Citrus Sinensis ID: 009920

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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--
Protein Sequence
MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATGRGGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLGPFPGGNSNRFSTPVGFSGGNGRGDSVLSSTTWNVWGNGSLNSATNPASPGAFLGSGSGNFEVSFGNNSVNWGPVSAPGGGSASGYSAGSMGYGSGDGNYGLGGGGFGRTSSAGVGPTSSFAGSTSGYEGSYGDSYRSGSGYGDPTWRSATPELDGSGSFSYGLGTVSTNVAAKSSEGFIGSYNVTSRQSTRGTTIFTFLIWYCFVRAIRDSAFLSAFTLWRENLDFFFFESVRFPYGEKI
Secondary Structure (PSIPRED)
cccccccEEEEcccccccHHHHHHHHHccccEEEEEEEEccccccccccEEEEEccHHHHHHHHHcccccccEEEEEccccccccccccccccccccccccccccccEEEccccccccHHHHHHHHHccccEEEEEEEEEccccccccEEEEEEcccHHHHHHHHcccEEEccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEcccccccccc
Secondary Structure Prediction (SSPRO)
ccccHHEEEEEcccccccHHHHHHHHHHHccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHcccccccccEEEEEEcccccHHccccccccccccccccHHHHEEEEEcccccccHHHHHHHHHHHccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHcccccEEccEEcEEEEcccccHHHcccccHHHHHHHcccccccHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccEEEEEEEEccccccc
Coil and Loop (DISEMBL)
mesdlgklfiggiswdtdEERLKEYFSRYGEVVEAVIMRDRatgrargfgfvvfadpavAERVIMDkhmidgrtveakkavprddqnmlnrntssihsspgpgrtkkifvgglastvtesDFKKYFDQFGTITDVVVMYdhntqrprgfgfitydsEEAVDRVLHKTFHELNGKMVEVkravpkefspgpsrssmigynnfgfnrptnlLNSFAQrynlspaggfgvrmdsrfsplatgrggispfggagygvgmnldgglspsyggssnfsnslgygrmlgpfpggnsnrfstpvgfsggngrgdsvlssttwnvwgngslnsatnpaspgaflgsgsgnfevsfgnnsvnwgpvsapgggsasgysagsmgygsgdgnyglggggfgrtssagvgptssfagstsgyegsygdsyrsgsgygdptwrsatpeldgsgsfsyglGTVSTNVaakssegfigsynvtsrqstrgttIFTFLIWYCFVRAIRDSAFLSAFTLWRENldffffesvrfpygeki
Flexible Loop (DISEMBL)
mesdlgklfiggiswdtdeeRLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMdkhmidgrtveakkavprddqnmlnrntssihsspgpgrtKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHElngkmvevkravpkefspgpsrsSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATGRGGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLGPFPGGNSNRFSTPVGFSGGNGRGDSVLSSTTWNVWGNGSLNSATNPASPGAFLGSGSGNFEVSFGNNSVNWGPVSAPGGGSASGYSAGSMGYGSGDGNYGLGGGGFGRTSSAGVGPTSSFAGSTSGYEGSYGDSYRSGSGYGDPTWRSATPELDGSGSFSYGLGTVSTNVAAKSSEGFIGsynvtsrqstrgTTIFTFLIWYCFVRAIRDSAFLSAFTLWRENLDFFFfesvrfpygeki
Low Complexity Region (SEG)
MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATGRGGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLGPFPGGNSNRFSTPVGFSGGNGRGDSVLSSTTWNVWGNGSLNSATNPASPGAFLGSGSGNFEVSFGNNSVNWGPVsapgggsasgysagsmgygsgdgnyglggggfgrtssagvgPTSSFAgstsgyegsygdsyrsgsgygDPTWRSATPELDGSGSFSYGLGTVSTNVAAKSSEGFIGSYNVTSRQSTRGTTIFTFLIWYCFVRAIRDSAFLSAFTLWRENLDFFFFESVRFPYGEKI
Disordered region (IsUnstruct)
*****GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDG**********************************KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEV*****************IGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATGRGGISPFGGAGYGVGMNLDG**************************************************************************************************************************************************************************************SYGLGTVSTNVAAKSSEGFIGSYNVTSRQSTRGTTIFTFLIWYCFVRAIRDSAFLSAFTLWRENLDFFFFESVRFPY****
Disordered Region (DISOPRED)
**SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTVEAKKA**********************GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEV***********************************AQRYNLSPAGGFGVR***************************************************************************************************************************************************************************************************************************V********************RQSTRGTTIFTFLIWYCFVRAIRDSAFLSAFTLWRENLDFFFFESVRFPYGE**
Disordered Region (DISEMBL)
MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATGRGGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLGPFPGGNSNRFSTPVGFSGGNGRGDSVLSSTTWNVWGNGSLNSATNPASPGAFLGSGSGNFEVSFGNNSVNWGPVSAPGGGSASGYSAGSMGYGSGDGNYGLGGGGFGRTSSAGVGPTSSFAGSTSGYEGSYGDSYRSGSGYGDPTWRSATPELDGSGSFSYGLGTVSTNVAAKSSEGFIGSYNVTSRQSTRGTTIFTFLIWYCFVRAIRDSAFLSAFTLWRENLDFFFFESVRFPYGEKI
Disordered Region (DISPRO)
***DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTVEAKKAVPR*****************GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFS**PSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATGRGGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLGPFPGGNSNRFSTPVGFSGGNGRGDSVLSSTTWNVWGNGSLNSATNPASPGAFLGSGSGNFEVSFGNNSVNWGPVSAPGGGSASGYSAGSMGYGSGDGNYGLGGGGFGRTSSAGVGPTSSFAGSTSGYEGSYGDSYRSGSGYGDPTWRSATPELDGSGSFSYGLGTVSTNVAAKSSEGFIGSYNVTSRQSTRGTTIFTFLIWYCFVRAIRDSAFLSAFTLWRENLDFFFFESVRFPYGEK*
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATGRGGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLGPFPGGNSNRFSTPVGFSGGNGRGDSVLSSTTWNVWGNGSLNSATNPASPGAFLGSGSGNFEVSFGNNSVNWGPVSAPGGGSASGYSAGSMGYGSGDGNYGLGGGGFGRTSSAGVGPTSSFAGSTSGYEGSYGDSYRSGSGYGDPTWRSATPELDGSGSFSYGLGTVSTNVAAKSSEGFIGSYNVTSRQSTRGTTIFTFLIWYCFVRAIRDSAFLSAFTLWRENLDFFFFESVRFPYGEKI
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	522	2.2.26 [Sep-21-2011]
Q8W034	411	Heterogeneous nuclear rib	no	no	0.360	0.457	0.567	6e-64
Q920Q6	346	RNA-binding protein Musas	yes	no	0.337	0.508	0.465	1e-47
Q96DH6	328	RNA-binding protein Musas	yes	no	0.337	0.536	0.465	3e-47
Q9VVE5	369	RNA-binding protein Musas	yes	no	0.331	0.468	0.478	2e-46
Q96EP5	407	DAZ-associated protein 1	no	no	0.348	0.447	0.454	1e-45
Q98SJ2	360	DAZ-associated protein 1	N/A	no	0.371	0.538	0.447	1e-45
Q9JII5	406	DAZ-associated protein 1	no	no	0.348	0.448	0.454	1e-45
O43347	362	RNA-binding protein Musas	no	no	0.325	0.469	0.475	3e-45
Q61474	362	RNA-binding protein Musas	no	no	0.325	0.469	0.475	5e-45
Q8K3P4	362	RNA-binding protein Musas	no	no	0.325	0.469	0.475	5e-45

>sp|Q8W034|RNP1_ARATH Heterogeneous nuclear ribonucleoprotein 1 OS=Arabidopsis thaliana GN=RNP1 PE=1 SV=1

 Score =  245 bits (625), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 109/192 (56%), Positives = 152/192 (79%), Gaps = 4/192 (2%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
           M+SD GKLF+GGISW+TDE++L+E+F+ YGEV +A++MRD+ TGR RGFGFV+F+DP+V 
Sbjct: 1   MDSDQGKLFVGGISWETDEDKLREHFTNYGEVSQAIVMRDKLTGRPRGFGFVIFSDPSVL 60

Query: 61  ERVIMDKHMIDGRTVEAKKAVPRDDQNMLNR----NTSSIHSSPGPGRTKKIFVGGLAST 116
           +RV+ +KH ID R V+ K+A+ R++Q +  R    NTS         +TKKIFVGGL  T
Sbjct: 61  DRVLQEKHSIDTREVDVKRAMSREEQQVSGRTGNLNTSRSSGGDAYNKTKKIFVGGLPPT 120

Query: 117 VTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMV 176
           +T+ +F++YF+ +G +TDV +MYD  T RPRGFGF+++DSE+AVD VLHKTFH+L+GK V
Sbjct: 121 LTDEEFRQYFEVYGPVTDVAIMYDQATNRPRGFGFVSFDSEDAVDSVLHKTFHDLSGKQV 180

Query: 177 EVKRAVPKEFSP 188
           EVKRA+PK+ +P
Sbjct: 181 EVKRALPKDANP 192

Involved in the packaging of pre-mRNA into hnRNP particles, transport of poly(A) mRNA from the nucleus to the cytoplasm and may modulate splice site selection.
Arabidopsis thaliana (taxid: 3702)

>sp|Q920Q6|MSI2H_MOUSE RNA-binding protein Musashi homolog 2 OS=Mus musculus GN=Msi2 PE=1 SV=1

 Score =  191 bits (485), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 89/191 (46%), Positives = 126/191 (65%), Gaps = 15/191 (7%)

Query: 2   ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
           + D GK+FIGG+SW T  + L++YFS++GE+ E ++MRD  T R+RGFGFV FADPA  +
Sbjct: 17  QHDPGKMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVD 76

Query: 62  RVI-MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTES 120
           +V+    H +D +T++ K A PR  Q  +              RTKKIFVGGL++     
Sbjct: 77  KVLGQPHHELDSKTIDPKVAFPRRAQPKMVT------------RTKKIFVGGLSANTVVE 124

Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR 180
           D K+YF+QFG + D ++M+D  T R RGFGF+T+++E+ V++V    FHE+N KMVE K+
Sbjct: 125 DVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEIHFHEINNKMVECKK 184

Query: 181 AVPKE--FSPG 189
           A PKE  F PG
Sbjct: 185 AQPKEVMFPPG 195

RNA binding protein that regulates the expression of target mRNAs at the translation level. May play a role in the proliferation and maintenance of stem cells in the central nervous system.

Mus musculus (taxid: 10090)

>sp|Q96DH6|MSI2H_HUMAN RNA-binding protein Musashi homolog 2 OS=Homo sapiens GN=MSI2 PE=1 SV=1

 Score =  190 bits (482), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 89/191 (46%), Positives = 126/191 (65%), Gaps = 15/191 (7%)

Query: 2   ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
           + D GK+FIGG+SW T  + L++YFS++GE+ E ++MRD  T R+RGFGFV FADPA  +
Sbjct: 17  QHDPGKMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVD 76

Query: 62  RVI-MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTES 120
           +V+    H +D +T++ K A PR  Q  +              RTKKIFVGGL++     
Sbjct: 77  KVLGQPHHELDSKTIDPKVAFPRRAQPKMVT------------RTKKIFVGGLSANTVVE 124

Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR 180
           D K+YF+QFG + D ++M+D  T R RGFGF+T+++E+ V++V    FHE+N KMVE K+
Sbjct: 125 DVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEIHFHEINNKMVECKK 184

Query: 181 AVPKE--FSPG 189
           A PKE  F PG
Sbjct: 185 AQPKEVMFPPG 195

RNA binding protein that regulates the expression of target mRNAs at the translation level. May play a role in the proliferation and maintenance of stem cells in the central nervous system.

Homo sapiens (taxid: 9606)

>sp|Q9VVE5|MSIR6_DROME RNA-binding protein Musashi homolog Rbp6 OS=Drosophila melanogaster GN=Rbp6 PE=2 SV=3

 Score =  187 bits (474), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 89/186 (47%), Positives = 121/186 (65%), Gaps = 13/186 (6%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
           + +D GK+FIGG+SW T  E L++YF RYG++ EA++M+D  T R+RGFGFV F+DP   
Sbjct: 24  VPNDPGKMFIGGLSWQTSPESLRDYFGRYGDISEAMVMKDPTTRRSRGFGFVTFSDPNSV 83

Query: 61  ERVIMD-KHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTE 119
           ++V+    H +DG+ V+ K A PR     +              RTKKIFVGGL++  T 
Sbjct: 84  DKVLTQGTHELDGKKVDPKVAFPRRAHPKMVT------------RTKKIFVGGLSAPTTL 131

Query: 120 SDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVK 179
            D K YF+QFG I D ++M+D  T R RGFGF+T+ SE+ VD+V    FHE+N KMVE K
Sbjct: 132 EDVKSYFEQFGPIEDAMLMFDKQTNRHRGFGFVTFQSEDVVDKVCEIHFHEINNKMVECK 191

Query: 180 RAVPKE 185
           +A PKE
Sbjct: 192 KAQPKE 197

RNA binding protein that regulates the expression of target mRNAs at the translation level. May play a role in the proliferation and maintenance of stem cells in the central nervous system.

Drosophila melanogaster (taxid: 7227)

>sp|Q96EP5|DAZP1_HUMAN DAZ-associated protein 1 OS=Homo sapiens GN=DAZAP1 PE=1 SV=1

 Score =  184 bits (468), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 84/185 (45%), Positives = 123/185 (66%), Gaps = 3/185 (1%)

Query: 4   DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV 63
           ++GKLF+GG+ W T +E L+ YFS+YGEVV+ VIM+D+ T ++RGFGFV F DP     V
Sbjct: 8   EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV 67

Query: 64  IMDK-HMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTK--KIFVGGLASTVTES 120
           +  + H +DGR ++ K   PR  Q    R        P    +K  KIFVGG+     E+
Sbjct: 68  LASRPHTLDGRNIDPKPCTPRGMQPERTRPKEGWQKGPRSDNSKSNKIFVGGIPHNCGET 127

Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR 180
           + ++YF +FG +T+VV++YD   QRPRGFGFIT++ E++VD+ ++  FH++ GK VEVKR
Sbjct: 128 ELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKR 187

Query: 181 AVPKE 185
           A P++
Sbjct: 188 AEPRD 192

RNA-binding protein, which may be required during spermatogenesis.

Homo sapiens (taxid: 9606)

>sp|Q98SJ2|DAZP1_XENLA DAZ-associated protein 1 OS=Xenopus laevis GN=dazap1 PE=1 SV=1

 Score =  184 bits (468), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 90/201 (44%), Positives = 130/201 (64%), Gaps = 7/201 (3%)

Query: 4   DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV 63
           ++GKLF+GG+ W T +E L+ YFS+YGEVV+ VIM+D+ T ++RGFGFV F DP     V
Sbjct: 8   EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV 67

Query: 64  IMDK-HMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGP---GRTKKIFVGGLASTVTE 119
           +  + H +DGR ++ K   PR  Q   +R               R+ KIFVGG+     E
Sbjct: 68  LASRPHTLDGRNIDPKPCTPRGMQPERSRPREGWQQKEPRTENSRSNKIFVGGIPHNCGE 127

Query: 120 SDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVK 179
           ++ K+YF++FG +T+VV++YD   QRPRGFGFIT++ E++VD+ ++  FH++ GK VEVK
Sbjct: 128 TELKEYFNRFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVK 187

Query: 180 RAVP---KEFSPGPSRSSMIG 197
           RA P   K  +PGP  S+  G
Sbjct: 188 RAEPRDSKSQTPGPPGSNQWG 208

RNA-binding protein, which is required during gametogenesis. May be involved in the actin-dependent anchoring of Vg1 mRNA in the vegetal cortex of the oocyte.

Xenopus laevis (taxid: 8355)

>sp|Q9JII5|DAZP1_MOUSE DAZ-associated protein 1 OS=Mus musculus GN=Dazap1 PE=2 SV=2

 Score =  184 bits (468), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 84/185 (45%), Positives = 123/185 (66%), Gaps = 3/185 (1%)

Query: 4   DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV 63
           ++GKLF+GG+ W T +E L+ YFS+YGEVV+ VIM+D+ T ++RGFGFV F DP     V
Sbjct: 8   EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV 67

Query: 64  IMDK-HMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTK--KIFVGGLASTVTES 120
           +  + H +DGR ++ K   PR  Q    R        P    +K  KIFVGG+     E+
Sbjct: 68  LASRPHTLDGRNIDPKPCTPRGMQPERTRPKEGWQKGPRSDSSKSNKIFVGGIPHNCGET 127

Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR 180
           + ++YF +FG +T+VV++YD   QRPRGFGFIT++ E++VD+ ++  FH++ GK VEVKR
Sbjct: 128 ELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKR 187

Query: 181 AVPKE 185
           A P++
Sbjct: 188 AEPRD 192

RNA-binding protein, which may be required during spermatogenesis.

Mus musculus (taxid: 10090)

>sp|O43347|MSI1H_HUMAN RNA-binding protein Musashi homolog 1 OS=Homo sapiens GN=MSI1 PE=1 SV=1

 Score =  183 bits (465), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 87/183 (47%), Positives = 120/183 (65%), Gaps = 13/183 (7%)

Query: 4   DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV 63
           D  K+FIGG+SW T +E L+EYF ++GEV E ++MRD  T R+RGFGFV F D A  ++V
Sbjct: 18  DPCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 77

Query: 64  I-MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDF 122
           +   +H +D +T++ K A PR  Q  +              RTKKIFVGGL+   T  D 
Sbjct: 78  LAQSRHELDSKTIDPKVAFPRRAQPKMVT------------RTKKIFVGGLSVNTTVEDV 125

Query: 123 KKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAV 182
           K+YF+QFG + D ++M+D  T R RGFGF+T++SE+ V++V    FHE+N KMVE K+A 
Sbjct: 126 KQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKAQ 185

Query: 183 PKE 185
           PKE
Sbjct: 186 PKE 188

RNA binding protein that regulates the expression of target mRNAs at the translation level. Regulates expression of the NOTCH1 antagonist NUMB. Binds RNA containing the sequence 5'-GUUAGUUAGUUAGUU-3' and other sequences containing the pattern 5'-[GA]U(1-3)AGU-3'. May play a role in the proliferation and maintenance of stem cells in the central nervous system.

Homo sapiens (taxid: 9606)

>sp|Q61474|MSI1H_MOUSE RNA-binding protein Musashi homolog 1 OS=Mus musculus GN=Msi1 PE=1 SV=1

 Score =  182 bits (463), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 87/183 (47%), Positives = 119/183 (65%), Gaps = 13/183 (7%)

Query: 4   DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV 63
           D  K+FIGG+SW T +E L+EYF ++GEV E ++MRD  T R+RGFGFV F D A  ++V
Sbjct: 18  DPCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 77

Query: 64  IMD-KHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDF 122
           +   +H +D +T++ K A PR  Q  +              RTKKIFVGGL+   T  D 
Sbjct: 78  LAQSRHELDSKTIDPKVAFPRRAQPKMVT------------RTKKIFVGGLSVNTTVEDV 125

Query: 123 KKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAV 182
           K YF+QFG + D ++M+D  T R RGFGF+T++SE+ V++V    FHE+N KMVE K+A 
Sbjct: 126 KHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKAQ 185

Query: 183 PKE 185
           PKE
Sbjct: 186 PKE 188

RNA binding protein that regulates the expression of target mRNAs at the translation level. Regulates expression of the NOTCH1 antagonist NUMB. Binds RNA containing the sequence 5'-GUUAGUUAGUUAGUU-3' and other sequences containing the pattern 5'-[GA]U(1-3)AGU-3'. May play a role in the proliferation and maintenance of stem cells in the central nervous system.

Mus musculus (taxid: 10090)

>sp|Q8K3P4|MSI1H_RAT RNA-binding protein Musashi homolog 1 OS=Rattus norvegicus GN=Msi1 PE=2 SV=1

 Score =  182 bits (462), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 87/183 (47%), Positives = 119/183 (65%), Gaps = 13/183 (7%)

Query: 4   DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV 63
           D  K+FIGG+SW T +E L+EYF ++GEV E ++MRD  T R+RGFGFV F D A  ++V
Sbjct: 18  DPCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 77

Query: 64  I-MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDF 122
           +   +H +D +T++ K A PR  Q  +              RTKKIFVGGL+   T  D 
Sbjct: 78  LAQSRHELDSKTIDPKVAFPRRAQPKMVT------------RTKKIFVGGLSVNTTVEDV 125

Query: 123 KKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAV 182
           K YF+QFG + D ++M+D  T R RGFGF+T++SE+ V++V    FHE+N KMVE K+A 
Sbjct: 126 KHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKAQ 185

Query: 183 PKE 185
           PKE
Sbjct: 186 PKE 188

RNA binding protein that regulates the expression of target mRNAs at the translation level. Regulates expression of the NOTCH1 antagonist NUMB. Binds RNA containing the sequence 5'-GUUAGUUAGUUAGUU-3' and other sequences containing the pattern 5'-[GA]U(1-3)AGU-3'. May play a role in the proliferation and maintenance of stem cells in the central nervous system.

Rattus norvegicus (taxid: 10116)

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	522
224061141	478	predicted protein [Populus trichocarpa]	0.906	0.989	0.773	0.0
255576302	478	Heterogeneous nuclear ribonucleoprotein	0.906	0.989	0.792	0.0
147783406	482	hypothetical protein VITISV_003519 [Viti	0.917	0.993	0.753	0.0
225460779	478	PREDICTED: uncharacterized protein LOC10	0.906	0.989	0.758	0.0
224114443	478	predicted protein [Populus trichocarpa]	0.906	0.989	0.747	0.0
357459939	481	Heterogeneous nuclear ribonucleoprotein	0.908	0.985	0.713	0.0
356527120	513	PREDICTED: uncharacterized protein LOC10	0.906	0.922	0.725	0.0
356552729	478	PREDICTED: uncharacterized protein LOC10	0.904	0.987	0.700	0.0
356566592	479	PREDICTED: uncharacterized protein LOC10	0.906	0.987	0.714	1e-180
449463715	480	PREDICTED: uncharacterized protein LOC10	0.906	0.985	0.656	1e-172

>gi|224061141|ref|XP_002300356.1| predicted protein [Populus trichocarpa] gi|222847614|gb|EEE85161.1| predicted protein [Populus trichocarpa]

 Score =  729 bits (1883), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 368/476 (77%), Positives = 407/476 (85%), Gaps = 3/476 (0%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
           MESDLGKLFIGGISWDTDEERLKEYFS+YGEVVEAVIMRDR TGRARGFGFVVFADP VA
Sbjct: 1   MESDLGKLFIGGISWDTDEERLKEYFSKYGEVVEAVIMRDRVTGRARGFGFVVFADPIVA 60

Query: 61  ERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTES 120
           ERVIM+KH++DGRTVEAKKAVPRDDQ++L+RNTSSIH SPGPGRTKKIFVGGLASTVTE+
Sbjct: 61  ERVIMEKHVVDGRTVEAKKAVPRDDQHILSRNTSSIHGSPGPGRTKKIFVGGLASTVTEN 120

Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR 180
           DFKKYF+QFG ITDVVVMYDHNT RPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR
Sbjct: 121 DFKKYFEQFGIITDVVVMYDHNTLRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR 180

Query: 181 AVPKEFSPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATGR 240
           AVPKE SPGPSRS ++GY N+G  R  N LN++AQ YN++  GGFG+RMDSRF+PLATGR
Sbjct: 181 AVPKELSPGPSRSPLMGY-NYGLTRANNFLNAYAQGYNMNSIGGFGMRMDSRFNPLATGR 239

Query: 241 GGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLGPFPGGNSNRFSTPVGFSG 300
            G +PF  AGYG+ MNL+  LSPSYGG SNFSN+  YGR+  P+  GN +R+STPVG+  
Sbjct: 240 SGFAPFSTAGYGMSMNLEPALSPSYGGVSNFSNTPAYGRISSPYYSGNPSRYSTPVGYGE 299

Query: 301 GNGRGDSVLSSTTWNVWGNGSLNSATNPASPGAFLGSGSGNFEVSFGNNSVNWG--PVSA 358
           GN R DS+LS TTWNVWGNGS N+ATNPASPG  LGS +GNF VSFGN+  NWG  PVSA
Sbjct: 300 GNARNDSLLSPTTWNVWGNGSHNTATNPASPGPLLGSRTGNFGVSFGNSGSNWGTSPVSA 359

Query: 359 PGGGSASGYSAGSMGYGSGDGNYGLGGGGFGRTSSAGVGPTSSFAGSTSGYEGSYGDSYR 418
            G GSASGY+ GSMGYGSGD NYGL G G+ R S  G  PTSSF+GS  GYEGSYGD YR
Sbjct: 360 QGRGSASGYTTGSMGYGSGDNNYGLSGAGYVRNSGTGAPPTSSFSGSAGGYEGSYGDLYR 419

Query: 419 SGSGYGDPTWRSATPELDGSGSFSYGLGTVSTNVAAKSSEGFIGSYNVTSRQSTRG 474
           SGS YGD TW+SATPELDG GSF YGLG V+++V  KSSEG+IGSY VTSRQS RG
Sbjct: 420 SGSVYGDSTWQSATPELDGCGSFGYGLGDVASDVTTKSSEGYIGSYGVTSRQSNRG 475

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255576302|ref|XP_002529044.1| Heterogeneous nuclear ribonucleoprotein 27C, putative [Ricinus communis] gi|223531524|gb|EEF33355.1| Heterogeneous nuclear ribonucleoprotein 27C, putative [Ricinus communis]

 Score =  726 bits (1874), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 377/476 (79%), Positives = 415/476 (87%), Gaps = 3/476 (0%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
           MESDLGKLFIGGISWDTDEERLKEYFS+YGEVVEAVIMRDR TGRARGFGFVVFADPAVA
Sbjct: 1   MESDLGKLFIGGISWDTDEERLKEYFSKYGEVVEAVIMRDRTTGRARGFGFVVFADPAVA 60

Query: 61  ERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTES 120
           ERVI+DKHMIDGRTVEAKKAVPRDDQ++LNRNTSSIH SPGPGRTKKIFVGGLASTVT++
Sbjct: 61  ERVIVDKHMIDGRTVEAKKAVPRDDQHILNRNTSSIHGSPGPGRTKKIFVGGLASTVTDN 120

Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR 180
           DFKKYF+QFG ITDVVVMYDHNTQRPRGFGFITYDSE+AVDRVLHKTFHELNGKMVEVKR
Sbjct: 121 DFKKYFEQFGNITDVVVMYDHNTQRPRGFGFITYDSEDAVDRVLHKTFHELNGKMVEVKR 180

Query: 181 AVPKEFSPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATGR 240
           AVPKE SPGPSRS +IGY N+G +R  N LN++AQ YN++  GGFG+RMDSRFSPLA+GR
Sbjct: 181 AVPKELSPGPSRSPLIGY-NYGLSRTNNFLNAYAQGYNMNSVGGFGMRMDSRFSPLASGR 239

Query: 241 GGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLGPFPGGNSNRFSTPVGFSG 300
            G  PFG  GYG+ MNL+ GL+PSYGG SNF NS GYGRML P+  GNS+R+STP+G+  
Sbjct: 240 SGFPPFGTTGYGMSMNLEPGLTPSYGGGSNFGNSPGYGRMLSPYYSGNSSRYSTPIGYGV 299

Query: 301 GNGRGDSVLSSTTWNVWGNGSLNSATNPASPGAFLGSGSGNFEVSFGNNSVNWGP--VSA 358
           GN R DSVLS TT NVWGNG LNSA NPASPGAFLGSGSG+F VSFGN+  NWGP  VSA
Sbjct: 300 GNARNDSVLSPTTRNVWGNGGLNSAANPASPGAFLGSGSGSFGVSFGNSGTNWGPSHVSA 359

Query: 359 PGGGSASGYSAGSMGYGSGDGNYGLGGGGFGRTSSAGVGPTSSFAGSTSGYEGSYGDSYR 418
            GGGSAS Y++GSMGYGSGD +YGLGGG +GR + +   P SSFAGS SGYEGSYGD YR
Sbjct: 360 QGGGSASAYTSGSMGYGSGDSSYGLGGGAYGRNNGSNAAPNSSFAGSNSGYEGSYGDLYR 419

Query: 419 SGSGYGDPTWRSATPELDGSGSFSYGLGTVSTNVAAKSSEGFIGSYNVTSRQSTRG 474
           SGS YGD TWRS TPEL+GSGSF YGL  ++ +V AKSSEG+IGSY VTSRQS RG
Sbjct: 420 SGSVYGDSTWRSGTPELEGSGSFGYGLSNIAADVTAKSSEGYIGSYGVTSRQSNRG 475

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147783406|emb|CAN75218.1| hypothetical protein VITISV_003519 [Vitis vinifera]

 Score =  694 bits (1791), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 363/482 (75%), Positives = 409/482 (84%), Gaps = 3/482 (0%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
           MESDLGKLFIGGISWDTDE+RLKEYF  YGEVVEAVIMRDR TGRARGFGFVVFADPAVA
Sbjct: 1   MESDLGKLFIGGISWDTDEDRLKEYFRTYGEVVEAVIMRDRTTGRARGFGFVVFADPAVA 60

Query: 61  ERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTES 120
           ERV+MDKHMIDGRTVEAKKAVPRDDQ++LNRNT SIH SPGPGRTKKIFVGGLASTVTES
Sbjct: 61  ERVVMDKHMIDGRTVEAKKAVPRDDQHLLNRNTGSIHGSPGPGRTKKIFVGGLASTVTES 120

Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR 180
           DFKKYFDQFGTI DVVVMYDHNTQRPRGFGFITYDSEEAV+RVLHKTFHELNGKMVEVKR
Sbjct: 121 DFKKYFDQFGTINDVVVMYDHNTQRPRGFGFITYDSEEAVERVLHKTFHELNGKMVEVKR 180

Query: 181 AVPKEFSPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATGR 240
           AVPKE SPGPSRS ++GY N+G  R  N LN++ Q YN+S  G +G+RMD RF+P+A+GR
Sbjct: 181 AVPKEHSPGPSRSPLVGY-NYGLGRNNNFLNNYGQGYNMSSVGSYGIRMDGRFNPVASGR 239

Query: 241 GGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLGPFPGGNSNRFSTPVGFSG 300
            G  PFG  GYG+GMNL+ GLSPSY G+S+FSN+ GYGR+L P+  GNSNR+STP+G++ 
Sbjct: 240 SGFPPFGAPGYGMGMNLEQGLSPSYSGNSSFSNNPGYGRILNPYYSGNSNRYSTPIGYNA 299

Query: 301 GNGRGDSVLSSTTWNVWGNGSLNSATNPASPGAFLGSGSGNFEVSFGNNSVNWG--PVSA 358
           GNGR DSVL+ST  NVWGNGSLN+ATNPASPGA+LGSG GNF VSFGN   NWG  P+ A
Sbjct: 300 GNGRSDSVLNSTPRNVWGNGSLNNATNPASPGAYLGSGGGNFGVSFGNGGANWGSSPIPA 359

Query: 359 PGGGSASGYSAGSMGYGSGDGNYGLGGGGFGRTSSAGVGPTSSFAGSTSGYEGSYGDSYR 418
            GGGSA G+++GS+ YGSGD +YGLGGGG+GR SS GV   SSFA ST GYEGSY + YR
Sbjct: 360 QGGGSALGFTSGSLNYGSGDSSYGLGGGGYGRNSSTGVAAASSFAPSTGGYEGSYEELYR 419

Query: 419 SGSGYGDPTWRSATPELDGSGSFSYGLGTVSTNVAAKSSEGFIGSYNVTSRQSTRGTTIF 478
           SGS Y D TWR+ T ELDG GSFSYGLG  +++V A S+E +IGSY+V +RQS RG T  
Sbjct: 420 SGSVYNDSTWRTPTSELDGPGSFSYGLGNAASDVTANSAEDYIGSYSVANRQSNRGNTFC 479

Query: 479 TF 480
            F
Sbjct: 480 LF 481

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225460779|ref|XP_002274589.1| PREDICTED: uncharacterized protein LOC100267443 [Vitis vinifera]

 Score =  691 bits (1782), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 361/476 (75%), Positives = 407/476 (85%), Gaps = 3/476 (0%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
           MESDLGKLFIGGISWDTDE+RLKEYF  YGEVVEAVIMRDR TGRARGFGFVVFADPAVA
Sbjct: 1   MESDLGKLFIGGISWDTDEDRLKEYFRTYGEVVEAVIMRDRTTGRARGFGFVVFADPAVA 60

Query: 61  ERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTES 120
           ERV+MDKHMIDGRTVEAKKAVPRDDQ++LNRNT SIH SPGPGRTKKIFVGGLASTVTES
Sbjct: 61  ERVVMDKHMIDGRTVEAKKAVPRDDQHLLNRNTGSIHGSPGPGRTKKIFVGGLASTVTES 120

Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR 180
           DFKKYFDQFGTI DVVVMYDHNTQRPRGFGFITYDSEEAV+RVLHKTFHELNGKMVEVKR
Sbjct: 121 DFKKYFDQFGTINDVVVMYDHNTQRPRGFGFITYDSEEAVERVLHKTFHELNGKMVEVKR 180

Query: 181 AVPKEFSPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATGR 240
           AVPKE SPGPSRS ++GY N+G  R  N LN++ Q YN+S  G +G+RMD RF+P+A+GR
Sbjct: 181 AVPKEHSPGPSRSPLVGY-NYGLGRNNNFLNNYGQGYNMSSVGSYGIRMDGRFNPVASGR 239

Query: 241 GGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLGPFPGGNSNRFSTPVGFSG 300
            G  PFG  GYG+GMNL+ GLSPSY G+S+FSN+ GYGR+L P+  GNSNR+STP+G++ 
Sbjct: 240 SGFPPFGAPGYGMGMNLEQGLSPSYSGNSSFSNNPGYGRILNPYYSGNSNRYSTPIGYNA 299

Query: 301 GNGRGDSVLSSTTWNVWGNGSLNSATNPASPGAFLGSGSGNFEVSFGNNSVNWG--PVSA 358
           GNGR DSVL+ST  NVWGNGSLN+ATNPASPGA+LGSG GNF VSFGN   NWG  P+ A
Sbjct: 300 GNGRSDSVLNSTPRNVWGNGSLNNATNPASPGAYLGSGGGNFGVSFGNGGANWGSSPIPA 359

Query: 359 PGGGSASGYSAGSMGYGSGDGNYGLGGGGFGRTSSAGVGPTSSFAGSTSGYEGSYGDSYR 418
            GGGSA G+++GS+ YGSGD +YGLGGGG+GR SS GV   SSFA ST GYEGSY + YR
Sbjct: 360 QGGGSALGFTSGSLNYGSGDSSYGLGGGGYGRNSSTGVAAASSFAPSTGGYEGSYEELYR 419

Query: 419 SGSGYGDPTWRSATPELDGSGSFSYGLGTVSTNVAAKSSEGFIGSYNVTSRQSTRG 474
           SGS Y D TWR+ T ELDG GSFSYGLG  +++V A S+E +IGSY+V +RQS RG
Sbjct: 420 SGSVYNDSTWRTPTSELDGPGSFSYGLGNAASDVTANSAEDYIGSYSVANRQSNRG 475

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224114443|ref|XP_002316761.1| predicted protein [Populus trichocarpa] gi|222859826|gb|EEE97373.1| predicted protein [Populus trichocarpa]

 Score =  675 bits (1741), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 356/476 (74%), Positives = 400/476 (84%), Gaps = 3/476 (0%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
           MESDLGKLFIGGISWDTDEERLKEYFS+YGEVVEAVIMRDRATGRARGFGFVVFAD  VA
Sbjct: 1   MESDLGKLFIGGISWDTDEERLKEYFSKYGEVVEAVIMRDRATGRARGFGFVVFADLTVA 60

Query: 61  ERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTES 120
           ERVIM+KH+IDGRTVEAKKAVPRDDQ++L+R+ S+IH SPGPGRTKKIFVGGLASTVTE+
Sbjct: 61  ERVIMEKHVIDGRTVEAKKAVPRDDQHILSRSISNIHGSPGPGRTKKIFVGGLASTVTEN 120

Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR 180
           +FKKYF+Q+G I DVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR
Sbjct: 121 EFKKYFEQYGIIIDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR 180

Query: 181 AVPKEFSPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATGR 240
           AVPKE SPGPSRS ++GYN+ G  R  N LNS+AQ YN+S  GGFG+RMD RF+PL TGR
Sbjct: 181 AVPKELSPGPSRSPLMGYNH-GLTRANNFLNSYAQGYNMSSVGGFGMRMDGRFNPLVTGR 239

Query: 241 GGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLGPFPGGNSNRFSTPVGFSG 300
            G +PFG +GYG  MNL+  LSPSYGG SNF N+  YGR+  P+   N +R+STP+G+  
Sbjct: 240 SGFAPFGTSGYGTSMNLEPVLSPSYGGGSNFGNAPAYGRISSPYYSSNPSRYSTPIGYGV 299

Query: 301 GNGRGDSVLSSTTWNVWGNGSLNSATNPASPGAFLGSGSGNFEVSFGNNSVNWG--PVSA 358
           GN R DS+LS  T NVWGNG LN+ATNP SPG  +GSGSG+F VSFGNN  NWG   VSA
Sbjct: 300 GNARNDSLLSPATRNVWGNGGLNTATNPGSPGPLVGSGSGSFGVSFGNNGANWGTSTVSA 359

Query: 359 PGGGSASGYSAGSMGYGSGDGNYGLGGGGFGRTSSAGVGPTSSFAGSTSGYEGSYGDSYR 418
            GGG ASGY++GSMGYG+GD NY  GG G+ R S A V PTSSF+GS  GYEGSYG+ YR
Sbjct: 360 QGGGIASGYTSGSMGYGNGDSNYSFGGSGYARNSGASVPPTSSFSGSIGGYEGSYGELYR 419

Query: 419 SGSGYGDPTWRSATPELDGSGSFSYGLGTVSTNVAAKSSEGFIGSYNVTSRQSTRG 474
           SGS YGD TWR+A PELDGSGSF YGLG V+++V  KSSEG+IGSY VTSRQS RG
Sbjct: 420 SGSVYGDSTWRTAIPELDGSGSFGYGLGDVASDVTTKSSEGYIGSYGVTSRQSNRG 475

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357459939|ref|XP_003600251.1| Heterogeneous nuclear ribonucleoprotein A1 [Medicago truncatula] gi|355489299|gb|AES70502.1| Heterogeneous nuclear ribonucleoprotein A1 [Medicago truncatula]

 Score =  664 bits (1714), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 341/478 (71%), Positives = 395/478 (82%), Gaps = 4/478 (0%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
           MESDLGKLFIGGISWDTDEERLKEYF+ YGEV+EAVIMRDRATGRARGFGFVVF+DPAVA
Sbjct: 1   MESDLGKLFIGGISWDTDEERLKEYFATYGEVIEAVIMRDRATGRARGFGFVVFSDPAVA 60

Query: 61  ERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTES 120
           ERVI+DKH+IDGRTVEAKKAVPRDDQ  +NR T S+  SPGPGRTKKIFVGGL ST+TES
Sbjct: 61  ERVIIDKHIIDGRTVEAKKAVPRDDQQNINRQTGSVQGSPGPGRTKKIFVGGLPSTITES 120

Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR 180
           DFK YFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL+KTFHELNGKMVEVKR
Sbjct: 121 DFKMYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLYKTFHELNGKMVEVKR 180

Query: 181 AVPKEFSPGPSRSSMIGYNNFGFN-RPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATG 239
           AVPKE SPGP+RS +IGYNN+  N R ++ LN++ Q Y++SP GGFGVRMD RFSPL  G
Sbjct: 181 AVPKELSPGPTRSPLIGYNNYSLNSRASSYLNNYGQGYSMSPIGGFGVRMDGRFSPLTGG 240

Query: 240 RGGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLGPFPGGNSNRFSTPVGFS 299
           R G +PFG  GYG+GMNL+ GLSP++GG+SNF N+LGYGR+  PF  GNS+R++TP+G++
Sbjct: 241 RTGFTPFGNTGYGMGMNLESGLSPNFGGNSNFGNNLGYGRIFSPFYSGNSSRYATPIGYN 300

Query: 300 GGNGRGDSVLSSTTWNVWGNGSLNSATNPASPGAFLGSGSGNFEVSFGNNSVNWGPVSAP 359
           GGNGRGDS+++ST+ NVWGNG L++A NP SPGAFLGSG G F VS GN+  NWG     
Sbjct: 301 GGNGRGDSLMNSTSRNVWGNGGLSNANNPVSPGAFLGSGGGAFGVSIGNSGTNWGAAIQG 360

Query: 360 GGGSASGYSAGSMG-YGSGDGNYGLGGGGFGRTSSAGVGPTSSFAGSTSGYEGSYGDSYR 418
            GG A+   A     Y  GD ++GLGG G+GR S+A   P+S+F  S  GY+GSYGD YR
Sbjct: 361 QGGGAASGYATGNNVYEGGDSSFGLGGVGYGRNSNAVANPSSTFNASAGGYDGSYGDLYR 420

Query: 419 SGSG--YGDPTWRSATPELDGSGSFSYGLGTVSTNVAAKSSEGFIGSYNVTSRQSTRG 474
           SGSG  Y D  WRSAT E+DGSGSFSYGLG ++++   K+SEG+IGSYNV SRQ  RG
Sbjct: 421 SGSGSVYNDSAWRSATSEIDGSGSFSYGLGGIASDDPVKTSEGYIGSYNVASRQPNRG 478

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356527120|ref|XP_003532161.1| PREDICTED: uncharacterized protein LOC100805131 [Glycine max]

 Score =  660 bits (1704), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 346/477 (72%), Positives = 401/477 (84%), Gaps = 4/477 (0%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
           MESDLGKLFIGGISWDTDEERLKEYF +YGEV+E VIMRDR TGRARGFGFVVF DP+VA
Sbjct: 35  MESDLGKLFIGGISWDTDEERLKEYFGKYGEVIETVIMRDRVTGRARGFGFVVFGDPSVA 94

Query: 61  ERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTES 120
           ERVIMDKH+IDGRTVEAKKAVPRDDQ  +NR + S H SPGPGRTKKIFVGGL ST+TES
Sbjct: 95  ERVIMDKHIIDGRTVEAKKAVPRDDQQNINRQSGSAHVSPGPGRTKKIFVGGLPSTITES 154

Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR 180
           DFK YFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL+KTFHELNGKMVEVKR
Sbjct: 155 DFKTYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLYKTFHELNGKMVEVKR 214

Query: 181 AVPKEFSPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATGR 240
           AVPKE SPGPSRS +IGY N+G  R +N LNS+AQ YN+SP GG+GVRMD RFSPL +GR
Sbjct: 215 AVPKELSPGPSRSPLIGY-NYGLTRASNYLNSYAQGYNMSPIGGYGVRMDGRFSPLTSGR 273

Query: 241 GGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLGPFPGGNSNRFSTPVGFSG 300
            G++PFG  GYG+G+NLD GLSP++GG+SN+ +++GYGR+  PF  GNS R++TP+G+SG
Sbjct: 274 SGLTPFGNTGYGMGVNLDSGLSPNFGGTSNYGSNVGYGRIFSPFYSGNSGRYTTPIGYSG 333

Query: 301 GNGRGDSVLSSTTWNVWGNGSLNSATNPASPGAFLGSGSGNFEVSFGNNSVNWGP-VSAP 359
           GNGR +S+++S + NVWGNG +N+A NP SP  FLGSGSG F VS GN+   WGP +SA 
Sbjct: 334 GNGRSNSLMNSPSRNVWGNGGINNANNPVSPSPFLGSGSGAFGVSIGNSGTGWGPSISAQ 393

Query: 360 GGGSASGYSAGSMGYGSGDGNYGLGGGGFGRTSSAGVGPTSSFAGSTSGYEGSYGDSYRS 419
           GGG+ASGY++G+  Y   D ++GLGGGG+GR SS GV P+SSF  ST GYEGSYGD YRS
Sbjct: 394 GGGAASGYASGNNVYEGADSSFGLGGGGYGRNSSTGVAPSSSFNVSTGGYEGSYGDLYRS 453

Query: 420 GSG--YGDPTWRSATPELDGSGSFSYGLGTVSTNVAAKSSEGFIGSYNVTSRQSTRG 474
           GSG  Y D  WRSA  E+DGSGSF YGLG ++++   KSSEG+IG+YNVTSRQ  RG
Sbjct: 454 GSGSVYNDSAWRSAASEIDGSGSFGYGLGGIASDDPVKSSEGYIGNYNVTSRQPNRG 510

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356552729|ref|XP_003544715.1| PREDICTED: uncharacterized protein LOC100788515 [Glycine max]

 Score =  646 bits (1667), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 334/477 (70%), Positives = 385/477 (80%), Gaps = 5/477 (1%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
           MESDLGKLFIGGISWDTD+ERLKEYF +YGEV+EAVIMRDR TGRARGFGFVVFADP+ A
Sbjct: 1   MESDLGKLFIGGISWDTDDERLKEYFGKYGEVIEAVIMRDRTTGRARGFGFVVFADPSAA 60

Query: 61  ERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTES 120
           ERVIMDKH+IDGRTVEAKKAVPRDDQ  +NR + SIH SP PGRTKKIFVGGL ST+TES
Sbjct: 61  ERVIMDKHIIDGRTVEAKKAVPRDDQQTINRQSGSIHGSPSPGRTKKIFVGGLPSTITES 120

Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR 180
           DFKKYFDQFGTI DVVVMYDHNTQRPRGFGFITYDSEEAVDRVL+KTFHELNGKMVEVKR
Sbjct: 121 DFKKYFDQFGTIADVVVMYDHNTQRPRGFGFITYDSEEAVDRVLYKTFHELNGKMVEVKR 180

Query: 181 AVPKEFSPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATGR 240
           AVPKE SPGP+RS +IGY N+G NR +  LNS+AQ +N++P GG+GVRMD RFSPL + R
Sbjct: 181 AVPKELSPGPTRSPLIGY-NYGLNRTSGFLNSYAQGFNMNPIGGYGVRMDGRFSPLTSAR 239

Query: 241 GGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLGPFPGGNSNRFSTPVGFSG 300
            G SPFG +GYG+G+NLD GL+PSYGG+S++  SLGY RM  PF  GNSNR++TP+G SG
Sbjct: 240 SGFSPFGSSGYGMGVNLDLGLNPSYGGTSSYGGSLGYARM-SPFNNGNSNRYTTPIGNSG 298

Query: 301 GNGRGDSVLSSTTWNVWGNGSLNSATN-PASPGAFLGSGSGNFEVSFGNNSVNWGP-VSA 358
           GNGR DS+++S + +VWGNG  N+A N P SPGA+LGSGSG F VS GN   NWGP V  
Sbjct: 299 GNGRSDSLMNSASRSVWGNGGQNNAANSPVSPGAYLGSGSGAFGVSIGNGGTNWGPSVPT 358

Query: 359 PGGGSASGYSAGSMGYGSGDGNYGLGGGGFGRTSSAGVGPTSSFAGSTSGYEGSYGDSYR 418
            GGG+A+GYS     Y  GD N  LGGGG+GR SS  V  +S+F   T  YEGSYG+ YR
Sbjct: 359 QGGGAATGYSTWGNSYDGGDNNISLGGGGYGRNSSPSVPQSSTFTAPTGDYEGSYGNLYR 418

Query: 419 SGSGYGDPTWRSATPELDGS-GSFSYGLGTVSTNVAAKSSEGFIGSYNVTSRQSTRG 474
           +GS Y D TWRSA  E+D S      GLG ++++   KSS+GFIG+YNV SRQ+ RG
Sbjct: 419 NGSVYSDSTWRSAASEIDASGSFGYGGLGGIASDDPVKSSDGFIGNYNVISRQTNRG 475

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356566592|ref|XP_003551514.1| PREDICTED: uncharacterized protein LOC100794390 [Glycine max]

 Score =  639 bits (1648), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 341/477 (71%), Positives = 397/477 (83%), Gaps = 4/477 (0%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
           MESDLGKLFIGGISWDTDEERLK+YF +YGEV+EAVIMRDR TGRARGFGFVVFADP+VA
Sbjct: 1   MESDLGKLFIGGISWDTDEERLKDYFGKYGEVIEAVIMRDRVTGRARGFGFVVFADPSVA 60

Query: 61  ERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTES 120
           ERVIMDKH+IDGRTVEAKKAVPRDDQ  +NR + S H+SPGPGRTKKIFVGGL ST+TES
Sbjct: 61  ERVIMDKHIIDGRTVEAKKAVPRDDQQNINRQSGSAHASPGPGRTKKIFVGGLPSTITES 120

Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR 180
           DFK YFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL+KTFHELNGKMVEVKR
Sbjct: 121 DFKMYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLYKTFHELNGKMVEVKR 180

Query: 181 AVPKEFSPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATGR 240
           AVPKE SPGPSRS +IGY N+G  R +N LNSFAQ YN+SP GG+G+RMD RFSPL +GR
Sbjct: 181 AVPKELSPGPSRSPLIGY-NYGLTRASNYLNSFAQGYNMSPIGGYGIRMDGRFSPLTSGR 239

Query: 241 GGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLGPFPGGNSNRFSTPVGFSG 300
            G +P G  GYG+G+N+D GLSP++GG+SN+ +++GYGR+  PF  GNS R++TP+G+SG
Sbjct: 240 SGFTPLGNTGYGMGVNMDSGLSPNFGGTSNYGSNVGYGRIFSPFYSGNSGRYTTPIGYSG 299

Query: 301 GNGRGDSVLSSTTWNVWGNGSLNSATNPASPGAFLGSGSGNFEVSFGNNSVNWGP-VSAP 359
           GNGR DS+++S + NVWGNG LN+A NP SP  FLGSGSG F VS GN+   WGP + A 
Sbjct: 300 GNGRSDSLMNSPSRNVWGNGGLNNANNPISPSPFLGSGSGAFGVSIGNSGTGWGPSLPAQ 359

Query: 360 GGGSASGYSAGSMGYGSGDGNYGLGGGGFGRTSSAGVGPTSSFAGSTSGYEGSYGDSYRS 419
           G G ASGY  G+  Y  GD ++GLGGGG+GR +S  V P+SSF  ST GYEGSYGD YRS
Sbjct: 360 GRGDASGYGTGNNVYEGGDSSFGLGGGGYGRNNSTSVTPSSSFNVSTGGYEGSYGDLYRS 419

Query: 420 GSG--YGDPTWRSATPELDGSGSFSYGLGTVSTNVAAKSSEGFIGSYNVTSRQSTRG 474
           GSG  Y +  WRS+  ++DGSGSF YGLG ++++   KSSEG+IG+YNVTSRQ  RG
Sbjct: 420 GSGSVYNNSAWRSSASDIDGSGSFGYGLGGIASDDPVKSSEGYIGNYNVTSRQPNRG 476

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449463715|ref|XP_004149577.1| PREDICTED: uncharacterized protein LOC101220541 [Cucumis sativus] gi|449517233|ref|XP_004165650.1| PREDICTED: uncharacterized protein LOC101224873 [Cucumis sativus]

 Score =  610 bits (1572), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 314/478 (65%), Positives = 373/478 (78%), Gaps = 5/478 (1%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
           MESDLGKLFIGGISWDTDEERL+EYF  YGEVVEAVIMRDR TGRARGFGFVVFADP VA
Sbjct: 1   MESDLGKLFIGGISWDTDEERLREYFGHYGEVVEAVIMRDRTTGRARGFGFVVFADPGVA 60

Query: 61  ERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTES 120
           ERVI+DKH+IDGRTVEAKKAVP+DDQNMLNR++ SIH SP  GRTKKIFVGGLASTVTE+
Sbjct: 61  ERVILDKHVIDGRTVEAKKAVPKDDQNMLNRSSGSIHGSPSSGRTKKIFVGGLASTVTEA 120

Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR 180
           DF+KYFDQFGTITDVVVMYDH+TQRPRGFGFITYDSEE VDRVLHKTFHELNGKMVEVKR
Sbjct: 121 DFQKYFDQFGTITDVVVMYDHSTQRPRGFGFITYDSEECVDRVLHKTFHELNGKMVEVKR 180

Query: 181 AVPKEFSPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATGR 240
           A+PKE +PGP+RS ++GY N+G +RP+  LNS+ Q YN+SP GG+GVR D R SP+ + R
Sbjct: 181 AIPKELTPGPNRSPLVGY-NYGMSRPSGFLNSYTQGYNMSPLGGYGVRPDGRLSPIISSR 239

Query: 241 GGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLGPFPGGNSNRFSTPVGFSG 300
            G+  FG A YGVG+NL+ G+   YG + N  NS    +ML  +  GNSNR+  P+G+SG
Sbjct: 240 TGVPHFGTANYGVGVNLEQGMRQGYGRTLNIMNSQAQEQMLNSYYNGNSNRYIAPIGYSG 299

Query: 301 GNGRGDSVLSSTTWNVWGNGSLNSATNPASPGAFLGSGSGNFEVSFGNNSVNWG--PVSA 358
           GNGRGDS LSS+TWNVWGNGS+++A + + PGAF GSG+GNF V++GNN  NW    V+ 
Sbjct: 300 GNGRGDSPLSSSTWNVWGNGSMSNAMSSSGPGAFSGSGTGNFRVAYGNNDDNWSSPAVAN 359

Query: 359 PGGGSASGYSAG-SMGYGSGDGNYGLGGGGFGRT-SSAGVGPTSSFAGSTSGYEGSYGDS 416
             G +  GY+ G + GY  GD N     GG+GR    + V    +F    +GYE SY D 
Sbjct: 360 HVGANVPGYTFGNNNGYAIGDNNGFGFRGGYGRNGVVSNVAARKAFVEMNNGYERSYRDL 419

Query: 417 YRSGSGYGDPTWRSATPELDGSGSFSYGLGTVSTNVAAKSSEGFIGSYNVTSRQSTRG 474
           YR  + + D TW+S  PELDGS SF YGLG ++++  AKSSE F+ SY+V+SRQSTRG
Sbjct: 420 YRDEAVHDDSTWQSTAPELDGSVSFGYGLGNLASDDPAKSSESFLASYDVSSRQSTRG 477

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	522
TAIR|locus:2077392	495	AT3G07810 [Arabidopsis thalian	0.674	0.711	0.664	3.2e-136
TAIR|locus:2133862	455	AT4G26650 [Arabidopsis thalian	0.614	0.705	0.594	1.3e-109
TAIR|locus:2173967	460	AT5G55550 [Arabidopsis thalian	0.622	0.706	0.597	2.8e-105
TAIR|locus:2050992	404	AT2G33410 [Arabidopsis thalian	0.636	0.821	0.452	1.4e-72
TAIR|locus:2129590	411	AT4G14300 [Arabidopsis thalian	0.641	0.815	0.438	3.5e-68
UNIPROTKB|E2R6E4	407	DAZAP1 "Uncharacterized protei	0.465	0.597	0.395	1.8e-48
UNIPROTKB|I3LB68	406	DAZAP1 "Uncharacterized protei	0.465	0.598	0.395	7.7e-48
UNIPROTKB|Q96EP5	407	DAZAP1 "DAZ-associated protein	0.465	0.597	0.395	1.6e-47
TAIR|locus:2007903	369	AT1G17640 [Arabidopsis thalian	0.545	0.772	0.385	2e-47
MGI|MGI:1923876	346	Msi2 "musashi RNA-binding prot	0.588	0.887	0.379	1.4e-46

TAIR|locus:2077392 AT3G07810 [Arabidopsis thaliana (taxid:3702)]

 Score = 1208 (430.3 bits), Expect = 3.2e-136, Sum P(2) = 3.2e-136
 Identities = 242/364 (66%), Positives = 285/364 (78%)

Query:     1 MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
             M+SD GKLFIGGISWDT+EERLKEYFS +GEV+EAVI++DR TGRARGFGFVVFADPAVA
Sbjct:     1 MQSDNGKLFIGGISWDTNEERLKEYFSSFGEVIEAVILKDRTTGRARGFGFVVFADPAVA 60

Query:    61 ERVIMDKHMIDGRTVEAKKAVPRDDQNMLNR-NTSSIHSSPG-PGRTKKIFVGGLASTVT 118
             E VI +KH IDGR VEAKKAVPRDDQNM+NR N+SSI  SPG PGRT+KIFVGGL S+VT
Sbjct:    61 EIVITEKHNIDGRLVEAKKAVPRDDQNMVNRSNSSSIQGSPGGPGRTRKIFVGGLPSSVT 120

Query:   119 ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEV 178
             ESDFK YF+QFGT TDVVVMYDHNTQRPRGFGFITYDSEEAV++VL KTFHELNGKMVEV
Sbjct:   121 ESDFKTYFEQFGTTTDVVVMYDHNTQRPRGFGFITYDSEEAVEKVLLKTFHELNGKMVEV 180

Query:   179 KRAVPKEFSPGPSRSSM-IGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLA 237
             KRAVPKE SPGPSRS +  GY+ +G NR  NLLN +AQ +N +  GG+G+RMD RFSP+ 
Sbjct:   181 KRAVPKELSPGPSRSPLGAGYS-YGVNRVNNLLNGYAQGFNPAAVGGYGLRMDGRFSPVG 239

Query:   238 TGRGGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLGPFPGGNSNRFSTPVG 297
              GR G + +  +GYG+ +N D GL   + G +N++ ++ YGR + P+  GN+NRF   VG
Sbjct:   240 AGRSGFANYS-SGYGMNVNFDQGLPTGFTGGTNYNGNVDYGRGMSPYYIGNTNRFGPAVG 298

Query:   298 FSGGNGRGDS-VLSSTTWNVWGN-GSLN---SATNPASPGAFLGSGSGNFEVS--FGNNS 350
             + GGNG G+S   SS T N+WGN G LN   + TN  S     GS SGN  +S  FGN+ 
Sbjct:   299 YEGGNGGGNSSFFSSVTRNLWGNNGGLNYNNNNTNSNSNTYMGGSSSGNNTLSGPFGNSG 358

Query:   351 VNWG 354
             VNWG
Sbjct:   359 VNWG 362

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005576 "extracellular region" evidence=ISM

TAIR|locus:2133862 AT4G26650 [Arabidopsis thaliana (taxid:3702)]

 Score = 993 (354.6 bits), Expect = 1.3e-109, Sum P(2) = 1.3e-109
 Identities = 218/367 (59%), Positives = 262/367 (71%)

Query:     3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
             SDLGKLFIGGISWDTDEERL+EYF +YG++VEAVIMRDR TGRARGFGF+VFADP+VAER
Sbjct:    12 SDLGKLFIGGISWDTDEERLQEYFGKYGDLVEAVIMRDRTTGRARGFGFIVFADPSVAER 71

Query:    63 VIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHS-SPGPG------RTKKIFVGGLAS 115
             VIMDKH+IDGRTVEAKKAVPRDDQ +L R+ S +H  SP  G      RTKKIFVGGL S
Sbjct:    72 VIMDKHIIDGRTVEAKKAVPRDDQQVLKRHASPMHLISPSHGGNGGGARTKKIFVGGLPS 131

Query:   116 TVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKM 175
             ++TE++FK YFDQFGTI DVVVMYDHNTQRPRGFGFIT+DSEE+VD VLHKTFHELNGKM
Sbjct:   132 SITEAEFKNYFDQFGTIADVVVMYDHNTQRPRGFGFITFDSEESVDMVLHKTFHELNGKM 191

Query:   176 VEVKRAVPKEFSPG-PSRSSMIGY-NNFGF--NRPT--NLLNSFAQRYNLSPAGGFGVRM 229
             VEVKRAVPKE S   P+RS +IGY NN+G   NR +  +  NSF   YN +  G  G   
Sbjct:   192 VEVKRAVPKELSSTTPNRSPLIGYGNNYGVVPNRSSANSYFNSFPPGYNNNNLGSAG--- 248

Query:   230 DSRFSPLATGRGGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLGP--FPGG 287
               RFSP+ +GR   S FG     +G+N +  L+ ++ G     N+LGY R+ G   F   
Sbjct:   249 --RFSPIGSGRNAFSSFG-----LGLNQELNLNSNFDG-----NTLGYSRIPGNQYFNSA 296

Query:   288 NSNRFSTPVGFSGGNGRGDSVLSSTTWNVWGNGSLNSATNPASPGAFLGSGSGNFEVSFG 347
             + NR+++P+G++    RGDS  + +  ++WGN S +S      PG  LG       VS G
Sbjct:   297 SPNRYNSPIGYN----RGDSAYNPSNRDLWGNRSDSSG-----PGWNLG-------VSVG 340

Query:   348 NNSVNWG 354
             NN  NWG
Sbjct:   341 NNRGNWG 347

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0042732 "D-xylose metabolic process" evidence=RCA

TAIR|locus:2173967 AT5G55550 [Arabidopsis thaliana (taxid:3702)]

 Score = 981 (350.4 bits), Expect = 2.8e-105, Sum P(2) = 2.8e-105
 Identities = 221/370 (59%), Positives = 261/370 (70%)

Query:     1 MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
             MESDLGKLFIGGISWDTDEERL++YFS YG+VVEAVIMRDRATGRARGFGF+VFADP V+
Sbjct:     1 MESDLGKLFIGGISWDTDEERLRDYFSNYGDVVEAVIMRDRATGRARGFGFIVFADPCVS 60

Query:    61 ERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIH-SSP---GPGRTKKIFVGGLAST 116
             ERVIMDKH+IDGRTVEAKKAVPRDDQ +L R+ S IH  SP   G GRTKKIFVGGL S+
Sbjct:    61 ERVIMDKHIIDGRTVEAKKAVPRDDQQVLKRHASPIHLMSPVHGGGGRTKKIFVGGLPSS 120

Query:   117 VTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMV 176
             +TE +FK YFDQFGTI DVVVMYDHNTQRPRGFGFIT+DS++AVDRVLHKTFHELNGK+V
Sbjct:   121 ITEEEFKNYFDQFGTIADVVVMYDHNTQRPRGFGFITFDSDDAVDRVLHKTFHELNGKLV 180

Query:   177 EVKRAVPKEFSPGPS-RSSMIGYNNFG--FNR-PTN-LLNSFAQR---YN-LSPAGGFGV 227
             EVKRAVPKE SP  + RS +    N+G   NR P N   N+FA     YN L P G    
Sbjct:   181 EVKRAVPKEISPVSNIRSPLASGVNYGGGSNRMPANSYFNNFAPGPGFYNSLGPVG---- 236

Query:   228 RMDSRFSP-LATGRGGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRM-LGP-F 284
                 RFSP + +GR  +S FG    G+  +L   L+PS  G+S+   + GY R+   P F
Sbjct:   237 ---RRFSPVIGSGRNAVSAFG---LGLNHDLSLNLNPSCDGTSS---TFGYNRIPSNPYF 287

Query:   285 PGGNSNRFSTPVGFSGGNGRGDSVLSSTTWNVWGNGSLNSATNPASPGAFLGSGSGNFEV 344
              G + NR+++P+G    + R +S  +S   ++WGN      T+ A PG        N  V
Sbjct:   288 NGASPNRYTSPIG----HNRTESPYNSNNRDLWGN-----RTDTAGPG-------WNLNV 331

Query:   345 SFGNNSVNWG 354
             S GNN  NWG
Sbjct:   332 SNGNNRGNWG 341

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

TAIR|locus:2050992 AT2G33410 [Arabidopsis thaliana (taxid:3702)]

 Score = 712 (255.7 bits), Expect = 1.4e-72, Sum P(2) = 1.4e-72
 Identities = 166/367 (45%), Positives = 215/367 (58%)

Query:     1 MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
             MESD GKLFIGGISWDTDE  L+EYFS +GEV++  +MR++ATGR RGFGFV F+DPAV 
Sbjct:     1 MESDQGKLFIGGISWDTDENLLREYFSNFGEVLQVTVMREKATGRPRGFGFVAFSDPAVI 60

Query:    61 ERVIMDKHMIDGRTVEAKKAVPRDDQNMLNR----NTSSIHSSPGPGRTKKIFVGGLAST 116
             +RV+ DKH ID R V+ K+A+ R++Q+   R    N S    S    RTKKIFVGGL   
Sbjct:    61 DRVLQDKHHIDNRDVDVKRAMSREEQSPAGRSGTFNASRNFDSGANVRTKKIFVGGLPPA 120

Query:   117 VTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMV 176
             +T  +F+ YF+ +G ++D V+M D  TQRPRGFGF+++DSE++VD VLHKTFH+LNGK V
Sbjct:   121 LTSDEFRAYFETYGPVSDAVIMIDQTTQRPRGFGFVSFDSEDSVDLVLHKTFHDLNGKQV 180

Query:   177 EVKRAVPKEFSPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDS-RF-S 234
             EVKRA+PK+ +PG +     G    G          F   Y  S   G+  R+DS R+  
Sbjct:   181 EVKRALPKDANPGIASGGGRGSGGAG---------GFPG-YGGSGGSGYEGRVDSNRYMQ 230

Query:   235 PLATGRGGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLG--YGRMLGPFPG-GNSNR 291
             P  TG  G  P+GG+GYG G    G     YGG   + N  G  YG    P  G G+  R
Sbjct:   231 PQNTG-SGYPPYGGSGYGTGYGY-GSNGVGYGGFGGYGNPAGAPYGNPSVPGAGFGSGPR 288

Query:   292 FS----TPVGFSGGNGRGDSVLSSTTWNVWGNGSLNSATNPASPGAFLGSGSGNFEVSFG 347
              S     P G+ G  G G++      W   G+G   SA      GA  G GS  +   +G
Sbjct:   289 SSWGAQAPSGY-GNVGYGNAA----PWG--GSGGPGSAVM-GQAGASAGYGSQGY--GYG 338

Query:   348 NNSVNWG 354
              N  ++G
Sbjct:   339 GNDSSYG 345

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2129590 AT4G14300 [Arabidopsis thaliana (taxid:3702)]

 Score = 692 (248.7 bits), Expect = 3.5e-68, P = 3.5e-68
 Identities = 159/363 (43%), Positives = 223/363 (61%)

Query:     1 MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
             M+SD GKLF+GGISW+TDE++L+E+F+ YGEV +A++MRD+ TGR RGFGFV+F+DP+V 
Sbjct:     1 MDSDQGKLFVGGISWETDEDKLREHFTNYGEVSQAIVMRDKLTGRPRGFGFVIFSDPSVL 60

Query:    61 ERVIMDKHMIDGRTVEAKKAVPRDDQNMLNR--NTSSIHSSPGPG--RTKKIFVGGLAST 116
             +RV+ +KH ID R V+ K+A+ R++Q +  R  N ++  SS G    +TKKIFVGGL  T
Sbjct:    61 DRVLQEKHSIDTREVDVKRAMSREEQQVSGRTGNLNTSRSSGGDAYNKTKKIFVGGLPPT 120

Query:   117 VTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMV 176
             +T+ +F++YF+ +G +TDV +MYD  T RPRGFGF+++DSE+AVD VLHKTFH+L+GK V
Sbjct:   121 LTDEEFRQYFEVYGPVTDVAIMYDQATNRPRGFGFVSFDSEDAVDSVLHKTFHDLSGKQV 180

Query:   177 EVKRAVPKEFSPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDS-RFSP 235
             EVKRA+PK+ +PG    SM G  + G+           Q Y  + +   G RMDS RF  
Sbjct:   181 EVKRALPKDANPGGGGRSMGGGGSGGY-----------QGYGGNESSYDG-RMDSNRFLQ 228

Query:   236 LATGRGGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLG-YGRMLGPFPG-GNSNRFS 293
               +   G+  +G +GYG G   +G     YG    ++ S G YG   G   G G +N   
Sbjct:   229 HQSVGNGLPSYGSSGYGAGYG-NGSNGAGYGAYGGYTGSAGGYGA--GATAGYGATNIPG 285

Query:   294 TPVGFSGG---NGRGDSVLSSTTWNV-WGNGSLNSATN-P-ASPGAFLGSGSGNFEVSFG 347
                G S G       D+  SS   N  +G+G+ +S    P A+P     SG  N    +G
Sbjct:   286 AGYGSSTGVAPRNSWDTPASSGYGNPGYGSGAAHSGYGVPGAAPPTQSPSGYSNQGYGYG 345

Query:   348 NNS 350
               S
Sbjct:   346 GYS 348

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0005829 "cytosol" evidence=RCA

UNIPROTKB|E2R6E4 DAZAP1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 470 (170.5 bits), Expect = 1.8e-48, Sum P(2) = 1.8e-48
 Identities = 100/253 (39%), Positives = 148/253 (58%)

Query:     4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV 63
             ++GKLF+GG+ W T +E L+ YFS+YGEVV+ VIM+D+ T ++RGFGFV F DP     V
Sbjct:     8 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV 67

Query:    64 IMDK-HMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTK--KIFVGGLASTVTES 120
             +  + H +DGR ++ K   PR  Q    R        P    +K  KIFVGG+     E+
Sbjct:    68 LASRPHTLDGRNIDPKPCTPRGMQPERTRPKEGWQKGPRSDNSKSNKIFVGGIPHNCGET 127

Query:   121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR 180
             + ++YF +FG +T+VV++YD   QRPRGFGFIT++ E++VD+ ++  FH++ GK VEVKR
Sbjct:   128 ELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKR 187

Query:   181 AVPKEF-SPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATG 239
             A P++  S  P +    G + +G     N  N +A +   +   G+G +    + P    
Sbjct:   188 AEPRDSKSQAPGQP---GASQWGSRVVPNAANGWAGQPPPTWQQGYGPQ--GMWVPAGQA 242

Query:   240 RGGISPFGGAGYG 252
              GG  P   AG G
Sbjct:   243 IGGYGP-PPAGRG 254

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|I3LB68 DAZAP1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 470 (170.5 bits), Expect = 7.7e-48, Sum P(2) = 7.7e-48
 Identities = 100/253 (39%), Positives = 148/253 (58%)

Query:     4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV 63
             ++GKLF+GG+ W T +E L+ YFS+YGEVV+ VIM+D+ T ++RGFGFV F DP     V
Sbjct:     8 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV 67

Query:    64 IMDK-HMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTK--KIFVGGLASTVTES 120
             +  + H +DGR ++ K   PR  Q    R        P    +K  KIFVGG+     E+
Sbjct:    68 LASRPHTLDGRNIDPKPCTPRGMQPERTRPKEGWQKGPRSDNSKSNKIFVGGIPHNCGET 127

Query:   121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR 180
             + ++YF +FG +T+VV++YD   QRPRGFGFIT++ E++VD+ ++  FH++ GK VEVKR
Sbjct:   128 ELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKR 187

Query:   181 AVPKEF-SPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATG 239
             A P++  S  P +    G + +G     N  N +A +   +   G+G +    + P    
Sbjct:   188 AEPRDSKSQAPGQP---GASQWGSRVVPNAANGWAGQPPPTWQQGYGPQ--GMWVPAGQA 242

Query:   240 RGGISPFGGAGYG 252
              GG  P   AG G
Sbjct:   243 IGGYGP-PPAGRG 254

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q96EP5 DAZAP1 "DAZ-associated protein 1" [Homo sapiens (taxid:9606)]

 Score = 470 (170.5 bits), Expect = 1.6e-47, Sum P(2) = 1.6e-47
 Identities = 100/253 (39%), Positives = 148/253 (58%)

Query:     4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV 63
             ++GKLF+GG+ W T +E L+ YFS+YGEVV+ VIM+D+ T ++RGFGFV F DP     V
Sbjct:     8 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV 67

Query:    64 IMDK-HMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTK--KIFVGGLASTVTES 120
             +  + H +DGR ++ K   PR  Q    R        P    +K  KIFVGG+     E+
Sbjct:    68 LASRPHTLDGRNIDPKPCTPRGMQPERTRPKEGWQKGPRSDNSKSNKIFVGGIPHNCGET 127

Query:   121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR 180
             + ++YF +FG +T+VV++YD   QRPRGFGFIT++ E++VD+ ++  FH++ GK VEVKR
Sbjct:   128 ELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKR 187

Query:   181 AVPKEF-SPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATG 239
             A P++  S  P +    G + +G     N  N +A +   +   G+G +    + P    
Sbjct:   188 AEPRDSKSQAPGQP---GASQWGSRVVPNAANGWAGQPPPTWQQGYGPQ--GMWVPAGQA 242

Query:   240 RGGISPFGGAGYG 252
              GG  P   AG G
Sbjct:   243 IGGYGP-PPAGRG 254

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007283 "spermatogenesis" evidence=IEA

GO:0030154 "cell differentiation" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

TAIR|locus:2007903 AT1G17640 [Arabidopsis thaliana (taxid:3702)]

 Score = 496 (179.7 bits), Expect = 2.0e-47, P = 2.0e-47
 Identities = 120/311 (38%), Positives = 168/311 (54%)

Query:     3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
             S  GKLF+GG+SW+T  E    YF ++GEVV++VIM DR TG  RGFGFV FAD AVAE+
Sbjct:    63 SSPGKLFVGGVSWETTAETFANYFGKFGEVVDSVIMTDRITGNPRGFGFVTFADSAVAEK 122

Query:    63 VIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDF 122
             V+ + H+ID R V+ K+ +PR D++   +  S         +T+KIFVGGL   + E + 
Sbjct:   123 VLEEDHVIDDRKVDLKRTLPRGDKDTDIKAVS---------KTRKIFVGGLPPLLEEDEL 173

Query:   123 KKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK-TFHELNGKMVEVKRA 181
             K YF  +G I +  +MYDH+T R RGFGF+T+ +E++VDR+      HEL  K VE+KRA
Sbjct:   174 KNYFCVYGDIIEHQIMYDHHTGRSRGFGFVTFQTEDSVDRLFSDGKVHELGDKQVEIKRA 233

Query:   182 VPKEFSPGPSRSSMIGYNNFG-FNRPTNLLNSFAQRYNL-SPAGGFGVRMDSRFSPLATG 239
              PK    G   +S   Y   G +++  +      + Y++ S  GG+G      +   A G
Sbjct:   234 EPKR--TGRD-NSFRSYGASGKYDQEDSYSGKANEDYSMYSGYGGYG-----GYGAYA-G 284

Query:   240 RGGISPFG----GAGYGVGMNLDGGL-SPSYGGSSNFSNSLGYGRMLGPFPGGNSNRFST 294
                ++P G    G GYG G    G + +  YG         GYG       GG  +  + 
Sbjct:   285 NSMVNPAGFYGYGGGYGYGYGYGGQMFNMGYGAGGYSHMGSGYGVAAAAAYGGGKSHGNG 344

Query:   295 PVGFSGGNGRG 305
               G S G G G
Sbjct:   345 NNGSSSGKGNG 355

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

MGI|MGI:1923876 Msi2 "musashi RNA-binding protein 2" [Mus musculus (taxid:10090)]

 Score = 488 (176.8 bits), Expect = 1.4e-46, P = 1.4e-46
 Identities = 131/345 (37%), Positives = 176/345 (51%)

Query:     2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
             + D GK+FIGG+SW T  + L++YFS++GE+ E ++MRD  T R+RGFGFV FADPA  +
Sbjct:    17 QHDPGKMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVD 76

Query:    62 RVI-MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGL-ASTVTE 119
             +V+    H +D +T++ K A PR  Q  +              RTKKIFVGGL A+TV E
Sbjct:    77 KVLGQPHHELDSKTIDPKVAFPRRAQPKMVT------------RTKKIFVGGLSANTVVE 124

Query:   120 SDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVK 179
              D K+YF+QFG + D ++M+D  T R RGFGF+T+++E+ V++V    FHE+N KMVE K
Sbjct:   125 -DVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEIHFHEINNKMVECK 183

Query:   180 RAVPKE--FSPGP-SRSSMIGYNNFGFNRPTNLLN--SFAQRYNLSPAGGFGVRMDSRFS 234
             +A PKE  F PG   R+  + Y    F     +L   +F   Y     G F      +F 
Sbjct:   184 KAQPKEVMFPPGTRGRARGLPYTMDAFMLGMGMLGYPNFVATYGRGYPG-FAPSYGYQFP 242

Query:   235 PLATGRGGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLGPFPGGNSNRFST 294
                    G  P   A         G +  SY    NF      G    P  G N  R   
Sbjct:   243 GFPAAAYG--PVAAAAVAAAR---GSVLNSYSAQPNF------GAPASP-AGSNPAR--- 287

Query:   295 PVGFSGGNGRGDSV-LSSTTWNVWGNGSLNSATNPASPGAFLGSG 338
             P GF G N  G    L        G G+  SA +P  PG+  G G
Sbjct:   288 PGGFPGANSPGPVADLYGPASQDSGVGNYISAASP-QPGSGFGHG 331

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003727 "single-stranded RNA binding" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005844 "polysome" evidence=IDA

GO:0008266 "poly(U) RNA binding" evidence=IDA

GO:0048864 "stem cell development" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	522
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	2e-46
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-35
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	3e-30
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	7e-28
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	5e-26
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	2e-25
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-25
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	3e-25
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	3e-25
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-24
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	2e-24
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	3e-24
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	3e-24
smart00360	73	smart00360, RRM, RNA recognition motif	3e-24
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	6e-24
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	8e-23
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	1e-22
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	2e-22
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	6e-22
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-21
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	1e-21
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-21
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-21
smart00360	73	smart00360, RRM, RNA recognition motif	9e-21
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	1e-20
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	3e-20
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	4e-20
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	6e-20
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	6e-20
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	7e-20
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	7e-20
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-19
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	2e-19
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	2e-19
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	5e-19
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	6e-19
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	7e-19
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	8e-19
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	8e-19
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	2e-18
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	2e-18
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-18
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	3e-18
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	3e-18
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-17
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	1e-17
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	2e-17
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	2e-17
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-17
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	7e-17
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	8e-17
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	9e-17
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	1e-16
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	1e-16
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	1e-16
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	1e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-16
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	4e-16
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	5e-16
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	5e-16
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	6e-16
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	8e-16
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	8e-16
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	8e-16
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	9e-16
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-15
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	3e-15
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-15
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	6e-15
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	6e-15
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	6e-15
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	9e-15
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-14
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-14
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-14
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-14
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-14
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	5e-14
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	5e-14
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	7e-14
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	1e-13
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	2e-13
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-13
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	3e-13
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	4e-13
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	5e-13
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	5e-13
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-13
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	8e-13
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-12
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-12
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	1e-12
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-12
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-12
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	3e-12
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	3e-12
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	3e-12
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-12
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	6e-12
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	6e-12
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	9e-12
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	1e-11
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	1e-11
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-11
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	3e-11
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-11
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	6e-11
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	2e-10
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-10
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	2e-10
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-10
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	2e-10
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	2e-10
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	2e-10
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	3e-10
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	3e-10
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	3e-10
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	4e-10
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	4e-10
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	4e-10
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	5e-10
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	5e-10
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	5e-10
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	5e-10
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	6e-10
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	6e-10
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	6e-10
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	8e-10
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	9e-10
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	9e-10
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	9e-10
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	1e-09
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	1e-09
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-09
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	2e-09
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	2e-09
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	2e-09
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	3e-09
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	3e-09
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	3e-09
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	4e-09
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	5e-09
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	5e-09
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	5e-09
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	6e-09
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	6e-09
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	7e-09
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	7e-09
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	9e-09
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	9e-09
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	1e-08
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	1e-08
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	1e-08
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	1e-08
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-08
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-08
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-08
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-08
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	2e-08
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	2e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-08
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	2e-08
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	2e-08
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	2e-08
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	4e-08
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	4e-08
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	5e-08
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	5e-08
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	5e-08
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	5e-08
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	5e-08
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	5e-08
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	6e-08
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	7e-08
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	7e-08
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	8e-08
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	8e-08
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	1e-07
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	1e-07
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	1e-07
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	1e-07
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	1e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-07
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-07
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-07
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	1e-07
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-07
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-07
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	2e-07
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-07
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-07
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	3e-07
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	3e-07
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	3e-07
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	4e-07
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	4e-07
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	4e-07
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	5e-07
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	5e-07
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	5e-07
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	5e-07
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	5e-07
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	5e-07
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	6e-07
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	6e-07
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	6e-07
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	6e-07
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	7e-07
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	7e-07
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	8e-07
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	8e-07
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	9e-07
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	9e-07
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	9e-07
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-06
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-06
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	1e-06
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	1e-06
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-06
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	2e-06
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-06
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-06
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	2e-06
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-06
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	2e-06
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	2e-06
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	2e-06
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-06
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	3e-06
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	3e-06
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	3e-06
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	3e-06
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	3e-06
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	3e-06
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	3e-06
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	3e-06
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	3e-06
cd12458	70	cd12458, RRM_AtC3H46_like, RNA recognition motif i	3e-06
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	3e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	3e-06
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	4e-06
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	4e-06
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	4e-06
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	4e-06
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	4e-06
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	5e-06
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	5e-06
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	6e-06
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	6e-06
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	7e-06
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	7e-06
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	7e-06
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	8e-06
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	9e-06
cd12429	74	cd12429, RRM_DNAJC17, RNA recognition motif in the	9e-06
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	9e-06
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-05
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	1e-05
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-05
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	1e-05
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	1e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	1e-05
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	1e-05
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	1e-05
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	1e-05
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	1e-05
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	1e-05
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	1e-05
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	1e-05
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	2e-05
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	2e-05
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	2e-05
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	2e-05
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	2e-05
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	2e-05
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	2e-05
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	2e-05
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	3e-05
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	3e-05
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	3e-05
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	4e-05
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	4e-05
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	4e-05
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	4e-05
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	4e-05
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	4e-05
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	4e-05
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	5e-05
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	5e-05
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	5e-05
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	5e-05
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	5e-05
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	6e-05
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	6e-05
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	6e-05
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	6e-05
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	6e-05
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	6e-05
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	6e-05
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	6e-05
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	7e-05
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	8e-05
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	8e-05
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	9e-05
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	9e-05
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	9e-05
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	9e-05
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	9e-05
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-04
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	1e-04
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	1e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-04
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	2e-04
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	2e-04
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	2e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	2e-04
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	2e-04
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	2e-04
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	2e-04
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	2e-04
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	2e-04
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-04
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	2e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	3e-04
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	3e-04
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	3e-04
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	3e-04
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	3e-04
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	4e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	4e-04
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	4e-04
cd12228	84	cd12228, RRM_ENOX, RNA recognition motif (RRM) in	4e-04
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	4e-04
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	4e-04
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	4e-04
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	5e-04
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	5e-04
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	5e-04
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	5e-04
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	5e-04
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	5e-04
cd12250	82	cd12250, RRM2_hnRNPR_like, RNA recognition motif 2	5e-04
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	6e-04
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	6e-04
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	6e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	6e-04
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	7e-04
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	7e-04
cd12348	75	cd12348, RRM1_SHARP, RNA recognition motif 1 in SM	7e-04
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	7e-04
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	7e-04
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	8e-04
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	8e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	8e-04
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	8e-04
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	8e-04
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	8e-04
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	9e-04
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	0.001
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	0.001
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	0.001
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	0.001
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	0.001
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	0.001
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	0.001
cd12658	76	cd12658, RRM1_MYEF2, RNA recognition motif 1 in ve	0.001
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	0.001
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	0.001
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	0.001
cd12444	112	cd12444, RRM1_CPEBs, RNA recognition motif 1 in cy	0.001
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.002
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.002
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	0.002
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	0.002
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	0.002
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	0.002
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	0.002
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	0.002
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	0.002
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	0.002
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	0.002
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	0.002
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	0.002
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	0.002
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	0.003
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	0.003
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	0.003
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	0.003
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	0.003
cd12281	92	cd12281, RRM1_TatSF1_like, RNA recognition motif 1	0.003
cd12265	86	cd12265, RRM_SLT11, RNA recognition motif of pre-m	0.003
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	0.003
cd12505	75	cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-	0.003
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	0.003
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	0.003
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	0.003
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	0.003
cd12536	85	cd12536, RRM1_RBM39, RNA recognition motif 1 in ve	0.003
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	0.004
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	0.004
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	0.004
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	0.004
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	0.004
cd12301	74	cd12301, RRM1_2_PAR10_like, RNA recognition motif	0.004
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	0.004
cd12678	74	cd12678, RRM_SLTM, RNA recognition motif in Scaffo	0.004
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	0.004
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	0.004
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	0.004
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	0.004

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

 Score =  156 bits (396), Expect = 2e-46
 Identities = 55/80 (68%), Positives = 70/80 (87%)

Query: 104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV 163
           RTKKIFVGGL   VTE+D +KYF QFGT+T+VVVMYDH  +RPRGFGFIT++SE++VD+V
Sbjct: 1   RTKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV 60

Query: 164 LHKTFHELNGKMVEVKRAVP 183
           +++ FH++NGK VEVKRA P
Sbjct: 61  VNEHFHDINGKKVEVKRAEP 80

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

 Score =  126 bits (320), Expect = 1e-35
 Identities = 45/72 (62%), Positives = 59/72 (81%), Gaps = 1/72 (1%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          LFIGG+SWDT EE L+EYFS+YGEVV+ VIM+D  TGR+RGFGFV FADP+  ++V+  K
Sbjct: 1  LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 68 -HMIDGRTVEAK 78
           H++DGR ++ K
Sbjct: 61 PHVLDGREIDPK 72

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

 Score =  112 bits (281), Expect = 3e-30
 Identities = 42/74 (56%), Positives = 55/74 (74%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           KIFVGGL++  TE D KKYF QFG + D ++M+D  T R RGFGF+T++SE+ VD+V   
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60

Query: 167 TFHELNGKMVEVKR 180
            FHE+N KMVE K+
Sbjct: 61  HFHEINNKMVECKK 74

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

 Score =  105 bits (265), Expect = 7e-28
 Identities = 46/75 (61%), Positives = 54/75 (72%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           KIFVGGL   VTE +FK+YF QFG + D  +M DH+T R RGFGF+T+DSE AV+RV   
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 167 TFHELNGKMVEVKRA 181
              EL GK VEVKRA
Sbjct: 61  GMLELGGKQVEVKRA 75

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

>gnl|CDD|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score =  100 bits (251), Expect = 5e-26
 Identities = 35/76 (46%), Positives = 57/76 (75%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          +FIGG++W+T ++ L+EYF ++GEV +  +MRD ATGR+RGFGF+ F  P     V+  +
Sbjct: 1  MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 68 HMIDGRTVEAKKAVPR 83
          H++DG+ ++ K+A+PR
Sbjct: 61 HILDGKIIDPKRAIPR 76

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|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 99.1 bits (247), Expect = 2e-25
 Identities = 43/81 (53%), Positives = 57/81 (70%), Gaps = 1/81 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          KLF+GG+SW+T +E L+ YFS+YGEVV+ VIM+D+ T R+RGFGFV F DP     V+  
Sbjct: 1  KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60

Query: 67 K-HMIDGRTVEAKKAVPRDDQ 86
            H +DGRT++ K   PR  Q
Sbjct: 61 GPHTLDGRTIDPKPCTPRGMQ 81

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|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 99.0 bits (247), Expect = 2e-25
 Identities = 31/77 (40%), Positives = 48/77 (62%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
           L + G+ W T E+ LK+YFS +GE++   + +D  TG+++GFGFV FAD     +V+  
Sbjct: 1  DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ 60

Query: 67 KHMIDGRTVEAKKAVPR 83
          +HMIDGR  + K    +
Sbjct: 61 RHMIDGRWCDVKIPNSK 77

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

 Score = 99.0 bits (246), Expect = 3e-25
 Identities = 41/78 (52%), Positives = 58/78 (74%)

Query: 104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV 163
           RTKKIFVGGL++     D K+YF+QFG + D ++M+D  T R RGFGF+T+++E+ V++V
Sbjct: 2   RTKKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKV 61

Query: 164 LHKTFHELNGKMVEVKRA 181
               FHE+N KMVE K+A
Sbjct: 62  CEIHFHEINNKMVECKKA 79

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

 Score = 98.6 bits (246), Expect = 3e-25
 Identities = 39/78 (50%), Positives = 57/78 (73%), Gaps = 1/78 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          KLFIGG+S++T ++ LK YFS++GE+ + V+M+D  T R+RGFGFV FA  +  +  +  
Sbjct: 1  KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 67 K-HMIDGRTVEAKKAVPR 83
          + H +DGR VE K+AVPR
Sbjct: 61 RPHKVDGREVEPKRAVPR 78

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

 Score = 96.9 bits (242), Expect = 1e-24
 Identities = 29/72 (40%), Positives = 46/72 (63%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           +F+GGL+   TE   ++YF ++G + D V+M D  T R RGFGF+T+    +VD+VL   
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 168 FHELNGKMVEVK 179
            H L+G+ ++ K
Sbjct: 61  PHVLDGREIDPK 72

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|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 96.3 bits (240), Expect = 2e-24
 Identities = 37/75 (49%), Positives = 54/75 (72%), Gaps = 1/75 (1%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD- 66
          +FIGG+SW T  E L+EYFS++GE+ E ++MRD  T R+RGFGFV F+DPA  ++V+   
Sbjct: 1  MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60

Query: 67 KHMIDGRTVEAKKAV 81
           H +DG+ ++ K A 
Sbjct: 61 PHELDGKKIDPKVAF 75

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

 Score = 95.9 bits (239), Expect = 3e-24
 Identities = 39/78 (50%), Positives = 54/78 (69%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+F+GGL+   T+   K YF Q+G ITD VVM D NT+R RGFGF+T+ S   VD  ++ 
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 167 TFHELNGKMVEVKRAVPK 184
             H+++G+ VE KRAVP+
Sbjct: 61  RPHKVDGREVEPKRAVPR 78

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

 Score = 95.9 bits (239), Expect = 3e-24
 Identities = 37/75 (49%), Positives = 50/75 (66%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           KIFVGGL+   TE   ++YF +FG I ++ +  D  T + RGF FIT+DSEE V ++L  
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60

Query: 167 TFHELNGKMVEVKRA 181
            FH + GK VEVK+A
Sbjct: 61  QFHVIGGKKVEVKKA 75

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|214636 smart00360, RRM, RNA recognition motif

 Score = 95.4 bits (238), Expect = 3e-24
 Identities = 27/72 (37%), Positives = 46/72 (63%), Gaps = 2/72 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           LF+G +  DT EE L+E FS++G+V    ++RD+ TG+++GF FV F     AE+ +  
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 65 MDKHMIDGRTVE 76
          ++   +DGR ++
Sbjct: 61 LNGKELDGRPLK 72

Length = 73

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

 Score = 94.7 bits (235), Expect = 6e-24
 Identities = 39/74 (52%), Positives = 54/74 (72%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           KIFVGGL+   T  D K+YF+QFG + D ++M+D  T R RGFGF+T++SE+ V++V   
Sbjct: 1   KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 167 TFHELNGKMVEVKR 180
            FHE+N KMVE K+
Sbjct: 61  HFHEINNKMVECKK 74

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

 Score = 91.5 bits (228), Expect = 8e-23
 Identities = 34/75 (45%), Positives = 52/75 (69%), Gaps = 1/75 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          K+F+GG+ + T ++ L++YFS++GE+ EAV++ DR TG++RG+GFV F D   AER   D
Sbjct: 2  KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 67 KH-MIDGRTVEAKKA 80
           + +IDGR      A
Sbjct: 62 PNPIIDGRKANVNLA 76

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

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

 Score = 91.3 bits (227), Expect = 1e-22
 Identities = 36/75 (48%), Positives = 50/75 (66%), Gaps = 1/75 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
          K+F+GG+  D  EE  KEYFS++G+VV+A +M+D  TGR+RGFGFV F   +  ERV   
Sbjct: 1  KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 66 DKHMIDGRTVEAKKA 80
              + G+ VE K+A
Sbjct: 61 GMLELGGKQVEVKRA 75

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

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

 Score = 90.3 bits (224), Expect = 2e-22
 Identities = 40/74 (54%), Positives = 56/74 (75%), Gaps = 1/74 (1%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          +F+GG+SWDT ++ LKEYFS++GEVV+  I  D  TGR+RGFGFV+F D A  E+V+  K
Sbjct: 1  MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 68 -HMIDGRTVEAKKA 80
           H +DGR ++ K+A
Sbjct: 61 EHKLDGRVIDPKRA 74

This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

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

 Score = 89.2 bits (222), Expect = 6e-22
 Identities = 32/73 (43%), Positives = 49/73 (67%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+FVGGL   VTE D ++YF Q+G +  V ++ D  T + RGF F+T+D  + VD+++ +
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

Query: 167 TFHELNGKMVEVK 179
            +H +NG  VEVK
Sbjct: 61  KYHTINGHRVEVK 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|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 88.1 bits (219), Expect = 1e-21
 Identities = 34/73 (46%), Positives = 47/73 (64%), Gaps = 1/73 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          KLF+GG+  D  EE L+EYFS+YG V    I+ D+ TG+ RGF FV F D    +++++ 
Sbjct: 1  KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

Query: 67 K-HMIDGRTVEAK 78
          K H I+G  VE K
Sbjct: 61 KYHTINGHRVEVK 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|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 88.5 bits (219), Expect = 1e-21
 Identities = 37/75 (49%), Positives = 56/75 (74%), Gaps = 1/75 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          K+F+GG+SWDT ++ LK+YF+++GEV +  I  D  TGR+RGFGF++F D +  E+V+  
Sbjct: 1  KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

Query: 67 K-HMIDGRTVEAKKA 80
          K H +DGR ++ KKA
Sbjct: 61 KEHRLDGRLIDPKKA 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|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 = 88.0 bits (219), Expect = 2e-21
 Identities = 30/77 (38%), Positives = 48/77 (62%), Gaps = 2/77 (2%)

Query: 6  GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI- 64
           KLF+ G+S  T E+ L+  FS++G V E ++M+D  TG +RGFGFV F     A+  I 
Sbjct: 2  NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 65 -MDKHMIDGRTVEAKKA 80
           ++   ++GR ++ +KA
Sbjct: 62 DLNGKELEGRVIKVEKA 78

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

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

 Score = 96.4 bits (240), Expect = 4e-21
 Identities = 69/276 (25%), Positives = 109/276 (39%), Gaps = 43/276 (15%)

Query: 16  DTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGR 73
             +E++L+E F+++GE+  A +M+D + GR+RGF FV F     A + +  M+   I   
Sbjct: 189 SVNEDKLRELFAKFGEITSAAVMKDGS-GRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLA 247

Query: 74  TVEAK----KAVPRDDQNML------NRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFK 123
               K    +A  R ++                  + G      ++V  L  TVT+   +
Sbjct: 248 KEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGV----NLYVKNLDDTVTDEKLR 303

Query: 124 KYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFH--ELNGKMVEVKRA 181
           + F + G IT   VM D      RGFGF+ + + E  +R +    H   L GK + V  A
Sbjct: 304 ELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAV-TEMHGRMLGGKPLYVALA 361

Query: 182 VPKEFSPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATGRG 241
             KE      R + +  + F   +P        Q    SP GG   +      P   G+G
Sbjct: 362 QRKE-----QRRAHL-QDQFMQLQP-----RMRQLPMGSPMGGAMGQ------PPYYGQG 404

Query: 242 GISPFGG--AGYGVGMNLDGGLSPSYGGSSNFSNSL 275
               F G   G+     +    +P   G     N L
Sbjct: 405 PQQQFNGQPLGWPRMSMM---PTPMGPGGPLRPNGL 437

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|214636 smart00360, RRM, RNA recognition motif

 Score = 85.7 bits (213), Expect = 9e-21
 Identities = 23/73 (31%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
            +FVG L    TE + ++ F +FG +  V ++ D  T + +GF F+ ++SEE  ++ L  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 167 -TFHELNGKMVEV 178
               EL+G+ ++V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 85.4 bits (211), Expect = 1e-20
 Identities = 37/75 (49%), Positives = 56/75 (74%), Gaps = 1/75 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
          K+FIGG+SWDT ++ L EY SR+GEV++  I  D  TGR+RGFGFV+F D A  ++V+ +
Sbjct: 1  KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60

Query: 66 DKHMIDGRTVEAKKA 80
           +H +DG+ ++ K+A
Sbjct: 61 KEHKLDGKLIDPKRA 75

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

>gnl|CDD|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 84.7 bits (209), Expect = 3e-20
 Identities = 37/75 (49%), Positives = 54/75 (72%), Gaps = 1/75 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
          K+FIGG+SW T +E L+EYF ++GEV E ++MRD  T R+RGFGFV F D A  ++V+  
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 66 DKHMIDGRTVEAKKA 80
           +H +D +T++ K A
Sbjct: 62 SRHELDSKTIDPKVA 76

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

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

 Score = 84.0 bits (208), Expect = 4e-20
 Identities = 33/74 (44%), Positives = 52/74 (70%), Gaps = 1/74 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
          K+F+GG+S +T E+ +K+YFS++G+V +A++M D+ T R RGFGFV F    V ++V  +
Sbjct: 1  KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60

Query: 66 DKHMIDGRTVEAKK 79
            H I+ + VE KK
Sbjct: 61 HFHEINNKMVECKK 74

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

 Score = 83.7 bits (207), Expect = 6e-20
 Identities = 32/79 (40%), Positives = 51/79 (64%)

Query: 104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV 163
           +  K+FVGGL    ++S  +++F ++G +T+ VVM D NT+R RGFGFIT+ S +  D  
Sbjct: 1   QLCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA 60

Query: 164 LHKTFHELNGKMVEVKRAV 182
           +    H ++G  +E+KRA 
Sbjct: 61  MEAQPHSIDGNQIELKRAK 79

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

 Score = 83.8 bits (207), Expect = 6e-20
 Identities = 35/79 (44%), Positives = 49/79 (62%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+FVGGL   V E D  ++F QFG +    V+ D  T + RGFGF+ + + ++ D+    
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60

Query: 167 TFHELNGKMVEVKRAVPKE 185
            FH +NG  VEVK+AVPKE
Sbjct: 61  KFHPINGHRVEVKKAVPKE 79

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

 Score = 90.0 bits (222), Expect = 7e-20
 Identities = 40/167 (23%), Positives = 72/167 (43%), Gaps = 12/167 (7%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            LF+G + +D  EE L+E F ++G V    ++RDR TG++RGF FV F     AE+ I  
Sbjct: 117 TLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEE 176

Query: 65  MDKHMIDGRTVEAKKAVPRDDQNM---------LNRNTSSIHSSPGPGRTKKIFVGGLAS 115
           ++   ++GR +  +KA P                 +  S   +     ++  ++VG L  
Sbjct: 177 LNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLE-KSDNLYVGNLPL 235

Query: 116 TVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDR 162
              E +    F   G I    +    + + P+   F+  ++ +    
Sbjct: 236 KTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALE 282

Length = 306

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

 Score = 83.6 bits (206), Expect = 7e-20
 Identities = 38/79 (48%), Positives = 58/79 (73%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           +K+F+GGL+   T+   + +F+Q+GT+TD VVM D NT+R RGFGF+TY S E VD  ++
Sbjct: 3   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMN 62

Query: 166 KTFHELNGKMVEVKRAVPK 184
              H+++G++VE KRAV +
Sbjct: 63  ARPHKVDGRVVEPKRAVSR 81

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|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 = 82.6 bits (204), Expect = 1e-19
 Identities = 36/77 (46%), Positives = 56/77 (72%), Gaps = 2/77 (2%)

Query: 6  GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI- 64
          GKLFIGG+S+DT+E+ L++ FS+YG++ E V+++DR T R+RGFGFV F +P  A+  + 
Sbjct: 1  GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMM 60

Query: 65 -MDKHMIDGRTVEAKKA 80
           M+   +DGR +   +A
Sbjct: 61 AMNGKSVDGRQIRVDQA 77

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

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

 Score = 82.8 bits (205), Expect = 2e-19
 Identities = 31/77 (40%), Positives = 47/77 (61%), Gaps = 1/77 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
          K+F+GG+  +  E  L++YFS++G V E V+M D    R RGFGF+ F      ++V+  
Sbjct: 4  KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNE 63

Query: 66 DKHMIDGRTVEAKKAVP 82
            H I+G+ VE K+A P
Sbjct: 64 HFHDINGKKVEVKRAEP 80

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|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 82.4 bits (203), Expect = 2e-19
 Identities = 37/75 (49%), Positives = 55/75 (73%), Gaps = 1/75 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
          K+FIGG+SW T  + L++YFS++GE+ E ++MRD  T R+RGFGFV FADPA  ++V+  
Sbjct: 1  KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60

Query: 66 DKHMIDGRTVEAKKA 80
            H +D +T++ K A
Sbjct: 61 PHHELDSKTIDPKVA 75

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

>gnl|CDD|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 81.2 bits (200), Expect = 5e-19
 Identities = 31/80 (38%), Positives = 51/80 (63%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           KKIFVGG+     E   + YF+++G I  + VM D  + + RGF F+T+D  + VD+++ 
Sbjct: 1   KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVV 60

Query: 166 KTFHELNGKMVEVKRAVPKE 185
           + +H +NG   EVK+A+ K+
Sbjct: 61  QKYHTINGHNCEVKKALSKQ 80

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

 Score = 80.8 bits (200), Expect = 6e-19
 Identities = 28/73 (38%), Positives = 46/73 (63%), Gaps = 3/73 (4%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          LF+G +  DT EE L+E FS++GE+    I+RD+  G+++GF FV F  P  AE+ +  +
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 66 DKHMIDGRTVEAK 78
          +   +DGR ++  
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|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 80.9 bits (199), Expect = 7e-19
 Identities = 35/79 (44%), Positives = 56/79 (70%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           +K+F+GGL+   T+   +++F+++GT+TD VVM D  T+R RGFGF+TY   E VD  + 
Sbjct: 3   RKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMS 62

Query: 166 KTFHELNGKMVEVKRAVPK 184
              H+++G++VE KRAV +
Sbjct: 63  ARPHKVDGRVVEPKRAVSR 81

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|241026 cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 80.8 bits (199), Expect = 8e-19
 Identities = 32/78 (41%), Positives = 51/78 (65%), Gaps = 1/78 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          K+F+GGI  DT+E  L++YF +YG++    +M DR +G+ RGF FV F D    +++++ 
Sbjct: 2  KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQ 61

Query: 67 K-HMIDGRTVEAKKAVPR 83
          K H I+G   E KKA+ +
Sbjct: 62 KYHTINGHNCEVKKALSK 79

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

 Score = 80.4 bits (198), Expect = 8e-19
 Identities = 34/74 (45%), Positives = 55/74 (74%), Gaps = 1/74 (1%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          +FIGG+SWDT ++ LK+YFS++GEVV+  +  D  TGR+RGFGFV+F +    ++V+  K
Sbjct: 1  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 68 -HMIDGRTVEAKKA 80
           H ++G+ ++ K+A
Sbjct: 61 EHKLNGKVIDPKRA 74

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|241020 cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins

 Score = 79.4 bits (196), Expect = 2e-18
 Identities = 32/75 (42%), Positives = 49/75 (65%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           +F+GGL+   T    ++YF +FG I + +VM D  T+R RGFGF+T+    +VD+VL + 
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60

Query: 168 FHELNGKMVEVKRAV 182
            HEL+GK ++ K A 
Sbjct: 61  PHELDGKKIDPKVAF 75

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|241024 cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins

 Score = 79.6 bits (196), Expect = 2e-18
 Identities = 29/77 (37%), Positives = 50/77 (64%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           KKIFVGG+     E   + YF+Q+G I  + +M D  + + RGF F+T+D  ++VD+++ 
Sbjct: 1   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 60

Query: 166 KTFHELNGKMVEVKRAV 182
           + +H +NG   EV++A+
Sbjct: 61  QKYHTVNGHNCEVRKAL 77

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 79.2 bits (196), Expect = 2e-18
 Identities = 28/71 (39%), Positives = 43/71 (60%), Gaps = 3/71 (4%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          LF+G +  DT EE LK+ FS++G +    I+RD  TGR++GF FV F D   AE+ +  +
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 66 DKHMIDGRTVE 76
          +   + GR + 
Sbjct: 60 NGKELGGRELR 70

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

>gnl|CDD|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 79.0 bits (194), Expect = 3e-18
 Identities = 41/82 (50%), Positives = 57/82 (69%), Gaps = 9/82 (10%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFA-----DPAVAE 61
          KLFIGG+S++T EE L+ Y+ ++G++ + V+MRD A+ R+RGFGFV F+     D A+A 
Sbjct: 4  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAA 63

Query: 62 RVIMDKHMIDGRTVEAKKAVPR 83
          R     H IDGR VE K+AV R
Sbjct: 64 R----PHTIDGRVVEPKRAVAR 81

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

 Score = 78.8 bits (195), Expect = 3e-18
 Identities = 29/78 (37%), Positives = 44/78 (56%), Gaps = 2/78 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L++G + ++  EE LK+ F ++GEV  A ++ DR TGR+RGFGFV       A   I  
Sbjct: 1  NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 65 MDKHMIDGRTVEAKKAVP 82
          ++     GRT+   +A P
Sbjct: 61 LNGTDFGGRTLTVNEARP 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|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 77.3 bits (190), Expect = 1e-17
 Identities = 36/80 (45%), Positives = 54/80 (67%), Gaps = 1/80 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          KLF+GG+  D  E  L E+FS++G V +A ++ D+ TG+ RGFGFV F +   A++  + 
Sbjct: 1  KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60

Query: 67 K-HMIDGRTVEAKKAVPRDD 85
          K H I+G  VE KKAVP+++
Sbjct: 61 KFHPINGHRVEVKKAVPKEE 80

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

>gnl|CDD|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 77.4 bits (190), Expect = 1e-17
 Identities = 38/84 (45%), Positives = 57/84 (67%), Gaps = 9/84 (10%)

Query: 5  LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFA-----DPAV 59
          L KLFIGG+S++T ++ L+E+F ++G + + V+MRD  T R+RGFGFV ++     D A+
Sbjct: 2  LRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAM 61

Query: 60 AERVIMDKHMIDGRTVEAKKAVPR 83
          + R     H +DGR VE K+AV R
Sbjct: 62 SAR----PHKVDGRVVEPKRAVSR 81

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|241021 cd12577, RRM1_Hrp1p, RNA recognition motif 1 in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins

 Score = 76.5 bits (188), Expect = 2e-17
 Identities = 34/77 (44%), Positives = 52/77 (67%), Gaps = 1/77 (1%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           +F+GGL    T+   ++YF QFG +TD  VM D  T R RGFGF+T+   ++V+ V+ K 
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVM-KK 59

Query: 168 FHELNGKMVEVKRAVPK 184
            H L+GK+++ KRA+P+
Sbjct: 60  EHILDGKIIDPKRAIPR 76

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|241206 cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 76.7 bits (188), Expect = 2e-17
 Identities = 33/79 (41%), Positives = 52/79 (65%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           +K+F+GGL+   TE   + Y++Q+G +TD VVM D  ++R RGFGF+T+     VD  + 
Sbjct: 3   RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMA 62

Query: 166 KTFHELNGKMVEVKRAVPK 184
              H ++G++VE KRAV +
Sbjct: 63  ARPHTIDGRVVEPKRAVAR 81

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

 Score = 84.2 bits (208), Expect = 2e-17
 Identities = 47/163 (28%), Positives = 83/163 (50%), Gaps = 6/163 (3%)

Query: 18  DEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFAD-PAVAERVIMDKHMIDGRTVE 76
            E  L E+FS+ G+V +   ++DR + R++G  +V F D  +V + + +   M+ GR + 
Sbjct: 102 RERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPII 161

Query: 77  AKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVV 136
            + +    ++             P      K++VG L   +TE + ++ F+ FG I DV 
Sbjct: 162 VQSSQAEKNRAAKAATHQPGDI-PNF---LKLYVGNLHFNITEQELRQIFEPFGDIEDVQ 217

Query: 137 VMYDHNTQRPRGFGFITY-DSEEAVDRVLHKTFHELNGKMVEV 178
           +  D  T R +GFGFI + D+EEA + +      EL G+ ++V
Sbjct: 218 LHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKV 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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 74.7 bits (184), Expect = 7e-17
 Identities = 33/76 (43%), Positives = 47/76 (61%), Gaps = 2/76 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           LF+G +SW  D+E LK  F ++G VV A ++ DR TGR+RGFG+V F  P  A++ I  
Sbjct: 1  TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 65 MDKHMIDGRTVEAKKA 80
          MD   +DGR +    +
Sbjct: 61 MDGKELDGRPINVDFS 76

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

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

 Score = 75.1 bits (184), Expect = 8e-17
 Identities = 38/84 (45%), Positives = 55/84 (65%), Gaps = 9/84 (10%)

Query: 5  LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFA-----DPAV 59
          L KLFIGG+S++T +E L+ +F ++G + + V+MRD  T R+RGFGFV ++     D A+
Sbjct: 2  LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAM 61

Query: 60 AERVIMDKHMIDGRTVEAKKAVPR 83
            R     H +DGR VE K+AV R
Sbjct: 62 NAR----PHKVDGRVVEPKRAVSR 81

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 = 74.6 bits (183), Expect = 9e-17
 Identities = 31/76 (40%), Positives = 50/76 (65%), Gaps = 1/76 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          K+F+GGI  DT+E  L++YF +YG++    IM DR +G+ RGF FV F D    +++++ 
Sbjct: 2  KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 61

Query: 67 K-HMIDGRTVEAKKAV 81
          K H ++G   E +KA+
Sbjct: 62 KYHTVNGHNCEVRKAL 77

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

 Score = 74.1 bits (182), Expect = 1e-16
 Identities = 30/74 (40%), Positives = 49/74 (66%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           +FVGGL+   T+ D K+YF +FG + D  +  D  T R RGFGF+ +    +V++VL + 
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 168 FHELNGKMVEVKRA 181
            H+L+G++++ KRA
Sbjct: 61  EHKLDGRVIDPKRA 74

This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 74

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

 Score = 74.6 bits (183), Expect = 1e-16
 Identities = 32/75 (42%), Positives = 50/75 (66%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+FVGGL+   ++ D K YF +FG +TD  +  D NT R RGFGFI +    +V++VL +
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

Query: 167 TFHELNGKMVEVKRA 181
             H L+G++++ K+A
Sbjct: 61  KEHRLDGRLIDPKKA 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|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 74.7 bits (183), Expect = 1e-16
 Identities = 34/78 (43%), Positives = 51/78 (65%), Gaps = 1/78 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          KLF+GGI  DT+E  L++YF  YG++    I+ DR +G+ RGFGFV F D    +++++ 
Sbjct: 2  KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQ 61

Query: 67 K-HMIDGRTVEAKKAVPR 83
          K H I+G   E +KA+ R
Sbjct: 62 KYHTINGHNAEVRKALSR 79

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|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 74.7 bits (183), Expect = 1e-16
 Identities = 27/80 (33%), Positives = 52/80 (65%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           KK+FVGG+     E   + YF+++G I  + ++ D  + + RGFGF+T+D  + VD+++ 
Sbjct: 1   KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVL 60

Query: 166 KTFHELNGKMVEVKRAVPKE 185
           + +H +NG   EV++A+ ++
Sbjct: 61  QKYHTINGHNAEVRKALSRQ 80

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

 Score = 73.1 bits (180), Expect = 2e-16
 Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 2/73 (2%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK- 166
           +FVG L    TE D ++ F +FG I  V ++ D    + +GF F+ ++S E  ++ L   
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 167 TFHELNGKMVEVK 179
              EL+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|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 72.7 bits (178), Expect = 4e-16
 Identities = 32/74 (43%), Positives = 49/74 (66%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           +F+GGL+   T+ D K YF +FG + D  +  D  T R RGFGF+ +   E+VD+V+ + 
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 168 FHELNGKMVEVKRA 181
            H+LNGK+++ KRA
Sbjct: 61  EHKLNGKVIDPKRA 74

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|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 72.5 bits (178), Expect = 5e-16
 Identities = 31/82 (37%), Positives = 46/82 (56%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+FVGGL+   T+   ++YF Q+G + D V+M D  T R RGFGF+ +     V  VL  
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60

Query: 167 TFHELNGKMVEVKRAVPKEFSP 188
             H L+G+ ++ K   P+   P
Sbjct: 61  GPHTLDGRTIDPKPCTPRGMQP 82

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

 Score = 72.5 bits (178), Expect = 5e-16
 Identities = 32/78 (41%), Positives = 49/78 (62%), Gaps = 1/78 (1%)

Query: 5  LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          L KLF+GG++  T +  L+ +F+RYG++ E V+M D  T R+RGFGF+ F+    A+  +
Sbjct: 2  LCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61

Query: 65 -MDKHMIDGRTVEAKKAV 81
              H IDG  +E K+A 
Sbjct: 62 EAQPHSIDGNQIELKRAK 79

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

 Score = 72.4 bits (177), Expect = 6e-16
 Identities = 34/75 (45%), Positives = 52/75 (69%), Gaps = 1/75 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
          K+F+GG+S +T  E +K+YF ++G+V +A++M D+ T R RGFGFV F +  V E+V  +
Sbjct: 5  KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEI 64

Query: 66 DKHMIDGRTVEAKKA 80
            H I+ + VE KKA
Sbjct: 65 HFHEINNKMVECKKA 79

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

 Score = 72.0 bits (177), Expect = 8e-16
 Identities = 29/75 (38%), Positives = 49/75 (65%), Gaps = 1/75 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
          K+F+GG+S +T EE+++EYF ++G +VE  +  D+ T + RGF F+ F      ++++  
Sbjct: 1  KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60

Query: 66 DKHMIDGRTVEAKKA 80
            H+I G+ VE KKA
Sbjct: 61 QFHVIGGKKVEVKKA 75

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|241203 cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 72.0 bits (176), Expect = 8e-16
 Identities = 32/75 (42%), Positives = 51/75 (68%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+F+GGL+   T+   ++YF QFG + + +VM D  T+R RGFGF+T+  +  VD+VL +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 167 TFHELNGKMVEVKRA 181
           + HEL+ K ++ K A
Sbjct: 62  SRHELDSKTIDPKVA 76

This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 77

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

 Score = 71.8 bits (177), Expect = 8e-16
 Identities = 26/71 (36%), Positives = 42/71 (59%), Gaps = 4/71 (5%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          L++  +     EE L+E+FS YG+V    ++R++   R RGF FV FA P  AE  +  +
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58

Query: 66 DKHMIDGRTVE 76
          +  ++DGRT+ 
Sbjct: 59 NGLVLDGRTLR 69

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

>gnl|CDD|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 71.9 bits (176), Expect = 9e-16
 Identities = 34/76 (44%), Positives = 46/76 (60%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           KKIFVGGL    TE   ++YF +FG I  + +  D  T + RGF FIT+  E+ V +VL 
Sbjct: 5   KKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLE 64

Query: 166 KTFHELNGKMVEVKRA 181
           K FH ++G   E+K A
Sbjct: 65  KKFHNVSGSKCEIKVA 80

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|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 = 71.9 bits (177), Expect = 1e-15
 Identities = 28/76 (36%), Positives = 49/76 (64%), Gaps = 1/76 (1%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS-EEAVDRVLH 165
           K+FV GL++  TE + +  F +FG + +V++M D  T   RGFGF+T++S E+A   +  
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 166 KTFHELNGKMVEVKRA 181
               EL G++++V++A
Sbjct: 63  LNGKELEGRVIKVEKA 78

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

>gnl|CDD|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 70.4 bits (172), Expect = 3e-15
 Identities = 29/75 (38%), Positives = 47/75 (62%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+F+GGL+   ++ D  +Y  +FG + D  +  D  T R RGFGF+ +    +VD+VL  
Sbjct: 1   KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60

Query: 167 TFHELNGKMVEVKRA 181
             H+L+GK+++ KRA
Sbjct: 61  KEHKLDGKLIDPKRA 75

This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 76

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

 Score = 70.4 bits (173), Expect = 3e-15
 Identities = 23/78 (29%), Positives = 46/78 (58%), Gaps = 1/78 (1%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           +IFVGG+    TE + + +F +FG++ DV ++ D      +G+GF+T++++E  +++L  
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVS-KGYGFVTFETQEDAEKILAM 62

Query: 167 TFHELNGKMVEVKRAVPK 184
                 GK + +  A+ K
Sbjct: 63  GNLNFRGKKLNIGPAIRK 80

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

 Score = 69.7 bits (170), Expect = 6e-15
 Identities = 32/74 (43%), Positives = 50/74 (67%), Gaps = 1/74 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
          K+F+GG+S +T  E +K+YF ++G+V +A++M D+ T R RGFGFV F    + E+V  +
Sbjct: 1  KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 66 DKHMIDGRTVEAKK 79
            H I+ + VE KK
Sbjct: 61 HFHEINNKMVECKK 74

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

 Score = 75.4 bits (184), Expect = 6e-15
 Identities = 37/179 (20%), Positives = 69/179 (38%), Gaps = 16/179 (8%)

Query: 77  AKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVV 136
            +      ++ +   + S             +FVG L   VTE D ++ F +FG +  V 
Sbjct: 87  ERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVR 146

Query: 137 VMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFH--ELNGKMVEVKRAVP----------- 183
           ++ D  T + RGF F+ ++SEE+ ++ + +  +  EL G+ + V++A P           
Sbjct: 147 LVRDRETGKSRGFAFVEFESEESAEKAI-EELNGKELEGRPLRVQKAQPASQPRSELSNN 205

Query: 184 --KEFSPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATGR 240
               F+   SR   +           NL    A+          G  + +   P   G+
Sbjct: 206 LDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGK 264

Length = 306

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

 Score = 69.2 bits (170), Expect = 6e-15
 Identities = 25/70 (35%), Positives = 37/70 (52%), Gaps = 5/70 (7%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           +FVG L    TE D K  F +FG I  + ++ D  T R +GF F+ ++ EE  ++ L   
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKAL--- 56

Query: 168 FHELNGKMVE 177
              LNGK + 
Sbjct: 57  -EALNGKELG 65

(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|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 68.8 bits (169), Expect = 9e-15
 Identities = 28/69 (40%), Positives = 43/69 (62%), Gaps = 5/69 (7%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          K+F+G ++ D  EE L++YFS++GEV +  I +       R F FV FADP VA+ +  +
Sbjct: 2  KVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP-----FRAFAFVTFADPEVAQSLCGE 56

Query: 67 KHMIDGRTV 75
           H+I G +V
Sbjct: 57 DHIIKGVSV 65

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|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 67.8 bits (166), Expect = 2e-14
 Identities = 27/78 (34%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
            + V GL    TE D K YF  FG +  V V  D  T + +GFGF+ +   E   +VL  
Sbjct: 1   DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVL-S 59

Query: 167 TFHELNGKMVEVKRAVPK 184
             H ++G+  +VK    K
Sbjct: 60  QRHMIDGRWCDVKIPNSK 77

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

 Score = 68.0 bits (167), Expect = 2e-14
 Identities = 28/78 (35%), Positives = 40/78 (51%), Gaps = 1/78 (1%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
            ++VG L   VTE D K  F QFG +T   V+ D  T R RGFGF+  ++ E  +  + K
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 167 TF-HELNGKMVEVKRAVP 183
               +  G+ + V  A P
Sbjct: 61  LNGTDFGGRTLTVNEARP 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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 67.6 bits (166), Expect = 2e-14
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL-HK 166
           ++V  L  +VTE D +++F  +G +  V ++   N  RPRGF F+ + S E  +  L   
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVR--NKDRPRGFAFVEFASPEDAEAALKKL 58

Query: 167 TFHELNGKMVE 177
               L+G+ + 
Sbjct: 59  NGLVLDGRTLR 69

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 = 67.7 bits (166), Expect = 2e-14
 Identities = 26/64 (40%), Positives = 43/64 (67%), Gaps = 1/64 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          ++F+GGI  DT EE L+++FSR+G V +  I+ DRA G ++G+GFV F     AE+++  
Sbjct: 4  RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRA-GVSKGYGFVTFETQEDAEKILAM 62

Query: 67 KHMI 70
           ++ 
Sbjct: 63 GNLN 66

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

 Score = 67.7 bits (166), Expect = 2e-14
 Identities = 24/70 (34%), Positives = 42/70 (60%), Gaps = 1/70 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADP-AVAERVIM 65
          KLF+G + W    + LKEYFS++G+V    +  D+ TG ++G+GFV F+    +   +  
Sbjct: 1  KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 66 DKHMIDGRTV 75
           KH+++G  +
Sbjct: 61 QKHILEGNKL 70

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|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 66.6 bits (162), Expect = 5e-14
 Identities = 31/75 (41%), Positives = 48/75 (64%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+F+GGL+   +    + YF +FG I + +VM D  T+R RGFGF+T+    +VD+VL +
Sbjct: 1   KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60

Query: 167 TFHELNGKMVEVKRA 181
             HEL+ K ++ K A
Sbjct: 61  PHHELDSKTIDPKVA 75

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

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

 Score = 66.9 bits (164), Expect = 5e-14
 Identities = 27/68 (39%), Positives = 38/68 (55%), Gaps = 2/68 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          L +  +++ T  + L+  F +YGEV +  I RDR T  +RGF FV F D   AE  +  M
Sbjct: 1  LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 66 DKHMIDGR 73
          D   +DGR
Sbjct: 61 DGKELDGR 68

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

 Score = 66.6 bits (163), Expect = 7e-14
 Identities = 28/77 (36%), Positives = 41/77 (53%), Gaps = 4/77 (5%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          +LF+G +  D  E+ LKE+F  +G V+E  I      GR   FGFVVF DP   ++++ +
Sbjct: 5  QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64

Query: 67 K--HMIDGRT--VEAKK 79
          K  +        VE KK
Sbjct: 65 KPIYFRGDHRLNVEEKK 81

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

 Score = 65.4 bits (160), Expect = 1e-13
 Identities = 27/77 (35%), Positives = 38/77 (49%), Gaps = 3/77 (3%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          +L +  + +   E  LK+ FS +G V E  I R    G+ +GF FV F   A AE+ I  
Sbjct: 1  RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIKG 59

Query: 65 MDKHMIDGRTVEAKKAV 81
          ++   I GR V    AV
Sbjct: 60 VNGKKIKGRPVAVDWAV 76

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|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 65.0 bits (158), Expect = 2e-13
 Identities = 30/75 (40%), Positives = 43/75 (57%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+FVGGL+   TE   K+YF  FG I ++ +  D  T   RGF F+TY  EE V ++L  
Sbjct: 1   KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60

Query: 167 TFHELNGKMVEVKRA 181
            +H++     E+K A
Sbjct: 61  RYHQIGSGKCEIKVA 75

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

 Score = 71.4 bits (175), Expect = 3e-13
 Identities = 45/189 (23%), Positives = 87/189 (46%), Gaps = 20/189 (10%)

Query: 3   SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
           S +G +F+  +    D + L + FS++G ++   +  D   G++RG+GFV F     A+ 
Sbjct: 86  SGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKA 144

Query: 63  VI--MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTES 120
            I  ++  +++ + V   + + + ++           ++P    T  ++V  L  +V E 
Sbjct: 145 AIQKVNGMLLNDKEVYVGRFIKKHERE----------AAPLKKFTN-LYVKNLDPSVNED 193

Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL-----HKTFHELNGKM 175
             ++ F +FG IT   VM D +  R RGF F+ ++  E   + +      K      GK 
Sbjct: 194 KLRELFAKFGEITSAAVMKDGS-GRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKK 252

Query: 176 VEVKRAVPK 184
           + V RA  +
Sbjct: 253 LYVGRAQKR 261

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|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 64.2 bits (157), Expect = 3e-13
 Identities = 26/76 (34%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           +K+FVG L   +TE D ++YF QFG +TDV +         R F F+T+   E    +  
Sbjct: 1   RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP-----FRAFAFVTFADPEVAQSLCG 55

Query: 166 KTFHELNGKMVEVKRA 181
           +  H + G  V V  A
Sbjct: 56  ED-HIIKGVSVHVSNA 70

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

 Score = 64.1 bits (157), Expect = 4e-13
 Identities = 22/75 (29%), Positives = 47/75 (62%), Gaps = 3/75 (4%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          +++  +  D D+E+LKE F +YG++  A +M+D   G+++GFGFV F +   A++ +  +
Sbjct: 4  VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 66 DKHMIDGRTVEAKKA 80
          +   ++G+ +   +A
Sbjct: 63 NGKEVNGKKLYVGRA 77

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|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 64.3 bits (156), Expect = 5e-13
 Identities = 28/75 (37%), Positives = 43/75 (57%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           KIFVGGL+    E   ++YF  FG +  + +  D+ T + RGF FIT+  EE V +++ K
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 167 TFHELNGKMVEVKRA 181
            +H +     E+K A
Sbjct: 61  KYHNVGLSKCEIKVA 75

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|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 = 64.1 bits (157), Expect = 5e-13
 Identities = 21/58 (36%), Positives = 34/58 (58%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          KLF+G +     EE ++  F  YG + E  I+RD+ TG+++G  FV F+    A++ I
Sbjct: 1  KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAI 58

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

 Score = 70.6 bits (173), Expect = 7e-13
 Identities = 52/184 (28%), Positives = 82/184 (44%), Gaps = 26/184 (14%)

Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
           L++G +  D  E +L + F  +G V+   + RD  T R+ G+G+V F +PA AER +  M
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 66  DKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKY 125
           +   + G+ +    +          R+ S   S  G      IFV  L  +V        
Sbjct: 63  NFKRLGGKPIRIMWS---------QRDPSLRRSGVG-----NIFVKNLDKSVDNKALFDT 108

Query: 126 FDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNG-----KMVEVKR 180
           F +FG I    V  D N  + RG+GF+ ++ EE+          ++NG     K V V R
Sbjct: 109 FSKFGNILSCKVATDENG-KSRGYGFVHFEKEESA----KAAIQKVNGMLLNDKEVYVGR 163

Query: 181 AVPK 184
            + K
Sbjct: 164 FIKK 167

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

 Score = 65.8 bits (160), Expect = 8e-13
 Identities = 37/79 (46%), Positives = 51/79 (64%), Gaps = 2/79 (2%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           KLFIGG+SW TD+  L++ F+ +G+VV+A ++ DR TGR+RGFGFV F D   A   I  
Sbjct: 36  KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95

Query: 65  MDKHMIDGRTVEAKKAVPR 83
           MD   ++GR +    A  R
Sbjct: 96  MDGKELNGRHIRVNPANDR 114

Length = 144

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

 Score = 62.6 bits (153), Expect = 1e-12
 Identities = 29/76 (38%), Positives = 43/76 (56%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
            KIFVGGL    T+   +KYF QFG I + VV+ D  T + RG+GF+T+  +E+ +R   
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 166 KTFHELNGKMVEVKRA 181
                ++G+   V  A
Sbjct: 61  DPNPIIDGRKANVNLA 76

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

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

 Score = 63.0 bits (154), Expect = 1e-12
 Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 7/80 (8%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--- 64
          +FI  + +D  EE LKE FS++GEV  A I++D+ TG ++G  FV F     A++ +   
Sbjct: 3  VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 65 ----MDKHMIDGRTVEAKKA 80
                   +DGR +    A
Sbjct: 63 DNAEDSGLSLDGRRLIVTLA 82

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

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

 Score = 63.4 bits (155), Expect = 1e-12
 Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 4/77 (5%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           K +FV  L    TES  ++ F+++G I  + ++ D  T +PRG+ FI ++ E    R + 
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHE----RDMK 57

Query: 166 KTFHELNGKMVEVKRAV 182
             +   +GK ++ +R +
Sbjct: 58  AAYKYADGKKIDGRRVL 74

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

 Score = 62.0 bits (151), Expect = 2e-12
 Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH- 165
            +FVG L+ +V +   K  F++FGT+    V+ D  T R RGFG++ ++S E   + +  
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 166 KTFHELNGKMVEVKRA 181
               EL+G+ + V  +
Sbjct: 61  MDGKELDGRPINVDFS 76

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

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

 Score = 62.3 bits (152), Expect = 2e-12
 Identities = 26/73 (35%), Positives = 42/73 (57%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+FVG L  TV   + K+YF QFG +    V +D  T   +G+GF+++ S + ++  L K
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 167 TFHELNGKMVEVK 179
             H L G  ++V+
Sbjct: 61  QKHILEGNKLQVQ 73

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

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

 Score = 62.2 bits (151), Expect = 3e-12
 Identities = 27/76 (35%), Positives = 50/76 (65%), Gaps = 1/76 (1%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS-EEAVDRVLH 165
           K+F+GGL+    E   ++ F ++G I++VVV+ D  TQR RGFGF+T+++ ++A D ++ 
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 166 KTFHELNGKMVEVKRA 181
                ++G+ + V +A
Sbjct: 62  MNGKSVDGRQIRVDQA 77

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

>gnl|CDD|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 = 61.9 bits (151), Expect = 3e-12
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 2/68 (2%)

Query: 9  FIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MD 66
          F+G I +D  EE+L E FS  G VV   ++ DR TG+ +G+GF  F D   A   I  ++
Sbjct: 2  FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 67 KHMIDGRT 74
           +  +GR 
Sbjct: 62 GYEFNGRA 69

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

 Score = 61.6 bits (150), Expect = 3e-12
 Identities = 27/77 (35%), Positives = 43/77 (55%), Gaps = 2/77 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MD 66
          LF+G +SW  +++ L+E+F   GEVV+  I +D   GR++GFG V FA    A++ +   
Sbjct: 2  LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALEKS 60

Query: 67 KHMIDGRTVEAKKAVPR 83
             + GR +    A  R
Sbjct: 61 GEELLGREIRVDLATER 77

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|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 = 61.2 bits (149), Expect = 4e-12
 Identities = 25/69 (36%), Positives = 38/69 (55%), Gaps = 2/69 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADP--AVAERVI 64
          +LF+  + + T EE L+E F  +GE+ E  +  D+ T R++GF FV F  P  AV     
Sbjct: 1  RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 65 MDKHMIDGR 73
          +D  +  GR
Sbjct: 61 LDGSIFQGR 69

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|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 = 61.0 bits (149), Expect = 6e-12
 Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 6/78 (7%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS-EEAVD--RV 163
           K+FVG L  T TE D +  F+++G I +V ++ D +T + +G  F+ + S EEA      
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 164 LH--KTFHELNGKMVEVK 179
           LH   T    +  +  VK
Sbjct: 61  LHGKVTMPGASRPLQ-VK 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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 66.9 bits (163), Expect = 6e-12
 Identities = 40/157 (25%), Positives = 74/157 (47%), Gaps = 22/157 (14%)

Query: 19  EERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVE 76
           +E ++  F+  GE+    ++RD+ TG++ G+GFV +  P  AE+ +  ++   +  +T++
Sbjct: 17  QEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIK 76

Query: 77  AKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVV 136
              A P  D                  +   ++V GL  T+T+ + +  F  FG I    
Sbjct: 77  VSYARPSSDSI----------------KGANLYVSGLPKTMTQHELESIFSPFGQIITSR 120

Query: 137 VMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNG 173
           ++ D+ T   +G GFI +D  +  DR +      LNG
Sbjct: 121 ILSDNVTGLSKGVGFIRFDKRDEADRAI----KTLNG 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|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 60.3 bits (147), Expect = 9e-12
 Identities = 24/78 (30%), Positives = 44/78 (56%), Gaps = 2/78 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          LF+  + +DT +E+L+E+FS  G +    +++D+ + + RGFG+V FA    A+R +   
Sbjct: 2  LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 66 DKHMIDGRTVEAKKAVPR 83
           K    GR +  + A  +
Sbjct: 62 KKTKFGGRKIHVEFAKKK 79

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

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

 Score = 60.3 bits (147), Expect = 1e-11
 Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 4/71 (5%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPA---VAERVI 64
          LF+  +++DT E +L+  F  YG +    ++RD+ TG+ RG+ F+ F        A +  
Sbjct: 4  LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKY- 62

Query: 65 MDKHMIDGRTV 75
           D   IDGR V
Sbjct: 63 ADGKKIDGRRV 73

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

 Score = 59.9 bits (146), Expect = 1e-11
 Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEAVDRVLHK 166
           ++VGGLA  V E      F  FG I D+ +  D+ TQ+ RGF F+ + + E+A   + + 
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 167 TFHELNGKMVEV 178
              EL G+ + V
Sbjct: 61  NESELFGRTIRV 72

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

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

 Score = 59.1 bits (144), Expect = 3e-11
 Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 2/78 (2%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS-EEAVDRVLHK 166
           ++V  L   + +   K+ F ++G IT   VM D    + +GFGF+ +++ E A   V   
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEG-KSKGFGFVNFENHEAAQKAVEEL 62

Query: 167 TFHELNGKMVEVKRAVPK 184
              E+NGK + V RA  K
Sbjct: 63  NGKEVNGKKLYVGRAQKK 80

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

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

 Score = 58.9 bits (143), Expect = 3e-11
 Identities = 23/77 (29%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           +FVG L+ +  + D +++F + G + DV +  D +  R +GFG + + +EE   + L K+
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDG-RSKGFGHVEFATEEGAQKALEKS 60

Query: 168 FHELNGKMVEVKRAVPK 184
             EL G+ + V  A  +
Sbjct: 61  GEELLGREIRVDLATER 77

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|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 = 58.5 bits (142), Expect = 4e-11
 Identities = 24/69 (34%), Positives = 40/69 (57%), Gaps = 6/69 (8%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEAVDRVLH 165
           ++FV  L  T TE + ++ F+ FG I++V +  D  T+R +GF F+++   E AV     
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAV----- 55

Query: 166 KTFHELNGK 174
           K + EL+G 
Sbjct: 56  KAYSELDGS 64

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

 Score = 58.0 bits (141), Expect = 6e-11
 Identities = 25/69 (36%), Positives = 41/69 (59%), Gaps = 3/69 (4%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L++  +    D+ERL+E FS +G +  A +M D   GR++GFGFV F+ P  A + +  
Sbjct: 3  NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTD-EKGRSKGFGFVCFSSPEEATKAVTE 61

Query: 65 MDKHMIDGR 73
          M+  +I G+
Sbjct: 62 MNGRIIGGK 70

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

 Score = 56.6 bits (137), Expect = 2e-10
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 9/80 (11%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           ++FVG L   +TE + K++F +FG + +V +       R   FGF+ +D  EAV ++L  
Sbjct: 5   QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64

Query: 167 T------FHELNGKMVEVKR 180
                   H LN   VE K+
Sbjct: 65  KPIYFRGDHRLN---VEEKK 81

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

 Score = 57.0 bits (138), Expect = 2e-10
 Identities = 24/70 (34%), Positives = 43/70 (61%), Gaps = 2/70 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          +F+G +S + D E L+  F+ +GE+ +A +++D  TG+++G+GFV F     AE  I  M
Sbjct: 2  IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 66 DKHMIDGRTV 75
          +   + GR +
Sbjct: 62 NGQWLGGRAI 71

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

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

 Score = 57.0 bits (138), Expect = 2e-10
 Identities = 23/70 (32%), Positives = 43/70 (61%), Gaps = 2/70 (2%)

Query: 6  GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADP--AVAERV 63
          G+LF+  + +   E+ L++ FS++GE+ E  +  D+ +G+++GF +V+F DP  AV    
Sbjct: 3  GRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYK 62

Query: 64 IMDKHMIDGR 73
           +D  +  GR
Sbjct: 63 ELDGKVFQGR 72

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

 Score = 56.5 bits (137), Expect = 2e-10
 Identities = 26/70 (37%), Positives = 41/70 (58%), Gaps = 1/70 (1%)

Query: 110 VGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS-EEAVDRVLHKTF 168
           V GL+   TE D ++ F ++G I  V V+YD  T R RGFGF+ ++S E+A +       
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNG 63

Query: 169 HELNGKMVEV 178
            E++G+ + V
Sbjct: 64  MEIDGRRIRV 73

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

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

 Score = 62.8 bits (152), Expect = 2e-10
 Identities = 40/183 (21%), Positives = 87/183 (47%), Gaps = 16/183 (8%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           ++++G IS++  E+ ++  F  +G +    +  D ATG+ +GF FV +  P  A+  +  
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQ 168

Query: 65  MDKHMIDGRTVEAKKA--VPRDDQ--NMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTES 120
           M+  M+ GR ++  +   +P+     +M+       +         +I+V  +   ++E+
Sbjct: 169 MNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFN---------RIYVASVHPDLSET 219

Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDR-VLHKTFHELNGKMVEVK 179
           D K  F+ FG I    +      +  +G+GFI Y++ ++    +      +L G+ + V 
Sbjct: 220 DIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVG 279

Query: 180 RAV 182
           + V
Sbjct: 280 KCV 282

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

 Score = 56.6 bits (137), Expect = 2e-10
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 3/72 (4%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          L +  +  D  +E L+  F   G +    I+RDR TG++ G+GFV + D   A++ I   
Sbjct: 3  LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAI--- 59

Query: 68 HMIDGRTVEAKK 79
          + ++G  +  K+
Sbjct: 60 NTLNGFEIRNKR 71

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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 56.7 bits (137), Expect = 2e-10
 Identities = 20/60 (33%), Positives = 40/60 (66%), Gaps = 1/60 (1%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           +IFVGG+     E+D +K+F Q+GT+ +V ++ D      +G+GF+T++++E   ++L +
Sbjct: 4   RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVS-KGYGFVTFETQEDAQKILQE 62

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|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 = 20/68 (29%), Positives = 39/68 (57%), Gaps = 2/68 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          LFI  +  +  ++ L + F+ +G V+ A +  D+ TG+++ FGFV + +P  A+  I  M
Sbjct: 1  LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 66 DKHMIDGR 73
          +   + G+
Sbjct: 61 NGFQVGGK 68

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

 Score = 56.1 bits (136), Expect = 3e-10
 Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 7/78 (8%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRAR-----GFGFVVFADPAVAER 62
          LF+  +++ T EE LK++F + G V    I + +           G+GFV F     A++
Sbjct: 3  LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 63 VI--MDKHMIDGRTVEAK 78
           +  +   ++DG  +E K
Sbjct: 63 ALKRLQGTVLDGHALELK 80

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

 Score = 55.9 bits (135), Expect = 3e-10
 Identities = 27/70 (38%), Positives = 43/70 (61%), Gaps = 6/70 (8%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD-SEEAVDRV 163
           + ++F+  LA T TE D +K F ++G +++V +  D  T++P+GF F+TY   E AV   
Sbjct: 2   SGRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAV--- 58

Query: 164 LHKTFHELNG 173
             K F EL+G
Sbjct: 59  --KAFAELDG 66

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

 Score = 56.1 bits (136), Expect = 4e-10
 Identities = 27/64 (42%), Positives = 37/64 (57%), Gaps = 2/64 (3%)

Query: 12 GISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKH--M 69
          G+S  T E  L+E FSRYG + +  ++ D+ TGR+RGFGFV F     A+      +   
Sbjct: 6  GLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGME 65

Query: 70 IDGR 73
          IDGR
Sbjct: 66 IDGR 69

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

 Score = 55.7 bits (135), Expect = 4e-10
 Identities = 23/73 (31%), Positives = 43/73 (58%), Gaps = 2/73 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          ++IG +     E  L++YFS++G V    + R + TG+++G+ FV F  P VA+ V   M
Sbjct: 2  VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 66 DKHMIDGRTVEAK 78
          + +++  R ++ K
Sbjct: 62 NNYLLFERLLKCK 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|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 55.6 bits (134), Expect = 4e-10
 Identities = 21/73 (28%), Positives = 42/73 (57%), Gaps = 2/73 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV--IM 65
          ++IG +     E+ LK+YFS++G V    + R + TG ++ +GF+ F +P VA      M
Sbjct: 2  IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSM 61

Query: 66 DKHMIDGRTVEAK 78
          + +++ G+ ++  
Sbjct: 62 NNYLLMGKVLQVH 74

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|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 55.4 bits (133), Expect = 5e-10
 Identities = 28/75 (37%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          K+F+GG+S DT EE++KEYF  +GE+    +  D  T   RGF FV + D    ++++  
Sbjct: 1  KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60

Query: 67 K-HMIDGRTVEAKKA 80
          + H I     E K A
Sbjct: 61 RYHQIGSGKCEIKVA 75

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

 Score = 55.3 bits (134), Expect = 5e-10
 Identities = 24/70 (34%), Positives = 40/70 (57%), Gaps = 2/70 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          L++GG++ + DE+ L   F  +G++ +  I  D  T + RGF FV F +P  A   I  M
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 66 DKHMIDGRTV 75
          ++  + GRT+
Sbjct: 61 NESELFGRTI 70

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

 Score = 55.7 bits (135), Expect = 5e-10
 Identities = 24/81 (29%), Positives = 49/81 (60%), Gaps = 3/81 (3%)

Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
          E+D  ++F+G +  +  +E L   FS+Y    +A ++RD+ TG+++G+GFV F+DP    
Sbjct: 4  ENDF-RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYL 62

Query: 62 RVI--MDKHMIDGRTVEAKKA 80
          + +  M+   +  R ++ +K+
Sbjct: 63 KAMKEMNGKYVGNRPIKLRKS 83

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

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

 Score = 55.7 bits (135), Expect = 5e-10
 Identities = 20/59 (33%), Positives = 33/59 (55%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          L++G +    DE  +   F+  GEV    I+R++ TG++ G+GFV FA    AE+ +  
Sbjct: 2  LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

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

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

 Score = 55.2 bits (134), Expect = 6e-10
 Identities = 21/52 (40%), Positives = 31/52 (59%)

Query: 13 ISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          +S D DE+ L+E F  +G +    + +D+ TG++RGF FV F     AER I
Sbjct: 7  LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAI 58

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|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 = 55.3 bits (134), Expect = 6e-10
 Identities = 20/76 (26%), Positives = 44/76 (57%), Gaps = 2/76 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          K+FIGG+     E+++KE    +G++    +++D ATG ++G+ F  + DP+V ++ I  
Sbjct: 2  KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61

Query: 67 KH--MIDGRTVEAKKA 80
           +   +  + +  ++A
Sbjct: 62 LNGMQLGDKKLTVQRA 77

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

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

 Score = 55.7 bits (135), Expect = 6e-10
 Identities = 27/70 (38%), Positives = 40/70 (57%), Gaps = 2/70 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER--VIM 65
          LF+G +S  T EE L+E FSRYG++    ++RD  TG ++G+ FV +     A R     
Sbjct: 6  LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 66 DKHMIDGRTV 75
           K +IDG  +
Sbjct: 66 HKLVIDGSEI 75

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

 Score = 54.7 bits (132), Expect = 8e-10
 Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 4/58 (6%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY----DSEEAVD 161
           IFVG L+  +     +  F  FG I+D  V+ D  T + +G+GF+++    D+E A+ 
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQ 59

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|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 54.8 bits (132), Expect = 9e-10
 Identities = 25/67 (37%), Positives = 45/67 (67%), Gaps = 1/67 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          ++F+GGI + T+E  L+++FS+YG V E  I+ DRA G ++G+GFV F     A++++ +
Sbjct: 4  RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRA-GVSKGYGFVTFETQEDAQKILQE 62

Query: 67 KHMIDGR 73
           + +  R
Sbjct: 63 ANRLCFR 69

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

 Score = 54.6 bits (132), Expect = 9e-10
 Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 3/73 (4%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          L +G +  +  +E+ +E  S +G V    ++   +TG ++G+GFV +A  A A +    K
Sbjct: 2  LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKA---K 58

Query: 68 HMIDGRTVEAKKA 80
          + +DG+ +  +K 
Sbjct: 59 NQLDGKQIGGRKL 71

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

 Score = 54.5 bits (132), Expect = 9e-10
 Identities = 24/62 (38%), Positives = 33/62 (53%), Gaps = 2/62 (3%)

Query: 19 EERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVE 76
          ++ LKE FS YG V +  +  DR     RG+ +V F  P  AE+ I  MD   IDG+ V 
Sbjct: 12 KDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEVT 71

Query: 77 AK 78
           +
Sbjct: 72 VE 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|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 54.6 bits (132), Expect = 1e-09
 Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 3/73 (4%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          +F+  + +    + LK+ F   G V+ A +  D   GR++GFG V+F  P  A+R I   
Sbjct: 1  IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTD-NDGRSKGFGTVLFESPEDAQRAIEMF 59

Query: 66 DKHMIDGRTVEAK 78
          + + ++GR +E +
Sbjct: 60 NGYDLEGRELEVR 72

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

>gnl|CDD|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins

 Score = 54.3 bits (131), Expect = 1e-09
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 7/75 (9%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRG-FGFITYDSEEAVDRVLHK 166
           +FV G     +E     YF  FG + +V++       + +G +  + +DS+E VD+VL +
Sbjct: 5   VFVSGFKRGTSEEQLMDYFSAFGPVMNVIM------DKDKGVYAIVEFDSKEGVDKVLSE 58

Query: 167 TFHELNGKMVEVKRA 181
             H LNG  + V+  
Sbjct: 59  PQHTLNGHRLRVRPR 73

This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS). . Length = 74

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

 Score = 54.1 bits (130), Expect = 1e-09
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 2/78 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          LF+  +++   +E L ++FS    +  AV++ D  TG +RG+GFV FA    A+  +  +
Sbjct: 2  LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 66 DKHMIDGRTVEAKKAVPR 83
              + GR +    A  R
Sbjct: 62 KNKKLHGRILRLDIAERR 79

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|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 54.2 bits (130), Expect = 2e-09
 Identities = 23/62 (37%), Positives = 39/62 (62%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          K+F+GG+S DT EE+++EYF  +GEV    +  D  T + RGF F+ F +    ++++  
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 67 KH 68
          K+
Sbjct: 61 KY 62

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

 Score = 53.9 bits (130), Expect = 2e-09
 Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 6/71 (8%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEAVDRV 163
           T ++FV  L  +  E D +K F +FG +++V V  D  + + +GF ++ + D E+AV   
Sbjct: 2   TGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAV--- 58

Query: 164 LHKTFHELNGK 174
             K + EL+GK
Sbjct: 59  --KAYKELDGK 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|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 23/65 (35%), Positives = 35/65 (53%), Gaps = 4/65 (6%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL-- 164
           +I V  L   VTE   +++F+  G +TDV VM      + R FGF+ + SEE   + +  
Sbjct: 2   RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRT-RDGKSRRFGFVGFKSEEDAQQAVKY 60

Query: 165 -HKTF 168
            +KTF
Sbjct: 61  FNKTF 65

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 53.3 bits (129), Expect = 3e-09
 Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 2/68 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          L++G +  D  E  L E FS  G V+   + RD  T R+ G+ +V F +PA AER +  +
Sbjct: 2  LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 66 DKHMIDGR 73
          +  +I G+
Sbjct: 62 NFDVIKGK 69

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

 Score = 53.1 bits (128), Expect = 3e-09
 Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS-EEAVDRVLHK 166
           IFV  L     ES   + F  FG +T+V V+ D  T + +G+GF+T  + EEA   +   
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 167 TFHELNGKMVEV 178
             + L G++++V
Sbjct: 64  NGYRLGGRVLQV 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|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 = 53.6 bits (129), Expect = 3e-09
 Identities = 17/61 (27%), Positives = 35/61 (57%)

Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
          + D  KLF+G I  + +E+ L+  F ++G++ E  +++D+ TG  +G  F+ +     A 
Sbjct: 2  DDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESAL 61

Query: 62 R 62
          +
Sbjct: 62 K 62

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|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 53.1 bits (127), Expect = 4e-09
 Identities = 25/75 (33%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          K+F+GG++ +  EE+++EYF  +GE+    +  D  T + RGF F+ F +    ++V+  
Sbjct: 6  KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLEK 65

Query: 67 K-HMIDGRTVEAKKA 80
          K H + G   E K A
Sbjct: 66 KFHNVSGSKCEIKVA 80

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|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 = 52.8 bits (127), Expect = 5e-09
 Identities = 27/80 (33%), Positives = 41/80 (51%), Gaps = 6/80 (7%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY---DSEEAVDRV 163
           K+FVG +   + E D +  F+QFG I ++ V+ D  T   +G  F+TY   +S       
Sbjct: 7   KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSA 66

Query: 164 LH--KTFHELNGKMVEVKRA 181
           LH  KT   +N  + +VK A
Sbjct: 67  LHEQKTLPGMNRPI-QVKPA 85

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

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

 Score = 52.8 bits (127), Expect = 5e-09
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          LF+G +S+D DE+ + E F  YGE+    +  D  +GR +GFG+V F+    A+  +  +
Sbjct: 1  LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 66 DKHMIDGRTV 75
              + GR V
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|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 52.3 bits (126), Expect = 5e-09
 Identities = 21/53 (39%), Positives = 32/53 (60%), Gaps = 1/53 (1%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEA 159
           ++VG L   +TE D +  F+ FG I  V +  D  T R +G+GFI + D+E+A
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDA 53

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

 Score = 52.2 bits (126), Expect = 6e-09
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 7/74 (9%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS-EEAVDRVLH 165
            ++V  L  ++ +   ++ F  FGTIT   VM D    R +GFGF+ + S EEA   V  
Sbjct: 3   NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKG-RSKGFGFVCFSSPEEATKAV-- 59

Query: 166 KTFHELNGKMVEVK 179
               E+NG+++  K
Sbjct: 60  ---TEMNGRIIGGK 70

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

 Score = 52.7 bits (127), Expect = 6e-09
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 9/74 (12%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNT----QRPRGFGFITYDSEEAVDR 162
           ++++G L S +TE    K F ++G I     ++ H +     +PRG+ F+T++++E  ++
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLF-HKSGPLKGQPRGYCFVTFETKEEAEK 59

Query: 163 VLHKTFHELNGKMV 176
            L      LNGK  
Sbjct: 60  ALKS----LNGKTA 69

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

 Score = 52.7 bits (127), Expect = 7e-09
 Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 2/59 (3%)

Query: 17 TDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGR 73
          T +E L+  FSR+G++    ++RD+ TG +  + F+ F      E     MD  +ID R
Sbjct: 15 TTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDR 73

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 52.2 bits (126), Expect = 7e-09
 Identities = 27/66 (40%), Positives = 40/66 (60%), Gaps = 3/66 (4%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           +FVGGL+ +VTESD ++ F +FGT++DV ++   +    RGF +I   + EA    L K 
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEA---QLKKC 58

Query: 168 FHELNG 173
              LNG
Sbjct: 59  KSTLNG 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|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins

 Score = 51.9 bits (125), Expect = 9e-09
 Identities = 19/55 (34%), Positives = 35/55 (63%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
          L++G + ++  E+ L+  F  +GE+    + RD  TGR++G+GF+ FAD   A++
Sbjct: 1  LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKK 55

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|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 52.2 bits (125), Expect = 9e-09
 Identities = 30/81 (37%), Positives = 39/81 (48%), Gaps = 4/81 (4%)

Query: 7  KLFIGGISWDT-DEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI- 64
          KL I  + W      +LK+ F RYG+V EA I R R  G+  GF FV       AE  + 
Sbjct: 2  KLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRG-GKLCGFAFVTMKKRKNAEIALE 60

Query: 65 -MDKHMIDGRTVEAKKAVPRD 84
            +   IDGR V    AV ++
Sbjct: 61 NTNGLEIDGRPVAVDWAVQKN 81

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|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 = 51.9 bits (125), Expect = 1e-08
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 5/76 (6%)

Query: 8  LFIGGISWDTDEERLKEYFSRYG--EVVEAVIMRDRATGRARGFGFVVFADPAVAERVIM 65
          L++G ++W T +E L+   +  G  +V        +A G+++GF +V FA  A A  V  
Sbjct: 1  LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAV-- 58

Query: 66 DKHMIDGRTVEAKKAV 81
           K  ++GR    KK V
Sbjct: 59 -KEKLEGREFNGKKCV 73

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

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 8/71 (11%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          +LF+G +  D  EE  KE FS+YGEV E  + ++      +GFGF+       AE+    
Sbjct: 3  RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDTRTNAEKAKAE 56

Query: 65 MDKHMIDGRTV 75
          +D  M  GR +
Sbjct: 57 LDGIMRKGRQL 67

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|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins

 Score = 51.5 bits (123), Expect = 1e-08
 Identities = 24/64 (37%), Positives = 39/64 (60%), Gaps = 3/64 (4%)

Query: 4  DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV 63
          D  +LF+G +  D D+  LKE+F +YG VVE   +R  + G+   FGFVVF D    +++
Sbjct: 2  DSHQLFVGNLPHDVDKSELKEFFQQYGNVVE---LRINSGGKLPNFGFVVFDDSEPVQKI 58

Query: 64 IMDK 67
          + ++
Sbjct: 59 LSNR 62

This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript. Length = 80

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 4/65 (6%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL-- 164
           ++ V  L   + E   +K F+ FGTITDV + Y  + +  R FGF+ Y +EE   + L  
Sbjct: 2   RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKF-RKFGFVGYKTEEEAQKALKH 60

Query: 165 -HKTF 168
            + +F
Sbjct: 61  FNNSF 65

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

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 15/59 (25%), Positives = 30/59 (50%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
           + +F+  L    TE + K+ F QFG +    ++ D  T   +G  F+ + ++E+  + L
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCL 59

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

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 1/78 (1%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL-HK 166
           +FV  L    T+   +++F + G I    V+ D  +++ RGFG++T+  EE   R L  K
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 167 TFHELNGKMVEVKRAVPK 184
              +  G+ + V+ A  K
Sbjct: 62  KKTKFGGRKIHVEFAKKK 79

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

>gnl|CDD|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 = 51.1 bits (123), Expect = 2e-08
 Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 4/73 (5%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           +F+  L +  T+ D  + F  FG +    V  D NT + + FGF++YD+ E+        
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESA----QAA 56

Query: 168 FHELNGKMVEVKR 180
              +NG  V  KR
Sbjct: 57  IKAMNGFQVGGKR 69

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

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

 Score = 51.3 bits (123), Expect = 2e-08
 Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 3/74 (4%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           I++G L     E + KKYF QFGT+ +V V     T   + +GFI + + E V  +  K+
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPE-VAAIAAKS 60

Query: 168 F--HELNGKMVEVK 179
              + L GK+++V 
Sbjct: 61  MNNYLLMGKVLQVH 74

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

 Score = 51.4 bits (124), Expect = 2e-08
 Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 12 GISWDTDEERLKEYFSRYGEV-VEAV-IMRDRATGRARGFGFVVFADPAVAERVI----- 64
          G+   T EE + +  S    V ++ V ++RD+ TG +RGF FV F     A + +     
Sbjct: 9  GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNN 68

Query: 65 MDKHMIDGRTV 75
          +D  +IDGR V
Sbjct: 69 LDPFVIDGRVV 79

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|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating protein-binding protein 2 (G3BP2) and similar proteins

 Score = 51.5 bits (123), Expect = 2e-08
 Identities = 26/64 (40%), Positives = 35/64 (54%)

Query: 4  DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV 63
          D  +LF+G +  D DE  LKE+F  +G VVE  I      G+   FGFVVF D    +R+
Sbjct: 4  DSHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQRI 63

Query: 64 IMDK 67
          +  K
Sbjct: 64 LGAK 67

This subgroup corresponds to the RRM of G3BP2, also termed GAP SH3 domain-binding protein 2, a cytoplasmic protein that interacts with both IkappaBalpha and IkappaBalpha/NF-kappaB complexes, indicating that G3BP2 may play a role in the control of nucleocytoplasmic distribution of IkappaBalpha and cytoplasmic anchoring of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing five PXXP motifs, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). It binds to the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity, through its N-terminal NTF2-like domain. The acidic domain is sufficient for the interaction of G3BP2 with the IkappaBalpha cytoplasmic retention sequence. Furthermore, G3BP2 might influence stability or translational efficiency of particular mRNAs by binding to RNA-containing structures within the cytoplasm through its RNA-binding domain. Length = 83

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

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 22/72 (30%), Positives = 41/72 (56%), Gaps = 6/72 (8%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIM---RDRATGRAR-GFGFVVFADPAVAER 62
          ++++  + +  DE+ L+  FS++GE VE++ +   +D   GR   GF FV F D + AE 
Sbjct: 2  EIYVRNLDFKLDEDDLRGIFSKFGE-VESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

Query: 63 VI-MDKHMIDGR 73
           + ++   + GR
Sbjct: 61 ALQLNGTELGGR 72

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|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 51.2 bits (123), Expect = 2e-08
 Identities = 26/69 (37%), Positives = 41/69 (59%), Gaps = 4/69 (5%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAV-IMRDRATGRARGFGFVVFADPAVAERVIMD 66
          L++G +    DE  +K  F+  GE V +V I+R++ TG   G+ FV FAD A AER +  
Sbjct: 2  LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCL-- 59

Query: 67 KHMIDGRTV 75
           H ++G+ +
Sbjct: 60 -HKLNGKPI 67

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

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

 Score = 51.1 bits (122), Expect = 2e-08
 Identities = 20/62 (32%), Positives = 34/62 (54%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          KLF+G +     E+ ++  F  +G V+E  I++D+ TG  +G  FV ++    A+R I  
Sbjct: 1  KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRA 60

Query: 67 KH 68
           H
Sbjct: 61 LH 62

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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 51.2 bits (122), Expect = 2e-08
 Identities = 29/91 (31%), Positives = 51/91 (56%), Gaps = 9/91 (9%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY--- 154
           ++P P     +F  GL+   TE D ++ F ++G I DV ++YD  ++R RGF F+ +   
Sbjct: 4   ANPDPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 61

Query: 155 -DSEEAVDRVLHKTFHELNGKMVEVKRAVPK 184
            D++EA +R       EL+G+ + V  ++ K
Sbjct: 62  DDAKEAKERA---NGMELDGRRIRVDFSITK 89

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|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 50.3 bits (121), Expect = 4e-08
 Identities = 22/56 (39%), Positives = 33/56 (58%), Gaps = 3/56 (5%)

Query: 18 DEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMID 71
           E+RL+E+F   GEV +  +MR R  G++R FGFV F     A++ +   +K  ID
Sbjct: 13 TEDRLREHFESKGEVTDVKVMRTR-DGKSRRFGFVGFKSEEDAQQAVKYFNKTFID 67

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

>gnl|CDD|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 = 49.8 bits (119), Expect = 4e-08
 Identities = 24/75 (32%), Positives = 43/75 (57%), Gaps = 2/75 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          +F+G I ++  EE+LK+ FS  G VV   ++ DR TG+ +G+GF  + D   A   +  +
Sbjct: 1  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 66 DKHMIDGRTVEAKKA 80
          + + ++GR +    A
Sbjct: 61 NGYELNGRQLRVDNA 75

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

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

 Score = 49.7 bits (119), Expect = 5e-08
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 6  GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADP--AVAERV 63
          G+LFI  +++   EE L++ FS+YG + E  +  D+ T + +GF FV +  P  AV    
Sbjct: 3  GRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFA 62

Query: 64 IMDKHMIDGR 73
           +D  +  GR
Sbjct: 63 ELDGTVFQGR 72

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

 Score = 49.7 bits (119), Expect = 5e-08
 Identities = 21/68 (30%), Positives = 39/68 (57%), Gaps = 2/68 (2%)

Query: 9  FIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADP-AVAERVIMDK 67
          +IG ++WD  E+ ++E+F    E+    +  D+ TG  +GFG V FAD  ++   + +D 
Sbjct: 3  YIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALKLDG 61

Query: 68 HMIDGRTV 75
           ++ GR +
Sbjct: 62 TVLCGRPI 69

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

 Score = 55.3 bits (133), Expect = 5e-08
 Identities = 39/209 (18%), Positives = 82/209 (39%), Gaps = 31/209 (14%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           +++IG +     E+++KE    +G++    +++D ATG ++G+ F  + DP+V +  I  
Sbjct: 297 RIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAA 356

Query: 65  MDKHMIDGRTVEAKKAVPRDDQNMLNR-NTSSIHSSPGPGRTKKIFVGGLAST------- 116
           ++        +  ++A    +Q  ++  N  +  +      ++ I   G   T       
Sbjct: 357 LNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTN 416

Query: 117 -VTESDF-------------KKYFDQFGTITDVVV---MYDHNTQRPRGFGFITYDSEEA 159
            VT  D              K  F ++G + ++V+     D N+    G  F+ Y     
Sbjct: 417 LVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADV-- 474

Query: 160 VDRVLHKTFHELNGKMVEVKRAVPKEFSP 188
             R   K    +NG+    +  V   +  
Sbjct: 475 --RSAEKAMEGMNGRKFNDRVVVAAFYGE 501

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

 Score = 49.9 bits (120), Expect = 5e-08
 Identities = 25/72 (34%), Positives = 43/72 (59%), Gaps = 6/72 (8%)

Query: 9  FIGGISWDTDEERLKEYFSRYGEVVEAV-IMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          F+G + +D +EE L+++F   G+V EAV I+RDR TG  +GFG+V+F         +   
Sbjct: 3  FVGNLPFDIEEEELRKHFEDCGDV-EAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL--- 58

Query: 68 HMIDGRTVEAKK 79
            ++G  ++ +K
Sbjct: 59 -KLNGIKLKGRK 69

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

>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 50.1 bits (120), Expect = 5e-08
 Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          +++  +  +   E LK  FS+YG VV   + R + TG  +GF F+ F  P  A++    K
Sbjct: 2  VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKAC--K 59

Query: 68 HMID 71
          H+ +
Sbjct: 60 HLNN 63

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|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 49.6 bits (119), Expect = 5e-08
 Identities = 19/68 (27%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 9  FIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADP-AVAERVIMDK 67
          F+G + + T  E L+E+F   G +    I+ D+ TG+ +GF ++ F D  +V   +++++
Sbjct: 3  FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLNE 62

Query: 68 HMIDGRTV 75
              GR +
Sbjct: 63 SEFRGRQI 70

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

 Score = 49.6 bits (118), Expect = 6e-08
 Identities = 33/78 (42%), Positives = 43/78 (55%), Gaps = 5/78 (6%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADP--AVAERVIM 65
          LF+ G+S DT EE LKE F      + A I+ DR TG ++GFGFV F+    A A +  M
Sbjct: 3  LFVKGLSEDTTEETLKESFD---GSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

Query: 66 DKHMIDGRTVEAKKAVPR 83
          +   IDG  V    A P+
Sbjct: 60 EDGEIDGNKVTLDFAKPK 77

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

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

 Score = 49.8 bits (119), Expect = 7e-08
 Identities = 22/57 (38%), Positives = 37/57 (64%), Gaps = 1/57 (1%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          +F+GGI    DE  ++ +F++YG V E  I+ DR TG ++G+GFV F D    ++++
Sbjct: 8  VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDDVDVQKIV 63

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

 Score = 49.3 bits (118), Expect = 7e-08
 Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 3/74 (4%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDR-VLHK 166
           IFVG L+  VT+ +  + F + G I +V ++          F FI ++ E+A  R V  +
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARAVESE 63

Query: 167 TFHELNGKMVEVKR 180
               L  K + V+ 
Sbjct: 64  NHSMLKNKTMHVQY 77

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

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

 Score = 49.3 bits (118), Expect = 8e-08
 Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 6/74 (8%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEA-VIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          L++ G+S  T    LK+ FS+YG+VV A ++   R+ G AR FGFV  A    A + I  
Sbjct: 2  LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPG-ARCFGFVTMASVEEAAKCIQH 60

Query: 65 MDKHMIDGR--TVE 76
          + +  + GR  +VE
Sbjct: 61 LHRTELHGRVISVE 74

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

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

 Score = 49.9 bits (119), Expect = 8e-08
 Identities = 29/103 (28%), Positives = 48/103 (46%), Gaps = 25/103 (24%)

Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--- 64
           LF+  + +D  EE L  +FS++G V  A+ + D++TGRA+G GFV F D       +   
Sbjct: 4   LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKNA 63

Query: 65  ----------------------MDKHMIDGRTVEAKKAVPRDD 85
                                 M +++++GR +    AV RD+
Sbjct: 64  PAAGSTSLLSGSSLTADIGDDVMPEYVLEGRVLSVTPAVVRDE 106

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|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 20/71 (28%), Positives = 38/71 (53%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           IFVG +    T  + +++F   GTI  + ++ D  T +P+GF +I +  + +V+  L   
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLN 61

Query: 168 FHELNGKMVEV 178
             E  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|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 12/76 (15%)

Query: 102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD 161
           P +   ++V G    +TE   KK F  FG I ++      + ++ +  GF+T++  E+ D
Sbjct: 1   PRKGNTLYVHGYG--LTEEILKKAFSPFGNIINI------SMEKEKNCGFVTFEKMESAD 52

Query: 162 RVLHKTFHELNGKMVE 177
           R +     ELNG  V+
Sbjct: 53  RAI----AELNGTTVQ 64

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

 Score = 49.0 bits (117), Expect = 1e-07
 Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          +F+G +S +  +  L   FS +    +A +M D  +GR+RG+GFV F     AE  I  M
Sbjct: 2  IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 66 DKHMIDGRTV 75
          +   +  R +
Sbjct: 62 NGKWLGSRPI 71

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

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 17/78 (21%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTIT--DVVVMYDHNTQRPRGFGFITYDSEEAVDRV- 163
           K+FVG L    T  + +  F+++GT+T  DVV          + +GF+  + EE  +   
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVTECDVV----------KNYGFVHMEEEEDAEDAI 50

Query: 164 --LHKTFHELNGKMVEVK 179
             L+   +E  GK + V+
Sbjct: 51  KALNG--YEFMGKRINVE 66

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

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 9/74 (12%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAV-IMRDRATGRARGFGFVVF-----ADPAVAE 61
          LFIG +  + DE+ L + FS +G +++   IMRD  TG ++GF F+ +     +D A+  
Sbjct: 4  LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 62 RVIMDKHMIDGRTV 75
             M+   +  R +
Sbjct: 64 ---MNGQYLCNRPI 74

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|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 = 23/71 (32%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          L++  ++  T  + L+  F +YG +V+  I  D  T R RGF +V F D   AE  +  +
Sbjct: 3  LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 66 DKHMIDGRTVE 76
          D+    GR +E
Sbjct: 63 DRTRFLGREIE 73

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

 Score = 49.2 bits (118), Expect = 1e-07
 Identities = 18/49 (36%), Positives = 35/49 (71%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFAD 56
          ++IGG+ ++  E  +   FS+YGE+V+  ++RD+ TG+++GF F+ + D
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYED 60

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

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 10/77 (12%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          L++  +   T EE+L+E FS YGEV     ++D        + FV F +   A + +  M
Sbjct: 4  LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55

Query: 66 DKHMIDGRTVEAKKAVP 82
          +   ++G  +E   A P
Sbjct: 56 NGKELEGSPIEVSLAKP 72

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

 Score = 48.8 bits (116), Expect = 1e-07
 Identities = 29/75 (38%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          LF+  I+ DT  E L+  F RYG +V+  +  D  T R RGF +V F D   AE  +  +
Sbjct: 3  LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62

Query: 66 DKHMIDGRTVEAKKA 80
          D+  I GR +E + A
Sbjct: 63 DRKWICGRQIEIQFA 77

This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|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 = 48.0 bits (115), Expect = 2e-07
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEAVDRVLHK 166
           +FVG +    TE    + F + G +    ++ D +T +P+G+GF  + D E A   + + 
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 167 TFHELNGKMVEV 178
             +E NG+ + V
Sbjct: 61  NGYEFNGRALRV 72

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

 Score = 48.5 bits (116), Expect = 2e-07
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
             ++V  +A      D ++ F ++G I DV +  D  T+RPRGF ++ ++     +  L+
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALY 60

Query: 166 KTFHE-LNGKMVEVKRA 181
                   G+ +E++ A
Sbjct: 61  YLDRTRFLGREIEIQFA 77

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

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 21/58 (36%), Positives = 33/58 (56%), Gaps = 4/58 (6%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEE----AVD 161
           I++GGL   +TE D    F Q+G I D+ ++ D  T + +GF F+ Y+ +     AVD
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVD 69

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|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 23/74 (31%), Positives = 41/74 (55%), Gaps = 8/74 (10%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           ++VGGL   VTE D + +F QFG I  + V+            F+T+ + EA ++   + 
Sbjct: 4   LYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQC------AFVTFTTREAAEKAAERL 57

Query: 168 FHEL--NGKMVEVK 179
           F++L  NG+ +++K
Sbjct: 58  FNKLIINGRRLKLK 71

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

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 16/57 (28%), Positives = 33/57 (57%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          ++I G+  +T +E L++    +G+++    + D+ T + +G+GFV F  P  A + I
Sbjct: 3  VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAI 59

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

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 17/67 (25%), Positives = 42/67 (62%), Gaps = 2/67 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADP-AVAERVIMD 66
          +F+  + +   E+ L++ FS+ GE+ +  ++++   G+++G+ +V F +  +V E + +D
Sbjct: 2  VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEALKLD 60

Query: 67 KHMIDGR 73
          + +I GR
Sbjct: 61 RELIKGR 67

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

 Score = 47.9 bits (115), Expect = 3e-07
 Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 4/61 (6%)

Query: 113 LASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELN 172
           L+    E D ++ F  FG I+ V +  D  T + RGF F+T+ + E  +R + K    LN
Sbjct: 7   LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEK----LN 62

Query: 173 G 173
           G
Sbjct: 63  G 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|240838 cd12392, RRM2_SART3, RNA recognition motif 2 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 47.8 bits (114), Expect = 3e-07
 Identities = 18/71 (25%), Positives = 40/71 (56%), Gaps = 3/71 (4%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          KLF+ G+ +   +E L++ F ++G V    ++ +R+ G+ +G  +V + + + A + +  
Sbjct: 4  KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRS-GKPKGLAYVEYENESSASQAVLK 62

Query: 65 MDKHMIDGRTV 75
          MD   I  +T+
Sbjct: 63 MDGTEIKEKTI 73

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

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

 Score = 47.5 bits (113), Expect = 3e-07
 Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 1/62 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          KLF+G +S   +E  ++  F+ +G + E  ++RD   G++RG  FV FA    A   I  
Sbjct: 3  KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRD-QNGQSRGCAFVTFASRQCALNAIKA 61

Query: 67 KH 68
           H
Sbjct: 62 MH 63

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

 Score = 47.5 bits (113), Expect = 4e-07
 Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK- 166
           +FV  LA +VT+ D   +F     I   VV+ D  T   RG+GF+T+   E     L K 
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 167 TFHELNGKMVEVKRAVPK 184
              +L+G+++ +  A  +
Sbjct: 62  KNKKLHGRILRLDIAERR 79

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

 Score = 47.3 bits (113), Expect = 4e-07
 Identities = 20/50 (40%), Positives = 32/50 (64%), Gaps = 1/50 (2%)

Query: 8  LFIGGISWDTDEERLKEYF-SRYGEVVEAVIMRDRATGRARGFGFVVFAD 56
          +F+G ++ D  +  L+E F +RY  V  A ++ D  TGR++G+GFV F D
Sbjct: 4  IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGD 53

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 46.4 bits (111), Expect = 4e-07
 Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 7/61 (11%)

Query: 22 LKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK 79
          L + FS +G V +  +++ +      GF FV F+    AE+ +  ++  +  GR +    
Sbjct: 1  LYKLFSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

Query: 80 A 80
          +
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|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 46.7 bits (111), Expect = 5e-07
 Identities = 23/67 (34%), Positives = 40/67 (59%), Gaps = 4/67 (5%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           IFVG L+  VT++     F  F + +D  VM+D  + R RG+GF+++ S++  +  +   
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAI--- 58

Query: 168 FHELNGK 174
            +E+NGK
Sbjct: 59  -NEMNGK 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|240843 cd12397, RRM2_Nop13p_fungi, RNA recognition motif 2 in yeast nucleolar protein 13 (Nop13p) and similar proteins

 Score = 47.1 bits (112), Expect = 5e-07
 Identities = 20/61 (32%), Positives = 34/61 (55%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          LF+G +S++T E+ L+ +F R G +    +M    +G+ +GF FV F +   A   +  K
Sbjct: 1  LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60

Query: 68 H 68
          H
Sbjct: 61 H 61

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

 Score = 46.9 bits (112), Expect = 5e-07
 Identities = 18/57 (31%), Positives = 36/57 (63%), Gaps = 2/57 (3%)

Query: 26 FSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA 80
          FS+YG+VV+  I++D+ T +++G  F++F D   A + +  ++   + GRT++   A
Sbjct: 22 FSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNNKELFGRTLKCSIA 78

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

>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 46.8 bits (112), Expect = 5e-07
 Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 6/52 (11%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEA 159
           ++VG L   +TE + ++ F  FG I +V V       + +G+ F+ +D+ EA
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRV------FKDKGYAFVRFDTHEA 48

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

 Score = 47.0 bits (112), Expect = 5e-07
 Identities = 17/46 (36%), Positives = 30/46 (65%)

Query: 19 EERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          ++ ++  FS  GE+    ++RD+ TG++ G+GFV + DP  AE+ I
Sbjct: 15 QDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAI 60

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

 Score = 46.8 bits (112), Expect = 5e-07
 Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 18/87 (20%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY----DSEEAVDR 162
           K++VG L    T+ + +  F+++G +  V V      + P GF F+ +    D+E+AV  
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWV-----ARNPPGFAFVEFEDPRDAEDAVR- 54

Query: 163 VLHKTFHELNGKMVEVKRAVPKEFSPG 189
                   L+G+ +     V  E S G
Sbjct: 55  -------ALDGRRIC-GNRVRVELSRG 73

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

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

 Score = 46.8 bits (112), Expect = 6e-07
 Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 1/67 (1%)

Query: 109 FVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK-T 167
           +VG L   VTE+   + F   G +  + V  D  T+R  G+ ++ + +    +R L    
Sbjct: 3   YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

Query: 168 FHELNGK 174
           F  + GK
Sbjct: 63  FDVIKGK 69

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

 Score = 46.9 bits (111), Expect = 6e-07
 Identities = 28/79 (35%), Positives = 45/79 (56%), Gaps = 7/79 (8%)

Query: 110 VGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY----DSEEAVDRVLH 165
           V GL+   TE D ++ F ++G +  V V+YD  T R RGF F+ +    DS+EA++   H
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAME---H 60

Query: 166 KTFHELNGKMVEVKRAVPK 184
               EL+G+ + V  ++ K
Sbjct: 61  ANGMELDGRRIRVDYSITK 79

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

>gnl|CDD|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 = 46.8 bits (112), Expect = 6e-07
 Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          + + G+ +   EE ++++FS      + + +     GR  G  +V FA P  A R +   
Sbjct: 2  VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKH 61

Query: 68 H-MIDGRTVE 76
          +  + GR +E
Sbjct: 62 NNKMGGRYIE 71

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|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 46.6 bits (111), Expect = 6e-07
 Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 5/70 (7%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           ++VGG+    TE + + YF   G I ++ +M   +T R RG  FIT+ +EEA  R L   
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRAL--- 57

Query: 168 FHELNGKMVE 177
              L+G+ + 
Sbjct: 58  --ALDGEDMG 65

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

 Score = 46.8 bits (112), Expect = 7e-07
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 4/71 (5%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIM-RDRATGRARGFGFVVFADPAVAERVI-- 64
          L++G +S+ T EE++ E FSR G+ ++ +IM  DR T    GF FV +     AE  +  
Sbjct: 1  LYVGNLSFYTTEEQIYELFSRCGD-IKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKY 59

Query: 65 MDKHMIDGRTV 75
          ++   +D R +
Sbjct: 60 LNGTKLDDRII 70

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

 Score = 46.6 bits (111), Expect = 7e-07
 Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 6/72 (8%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           K++ V  +     + D ++ F QFG I DV +++  N +  +GFGF+T+ +    DR   
Sbjct: 1   KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIF--NERGSKGFGFVTFANSADADRAR- 57

Query: 166 KTFHELNGKMVE 177
               +L+G +VE
Sbjct: 58  ---EKLHGTVVE 66

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

 Score = 46.5 bits (110), Expect = 8e-07
 Identities = 17/58 (29%), Positives = 33/58 (56%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
           K+FVG +  T+TE + +  F++ G + +V ++ D  T   +G  F+ Y + +  DR +
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAI 58

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|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 = 46.3 bits (110), Expect = 8e-07
 Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEAVDRVLHK 166
           +FVG +    TE   K  F + G +    ++YD  T +P+G+GF  Y D E A+  + + 
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 167 TFHELNGKMVEVKRA 181
             +ELNG+ + V  A
Sbjct: 61  NGYELNGRQLRVDNA 75

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

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

 Score = 46.1 bits (110), Expect = 9e-07
 Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 4/63 (6%)

Query: 110 VGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY----DSEEAVDRVLH 165
           V  L    T  D ++ F+++G + DV +  D  T+  RGF F+ +    D+E+A+D +  
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 166 KTF 168
           K  
Sbjct: 63  KEL 65

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

 Score = 46.0 bits (110), Expect = 9e-07
 Identities = 20/74 (27%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           +++G L     E + +KYF QFGT+T + +     T + +G+ F+ ++S E V +++ +T
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPE-VAKIVAET 60

Query: 168 FHE--LNGKMVEVK 179
            +   L  ++++ K
Sbjct: 61  MNNYLLFERLLKCK 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|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 46.5 bits (111), Expect = 9e-07
 Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 7/76 (9%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMY---DHNTQRPRGFGFITYDSEEAVD 161
           T  ++VG L   VTE    + F +FG +  V +M+   +   +R R  GF+ + +    +
Sbjct: 1   TTNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAE 60

Query: 162 RVLHKTFHELNGKMVE 177
           R L     EL+GK V 
Sbjct: 61  RAL----DELDGKDVM 72

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

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

 Score = 45.8 bits (109), Expect = 1e-06
 Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 4/68 (5%)

Query: 113 LASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELN 172
           L   +T+ + +  F+  G I    ++ D  T +  G+GF+ Y  E    + ++     LN
Sbjct: 8   LPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINT----LN 63

Query: 173 GKMVEVKR 180
           G  +  KR
Sbjct: 64  GFEIRNKR 71

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

 Score = 46.2 bits (110), Expect = 1e-06
 Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 5/77 (6%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEAVD--RVL 164
           ++V  L  ++T +D  K F ++G +  V ++ D  T++ +G  FI + D E+A    + L
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 165 HKTFHELNGKMVEVKRA 181
           +    EL G+ ++   A
Sbjct: 64  NNK--ELFGRTLKCSIA 78

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

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

 Score = 45.9 bits (109), Expect = 1e-06
 Identities = 22/77 (28%), Positives = 43/77 (55%), Gaps = 6/77 (7%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEA-VIMRDRATGRARGFGFVVFADPAVAERVIM 65
          +L +  I +   +  L++ F ++G +++  +I  +R +   +GFGFV FA+ A A+R   
Sbjct: 2  RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGS---KGFGFVTFANSADADRARE 58

Query: 66 DKH--MIDGRTVEAKKA 80
            H  +++GR +E   A
Sbjct: 59 KLHGTVVEGRKIEVNNA 75

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

 Score = 46.1 bits (109), Expect = 1e-06
 Identities = 20/57 (35%), Positives = 35/57 (61%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          L++ G+     ++ L++ FS+YG ++ + I+RD+ TG +RG GF+ F     AE  I
Sbjct: 3  LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAI 59

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

 Score = 49.9 bits (119), Expect = 2e-06
 Identities = 22/71 (30%), Positives = 42/71 (59%), Gaps = 2/71 (2%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADP--AVAERVI 64
           KL++G + ++  E+ L++ F  +G++ +  + RD  TGR++GFGF+ F D   A     +
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEV 247

Query: 65  MDKHMIDGRTV 75
           M+   + GR +
Sbjct: 248 MNGFELAGRPI 258

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 10/70 (14%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           ++FVG L + +TE +FK+ F ++G +++V +       + +GFGFI  D+    ++   K
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGEVSEVFL------NKEKGFGFIRLDTRTNAEKA--K 54

Query: 167 TFHELNGKMV 176
              EL+G M 
Sbjct: 55  A--ELDGIMR 62

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

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 11/79 (13%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVV-------MYDHNTQRPRGFGFITYDSEEA 159
           +I+V  L   + E D +  F +FG +  + +           N     GF F+T+    +
Sbjct: 2   EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLN----NGFAFVTFKDASS 57

Query: 160 VDRVLHKTFHELNGKMVEV 178
            +  L     EL G+ + V
Sbjct: 58  AENALQLNGTELGGRKISV 76

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

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 2/57 (3%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          +F+G +S D  +E L E FSR+G+++E  +++ RA      F F+ F     A R +
Sbjct: 6  IFVGQLSPDVTKEELNERFSRHGKILEVNLIK-RANHT-NAFAFIKFEREQAAARAV 60

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

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 10/71 (14%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          KLF+G +   T  E L+  F +YG V E  ++++        +GFV   +   AE  I  
Sbjct: 1  KLFVGNLPDATTSEELRALFEKYGTVTECDVVKN--------YGFVHMEEEEDAEDAIKA 52

Query: 65 MDKHMIDGRTV 75
          ++ +   G+ +
Sbjct: 53 LNGYEFMGKRI 63

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 18/67 (26%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           +FV  L  +V E + +K F + G ITDV ++ ++   + +G+ ++ +++EE+V   L   
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEALKLD 60

Query: 168 FHELNGK 174
              + G+
Sbjct: 61  RELIKGR 67

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

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 20/54 (37%), Positives = 31/54 (57%), Gaps = 1/54 (1%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEA 159
           +K+FVG L+    E+D +  F  FG+I +  V+ D N Q  RG  F+T+ S + 
Sbjct: 2   RKLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQS-RGCAFVTFASRQC 54

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|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 45.2 bits (107), Expect = 2e-06
 Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 11/75 (14%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          K+F+G +  DT +E L+  F  YG V+   +MR         F FV     A A+R I +
Sbjct: 2  KIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ--------FAFVHLRGEAAADRAIEE 53

Query: 67 KHMIDGRTVEAKKAV 81
           +   GR +  +K V
Sbjct: 54 LN---GRELHGRKLV 65

This subgroup corresponds to the RRM1 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 = 69

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

 Score = 45.4 bits (108), Expect = 2e-06
 Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD 161
           +FVG L + VTE    + F Q G +  V +  D N + P+ F F+T+  E +V 
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGK-PKSFAFVTFKHEVSVP 56

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 18/49 (36%), Positives = 29/49 (59%)

Query: 9  FIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADP 57
          F+  +S    E  L E+FS+ G+V +  I+RDR + R++G  +V F D 
Sbjct: 3  FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDE 51

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEE-AVDRVLH 165
           +I+V  +   ++E D K  F+ FG I    +  D  T + +G+GFI Y++ + A D +  
Sbjct: 2   RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIAS 61

Query: 166 KTFHELNGKMVEVKRA 181
               +L G+ + V +A
Sbjct: 62  MNLFDLGGQQLRVGKA 77

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

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 15/65 (23%), Positives = 35/65 (53%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          ++++  +  D  E+ +K  F  +G++    +  D  TG+ +G+GF+ + +P  A+  I  
Sbjct: 2  RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIAS 61

Query: 67 KHMID 71
           ++ D
Sbjct: 62 MNLFD 66

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

 Score = 46.6 bits (110), Expect = 3e-06
 Identities = 27/88 (30%), Positives = 45/88 (51%), Gaps = 1/88 (1%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
           + K+F+GGL+    ++  +  F  FG + D  V+ D  T R RGFGF+ ++ E A    +
Sbjct: 34  STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAI 93

Query: 165 HKT-FHELNGKMVEVKRAVPKEFSPGPS 191
            +    ELNG+ + V  A  +  +P   
Sbjct: 94  SEMDGKELNGRHIRVNPANDRPSAPRAY 121

Length = 144

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

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 26/77 (33%), Positives = 43/77 (55%), Gaps = 11/77 (14%)

Query: 108 IFVGGLASTVTESDFKKYFDQFG-TITDVVVMYDHNTQRP--RGFGFITYDSEEAVDRV- 163
           ++V GL+ST   +D K+ F ++G  +   +V    N + P  R FGF+T  S E   +  
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVT---NARSPGARCFGFVTMASVEEAAKCI 58

Query: 164 --LHKTFHELNGKMVEV 178
             LH+T  EL+G+++ V
Sbjct: 59  QHLHRT--ELHGRVISV 73

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

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

 Score = 45.3 bits (107), Expect = 3e-06
 Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           +FV  +A      D ++ F ++G I DV V  D  T+RPRGF ++ ++     +  LH  
Sbjct: 3   LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62

Query: 168 FHE-LNGKMVEVKRA 181
             + + G+ +E++ A
Sbjct: 63  DRKWICGRQIEIQFA 77

This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 44.5 bits (106), Expect = 3e-06
 Identities = 17/52 (32%), Positives = 28/52 (53%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEA 159
           +++ GL    T+ D +K    FG I     + D  T + +G+GF+ +DS EA
Sbjct: 3   VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEA 54

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|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 44.7 bits (106), Expect = 3e-06
 Identities = 23/67 (34%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MD 66
          +++GGI + + E+ ++ YFS  GE+ E  +M    TGR RG  F+ F     A+R + +D
Sbjct: 1  VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALALD 60

Query: 67 KHMIDGR 73
             + GR
Sbjct: 61 GEDMGGR 67

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

 Score = 45.1 bits (106), Expect = 3e-06
 Identities = 22/66 (33%), Positives = 38/66 (57%), Gaps = 2/66 (3%)

Query: 19 EERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVE 76
          +E LK  F   GE+    ++RD+ TG++ G+GFV + DP  AE+ I  ++   +  +T++
Sbjct: 18 QEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIK 77

Query: 77 AKKAVP 82
             A P
Sbjct: 78 VSYARP 83

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|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 45.0 bits (106), Expect = 3e-06
 Identities = 25/82 (30%), Positives = 43/82 (52%), Gaps = 1/82 (1%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEAVDRVLHK 166
           +FV  +A      D ++ F ++G I DV V  D  T+RPRGF +I + D  +A D + + 
Sbjct: 3   LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62

Query: 167 TFHELNGKMVEVKRAVPKEFSP 188
               + G+ +E++ A     +P
Sbjct: 63  NRKWVCGRQIEIQFAQGDRKTP 84

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 44.7 bits (105), Expect = 3e-06
 Identities = 23/77 (29%), Positives = 43/77 (55%), Gaps = 5/77 (6%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV-- 163
           + ++V GL+ST   +D K  F ++G +    V+ +  +   R +GF+T  + E   +   
Sbjct: 2   RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCIN 61

Query: 164 -LHKTFHELNGKMVEVK 179
            LH+T  EL+G+M+ V+
Sbjct: 62  HLHRT--ELHGRMISVE 76

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

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 44.9 bits (107), Expect = 3e-06
 Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 3/57 (5%)

Query: 107 KIFVGGLASTVTESDFKKYFDQF-GTITDVVVMYDHNTQRPRGFGFITY-DSEEAVD 161
           ++ V  L +++TE++ K++F +  G ITDV ++   +  + R   FI Y   EEA  
Sbjct: 2   RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTED-GKSRRIAFIGYKTEEEAQK 57

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

>gnl|CDD|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis thaliana zinc finger CCCH domain-containing protein 46 (AtC3H46) and similar proteins

 Score = 44.8 bits (106), Expect = 3e-06
 Identities = 28/66 (42%), Positives = 38/66 (57%), Gaps = 5/66 (7%)

Query: 115 STVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK-TFHELNG 173
           S  TE D  +YF QFG + DV + Y    Q+ R FGF+T+++ E V R+L K   H + G
Sbjct: 9   SRFTEEDVSEYFGQFGPVLDVRIPY----QQKRMFGFVTFENAETVKRILSKGNPHFICG 64

Query: 174 KMVEVK 179
             V VK
Sbjct: 65  SRVRVK 70

This subfamily corresponds to the RRM domain in AtC3H46, a putative RNA-binding protein that contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCCH class of zinc finger, typically C-X8-C-X5-C-X3-H. It may possess ribonuclease activity. . Length = 70

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 44.5 bits (105), Expect = 3e-06
 Identities = 21/50 (42%), Positives = 32/50 (64%), Gaps = 6/50 (12%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
           ++FVG L + +TE DFKK F+++G  ++V +       R RGFGFI  +S
Sbjct: 3   RLFVGNLPTDITEEDFKKLFEKYGEPSEVFI------NRDRGFGFIRLES 46

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 44.5 bits (106), Expect = 3e-06
 Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 2/74 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          +++G +     EE L E F + G VV   I +DR T   +G+GFV F     A+  I   
Sbjct: 1  VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 68 HMID--GRTVEAKK 79
          +MI   G+ +   K
Sbjct: 61 NMIKLYGKPIRVNK 74

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

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

 Score = 44.6 bits (106), Expect = 4e-06
 Identities = 26/80 (32%), Positives = 36/80 (45%), Gaps = 2/80 (2%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVV-VMYDHNTQRPRGFGFITYDSEEAVDRVL-H 165
           +F+G L   V E      F  FG I     +M D +T   +GF FI+YDS EA D  +  
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 166 KTFHELNGKMVEVKRAVPKE 185
                L  + + V  A  K+
Sbjct: 64  MNGQYLCNRPITVSYAFKKD 83

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

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

 Score = 43.7 bits (104), Expect = 4e-06
 Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 10/61 (16%)

Query: 122 FKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV---LHKTFHELNGKMVEV 178
             K F  FG +  + ++         GF F+ + +EEA ++    L+       G+ + V
Sbjct: 1   LYKLFSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVL--FGGRPLRV 53

Query: 179 K 179
            
Sbjct: 54  D 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|240729 cd12283, RRM1_RBM39_like, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 44.1 bits (105), Expect = 4e-06
 Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 5/69 (7%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           +FV  L+  V E D  ++F + G + DV ++ D N++R +G  ++ +  EE+V   L   
Sbjct: 2   VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL--- 58

Query: 168 FHELNGKMV 176
              L G+ +
Sbjct: 59  --GLTGQRL 65

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

 Score = 44.5 bits (105), Expect = 4e-06
 Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEE 158
           K+FVG L    TE + ++ F  +G + D+ +M D   Q  RG  F+ Y S+E
Sbjct: 1   KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQ-SRGCAFVKYSSKE 51

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

 Score = 44.3 bits (105), Expect = 4e-06
 Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 1/67 (1%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MD 66
          LF+G + +DT  E L  +F   G      ++ D+ TG+++G  FV F       + + + 
Sbjct: 3  LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62

Query: 67 KHMIDGR 73
            ++ GR
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|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 = 44.4 bits (105), Expect = 5e-06
 Identities = 18/50 (36%), Positives = 29/50 (58%), Gaps = 2/50 (4%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGR--ARGFGFVVF 54
          K+F+G I     E+ L+E F +YG V +  ++RDR+     ++G  FV F
Sbjct: 3  KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTF 52

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

 Score = 44.2 bits (105), Expect = 5e-06
 Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 12/71 (16%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD----SEEAVDRV 163
           ++V GL  T+T+ + +  F  +G I    ++ D+ T   RG GFI +D    +E A+   
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKA- 61

Query: 164 LHKTFHELNGK 174
                  LNG 
Sbjct: 62  -------LNGT 65

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

 Score = 44.1 bits (104), Expect = 6e-06
 Identities = 17/57 (29%), Positives = 31/57 (54%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          L++  +     E+ L++ F  YG +V+  ++RD++TG  RG  FV +     A+  I
Sbjct: 3  LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAI 59

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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 43.9 bits (104), Expect = 6e-06
 Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 5  LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          L +LF+  I     EE L+E F  +G++    I++D+ TG ++GFG+V F  P+ A   +
Sbjct: 1  LTRLFVV-IPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 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|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 43.8 bits (104), Expect = 7e-06
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 6/72 (8%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEAVDRVLH 165
           +IFVG L + VT+    + F ++ +     V+ D  T + +G+GF+++ D  + +     
Sbjct: 8   RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYL----- 62

Query: 166 KTFHELNGKMVE 177
           K   E+NGK V 
Sbjct: 63  KAMKEMNGKYVG 74

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

 Score = 43.9 bits (104), Expect = 7e-06
 Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 7/82 (8%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
           +  +++G L+  VTE D K  F+++G I  +      +   PRG  ++  ++ +   R L
Sbjct: 2   STTLWIGHLSKKVTEEDLKNLFEEYGEIQSI------DMIPPRGCAYVCMETRQDAHRAL 55

Query: 165 HK-TFHELNGKMVEVKRAVPKE 185
            K    +L GK ++V  A  K 
Sbjct: 56  QKLRNVKLAGKKIKVAWAPNKG 77

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

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

 Score = 47.7 bits (113), Expect = 7e-06
 Identities = 35/143 (24%), Positives = 57/143 (39%), Gaps = 14/143 (9%)

Query: 16  DTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTV 75
           D  +  L   F   G +    IMRD  TG + G+ FV F   A ++R I + + I  R  
Sbjct: 118 DMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNK 177

Query: 76  EAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDV 135
             K +  R     +              +   ++V  L  T+T+      F ++G I   
Sbjct: 178 RLKVSYARPGGESI--------------KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQK 223

Query: 136 VVMYDHNTQRPRGFGFITYDSEE 158
            ++ D  T  PRG  F+ ++  E
Sbjct: 224 NILRDKLTGTPRGVAFVRFNKRE 246

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

 Score = 43.6 bits (103), Expect = 8e-06
 Identities = 16/62 (25%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
            K+FV GL  +VT+ + +K F + G +  V ++ + +  +P+G  ++ Y++E +  + + 
Sbjct: 3   HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSG-KPKGLAYVEYENESSASQAVL 61

Query: 166 KT 167
           K 
Sbjct: 62  KM 63

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

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

 Score = 43.6 bits (103), Expect = 9e-06
 Identities = 19/72 (26%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 6  GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI- 64
           ++++G IS++  E+ +++ FS +G +    +  D  T + +GF FV +  P  A+  + 
Sbjct: 1  CRVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALE 60

Query: 65 -MDKHMIDGRTV 75
           M+  M+ GR +
Sbjct: 61 QMNGVMLGGRNI 72

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

 Score = 43.4 bits (103), Expect = 9e-06
 Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 12/61 (19%)

Query: 13 ISWDT-------DEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIM 65
          + W          E+ L++ FS+YG+ V  V++  +  G A     V FA    AE  + 
Sbjct: 5  VKWKRKKGNGDYSEDELRKIFSKYGD-VSDVVVSSKKKGSA----IVEFASKKAAEAAVE 59

Query: 66 D 66
          +
Sbjct: 60 N 60

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

>gnl|CDD|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 43.1 bits (102), Expect = 9e-06
 Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 9/79 (11%)

Query: 108 IFVGGLASTVTESDFKKYF-DQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           +++G L+S V ESD ++ F +    ++ V+V       +  G+ F+    +   D+ + K
Sbjct: 1   LYIGNLSSDVNESDLRQLFEEHKIPVSSVLV-------KKGGYAFVDCPDQSWADKAIEK 53

Query: 167 -TFHELNGKMVEVKRAVPK 184
                L GK++EV+ +VPK
Sbjct: 54  LNGKILQGKVIEVEHSVPK 72

Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. Length = 73

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

 Score = 42.9 bits (102), Expect = 1e-05
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS-EEAVDRVLHK 166
           + VG L   V +   K+ F  +GT+ DV +  D     PRG+ ++ ++S E+A   + H 
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 167 TFHELNGKMVEVK 179
              +++G+ V V+
Sbjct: 61  DGGQIDGQEVTVE 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|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 42.9 bits (102), Expect = 1e-05
 Identities = 20/72 (27%), Positives = 40/72 (55%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           +FVG L   + E + +K+F+  G +  V ++ D  T   +GFG++ + ++++V   L   
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLN 61

Query: 168 FHELNGKMVEVK 179
             +L G+ + VK
Sbjct: 62  GIKLKGRKIRVK 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|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 17/73 (23%), Positives = 35/73 (47%), Gaps = 14/73 (19%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS-EEAVDRVL 164
           K ++V  L  + TE   ++ F ++G +  V         + + + F+ ++  ++AV    
Sbjct: 2   KVLYVRNLPLSTTEEQLRELFSEYGEVERVK--------KIKDYAFVHFEERDDAV---- 49

Query: 165 HKTFHELNGKMVE 177
            K   E+NGK +E
Sbjct: 50  -KAMEEMNGKELE 61

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

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 5/68 (7%)

Query: 108 IFVGGLASTVTESDFKKYFDQ-FGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           IFVG LA  VT+   ++ F   + ++    V+ D  T R +G+GF+ +  E+  DR L  
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRAL-- 61

Query: 167 TFHELNGK 174
              E+NG 
Sbjct: 62  --TEMNGV 67

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

 Score = 43.4 bits (102), Expect = 1e-05
 Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 4/57 (7%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD----SEEAV 160
           ++V GL  T+T+ + ++ F Q+G I    ++ D  T   RG GFI +D    +EEA+
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAI 59

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|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 43.1 bits (101), Expect = 1e-05
 Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 2/75 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          LF+  ++  T  E L+  F RYG +V+  +  D  T R RGF ++ F D   AE  +  +
Sbjct: 3  LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62

Query: 66 DKHMIDGRTVEAKKA 80
          ++  + GR +E + A
Sbjct: 63 NRKWVCGRQIEIQFA 77

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

 Score = 43.3 bits (102), Expect = 1e-05
 Identities = 17/51 (33%), Positives = 28/51 (54%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEE 158
           ++V  L   +TE + +K F+ +G I    ++ D +T  PRG  F+ YD  E
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKRE 53

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|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 26/69 (37%), Positives = 38/69 (55%), Gaps = 3/69 (4%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          +L +  + +D  EE L+E F R GEV +  I  DR +GR+ G   VVF     AER I  
Sbjct: 2  RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQ 60

Query: 65 MDKHMIDGR 73
           +  ++DG+
Sbjct: 61 FNGVLLDGQ 69

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

 Score = 43.3 bits (102), Expect = 1e-05
 Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 5/70 (7%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           ++VG L   VTE   K+ F   G + +V ++ D N  +   +GF+ Y      +  L   
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKN-NKGVNYGFVEYHQSHDAEIALQT- 58

Query: 168 FHELNGKMVE 177
              LNG+ +E
Sbjct: 59  ---LNGRQIE 65

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

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 25/87 (28%), Positives = 44/87 (50%), Gaps = 14/87 (16%)

Query: 103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY----DSEE 158
            RT  +FV  + S V + + +  F+QFG   D+  +Y     + RGF  ++Y     +  
Sbjct: 1   SRT--LFVRNINSNVEDEELRALFEQFG---DIRTLYT--ACKHRGFIMVSYYDIRAARR 53

Query: 159 AVDRVLHKTFHELNGKMVEVKRAVPKE 185
           A  R L  T  EL G+ +++  ++PK+
Sbjct: 54  AK-RALQGT--ELGGRKLDIHFSIPKD 77

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 18/79 (22%), Positives = 38/79 (48%), Gaps = 7/79 (8%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          LF+  I+ + ++E L+  F ++G+ +  +        + RGF  V + D   A R    +
Sbjct: 4  LFVRNINSNVEDEELRALFEQFGD-IRTLYT----ACKHRGFIMVSYYDIRAARRAKRAL 58

Query: 66 DKHMIDGRTVEAKKAVPRD 84
              + GR ++   ++P+D
Sbjct: 59 QGTELGGRKLDIHFSIPKD 77

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

>gnl|CDD|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 43.1 bits (101), Expect = 1e-05
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFIT-YDSEEAVDRVLHK 166
           +FVG L+  +T  D K  F  FG I+D  V+ D  T + +G+GF++ Y+  +A + ++H 
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 167 TFHELNGKMVEVKRA 181
               L G+ +    A
Sbjct: 64  GGQWLGGRQIRTNWA 78

This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

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

 Score = 43.2 bits (101), Expect = 1e-05
 Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          L +  +  +  ++ L+  FS  GEV  A ++RD+  G + G+GFV + +   AER I  +
Sbjct: 4  LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 66 DKHMIDGRTVEAKKAVP 82
          +   +  +T++   A P
Sbjct: 64 NGLRLQSKTIKVSYARP 80

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|240725 cd12279, RRM_TUT1, RNA recognition motif in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 17/74 (22%), Positives = 37/74 (50%), Gaps = 6/74 (8%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD- 66
          +F+ G    T EE+L +YFS +G V+  ++ +D+       +  V F      ++V+ + 
Sbjct: 5  VFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKDKGV-----YAIVEFDSKEGVDKVLSEP 59

Query: 67 KHMIDGRTVEAKKA 80
          +H ++G  +  +  
Sbjct: 60 QHTLNGHRLRVRPR 73

This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS). . Length = 74

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

 Score = 42.6 bits (100), Expect = 2e-05
 Identities = 21/43 (48%), Positives = 28/43 (65%)

Query: 12 GISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVF 54
          G+S  T E  L+E FSRYG +    ++ D+ TGR+RGF FV F
Sbjct: 6  GLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYF 48

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|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 42.2 bits (99), Expect = 2e-05
 Identities = 22/55 (40%), Positives = 29/55 (52%), Gaps = 6/55 (10%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
          +LF+G +  D  EE  K+ F +YGE  E  I RD      RGFGF+      +AE
Sbjct: 3  RLFVGNLPTDITEEDFKKLFEKYGEPSEVFINRD------RGFGFIRLESRTLAE 51

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 42.4 bits (100), Expect = 2e-05
 Identities = 15/53 (28%), Positives = 30/53 (56%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEA 159
           +++VG ++  + E   ++ F  FG I  + + +D  T + +GF F+ Y+  EA
Sbjct: 2   RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEA 54

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|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 42.6 bits (100), Expect = 2e-05
 Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 8/62 (12%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          KLF+G +  +  E+ ++  F +YG+V+E  I+++        +GFV   D   A+  I +
Sbjct: 2  KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--------YGFVHMDDKTAADEAIRN 53

Query: 67 KH 68
           H
Sbjct: 54 LH 55

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|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 42.6 bits (100), Expect = 2e-05
 Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 9/74 (12%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+FVG L    TE + +  F+Q+G + +  ++        + +GF+  D + A D  +  
Sbjct: 2   KLFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIRN 53

Query: 167 TFH-ELNGKMVEVK 179
             H +L+G  + V+
Sbjct: 54  LHHYKLHGVAINVE 67

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|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 3/71 (4%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          KLFIG +S   +E  ++  FS +G++ E  I+R    G +RG  FV F   A+A+  I  
Sbjct: 3  KLFIGMVSKKCNENDIRVMFSPFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAI-- 59

Query: 67 KHMIDGRTVEA 77
          K M   +T+E 
Sbjct: 60 KAMHQAQTMEG 70

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|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 23/74 (31%), Positives = 43/74 (58%), Gaps = 4/74 (5%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV--I 64
          ++F+  + +D   ++LKE FS+ G V+ A I  +   G+++G G V F  P  AE+   +
Sbjct: 1  QIFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKME--NGKSKGCGTVRFDSPESAEKACRL 58

Query: 65 MDKHMIDGRTVEAK 78
          M+   I+GR ++ +
Sbjct: 59 MNGIKINGREIDVR 72

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, 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 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

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

 Score = 41.9 bits (99), Expect = 3e-05
 Identities = 16/45 (35%), Positives = 26/45 (57%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFV 52
          +F+  +  D DE  L + FS +G V    ++RD  T + +G+GFV
Sbjct: 4  IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFV 48

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|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 42.2 bits (100), Expect = 3e-05
 Identities = 18/45 (40%), Positives = 28/45 (62%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFV 52
          LF+GG+S    E  L+E FSR+G V +  I++ +  G  RGF ++
Sbjct: 2  LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYI 46

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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 42.0 bits (99), Expect = 3e-05
 Identities = 14/39 (35%), Positives = 24/39 (61%)

Query: 116 TVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY 154
           + TE D ++ F +FG I  V ++ D NT   +GFG++ +
Sbjct: 11  SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKF 49

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

 Score = 41.5 bits (98), Expect = 4e-05
 Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 4/67 (5%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           +++G L   + E+     F + G +T V ++ +  T +  G+GF+ + + EA ++ L   
Sbjct: 2   LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS- 60

Query: 168 FHELNGK 174
              LNGK
Sbjct: 61  ---LNGK 64

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

 Score = 41.8 bits (99), Expect = 4e-05
 Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 6/80 (7%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFG--TITDVVVMYDHNTQRPRGFGFITY----DSEE 158
           T  + + GL    TE D  +         I DV ++ D  T   RGF F+ +    D+ +
Sbjct: 2   TNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQ 61

Query: 159 AVDRVLHKTFHELNGKMVEV 178
            +D + +     ++G++V V
Sbjct: 62  WMDALNNLDPFVIDGRVVRV 81

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

 Score = 41.8 bits (98), Expect = 4e-05
 Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          KLF+G ++    E+ ++E FS YG V +  +MRD    ++RG  FV ++   +A+  I
Sbjct: 1  KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMK-QSRGCAFVKYSSKEMAQAAI 57

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

 Score = 41.6 bits (97), Expect = 4e-05
 Identities = 19/57 (33%), Positives = 34/57 (59%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          L++ G+     ++ L++ FS+YG ++ + I+ D+ TG +RG GF+ F     AE  I
Sbjct: 5  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 61

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|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 41.6 bits (98), Expect = 4e-05
 Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 9/84 (10%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVI----MRDRATGRARGFG--FVVFADPAVA 60
          +++I  +S+ + EE L+E+   + E V  +I    +R   + R R  G  +  F+ P  A
Sbjct: 1  RVYISNLSYSSSEEDLEEFLKDF-EPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQA 59

Query: 61 ERVI--MDKHMIDGRTVEAKKAVP 82
          E+V+  ++  +   R +  K  VP
Sbjct: 60 EKVVKDLNGKVFKNRKLFVKLHVP 83

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

 Score = 41.4 bits (98), Expect = 4e-05
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           IF+  L  ++        F  FG I    V  D N    +G+GF+ +++EEA  R + K 
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGG-SKGYGFVHFETEEAAVRAIEK- 62

Query: 168 FHELNGKMVEVKR 180
              +NG ++  K+
Sbjct: 63  ---VNGMLLNDKK 72

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

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

 Score = 41.7 bits (98), Expect = 4e-05
 Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 8  LFIGGISWDTDEERLKEYF-SRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          +F+G +S + +E  L   F SR+     A IM D  TG +RG+GFV F+D    +R +++
Sbjct: 4  IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63

Query: 67 KH 68
            
Sbjct: 64 MQ 65

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

 Score = 41.6 bits (97), Expect = 5e-05
 Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          L +  +  +  +E  +  F   GE+    ++RD+ TG++ G+GFV + DP  AE+ I  +
Sbjct: 5  LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 66 DKHMIDGRTVEAKKAVP 82
          +   +  +T++   A P
Sbjct: 65 NGLRLQTKTIKVSYARP 81

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|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 = 5e-05
 Identities = 23/84 (27%), Positives = 37/84 (44%), Gaps = 23/84 (27%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          +F+  + +    ++LKE F   G+VV A I  D+  G++RG G V F  P          
Sbjct: 1  IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDK-EGKSRGMGVVQFEHP---------- 49

Query: 68 HMIDGRTVEAKKAVPRDDQNMLNR 91
                 +EA +A+     +M N 
Sbjct: 50 -------IEAVQAI-----SMFNG 61

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

 Score = 41.7 bits (97), Expect = 5e-05
 Identities = 19/57 (33%), Positives = 34/57 (59%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          L++ G+     ++ L++ FS+YG ++ + I+ D+ TG +RG GF+ F     AE  I
Sbjct: 8  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 64

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|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 41.2 bits (97), Expect = 5e-05
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 14/69 (20%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEAVDRVLH 165
           ++++G L     E D +++F  +G I ++ +          GFGF+ + D  +A D V  
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRIREINLKN--------GFGFVEFEDPRDADDAV-- 50

Query: 166 KTFHELNGK 174
              +ELNGK
Sbjct: 51  ---YELNGK 56

This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 70

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

 Score = 41.2 bits (97), Expect = 5e-05
 Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 4/63 (6%)

Query: 17 TDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTVE 76
          TDEE  +  F   G V    I+RD+ TG + GFGFV +     A+R I     ++G  ++
Sbjct: 13 TDEE-FRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAI---RTLNGLQLQ 68

Query: 77 AKK 79
           K+
Sbjct: 69 NKR 71

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

 Score = 41.1 bits (97), Expect = 6e-05
 Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 13/75 (17%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY----DSEEAVDR 162
           ++ V  L    TE+D KK F  FG + +V +       + +GF F+ +    D+E+A+  
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRK-PDGKKKGFAFVQFTSKADAEKAIK- 58

Query: 163 VLHKTFHELNGKMVE 177
                   +NGK ++
Sbjct: 59  -------GVNGKKIK 66

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

>gnl|CDD|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 = 6e-05
 Identities = 20/49 (40%), Positives = 31/49 (63%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFAD 56
          L + G+S  T E  L+E FS+YG + +  I+ D+ + R+RGF FV F +
Sbjct: 12 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

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

 Score = 40.9 bits (96), Expect = 6e-05
 Identities = 16/57 (28%), Positives = 30/57 (52%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
           +FVG L+   TE + + +F + G I  V +M   ++ + +GF F+ ++  E     L
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 57

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

 Score = 41.0 bits (97), Expect = 6e-05
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 5/76 (6%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD---RVL 164
           ++VG L   VTE    + F Q G + +V +  D  TQ  +G+GF+ + SEE  D   +++
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 165 HKTFHELNGKMVEVKR 180
           +    +L GK + V +
Sbjct: 61  NMI--KLYGKPIRVNK 74

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

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

 Score = 41.2 bits (96), Expect = 6e-05
 Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 4/61 (6%)

Query: 104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD----SEEA 159
           R   ++V GL  T+T+ + ++ F Q+G I    ++ D  T   RG GFI +D    +EEA
Sbjct: 1   RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 60

Query: 160 V 160
           +
Sbjct: 61  I 61

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

 Score = 41.3 bits (96), Expect = 6e-05
 Identities = 18/57 (31%), Positives = 34/57 (59%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          L+I G+  +T ++ L +    YG++V    + D+ T + +G+GFV F  PA A++ +
Sbjct: 10 LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAV 66

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|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 41.2 bits (96), Expect = 6e-05
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 12/72 (16%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           K +FV  LA+TVTE   +K F +FG +  V  + D        + F+ ++  +A  R + 
Sbjct: 2   KVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVHFEERDAAVRAM- 52

Query: 166 KTFHELNGKMVE 177
               E+NGK +E
Sbjct: 53  ---DEMNGKEIE 61

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind 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. hnRNP R 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, as well as 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; hnRNP R binds RNA through its RRM domains. . Length = 72

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

 Score = 41.1 bits (96), Expect = 6e-05
 Identities = 18/57 (31%), Positives = 34/57 (59%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          L++ G+     ++ +++ FS+YG ++ + I+ D+ TG +RG GF+ F     AE  I
Sbjct: 4  LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAI 60

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

 Score = 41.3 bits (96), Expect = 7e-05
 Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 4/61 (6%)

Query: 104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD----SEEA 159
           R   ++V GL  T+T+ + ++ F Q+G I    ++ D  T   RG GFI +D    +EEA
Sbjct: 4   RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 63

Query: 160 V 160
           +
Sbjct: 64  I 64

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

 Score = 40.4 bits (95), Expect = 8e-05
 Identities = 20/71 (28%), Positives = 33/71 (46%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           +FVG L    T  D   +F   G    V ++ D  T + +G  F+ +D+ EA+ + L   
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62

Query: 168 FHELNGKMVEV 178
              L G+ + V
Sbjct: 63  HTLLKGRKINV 73

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

>gnl|CDD|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 = 40.6 bits (95), Expect = 8e-05
 Identities = 21/57 (36%), Positives = 33/57 (57%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          LFI  +  +  +  L + F  +G V+ A +  DRAT +++ FGFV F +PA A+  I
Sbjct: 7  LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAI 63

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

 Score = 41.1 bits (96), Expect = 9e-05
 Identities = 24/76 (31%), Positives = 46/76 (60%), Gaps = 15/76 (19%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRP-RG----FGFITYDSEEAV 160
           + +F+G L  TVTE+D ++ FD+FG IT+V      + +RP RG    +GF+ +++ +  
Sbjct: 8   RTLFLGNLDITVTETDLRRAFDRFGVITEV------DIKRPGRGQTSTYGFLKFENLD-- 59

Query: 161 DRVLHKTFHELNGKMV 176
             + H+    ++GK++
Sbjct: 60  --MAHRAKLAMSGKVL 73

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

 Score = 40.5 bits (95), Expect = 9e-05
 Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 8/70 (11%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           ++ G   ++   SD K+ F+  G +  V ++    ++  +   FIT+++ EA        
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQ----LA 53

Query: 168 FHELNGKMVE 177
              LNG  V+
Sbjct: 54  IETLNGASVD 63

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|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 40.2 bits (94), Expect = 9e-05
 Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 8/74 (10%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE--RVI 64
          +LF+G +  D  EE +++ F +YG+  E  I +D      +GFGF+      +AE  +  
Sbjct: 3  RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAEIAKAE 56

Query: 65 MDKHMIDGRTVEAK 78
          +D   + G+ +  +
Sbjct: 57 LDNMPLRGKQLRVR 70

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 40.8 bits (96), Expect = 9e-05
 Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 8/60 (13%)

Query: 117 VTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD--SEEAVDRVLHKTFHELNGK 174
           VTE D ++ F  FG I D+ V+ D  T+  +G  ++ +   S  A      +   E+NGK
Sbjct: 14  VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAA------RAMEEMNGK 67

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

 Score = 40.8 bits (95), Expect = 9e-05
 Identities = 18/59 (30%), Positives = 35/59 (59%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          L+I G+     ++ +++ FSR+G ++ + ++ D+ATG +RG  F+ F   + AE  I  
Sbjct: 3  LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61

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

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

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 18/52 (34%), Positives = 32/52 (61%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEA 159
           +FVG L+    E    + F ++G I+ V +  D ++ RP+GFG++ + S+EA
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEA 52

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|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 40.5 bits (94), Expect = 1e-04
 Identities = 24/75 (32%), Positives = 44/75 (58%), Gaps = 2/75 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          +F+G +S +   E +K  F+ +G++ +A +++D ATG+++G+GFV F +   AE  I  M
Sbjct: 4  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 66 DKHMIDGRTVEAKKA 80
              + GR +    A
Sbjct: 64 GGQWLGGRQIRTNWA 78

This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

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

 Score = 40.5 bits (94), Expect = 1e-04
 Identities = 21/46 (45%), Positives = 28/46 (60%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFIT 153
           IFV  LA    ES   + F  FG +T+V V+ D NT + +GFGF+T
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVT 51

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

 Score = 43.4 bits (102), Expect = 2e-04
 Identities = 24/120 (20%), Positives = 51/120 (42%), Gaps = 6/120 (5%)

Query: 64  IMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPG----PGRTKKIFVGGLASTVTE 119
           ++         V  + A  R      +  T+ + +        G    IFV  L+    E
Sbjct: 225 VLAHQQQQHA-VAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDE 283

Query: 120 SDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS-EEAVDRVLHKTFHELNGKMVEV 178
           +   + F  FG + +V ++ D  T + +G+GF++  + +EA   +L    + L  ++++V
Sbjct: 284 TVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQV 343

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|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 5/70 (7%)

Query: 108 IFVGGLASTVTESDFKKYFDQFG-TITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           +++G L   + E+  K+ F   G T+  V ++ +  T  P G+ F+ +  E   +R LHK
Sbjct: 2   LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61

Query: 167 TFHELNGKMV 176
               LNGK +
Sbjct: 62  ----LNGKPI 67

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

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

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 25/72 (34%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRA---TGRARGFGFVVFADPAVAERVI 64
          L++G ++    EE L + F R+G +    IM  R      R R  GFV F + A AER  
Sbjct: 4  LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERA- 62

Query: 65 MDKHMIDGRTVE 76
          +D+  +DG+ V 
Sbjct: 63 LDE--LDGKDVM 72

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 39.8 bits (93), Expect = 2e-04
 Identities = 16/55 (29%), Positives = 33/55 (60%), Gaps = 2/55 (3%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRP--RGFGFITYDSEEA 159
           K+FVG +  + +E D ++ F+Q+G +  + V+ D +   P  +G  F+T+ + +A
Sbjct: 3   KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKA 57

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 20/57 (35%), Positives = 32/57 (56%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          L++ G+     ++ L+  FS YG ++ + I+ D  TG +RG GF+ F     AER I
Sbjct: 3  LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAI 59

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

 Score = 40.1 bits (93), Expect = 2e-04
 Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 4/60 (6%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY----DSEEAVDRV 163
           +FVG L+  +T  D K  F  FG I+D  V+ D  T + +G+GF+++    D+E A+ ++
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

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

 Score = 39.7 bits (92), Expect = 2e-04
 Identities = 23/75 (30%), Positives = 43/75 (57%), Gaps = 2/75 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          +F+G +S +   + +K  F+ +G + +A +++D ATG+++G+GFV F +   AE  I  M
Sbjct: 4  VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 66 DKHMIDGRTVEAKKA 80
              + GR +    A
Sbjct: 64 GGQWLGGRQIRTNWA 78

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

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

 Score = 40.2 bits (93), Expect = 2e-04
 Identities = 18/57 (31%), Positives = 33/57 (57%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          L+I G+   T ++ L +    YG++V    + D+ T + +G+GFV F  PA A++ +
Sbjct: 7  LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAV 63

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

 Score = 39.7 bits (92), Expect = 2e-04
 Identities = 17/57 (29%), Positives = 33/57 (57%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          L+I G+   T ++ L +    YG++V    + D+ T + +G+GFV F  P+ A++ +
Sbjct: 4  LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 60

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|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 40.0 bits (94), Expect = 2e-04
 Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 7/59 (11%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRG--FGFITYDSEEAVDRVL 164
           I+VG +    T S+ ++ F  FG I ++ + +     R  G  +GF+TY       R +
Sbjct: 5   IYVGKIPIDTTRSELRQRFQPFGEIEEITLHF-----RDDGDNYGFVTYRYACDAFRAI 58

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

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

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 14/71 (19%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRP--RGFGFITYDSEEAVDRVLH 165
           +FVGGL   VTE + +  F  FG I  V +        P  +G GF+ +    A +  + 
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKI--------PPGKGCGFVQFVHRAAAEAAIQ 55

Query: 166 KTFHELNGKMV 176
           +    L G ++
Sbjct: 56  Q----LQGTII 62

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

 Score = 40.1 bits (93), Expect = 2e-04
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEAVDRVLHK 166
           IF+  L     E    + F  FG +T+V V+ D NT + +GFGF+T  + EEA   +   
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 167 TFHELNGKMVEV 178
             + L  K+++V
Sbjct: 64  NGYRLGDKILQV 75

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

 Score = 39.5 bits (93), Expect = 3e-04
 Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 6/79 (7%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPR-----GFGFITYDSEEAVDR 162
           +FV  L    TE   KK+F++ G +  V +    + + P      G+GF+ + S+EA  +
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 163 VLHKTFH-ELNGKMVEVKR 180
            L +     L+G  +E+K 
Sbjct: 63  ALKRLQGTVLDGHALELKL 81

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|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 = 3e-04
 Identities = 21/58 (36%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 108 IFVGGLASTVTESDFKKYF-DQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
           IFVG L+  V ESD    F  +F +     +M D  T   RG+GF+ +  E    R L
Sbjct: 4   IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRAL 61

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|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 39.1 bits (91), Expect = 3e-04
 Identities = 15/55 (27%), Positives = 30/55 (54%), Gaps = 6/55 (10%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD 161
           ++FVG L   +TE + +K F+++G   ++ +  D      +GFGFI  ++    +
Sbjct: 3   RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHKD------KGFGFIRLETRTLAE 51

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 39.6 bits (93), Expect = 3e-04
 Identities = 20/62 (32%), Positives = 29/62 (46%), Gaps = 3/62 (4%)

Query: 18 DEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTVEA 77
          DE  LK+   +YGEV E  I     T +  G   VVF     A+R + +K  ++  +V  
Sbjct: 15 DEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCV-EK--LNQTSVMG 71

Query: 78 KK 79
          K 
Sbjct: 72 KI 73

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

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 39.1 bits (91), Expect = 3e-04
 Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 3/77 (3%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL--- 164
           +FVG L     E    + F + G I  V ++ D  T   +GF ++ +  E AV++ L   
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLN 61

Query: 165 HKTFHELNGKMVEVKRA 181
            K F  +  + + V R 
Sbjct: 62  EKKFPPMLPRELRVSRC 78

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

 Score = 39.2 bits (92), Expect = 4e-04
 Identities = 16/66 (24%), Positives = 30/66 (45%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
             +FVG L+   TE   ++ F ++G I  + ++ D  T   +G+ F+ Y+ E    R   
Sbjct: 4   LTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYR 63

Query: 166 KTFHEL 171
                +
Sbjct: 64  DAHKLV 69

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

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 7/71 (9%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          K+++G +     +  L++ F +YG +    + R        GF FV F DP  AE  +  
Sbjct: 1  KVYVGNLGPRATKRELEDEFEKYGPLRSVWVAR-----NPPGFAFVEFEDPRDAEDAVRA 55

Query: 65 MDKHMIDGRTV 75
          +D   I G  V
Sbjct: 56 LDGRRICGNRV 66

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

 Score = 39.0 bits (90), Expect = 4e-04
 Identities = 16/57 (28%), Positives = 29/57 (50%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
           +++ GL    T+ D  K    +G I     + D NT + +G+GF+ +DS  A  + +
Sbjct: 7   LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAV 63

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|240674 cd12228, RRM_ENOX, RNA recognition motif (RRM) in the cell surface Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or ENOX) proteins

 Score = 39.3 bits (92), Expect = 4e-04
 Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 7/59 (11%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
           K +FVGGL    TE   ++ F+Q G I  +           + F  I +  E AVD+ +
Sbjct: 7   KTVFVGGLPENATEEIIREVFEQCGEIIAI-------RMSKKNFCHIRFAEEFAVDKAI 58

This subgroup corresponds to the conserved RNA recognition motif (RRM) in ECTO-NOX proteins (also termed ENOX), comprising a family of plant and animal NAD(P)H oxidases exhibiting both, oxidative and protein disulfide isomerase-like, activities. They are growth-related and drive cell enlargement, and may play roles in aging and neurodegenerative diseases. ENOX proteins function as terminal oxidases of plasma membrane electron transport (PMET) through catalyzing electron transport from plasma membrane quinones to extracellular oxygen, forming water as a product. They are also hydroquinone oxidases that oxidize externally supplied NADH, hence NOX. ENOX proteins harbor a di-copper center that lack flavin. ENOX proteins display protein disulfide interchange activity that is also possessed by protein disulfide isomerase. In contrast to the classic protein disulfide isomerases, ENOX proteins lack the double CXXC motif. This family includes two ENOX proteins, ENOX1 and ENOX2. ENOX1, also termed candidate growth-related and time keeping constitutive hydroquinone [NADH] oxidase (cCNOX), or cell proliferation-inducing gene 38 protein, or Constitutive Ecto-NOX (cNOX), is the constitutively expressed cell surface NADH (ubiquinone) oxidase that is ubiquitous and refractory to drugs. ENOX2, also termed APK1 antigen, or cytosolic ovarian carcinoma antigen 1, or tumor-associated hydroquinone oxidase (tNOX), is a cancer-specific variant of ENOX1 and plays a key role in cell proliferation and tumor progression. In contrast to ENOX1, ENOX2 is drug-responsive and harbors a drug binding site to which the cancer-specific S-peptide tagged pan-ENOX2 recombinant (scFv) is directed. Moreover, ENOX2 is specifically inhibited by a variety of quinone site inhibitors that have anticancer activity and is unique to the surface of cancer cells. ENOX proteins contain many functional motifs. Length = 84

>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 38.3 bits (89), Expect = 4e-04
 Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 12/74 (16%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           KIFVG +++T T  + +  F++FG + +   + D+       F  +  + E         
Sbjct: 2   KIFVGNVSATCTSDELRGLFEEFGRVVECDKVKDY------AFVHMEREEEALA------ 49

Query: 167 TFHELNGKMVEVKR 180
               LNGK V+ +R
Sbjct: 50  AIEALNGKEVKGRR 63

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|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 = 39.1 bits (92), Expect = 4e-04
 Identities = 27/71 (38%), Positives = 34/71 (47%), Gaps = 11/71 (15%)

Query: 18 DEER------LKEYFSRYGEVVEAVIMRDRATGR-ARGFG--FVVFADPAVAERVI--MD 66
          DEE       +KE   +YG+V+  VI R  A G    G G  FV FAD   A++    + 
Sbjct: 18 DEEYEEILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALA 77

Query: 67 KHMIDGRTVEA 77
              DGRTV A
Sbjct: 78 GRKFDGRTVVA 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|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 38.4 bits (89), Expect = 4e-04
 Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 9/79 (11%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEE-AVDRVL 164
           K +FV  LA+TVTE   +K F QFG +  V  + D        + FI +D  + AV  + 
Sbjct: 2   KVLFVRNLANTVTEEILEKAFGQFGKLERVKKLKD--------YAFIHFDERDGAVKAME 53

Query: 165 HKTFHELNGKMVEVKRAVP 183
                EL G+ +E+  A P
Sbjct: 54  EMNGKELEGENIEIVFAKP 72

This subgroup corresponds to the RRM3 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 that is 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 = 72

>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating protein-binding protein 2 (G3BP2) and similar proteins

 Score = 38.8 bits (90), Expect = 5e-04
 Identities = 18/60 (30%), Positives = 33/60 (55%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
           + ++FVG L   + ES+ K++F  FG + ++ +       +   FGF+ +D  E V R+L
Sbjct: 5   SHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQRIL 64

This subgroup corresponds to the RRM of G3BP2, also termed GAP SH3 domain-binding protein 2, a cytoplasmic protein that interacts with both IkappaBalpha and IkappaBalpha/NF-kappaB complexes, indicating that G3BP2 may play a role in the control of nucleocytoplasmic distribution of IkappaBalpha and cytoplasmic anchoring of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing five PXXP motifs, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). It binds to the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity, through its N-terminal NTF2-like domain. The acidic domain is sufficient for the interaction of G3BP2 with the IkappaBalpha cytoplasmic retention sequence. Furthermore, G3BP2 might influence stability or translational efficiency of particular mRNAs by binding to RNA-containing structures within the cytoplasm through its RNA-binding domain. Length = 83

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

 Score = 38.5 bits (90), Expect = 5e-04
 Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
           +++G LA  +TE D +++F     IT V +  D  T   +GFG + +  EE++D  L
Sbjct: 2   VYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAAL 57

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

 Score = 38.6 bits (90), Expect = 5e-04
 Identities = 20/79 (25%), Positives = 47/79 (59%), Gaps = 6/79 (7%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK- 166
           +FVGG+   + E++ + +F ++G++ +V ++ D  T   +G+GF+++  +  V +++   
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDDVDVQKIVESQ 66

Query: 167 -TFHELNGKMVEVKRAVPK 184
             FH   GK +++  A+ K
Sbjct: 67  INFH---GKKLKLGPAIRK 82

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

 Score = 39.5 bits (92), Expect = 5e-04
 Identities = 15/57 (26%), Positives = 28/57 (49%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
           +FV  L    TE     +F +FG++   + + D +T R +G GF+ +  +   +  L
Sbjct: 4   LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

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

 Score = 38.8 bits (90), Expect = 5e-04
 Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 4/57 (7%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD----SEEAV 160
           ++V GL  T+++ + ++ F Q+G I    ++ D  T   RG GFI +D    +EEA+
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAI 60

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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 38.5 bits (90), Expect = 5e-04
 Identities = 20/70 (28%), Positives = 38/70 (54%), Gaps = 3/70 (4%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          +LFI        E+ L+E F+ +GE+ +  +++D+ T  ++G  +V FA  + A R +  
Sbjct: 5  RLFIV-CGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEE 63

Query: 65 MDKHMIDGRT 74
          M+   + G T
Sbjct: 64 MNGKCLGGDT 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|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 38.4 bits (90), Expect = 5e-04
 Identities = 24/80 (30%), Positives = 36/80 (45%), Gaps = 10/80 (12%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATG--RARGFGFVVFAD---PAVAE 61
          +LF+GGI     +E + E FS+  E V  VI+        + RGF FV +      A+A 
Sbjct: 3  RLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRAAAMAR 62

Query: 62 RVIMDKHMIDGRTVEAKKAV 81
          R      ++ GR +     V
Sbjct: 63 R-----KLVPGRILLWGHEV 77

This subfamily corresponds to the RRM2 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 bind 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), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains); DND1 harbors only two RRMs. . Length = 82

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

 Score = 38.7 bits (89), Expect = 6e-04
 Identities = 21/81 (25%), Positives = 35/81 (43%), Gaps = 4/81 (4%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           +++ GL    T+ D  K    +G I     + D  T + +G+GF+ +DS  A      K 
Sbjct: 10  LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAA----QKA 65

Query: 168 FHELNGKMVEVKRAVPKEFSP 188
              L    V+ + A  +E  P
Sbjct: 66  VSALKASGVQAQMAKQQEQDP 86

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

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

 Score = 38.6 bits (89), Expect = 6e-04
 Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          L +  +  +  +E  K  F   GE+    ++RD+ TG++ G+GFV + DP  A++ I  +
Sbjct: 6  LIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTL 65

Query: 66 DKHMIDGRTVEAKKAVP 82
          +   +  +T++   A P
Sbjct: 66 NGLKLQTKTIKVSYARP 82

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|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 = 19/77 (24%), Positives = 41/77 (53%), Gaps = 4/77 (5%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADP-AVAERVIMD 66
          +++G + + +  E L+ +FS  G +    I+ D+ +G  +G+ ++ FA   +V   V +D
Sbjct: 2  VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVALD 61

Query: 67 KHMIDGRTVEAKKAVPR 83
          +    GR +   K +P+
Sbjct: 62 ESSFRGRVI---KVLPK 75

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|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 38.0 bits (89), Expect = 6e-04
 Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 6/52 (11%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEA 159
           ++VGGL    + ++ ++ FD+FG I  +   YD      R + +I Y+S EA
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRID--YDPG----RNYAYIEYESIEA 46

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|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 37.9 bits (88), Expect = 7e-04
 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 12/76 (15%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           KIFVG +    ++ + +  F+ +G +    VM        R F F+    E A DR +  
Sbjct: 2   KIFVGNVDEDTSQEELRALFEAYGAVLSCAVM--------RQFAFVHLRGEAAADRAI-- 51

Query: 167 TFHELNGKMVEVKRAV 182
              ELNG+ +  ++ V
Sbjct: 52  --EELNGRELHGRKLV 65

This subgroup corresponds to the RRM1 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 = 69

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

 Score = 38.4 bits (90), Expect = 7e-04
 Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 8/76 (10%)

Query: 104 RTKKIFVGGLASTVTESD-FKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEAVD 161
            ++ +FV  L  T  +    +K F Q G  T   +    N Q PRGF F+ Y  +E+A  
Sbjct: 1   HSRCLFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPNGQ-PRGFAFVEYATAEDA-- 57

Query: 162 RVLHKTFHELNGKMVE 177
               +    LNG  ++
Sbjct: 58  ---EEAQQALNGHSLQ 70

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|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 38.2 bits (89), Expect = 7e-04
 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 1/67 (1%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          L++G +  +  EER+ E+F RYG V    I+  R +       FV F D   A++     
Sbjct: 2  LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVA-AFVDFVDIKSAQKAHNAV 60

Query: 68 HMIDGRT 74
          + +  R 
Sbjct: 61 NKMGDRD 67

This subfamily corresponds to the RRM1 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 = 75

>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 38.2 bits (89), Expect = 7e-04
 Identities = 19/76 (25%), Positives = 41/76 (53%), Gaps = 13/76 (17%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRG----FGFITYDSEEAV 160
           T+ +FVG L  T+TE + ++ F+++G + DV +      + PRG    + F+ +     +
Sbjct: 2   TRTLFVGNLEITITEEELRRAFERYGVVEDVDI-----KRPPRGQGNAYAFVKF---LNL 53

Query: 161 DRVLHKTFHELNGKMV 176
           D + H+    ++G+ +
Sbjct: 54  D-MAHRAKVAMSGQYI 68

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

 Score = 38.5 bits (89), Expect = 7e-04
 Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 1/79 (1%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEAVDRVLHK 166
           IFV  L+    ES   + F  FG +T+V V+ D  T + +GFGF+T  + +EA   +   
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 167 TFHELNGKMVEVKRAVPKE 185
             + L  ++++V     K+
Sbjct: 64  NGYRLGDRVLQVSFKTSKQ 82

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

>gnl|CDD|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 38.1 bits (89), Expect = 8e-04
 Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEA 159
           ++V  L    T    K  F ++GT+  V +    +T   +GF FI +   EEA
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEA 54

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

 Score = 37.9 bits (89), Expect = 8e-04
 Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 5/64 (7%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY----DSEEAVDRV 163
           ++VG L+   TE    + F + G I  +++  D  T+ P GF F+ Y    D+E AV + 
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAV-KY 59

Query: 164 LHKT 167
           L+ T
Sbjct: 60  LNGT 63

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

 Score = 37.7 bits (88), Expect = 8e-04
 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADP 57
          LF+G +     EE L E F + G +    I +D   G+ + F FV F   
Sbjct: 4  LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDP-NGKPKSFAFVTFKHE 52

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|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 38.0 bits (89), Expect = 8e-04
 Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 12/79 (15%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY----DSEEAVDR 162
           ++ V  L   VTE D ++ F + G +  V + YD  + R  G   + +    D+E A+  
Sbjct: 2   RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAI-- 58

Query: 163 VLHKTFH--ELNGKMVEVK 179
              K F+   L+G+ ++V+
Sbjct: 59  ---KQFNGVLLDGQPMQVE 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|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 37.6 bits (87), Expect = 8e-04
 Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 8/74 (10%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE--RVI 64
          +LF+G +  D  E+  K+ F++YGE  E  I       + +GFGF+     A+AE  +  
Sbjct: 3  RLFVGNLPADITEDEFKKLFAKYGEPGEVFI------NKGKGFGFIKLESRALAEIAKAE 56

Query: 65 MDKHMIDGRTVEAK 78
          +D   + GR +  +
Sbjct: 57 LDDTPMRGRQLRVR 70

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|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 38.0 bits (88), Expect = 8e-04
 Identities = 22/74 (29%), Positives = 43/74 (58%), Gaps = 4/74 (5%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV--I 64
          ++F+  + +D   + LK+ F+  G V+ A I  +   G+++G G V F  P VAER   +
Sbjct: 1  QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVRFESPEVAERACRM 58

Query: 65 MDKHMIDGRTVEAK 78
          M+ + ++GR ++ +
Sbjct: 59 MNGYKLNGREIDVR 72

This subgroup corresponds to the RRM3 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. 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). . Length = 77

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

 Score = 37.6 bits (88), Expect = 9e-04
 Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK- 166
           IFV  L  +VT  D K  F + G +    V  D++  R +GFG + ++S E   R +   
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDG-RSKGFGTVLFESPEDAQRAIEMF 59

Query: 167 TFHELNGKMVEVK 179
             ++L G+ +EV+
Sbjct: 60  NGYDLEGRELEVR 72

This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 72

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 6/75 (8%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS-EEAVDRVLHK 166
           + VG L    T+  F++    FG +    ++Y  +T   +G+GF+ Y S   A+     K
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASAL-----K 56

Query: 167 TFHELNGKMVEVKRA 181
             ++L+GK +  ++ 
Sbjct: 57  AKNQLDGKQIGGRKL 71

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 15/55 (27%), Positives = 26/55 (47%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDR 162
           +FV  L    T+ D +  F +FG I    V+ D  T     + FI ++++E  + 
Sbjct: 6   LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEE 60

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins

 Score = 38.0 bits (88), Expect = 0.001
 Identities = 17/60 (28%), Positives = 36/60 (60%), Gaps = 3/60 (5%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
           + ++FVG L   V +S+ K++F Q+G + ++ +   ++  +   FGF+ +D  E V ++L
Sbjct: 3   SHQLFVGNLPHDVDKSELKEFFQQYGNVVELRI---NSGGKLPNFGFVVFDDSEPVQKIL 59

This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript. Length = 80

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

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 4/57 (7%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD----SEEAV 160
           +++ GL  T+T+ D +  F +FG I +  V+ D  T   RG  FI +D    +EEA+
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAI 59

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

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 37.6 bits (87), Expect = 0.001
 Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 4/77 (5%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIM-- 65
          +F+G + ++  EE L   F + G +    I+RD  T   +GF +V F D    E+ ++  
Sbjct: 2  VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLN 61

Query: 66 --DKHMIDGRTVEAKKA 80
                +  R +   + 
Sbjct: 62 EKKFPPMLPRELRVSRC 78

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

 Score = 37.9 bits (89), Expect = 0.001
 Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 7/57 (12%)

Query: 8  LFIGGISWDTDEERLK----EYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
          L+I  ++    ++ LK      FS++G V++ V  +   T + RG  FVVF D   A
Sbjct: 2  LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASK---TLKMRGQAFVVFKDVESA 55

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|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 37.9 bits (89), Expect = 0.001
 Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 6  GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIM 65
           ++F+G I  D  E+ L   F + G + E  +M D + G  RG+ FV + +   A+R + 
Sbjct: 2  CEVFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFS-GLNRGYAFVTYTNKEAAQRAVK 60

Query: 66 DKHMIDGRT 74
            H  + R 
Sbjct: 61 QLHNYEIRP 69

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|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 4/76 (5%)

Query: 7  KLFIGGISWDTDEERLKEYF-SRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI- 64
          ++FI  I +D   + +K+    + GEV    + +D A G++RG G V F D    ++ + 
Sbjct: 1  RVFISNIPYDMKWQAIKDLMREKVGEVTYVELFKD-AEGKSRGCGVVEFKDEEFVKKALE 59

Query: 65 -MDKHMIDGRTVEAKK 79
           M+K+ ++GR +  K+
Sbjct: 60 VMNKYDLNGRPLNIKE 75

This subgroup corresponds to the RRM1 of MEF-2, also termed MyEF-2 or MST156, 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 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 37.7 bits (88), Expect = 0.001
 Identities = 21/50 (42%), Positives = 32/50 (64%), Gaps = 2/50 (4%)

Query: 8  LFIGGISWDTDEERLKEYFS-RYGEVVEAVIMRDRATGRARGFGFVVFAD 56
          LF+G ++ D D+ +L E+FS RY     A ++ D   G +RG+GFV F+D
Sbjct: 4  LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLD-QNGNSRGYGFVRFSD 52

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 37.8 bits (88), Expect = 0.001
 Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 4/79 (5%)

Query: 107 KIFVGGLASTVTESDFK----KYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDR 162
            IFV G  S++ E D +    ++F   G IT V +  D  T   +GF +I + S + V++
Sbjct: 1   TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60

Query: 163 VLHKTFHELNGKMVEVKRA 181
            L     +L G  + V  A
Sbjct: 61  ALELDGSDLGGGNLVVDEA 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|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 = 37.3 bits (87), Expect = 0.001
 Identities = 23/57 (40%), Positives = 28/57 (49%), Gaps = 2/57 (3%)

Query: 9  FIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIM 65
           +GGI     E+ LKE+FS  GEV    +  DR    AR F FV FAD   A   + 
Sbjct: 4  HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQH-SAR-FAFVEFADAESALSALN 58

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|240890 cd12444, RRM1_CPEBs, RNA recognition motif 1 in cytoplasmic polyadenylation element-binding protein CPEB-1, CPEB-2, CPEB-3, CPEB-4 and similar protiens

 Score = 38.4 bits (89), Expect = 0.001
 Identities = 21/90 (23%), Positives = 36/90 (40%), Gaps = 22/90 (24%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTIT----------------------DVVVMYDHNT 143
           +K+FVGGL   +TE+D    F +FG++                           +     
Sbjct: 1   RKVFVGGLPWDITEADILNSFRRFGSLQVDWPGKHYECKSDSDPSLCNEKSDGSINGDKG 60

Query: 144 QRPRGFGFITYDSEEAVDRVLHKTFHELNG 173
           Q P+G+ F+ ++ E +V  +L     E  G
Sbjct: 61  QHPKGYVFLLFEKERSVRSLLLACSEEEGG 90

This subfamily corresponds to the RRM1 of the CPEB family of proteins that bind to defined groups of mRNAs and act as either translational repressors or activators to regulate their translation. CPEB proteins are well conserved in both, vertebrates and invertebrates. Based on sequence similarity, RNA-binding specificity, and functional regulation of translation, the CPEB proteins have been classified into two subfamilies. The first subfamily includes CPEB-1 and related proteins. CPEB-1 is an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. Otherwise, it may function as a translational inhibitor when dephosphorylated and bind to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm. The second subfamily includes CPEB-2, CPEB-3, CPEB-4, and related protiens. Due to high sequence similarity, members in this subfamily may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. CPEB-2 impedes target RNA translation at elongation; it directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All CPEB proteins are nucleus-cytoplasm shuttling proteins. They contain an N-terminal unstructured region, followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. CPEB-2, -3, and -4 have conserved nuclear export signals that are not present in CPEB-1. . Length = 112

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

 Score = 40.3 bits (94), Expect = 0.002
 Identities = 21/72 (29%), Positives = 38/72 (52%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           +FV  LA    E D  ++F + G + DV  + D N++R +G  ++ +   E+V + L  T
Sbjct: 92  VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALT 151

Query: 168 FHELNGKMVEVK 179
              L G+ + V+
Sbjct: 152 GQMLLGRPIIVQ 163

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

 Score = 40.3 bits (94), Expect = 0.002
 Identities = 18/45 (40%), Positives = 27/45 (60%)

Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFV 52
           +F+  +S DTDE  L + F  +G V    I+RD  T + +G+GFV
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFV 316

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

 Score = 40.8 bits (95), Expect = 0.002
 Identities = 25/103 (24%), Positives = 45/103 (43%), Gaps = 24/103 (23%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           +++VG ++  + E   ++ FD FG I  + + +D  T + +GF F+ Y+  EA    L  
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLAL-- 166

Query: 167 TFHELNGKMVEVKRAVPKEFSPGPSRSSMIGYNNFGFNRPTNL 209
              ++NG                     M+G  N    RP+N+
Sbjct: 167 --EQMNG--------------------QMLGGRNIKVGRPSNM 187

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|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 = 36.8 bits (86), Expect = 0.002
 Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 8/70 (11%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          +++G +     EE L+  FS +G + E  + +D      +G+ FV F     A   I  +
Sbjct: 3  VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIVAV 56

Query: 66 DKHMIDGRTV 75
          +   I+G+TV
Sbjct: 57 NGTSINGQTV 66

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

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

 Score = 37.0 bits (85), Expect = 0.002
 Identities = 21/61 (34%), Positives = 33/61 (54%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          L++ G+S  T    LK  FS+YG+VV A ++ +  +  AR +GFV  +    A + I   
Sbjct: 4  LWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHL 63

Query: 68 H 68
          H
Sbjct: 64 H 64

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

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

 Score = 36.4 bits (84), Expect = 0.002
 Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 4/69 (5%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          L++G +     E+ LK+ F   G V    I+ D+   +   +GFV +     AE  +   
Sbjct: 1  LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK-NNKGVNYGFVEYHQSHDAEIAL--- 56

Query: 68 HMIDGRTVE 76
            ++GR +E
Sbjct: 57 QTLNGRQIE 65

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|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 36.8 bits (85), Expect = 0.002
 Identities = 18/50 (36%), Positives = 30/50 (60%), Gaps = 6/50 (12%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
           ++FVG L + +TE +FKK F ++G   +V +       + +GFGFI  +S
Sbjct: 3   RLFVGNLPADITEDEFKKLFAKYGEPGEVFI------NKGKGFGFIKLES 46

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|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          +F+  + +    ++LKE FS  G VV A I+ D+  G++RG G V F  P  A + I
Sbjct: 3  VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDK-DGKSRGIGTVTFEQPIEAVQAI 58

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

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 4/65 (6%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          LF+G +     EE L E F + G + +  I +D+  G+ + FGFV F      E V    
Sbjct: 4  LFVGNLECRVREEILYELFLQAGPLTKVTICKDK-EGKPKSFGFVCFKHS---ESVPYAI 59

Query: 68 HMIDG 72
           +++G
Sbjct: 60 ALLNG 64

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|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 = 36.8 bits (86), Expect = 0.002
 Identities = 11/55 (20%), Positives = 24/55 (43%), Gaps = 1/55 (1%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
            K+ V  +    T+ + ++ F  FG +   V +        RGF F+ + +++  
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKS-VRLPKKFDGSHRGFAFVEFVTKQEA 54

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

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 16/72 (22%), Positives = 36/72 (50%), Gaps = 2/72 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          +F+ G+  +  EE + + F+ +GE+    +  DR TG  +G+  + +     A+  I  +
Sbjct: 9  IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 66 DKHMIDGRTVEA 77
          +   + G+T+  
Sbjct: 69 NGKELLGQTISV 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|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 12/68 (17%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           ++F+G L     E D +++F  +G I D+ +         RGFGF+ +D     D  +  
Sbjct: 1   RVFIGRLNPAAREKDVERFFKGYGRIRDIDL--------KRGFGFVEFDDPRDADDAV-- 50

Query: 167 TFHELNGK 174
             +EL+GK
Sbjct: 51  --YELDGK 56

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

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

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 13/31 (41%), Positives = 21/31 (67%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDV 135
           T+ +F+G L  T T SD ++ F++FG I D+
Sbjct: 2   TRTLFIGNLEKTTTYSDLREAFERFGEIIDI 32

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

 Score = 37.0 bits (85), Expect = 0.002
 Identities = 19/46 (41%), Positives = 27/46 (58%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFIT 153
           IFV  L+    ES   + F  FG + +V V+ D NT + +GFGF+T
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVT 51

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|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 16/77 (20%), Positives = 35/77 (45%), Gaps = 4/77 (5%)

Query: 7  KLFIGGISWDTDEERLKEYFSR-YGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI- 64
          +L +  +     E  LKE+FS+  GE+ +  ++R    G++R   F+ +     A++   
Sbjct: 2  RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTE-DGKSRRIAFIGYKTEEEAQKAKD 60

Query: 65 -MDKHMIDGRTVEAKKA 80
            +   I+   +  + A
Sbjct: 61 YFNNTYINTSKISVEFA 77

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

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

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 18/70 (25%), Positives = 29/70 (41%), Gaps = 8/70 (11%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          L+IG +S    EE LK  F  YGE+    ++        RG  +V       A R +  +
Sbjct: 5  LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMI------PPRGCAYVCMETRQDAHRALQKL 58

Query: 66 DKHMIDGRTV 75
              + G+ +
Sbjct: 59 RNVKLAGKKI 68

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

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

 Score = 36.6 bits (85), Expect = 0.003
 Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 4/68 (5%)

Query: 113 LASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELN 172
           L  T+T+ +F+  F   G + +  ++ D  T    GFGF+ Y S E   R +      LN
Sbjct: 8   LPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRT----LN 63

Query: 173 GKMVEVKR 180
           G  ++ KR
Sbjct: 64  GLQLQNKR 71

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|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 = 36.1 bits (84), Expect = 0.003
 Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 6/57 (10%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          +F+GG+     E+ L+  F  +GE+V   I         +G GFV F   A AE  I
Sbjct: 4  VFVGGLDPAVTEDELRSLFGPFGEIVYVKI------PPGKGCGFVQFVHRAAAEAAI 54

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|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 = 36.1 bits (84), Expect = 0.003
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFA 55
          KL +  + ++  ++ L+E FS +G+V  +V +  +  G  RGF FV F 
Sbjct: 2  KLIVRNVPFEATKKELRELFSPFGQVK-SVRLPKKFDGSHRGFAFVEFV 49

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|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 36.7 bits (86), Expect = 0.003
 Identities = 21/93 (22%), Positives = 38/93 (40%), Gaps = 21/93 (22%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPR------------GFGFIT 153
             ++V GL   +T  +F + F + G     ++  D  T +P+            G     
Sbjct: 2   TNVYVSGLPLDITVEEFVEVFSKCG-----IIKEDPETGKPKIKLYRDENGNLKGDALCC 56

Query: 154 YDSEEAVD---RVLHKTFHELNGKMVEVKRAVP 183
           Y  EE+V+   ++L  T     G  ++V+RA  
Sbjct: 57  YLKEESVELAIQLLDGT-EIGRGYKMKVERAKF 88

This subfamily corresponds to the RRM1 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 = 92

>gnl|CDD|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing factor SLT11 and similar proteins

 Score = 36.6 bits (85), Expect = 0.003
 Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 6/56 (10%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV 63
           F+ G+  D  E ++++YF ++G+  ++VI+  RA       GFV F     AE+ 
Sbjct: 5  FFLFGVEDDLPEYKIRDYFEQFGK-SKSVIVNHRA-----KCGFVRFETREAAEKF 54

This subfamily corresponds to the RRM of SLT11, also known as extracellular mutant protein 2, or synthetic lethality with U2 protein 11, and is a splicing factor required for spliceosome assembly in yeast. It contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). SLT11 can facilitate the cooperative formation of U2/U6 helix II in association with stem II in the yeast spliceosome by utilizing its RNA-annealing and -binding activities. . Length = 86

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

 Score = 36.3 bits (84), Expect = 0.003
 Identities = 18/62 (29%), Positives = 25/62 (40%), Gaps = 8/62 (12%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          +L++     DT E  ++E FS YG V E  ++          F FV F     A R    
Sbjct: 1  RLYVRPFPPDTSESAIREIFSPYGAVKEVKMI--------SNFAFVEFESLESAIRAKDS 52

Query: 67 KH 68
           H
Sbjct: 53 VH 54

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|240949 cd12505, RRM2_GRSF1, RNA recognition motif 2 in G-rich sequence factor 1 (GRSF-1) and similar proteins

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 16/66 (24%), Positives = 32/66 (48%), Gaps = 1/66 (1%)

Query: 12 GISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIM-DKHMI 70
          G+ +   E+ + ++F     V + V++     GR  G  +V FA P +A + ++  +  I
Sbjct: 8  GLPYSCTEDDIIDFFRGLDIVDDGVVIVLNRRGRKTGEAYVQFATPEMANKALLKHREEI 67

Query: 71 DGRTVE 76
            R +E
Sbjct: 68 GNRYIE 73

This subfamily corresponds to the RRM2 of GRSF-1, 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. GRSF-1 contains three potential RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic alpha-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity. . Length = 75

>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 36.3 bits (84), Expect = 0.003
 Identities = 19/77 (24%), Positives = 41/77 (53%), Gaps = 4/77 (5%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADP-AVAERVIMD 66
          +++G + +    E L+ +F   G V    I+ D+ +G  +GF ++ F+D  +V   + +D
Sbjct: 2  VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALALD 61

Query: 67 KHMIDGRTVEAKKAVPR 83
          + +  GR +   K +P+
Sbjct: 62 ESLFRGRQI---KVMPK 75

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

 Score = 36.6 bits (84), Expect = 0.003
 Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 2/80 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          LFI  +  +  ++ L + F  +G VV A +  D+ T  ++ FGFV + +P  A+  I  M
Sbjct: 10 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69

Query: 66 DKHMIDGRTVEAKKAVPRDD 85
          +   I  + ++ +    ++D
Sbjct: 70 NGFQIGMKRLKVQLKRSKND 89

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|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 36.1 bits (83), Expect = 0.003
 Identities = 18/58 (31%), Positives = 29/58 (50%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          ++F+G I  D  E+ L   F + G + +  +M D  TG  RG+ FV F     A+  +
Sbjct: 3  EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQEAV 60

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

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 3/71 (4%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          L+I  +    DE+ L+     YG+V+   I+RD + G++RG GF         E +I   
Sbjct: 3  LYISNLPLHMDEQDLETMLKPYGQVISTRILRD-SKGQSRGVGFARMESREKCEDIISKF 61

Query: 68 H--MIDGRTVE 76
          +   + G    
Sbjct: 62 NGKYLKGEGEP 72

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

 Score = 36.6 bits (84), Expect = 0.003
 Identities = 13/56 (23%), Positives = 30/56 (53%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
            + +F   LA+ +   D +++F   G + DV ++ D N++R +G  ++ +    +V
Sbjct: 1   ARTVFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSV 56

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

 Score = 36.1 bits (84), Expect = 0.004
 Identities = 23/80 (28%), Positives = 41/80 (51%), Gaps = 6/80 (7%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRA---TGRARGFGFVVFADPAVAERV 63
          +L+IG +     E  L + FS+YG++ +   +  ++    G+ RG+ FV F     AE+ 
Sbjct: 1  RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 64 IMDKHMIDGRTVEAKKAVPR 83
          +     ++G+T   KK V R
Sbjct: 61 LKS---LNGKTALGKKLVVR 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|241094 cd12650, RRM1_Hu, RNA recognition motif 1 in the Hu proteins family

 Score = 35.9 bits (83), Expect = 0.004
 Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 5/76 (6%)

Query: 104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV 163
           +T  I V  L   +T+ + +  F   G I    ++ D  T +  G+GF+ Y   E  ++ 
Sbjct: 1   KTNLI-VNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKA 59

Query: 164 LHKTFHELNGKMVEVK 179
           ++     LNG  ++ K
Sbjct: 60  INT----LNGLRLQNK 71

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

 Score = 35.9 bits (82), Expect = 0.004
 Identities = 15/57 (26%), Positives = 28/57 (49%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
           +++ GL    T+ D  K    +G I     + D  T + +G+GF+ +DS  A  + +
Sbjct: 4   LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 60

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

 Score = 36.2 bits (83), Expect = 0.004
 Identities = 16/49 (32%), Positives = 27/49 (55%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFAD 56
          +F+  +S + DE  L + F  +G V    ++RD  T + +GFGFV   +
Sbjct: 4  IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTN 52

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

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
           + +FVG L   V E    + F Q G +T V +  D    +P+ FGF+ +   E+V
Sbjct: 2   RTLFVGNLECRVREEILYELFLQAGPLTKVTICKDKEG-KPKSFGFVCFKHSESV 55

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|240747 cd12301, RRM1_2_PAR10_like, RNA recognition motif 1 and 2 in poly [ADP-ribose] polymerase PARP-10, RNA recognition motif 2 in PARP-14, RNA recognition motif in N-myc-interactor (Nmi), interferon-induced 35 kDa protein (IFP 35), RNA-binding protein 43 (RBM43) and similar proteins

 Score = 36.1 bits (84), Expect = 0.004
 Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 10/71 (14%)

Query: 12 GISWDTDEERLKEYF--SRY--GEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MD 66
          G+     +++L+ YF   R   G  V  V    R  G A     V FAD  VAERV+   
Sbjct: 7  GLPETVSDDKLELYFENKRRSGGGDVTRVQ-YLREKGSA----LVTFADFKVAERVVKQK 61

Query: 67 KHMIDGRTVEA 77
          KH ++G  +  
Sbjct: 62 KHPLNGTQLSV 72

This subfamily corresponds to the RRM1 and RRM2 of PARP-10, RRM2 of PARP-14, RRM of N-myc-interactor (Nmi), interferon-induced 35 kDa protein (IFP 35) and RNA-binding protein 43 (RBM43). PARP-10 is a novel oncoprotein c-Myc-interacting protein with poly(ADP-ribose) polymerase activity. It is localized to the nuclear and cytoplasmic compartments. In addition to PARP activity, PARP-10 is also involved in the control of cell proliferation by inhibiting c-Myc- and E1A-mediated cotransformation of primary cells. PARP-10 may also play a role in nuclear processes including the regulation of chromatin, gene transcription, and nuclear/cytoplasmic transport. PARP-10 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two overlapping C-terminal domains composed of a glycine-rich region and a region with homology to catalytic domains of PARP enzymes (PARP domain). In addition, PARP-10 contains two ubiquitin-interacting motifs (UIM). PARP-14, also termed aggressive lymphoma protein 2, is a member of the B aggressive lymphoma (BAL) family of macrodomain-containing PARPs. Like PARP-10, PARP-14 also includes two RRMs at the N-terminus. Nmi, also termed N-myc and STAT interactor, is an interferon inducible protein that interacts with c-Myc, N-Myc, Max and c-Fos, and other transcription factors containing bHLH-ZIP, bHLH or ZIP domains. Besides binding Myc proteins, Nmi also associates with all the Stat family of transcription factors except Stat2. In response to cytokine (e.g. IL-2 and IFN-gamma) stimulation, Nmi can enhance Stat-mediated transcriptional activity through recruiting the Stat1 and Stat5 transcriptional coactivators, CREB-binding protein (CBP) and p300. IFP 35 is an interferon-induced leucine zipper protein that can specifically form homodimers. Distinct from known bZIP proteins, IFP 35 lacks a basic domain critical for DNA binding. In addition, IFP 35 may negatively regulate other bZIP transcription factors by protein-protein interaction. For instance, it can form heterodimers with B-ATF, a member of the AP1 transcription factor family. Both Nmi and IFP35 harbor one RRM. RBM43 is a putative RNA-binding protein containing one RRM, but its biological function remains unclear. . Length = 74

>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 20/55 (36%), Positives = 26/55 (47%), Gaps = 2/55 (3%)

Query: 108 IFVGGLASTVTESDFKKYFDQFG-TITDVVVMYDHNTQRPRGFGFITYDS-EEAV 160
           I + GL  +VTE D +      G    DV +M    T   RGF F+ + S EEA 
Sbjct: 5   IMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEFMSLEEAT 59

This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 81

>gnl|CDD|241122 cd12678, RRM_SLTM, RNA recognition motif in Scaffold attachment factor (SAF)-like transcription modulator (SLTM) and similar proteins

 Score = 35.8 bits (82), Expect = 0.004
 Identities = 21/75 (28%), Positives = 39/75 (52%), Gaps = 5/75 (6%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV---L 164
           ++V GL+S    +D K  F ++G +    V+ +  +   + +G +T  S   V R    L
Sbjct: 2   LWVSGLSSNTKAADLKNLFGKYGKVLSAKVVTNARSPGAKCYGIVTMSSSAEVARCISHL 61

Query: 165 HKTFHELNGKMVEVK 179
           H+T  EL+G+ + V+
Sbjct: 62  HRT--ELHGQQISVE 74

This subgroup corresponds to the RRM domain of SLTM, also termed modulator of estrogen-induced transcription, which shares high sequence similarity with scaffold attachment factor B1 (SAFB1). It contains a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. To a large extent, SLTM co-localizes with SAFB1 in the nucleus, which suggests that they share similar functions, such as the inhibition of an oestrogen reporter gene. However, rather than mediating a specific inhibitory effect on oestrogen action, SLTM is shown to exert a generalized inhibitory effect on gene expression associated with induction of apoptosis in a wide range of cell lines. . Length = 74

>gnl|CDD|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 35.8 bits (83), Expect = 0.004
 Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 7/60 (11%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY----DSEEAVDR 162
           +I+VG L   + E D +  F ++G I  + +    N +R   F F+ +    D+E+AV  
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGPIKAIDL---KNRRRGPPFAFVEFEDPRDAEDAVRG 57

This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. . Length = 72

>gnl|CDD|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 = 16/58 (27%), Positives = 30/58 (51%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          ++F+G I  D  E+ L   F + G + +  +M D  +G+ RG+ F+ F     A+  +
Sbjct: 3  EVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAV 60

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

 Score = 39.2 bits (91), Expect = 0.004
 Identities = 19/65 (29%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE 157
           S   PGR  ++FVG +   + E +    F++ G I ++ +M D + Q  RG+ F+T+  +
Sbjct: 51  SGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQN-RGYAFVTFCGK 109

Query: 158 EAVDR 162
           E    
Sbjct: 110 EEAKE 114

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

>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 35.9 bits (83), Expect = 0.004
 Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 4/76 (5%)

Query: 7  KLFIGGISWDTDEERLKEYF-SRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI- 64
          ++FI  I +D   + LK+ F  + GEV    + +D   G++RG G V F D    ++ + 
Sbjct: 1  RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKD-EEGKSRGCGVVEFKDKESVQKALE 59

Query: 65 -MDKHMIDGRTVEAKK 79
           M+++ + GR +  K+
Sbjct: 60 TMNRYELKGRKLVVKE 75

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	522
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.97
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.97
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.96
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.96
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.96
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.96
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.96
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.96
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.95
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.94
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.94
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.93
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.92
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.92
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.92
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.92
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.92
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.91
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.91
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.9
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.88
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.88
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.86
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.85
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.85
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.84
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.84
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.83
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.81
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.79
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.78
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.77
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.75
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.74
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.7
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.7
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.65
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.63
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.61
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.6
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.6
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.59
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.57
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.55
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.55
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.55
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.54
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.53
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.51
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.51
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.5
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.47
KOG0122	270	consensus Translation initiation factor 3, subunit	99.46
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.45
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.43
PLN03120	260	nucleic acid binding protein; Provisional	99.43
KOG0122	270	consensus Translation initiation factor 3, subunit	99.42
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.41
PLN03121	243	nucleic acid binding protein; Provisional	99.4
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.4
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.4
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.4
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.37
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.37
PLN03120	260	nucleic acid binding protein; Provisional	99.36
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.35
smart00362	72	RRM_2 RNA recognition motif.	99.34
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.34
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.33
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.32
PLN03213	759	repressor of silencing 3; Provisional	99.32
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.31
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.3
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.3
smart00360	71	RRM RNA recognition motif.	99.3
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.29
smart00362	72	RRM_2 RNA recognition motif.	99.28
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.28
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.28
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.28
smart00360	71	RRM RNA recognition motif.	99.28
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.27
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.26
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.25
PLN03213	759	repressor of silencing 3; Provisional	99.23
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.23
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.23
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.22
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.21
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.2
PLN03121	243	nucleic acid binding protein; Provisional	99.19
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.19
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.18
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.16
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.13
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.13
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.13
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.13
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.12
KOG4210	285	consensus Nuclear localization sequence binding pr	99.12
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.12
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.07
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.06
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.06
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	99.03
smart00361	70	RRM_1 RNA recognition motif.	99.01
smart00361	70	RRM_1 RNA recognition motif.	99.0
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.97
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.97
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.94
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.93
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.91
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.91
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.9
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.88
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.8
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.76
KOG0226	290	consensus RNA-binding proteins [General function p	98.75
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.75
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.73
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.68
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.65
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.64
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.57
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.57
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.56
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.53
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.52
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.52
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.46
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.43
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.42
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.34
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.33
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.32
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.31
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.26
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.24
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.24
KOG0226	290	consensus RNA-binding proteins [General function p	98.23
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.21
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.09
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.08
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.06
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.9
KOG0151	877	consensus Predicted splicing regulator, contains R	97.82
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.66
KOG0151	877	consensus Predicted splicing regulator, contains R	97.65
KOG1855	484	consensus Predicted RNA-binding protein [General f	97.6
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.59
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.54
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.54
KOG4210	285	consensus Nuclear localization sequence binding pr	97.35
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.21
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.16
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.13
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.1
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.05
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	96.97
KOG3152	278	consensus TBP-binding protein, activator of basal	96.93
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.93
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.83
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	96.81
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.61
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.58
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.43
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.32
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.3
KOG2314	698	consensus Translation initiation factor 3, subunit	96.28
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.13
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.09
KOG2591	684	consensus c-Mpl binding protein, contains La domai	95.88
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	95.79
KOG3152	278	consensus TBP-binding protein, activator of basal	95.71
KOG2135	526	consensus Proteins containing the RNA recognition	95.64
KOG1996	378	consensus mRNA splicing factor [RNA processing and	95.63
KOG2314	698	consensus Translation initiation factor 3, subunit	95.62
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.52
KOG1996	378	consensus mRNA splicing factor [RNA processing and	95.49
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	95.36
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	95.34
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	95.26
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	95.24
KOG2135	526	consensus Proteins containing the RNA recognition	95.19
KOG2591	684	consensus c-Mpl binding protein, contains La domai	94.98
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	94.65
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	94.65
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	94.35
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	94.29
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	94.2
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	93.97
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	93.45
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	93.18
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	91.96
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	91.7
KOG2318	650	consensus Uncharacterized conserved protein [Funct	91.43
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	91.29
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	90.27
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	90.25
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	90.21
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	89.9
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	89.02
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	88.9
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	88.08
KOG2068	327	consensus MOT2 transcription factor [Transcription	87.73
KOG2068	327	consensus MOT2 transcription factor [Transcription	87.32
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	87.27
KOG3973	465	consensus Uncharacterized conserved glycine-rich p	87.21
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	86.63
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	85.46
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	84.54
smart00596	69	PRE_C2HC PRE_C2HC domain.	83.6
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	82.94
COG5594	827	Uncharacterized integral membrane protein [Functio	82.54
PF07530	68	PRE_C2HC: Associated with zinc fingers; InterPro:	82.49
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	81.94
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	81.88
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	80.79

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=5.4e-34  Score=296.05  Aligned_cols=168  Identities=22%  Similarity=0.394  Sum_probs=153.5

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++||++|+++|++||+|++|+|++|+.|+++||||||+|.++++|++||  +++++|.+++|+|.++
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a  184 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYA  184 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecc
Confidence            46789999999999999999999999999999999999999999999999999999999999  8999999999999988


Q ss_pred             CCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHH
Q 009920           81 VPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV  160 (522)
Q Consensus        81 ~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A  160 (522)
                      .+..+.                ...++|||.|||+++||++|+++|++||+|++|+|++|+.++++||||||+|+++++|
T Consensus       185 ~p~~~~----------------~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A  248 (346)
T TIGR01659       185 RPGGES----------------IKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEA  248 (346)
T ss_pred             cccccc----------------cccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHH
Confidence            653211                2346899999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcC-CccCC--eEEEEEEcCCCCC
Q 009920          161 DRVLHKTF-HELNG--KMVEVKRAVPKEF  186 (522)
Q Consensus       161 ~~Al~~~~-~~l~G--r~I~V~~a~pk~~  186 (522)
                      ++||++++ ..|++  ++|+|++++.+.+
T Consensus       249 ~~Ai~~lng~~~~g~~~~l~V~~a~~~~~  277 (346)
T TIGR01659       249 QEAISALNNVIPEGGSQPLTVRLAEEHGK  277 (346)
T ss_pred             HHHHHHhCCCccCCCceeEEEEECCcccc
Confidence            99999999 66665  7899999886543

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).

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

Probab=99.97  E-value=7.3e-31  Score=266.22  Aligned_cols=236  Identities=51%  Similarity=0.910  Sum_probs=195.6

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      .+.++|||++|+|+++||.|+++|.+||+|.+|+||+|+.++++|+|+||+|++++...++| ...|.|+++.|+++.+.
T Consensus         4 ~~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    4 GESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             cCCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceecc
Confidence            47899999999999999999999999999999999999999999999999999999999999 77899999999999999


Q ss_pred             CCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHH
Q 009920           82 PRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD  161 (522)
Q Consensus        82 ~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~  161 (522)
                      ++.++....+.          ..+++|||+.||.++++++|++.|++||.|.++.++.|+.+.++++|+||+|+++++++
T Consensus        84 ~r~~~~~~~~~----------~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVd  153 (311)
T KOG4205|consen   84 SREDQTKVGRH----------LRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVD  153 (311)
T ss_pred             Ccccccccccc----------cceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccc
Confidence            99887755433          26889999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcCCccCCeEEEEEEcCCCCCCCCCCCCC-CCCCC-CCCCCCCCCccccccccCCCCCCCCCCCCCCC-CCCCCCC
Q 009920          162 RVLHKTFHELNGKMVEVKRAVPKEFSPGPSRSS-MIGYN-NFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDS-RFSPLAT  238 (522)
Q Consensus       162 ~Al~~~~~~l~Gr~I~V~~a~pk~~~~~~~r~~-~gG~~-~~G~~~~~~~~~~~~~g~~~~~~GG~ggr~gg-r~g~~gG  238 (522)
                      +++.+..++|++++|+|+.|.||+......... ..++. .++..+...++..+.+++++.....|+.++.+ ++++...
T Consensus       154 kv~~~~f~~~~gk~vevkrA~pk~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~~~g~~~~~~~~~~~~~~~~~~~~~~~  233 (311)
T KOG4205|consen  154 KVTLQKFHDFNGKKVEVKRAIPKEVMQSTKSSVSTRGKGNNLGNGRTGFFLKKYFKGYGPVGMSDYGGRPVGRRYGPLFN  233 (311)
T ss_pred             eecccceeeecCceeeEeeccchhhccccccccccccccccccccccccccchhccccCccccccccccccccccccccC
Confidence            999999999999999999999999876554211 11212 34444444555666667766655555555543 4444433


Q ss_pred             CCCCCCCCCC
Q 009920          239 GRGGISPFGG  248 (522)
Q Consensus       239 GrGG~gg~gg  248 (522)
                      .+.++..++.
T Consensus       234 ~g~g~~~~~~  243 (311)
T KOG4205|consen  234 GGSGYPEFGN  243 (311)
T ss_pred             CCccccccCc
Confidence            4445555553

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

Probab=99.97  E-value=2.4e-29  Score=274.78  Aligned_cols=180  Identities=21%  Similarity=0.464  Sum_probs=156.7

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||++++|++|+++|++||+|++|+|++|+.|+++||||||+|.++++|++||  ++++.|++|+|+|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            35689999999999999999999999999999999999999999999999999999999999  8999999999999865


Q ss_pred             CCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHH
Q 009920           81 VPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV  160 (522)
Q Consensus        81 ~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A  160 (522)
                      ..........     ..........++|||+|||+++++++|+++|++||.|++|+|++|+.++++||||||+|+++++|
T Consensus       185 ~~~p~a~~~~-----~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A  259 (612)
T TIGR01645       185 SNMPQAQPII-----DMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQ  259 (612)
T ss_pred             cccccccccc-----ccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHH
Confidence            4321111000     00011123457999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcC-CccCCeEEEEEEcCCCCCC
Q 009920          161 DRVLHKTF-HELNGKMVEVKRAVPKEFS  187 (522)
Q Consensus       161 ~~Al~~~~-~~l~Gr~I~V~~a~pk~~~  187 (522)
                      ++||+.++ .+|+|+.|+|.++.++...
T Consensus       260 ~kAI~amNg~elgGr~LrV~kAi~pP~~  287 (612)
T TIGR01645       260 SEAIASMNLFDLGGQYLRVGKCVTPPDA  287 (612)
T ss_pred             HHHHHHhCCCeeCCeEEEEEecCCCccc
Confidence            99999999 8999999999999976543

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.96  E-value=6.9e-29  Score=258.13  Aligned_cols=166  Identities=25%  Similarity=0.505  Sum_probs=151.9

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      +.++|||+|||.+++|+||+++|++||+|.+|+|++++.+++++|||||+|.++++|++||  +++..|.+++|.|+++.
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            4689999999999999999999999999999999999999999999999999999999999  89999999999999986


Q ss_pred             CCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHH
Q 009920           82 PRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD  161 (522)
Q Consensus        82 ~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~  161 (522)
                      ++...                ....+|||.|||..+++++|+++|++||.|+.++|+.++.++.++|||||+|++.++|+
T Consensus        82 ~~~~~----------------~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~  145 (352)
T TIGR01661        82 PSSDS----------------IKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEAD  145 (352)
T ss_pred             ccccc----------------cccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHH
Confidence            64321                23468999999999999999999999999999999999988899999999999999999


Q ss_pred             HHHHhcC-CccCC--eEEEEEEcCCCC
Q 009920          162 RVLHKTF-HELNG--KMVEVKRAVPKE  185 (522)
Q Consensus       162 ~Al~~~~-~~l~G--r~I~V~~a~pk~  185 (522)
                      +||+.++ ..+.+  ++|.|+++..+.
T Consensus       146 ~ai~~l~g~~~~g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       146 RAIKTLNGTTPSGCTEPITVKFANNPS  172 (352)
T ss_pred             HHHHHhCCCccCCCceeEEEEECCCCC
Confidence            9999888 66666  678999887654

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

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

Probab=99.96  E-value=8.4e-29  Score=266.68  Aligned_cols=177  Identities=26%  Similarity=0.469  Sum_probs=155.9

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      ++.++|||+|||+++++++|+++|++||+|++|+|++++.+++++|||||+|.+.++|++|| +++..|.+++|.|+.+.
T Consensus        87 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~~  166 (457)
T TIGR01622        87 RDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQ  166 (457)
T ss_pred             cCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEeecc
Confidence            56789999999999999999999999999999999999999999999999999999999999 99999999999998765


Q ss_pred             CCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHH
Q 009920           82 PRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD  161 (522)
Q Consensus        82 ~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~  161 (522)
                      .+..........    ........++|||+|||..+|+++|+++|++||.|+.|.|+.++.+++++|||||+|.+.++|+
T Consensus       167 ~~~~~~~~~~~~----~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~  242 (457)
T TIGR01622       167 AEKNRAAKAATH----QPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAK  242 (457)
T ss_pred             hhhhhhhhcccc----cCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHH
Confidence            443322111100    0111123789999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcC-CccCCeEEEEEEcCC
Q 009920          162 RVLHKTF-HELNGKMVEVKRAVP  183 (522)
Q Consensus       162 ~Al~~~~-~~l~Gr~I~V~~a~p  183 (522)
                      +||+.++ .+|.+++|+|.++..
T Consensus       243 ~A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       243 EALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             HHHHhcCCcEECCEEEEEEEccC
Confidence            9999888 899999999999884

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.

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

Probab=99.96  E-value=4e-28  Score=248.24  Aligned_cols=178  Identities=26%  Similarity=0.424  Sum_probs=148.4

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccC-CeEEEEeec
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMID-GRTVEAKKA   80 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~-Gr~I~V~~a   80 (522)
                      ..|.|||+.||.|+.|+||+.+|++.|+|.+++||+|+.++.+||||||.|+++++|++||  +|+++|. ||.|.|..+
T Consensus        82 ~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~S  161 (506)
T KOG0117|consen   82 RGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVS  161 (506)
T ss_pred             CCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEe
Confidence            4689999999999999999999999999999999999999999999999999999999999  8999884 888887665


Q ss_pred             CCCccccc------------------------------------ccc---------------------------------
Q 009920           81 VPRDDQNM------------------------------------LNR---------------------------------   91 (522)
Q Consensus        81 ~~k~~~~~------------------------------------~~~---------------------------------   91 (522)
                      ..+...-.                                    .++                                 
T Consensus       162 van~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~t  241 (506)
T KOG0117|consen  162 VANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAIT  241 (506)
T ss_pred             eecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcce
Confidence            33311000                                    000                                 


Q ss_pred             ----ccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhc
Q 009920           92 ----NTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT  167 (522)
Q Consensus        92 ----~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~  167 (522)
                          ............+.+.|||+||+.++|||.|+++|++||.|++|+.++|        ||||+|.++++|.+|++.+
T Consensus       242 VdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~  313 (506)
T KOG0117|consen  242 VDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKET  313 (506)
T ss_pred             eeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHh
Confidence                0000000112345578999999999999999999999999999999977        9999999999999999999


Q ss_pred             C-CccCCeEEEEEEcCCCCCCCC
Q 009920          168 F-HELNGKMVEVKRAVPKEFSPG  189 (522)
Q Consensus       168 ~-~~l~Gr~I~V~~a~pk~~~~~  189 (522)
                      + ++|+|..|+|.+|+|..+.+.
T Consensus       314 ngkeldG~~iEvtLAKP~~k~k~  336 (506)
T KOG0117|consen  314 NGKELDGSPIEVTLAKPVDKKKK  336 (506)
T ss_pred             cCceecCceEEEEecCChhhhcc
Confidence            9 999999999999999876553

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.96  E-value=2.9e-28  Score=253.47  Aligned_cols=183  Identities=21%  Similarity=0.408  Sum_probs=152.3

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCC--eEEEEee
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDG--RTVEAKK   79 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~G--r~I~V~~   79 (522)
                      ..++|||+|||.++++++|+++|++||+|..++|++++.++.+++||||+|.+.++|++||  +++..+.+  ++|.|++
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            4678999999999999999999999999999999999888899999999999999999999  88888876  5778887


Q ss_pred             cCCCcccccc--cc-------ccCC-------------------------------------------------CCC---
Q 009920           80 AVPRDDQNML--NR-------NTSS-------------------------------------------------IHS---   98 (522)
Q Consensus        80 a~~k~~~~~~--~~-------~~~~-------------------------------------------------~~~---   98 (522)
                      +.........  ..       ....                                                 ...   
T Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (352)
T TIGR01661       168 ANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPP  247 (352)
T ss_pred             CCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCc
Confidence            7544311000  00       0000                                                 000   


Q ss_pred             ---------------CCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHH
Q 009920           99 ---------------SPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV  163 (522)
Q Consensus        99 ---------------~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~A  163 (522)
                                     ........+|||+|||+++++++|+++|++||.|++|+|++|+.|+++||||||+|++.++|.+|
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                           00012233699999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhcC-CccCCeEEEEEEcCCCCC
Q 009920          164 LHKTF-HELNGKMVEVKRAVPKEF  186 (522)
Q Consensus       164 l~~~~-~~l~Gr~I~V~~a~pk~~  186 (522)
                      |+.++ ..|+||+|+|.++.+|..
T Consensus       328 i~~lnG~~~~gr~i~V~~~~~~~~  351 (352)
T TIGR01661       328 ILSLNGYTLGNRVLQVSFKTNKAY  351 (352)
T ss_pred             HHHhCCCEECCeEEEEEEccCCCC
Confidence            99888 899999999999998764

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

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

Probab=99.96  E-value=1.2e-27  Score=261.13  Aligned_cols=175  Identities=25%  Similarity=0.403  Sum_probs=138.9

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccC-CeEEEEeec
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMID-GRTVEAKKA   80 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~-Gr~I~V~~a   80 (522)
                      ..++|||+|||++++|++|+++|++||+|.+|+|++| .++++||||||+|.++|+|++||  +++.+|. ++.|.|..+
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence            4589999999999999999999999999999999999 68999999999999999999999  7777774 565554433


Q ss_pred             CCCcc----------c--------------------------cc----------------------ccccc---------
Q 009920           81 VPRDD----------Q--------------------------NM----------------------LNRNT---------   93 (522)
Q Consensus        81 ~~k~~----------~--------------------------~~----------------------~~~~~---------   93 (522)
                      .....          .                          ..                      .....         
T Consensus       136 ~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~  215 (578)
T TIGR01648       136 VDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIA  215 (578)
T ss_pred             ccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEE
Confidence            21000          0                          00                      00000         


Q ss_pred             -----CCC-CCCCCCCCcceeEecCCCCCCCHHHHHHHHhhc--CCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHH
Q 009920           94 -----SSI-HSSPGPGRTKKIFVGGLASTVTESDFKKYFDQF--GTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH  165 (522)
Q Consensus        94 -----~~~-~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~f--G~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~  165 (522)
                           ... .........++|||+|||+++||++|+++|++|  |+|++|++++        +||||+|+++++|++||+
T Consensus       216 VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r--------gfAFVeF~s~e~A~kAi~  287 (578)
T TIGR01648       216 VDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR--------DYAFVHFEDREDAVKAMD  287 (578)
T ss_pred             EEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec--------CeEEEEeCCHHHHHHHHH
Confidence                 000 000112345789999999999999999999999  9999998764        499999999999999999


Q ss_pred             hcC-CccCCeEEEEEEcCCCCCC
Q 009920          166 KTF-HELNGKMVEVKRAVPKEFS  187 (522)
Q Consensus       166 ~~~-~~l~Gr~I~V~~a~pk~~~  187 (522)
                      .++ .+|++++|+|++++|+...
T Consensus       288 ~lnG~~i~Gr~I~V~~Akp~~~~  310 (578)
T TIGR01648       288 ELNGKELEGSEIEVTLAKPVDKK  310 (578)
T ss_pred             HhCCCEECCEEEEEEEccCCCcc
Confidence            888 8999999999999987654

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.

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

Probab=99.96  E-value=1e-28  Score=251.47  Aligned_cols=174  Identities=27%  Similarity=0.495  Sum_probs=153.4

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH---HcccccCC--eEEE
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI---MDKHMIDG--RTVE   76 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl---~~~~~i~G--r~I~   76 (522)
                      |.+.-+|||+-||+.++|+||+++||+||.|.+|.|++||.|+.++|||||.|.+.++|.+|+   .|.+.|.|  ..|.
T Consensus        31 d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvq  110 (510)
T KOG0144|consen   31 DGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQ  110 (510)
T ss_pred             CchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCccee
Confidence            356778999999999999999999999999999999999999999999999999999999999   44555654  5777


Q ss_pred             EeecCCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecC
Q 009920           77 AKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS  156 (522)
Q Consensus        77 V~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s  156 (522)
                      |++|..+.+..               .+.++|||+-|++.+||+||+++|.+||.|++|.|++|.. +.+||||||+|.+
T Consensus       111 vk~Ad~E~er~---------------~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~-~~sRGcaFV~fst  174 (510)
T KOG0144|consen  111 VKYADGERERI---------------VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPD-GLSRGCAFVKFST  174 (510)
T ss_pred             ecccchhhhcc---------------ccchhhhhhhccccccHHHHHHHHHhhCccchhhheeccc-ccccceeEEEEeh
Confidence            77776554332               3567999999999999999999999999999999999987 8999999999999


Q ss_pred             HHHHHHHHHhcC--CccCC--eEEEEEEcCCCCCCCCCC
Q 009920          157 EEAVDRVLHKTF--HELNG--KMVEVKRAVPKEFSPGPS  191 (522)
Q Consensus       157 ~e~A~~Al~~~~--~~l~G--r~I~V~~a~pk~~~~~~~  191 (522)
                      +|.|..||+.++  +++.|  .+|.|++|++++++..+.
T Consensus       175 ke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~~~~  213 (510)
T KOG0144|consen  175 KEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKDGKR  213 (510)
T ss_pred             HHHHHHHHHhhccceeeccCCCceEEEecccCCCchHHH
Confidence            999999999998  47777  579999999988776544

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

Probab=99.95  E-value=9e-28  Score=232.39  Aligned_cols=176  Identities=28%  Similarity=0.499  Sum_probs=154.1

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCC
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~   82 (522)
                      +-.|||+.|..+++-|+||+.|.+||+|.+++|++|..|.++|||+||.|..+++|+.||  |+++-|..|.|+-.||..
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            456999999999999999999999999999999999999999999999999999999999  999999999999999987


Q ss_pred             CccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHH
Q 009920           83 RDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDR  162 (522)
Q Consensus        83 k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~  162 (522)
                      |..............-.....+.++|||+|++..+||++|++.|++||+|.+|+|.++      +||+||.|++.|+|.+
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            7633222222211112334457889999999999999999999999999999999988      5699999999999999


Q ss_pred             HHHhcC-CccCCeEEEEEEcCCCCC
Q 009920          163 VLHKTF-HELNGKMVEVKRAVPKEF  186 (522)
Q Consensus       163 Al~~~~-~~l~Gr~I~V~~a~pk~~  186 (522)
                      ||..++ .+|.|+.|++.|-+....
T Consensus       216 AIv~mNntei~G~~VkCsWGKe~~~  240 (321)
T KOG0148|consen  216 AIVQMNNTEIGGQLVRCSWGKEGDD  240 (321)
T ss_pred             HHHHhcCceeCceEEEEeccccCCC
Confidence            999888 899999999999875543

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

Probab=99.94  E-value=1.9e-26  Score=254.87  Aligned_cols=166  Identities=29%  Similarity=0.505  Sum_probs=148.7

Q ss_pred             EEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCCCc
Q 009920            7 KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVPRD   84 (522)
Q Consensus         7 ~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~k~   84 (522)
                      .|||+|||.++||++|+++|++||+|++|+|++|+.|++++|||||+|.++++|++||  ++...|.+++|+|.++....
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  78888999999999875432


Q ss_pred             cccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHH
Q 009920           85 DQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL  164 (522)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al  164 (522)
                      ...              .....+|||.|||.++++++|+++|++||.|.+|+|+.+. ++++||||||+|+++++|++|+
T Consensus        82 ~~~--------------~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~-~g~skg~afV~F~~~e~A~~Ai  146 (562)
T TIGR01628        82 SLR--------------RSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAI  146 (562)
T ss_pred             ccc--------------ccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC-CCCcccEEEEEECCHHHHHHHH
Confidence            111              1234579999999999999999999999999999999886 4788999999999999999999


Q ss_pred             HhcC-CccCCeEEEEEEcCCCCCC
Q 009920          165 HKTF-HELNGKMVEVKRAVPKEFS  187 (522)
Q Consensus       165 ~~~~-~~l~Gr~I~V~~a~pk~~~  187 (522)
                      ++++ ..++++.|.|....++..+
T Consensus       147 ~~lng~~~~~~~i~v~~~~~~~~~  170 (562)
T TIGR01628       147 QKVNGMLLNDKEVYVGRFIKKHER  170 (562)
T ss_pred             HHhcccEecCceEEEecccccccc
Confidence            9998 8999999999876655443

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

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

Probab=99.94  E-value=2.1e-26  Score=254.53  Aligned_cols=182  Identities=28%  Similarity=0.520  Sum_probs=156.0

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccC----CeEEEE
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMID----GRTVEA   77 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~----Gr~I~V   77 (522)
                      ..++|||+|||+++||++|+++|++||+|++++|+++. +++++|||||+|.++++|++|+  +++..|.    ++.|.|
T Consensus       177 ~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~-~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v  255 (562)
T TIGR01628       177 KFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYV  255 (562)
T ss_pred             CCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEe
Confidence            45779999999999999999999999999999999986 5899999999999999999999  8999999    999999


Q ss_pred             eecCCCcccccccccc--CCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEec
Q 009920           78 KKAVPRDDQNMLNRNT--SSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD  155 (522)
Q Consensus        78 ~~a~~k~~~~~~~~~~--~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~  155 (522)
                      .++.++.+........  .............+|||+||++++|+++|+++|++||.|++|+|+.| .++++||||||+|+
T Consensus       256 ~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~  334 (562)
T TIGR01628       256 GRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFS  334 (562)
T ss_pred             ecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeC
Confidence            9887765542211111  00111112345678999999999999999999999999999999999 56899999999999


Q ss_pred             CHHHHHHHHHhcC-CccCCeEEEEEEcCCCCCC
Q 009920          156 SEEAVDRVLHKTF-HELNGKMVEVKRAVPKEFS  187 (522)
Q Consensus       156 s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk~~~  187 (522)
                      ++++|++|++.++ ..|+||+|.|.++.+++.+
T Consensus       335 ~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~~~  367 (562)
T TIGR01628       335 NPEEANRAVTEMHGRMLGGKPLYVALAQRKEQR  367 (562)
T ss_pred             CHHHHHHHHHHhcCCeeCCceeEEEeccCcHHH
Confidence            9999999999888 8999999999999987653

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

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

Probab=99.93  E-value=4.6e-25  Score=240.68  Aligned_cols=178  Identities=18%  Similarity=0.346  Sum_probs=143.4

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhcc------------CCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-Hccc
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRY------------GEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKH   68 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~------------G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~   68 (522)
                      ++..++|||+|||+++|+++|+++|+++            ..|..+.+      .+.++||||+|.++|+|++|| +++.
T Consensus       172 ~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al~l~g~  245 (509)
T TIGR01642       172 TRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAMALDSI  245 (509)
T ss_pred             CccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhhcCCCe
Confidence            4678999999999999999999999975            23444444      345789999999999999999 9999


Q ss_pred             ccCCeEEEEeecCCCcccccc-----cccc----C----CCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEE
Q 009920           69 MIDGRTVEAKKAVPRDDQNML-----NRNT----S----SIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDV  135 (522)
Q Consensus        69 ~i~Gr~I~V~~a~~k~~~~~~-----~~~~----~----~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v  135 (522)
                      .|.++.|.|............     ....    .    ...........++|||+|||..+|+++|+++|++||.|+.+
T Consensus       246 ~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~  325 (509)
T TIGR01642       246 IYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAF  325 (509)
T ss_pred             EeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEE
Confidence            999999999765432211000     0000    0    00111123456799999999999999999999999999999


Q ss_pred             EEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCCC
Q 009920          136 VVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPKE  185 (522)
Q Consensus       136 ~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk~  185 (522)
                      .|++++.+++++|||||+|.+.++|++||+.++ ..|.+++|.|+++....
T Consensus       326 ~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~  376 (509)
T TIGR01642       326 NLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGA  376 (509)
T ss_pred             EEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCC
Confidence            999999999999999999999999999999888 89999999999987543

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

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

Probab=99.92  E-value=4.7e-25  Score=212.32  Aligned_cols=169  Identities=25%  Similarity=0.489  Sum_probs=154.3

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      ++..++|.|.-||..+|+|||+.+|...|+|++|++++|+-++.+.||+||.|.+++||++|+  +++..+..++|+|.+
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            345678999999999999999999999999999999999999999999999999999999999  999999999999999


Q ss_pred             cCCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHH
Q 009920           80 AVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEA  159 (522)
Q Consensus        80 a~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~  159 (522)
                      +.|..+.                .+...|||.+||+++|..||+++|++||.|...+|+.|..|+.+||.+||.|+-+++
T Consensus       118 ARPSs~~----------------Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~E  181 (360)
T KOG0145|consen  118 ARPSSDS----------------IKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIE  181 (360)
T ss_pred             ccCChhh----------------hcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhH
Confidence            9876543                345689999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcC-CccCC--eEEEEEEcCCCCC
Q 009920          160 VDRVLHKTF-HELNG--KMVEVKRAVPKEF  186 (522)
Q Consensus       160 A~~Al~~~~-~~l~G--r~I~V~~a~pk~~  186 (522)
                      |++||+.++ ++--|  .+|.|+++..+..
T Consensus       182 Ae~AIk~lNG~~P~g~tepItVKFannPsq  211 (360)
T KOG0145|consen  182 AEEAIKGLNGQKPSGCTEPITVKFANNPSQ  211 (360)
T ss_pred             HHHHHHhccCCCCCCCCCCeEEEecCCccc
Confidence            999999888 54444  6899999986543

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

Probab=99.92  E-value=2.8e-24  Score=233.56  Aligned_cols=175  Identities=18%  Similarity=0.304  Sum_probs=141.8

Q ss_pred             CCCcEEEECCCCC-CCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            3 SDLGKLFIGGISW-DTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         3 ~d~r~LfVgnLP~-~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      ...++|||+|||+ ++|+++|+++|++||.|++|+|++++     ++||||+|.++++|++||  ++++.|.+++|+|.+
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~  347 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCP  347 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            3568999999998 69999999999999999999999874     589999999999999999  999999999999998


Q ss_pred             cCCCccccccccc------------cCCCC--C-------CCCCCCcceeEecCCCCCCCHHHHHHHHhhcCC--eeEEE
Q 009920           80 AVPRDDQNMLNRN------------TSSIH--S-------SPGPGRTKKIFVGGLASTVTESDFKKYFDQFGT--ITDVV  136 (522)
Q Consensus        80 a~~k~~~~~~~~~------------~~~~~--~-------~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~--I~~v~  136 (522)
                      ++.+.........            ....+  .       .....++++|||.|||.++|+++|+++|++||.  |+.|+
T Consensus       348 s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik  427 (481)
T TIGR01649       348 SKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFK  427 (481)
T ss_pred             cccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEE
Confidence            7654321110000            00000  0       001235679999999999999999999999998  88888


Q ss_pred             EEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeE------EEEEEcCCC
Q 009920          137 VMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKM------VEVKRAVPK  184 (522)
Q Consensus       137 i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~------I~V~~a~pk  184 (522)
                      +..++.  ..+++|||+|++.++|++||.+++ ++|.++.      |+|++++++
T Consensus       428 ~~~~~~--~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       428 FFPKDN--ERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             EecCCC--CcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccCC
Confidence            865443  257899999999999999999988 7999885      999999865

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

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

Probab=99.92  E-value=4e-24  Score=232.29  Aligned_cols=167  Identities=16%  Similarity=0.226  Sum_probs=139.1

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH----HcccccCCeEEEEeec
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI----MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl----~~~~~i~Gr~I~V~~a   80 (522)
                      +++|||+|||+++||++|+++|++||+|++|+|+++      |+||||+|.++|+|++||    ++...|.+++|.|+++
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s   75 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYS   75 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEec
Confidence            689999999999999999999999999999999864      479999999999999999    2678999999999999


Q ss_pred             CCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHH
Q 009920           81 VPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV  160 (522)
Q Consensus        81 ~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A  160 (522)
                      ..++......    ............+|+|.||++++|+++|+++|++||.|++|.|++++.    +++|||+|++.++|
T Consensus        76 ~~~~~~~~~~----~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~----~~~afVef~~~~~A  147 (481)
T TIGR01649        76 TSQEIKRDGN----SDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNN----VFQALVEFESVNSA  147 (481)
T ss_pred             CCcccccCCC----CcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCC----ceEEEEEECCHHHH
Confidence            7654222111    000111223456899999999999999999999999999999987653    46899999999999


Q ss_pred             HHHHHhcC-CccCC--eEEEEEEcCCCC
Q 009920          161 DRVLHKTF-HELNG--KMVEVKRAVPKE  185 (522)
Q Consensus       161 ~~Al~~~~-~~l~G--r~I~V~~a~pk~  185 (522)
                      ++|++.++ .+|.+  +.|+|++++++.
T Consensus       148 ~~A~~~Lng~~i~~~~~~l~v~~sk~~~  175 (481)
T TIGR01649       148 QHAKAALNGADIYNGCCTLKIEYAKPTR  175 (481)
T ss_pred             HHHHHHhcCCcccCCceEEEEEEecCCC
Confidence            99999888 78865  589999988754

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).

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

Probab=99.92  E-value=1.5e-24  Score=226.39  Aligned_cols=181  Identities=27%  Similarity=0.490  Sum_probs=151.7

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCC
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~   82 (522)
                      .-+|+|+||||.|.+.+|+.+|+.||.|++|.|.+.++ ++..|||||+|.+..+|++||  +|.++|++|+|-|.||++
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~d-gklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~  195 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKD-GKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVD  195 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCC-CCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecc
Confidence            46899999999999999999999999999999998776 555599999999999999999  999999999999999987


Q ss_pred             Cccccccc----------------cc--c------------------C--C------------------CCC--------
Q 009920           83 RDDQNMLN----------------RN--T------------------S--S------------------IHS--------   98 (522)
Q Consensus        83 k~~~~~~~----------------~~--~------------------~--~------------------~~~--------   98 (522)
                      +...+...                ..  .                  .  .                  ...        
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            64322100                00  0                  0  0                  000        


Q ss_pred             ----------CCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC
Q 009920           99 ----------SPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF  168 (522)
Q Consensus        99 ----------~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~  168 (522)
                                .......++|||+|||+++||++|.++|++||+|..+.|+.++.|++++|.|||.|.++.++++||++..
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                      0001112689999999999999999999999999999999999999999999999999999999999872


Q ss_pred             -------CccCCeEEEEEEcCCCCC
Q 009920          169 -------HELNGKMVEVKRAVPKEF  186 (522)
Q Consensus       169 -------~~l~Gr~I~V~~a~pk~~  186 (522)
                             ..|+||.|.|..|.++..
T Consensus       356 pa~e~g~~ll~GR~Lkv~~Av~Rke  380 (678)
T KOG0127|consen  356 PASEDGSVLLDGRLLKVTLAVTRKE  380 (678)
T ss_pred             ccCCCceEEEeccEEeeeeccchHH
Confidence                   368999999999998764

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

Probab=99.92  E-value=1.8e-24  Score=225.62  Aligned_cols=186  Identities=22%  Similarity=0.458  Sum_probs=158.9

Q ss_pred             CCCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEe
Q 009920            1 MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAK   78 (522)
Q Consensus         1 me~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~   78 (522)
                      |+++..||||++||++++.++|.++|+.+|+|..|.++.++.+..+|||+||.|+-.|++++|+  .+...+.||.|.|+
T Consensus         1 ~n~~g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~   80 (678)
T KOG0127|consen    1 ENKSGATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVD   80 (678)
T ss_pred             CCCCCceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccc
Confidence            4556689999999999999999999999999999999999999999999999999999999999  77788999999999


Q ss_pred             ecCCCccccccccccCCC-----CC-CC----CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcce
Q 009920           79 KAVPRDDQNMLNRNTSSI-----HS-SP----GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRG  148 (522)
Q Consensus        79 ~a~~k~~~~~~~~~~~~~-----~~-~~----~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG  148 (522)
                      .+.++...+.........     .. .+    ...+.-+|.|+|||+.+.+.+|+.+|++||.|.+|.|++.+++ +..|
T Consensus        81 ~A~~R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dg-klcG  159 (678)
T KOG0127|consen   81 PAKKRARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDG-KLCG  159 (678)
T ss_pred             cccccccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCC-Cccc
Confidence            998876554211111100     00 00    1123568999999999999999999999999999999987774 4559


Q ss_pred             EEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCCCCC
Q 009920          149 FGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPKEFS  187 (522)
Q Consensus       149 ~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk~~~  187 (522)
                      ||||+|....+|++||+.++ ++|+||+|.|+||.++...
T Consensus       160 FaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~y  199 (678)
T KOG0127|consen  160 FAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTY  199 (678)
T ss_pred             eEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccccc
Confidence            99999999999999999999 8999999999999998754

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

Probab=99.91  E-value=1.2e-23  Score=229.42  Aligned_cols=181  Identities=18%  Similarity=0.369  Sum_probs=147.2

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      ..++|||+|||+++|+++|+++|++||+|+.+.|++++.+++++|||||+|.++++|++||  ++++.|.+++|.|+++.
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  89999999999999986


Q ss_pred             CCcccccccccc---------C---CCCCCCCCCCcceeEecCCCCC--C--------CHHHHHHHHhhcCCeeEEEEEe
Q 009920           82 PRDDQNMLNRNT---------S---SIHSSPGPGRTKKIFVGGLAST--V--------TESDFKKYFDQFGTITDVVVMY  139 (522)
Q Consensus        82 ~k~~~~~~~~~~---------~---~~~~~~~~~~~~~LfVgnLp~~--v--------teedL~~~F~~fG~I~~v~i~~  139 (522)
                      ............         .   .........++++|+|.||...  +        ..++|+++|++||.|++|.|++
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            543322111110         0   0000112335788999999642  1        2368999999999999999987


Q ss_pred             cC---CCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCC
Q 009920          140 DH---NTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPK  184 (522)
Q Consensus       140 d~---~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk  184 (522)
                      +.   .+...+|++||+|+++++|++||+.|+ ..|+|+.|.|.+....
T Consensus       454 ~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~~  502 (509)
T TIGR01642       454 PNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGED  502 (509)
T ss_pred             cCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCHH
Confidence            53   344567999999999999999999999 8999999999997643

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

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

Probab=99.91  E-value=2.6e-24  Score=198.13  Aligned_cols=168  Identities=30%  Similarity=0.474  Sum_probs=152.4

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      ...+|||+||+..++|+-|.|+|-+.|+|++++|.+|+.+...+|||||+|.++|+|+-|+  ++...+-+|+|+|.++.
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            4579999999999999999999999999999999999999999999999999999999999  89889999999999887


Q ss_pred             CCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeE-EEEEecCCCCCcceEEEEEecCHHHH
Q 009920           82 PRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITD-VVVMYDHNTQRPRGFGFITYDSEEAV  160 (522)
Q Consensus        82 ~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~-v~i~~d~~tg~~rG~aFVeF~s~e~A  160 (522)
                      ...+..               ....+|||+||.+.++|..|.++|+.||+|.. .+|++|++|+.+++|+||.|++.|++
T Consensus        88 ~~~~nl---------------~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeas  152 (203)
T KOG0131|consen   88 AHQKNL---------------DVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEAS  152 (203)
T ss_pred             cccccc---------------cccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHH
Confidence            222111               23478999999999999999999999999755 59999999999999999999999999


Q ss_pred             HHHHHhcC-CccCCeEEEEEEcCCCCC
Q 009920          161 DRVLHKTF-HELNGKMVEVKRAVPKEF  186 (522)
Q Consensus       161 ~~Al~~~~-~~l~Gr~I~V~~a~pk~~  186 (522)
                      .+|++.++ +.+..++|.|+++..+..
T Consensus       153 d~ai~s~ngq~l~nr~itv~ya~k~~~  179 (203)
T KOG0131|consen  153 DAAIGSMNGQYLCNRPITVSYAFKKDT  179 (203)
T ss_pred             HHHHHHhccchhcCCceEEEEEEecCC
Confidence            99999999 889999999999986654

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

Probab=99.90  E-value=6.7e-24  Score=207.42  Aligned_cols=147  Identities=24%  Similarity=0.535  Sum_probs=136.4

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCCC
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVPR   83 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~k   83 (522)
                      -+|||+|||.++++.+|+.+|++||+|++|.|+++        |+||..+|+..|+.||  ++.-+|++..|.|+.++.+
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            37999999999999999999999999999999986        9999999999999999  8888999999999988765


Q ss_pred             ccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHH
Q 009920           84 DDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV  163 (522)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~A  163 (522)
                      .                  ..+.+|+|+||.+.++.+||++.|++||+|.+++|++|        |+||+|+..++|..|
T Consensus        75 s------------------k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~a  128 (346)
T KOG0109|consen   75 S------------------KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEA  128 (346)
T ss_pred             C------------------CCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHH
Confidence            2                  24678999999999999999999999999999999976        999999999999999


Q ss_pred             HHhcC-CccCCeEEEEEEcCCCCC
Q 009920          164 LHKTF-HELNGKMVEVKRAVPKEF  186 (522)
Q Consensus       164 l~~~~-~~l~Gr~I~V~~a~pk~~  186 (522)
                      ++.++ .+++|++++|..+..+-+
T Consensus       129 ir~l~~~~~~gk~m~vq~stsrlr  152 (346)
T KOG0109|consen  129 IRGLDNTEFQGKRMHVQLSTSRLR  152 (346)
T ss_pred             Hhcccccccccceeeeeeeccccc
Confidence            99888 899999999999887653

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

Probab=99.88  E-value=1.4e-21  Score=210.54  Aligned_cols=176  Identities=22%  Similarity=0.388  Sum_probs=141.8

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCC
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~   82 (522)
                      .++|||+|||.++||++|+++|++||+|..|.|++++.++++++||||+|.+.++|++|+  +++..|.+++|.|.++..
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            589999999999999999999999999999999999998999999999999999999999  899999999999999653


Q ss_pred             Cccccccc------------------------------cc---------c-------------------CC---------
Q 009920           83 RDDQNMLN------------------------------RN---------T-------------------SS---------   95 (522)
Q Consensus        83 k~~~~~~~------------------------------~~---------~-------------------~~---------   95 (522)
                      ........                              ..         .                   ..         
T Consensus       266 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  345 (457)
T TIGR01622       266 STYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALA  345 (457)
T ss_pred             CCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhccccccccccccccccccccccc
Confidence            21100000                              00         0                   00         


Q ss_pred             -------CCCCCCCCCcceeEecCCCCCCC----------HHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHH
Q 009920           96 -------IHSSPGPGRTKKIFVGGLASTVT----------ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEE  158 (522)
Q Consensus        96 -------~~~~~~~~~~~~LfVgnLp~~vt----------eedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e  158 (522)
                             .........+++|+|.||....+          ++||++.|++||.|++|.|...    ...|++||+|.+++
T Consensus       346 ~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~----~~~G~~fV~F~~~e  421 (457)
T TIGR01622       346 IMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTK----NSAGKIYLKFSSVD  421 (457)
T ss_pred             cccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCC----CCceeEEEEECCHH
Confidence                   00000124567899999955544          3689999999999999988733    45799999999999


Q ss_pred             HHHHHHHhcC-CccCCeEEEEEEcCCC
Q 009920          159 AVDRVLHKTF-HELNGKMVEVKRAVPK  184 (522)
Q Consensus       159 ~A~~Al~~~~-~~l~Gr~I~V~~a~pk  184 (522)
                      +|++|++.|+ ..|+|++|.|.+....
T Consensus       422 ~A~~A~~~lnGr~f~gr~i~~~~~~~~  448 (457)
T TIGR01622       422 AALAAFQALNGRYFGGKMITAAFVVND  448 (457)
T ss_pred             HHHHHHHHhcCcccCCeEEEEEEEcHH
Confidence            9999999999 8999999999987643

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.

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

Probab=99.88  E-value=9.7e-20  Score=189.34  Aligned_cols=174  Identities=21%  Similarity=0.412  Sum_probs=145.6

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecCC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~~   82 (522)
                      +.-.|-|++|||+||++||++||+.+. |+++++.+  .+++.+|-|||||.+.|++++|| +++..+..|-|+|..+..
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~~   85 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR--RNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAGG   85 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEEec--cCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccCC
Confidence            445688999999999999999999994 77766655  47999999999999999999999 889999999999999988


Q ss_pred             CccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeE-EEEEecCCCCCcceEEEEEecCHHHHH
Q 009920           83 RDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITD-VVVMYDHNTQRPRGFGFITYDSEEAVD  161 (522)
Q Consensus        83 k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~-v~i~~d~~tg~~rG~aFVeF~s~e~A~  161 (522)
                      ++......+.....     ......|-+++||+.||++||.++|+..-.|.+ |.++.|+. .++.|.|||+|++.|+|+
T Consensus        86 ~e~d~~~~~~g~~s-----~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~r-gR~tGEAfVqF~sqe~ae  159 (510)
T KOG4211|consen   86 AEADWVMRPGGPNS-----SANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQR-GRPTGEAFVQFESQESAE  159 (510)
T ss_pred             ccccccccCCCCCC-----CCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCC-CCcccceEEEecCHHHHH
Confidence            77655443322211     135678999999999999999999999866666 44555655 679999999999999999


Q ss_pred             HHHHhcCCccCCeEEEEEEcCCCCC
Q 009920          162 RVLHKTFHELNGKMVEVKRAVPKEF  186 (522)
Q Consensus       162 ~Al~~~~~~l~Gr~I~V~~a~pk~~  186 (522)
                      +||+++.+.|..|.|+|..+...+.
T Consensus       160 ~Al~rhre~iGhRYIEvF~Ss~~e~  184 (510)
T KOG4211|consen  160 IALGRHRENIGHRYIEVFRSSRAEV  184 (510)
T ss_pred             HHHHHHHHhhccceEEeehhHHHHH
Confidence            9999999999999999998775543

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

Probab=99.86  E-value=4.9e-21  Score=184.70  Aligned_cols=180  Identities=27%  Similarity=0.461  Sum_probs=149.3

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCC--eEEEEeec
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDG--RTVEAKKA   80 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~G--r~I~V~~a   80 (522)
                      ..+|||.+||+.+|.+||+++|++||.|...+|+.|..|+.+||.+||.|...++|++||  ++++.-.+  .+|.|+.+
T Consensus       127 ~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFa  206 (360)
T KOG0145|consen  127 DANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFA  206 (360)
T ss_pred             ccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEec
Confidence            467999999999999999999999999999999999999999999999999999999999  77776544  57888887


Q ss_pred             CCCcccccc-----------ccccCCCCC------------------------------------CCCCCCcceeEecCC
Q 009920           81 VPRDDQNML-----------NRNTSSIHS------------------------------------SPGPGRTKKIFVGGL  113 (522)
Q Consensus        81 ~~k~~~~~~-----------~~~~~~~~~------------------------------------~~~~~~~~~LfVgnL  113 (522)
                      .........           .+...+.|.                                    +..+...-+|||-||
T Consensus       207 nnPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciFvYNL  286 (360)
T KOG0145|consen  207 NNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCIFVYNL  286 (360)
T ss_pred             CCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCeeEEEEEec
Confidence            543221110           000000000                                    111222358999999


Q ss_pred             CCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCC
Q 009920          114 ASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPK  184 (522)
Q Consensus       114 p~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk  184 (522)
                      ..+++|.-|.++|.+||.|..|+|++|..|.+.|||+||++.+-++|..||..++ ..|.+|.|.|.+...|
T Consensus       287 spd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk  358 (360)
T KOG0145|consen  287 SPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNK  358 (360)
T ss_pred             CCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecCC
Confidence            9999999999999999999999999999999999999999999999999999998 8999999999998755

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

Probab=99.85  E-value=2e-21  Score=194.57  Aligned_cols=176  Identities=22%  Similarity=0.501  Sum_probs=152.7

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCC
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~   82 (522)
                      .|+|||+.|.++..||.|+..|..||+|++|.+.-|+.|+++|+||||||+-+|.|+.|+  ||...+.||.|+|.+...
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsN  192 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSN  192 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCC
Confidence            489999999999999999999999999999999999999999999999999999999999  999999999999974322


Q ss_pred             Ccccc-ccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHH
Q 009920           83 RDDQN-MLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD  161 (522)
Q Consensus        83 k~~~~-~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~  161 (522)
                      -...+ ....-      ..+...-.+|||..+..+++|+||+.+|+.||+|+.|.+.+++.+...|||+||||++..+..
T Consensus       193 mpQAQpiID~v------qeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~  266 (544)
T KOG0124|consen  193 MPQAQPIIDMV------QEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQS  266 (544)
T ss_pred             CcccchHHHHH------HHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchH
Confidence            11100 00000      001123468999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcC-CccCCeEEEEEEcCCCCC
Q 009920          162 RVLHKTF-HELNGKMVEVKRAVPKEF  186 (522)
Q Consensus       162 ~Al~~~~-~~l~Gr~I~V~~a~pk~~  186 (522)
                      .||..|+ .+|.|..|+|-.+..+..
T Consensus       267 eAiasMNlFDLGGQyLRVGk~vTPP~  292 (544)
T KOG0124|consen  267 EAIASMNLFDLGGQYLRVGKCVTPPD  292 (544)
T ss_pred             HHhhhcchhhcccceEecccccCCCc
Confidence            9999999 899999999998875543

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

Probab=99.85  E-value=2e-20  Score=195.83  Aligned_cols=156  Identities=29%  Similarity=0.486  Sum_probs=142.7

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCCC
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVPR   83 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~k   83 (522)
                      ..|||+   +++||..|.++|+++++|++++|++|. |  +-|||||.|.++++|++||  ++-..|++++|+|-|+...
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            368999   899999999999999999999999998 6  9999999999999999999  8999999999999987643


Q ss_pred             ccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHH
Q 009920           84 DDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV  163 (522)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~A  163 (522)
                      ..                     .|||.||+++++.++|.++|+.||.|..|++.+|++-  ++|| ||+|+++++|++|
T Consensus        76 ~~---------------------~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g--~kg~-FV~f~~e~~a~~a  131 (369)
T KOG0123|consen   76 PS---------------------LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG--SKGY-FVQFESEESAKKA  131 (369)
T ss_pred             Cc---------------------eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC--ceee-EEEeCCHHHHHHH
Confidence            22                     1999999999999999999999999999999999874  9999 9999999999999


Q ss_pred             HHhcC-CccCCeEEEEEEcCCCCCCCCCC
Q 009920          164 LHKTF-HELNGKMVEVKRAVPKEFSPGPS  191 (522)
Q Consensus       164 l~~~~-~~l~Gr~I~V~~a~pk~~~~~~~  191 (522)
                      |++++ ..+.+++|.|....+++.+..+.
T Consensus       132 i~~~ng~ll~~kki~vg~~~~~~er~~~~  160 (369)
T KOG0123|consen  132 IEKLNGMLLNGKKIYVGLFERKEEREAPL  160 (369)
T ss_pred             HHHhcCcccCCCeeEEeeccchhhhcccc
Confidence            99999 89999999999998877654433

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

Probab=99.84  E-value=5.2e-21  Score=185.07  Aligned_cols=184  Identities=21%  Similarity=0.406  Sum_probs=152.5

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hccc-ccCC--eEEEEe
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKH-MIDG--RTVEAK   78 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~-~i~G--r~I~V~   78 (522)
                      |+++|||+.|.+.-.|||++.+|..||+|++|.+.+.++ +.+||||||+|.+..+|+.||  ++.. .+.|  ..|.|+
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            679999999999999999999999999999999999885 999999999999999999999  6553 4443  577788


Q ss_pred             ecCCCccccccc--------------------------------------------------------------------
Q 009920           79 KAVPRDDQNMLN--------------------------------------------------------------------   90 (522)
Q Consensus        79 ~a~~k~~~~~~~--------------------------------------------------------------------   90 (522)
                      .+...+++....                                                                    
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            876654311000                                                                    


Q ss_pred             ----------ccc-------------------------C-----------------CCC---------------------
Q 009920           91 ----------RNT-------------------------S-----------------SIH---------------------   97 (522)
Q Consensus        91 ----------~~~-------------------------~-----------------~~~---------------------   97 (522)
                                .++                         .                 ...                     
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                         0                 000                     


Q ss_pred             ---------------------CCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecC
Q 009920           98 ---------------------SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS  156 (522)
Q Consensus        98 ---------------------~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s  156 (522)
                                           ...+..+.+.|||-.||.+..+.||-++|-.||.|+..++..|+.|..+|+|+||.|++
T Consensus       257 ypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDN  336 (371)
T KOG0146|consen  257 YPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDN  336 (371)
T ss_pred             cchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCC
Confidence                                 00112344789999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhcC-CccCCeEEEEEEcCCCCCCC
Q 009920          157 EEAVDRVLHKTF-HELNGKMVEVKRAVPKEFSP  188 (522)
Q Consensus       157 ~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk~~~~  188 (522)
                      +.++++||+.|+ ..|.=|+|+|..++||+..+
T Consensus       337 p~SaQaAIqAMNGFQIGMKRLKVQLKRPkdanR  369 (371)
T KOG0146|consen  337 PASAQAAIQAMNGFQIGMKRLKVQLKRPKDANR  369 (371)
T ss_pred             chhHHHHHHHhcchhhhhhhhhhhhcCccccCC
Confidence            999999999999 89999999999999998643

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

Probab=99.84  E-value=1.5e-21  Score=205.13  Aligned_cols=183  Identities=25%  Similarity=0.457  Sum_probs=157.3

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeec
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a   80 (522)
                      |+|.++||+-.|+..+++.+|.+||+.+|+|.+|.|+.|+.+.++||.|||+|.|.+.+..|| +.++.+.+.+|.|+..
T Consensus       176 ERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq~s  255 (549)
T KOG0147|consen  176 ERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQLS  255 (549)
T ss_pred             HHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEeccc
Confidence            578899999999999999999999999999999999999999999999999999999999999 9999999999999876


Q ss_pred             CCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHH
Q 009920           81 VPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV  160 (522)
Q Consensus        81 ~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A  160 (522)
                      ........  ..........-..+..+|+|+||.++++|++|+.+|++||.|..|.+++|.+|++.|||+||+|.+.++|
T Consensus       256 Eaeknr~a--~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~a  333 (549)
T KOG0147|consen  256 EAEKNRAA--NASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDA  333 (549)
T ss_pred             HHHHHHHH--hccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHH
Confidence            54433311  1111111111123444599999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcC-CccCCeEEEEEEcCCCCC
Q 009920          161 DRVLHKTF-HELNGKMVEVKRAVPKEF  186 (522)
Q Consensus       161 ~~Al~~~~-~~l~Gr~I~V~~a~pk~~  186 (522)
                      ++|++.++ .+|.|+.|+|.....+..
T Consensus       334 r~a~e~lngfelAGr~ikV~~v~~r~~  360 (549)
T KOG0147|consen  334 RKALEQLNGFELAGRLIKVSVVTERVD  360 (549)
T ss_pred             HHHHHHhccceecCceEEEEEeeeecc
Confidence            99999999 899999999988765543

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

Probab=99.83  E-value=2.3e-20  Score=200.80  Aligned_cols=174  Identities=24%  Similarity=0.425  Sum_probs=147.1

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCC---CCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRAT---GRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~t---g~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      .++|||.||++++|.++|+++|.+.|.|.+|.|.+.++.   -.|.||+||+|.++++|++|+  ++.+.|+|+.|+|+.
T Consensus       515 ~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~  594 (725)
T KOG0110|consen  515 ETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKI  594 (725)
T ss_pred             chhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEe
Confidence            445999999999999999999999999999988766532   135699999999999999999  788999999999999


Q ss_pred             cCCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHH
Q 009920           80 AVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEA  159 (522)
Q Consensus        80 a~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~  159 (522)
                      +..+......       ...+......+|+|+|||+.++..+|+++|..||.|++|+|++.......+|||||+|.++++
T Consensus       595 S~~k~~~~~g-------K~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~e  667 (725)
T KOG0110|consen  595 SENKPASTVG-------KKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPRE  667 (725)
T ss_pred             ccCccccccc-------cccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHH
Confidence            8722221111       111122336799999999999999999999999999999999886666779999999999999


Q ss_pred             HHHHHHhcC-CccCCeEEEEEEcCCCC
Q 009920          160 VDRVLHKTF-HELNGKMVEVKRAVPKE  185 (522)
Q Consensus       160 A~~Al~~~~-~~l~Gr~I~V~~a~pk~  185 (522)
                      |.+|+..+. ..|.||+|.++||....
T Consensus       668 a~nA~~al~STHlyGRrLVLEwA~~d~  694 (725)
T KOG0110|consen  668 AKNAFDALGSTHLYGRRLVLEWAKSDN  694 (725)
T ss_pred             HHHHHHhhcccceechhhheehhccch
Confidence            999999998 78999999999998543

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

Probab=99.81  E-value=6.3e-20  Score=187.58  Aligned_cols=182  Identities=23%  Similarity=0.409  Sum_probs=150.2

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hcc-cccC--CeEEEEe
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDK-HMID--GRTVEAK   78 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~-~~i~--Gr~I~V~   78 (522)
                      ++++|||+.|++.+||+||+++|.+||.|++|.|++|.+ +.+||||||.|.++|.|..||  +|. +.+.  ..+|.|+
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~-~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVk  201 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPD-GLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVK  201 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheeccc-ccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEE
Confidence            478999999999999999999999999999999999985 999999999999999999999  554 3444  4689999


Q ss_pred             ecCCCcccccccc-------------------------------------------------------------------
Q 009920           79 KAVPRDDQNMLNR-------------------------------------------------------------------   91 (522)
Q Consensus        79 ~a~~k~~~~~~~~-------------------------------------------------------------------   91 (522)
                      +|.+++++.....                                                                   
T Consensus       202 FADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~L~~l~a~~~qq~~~~~  281 (510)
T KOG0144|consen  202 FADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLPPLGPLNATQLQQAAALA  281 (510)
T ss_pred             ecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccccCCCCcchhHHHHHHHhh
Confidence            9987654211000                                                                   


Q ss_pred             --------cc-CCCC-------------C---------------------------------------------------
Q 009920           92 --------NT-SSIH-------------S---------------------------------------------------   98 (522)
Q Consensus        92 --------~~-~~~~-------------~---------------------------------------------------   98 (522)
                              .. ....             .                                                   
T Consensus       282 ~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~~n~~~~~a~a~~~sp~a  361 (510)
T KOG0144|consen  282 AAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPANYNLAGGMAGAGTTSPVA  361 (510)
T ss_pred             hhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchhcccccccccccccCccc
Confidence                    00 0000             0                                                   


Q ss_pred             --------------------------------------------------------CCCCCCcceeEecCCCCCCCHHHH
Q 009920           99 --------------------------------------------------------SPGPGRTKKIFVGGLASTVTESDF  122 (522)
Q Consensus        99 --------------------------------------------------------~~~~~~~~~LfVgnLp~~vteedL  122 (522)
                                                                              ..+..+...|||.+||.+.-+.||
T Consensus       362 a~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpeGanlfiyhlPqefgdq~l  441 (510)
T KOG0144|consen  362 ASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPEGANLFIYHLPQEFGDQDL  441 (510)
T ss_pred             ccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCCccceeeeeCchhhhhHHH
Confidence                                                                    000011245999999999999999


Q ss_pred             HHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCCCC
Q 009920          123 KKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPKEF  186 (522)
Q Consensus       123 ~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk~~  186 (522)
                      -..|..||.|+..++..|+.|+-+|+|+||.|++..+|.+||..|+ ..|..|+++|..++.+..
T Consensus       442 ~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~~~n  506 (510)
T KOG0144|consen  442 IATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRDRNN  506 (510)
T ss_pred             HHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeeccCC
Confidence            9999999999999999999999999999999999999999999999 899999999999876643

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

Probab=99.79  E-value=1.1e-18  Score=182.77  Aligned_cols=171  Identities=23%  Similarity=0.472  Sum_probs=150.9

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      +|...|||+||++++|.++|.++|+.||+|++|+++++.+ + ++|| ||+|.++++|++|+  +|+..+.+++|.|-..
T Consensus        74 rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~  150 (369)
T KOG0123|consen   74 RDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLF  150 (369)
T ss_pred             cCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeec
Confidence            4566699999999999999999999999999999999975 4 9999 99999999999999  9999999999999888


Q ss_pred             CCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHH
Q 009920           81 VPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV  160 (522)
Q Consensus        81 ~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A  160 (522)
                      ..+++.......        .......++|.+++.++++++|+++|..+|+|..+.++.+.. +++++|+||+|++.++|
T Consensus       151 ~~~~er~~~~~~--------~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~-g~~~~~gfv~f~~~e~a  221 (369)
T KOG0123|consen  151 ERKEEREAPLGE--------YKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSI-GKSKGFGFVNFENPEDA  221 (369)
T ss_pred             cchhhhcccccc--------hhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCC-CCCCCccceeecChhHH
Confidence            776654432221        123556799999999999999999999999999999999987 45899999999999999


Q ss_pred             HHHHHhcC-CccCCeEEEEEEcCCCC
Q 009920          161 DRVLHKTF-HELNGKMVEVKRAVPKE  185 (522)
Q Consensus       161 ~~Al~~~~-~~l~Gr~I~V~~a~pk~  185 (522)
                      +.|++.++ ..+.++.+.|..+..+.
T Consensus       222 ~~av~~l~~~~~~~~~~~V~~aqkk~  247 (369)
T KOG0123|consen  222 KKAVETLNGKIFGDKELYVGRAQKKS  247 (369)
T ss_pred             HHHHHhccCCcCCccceeecccccch
Confidence            99999999 78888999999888744

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

Probab=99.78  E-value=4.8e-19  Score=172.07  Aligned_cols=140  Identities=21%  Similarity=0.471  Sum_probs=120.7

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHHHcccccCCeEEEEeecC
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl~~~~~i~Gr~I~V~~a~   81 (522)
                      +++-|+|||+||..++||+-|..||.+.|+|+.|+|+.+                                 +|+|.++.
T Consensus         3 ~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~---------------------------------e~~v~wa~   49 (321)
T KOG0148|consen    3 SDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFD---------------------------------ELKVNWAT   49 (321)
T ss_pred             CCCCceEEeeccChhhHHHHHHHHHHhccccccceeehh---------------------------------hhcccccc
Confidence            356799999999999999999999999999999999986                                 34555554


Q ss_pred             CCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHH
Q 009920           82 PRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD  161 (522)
Q Consensus        82 ~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~  161 (522)
                      ....+.+           +.......|||+.|...++-|+|++.|.+||+|.+++|++|..|.++|||+||.|..+++|+
T Consensus        50 ~p~nQsk-----------~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAE  118 (321)
T KOG0148|consen   50 APGNQSK-----------PTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAE  118 (321)
T ss_pred             CcccCCC-----------CccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHH
Confidence            4311111           11123457999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcC-CccCCeEEEEEEcCCCC
Q 009920          162 RVLHKTF-HELNGKMVEVKRAVPKE  185 (522)
Q Consensus       162 ~Al~~~~-~~l~Gr~I~V~~a~pk~  185 (522)
                      +||+.|+ .-|..|.|+-.||..|.
T Consensus       119 nAI~~MnGqWlG~R~IRTNWATRKp  143 (321)
T KOG0148|consen  119 NAIQQMNGQWLGRRTIRTNWATRKP  143 (321)
T ss_pred             HHHHHhCCeeeccceeeccccccCc
Confidence            9999999 89999999999998776

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

Probab=99.77  E-value=2.5e-17  Score=152.22  Aligned_cols=156  Identities=21%  Similarity=0.330  Sum_probs=126.6

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      +.+++|||+|||.++-|+||+++|-|||.|.+|.|...   .....||||+|+++.+|+.||  .+.-.++++.|.|+.+
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            56899999999999999999999999999999988543   345679999999999999999  8999999999999988


Q ss_pred             CCCcccccccc----------ccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEE
Q 009920           81 VPRDDQNMLNR----------NTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFG  150 (522)
Q Consensus        81 ~~k~~~~~~~~----------~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~a  150 (522)
                      ..-.......-          ......-.+......+|.|.+||.+.+|+||+++..+-|.|....+.+|       |.+
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            65432111000          0000011222334568999999999999999999999999999998877       379


Q ss_pred             EEEecCHHHHHHHHHhcC
Q 009920          151 FITYDSEEAVDRVLHKTF  168 (522)
Q Consensus       151 FVeF~s~e~A~~Al~~~~  168 (522)
                      .|+|...|+++-|+.+++
T Consensus       154 vV~~~r~eDMkYAvr~ld  171 (241)
T KOG0105|consen  154 VVEYLRKEDMKYAVRKLD  171 (241)
T ss_pred             eeeeeehhhHHHHHHhhc
Confidence            999999999999999887

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

Probab=99.75  E-value=3.4e-17  Score=150.34  Aligned_cols=84  Identities=31%  Similarity=0.598  Sum_probs=79.2

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ...++|||+|||+++||++|+++|++||+|++|+|++|+.|+++||||||+|+++++|++||+.++ ++|++++|+|+++
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a  111 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPA  111 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeC
Confidence            456799999999999999999999999999999999999999999999999999999999999877 8999999999999


Q ss_pred             CCCCC
Q 009920          182 VPKEF  186 (522)
Q Consensus       182 ~pk~~  186 (522)
                      .+++.
T Consensus       112 ~~~~~  116 (144)
T PLN03134        112 NDRPS  116 (144)
T ss_pred             CcCCC
Confidence            87654

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

Probab=99.74  E-value=1e-16  Score=176.03  Aligned_cols=79  Identities=20%  Similarity=0.484  Sum_probs=75.2

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      ..++|||+|||+++++++|+++|++||+|++|+|++++.++++||||||+|.++++|++||  +|...|.|+.|+|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            3479999999999999999999999999999999999999999999999999999999999  99999999999998876


Q ss_pred             C
Q 009920           82 P   82 (522)
Q Consensus        82 ~   82 (522)
                      +
T Consensus       283 ~  283 (612)
T TIGR01645       283 T  283 (612)
T ss_pred             C
Confidence            4

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.

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.70  E-value=4.2e-16  Score=159.64  Aligned_cols=177  Identities=27%  Similarity=0.418  Sum_probs=144.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHh-ccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFS-RYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~-~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      +..|.+||.|||+++..++||++|. +.|+|+.|.++.|.. +|+||||.|||+++|.++||+  ++++++.+|+|.|+.
T Consensus        42 ~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~-GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKE  120 (608)
T KOG4212|consen   42 ARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDES-GKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKE  120 (608)
T ss_pred             cccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccC-CCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEec
Confidence            3456799999999999999999996 579999999999974 999999999999999999999  999999999999986


Q ss_pred             cCCCccccc---------------------------------------------ccc--cc-------------------
Q 009920           80 AVPRDDQNM---------------------------------------------LNR--NT-------------------   93 (522)
Q Consensus        80 a~~k~~~~~---------------------------------------------~~~--~~-------------------   93 (522)
                      ....+..+.                                             +.+  ..                   
T Consensus       121 d~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~  200 (608)
T KOG4212|consen  121 DHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLS  200 (608)
T ss_pred             cCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccch
Confidence            654211000                                             000  00                   


Q ss_pred             ----CCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-
Q 009920           94 ----SSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-  168 (522)
Q Consensus        94 ----~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-  168 (522)
                          .+.+ ...+....++||.||.+.+..+.|++.|...|.|+.|.+-.|++ +.++|+|.++|+.+-.|-.||.+++ 
T Consensus       201 ~~Flr~~h-~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKe-G~s~G~~vi~y~hpveavqaIsml~~  278 (608)
T KOG4212|consen  201 ASFLRSLH-IFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKE-GNSRGFAVIEYDHPVEAVQAISMLDR  278 (608)
T ss_pred             hhhhhhcc-CCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccc-cccCCeeEEEecchHHHHHHHHhhcc
Confidence                0000 11233456899999999999999999999999999999999998 5899999999999999999999998 


Q ss_pred             CccCCeEEEEEEcC
Q 009920          169 HELNGKMVEVKRAV  182 (522)
Q Consensus       169 ~~l~Gr~I~V~~a~  182 (522)
                      .-+..++..|....
T Consensus       279 ~g~~~~~~~~Rl~~  292 (608)
T KOG4212|consen  279 QGLFDRRMTVRLDR  292 (608)
T ss_pred             CCCccccceeeccc
Confidence            56666777776644

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

Probab=99.70  E-value=9e-17  Score=147.58  Aligned_cols=83  Identities=45%  Similarity=0.808  Sum_probs=78.0

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++||++|+++|++||+|++|+|++++.|+++|+||||+|+++|+|++||  ++.++|++++|+|+++
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a  111 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPA  111 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeC
Confidence            35789999999999999999999999999999999999999999999999999999999999  7899999999999998


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      .++..
T Consensus       112 ~~~~~  116 (144)
T PLN03134        112 NDRPS  116 (144)
T ss_pred             CcCCC
Confidence            76543

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

Probab=99.65  E-value=2.4e-16  Score=151.82  Aligned_cols=161  Identities=26%  Similarity=0.478  Sum_probs=130.3

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCCC
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVPR   83 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~k   83 (522)
                      .+|||++||+.+.+++|++||.+||+|.+|.|..        +|+||+|.++.+|+.|+  ++..+|.+.++.|+++...
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 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            5799999999999999999999999999888755        58999999999999999  9999999988888888754


Q ss_pred             cccccccc----ccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHH
Q 009920           84 DDQNMLNR----NTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEA  159 (522)
Q Consensus        84 ~~~~~~~~----~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~  159 (522)
                      ........    ........+.....+.|+|.+|+..+.+++|+++|.++|++....+.        +.++||+|.++++
T Consensus        74 ~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~~--------~~~~~v~Fs~~~d  145 (216)
T KOG0106|consen   74 RRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDAR--------RNFAFVEFSEQED  145 (216)
T ss_pred             ccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhhh--------ccccceeehhhhh
Confidence            32221111    11112222333456789999999999999999999999999555442        4489999999999


Q ss_pred             HHHHHHhcC-CccCCeEEEEEEcC
Q 009920          160 VDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       160 A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      +++|+++++ .+|.++.|+|....
T Consensus       146 a~ra~~~l~~~~~~~~~l~~~~~~  169 (216)
T KOG0106|consen  146 AKRALEKLDGKKLNGRRISVEKNS  169 (216)
T ss_pred             hhhcchhccchhhcCceeeecccC
Confidence            999999999 89999999995443

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

Probab=99.63  E-value=6.8e-15  Score=140.76  Aligned_cols=170  Identities=16%  Similarity=0.326  Sum_probs=134.1

Q ss_pred             CcEEEECCCCCCCCHHHHHH----HHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEe
Q 009920            5 LGKLFIGGISWDTDEERLKE----YFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAK   78 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e----~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~   78 (522)
                      .+||||.||+..+..+||++    +|++||+|.+|...+   |.+.||.|||.|.+.+.|..|+  +++..+-++.++|.
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriq   85 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQ   85 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhhee
Confidence            44999999999999999998    999999999888876   4689999999999999999999  99999999999999


Q ss_pred             ecCCCcccccccc-------------------ccCCCC---------------CCCCCCCcceeEecCCCCCCCHHHHHH
Q 009920           79 KAVPRDDQNMLNR-------------------NTSSIH---------------SSPGPGRTKKIFVGGLASTVTESDFKK  124 (522)
Q Consensus        79 ~a~~k~~~~~~~~-------------------~~~~~~---------------~~~~~~~~~~LfVgnLp~~vteedL~~  124 (522)
                      +|..+.+.....+                   ++....               ......+...||+.|||..++.+.|..
T Consensus        86 yA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~  165 (221)
T KOG4206|consen   86 YAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSD  165 (221)
T ss_pred             cccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHHH
Confidence            8866543221100                   000000               012244667899999999999999999


Q ss_pred             HHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccC-CeEEEEEEcC
Q 009920          125 YFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELN-GKMVEVKRAV  182 (522)
Q Consensus       125 ~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~-Gr~I~V~~a~  182 (522)
                      +|++|.-.++|+++...     ++.|||+|.++..+..|.+.+. ..|- ...+.|++++
T Consensus       166 lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  166 LFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            99999999999998643     4599999999888888887766 3333 6677776654

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

Probab=99.61  E-value=3.7e-15  Score=157.27  Aligned_cols=172  Identities=21%  Similarity=0.416  Sum_probs=130.6

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCCC
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVPR   83 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~k   83 (522)
                      ++|||+||+.+++|++|+.+|++||.|+.|.+++|.+|+++|||+||+|.++++|++|+  +|+.+|.|+.|+|.....+
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            44999999999999999999999999999999999989999999999999999999998  9999999999998554332


Q ss_pred             cccccc-----cc---------------cc------------------------------------CCCCCCCCC-----
Q 009920           84 DDQNML-----NR---------------NT------------------------------------SSIHSSPGP-----  102 (522)
Q Consensus        84 ~~~~~~-----~~---------------~~------------------------------------~~~~~~~~~-----  102 (522)
                      .+....     ..               .+                                    .......+.     
T Consensus       359 ~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~  438 (549)
T KOG0147|consen  359 VDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASPA  438 (549)
T ss_pred             cccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCccccccc
Confidence            221110     00               00                                    000001111     


Q ss_pred             --CCcceeEecCC--CCCCC--------HHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-C
Q 009920          103 --GRTKKIFVGGL--ASTVT--------ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-H  169 (522)
Q Consensus       103 --~~~~~LfVgnL--p~~vt--------eedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~  169 (522)
                        .++.++.|.|+  |.+.|        .|||.+.+.+||.|.+|.|.+.     +-|+.||.|.++++|.+|+..++ .
T Consensus       439 ~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~n-----s~g~VYvrc~s~~~A~~a~~alhgr  513 (549)
T KOG0147|consen  439 FDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKN-----SAGCVYVRCPSAEAAGTAVKALHGR  513 (549)
T ss_pred             cCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccC-----CCceEEEecCcHHHHHHHHHHHhhh
Confidence              33445566665  22222        2678888899999977766533     23899999999999999999999 7


Q ss_pred             ccCCeEEEEEEcC
Q 009920          170 ELNGKMVEVKRAV  182 (522)
Q Consensus       170 ~l~Gr~I~V~~a~  182 (522)
                      .|.+|+|..++-.
T Consensus       514 WF~gr~Ita~~~~  526 (549)
T KOG0147|consen  514 WFAGRMITAKYLP  526 (549)
T ss_pred             hhccceeEEEEee
Confidence            9999999998753

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

Probab=99.60  E-value=4e-14  Score=147.81  Aligned_cols=176  Identities=20%  Similarity=0.295  Sum_probs=134.1

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEE-EeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAV-IMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~-i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      ....|.|++||+.|||+||.+||+.+-.|.+.. ++.++ .+++.|.|||+|++.|.|++|| .+++.|..|-|+|.++.
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGRHRENIGHRYIEVFRSS  180 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHHHHHhhccceEEeehhH
Confidence            356899999999999999999999997777733 45554 4889999999999999999999 99999999999997663


Q ss_pred             CCcccccc------------------ccc-----------c--------------------------------------C
Q 009920           82 PRDDQNML------------------NRN-----------T--------------------------------------S   94 (522)
Q Consensus        82 ~k~~~~~~------------------~~~-----------~--------------------------------------~   94 (522)
                      ..+.....                  .+.           .                                      .
T Consensus       181 ~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~gs~~~~~~~~~~  260 (510)
T KOG4211|consen  181 RAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFGSYGGGRDPNYP  260 (510)
T ss_pred             HHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCccccccccccccccccccccC
Confidence            32211110                  000           0                                      0


Q ss_pred             C---CCCC-------CCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHH
Q 009920           95 S---IHSS-------PGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL  164 (522)
Q Consensus        95 ~---~~~~-------~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al  164 (522)
                      .   .+..       ........++.++||+..++.+|..+|...-++ .|+|...+ +++..|.|+|+|.+.++|..|+
T Consensus       261 ~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~-~v~i~ig~-dGr~TGEAdveF~t~edav~Am  338 (510)
T KOG4211|consen  261 VSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPY-RVHIEIGP-DGRATGEADVEFATGEDAVGAM  338 (510)
T ss_pred             CCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCce-eEEEEeCC-CCccCCcceeecccchhhHhhh
Confidence            0   0000       000112578999999999999999999987665 55555544 4888999999999999999999


Q ss_pred             HhcCCccCCeEEEEEEcC
Q 009920          165 HKTFHELNGKMVEVKRAV  182 (522)
Q Consensus       165 ~~~~~~l~Gr~I~V~~a~  182 (522)
                      .+....+..+-|++....
T Consensus       339 skd~anm~hrYVElFln~  356 (510)
T KOG4211|consen  339 GKDGANMGHRYVELFLNG  356 (510)
T ss_pred             ccCCcccCcceeeecccC
Confidence            999989999999987764

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.60  E-value=1e-14  Score=142.25  Aligned_cols=159  Identities=26%  Similarity=0.485  Sum_probs=121.4

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCC
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~   82 (522)
                      .++|||+|||+++|+++|+++|++||+|..+.|..++.++++++||||+|.++++|.+|+  ++...|.+++|.|.++..
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            489999999999999999999999999999999999989999999999999999999999  788999999999999653


Q ss_pred             ----Ccccccc----ccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEe
Q 009920           83 ----RDDQNML----NRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY  154 (522)
Q Consensus        83 ----k~~~~~~----~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF  154 (522)
                          +......    ..................+++.+++..+++.++...|..++.+..+.+.............++.+
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  274 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGN  274 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCCCcccccccccch
Confidence                2211100    00111122233345677899999999999999999999999997777776655444433334333


Q ss_pred             cCHHHHHHH
Q 009920          155 DSEEAVDRV  163 (522)
Q Consensus       155 ~s~e~A~~A  163 (522)
                      .....+...
T Consensus       275 ~~~~~~~~~  283 (306)
T COG0724         275 EASKDALES  283 (306)
T ss_pred             hHHHhhhhh
Confidence            333333333

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.59  E-value=2e-15  Score=144.80  Aligned_cols=79  Identities=42%  Similarity=0.875  Sum_probs=74.3

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecCC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~~   82 (522)
                      .-+||||++|||++++|+|+++||+||+|++++|+.|+.|+|+|||+||+|+|.|.|++|+ .-+..|+||+..++.|.-
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLASL   90 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchhhh
Confidence            4579999999999999999999999999999999999999999999999999999999999 557889999999988754

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

Probab=99.57  E-value=2.2e-14  Score=155.06  Aligned_cols=175  Identities=20%  Similarity=0.296  Sum_probs=132.0

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      ++..+.|+|+|||..+..++|.+.|..||+|..+.|.+.-      --++|+|.++.+|++|+  +.-..+...++.+.|
T Consensus       382 ~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp~~G------~~aiv~fl~p~eAr~Afrklaysr~k~~plyle~  455 (725)
T KOG0110|consen  382 ERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLPPGG------TGAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEW  455 (725)
T ss_pred             hhhcceeeeccCccccccHHHHHHhhcccccceeecCccc------ceeeeeecCccchHHHHHHhchhhhccCcccccc
Confidence            3567889999999999999999999999999988554321      14999999999999999  666666666666655


Q ss_pred             cCCCccc-----ccc-----c--------c---ccCCCCC--C-----------CCCCCcceeEecCCCCCCCHHHHHHH
Q 009920           80 AVPRDDQ-----NML-----N--------R---NTSSIHS--S-----------PGPGRTKKIFVGGLASTVTESDFKKY  125 (522)
Q Consensus        80 a~~k~~~-----~~~-----~--------~---~~~~~~~--~-----------~~~~~~~~LfVgnLp~~vteedL~~~  125 (522)
                      +.....+     ...     .        +   .......  .           ......++|||.||++++|.++|+.+
T Consensus       456 aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~  535 (725)
T KOG0110|consen  456 APEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLEDL  535 (725)
T ss_pred             ChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHHH
Confidence            5322111     000     0        0   0000000  0           01112234999999999999999999


Q ss_pred             HhhcCCeeEEEEEecCCCC---CcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          126 FDQFGTITDVVVMYDHNTQ---RPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       126 F~~fG~I~~v~i~~d~~tg---~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      |.+.|.|..+.|.+.++..   .+.||+||+|.++++|++|++.|+ +.|+|+.|.|+++.
T Consensus       536 F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  536 FSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             HHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            9999999999888766432   345999999999999999999999 99999999999988

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.55  E-value=4.8e-15  Score=149.94  Aligned_cols=181  Identities=22%  Similarity=0.333  Sum_probs=141.2

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhc---c-CCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEe
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSR---Y-GEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAK   78 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~---~-G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~   78 (522)
                      +.-.|.+++||+++++.||.+||.+   . +.++.|.+++.+ +++..|-|||.|..+++|+.|| +++..|..|.|++.
T Consensus       160 ~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElF  238 (508)
T KOG1365|consen  160 NQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELF  238 (508)
T ss_pred             cceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHH
Confidence            3456788999999999999999963   2 245556666654 5999999999999999999999 89999999999998


Q ss_pred             ecCCCccccccccccC---------------CCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCC-eeE--EEEEec
Q 009920           79 KAVPRDDQNMLNRNTS---------------SIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGT-ITD--VVVMYD  140 (522)
Q Consensus        79 ~a~~k~~~~~~~~~~~---------------~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~-I~~--v~i~~d  140 (522)
                      +++..+-++..++...               .....+......+|-+++||++++.|||-++|..|-. |..  |.++.+
T Consensus       239 RSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N  318 (508)
T KOG1365|consen  239 RSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN  318 (508)
T ss_pred             HHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc
Confidence            8877665554433221               1111222334678999999999999999999998865 333  666666


Q ss_pred             CCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCCCC
Q 009920          141 HNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPKEF  186 (522)
Q Consensus       141 ~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk~~  186 (522)
                      .+ +++.|.|||+|.++|+|.+|.++.+ +..+.|.|+|..+.-.+.
T Consensus       319 ~q-GrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~eel  364 (508)
T KOG1365|consen  319 GQ-GRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSVEEL  364 (508)
T ss_pred             CC-CCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccHHHH
Confidence            55 8999999999999999999999988 455699999988775543

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.55  E-value=2.5e-14  Score=141.18  Aligned_cols=100  Identities=20%  Similarity=0.350  Sum_probs=93.9

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      ..++-+||||.-|+.+++|.+|++.|+.||+|+.|.|+.|+.|+++||||||+|+++.++++|.+..+ .+|+++.|.|+
T Consensus        97 ~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VD  176 (335)
T KOG0113|consen   97 IGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVD  176 (335)
T ss_pred             cCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEE
Confidence            44788999999999999999999999999999999999999999999999999999999999999888 89999999999


Q ss_pred             EcCCCCCCCCCCCCCCCCCCC
Q 009920          180 RAVPKEFSPGPSRSSMIGYNN  200 (522)
Q Consensus       180 ~a~pk~~~~~~~r~~~gG~~~  200 (522)
                      +...+..+.+.+|..++|.++
T Consensus       177 vERgRTvkgW~PRRLGGGLGg  197 (335)
T KOG0113|consen  177 VERGRTVKGWLPRRLGGGLGG  197 (335)
T ss_pred             ecccccccccccccccCCcCC
Confidence            999999999999888777653

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.55  E-value=8.1e-15  Score=140.70  Aligned_cols=81  Identities=36%  Similarity=0.645  Sum_probs=77.0

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcC
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAV  182 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~  182 (522)
                      ..-+||||++|+|+++.|+|+++|++||+|++++|+.|+.|+++|||+||+|.|.|+|++|++..+..|+||+..|.+|.
T Consensus        10 T~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   10 TTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLAS   89 (247)
T ss_pred             ceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchhh
Confidence            35579999999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             C
Q 009920          183 P  183 (522)
Q Consensus       183 p  183 (522)
                      -
T Consensus        90 l   90 (247)
T KOG0149|consen   90 L   90 (247)
T ss_pred             h
Confidence            3

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.54  E-value=2.6e-14  Score=149.01  Aligned_cols=85  Identities=21%  Similarity=0.345  Sum_probs=79.6

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      .....++|||++||+++||++|+++|++||+|++|+|++|+.++++||||||+|.++++|++||+.++ .+|.+++|+|+
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            34567899999999999999999999999999999999999999999999999999999999999888 89999999999


Q ss_pred             EcCCCC
Q 009920          180 RAVPKE  185 (522)
Q Consensus       180 ~a~pk~  185 (522)
                      ++++..
T Consensus       183 ~a~p~~  188 (346)
T TIGR01659       183 YARPGG  188 (346)
T ss_pred             cccccc
Confidence            988754

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).

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

Probab=99.53  E-value=3.1e-14  Score=156.27  Aligned_cols=120  Identities=18%  Similarity=0.270  Sum_probs=97.5

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhcc--CCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRY--GEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~--G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .++|||+|||+++||++|+++|++|  |+|++|++++        +||||+|.++++|++||  ++.++|++++|+|.++
T Consensus       233 ~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r--------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~A  304 (578)
T TIGR01648       233 VKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR--------DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLA  304 (578)
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec--------CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            5789999999999999999999999  9999998764        49999999999999999  8999999999999999


Q ss_pred             CCCccccccc------------cccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCe
Q 009920           81 VPRDDQNMLN------------RNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTI  132 (522)
Q Consensus        81 ~~k~~~~~~~------------~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I  132 (522)
                      +++.......            ..............+.++++.+|++.++++.+.++|..+|.|
T Consensus       305 kp~~~~~~~~~~rg~gg~~~~~~~~~~~~g~~~sp~s~~~~~g~~~~~~~~~~~~~~f~~~g~~  368 (578)
T TIGR01648       305 KPVDKKSYVRYTRGTGGRGKERQAARQSLGQVYDPASRSLAYEDYYYHPPYAPSLHFPRMPGPI  368 (578)
T ss_pred             cCCCcccccccccccCCCcccccccccccCcccCccccccccccccccccccchhhccccCccc
Confidence            8865442110            000011112223467899999999999999999999998763

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.

>PF00076 RRM_1: RNA recognition motif

Probab=99.51  E-value=6.5e-14  Score=110.77  Aligned_cols=68  Identities=31%  Similarity=0.771  Sum_probs=64.7

Q ss_pred             EEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEE
Q 009920            8 LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVE   76 (522)
Q Consensus         8 LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~   76 (522)
                      |||+|||+++|+++|+++|++||+|..++++.+ .+++.+++|||+|.++++|++|+  +++..+.+++|+
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 56899999999999999999999  899999999874

(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 ....

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=99.51  E-value=2.2e-13  Score=143.24  Aligned_cols=178  Identities=22%  Similarity=0.408  Sum_probs=129.0

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCC-CC--Cccc---EEEEEecCHHHHHHHHHcccccCCeEEE
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRA-TG--RARG---FGFVVFADPAVAERVIMDKHMIDGRTVE   76 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~-tg--~srG---~aFVeF~~~e~A~kAl~~~~~i~Gr~I~   76 (522)
                      .-+++|||++||++++|++|...|..||.|. |......+ .+  -++|   |+|+.|+++..+++.|..-.+ ...+.-
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~-~~~~~y  334 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE-GEGNYY  334 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh-cccceE
Confidence            4578999999999999999999999999874 44442111 11  2467   999999999998887722222 222333


Q ss_pred             EeecCCCcccccc-------ccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHh-hcCCeeEEEEEecCCCCCcce
Q 009920           77 AKKAVPRDDQNML-------NRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFD-QFGTITDVVVMYDHNTQRPRG  148 (522)
Q Consensus        77 V~~a~~k~~~~~~-------~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~-~fG~I~~v~i~~d~~tg~~rG  148 (522)
                      ++...++.+.+..       .....-.......++.+||||+.||..++.++|..+|+ .||.|.-+-|-+|++-+.|||
T Consensus       335 f~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkG  414 (520)
T KOG0129|consen  335 FKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKG  414 (520)
T ss_pred             EEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCC
Confidence            3333332222211       11111122344567889999999999999999999998 699999999999999999999


Q ss_pred             EEEEEecCHHHHHHHHHhcCCccC----CeEEEEEEcC
Q 009920          149 FGFITYDSEEAVDRVLHKTFHELN----GKMVEVKRAV  182 (522)
Q Consensus       149 ~aFVeF~s~e~A~~Al~~~~~~l~----Gr~I~V~~a~  182 (522)
                      -+-|+|.+..+-.+||++-..+|+    .|+|+|+.-.
T Consensus       415 aGRVtFsnqqsYi~AIsarFvql~h~d~~KRVEIkPYv  452 (520)
T KOG0129|consen  415 AGRVTFSNQQAYIKAISARFVQLDHTDIDKRVEIKPYV  452 (520)
T ss_pred             cceeeecccHHHHHHHhhheEEEeccccceeeeeccee
Confidence            999999999999999997654333    3677776543

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

Probab=99.50  E-value=5.7e-13  Score=133.91  Aligned_cols=177  Identities=15%  Similarity=0.327  Sum_probs=135.0

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEE--------EEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCe
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVE--------AVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGR   73 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~--------v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr   73 (522)
                      -++.|||.|||.++|.+|+.++|++||.|..        |+|.++.. |+.||=|.|.|...|.++.|+  ++...+.++
T Consensus       133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~  211 (382)
T KOG1548|consen  133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDELRGK  211 (382)
T ss_pred             cCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCcccccCc
Confidence            3456999999999999999999999997743        67888865 999999999999999999999  999999999


Q ss_pred             EEEEeecCCCcccc--c-------------cccc-------cCCCCCCCCCCCcceeEecCCCC----CCC-------HH
Q 009920           74 TVEAKKAVPRDDQN--M-------------LNRN-------TSSIHSSPGPGRTKKIFVGGLAS----TVT-------ES  120 (522)
Q Consensus        74 ~I~V~~a~~k~~~~--~-------------~~~~-------~~~~~~~~~~~~~~~LfVgnLp~----~vt-------ee  120 (522)
                      +|+|+.|+-+..-.  .             ....       .............++|.|.|+=.    ..+       ++
T Consensus       212 ~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlke  291 (382)
T KOG1548|consen  212 KLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKE  291 (382)
T ss_pred             EEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHHH
Confidence            99998874321100  0             0000       00001122234457888888721    222       36


Q ss_pred             HHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCCC
Q 009920          121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPKE  185 (522)
Q Consensus       121 dL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk~  185 (522)
                      ||++-+++||.|..|.|.-.    .|.|.+.|.|.+.++|+.||+.|+ ..++||+|..+...-+.
T Consensus       292 dl~eec~K~G~v~~vvv~d~----hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~t  353 (382)
T KOG1548|consen  292 DLTEECEKFGQVRKVVVYDR----HPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGKT  353 (382)
T ss_pred             HHHHHHHHhCCcceEEEecc----CCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCcc
Confidence            77788899999999988744    357899999999999999999999 89999999988765443

>PF00076 RRM_1: RNA recognition motif

Probab=99.47  E-value=2.5e-13  Score=107.40  Aligned_cols=69  Identities=30%  Similarity=0.756  Sum_probs=65.2

Q ss_pred             eEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEE
Q 009920          108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVE  177 (522)
Q Consensus       108 LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~  177 (522)
                      |||+|||.++|+++|+++|++||.|..+.++.+ .+++.+++|||+|+++++|++|++.++ ..+++++|+
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 668899999999999999999999777 899999885

(a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.46  E-value=1.6e-13  Score=132.31  Aligned_cols=81  Identities=27%  Similarity=0.468  Sum_probs=78.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .|+++|.|.|||.+++|++|+++|.+||.|..|.|.+|++|+.+||||||.|.+.++|.+||  ++++-++.-.|.|+|+
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws  266 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS  266 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec
Confidence            46788999999999999999999999999999999999999999999999999999999999  9999999999999999


Q ss_pred             CCC
Q 009920           81 VPR   83 (522)
Q Consensus        81 ~~k   83 (522)
                      +|+
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            886

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.45  E-value=2.8e-13  Score=108.09  Aligned_cols=68  Identities=34%  Similarity=0.729  Sum_probs=62.2

Q ss_pred             EEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEE
Q 009920            8 LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVE   76 (522)
Q Consensus         8 LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~   76 (522)
                      |||+|||+++++++|+++|+++|.|..++++++++ ++.+++|||+|.++++|++|+  .+++.|++++|+
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 899999999999999999999  556899999885

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.43  E-value=5.4e-13  Score=133.24  Aligned_cols=87  Identities=22%  Similarity=0.536  Sum_probs=78.6

Q ss_pred             CCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEE
Q 009920          100 PGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEV  178 (522)
Q Consensus       100 ~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V  178 (522)
                      +.....++|+|.|||+...|.||+.+|++||+|.+|+|+.+.  .-+|||+||+|++.+||++|.++++ ..++||+|+|
T Consensus        91 ~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEV  168 (376)
T KOG0125|consen   91 SSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEV  168 (376)
T ss_pred             CCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEE
Confidence            344567899999999999999999999999999999999874  5689999999999999999999999 8999999999


Q ss_pred             EEcCCCCCCC
Q 009920          179 KRAVPKEFSP  188 (522)
Q Consensus       179 ~~a~pk~~~~  188 (522)
                      ..|.++-..+
T Consensus       169 n~ATarV~n~  178 (376)
T KOG0125|consen  169 NNATARVHNK  178 (376)
T ss_pred             eccchhhccC
Confidence            9999875443

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.43  E-value=6.6e-13  Score=131.35  Aligned_cols=78  Identities=21%  Similarity=0.337  Sum_probs=72.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      +..++|||+|||+++||++|+++|+.||+|++|+|++++.   .++||||+|.++++|++|| +++..|.+++|+|.++.
T Consensus         2 ~~~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~   78 (260)
T PLN03120          2 MQVRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAE   78 (260)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEecc
Confidence            3478999999999999999999999999999999999864   5799999999999999999 99999999999999976


Q ss_pred             CC
Q 009920           82 PR   83 (522)
Q Consensus        82 ~k   83 (522)
                      ..
T Consensus        79 ~~   80 (260)
T PLN03120         79 DY   80 (260)
T ss_pred             CC
Confidence            54

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.42  E-value=6.2e-13  Score=128.26  Aligned_cols=83  Identities=24%  Similarity=0.451  Sum_probs=79.2

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+..+|-|.||+++++|+||+++|.+||.|.+|.|.+|++|+.+||||||+|.++++|.+||+.++ +-++.-.|.|+|
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEw  265 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEW  265 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEe
Confidence            3467889999999999999999999999999999999999999999999999999999999999999 889999999999


Q ss_pred             cCCC
Q 009920          181 AVPK  184 (522)
Q Consensus       181 a~pk  184 (522)
                      ++|+
T Consensus       266 skP~  269 (270)
T KOG0122|consen  266 SKPS  269 (270)
T ss_pred             cCCC
Confidence            9986

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

Probab=99.41  E-value=5.5e-12  Score=129.04  Aligned_cols=170  Identities=15%  Similarity=0.247  Sum_probs=132.3

Q ss_pred             CcEEEECCCCCC-CCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            5 LGKLFIGGISWD-TDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         5 ~r~LfVgnLP~~-~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      .+.|-|.||-.+ +|++.|..+|.-||+|..|+|+.++.+     -|.|+|.|...|+.|+  ++++.|.+++|+|..++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd-----~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKD-----NALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCc-----ceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            478889999887 899999999999999999999998653     7999999999999999  99999999999998876


Q ss_pred             CCccccccccccC----------CCCC---------CCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCC
Q 009920           82 PRDDQNMLNRNTS----------SIHS---------SPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHN  142 (522)
Q Consensus        82 ~k~~~~~~~~~~~----------~~~~---------~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~  142 (522)
                      ...-+...+..+.          ..+.         .....++.+|++.|+|.+++||||++.|..-|-+++......  
T Consensus       372 H~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~--  449 (492)
T KOG1190|consen  372 HTNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQ--  449 (492)
T ss_pred             CccccCCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecC--
Confidence            5543322211110          1111         112256789999999999999999999998877654433322  


Q ss_pred             CCCcceEEEEEecCHHHHHHHHHhcC-CccCCe-EEEEEEcCC
Q 009920          143 TQRPRGFGFITYDSEEAVDRVLHKTF-HELNGK-MVEVKRAVP  183 (522)
Q Consensus       143 tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr-~I~V~~a~p  183 (522)
                        +.+-+|++++++.|+|..|+..++ +.+... .++|++++.
T Consensus       450 --kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks  490 (492)
T KOG1190|consen  450 --KDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKS  490 (492)
T ss_pred             --CCcceeecccCChhHhhhhccccccccCCCCceEEEEeecc
Confidence              223399999999999999988887 777765 899998763

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.40  E-value=2.3e-12  Score=125.67  Aligned_cols=80  Identities=18%  Similarity=0.188  Sum_probs=73.8

Q ss_pred             CCCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEee
Q 009920            1 MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKK   79 (522)
Q Consensus         1 me~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~   79 (522)
                      |..+..+|||+||++++||++|++||+.||+|.+|+|+++.   +.+++|||+|+++++|+.|| +++..|.+++|.|..
T Consensus         1 m~~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~   77 (243)
T PLN03121          1 MYPGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVLLSGATIVDQRVCITR   77 (243)
T ss_pred             CCCCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEe
Confidence            77888999999999999999999999999999999999984   45689999999999999999 999999999999988


Q ss_pred             cCCC
Q 009920           80 AVPR   83 (522)
Q Consensus        80 a~~k   83 (522)
                      ....
T Consensus        78 ~~~y   81 (243)
T PLN03121         78 WGQY   81 (243)
T ss_pred             Cccc
Confidence            7643

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

Probab=99.40  E-value=5e-12  Score=127.57  Aligned_cols=179  Identities=16%  Similarity=0.310  Sum_probs=135.1

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      .-.+|||..+++|.+|+||+.+|+.||+|+.|.+.+++....+|||+||||.+......|+  ||-..+.|..|+|-++.
T Consensus       209 ~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  209 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             hhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccccc
Confidence            3468999999999999999999999999999999999999999999999999999999999  89899999999886654


Q ss_pred             CCcccccc-------------------------------------------c----------------------------
Q 009920           82 PRDDQNML-------------------------------------------N----------------------------   90 (522)
Q Consensus        82 ~k~~~~~~-------------------------------------------~----------------------------   90 (522)
                      ........                                           +                            
T Consensus       289 TPP~aLl~Pat~s~~P~aaaVAaAAaTAKi~A~eAvAg~avlg~~G~~~~vSpA~~aa~p~~~l~qa~~a~~~pgvi~~v  368 (544)
T KOG0124|consen  289 TPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGSAVLGTVGAPGLVSPAPRAAQPLGTLPQAVMAAQAPGVITGV  368 (544)
T ss_pred             CCCchhcCCCCcccCchHHHHHHHHHHHHHHHHHHhccCCcccccCCccccCccccccCCCCCccccchhccCCceeccC
Confidence            33110000                                           0                            


Q ss_pred             ---ccc--------------------------------C--------------CCCC--------------CCCCCCcce
Q 009920           91 ---RNT--------------------------------S--------------SIHS--------------SPGPGRTKK  107 (522)
Q Consensus        91 ---~~~--------------------------------~--------------~~~~--------------~~~~~~~~~  107 (522)
                         ++.                                .              ..+.              .-...+++.
T Consensus       369 tP~~P~iP~~i~p~g~v~P~LA~ppT~g~L~kkkeKe~eelqpkl~~~~~L~~QE~msI~G~sARhlvMqkLmR~~~S~V  448 (544)
T KOG0124|consen  369 TPARPPIPVTIPPVGVVNPILASPPTLGLLEKKKEKEEEELQPKLERPEMLSEQEHMSISGSSARHLVMQKLMRKQESTV  448 (544)
T ss_pred             CCCCCCCCccCCCcceechhhcCCCchhhcchhhhhhHhhhcccccCHHHhhhhhCccccCccHHHHHHHHHhccccCcE
Confidence               000                                0              0000              001122345


Q ss_pred             eEecCC--CCCCCH---HHHHHHHhhcCCeeEEEEEecCCCCCc----ceEEEEEecCHHHHHHHHHhcC-CccCCeEEE
Q 009920          108 IFVGGL--ASTVTE---SDFKKYFDQFGTITDVVVMYDHNTQRP----RGFGFITYDSEEAVDRVLHKTF-HELNGKMVE  177 (522)
Q Consensus       108 LfVgnL--p~~vte---edL~~~F~~fG~I~~v~i~~d~~tg~~----rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~  177 (522)
                      |.++|.  |.+++|   .+|++.+.+||.|.+|.|...+.+..-    -=-.||+|....++.+|++.++ ..|.||+|.
T Consensus       449 ivLRNMV~P~DiDe~LegEi~EECgKfG~V~rViI~nekq~e~edaeiiVKIFVefS~~~e~~rak~ALdGRfFgGr~Vv  528 (544)
T KOG0124|consen  449 IVLRNMVDPKDIDEDLEGEITEECGKFGAVNRVIIYNEKQGEEEDAEIIVKIFVEFSIASETHRAKQALDGRFFGGRKVV  528 (544)
T ss_pred             EEEeccCChhhhhhHHHHHHHHHHhcccceeEEEEEecccccccchhhhheeeeeechhhHHHHHHHhhccceecCceee
Confidence            777776  555554   688999999999999999887765421    1136999999999999999999 889999987


Q ss_pred             EEEcC
Q 009920          178 VKRAV  182 (522)
Q Consensus       178 V~~a~  182 (522)
                      .+.-.
T Consensus       529 AE~YD  533 (544)
T KOG0124|consen  529 AEVYD  533 (544)
T ss_pred             hhhhh
Confidence            76543

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.40  E-value=1.2e-12  Score=104.44  Aligned_cols=69  Identities=28%  Similarity=0.685  Sum_probs=64.4

Q ss_pred             eEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEE
Q 009920          108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVE  177 (522)
Q Consensus       108 LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~  177 (522)
                      |+|.|||++++++||+++|+.+|.|.++.+..+++ ++++++|||+|.++++|++|++.++ ..|+|++|+
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            79999999999999999999999999999999988 8999999999999999999999999 899999985

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.40  E-value=6.6e-13  Score=122.36  Aligned_cols=76  Identities=28%  Similarity=0.518  Sum_probs=70.5

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCC
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~   82 (522)
                      .++|||+||+.++++.||+.+|.+||+|.+|+|.+++.     |||||||+++.+|++|+  |++..|++..|.|+.+.-
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPP-----GfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPP-----GFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCC-----CceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            68999999999999999999999999999999998764     89999999999999999  999999999999998865


Q ss_pred             Ccc
Q 009920           83 RDD   85 (522)
Q Consensus        83 k~~   85 (522)
                      +..
T Consensus        85 ~~r   87 (195)
T KOG0107|consen   85 RPR   87 (195)
T ss_pred             Ccc
Confidence            543

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.37  E-value=9.2e-13  Score=115.64  Aligned_cols=82  Identities=23%  Similarity=0.375  Sum_probs=76.9

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      +++++|||+||+.-++||+|.|+|+++|+|..|.|=.|+.+.++-|||||+|.+.++|+.||  .+.+.++.+.|.|.|.
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            57899999999999999999999999999999999999999999999999999999999999  9999999999999887


Q ss_pred             CCCc
Q 009920           81 VPRD   84 (522)
Q Consensus        81 ~~k~   84 (522)
                      .--.
T Consensus       114 ~GF~  117 (153)
T KOG0121|consen  114 AGFV  117 (153)
T ss_pred             ccch
Confidence            5443

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

Probab=99.37  E-value=9e-12  Score=118.75  Aligned_cols=160  Identities=14%  Similarity=0.275  Sum_probs=111.2

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEee-cCCCCCcccEEEEEecCHHHHHHHH--HcccccC---CeEEEEe
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMR-DRATGRARGFGFVVFADPAVAERVI--MDKHMID---GRTVEAK   78 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~-d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~---Gr~I~V~   78 (522)
                      -|+|||.+||.|+...||..+|..|--.+.+.|.. ++.....+-+|||.|.+..+|.+|+  +++..++   +..|.|+
T Consensus        34 VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiE  113 (284)
T KOG1457|consen   34 VRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIE  113 (284)
T ss_pred             cceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEee
Confidence            69999999999999999999999986555555533 3433345689999999999999999  8888876   5677776


Q ss_pred             ecCCCcc--cccccccc-------------------CCCCC-----------------C---------------------
Q 009920           79 KAVPRDD--QNMLNRNT-------------------SSIHS-----------------S---------------------   99 (522)
Q Consensus        79 ~a~~k~~--~~~~~~~~-------------------~~~~~-----------------~---------------------   99 (522)
                      .++...+  +.+....+                   ...+.                 .                     
T Consensus       114 lAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P~a  193 (284)
T KOG1457|consen  114 LAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAPSA  193 (284)
T ss_pred             ehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCCcc
Confidence            6643322  11110000                   00000                 0                     


Q ss_pred             -----------CCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC
Q 009920          100 -----------PGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF  168 (522)
Q Consensus       100 -----------~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~  168 (522)
                                 .......+|||.||..+|||++|+.+|+.|--...++|...  .+  ...|||+|++.+.|..|+..+.
T Consensus       194 ~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~g--~~vaf~~~~~~~~at~am~~lq  269 (284)
T KOG1457|consen  194 NAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--GG--MPVAFADFEEIEQATDAMNHLQ  269 (284)
T ss_pred             cchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--CC--cceEeecHHHHHHHHHHHHHhh
Confidence                       00011247999999999999999999999976666666432  12  3378999999888888885443

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.36  E-value=3.9e-12  Score=125.92  Aligned_cols=78  Identities=17%  Similarity=0.282  Sum_probs=71.3

Q ss_pred             cceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcCCC
Q 009920          105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPK  184 (522)
Q Consensus       105 ~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~pk  184 (522)
                      .++|||+|||+.+||++|+++|+.||+|++|.|+.|++   +++||||+|+++++|++||.+++..|.+++|+|+++..-
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   478999999999999999976669999999999998754


Q ss_pred             C
Q 009920          185 E  185 (522)
Q Consensus       185 ~  185 (522)
                      +
T Consensus        81 ~   81 (260)
T PLN03120         81 Q   81 (260)
T ss_pred             C
Confidence            3

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.35  E-value=4.9e-12  Score=135.19  Aligned_cols=180  Identities=18%  Similarity=0.360  Sum_probs=137.1

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      ..+++||.+||...++++++|+++.||++....++++..++-+++|||.+|.++.....|+  +++..+.+++|.|..|.
T Consensus       288 ~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~  367 (500)
T KOG0120|consen  288 SPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAI  367 (500)
T ss_pred             ccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhh
Confidence            4578999999999999999999999999999999999999999999999999999999999  99999999999998886


Q ss_pred             CCccccccccccCC--C---CC---CCCCCCcceeEecCC--CCCC-CH-------HHHHHHHhhcCCeeEEEEEecCC-
Q 009920           82 PRDDQNMLNRNTSS--I---HS---SPGPGRTKKIFVGGL--ASTV-TE-------SDFKKYFDQFGTITDVVVMYDHN-  142 (522)
Q Consensus        82 ~k~~~~~~~~~~~~--~---~~---~~~~~~~~~LfVgnL--p~~v-te-------edL~~~F~~fG~I~~v~i~~d~~-  142 (522)
                      ..........+...  .   ..   .....++..|.+.|+  |.++ .+       |+|+..+.+||.|..|.|.++-. 
T Consensus       368 ~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~  447 (500)
T KOG0120|consen  368 VGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPD  447 (500)
T ss_pred             ccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCC
Confidence            65443333222100  0   00   111223344444443  1121 22       35566667899999999988722 


Q ss_pred             --CCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCC
Q 009920          143 --TQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVP  183 (522)
Q Consensus       143 --tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~p  183 (522)
                        ..-..|-.||||.+.+++++|++.|. .++++|.|...+-.+
T Consensus       448 ~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  448 ENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             CCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence              22335778999999999999999999 899999999888654

>smart00362 RRM_2 RNA recognition motif

Probab=99.34  E-value=5.7e-12  Score=98.38  Aligned_cols=70  Identities=36%  Similarity=0.696  Sum_probs=64.8

Q ss_pred             EEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEe
Q 009920            7 KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAK   78 (522)
Q Consensus         7 ~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~   78 (522)
                      +|||.|||.++++++|+++|++||+|.++++++++  +.++++|||+|.++++|++|+  +++..+.+++|+|+
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            58999999999999999999999999999999876  678999999999999999999  77789999998873

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.34  E-value=1.6e-12  Score=122.60  Aligned_cols=83  Identities=23%  Similarity=0.469  Sum_probs=78.8

Q ss_pred             CCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEE
Q 009920          100 PGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEV  178 (522)
Q Consensus       100 ~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V  178 (522)
                      +..+....|.|-||.+.++.++|+.+|++||.|-+|.|+.|+.|.+++|||||.|.+..+|+.|++.|+ ..|+|+.|.|
T Consensus         8 Pdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrV   87 (256)
T KOG4207|consen    8 PDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRV   87 (256)
T ss_pred             CCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeee
Confidence            344567899999999999999999999999999999999999999999999999999999999999999 8999999999


Q ss_pred             EEcC
Q 009920          179 KRAV  182 (522)
Q Consensus       179 ~~a~  182 (522)
                      ++|+
T Consensus        88 q~ar   91 (256)
T KOG4207|consen   88 QMAR   91 (256)
T ss_pred             hhhh
Confidence            9987

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.33  E-value=3e-12  Score=112.49  Aligned_cols=83  Identities=20%  Similarity=0.390  Sum_probs=77.8

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ..+++|||+||++.++||+|.++|+++|+|+.|.+-.|+.+..+-|||||+|.+.++|+.||+.++ ..|+.++|.|+|.
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            357899999999999999999999999999999999999999999999999999999999999988 8999999999997


Q ss_pred             CCCC
Q 009920          182 VPKE  185 (522)
Q Consensus       182 ~pk~  185 (522)
                      .--.
T Consensus       114 ~GF~  117 (153)
T KOG0121|consen  114 AGFV  117 (153)
T ss_pred             ccch
Confidence            6443

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.32  E-value=4.9e-12  Score=125.10  Aligned_cols=81  Identities=26%  Similarity=0.554  Sum_probs=75.3

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ..-+||||.-|+.+++|.+|++.|++||+|+.|.|++++.|++++|||||+|+++.+..+|.  .+...|+++.|.|..-
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            45689999999999999999999999999999999999999999999999999999999999  7889999999999765


Q ss_pred             CCC
Q 009920           81 VPR   83 (522)
Q Consensus        81 ~~k   83 (522)
                      ..+
T Consensus       179 RgR  181 (335)
T KOG0113|consen  179 RGR  181 (335)
T ss_pred             ccc
Confidence            433

>PLN03213 repressor of silencing 3; Provisional

Probab=99.32  E-value=1.8e-12  Score=134.92  Aligned_cols=76  Identities=21%  Similarity=0.387  Sum_probs=69.9

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCH--HHHHHHH--HcccccCCeEEEEee
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADP--AVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~--e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      ...+|||+||++++++++|+++|.+||.|.+|.|++  +|+  ||||||+|.+.  +++++||  +++.+++|+.|+|..
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            457899999999999999999999999999999994  456  99999999987  6899999  999999999999999


Q ss_pred             cCCC
Q 009920           80 AVPR   83 (522)
Q Consensus        80 a~~k   83 (522)
                      |++.
T Consensus        85 AKP~   88 (759)
T PLN03213         85 AKEH   88 (759)
T ss_pred             ccHH
Confidence            9775

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

Probab=99.31  E-value=1.5e-11  Score=127.25  Aligned_cols=119  Identities=22%  Similarity=0.411  Sum_probs=92.9

Q ss_pred             cCHHHHHHHHHcccccCCeEEEEeecCCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeE
Q 009920           55 ADPAVAERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITD  134 (522)
Q Consensus        55 ~~~e~A~kAl~~~~~i~Gr~I~V~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~  134 (522)
                      .+.|+|.++|+..+   +..|+|+..+.+..-....      -..+.+...+.|||+.||.++.|+||.-+|++.|+|-+
T Consensus        42 ~~~eaal~al~E~t---gy~l~ve~gqrk~ggPpP~------weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~e  112 (506)
T KOG0117|consen   42 QSEEAALKALLERT---GYTLVVENGQRKYGGPPPG------WEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYE  112 (506)
T ss_pred             ccHHHHHHHHHHhc---CceEEEeccccccCCCCCc------ccCCCCCCCceEEecCCCccccchhhHHHHHhccceee
Confidence            34677778874433   4567776655443221111      22223367889999999999999999999999999999


Q ss_pred             EEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-Ccc-CCeEEEEEEcC
Q 009920          135 VVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HEL-NGKMVEVKRAV  182 (522)
Q Consensus       135 v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l-~Gr~I~V~~a~  182 (522)
                      ++||+|+.++.+||||||+|.+.++|++||+.++ ++| .||.|.|+.+.
T Consensus       113 lRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Sv  162 (506)
T KOG0117|consen  113 LRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSV  162 (506)
T ss_pred             EEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEee
Confidence            9999999999999999999999999999999988 655 57888877654

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.30  E-value=1e-11  Score=120.99  Aligned_cols=79  Identities=34%  Similarity=0.720  Sum_probs=76.2

Q ss_pred             cceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCC
Q 009920          105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVP  183 (522)
Q Consensus       105 ~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~p  183 (522)
                      .++|||+|||..+|+++|+++|.+||.|..|.|+.|+.+++++|+|||+|.++++|+.|++.++ ..|.+++|.|.++.+
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            6899999999999999999999999999999999999999999999999999999999999999 899999999999654

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.30  E-value=2.3e-12  Score=122.36  Aligned_cols=87  Identities=32%  Similarity=0.621  Sum_probs=81.9

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      .+.++|||++|..+|+|.-|...|-+||.|++|.|+.|.++++.|||+||+|+..|+|.+||..|+ .+|.||.|+|.+|
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            456799999999999999999999999999999999999999999999999999999999999999 8999999999999


Q ss_pred             CCCCCCCC
Q 009920          182 VPKEFSPG  189 (522)
Q Consensus       182 ~pk~~~~~  189 (522)
                      +|.+.+.+
T Consensus        88 kP~kikeg   95 (298)
T KOG0111|consen   88 KPEKIKEG   95 (298)
T ss_pred             CCccccCC
Confidence            99875543

>smart00360 RRM RNA recognition motif

Probab=99.30  E-value=1e-11  Score=96.52  Aligned_cols=69  Identities=35%  Similarity=0.739  Sum_probs=64.3

Q ss_pred             ECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEe
Q 009920           10 IGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAK   78 (522)
Q Consensus        10 VgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~   78 (522)
                      |.|||+++++++|+++|++||+|.++.+.+++.+++++++|||+|.+.++|++|+  +++..+.+++|.|+
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            6799999999999999999999999999998888899999999999999999999  77788899988773

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.29  E-value=3.1e-12  Score=120.62  Aligned_cols=78  Identities=35%  Similarity=0.608  Sum_probs=74.7

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      ....|.|-||.+.++.++|+.+|++||.|.+|.|.+|+.|..++|||||.|.++.+|++||  |+..+|++++|.|+.|.
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            4678999999999999999999999999999999999999999999999999999999999  99999999999998764

>smart00362 RRM_2 RNA recognition motif

Probab=99.28  E-value=1.9e-11  Score=95.41  Aligned_cols=71  Identities=34%  Similarity=0.687  Sum_probs=66.1

Q ss_pred             eeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       107 ~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      +|+|.+||..+++++|+++|++||+|+++.++.++  +.++++|||+|.+.++|++|++.++ ..+.+++|+|+
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            58999999999999999999999999999999876  6788999999999999999999988 89999999874

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.28  E-value=6.5e-12  Score=125.60  Aligned_cols=82  Identities=26%  Similarity=0.577  Sum_probs=75.4

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      .-++|+|.|||+..-|.||+..|++||+|.+|.|+.+.  .-||||+||+|++++||++|-  +++..|.||+|+|..+.
T Consensus        95 ~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~AT  172 (376)
T KOG0125|consen   95 TPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNAT  172 (376)
T ss_pred             CCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccc
Confidence            35799999999999999999999999999999999985  469999999999999999998  99999999999999998


Q ss_pred             CCcccc
Q 009920           82 PRDDQN   87 (522)
Q Consensus        82 ~k~~~~   87 (522)
                      .+...+
T Consensus       173 arV~n~  178 (376)
T KOG0125|consen  173 ARVHNK  178 (376)
T ss_pred             hhhccC
Confidence            875443

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.28  E-value=3.2e-12  Score=135.73  Aligned_cols=80  Identities=35%  Similarity=0.657  Sum_probs=76.6

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCCC
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVPR   83 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~k   83 (522)
                      +.|||+|||++++|++|.++|++.|.|.+++++.|++|+++|||+|++|.+.++|++|+  ++..++.+|+|+|.++...
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  9999999999999998665


Q ss_pred             cc
Q 009920           84 DD   85 (522)
Q Consensus        84 ~~   85 (522)
                      +.
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            44

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.28  E-value=8.5e-11  Score=121.17  Aligned_cols=71  Identities=18%  Similarity=0.292  Sum_probs=65.3

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ++|||+|||+++||+.|++-|..||.|..++|+..   +++||  .|.|.++++|++|+.+++ ..|+||.|+|++.
T Consensus       537 ~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~---GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  537 CQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMEN---GKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             cEEEEecCCccccHHHHHHHHHhccceehhhhhcc---CCccc--eEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            67999999999999999999999999999999644   67776  899999999999999999 8999999999873

>smart00360 RRM RNA recognition motif

Probab=99.28  E-value=1.9e-11  Score=94.94  Aligned_cols=70  Identities=36%  Similarity=0.721  Sum_probs=65.9

Q ss_pred             ecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          110 VGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       110 VgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      |.+||..+++++|+++|++||.|.++.+..++.+.+++++|||+|.+.++|++|++.++ ..+.+++|+|+
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            57899999999999999999999999999998889999999999999999999999998 88999999874

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.27  E-value=1.1e-11  Score=114.39  Aligned_cols=77  Identities=21%  Similarity=0.513  Sum_probs=70.4

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      ..++|||+||+..+++.||+.+|..||+|..|.|...     +.|||||||+++.+|+.|+..|+ ++|+|..|.|++..
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            4689999999999999999999999999999998764     46899999999999999999999 89999999999987


Q ss_pred             CCC
Q 009920          183 PKE  185 (522)
Q Consensus       183 pk~  185 (522)
                      -+.
T Consensus        84 G~~   86 (195)
T KOG0107|consen   84 GRP   86 (195)
T ss_pred             CCc
Confidence            443

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=99.26  E-value=1.7e-11  Score=131.15  Aligned_cols=181  Identities=23%  Similarity=0.413  Sum_probs=145.4

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhcc------------CCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-Hccc
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRY------------GEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKH   68 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~------------G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~   68 (522)
                      ....++++|.+||..++|+.+..+|..-            -.|+.+.|-..+      .||||+|.+.++|..|+ ++..
T Consensus       172 t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~~------nfa~ie~~s~~~at~~~~~~~~  245 (500)
T KOG0120|consen  172 TRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLEK------NFAFIEFRSISEATEAMALDGI  245 (500)
T ss_pred             hhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecccc------cceeEEecCCCchhhhhcccch
Confidence            3567899999999999999999999653            236666665544      49999999999999999 8888


Q ss_pred             ccCCeEEEEeecCCCccccccccc-------cCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecC
Q 009920           69 MIDGRTVEAKKAVPRDDQNMLNRN-------TSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDH  141 (522)
Q Consensus        69 ~i~Gr~I~V~~a~~k~~~~~~~~~-------~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~  141 (522)
                      .+.++.+.+...............       .............++|||++||..+++++++++.+.||+++...++.|.
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            889988888655433222111100       1111122334566899999999999999999999999999999999999


Q ss_pred             CCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCCCCCC
Q 009920          142 NTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPKEFSP  188 (522)
Q Consensus       142 ~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk~~~~  188 (522)
                      .++.+|+|||.+|.+......|+.-++ .++.+++|.|..|.+.....
T Consensus       326 ~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~  373 (500)
T KOG0120|consen  326 ATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNA  373 (500)
T ss_pred             ccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhc
Confidence            999999999999999999999999999 89999999999998765543

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

Probab=99.25  E-value=1.6e-11  Score=125.65  Aligned_cols=171  Identities=11%  Similarity=0.221  Sum_probs=122.8

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH----HcccccCCeEEEE
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI----MDKHMIDGRTVEA   77 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl----~~~~~i~Gr~I~V   77 (522)
                      ...++.|.|+||||+++|+||.+++.+||.|+++.+++.++      .|||||+|++.|...+    .--..+.+++|.|
T Consensus        25 ~~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGkn------QAflem~d~~sAvtmv~~y~~~~p~lr~~~~yi   98 (492)
T KOG1190|consen   25 AEPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGKN------QAFLEMADEESAVTMVNYYTSVTPVLRGQPIYI   98 (492)
T ss_pred             cCCcceeEeccCCccccHHHHHHhcccccceeeeeeeccch------hhhhhhcchhhhhheeecccccCccccCcceee
Confidence            34678999999999999999999999999999999988765      8999999999998865    2223566777777


Q ss_pred             eecCCCccccccc--------------------ccc----CCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCee
Q 009920           78 KKAVPRDDQNMLN--------------------RNT----SSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTIT  133 (522)
Q Consensus        78 ~~a~~k~~~~~~~--------------------~~~----~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~  133 (522)
                      .++..++-.....                    .+.    ......+.+...-+++|.++-+.++-|-|.++|++||.|.
T Consensus        99 q~sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~Vl  178 (492)
T KOG1190|consen   99 QYSNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVL  178 (492)
T ss_pred             hhhhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeE
Confidence            6553221111000                    000    0001122333456789999999999999999999999998


Q ss_pred             EEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCC--eEEEEEEcC
Q 009920          134 DVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNG--KMVEVKRAV  182 (522)
Q Consensus       134 ~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~G--r~I~V~~a~  182 (522)
                      +|.-....+  ..  .|+|+|.+.+.|+.|...++ ..|-.  +.|+|++++
T Consensus       179 KIiTF~Knn--~F--QALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sk  226 (492)
T KOG1190|consen  179 KIITFTKNN--GF--QALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSK  226 (492)
T ss_pred             EEEEEeccc--ch--hhhhhccchhhHHHHHHhccCCcccCceeEEEeehhh
Confidence            876554322  12  58999999999999998888 54443  344555443

>PLN03213 repressor of silencing 3; Provisional

Probab=99.23  E-value=2.8e-11  Score=126.17  Aligned_cols=78  Identities=22%  Similarity=0.463  Sum_probs=71.3

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCH--HHHHHHHHhcC-CccCCeEEEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE--EAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~--e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      ....+|||+||++.++++||+++|..||.|++|.|+  ++|+  ||||||+|.+.  +++++||+.++ .++.|+.|+|.
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            456799999999999999999999999999999999  4456  89999999987  78999999999 89999999999


Q ss_pred             EcCCC
Q 009920          180 RAVPK  184 (522)
Q Consensus       180 ~a~pk  184 (522)
                      .|+|.
T Consensus        84 KAKP~   88 (759)
T PLN03213         84 KAKEH   88 (759)
T ss_pred             eccHH
Confidence            99874

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=99.23  E-value=2.8e-11  Score=122.94  Aligned_cols=179  Identities=20%  Similarity=0.303  Sum_probs=132.5

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      ++...|..++|||..++.+|..+|+-.-.+.-.+.+.....++-.+++.|.|.|+|.-+.|+ .+++.+..|.|+|.++.
T Consensus        58 ~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryievYka~  137 (508)
T KOG1365|consen   58 DDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYIEVYKAT  137 (508)
T ss_pred             CcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHhhhhhccCCceeeeccC
Confidence            45666788999999999999999986643333333333334677799999999999999999 89999999999999888


Q ss_pred             CCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhc----CCeeEEEEEecCCCCCcceEEEEEecCH
Q 009920           82 PRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQF----GTITDVVVMYDHNTQRPRGFGFITYDSE  157 (522)
Q Consensus        82 ~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~f----G~I~~v~i~~d~~tg~~rG~aFVeF~s~  157 (522)
                      ..+-.....-.......-.....--.|-+++||+++++.|+.++|.+.    +.++.|-+++.+ .+++.|-|||.|..+
T Consensus       138 ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~e  216 (508)
T KOG1365|consen  138 GEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACE  216 (508)
T ss_pred             chhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCH
Confidence            765433221111111111112233467889999999999999999743    234455555554 489999999999999


Q ss_pred             HHHHHHHHhcCCccCCeEEEEEEcC
Q 009920          158 EAVDRVLHKTFHELNGKMVEVKRAV  182 (522)
Q Consensus       158 e~A~~Al~~~~~~l~Gr~I~V~~a~  182 (522)
                      ++|++||.++...|.-|.|+|.++.
T Consensus       217 e~aq~aL~khrq~iGqRYIElFRST  241 (508)
T KOG1365|consen  217 EDAQFALRKHRQNIGQRYIELFRST  241 (508)
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHh
Confidence            9999999998888888888776554

>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=99.23  E-value=6e-11  Score=93.02  Aligned_cols=72  Identities=36%  Similarity=0.703  Sum_probs=66.0

Q ss_pred             EEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            7 KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         7 ~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      +|+|.+||+++++++|+++|+.+|+|..+.+++++.+ +.+++|||+|.++++|+.|+  ++...+++++|.|.+
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            5899999999999999999999999999999988765 78999999999999999999  777779999998863

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).

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

Probab=99.22  E-value=2e-11  Score=113.33  Aligned_cols=80  Identities=26%  Similarity=0.473  Sum_probs=77.1

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ....+|||+||+..++++.|.++|-+.|+|+++.|++|+.++..+|||||||.++|+|+-|++.++ .+|-||+|+|..+
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            456799999999999999999999999999999999999999999999999999999999999999 7999999999999


Q ss_pred             C
Q 009920          182 V  182 (522)
Q Consensus       182 ~  182 (522)
                      .
T Consensus        87 s   87 (203)
T KOG0131|consen   87 S   87 (203)
T ss_pred             c
Confidence            8

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

Probab=99.21  E-value=6e-11  Score=110.30  Aligned_cols=76  Identities=17%  Similarity=0.441  Sum_probs=68.6

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      .+++|||+|||.++.|.||+++|.+||.|.+|.+...   ..+..||||+|+++.+|+.||.--+ -++++.+|.|+++.
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            4679999999999999999999999999999998654   3445699999999999999999888 79999999999975

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.20  E-value=3.3e-12  Score=118.38  Aligned_cols=79  Identities=29%  Similarity=0.630  Sum_probs=74.8

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      +|+--|||++||++.||.||.-+|++||+|++|.+++|+.||+++||||+.|++......|+  +|+..|.+|.|+|...
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            56778999999999999999999999999999999999999999999999999999999999  9999999999999765


Q ss_pred             C
Q 009920           81 V   81 (522)
Q Consensus        81 ~   81 (522)
                      .
T Consensus       113 ~  113 (219)
T KOG0126|consen  113 S  113 (219)
T ss_pred             c
Confidence            3

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.19  E-value=1e-10  Score=114.32  Aligned_cols=79  Identities=18%  Similarity=0.207  Sum_probs=71.2

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcCC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVP  183 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~p  183 (522)
                      ...+|||.||++.+||+||+++|+.||+|++|+|++|..   .+++|||+|+++++|+.||.+.+..|.+++|.|.....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~e---t~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGE---YACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCC---cceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCcc
Confidence            357999999999999999999999999999999999854   45799999999999999998877999999999998764


Q ss_pred             CC
Q 009920          184 KE  185 (522)
Q Consensus       184 k~  185 (522)
                      ..
T Consensus        81 y~   82 (243)
T PLN03121         81 YE   82 (243)
T ss_pred             cc
Confidence            43

>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=99.19  E-value=1.3e-10  Score=91.02  Aligned_cols=73  Identities=33%  Similarity=0.709  Sum_probs=67.4

Q ss_pred             eeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       107 ~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      +|+|.+||..+++++|+++|+.+|.|..+.+..++.+ .++++|||+|.+.++|+.|++.++ ..+++++|+|.+
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            4899999999999999999999999999999988775 778999999999999999999999 569999999864

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.18  E-value=1.7e-11  Score=116.58  Aligned_cols=86  Identities=29%  Similarity=0.518  Sum_probs=80.7

Q ss_pred             CCCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEe
Q 009920            1 MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAK   78 (522)
Q Consensus         1 me~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~   78 (522)
                      |..+-|+|||++|..++||.-|...|-+||.|++|.|..|.++.+.|+|+||+|...|+|.+||  |+..++.||.|+|.
T Consensus         6 ~a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN   85 (298)
T KOG0111|consen    6 MANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVN   85 (298)
T ss_pred             ccccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEe
Confidence            3456799999999999999999999999999999999999999999999999999999999999  99999999999999


Q ss_pred             ecCCCccc
Q 009920           79 KAVPRDDQ   86 (522)
Q Consensus        79 ~a~~k~~~   86 (522)
                      .|+|....
T Consensus        86 ~AkP~kik   93 (298)
T KOG0111|consen   86 LAKPEKIK   93 (298)
T ss_pred             ecCCcccc
Confidence            99886544

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

Probab=99.16  E-value=3.1e-09  Score=108.04  Aligned_cols=163  Identities=15%  Similarity=0.179  Sum_probs=124.8

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH----HcccccCCeEEEEee
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI----MDKHMIDGRTVEAKK   79 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl----~~~~~i~Gr~I~V~~   79 (522)
                      .+-.|.|++|-..++|.||.|.++.||+|.-+.+|..+      ..|.|+|+|.+-|+.++    .+...|.++.-.+.+
T Consensus        30 ~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~------r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~Ny  103 (494)
T KOG1456|consen   30 PSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHK------RQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFNY  103 (494)
T ss_pred             CCceEEEeccccccchhHHHHHHhcCCceEEEEecccc------ceeeeeeccccchhhheehhccCcccccCchhhccc
Confidence            34578999999999999999999999999888877654      38999999999999998    455667777777766


Q ss_pred             cCCCccccccccccCCCCCCCCCCCccee--EecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCH
Q 009920           80 AVPRDDQNMLNRNTSSIHSSPGPGRTKKI--FVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE  157 (522)
Q Consensus        80 a~~k~~~~~~~~~~~~~~~~~~~~~~~~L--fVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~  157 (522)
                      ++.+...+..    .   .  .....+.|  -|-|--+.+|.+-|.+++..+|+|.+|.|++.  ++-   .|.|||++.
T Consensus       104 Stsq~i~R~g----~---e--s~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ngV---QAmVEFdsv  169 (494)
T KOG1456|consen  104 STSQCIERPG----D---E--SATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NGV---QAMVEFDSV  169 (494)
T ss_pred             chhhhhccCC----C---C--CCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cce---eeEEeechh
Confidence            6443322211    0   0  11223333  34455578999999999999999999999865  233   699999999


Q ss_pred             HHHHHHHHhcC-CccC-C-eEEEEEEcCCCCC
Q 009920          158 EAVDRVLHKTF-HELN-G-KMVEVKRAVPKEF  186 (522)
Q Consensus       158 e~A~~Al~~~~-~~l~-G-r~I~V~~a~pk~~  186 (522)
                      +.|++|.+.++ .+|- | ..|+|++|+|.+.
T Consensus       170 ~~AqrAk~alNGADIYsGCCTLKIeyAkP~rl  201 (494)
T KOG1456|consen  170 EVAQRAKAALNGADIYSGCCTLKIEYAKPTRL  201 (494)
T ss_pred             HHHHHHHhhcccccccccceeEEEEecCccee
Confidence            99999999999 5543 3 6789999998764

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

Probab=99.13  E-value=1.9e-09  Score=109.48  Aligned_cols=175  Identities=16%  Similarity=0.212  Sum_probs=131.8

Q ss_pred             CCcEEEECCCCCC-CCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            4 DLGKLFIGGISWD-TDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         4 d~r~LfVgnLP~~-~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      +.+.++|-+|... ++.+.|..+|..||.|+.|++|+.+.     +-|.||+-|..+.++|+  +++..+.|.+|.|..+
T Consensus       286 ~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~-----gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~S  360 (494)
T KOG1456|consen  286 PGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKP-----GTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVS  360 (494)
T ss_pred             CCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeeccc-----ceeEEEcCcHHHHHHHHHHhccCccccceEEEeec
Confidence            4678999999887 78899999999999999999999875     68999999999999999  9999999999999877


Q ss_pred             CCCccccc----------------cccc-c----CCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCC-eeEEEEE
Q 009920           81 VPRDDQNM----------------LNRN-T----SSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGT-ITDVVVM  138 (522)
Q Consensus        81 ~~k~~~~~----------------~~~~-~----~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~-I~~v~i~  138 (522)
                      +..--...                .+++ .    .......-..++++|+.-|.|..+|||.|-++|....+ -++|+|.
T Consensus       361 kQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~svkvF  440 (494)
T KOG1456|consen  361 KQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSVKVF  440 (494)
T ss_pred             cccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcceEEee
Confidence            54311110                0000 0    01111223457889999999999999999999987654 3566666


Q ss_pred             ecCCCCCcceEEEEEecCHHHHHHHHHhcCC-ccCCe------EEEEEEcCCCC
Q 009920          139 YDHNTQRPRGFGFITYDSEEAVDRVLHKTFH-ELNGK------MVEVKRAVPKE  185 (522)
Q Consensus       139 ~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~-~l~Gr------~I~V~~a~pk~  185 (522)
                      .-+. .++ -.+++||++.++|..||.+++| .|++.      .+++.++.++.
T Consensus       441 p~ks-erS-ssGllEfe~~s~Aveal~~~NH~pi~~p~gs~PfilKlcfsts~~  492 (494)
T KOG1456|consen  441 PLKS-ERS-SSGLLEFENKSDAVEALMKLNHYPIEGPNGSFPFILKLCFSTSKH  492 (494)
T ss_pred             cccc-ccc-ccceeeeehHHHHHHHHHHhccccccCCCCCCCeeeeeeeccccc
Confidence            5553 333 2689999999999999999984 56553      35666665543

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.13  E-value=1.1e-10  Score=103.43  Aligned_cols=84  Identities=24%  Similarity=0.376  Sum_probs=78.3

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ...-.|||.++.+.+||+||.+.|..||+|+.|.+-.|+.|+-.||||+|+|++.+.|++|+..++ .+|.++.|.|.|+
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~  149 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWC  149 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEE
Confidence            445689999999999999999999999999999999999999999999999999999999999999 8999999999998


Q ss_pred             CCCCC
Q 009920          182 VPKEF  186 (522)
Q Consensus       182 ~pk~~  186 (522)
                      --+..
T Consensus       150 Fv~gp  154 (170)
T KOG0130|consen  150 FVKGP  154 (170)
T ss_pred             EecCC
Confidence            75543

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.13  E-value=1.4e-10  Score=98.46  Aligned_cols=81  Identities=22%  Similarity=0.366  Sum_probs=72.7

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      ..+.|||+|||+++|.||+.++|.+||.|..|+|=.++.   .+|-|||+|++..+|++|+  ++...++++.+.|-..+
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            467899999999999999999999999999999977655   5899999999999999999  99999999999998877


Q ss_pred             CCcccc
Q 009920           82 PRDDQN   87 (522)
Q Consensus        82 ~k~~~~   87 (522)
                      +.+..+
T Consensus        94 ~~~~~~   99 (124)
T KOG0114|consen   94 PEDAFK   99 (124)
T ss_pred             HHHHHH
Confidence            665443

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.13  E-value=8.1e-11  Score=104.34  Aligned_cols=79  Identities=23%  Similarity=0.433  Sum_probs=74.7

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCCC
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVPR   83 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~k   83 (522)
                      -.|||.++..++||++|.+.|..||+|+++.+-.|+.|+-.||||.|+|++.++|++|+  +|...|.+++|+|.|+-.+
T Consensus        73 wIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~  152 (170)
T KOG0130|consen   73 WIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVK  152 (170)
T ss_pred             EEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEec
Confidence            36899999999999999999999999999999999999999999999999999999999  9999999999999998654


Q ss_pred             c
Q 009920           84 D   84 (522)
Q Consensus        84 ~   84 (522)
                      .
T Consensus       153 g  153 (170)
T KOG0130|consen  153 G  153 (170)
T ss_pred             C
Confidence            3

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.12  E-value=3.2e-10  Score=96.36  Aligned_cols=81  Identities=17%  Similarity=0.383  Sum_probs=73.4

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      +...+.|||.|||+++|.|++-++|.+||+|..|+|-..++|   +|.|||.|++..+|++|++.+. ..+.++.+.|-+
T Consensus        15 pevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~T---rGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vly   91 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKET---RGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLY   91 (124)
T ss_pred             hhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCc---CceEEEEehHhhhHHHHHHHhcccccCCceEEEEe
Confidence            346778999999999999999999999999999999877654   8899999999999999999998 799999999998


Q ss_pred             cCCCC
Q 009920          181 AVPKE  185 (522)
Q Consensus       181 a~pk~  185 (522)
                      -.+.+
T Consensus        92 yq~~~   96 (124)
T KOG0114|consen   92 YQPED   96 (124)
T ss_pred             cCHHH
Confidence            77654

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=99.12  E-value=7.9e-11  Score=119.67  Aligned_cols=178  Identities=21%  Similarity=0.297  Sum_probs=145.4

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-Hcc-cccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDK-HMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~-~~i~Gr~I~V~~a~   81 (522)
                      ..+++|++++.+.+.+.++..++.+.|.+..+.+........+++++.|.|+.++.+..|| +.. ..+..+.+......
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            5788999999999999999999999999888888887778899999999999999999999 555 46677777665554


Q ss_pred             CCccccccccccCCCCCCCCCCCcceeE-ecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHH
Q 009920           82 PRDDQNMLNRNTSSIHSSPGPGRTKKIF-VGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV  160 (522)
Q Consensus        82 ~k~~~~~~~~~~~~~~~~~~~~~~~~Lf-VgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A  160 (522)
                      .+..+..      ............+++ |.+|++.+++++|+.+|..++.|..++++.++.+...+++++|+|.+.+..
T Consensus       167 ~~~~~~~------n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~  240 (285)
T KOG4210|consen  167 RRGLRPK------NKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSK  240 (285)
T ss_pred             ccccccc------chhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhH
Confidence            4431110      000011123444555 999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcCCccCCeEEEEEEcCCCCCC
Q 009920          161 DRVLHKTFHELNGKMVEVKRAVPKEFS  187 (522)
Q Consensus       161 ~~Al~~~~~~l~Gr~I~V~~a~pk~~~  187 (522)
                      ++++....+.+.++++.|.+..++...
T Consensus       241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~  267 (285)
T KOG4210|consen  241 KLALNDQTRSIGGRPLRLEEDEPRPKS  267 (285)
T ss_pred             HHHhhcccCcccCcccccccCCCCccc
Confidence            999988348999999999999887654

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

Probab=99.12  E-value=5.8e-11  Score=121.29  Aligned_cols=89  Identities=47%  Similarity=0.795  Sum_probs=83.8

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcCC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVP  183 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~p  183 (522)
                      +.++|||++|+++++||.|++.|.+||+|.+|.+++|+.++++|||+||+|++++.+.++|....|.|+++.|+++.|.|
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            67899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCC
Q 009920          184 KEFSPGPSR  192 (522)
Q Consensus       184 k~~~~~~~r  192 (522)
                      +.......+
T Consensus        85 r~~~~~~~~   93 (311)
T KOG4205|consen   85 REDQTKVGR   93 (311)
T ss_pred             ccccccccc
Confidence            987655443

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.07  E-value=2.5e-10  Score=121.48  Aligned_cols=81  Identities=27%  Similarity=0.572  Sum_probs=77.7

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCC
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPK  184 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk  184 (522)
                      ++|||+|+|++++|++|.++|+..|.|.+++++.|++|+++|||+|++|.+++++++|++.++ .++.+|+|+|.++...
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            799999999999999999999999999999999999999999999999999999999999999 8999999999998755


Q ss_pred             CC
Q 009920          185 EF  186 (522)
Q Consensus       185 ~~  186 (522)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            43

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=99.06  E-value=1.3e-09  Score=115.33  Aligned_cols=81  Identities=23%  Similarity=0.422  Sum_probs=71.8

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcCCCC
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKE  185 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~pk~  185 (522)
                      .+|||.|||.++++++|+++|.+||.|++..|.......+..+|+||+|.+.++++.||++....|++++|.|+..++..
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek~~~~  368 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEKRPGF  368 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEeccccc
Confidence            45999999999999999999999999999988876533444489999999999999999999899999999999987654


Q ss_pred             C
Q 009920          186 F  186 (522)
Q Consensus       186 ~  186 (522)
                      .
T Consensus       369 ~  369 (419)
T KOG0116|consen  369 R  369 (419)
T ss_pred             c
Confidence            3

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.06  E-value=2.9e-11  Score=112.13  Aligned_cols=79  Identities=25%  Similarity=0.535  Sum_probs=74.3

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      ++.-|||++||+++||.||-.+|++||+|++|.+++|+.|++++||||+.|++..+..-|+.-++ ..|.+|.|+|....
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            56689999999999999999999999999999999999999999999999999999998998888 89999999998654

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=99.03  E-value=1.4e-11  Score=135.80  Aligned_cols=152  Identities=22%  Similarity=0.311  Sum_probs=129.9

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      ++..++||.||+..+.+++|.+.|..++.+..+.|..-+++++.||+|||+|..++++.+|| ++...+.+         
T Consensus       665 R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g---------  735 (881)
T KOG0128|consen  665 RDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG---------  735 (881)
T ss_pred             HHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh---------
Confidence            45678999999999999999999999988877777655667899999999999999999999 44443333         


Q ss_pred             CCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHH
Q 009920           82 PRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD  161 (522)
Q Consensus        82 ~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~  161 (522)
                                             ..+|+|.++|+..|.++|+.++.++|.++++.++..+. ++++|.|+|.|.++.++.
T Consensus       736 -----------------------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~-gkpkg~a~v~y~~ea~~s  791 (881)
T KOG0128|consen  736 -----------------------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRA-GKPKGKARVDYNTEADAS  791 (881)
T ss_pred             -----------------------hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhc-cccccceeccCCCcchhh
Confidence                                   23689999999999999999999999999999877765 899999999999999999


Q ss_pred             HHHHhcC-CccCCeEEEEEEcCCCCCC
Q 009920          162 RVLHKTF-HELNGKMVEVKRAVPKEFS  187 (522)
Q Consensus       162 ~Al~~~~-~~l~Gr~I~V~~a~pk~~~  187 (522)
                      +++.+.+ ..++-+-++|....|..++
T Consensus       792 ~~~~s~d~~~~rE~~~~v~vsnp~~~K  818 (881)
T KOG0128|consen  792 RKVASVDVAGKRENNGEVQVSNPERDK  818 (881)
T ss_pred             hhcccchhhhhhhcCccccccCCcccc
Confidence            9998887 6777788888887764443

>smart00361 RRM_1 RNA recognition motif

Probab=99.01  E-value=1.2e-09  Score=87.78  Aligned_cols=61  Identities=23%  Similarity=0.492  Sum_probs=54.7

Q ss_pred             HHHHHHHHh----hcCCeeEEE-EEecCCC--CCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          119 ESDFKKYFD----QFGTITDVV-VMYDHNT--QRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       119 eedL~~~F~----~fG~I~~v~-i~~d~~t--g~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      +++|+++|+    +||.|.+|. |+.++.+  ++++|++||+|.++++|++|++.++ ..+++|+|++.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            678888888    999999995 7777777  8999999999999999999999988 89999999873

>smart00361 RRM_1 RNA recognition motif

Probab=99.00  E-value=1.3e-09  Score=87.55  Aligned_cols=60  Identities=33%  Similarity=0.521  Sum_probs=53.9

Q ss_pred             CHHHHHHHHh----ccCCeEEEE-EeecCCC--CCcccEEEEEecCHHHHHHHH--HcccccCCeEEEE
Q 009920           18 DEERLKEYFS----RYGEVVEAV-IMRDRAT--GRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEA   77 (522)
Q Consensus        18 teedL~e~F~----~~G~V~~v~-i~~d~~t--g~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V   77 (522)
                      .+++|+++|+    +||+|.+|. |+.++.+  +++|||+||+|.++++|++|+  +++..++++.|.+
T Consensus         1 ~~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        1 KDEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             CchhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            3678999998    999999995 7777666  899999999999999999999  8999999999976

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

Probab=98.97  E-value=8.2e-10  Score=109.16  Aligned_cols=72  Identities=22%  Similarity=0.554  Sum_probs=67.7

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCC
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPK  184 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk  184 (522)
                      .+|||+|||..+++.+|+.+|++||+|.+|+|+++        |+||+.+++.+++.||..++ -+|+|..|.|+.++.|
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            47999999999999999999999999999999966        99999999999999999877 6999999999999877


Q ss_pred             C
Q 009920          185 E  185 (522)
Q Consensus       185 ~  185 (522)
                      .
T Consensus        75 s   75 (346)
T KOG0109|consen   75 S   75 (346)
T ss_pred             C
Confidence            3

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.97  E-value=8.7e-10  Score=111.28  Aligned_cols=85  Identities=20%  Similarity=0.349  Sum_probs=78.8

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+...|||-.|.+-+|++||+-+|+.||+|+.|.|++|..|+.+-.||||||++.+++++|.-+|+ ..|+.++|+|.+
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            3567899999999999999999999999999999999999999999999999999999999999888 799999999998


Q ss_pred             cCCCCC
Q 009920          181 AVPKEF  186 (522)
Q Consensus       181 a~pk~~  186 (522)
                      +..-.+
T Consensus       316 SQSVsk  321 (479)
T KOG0415|consen  316 SQSVSK  321 (479)
T ss_pred             hhhhhh
Confidence            775444

>PF13893 RRM_5: RNA recognition motif

Probab=98.94  E-value=2.8e-09  Score=81.58  Aligned_cols=55  Identities=25%  Similarity=0.593  Sum_probs=49.3

Q ss_pred             HHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          122 FKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       122 L~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      |+++|++||+|+++.+..++     +++|||+|.+.++|++|++.++ ..+.|++|+|+++
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68999999999999998664     5699999999999999999888 8999999999985

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

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

Probab=98.93  E-value=9.5e-10  Score=107.45  Aligned_cols=84  Identities=30%  Similarity=0.518  Sum_probs=79.5

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .|.|+|||-.||.+..+.||...|-.||.|++.+|..|+.|..+|.|+||.|.++..|+.||  ||+..|.-++|+|...
T Consensus       283 PeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLK  362 (371)
T KOG0146|consen  283 PEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLK  362 (371)
T ss_pred             CCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhc
Confidence            47899999999999999999999999999999999999999999999999999999999999  9999999999999888


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      .|++..
T Consensus       363 RPkdan  368 (371)
T KOG0146|consen  363 RPKDAN  368 (371)
T ss_pred             CccccC
Confidence            777653

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.91  E-value=2.2e-09  Score=117.60  Aligned_cols=107  Identities=18%  Similarity=0.339  Sum_probs=84.6

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCC
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~   82 (522)
                      +|||||+.||+.++|+||+++|+.||+|.+|+++..      |+||||++....+|++||  ++++.+..+.|+|.|+.-
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            689999999999999999999999999999999764      579999999999999999  899999999999999987


Q ss_pred             CccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhh
Q 009920           83 RDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQ  128 (522)
Q Consensus        83 k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~  128 (522)
                      +..+...+.-.           ...|=|.-||++.-.+||+.+++.
T Consensus       495 ~G~kse~k~~w-----------D~~lGVt~IP~~kLt~dl~~~~eg  529 (894)
T KOG0132|consen  495 KGPKSEYKDYW-----------DVELGVTYIPWEKLTDDLEAWCEG  529 (894)
T ss_pred             CCcchhhhhhh-----------hcccCeeEeehHhcCHHHHHhhhh
Confidence            65443211100           112234445776555558887764

>PF13893 RRM_5: RNA recognition motif

Probab=98.91  E-value=4.9e-09  Score=80.25  Aligned_cols=54  Identities=35%  Similarity=0.662  Sum_probs=48.8

Q ss_pred             HHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920           22 LKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus        22 L~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      |+++|++||+|+++++.+++     +++|||+|.+.++|++|+  +++..+.+++|+|+++
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            78999999999999998764     579999999999999999  8999999999999875

(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 ....

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.90  E-value=1.8e-09  Score=109.10  Aligned_cols=81  Identities=28%  Similarity=0.507  Sum_probs=76.6

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      ......|||..|.+-+|+++|.-+|+.||+|.+|.|++|..|+.+..||||+|.+++++++|.  |++..|+.++|.|..
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            456789999999999999999999999999999999999999999999999999999999999  999999999999987


Q ss_pred             cCC
Q 009920           80 AVP   82 (522)
Q Consensus        80 a~~   82 (522)
                      ++.
T Consensus       316 SQS  318 (479)
T KOG0415|consen  316 SQS  318 (479)
T ss_pred             hhh
Confidence            754

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.88  E-value=3.2e-10  Score=108.04  Aligned_cols=134  Identities=25%  Similarity=0.302  Sum_probs=113.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      +..++|||.||...++|+-|.|+|-+-|+|..|.|..+++ .+.| ||||.|+++-.+.-|+  +|+..+.+++|.++. 
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 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTL-   83 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccchhhccc-
Confidence            4578999999999999999999999999999999988875 6777 9999999999999998  788888777766643 


Q ss_pred             CCCccccccccccCCCCCCCCCCCcceeEecC----CCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecC
Q 009920           81 VPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGG----LASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS  156 (522)
Q Consensus        81 ~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgn----Lp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s  156 (522)
                                                  +.++    |.+.++++.+.+.|..-++|+.+++..+.+ ++++-+.||++..
T Consensus        84 ----------------------------r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d-~rnrn~~~~~~qr  134 (267)
T KOG4454|consen   84 ----------------------------RCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDND-GRNRNFGFVTYQR  134 (267)
T ss_pred             ----------------------------ccCCCcchhhhhcchhhheeeecccCCCCCcccccccc-CCccCccchhhhh
Confidence                                        2222    567789999999999999999999998876 7788899999988


Q ss_pred             HHHHHHHHHhcC
Q 009920          157 EEAVDRVLHKTF  168 (522)
Q Consensus       157 ~e~A~~Al~~~~  168 (522)
                      ..+.-.++....
T Consensus       135 ~~~~P~~~~~y~  146 (267)
T KOG4454|consen  135 LCAVPFALDLYQ  146 (267)
T ss_pred             hhcCcHHhhhhc
Confidence            777777765543

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.80  E-value=1.3e-08  Score=111.55  Aligned_cols=78  Identities=28%  Similarity=0.551  Sum_probs=71.2

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      .-++||||+.|+..++|+||+.+|+.||+|..|.++.      +|++|||.+.+.++|++||++|. ..+..+.|+|.|+
T Consensus       419 V~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~------~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa  492 (894)
T KOG0132|consen  419 VCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP------PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWA  492 (894)
T ss_pred             EeeeeeeeccccchhhHHHHHHHHHhcccceeEeecc------CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeee
Confidence            4468999999999999999999999999999999874      47799999999999999999998 8999999999999


Q ss_pred             CCCCC
Q 009920          182 VPKEF  186 (522)
Q Consensus       182 ~pk~~  186 (522)
                      .-+..
T Consensus       493 ~g~G~  497 (894)
T KOG0132|consen  493 VGKGP  497 (894)
T ss_pred             ccCCc
Confidence            86643

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.76  E-value=1.5e-08  Score=107.57  Aligned_cols=78  Identities=32%  Similarity=0.549  Sum_probs=73.8

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCC
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~   82 (522)
                      .++|||.+|+..+-..+|+.+|++||+|+-++|+.+..+.-.|+|+||+|.+.++|.+||  ++.++|+++.|.|++++.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            588999999999999999999999999999999999888889999999999999999999  999999999999988754

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.75  E-value=5.5e-09  Score=101.74  Aligned_cols=166  Identities=19%  Similarity=0.335  Sum_probs=123.9

Q ss_pred             EEECCCCCCCCHHH-H--HHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCC
Q 009920            8 LFIGGISWDTDEER-L--KEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         8 LfVgnLP~~~teed-L--~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~   82 (522)
                      +++.++-.++..+- |  ...|+.+-.+...+++++.. ...++++|+.|+....-.++.  .+++.|.-+.|++...+.
T Consensus        99 p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p-~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gts  177 (290)
T KOG0226|consen   99 PFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRP-QPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTS  177 (290)
T ss_pred             ccccccccccCCCCCCcchhhhccchhhhhhhhhhcCC-CccCcccccCcchhhhhhhhccccccccccCcceeeccccc
Confidence            44555544544443 3  56677776666677777765 677889999999888777776  445555555554443333


Q ss_pred             CccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHH
Q 009920           83 RDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDR  162 (522)
Q Consensus        83 k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~  162 (522)
                      -++....          .-.....+||.+.|-.+++++.|.+.|.+|-.-...++++|+.|++++||+||.|.+.+++.+
T Consensus       178 wedPsl~----------ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~r  247 (290)
T KOG0226|consen  178 WEDPSLA----------EWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVR  247 (290)
T ss_pred             cCCcccc----------cCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHH
Confidence            3222211          122456799999999999999999999999888889999999999999999999999999999


Q ss_pred             HHHhcC-CccCCeEEEEEEcCCC
Q 009920          163 VLHKTF-HELNGKMVEVKRAVPK  184 (522)
Q Consensus       163 Al~~~~-~~l~Gr~I~V~~a~pk  184 (522)
                      |+..|+ +.++.|.|++....-+
T Consensus       248 Amrem~gkyVgsrpiklRkS~wk  270 (290)
T KOG0226|consen  248 AMREMNGKYVGSRPIKLRKSEWK  270 (290)
T ss_pred             HHHhhcccccccchhHhhhhhHH
Confidence            999999 8889899887655433

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.75  E-value=3.2e-08  Score=100.19  Aligned_cols=81  Identities=30%  Similarity=0.607  Sum_probs=71.2

Q ss_pred             CCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC--CccCCeEE
Q 009920           99 SPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF--HELNGKMV  176 (522)
Q Consensus        99 ~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~--~~l~Gr~I  176 (522)
                      ++.....++|||++|-..++|.||+++|.+||+|+.|+++..+      ++|||+|.+.++|+.|.++..  ..|+|++|
T Consensus       222 pPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl  295 (377)
T KOG0153|consen  222 PPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFNKLVINGFRL  295 (377)
T ss_pred             CCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcceeeecceEE
Confidence            3344556899999999999999999999999999999998653      499999999999999998876  58999999


Q ss_pred             EEEEcCCCC
Q 009920          177 EVKRAVPKE  185 (522)
Q Consensus       177 ~V~~a~pk~  185 (522)
                      +|.|..++.
T Consensus       296 ~i~Wg~~~~  304 (377)
T KOG0153|consen  296 KIKWGRPKQ  304 (377)
T ss_pred             EEEeCCCcc
Confidence            999999843

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.73  E-value=4e-08  Score=99.48  Aligned_cols=75  Identities=28%  Similarity=0.570  Sum_probs=69.3

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH---HcccccCCeEEEEe
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI---MDKHMIDGRTVEAK   78 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl---~~~~~i~Gr~I~V~   78 (522)
                      |...++|||++|-..++|.+|+++|.+||+|..++++..+      ++|||+|.+.+.|++|.   .++..|+|++|.|.
T Consensus       225 D~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~  298 (377)
T KOG0153|consen  225 DTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIK  298 (377)
T ss_pred             ccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcceeeecceEEEEE
Confidence            4567899999998899999999999999999999998864      49999999999999998   78889999999999


Q ss_pred             ecCC
Q 009920           79 KAVP   82 (522)
Q Consensus        79 ~a~~   82 (522)
                      |..+
T Consensus       299 Wg~~  302 (377)
T KOG0153|consen  299 WGRP  302 (377)
T ss_pred             eCCC
Confidence            9988

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.68  E-value=1.2e-08  Score=113.47  Aligned_cols=159  Identities=22%  Similarity=0.346  Sum_probs=124.6

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .++++||++||+..+++.+|+..|..+|.|.+|.|-+-+. ++-.-|+||.|.+.+.+-+|+  +....|..-.+.+..-
T Consensus       370 ~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~-~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG  448 (975)
T KOG0112|consen  370 RATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI-KTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLG  448 (975)
T ss_pred             hhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC-CcccchhhhhhhccccCcccchhhcCCccccCccccccc
Confidence            4678999999999999999999999999999999866532 455569999999999888887  4444443223333222


Q ss_pred             CCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHH
Q 009920           81 VPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV  160 (522)
Q Consensus        81 ~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A  160 (522)
                      .+                  ....++.++|++|..++....|.+.|..||.|..|.+-...    +  ||+|.|++...+
T Consensus       449 ~~------------------kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq----~--yayi~yes~~~a  504 (975)
T KOG0112|consen  449 QP------------------KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQ----P--YAYIQYESPPAA  504 (975)
T ss_pred             cc------------------ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccCC----c--ceeeecccCccc
Confidence            21                  22467789999999999999999999999999988775432    2  999999999999


Q ss_pred             HHHHHhcC-CccCC--eEEEEEEcCCCCC
Q 009920          161 DRVLHKTF-HELNG--KMVEVKRAVPKEF  186 (522)
Q Consensus       161 ~~Al~~~~-~~l~G--r~I~V~~a~pk~~  186 (522)
                      ++|++.+. ..|.+  ++|.|.++.+...
T Consensus       505 q~a~~~~rgap~G~P~~r~rvdla~~~~~  533 (975)
T KOG0112|consen  505 QAATHDMRGAPLGGPPRRLRVDLASPPGA  533 (975)
T ss_pred             hhhHHHHhcCcCCCCCcccccccccCCCC
Confidence            99998776 55554  7799999886544

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.65  E-value=6.1e-08  Score=105.17  Aligned_cols=179  Identities=12%  Similarity=0.054  Sum_probs=125.9

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      .|.+.+-+++.++++++.|+++||... .|..+.|..+...+-..|-++|+|....++++|+ .+...+-.|.|++..+.
T Consensus       309 ~d~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~rn~~~~~~R~~q~~P~g  387 (944)
T KOG4307|consen  309 SDKYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTRNPSDDVNRPFQTGPPG  387 (944)
T ss_pred             chhheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhcCchhhhhcceeecCCC
Confidence            567888899999999999999999754 2444455555443444789999999999999999 66666677888886554


Q ss_pred             CCccccc-----ccc--ccCCCCC----------------CCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEE
Q 009920           82 PRDDQNM-----LNR--NTSSIHS----------------SPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVM  138 (522)
Q Consensus        82 ~k~~~~~-----~~~--~~~~~~~----------------~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~  138 (522)
                      .....-.     ...  .....|.                ........+|||..||..+++.++.++|...-.|++...+
T Consensus       388 ~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~l  467 (944)
T KOG4307|consen  388 NLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIEL  467 (944)
T ss_pred             ccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEe
Confidence            3322110     000  0000000                0112345689999999999999999999998888884444


Q ss_pred             ecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          139 YDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       139 ~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      ....+.+.++.|||+|..++++.+|+.-.. +.+..|.|+|.-..
T Consensus       468 t~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~  512 (944)
T KOG4307|consen  468 TRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIA  512 (944)
T ss_pred             ccCCcccccchhhheeccccccchhhhcccccccCceEEEeechh
Confidence            444557888999999999777777665544 67888888887533

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.64  E-value=1.6e-07  Score=89.24  Aligned_cols=80  Identities=24%  Similarity=0.453  Sum_probs=73.5

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhcc-CCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRY-GEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~-G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...-++|..||.-+.|.+|..+|.++ |.|..+++.|++.||.+|+||||+|+++|+|+-|.  ||+-.+.++.|+|...
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            34568999999999999999999998 88888899899999999999999999999999998  9999999999999887


Q ss_pred             CCC
Q 009920           81 VPR   83 (522)
Q Consensus        81 ~~k   83 (522)
                      .+.
T Consensus       128 ppe  130 (214)
T KOG4208|consen  128 PPE  130 (214)
T ss_pred             Cch
Confidence            665

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.57  E-value=1.2e-07  Score=100.71  Aligned_cols=79  Identities=25%  Similarity=0.572  Sum_probs=74.4

Q ss_pred             cceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCC
Q 009920          105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVP  183 (522)
Q Consensus       105 ~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~p  183 (522)
                      .+.|||.+|...+...||+.+|++||.|+-.+|+++..+.-.++|+||++.+.++|.+||+.++ .+|.|++|.|+.++.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            3579999999999999999999999999999999998888899999999999999999999999 899999999998763

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.57  E-value=1.1e-07  Score=100.88  Aligned_cols=79  Identities=27%  Similarity=0.454  Sum_probs=68.6

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecCC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~~   82 (522)
                      +..+|||+|||.++++++|+++|.+||+|+...|......++...|+||+|.+.++++.|| .+...|.+++|.|+...+
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEeccc
Confidence            4566999999999999999999999999999998775533555599999999999999999 778889999999986544

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

Probab=98.56  E-value=1.8e-07  Score=90.10  Aligned_cols=80  Identities=23%  Similarity=0.444  Sum_probs=72.1

Q ss_pred             CcceeEecCCCCCCCHHHHHH----HHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEE
Q 009920          104 RTKKIFVGGLASTVTESDFKK----YFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEV  178 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~----~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V  178 (522)
                      +..+|||.||++.+..++|++    +|++||.|.+|...+   |.+.||.|||.|++.+.|-.|+..++ .-+-||+++|
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mri   84 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRI   84 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhhe
Confidence            445999999999999999998    999999999998875   46789999999999999999999988 7899999999


Q ss_pred             EEcCCCCC
Q 009920          179 KRAVPKEF  186 (522)
Q Consensus       179 ~~a~pk~~  186 (522)
                      .+|+.+..
T Consensus        85 qyA~s~sd   92 (221)
T KOG4206|consen   85 QYAKSDSD   92 (221)
T ss_pred             ecccCccc
Confidence            99987654

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.53  E-value=7.5e-08  Score=102.78  Aligned_cols=169  Identities=17%  Similarity=0.187  Sum_probs=109.0

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ..+++|+|-|||.++++++|+++|+.||+|.+|+.-+.     .++.+||+|-|..+|++|+  ++..+|.+++|+....
T Consensus        73 ~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~-----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~~~  147 (549)
T KOG4660|consen   73 MNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN-----KRGIVFVEFYDVRDAERALKALNRREIAGKRIKRPGG  147 (549)
T ss_pred             CccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc-----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCCCc
Confidence            46799999999999999999999999999999665443     4689999999999999999  8999999998882211


Q ss_pred             CCCccccccc-----ccc-CCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEe
Q 009920           81 VPRDDQNMLN-----RNT-SSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY  154 (522)
Q Consensus        81 ~~k~~~~~~~-----~~~-~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF  154 (522)
                      ..+.......     .-. ......+..-....+|+- |++.++..-++.++.-++.++. +..     ..-+-.-||+|
T Consensus       148 ~~~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g~-l~P~~s~~~~~~~~~~~~~~~~-~~~-----~~~~hq~~~~~  220 (549)
T KOG4660|consen  148 ARRAMGLQSGTSFLNHFGSPLANSPPGGWPRGQLFGM-LSPTRSSILLEHISSVDGSSPG-RET-----PLLNHQRFVEF  220 (549)
T ss_pred             ccccchhcccchhhhhccchhhcCCCCCCcCCcceee-eccchhhhhhhcchhccCcccc-ccc-----cchhhhhhhhh
Confidence            1111111000     000 011111222223344443 8998888878888888887765 222     11112567888


Q ss_pred             cCHHHHHHHHHhcCCccCCeEEEEEEcCC
Q 009920          155 DSEEAVDRVLHKTFHELNGKMVEVKRAVP  183 (522)
Q Consensus       155 ~s~e~A~~Al~~~~~~l~Gr~I~V~~a~p  183 (522)
                      .+..++..++..+...+.++...+++..+
T Consensus       221 ~~~~s~a~~~~~~G~~~s~~~~v~t~S~~  249 (549)
T KOG4660|consen  221 ADNRSYAFSEPRGGFLISNSSGVITFSGP  249 (549)
T ss_pred             ccccchhhcccCCceecCCCCceEEecCC
Confidence            88887755544333445555545555443

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.52  E-value=2.9e-07  Score=87.55  Aligned_cols=84  Identities=21%  Similarity=0.385  Sum_probs=74.7

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhc-CCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQF-GTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEV  178 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~f-G~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V  178 (522)
                      .......++|..+|.-+.+.+|..+|.+| |.|..+++-+++.|+.+||||||||+++|.|+-|.+.|| -.|.++.|.|
T Consensus        45 ~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c  124 (214)
T KOG4208|consen   45 EQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLEC  124 (214)
T ss_pred             ccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeee
Confidence            34556789999999999999999999988 788888998999999999999999999999999999888 6788899999


Q ss_pred             EEcCCC
Q 009920          179 KRAVPK  184 (522)
Q Consensus       179 ~~a~pk  184 (522)
                      .+-.|.
T Consensus       125 ~vmppe  130 (214)
T KOG4208|consen  125 HVMPPE  130 (214)
T ss_pred             EEeCch
Confidence            886554

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.52  E-value=3.5e-07  Score=90.46  Aligned_cols=84  Identities=25%  Similarity=0.450  Sum_probs=76.6

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ....+|.|.|||..|+++||+++|++|++++.+.|..|+. +++.|.|-|.|+..++|++|+++++ ..|+|+.+++...
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~-G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i  159 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRA-GRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEII  159 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCC-CCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEe
Confidence            3457899999999999999999999999999999999876 8899999999999999999999998 8999999999988


Q ss_pred             CCCCCC
Q 009920          182 VPKEFS  187 (522)
Q Consensus       182 ~pk~~~  187 (522)
                      .+....
T Consensus       160 ~~~~~~  165 (243)
T KOG0533|consen  160 SSPSQS  165 (243)
T ss_pred             cCcccc
Confidence            766554

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.46  E-value=6e-07  Score=88.85  Aligned_cols=83  Identities=25%  Similarity=0.424  Sum_probs=73.5

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      |...++|+|.|||..++++||+|+|++|++++.+.|..++ ++++.|.|=|.|...++|++|+  ++...++++.|++..
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 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            3445789999999999999999999999999888888887 5999999999999999999999  888999999999887


Q ss_pred             cCCCcc
Q 009920           80 AVPRDD   85 (522)
Q Consensus        80 a~~k~~   85 (522)
                      ..+...
T Consensus       159 i~~~~~  164 (243)
T KOG0533|consen  159 ISSPSQ  164 (243)
T ss_pred             ecCccc
Confidence            655433

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.43  E-value=3.7e-07  Score=90.21  Aligned_cols=84  Identities=24%  Similarity=0.367  Sum_probs=77.7

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR  180 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~  180 (522)
                      ...+...+||+|+.+.+|.++++.+|+.||.|..|.|++|+.++.+|+|+||+|++.+.+++|+++...+|.++.|+|.+
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVTL  176 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceeee
Confidence            34567899999999999999999999999999999999999999999999999999999999999555999999999999


Q ss_pred             cCCC
Q 009920          181 AVPK  184 (522)
Q Consensus       181 a~pk  184 (522)
                      .+-+
T Consensus       177 ~r~~  180 (231)
T KOG4209|consen  177 KRTN  180 (231)
T ss_pred             eeee
Confidence            8765

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.42  E-value=2e-06  Score=93.61  Aligned_cols=76  Identities=18%  Similarity=0.132  Sum_probs=64.9

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEE-EEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVE-AVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~-v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      ...|||..||..+++.++.++|.+.-.|++ |.|.+.+ +.+.++.|||+|..++++.+|+  .+++.+..|.|+|....
T Consensus       434 g~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~  512 (944)
T KOG4307|consen  434 GGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIA  512 (944)
T ss_pred             cceEEeccCCccccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEeechh
Confidence            457999999999999999999999888888 5555544 6889999999999999998888  78888889999986543

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

Probab=98.34  E-value=1.5e-06  Score=88.27  Aligned_cols=81  Identities=26%  Similarity=0.422  Sum_probs=73.2

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCee--------EEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-Ccc
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTIT--------DVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HEL  171 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~--------~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l  171 (522)
                      .+...+.|||.+||.++|.+++.++|.+||.|.        .|++.++.. ++.||-|+|.|--+++++-|++.++ ..|
T Consensus       130 ~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~  208 (382)
T KOG1548|consen  130 EPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDEL  208 (382)
T ss_pred             ccccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCcccc
Confidence            345567799999999999999999999999885        377888876 8999999999999999999999999 899


Q ss_pred             CCeEEEEEEcC
Q 009920          172 NGKMVEVKRAV  182 (522)
Q Consensus       172 ~Gr~I~V~~a~  182 (522)
                      .|++|+|+.|+
T Consensus       209 rg~~~rVerAk  219 (382)
T KOG1548|consen  209 RGKKLRVERAK  219 (382)
T ss_pred             cCcEEEEehhh
Confidence            99999999887

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.33  E-value=2.7e-07  Score=88.35  Aligned_cols=78  Identities=17%  Similarity=0.243  Sum_probs=71.0

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ...++|||.|+-..|+||.|.++|-+-|+|.+|.|..+++ ++.| ||||+|+++..+.-|++.++ .+|.++.|.|+.-
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~~~r   84 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            4567999999999999999999999999999999998887 5566 99999999999999999999 7999999988875


Q ss_pred             C
Q 009920          182 V  182 (522)
Q Consensus       182 ~  182 (522)
                      .
T Consensus        85 ~   85 (267)
T KOG4454|consen   85 C   85 (267)
T ss_pred             c
Confidence            4

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.32  E-value=3.2e-06  Score=72.43  Aligned_cols=77  Identities=19%  Similarity=0.184  Sum_probs=63.8

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhcc--CCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccC----CeEEEE
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRY--GEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMID----GRTVEA   77 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~--G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~----Gr~I~V   77 (522)
                      +||+|+|||...|.++|.+++.+.  |...-+.+..|-.+..+.|||||-|.++++|.+..  .+++.+.    .+.++|
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            789999999999999999999763  77777889999888999999999999999999988  6665543    455566


Q ss_pred             eecCC
Q 009920           78 KKAVP   82 (522)
Q Consensus        78 ~~a~~   82 (522)
                      .+|.-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            66543

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.31  E-value=7.6e-07  Score=88.02  Aligned_cols=82  Identities=20%  Similarity=0.417  Sum_probs=75.8

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeec
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a   80 (522)
                      +.+.+.|||+|+...+|.++|+.+|+.||.|..+.|.+++.++.+|+|+||+|.+.+.+++++ ++...|.++.|+|.+.
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt~~  177 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVTLK  177 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceeeee
Confidence            457889999999999999999999999999999999999999899999999999999999999 8999999999999766


Q ss_pred             CCC
Q 009920           81 VPR   83 (522)
Q Consensus        81 ~~k   83 (522)
                      ...
T Consensus       178 r~~  180 (231)
T KOG4209|consen  178 RTN  180 (231)
T ss_pred             eee
Confidence            443

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.26  E-value=2.3e-06  Score=87.48  Aligned_cols=84  Identities=24%  Similarity=0.400  Sum_probs=76.5

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCee--------EEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccC
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTIT--------DVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELN  172 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~--------~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~  172 (522)
                      .....+|||-.||..+++++|.++|.++++|+        .|.|.+|++|.++|+-|.|+|++..+|++||+... +++.
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            34567899999999999999999999999885        36788999999999999999999999999999988 8999


Q ss_pred             CeEEEEEEcCCCC
Q 009920          173 GKMVEVKRAVPKE  185 (522)
Q Consensus       173 Gr~I~V~~a~pk~  185 (522)
                      +.+|+|.+|..+.
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999999987655

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.24  E-value=8.1e-07  Score=91.22  Aligned_cols=165  Identities=13%  Similarity=0.152  Sum_probs=120.1

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCC---CCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEee
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRAT---GRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKK   79 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~t---g~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~   79 (522)
                      ....|-|.||.+.+|.++++.+|.-+|+|.++.|+.+..+   ......|||.|.|...+..|. +.++.+-++.|.|..
T Consensus         6 ~~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p   85 (479)
T KOG4676|consen    6 SLGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRP   85 (479)
T ss_pred             CCceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEe
Confidence            3457899999999999999999999999999999885443   345678999999999999998 888888788877765


Q ss_pred             cCCCccccc-----------ccc-------------------ccCCCCCCCC----------CCCcceeEecCCCCCCCH
Q 009920           80 AVPRDDQNM-----------LNR-------------------NTSSIHSSPG----------PGRTKKIFVGGLASTVTE  119 (522)
Q Consensus        80 a~~k~~~~~-----------~~~-------------------~~~~~~~~~~----------~~~~~~LfVgnLp~~vte  119 (522)
                      .........           ...                   .+......|.          +....+|+|.+|+..+..
T Consensus        86 ~~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l  165 (479)
T KOG4676|consen   86 YGDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAIL  165 (479)
T ss_pred             cCCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcc
Confidence            432221110           000                   0000000000          112257999999999999


Q ss_pred             HHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccC
Q 009920          120 SDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELN  172 (522)
Q Consensus       120 edL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~  172 (522)
                      .++.+.|+.+|+|....+.....    .-+|-|+|......+.|+++++.++.
T Consensus       166 ~e~~e~f~r~Gev~ya~~ask~~----s~~c~~sf~~qts~~halr~~gre~k  214 (479)
T KOG4676|consen  166 PESGESFERKGEVSYAHTASKSR----SSSCSHSFRKQTSSKHALRSHGRERK  214 (479)
T ss_pred             hhhhhhhhhcchhhhhhhhccCC----CcchhhhHhhhhhHHHHHHhcchhhh
Confidence            99999999999998776654332    23778999999999999998875444

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

Probab=98.24  E-value=1.2e-06  Score=84.96  Aligned_cols=74  Identities=27%  Similarity=0.566  Sum_probs=66.0

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCC
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPK  184 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk  184 (522)
                      .+|||++||+.+.+++|+++|..||.|.+|.+.        .+|+||+|++..+|+.|+..++ ++|.+.++.|++++.+
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            479999999999999999999999999999886        3589999999999999999988 7899888888888865


Q ss_pred             CCC
Q 009920          185 EFS  187 (522)
Q Consensus       185 ~~~  187 (522)
                      ...
T Consensus        74 ~~~   76 (216)
T KOG0106|consen   74 RRG   76 (216)
T ss_pred             ccc
Confidence            443

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.23  E-value=7.7e-07  Score=86.98  Aligned_cols=81  Identities=27%  Similarity=0.574  Sum_probs=74.0

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .++-+||++.|-.++++|.|-..|.+|-.-...++++++.|++++||+||.|.+++++.+|+  |+...+..|.|++..+
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            56788999999999999999999999988888899999999999999999999999999999  9999999998888765


Q ss_pred             CCC
Q 009920           81 VPR   83 (522)
Q Consensus        81 ~~k   83 (522)
                      .-+
T Consensus       268 ~wk  270 (290)
T KOG0226|consen  268 EWK  270 (290)
T ss_pred             hHH
Confidence            443

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.21  E-value=1.4e-07  Score=97.50  Aligned_cols=148  Identities=22%  Similarity=0.361  Sum_probs=118.1

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCC-eEEEEEeecCCCCCcccEEEEEecCHHHHHHHH---HcccccCCeEEEEeecC
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGE-VVEAVIMRDRATGRARGFGFVVFADPAVAERVI---MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~-V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl---~~~~~i~Gr~I~V~~a~   81 (522)
                      .+|||+||.+.++..+|+.+|...-. +..-.+++       .+|+||.+.+...|.+|+   ..+.++.|++++++...
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 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK-------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSV   74 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee-------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchh
Confidence            57999999999999999999976411 11112333       369999999999999999   34568999999998877


Q ss_pred             CCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEE-EecCCCCCcceEEEEEecCHHHH
Q 009920           82 PRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVV-MYDHNTQRPRGFGFITYDSEEAV  160 (522)
Q Consensus        82 ~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i-~~d~~tg~~rG~aFVeF~s~e~A  160 (522)
                      ++..                  +++++-|.|+|..+.++.|..++.+|+.|+.|.. ..|++|-    ..-|+|.+.+.+
T Consensus        75 ~kkq------------------rsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~eta----vvnvty~~~~~~  132 (584)
T KOG2193|consen   75 PKKQ------------------RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETA----VVNVTYSAQQQH  132 (584)
T ss_pred             hHHH------------------HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHH----HHHHHHHHHHHH
Confidence            6543                  3456889999999999999999999999998855 3444432    345788999999


Q ss_pred             HHHHHhcC-CccCCeEEEEEEcC
Q 009920          161 DRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       161 ~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      +.||.+++ +.|....++|.+--
T Consensus       133 ~~ai~kl~g~Q~en~~~k~~YiP  155 (584)
T KOG2193|consen  133 RQAIHKLNGPQLENQHLKVGYIP  155 (584)
T ss_pred             HHHHHhhcchHhhhhhhhcccCc
Confidence            99999998 79999999988743

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.09  E-value=4.1e-06  Score=89.80  Aligned_cols=71  Identities=20%  Similarity=0.377  Sum_probs=63.7

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVE  177 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~  177 (522)
                      .....+|+|-|||.+|++++|+++|+.||+|+.|+.-     ...++.+||+|-|..+|++|++.++ .+|.+++|+
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t-----~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRET-----PNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcc-----cccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            4567899999999999999999999999999986553     4457899999999999999999999 899999998

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.08  E-value=2.6e-07  Score=102.73  Aligned_cols=165  Identities=16%  Similarity=0.153  Sum_probs=125.6

Q ss_pred             CcEEEECCCCCCCCHH-HHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecCC
Q 009920            5 LGKLFIGGISWDTDEE-RLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         5 ~r~LfVgnLP~~~tee-dL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~~   82 (522)
                      .+++.+.++-+...++ .++..|+.++.|+.|++......-..--+.++++..+..++.|. .....+..+.+.|..+.+
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            3556677777776555 57888999999999998763221112228899999999999999 777788888887777766


Q ss_pred             CccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHH
Q 009920           83 RDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDR  162 (522)
Q Consensus        83 k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~  162 (522)
                      +.......-.      +.......++||.||+..+.++||...|..++.|..++|...+++++.||+|+|+|..++++.+
T Consensus       651 ~~~~~~~kvs------~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~a  724 (881)
T KOG0128|consen  651 EEKEENFKVS------PNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGA  724 (881)
T ss_pred             hhhhhccCcC------chHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhh
Confidence            5532211100      0011245689999999999999999999999999888888788889999999999999999999


Q ss_pred             HHHhcCCccCCeE
Q 009920          163 VLHKTFHELNGKM  175 (522)
Q Consensus       163 Al~~~~~~l~Gr~  175 (522)
                      |+...+..+.++.
T Consensus       725 aV~f~d~~~~gK~  737 (881)
T KOG0128|consen  725 AVAFRDSCFFGKI  737 (881)
T ss_pred             hhhhhhhhhhhhh
Confidence            9998885555533

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.06  E-value=2.5e-05  Score=66.89  Aligned_cols=78  Identities=15%  Similarity=0.252  Sum_probs=66.4

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhc--CCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccC----CeEEEE
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQF--GTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELN----GKMVEV  178 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~f--G~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~----Gr~I~V  178 (522)
                      ++|.|+|+|...|.++|.+++...  +...-+-++.|..+....|||||.|.++++|.+-.+..+ +.+.    .|.++|
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            589999999999999999999763  566777888999889999999999999999999888776 5443    577899


Q ss_pred             EEcCC
Q 009920          179 KRAVP  183 (522)
Q Consensus       179 ~~a~p  183 (522)
                      .+|+-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            88864

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

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

Probab=97.90  E-value=0.0001  Score=71.10  Aligned_cols=87  Identities=17%  Similarity=0.302  Sum_probs=66.7

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEE-ecCCCCCcceEEEEEecCHHHHHHHHHhcC-Ccc---CCeE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVM-YDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HEL---NGKM  175 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~-~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l---~Gr~  175 (522)
                      .+...++|||.+||.++...||..+|..|---+.+.|. .++..+-.+-+|||+|.+..+|++|+.+++ ..|   .+..
T Consensus        30 ~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~st  109 (284)
T KOG1457|consen   30 EPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGST  109 (284)
T ss_pred             cccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCce
Confidence            34568899999999999999999999998655555443 333333345699999999999999999988 444   3577


Q ss_pred             EEEEEcCCCCCC
Q 009920          176 VEVKRAVPKEFS  187 (522)
Q Consensus       176 I~V~~a~pk~~~  187 (522)
                      |++++|+...+.
T Consensus       110 LhiElAKSNtK~  121 (284)
T KOG1457|consen  110 LHIELAKSNTKR  121 (284)
T ss_pred             eEeeehhcCccc
Confidence            888888765543

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=97.82  E-value=3.5e-05  Score=84.56  Aligned_cols=81  Identities=26%  Similarity=0.410  Sum_probs=70.5

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecC---CCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEE
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDR---ATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEA   77 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~---~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V   77 (522)
                      ...++|||.||++.++|+.|...|..||+|..++||--+   +.-+.+-|+||.|-+..+|++|+  +++..+...++++
T Consensus       172 P~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~  251 (877)
T KOG0151|consen  172 PQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKL  251 (877)
T ss_pred             CcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeee
Confidence            346899999999999999999999999999999997533   23456789999999999999999  9999999999999


Q ss_pred             eecCCC
Q 009920           78 KKAVPR   83 (522)
Q Consensus        78 ~~a~~k   83 (522)
                      -|.++-
T Consensus       252 gWgk~V  257 (877)
T KOG0151|consen  252 GWGKAV  257 (877)
T ss_pred             cccccc
Confidence            887543

>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=97.66  E-value=0.00011  Score=63.97  Aligned_cols=53  Identities=32%  Similarity=0.497  Sum_probs=36.1

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI   64 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl   64 (522)
                      +.|.|.+++.+++-++|+++|++|++|..|.+.+...      .|+|.|.+++.|++|+
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~------~g~VRf~~~~~A~~a~   54 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT------EGYVRFKTPEAAQKAL   54 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S------EEEEEESS---HHHHH
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC------EEEEEECCcchHHHHH
Confidence            4689999999999999999999999999999987654      7999999999999999

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=97.65  E-value=7.1e-05  Score=82.17  Aligned_cols=83  Identities=20%  Similarity=0.403  Sum_probs=72.4

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecC---CCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDH---NTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEV  178 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~---~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V  178 (522)
                      ..++.|||+||+..++|+.|...|..||+|..|+|+..+   +..+.+-++||.|.+..+|++|++.++ ..+....+++
T Consensus       172 P~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~  251 (877)
T KOG0151|consen  172 PQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKL  251 (877)
T ss_pred             CcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeee
Confidence            456789999999999999999999999999999998653   345567799999999999999999998 7889999999


Q ss_pred             EEcCCCC
Q 009920          179 KRAVPKE  185 (522)
Q Consensus       179 ~~a~pk~  185 (522)
                      -|.++-.
T Consensus       252 gWgk~V~  258 (877)
T KOG0151|consen  252 GWGKAVP  258 (877)
T ss_pred             ccccccc
Confidence            9986443

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=97.60  E-value=5.4e-05  Score=78.98  Aligned_cols=68  Identities=15%  Similarity=0.227  Sum_probs=58.0

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEec---CCCC--Cc--------ceEEEEEecCHHHHHHHHHhcC
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYD---HNTQ--RP--------RGFGFITYDSEEAVDRVLHKTF  168 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d---~~tg--~~--------rG~aFVeF~s~e~A~~Al~~~~  168 (522)
                      +.+.++|.+.|||.+-.-+.|.+||..+|.|+.|+|++.   ++..  .+        +=+|+|||+..++|.+|.++++
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            357899999999999999999999999999999999876   3222  11        3479999999999999999997


Q ss_pred             C
Q 009920          169 H  169 (522)
Q Consensus       169 ~  169 (522)
                      .
T Consensus       308 ~  308 (484)
T KOG1855|consen  308 P  308 (484)
T ss_pred             h
Confidence            4

>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=97.59  E-value=9.4e-05  Score=64.44  Aligned_cols=69  Identities=25%  Similarity=0.415  Sum_probs=44.2

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-C-----ccCCeEEEEE
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-H-----ELNGKMVEVK  179 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~-----~l~Gr~I~V~  179 (522)
                      ..|+|.+++..++.++|+++|++|+.|..|.+.+...      .|+|.|.++++|++|++++. .     .|.+..+.++
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~------~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT------EGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S------EEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC------EEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            3588889999999999999999999999999986544      79999999999999998765 2     4666666655


Q ss_pred             E
Q 009920          180 R  180 (522)
Q Consensus       180 ~  180 (522)
                      .
T Consensus        76 v   76 (105)
T PF08777_consen   76 V   76 (105)
T ss_dssp             -
T ss_pred             E
Confidence            4

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.54  E-value=0.00032  Score=58.06  Aligned_cols=67  Identities=16%  Similarity=0.324  Sum_probs=44.5

Q ss_pred             cEEEECCCCCCCCHHHH----HHHHhccC-CeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEe
Q 009920            6 GKLFIGGISWDTDEERL----KEYFSRYG-EVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAK   78 (522)
Q Consensus         6 r~LfVgnLP~~~teedL----~e~F~~~G-~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~   78 (522)
                      ..|+|.|||.+.+...|    +.+++.+| +|.+|  .        .+-|+|.|.++|.|++|+  |++..+.|++|.|.
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--S--------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--e--------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            56999999999887665    55666774 66544  2        247999999999999999  99999999999998


Q ss_pred             ecCC
Q 009920           79 KAVP   82 (522)
Q Consensus        79 ~a~~   82 (522)
                      ....
T Consensus        73 ~~~~   76 (90)
T PF11608_consen   73 FSPK   76 (90)
T ss_dssp             SS--
T ss_pred             EcCC
Confidence            7743

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.54  E-value=7.5e-05  Score=76.64  Aligned_cols=83  Identities=25%  Similarity=0.371  Sum_probs=73.3

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeE--------EEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVV--------EAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDG   72 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~--------~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~G   72 (522)
                      .+.-+|||-.||..+++++|.++|.+++.|.        .|+|-++++|.+.|+-|.|.|.|+..|+.|+  .+...+++
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~g  143 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCG  143 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccC
Confidence            3456899999999999999999999998774        4667889999999999999999999999999  88999999


Q ss_pred             eEEEEeecCCCcc
Q 009920           73 RTVEAKKAVPRDD   85 (522)
Q Consensus        73 r~I~V~~a~~k~~   85 (522)
                      .+|+|..+..+..
T Consensus       144 n~ikvs~a~~r~~  156 (351)
T KOG1995|consen  144 NTIKVSLAERRTG  156 (351)
T ss_pred             CCchhhhhhhccC
Confidence            9999987766543

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.35  E-value=0.00012  Score=74.69  Aligned_cols=80  Identities=24%  Similarity=0.508  Sum_probs=71.6

Q ss_pred             cEEE-ECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHHH-cccccCCeEEEEeecCCC
Q 009920            6 GKLF-IGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIM-DKHMIDGRTVEAKKAVPR   83 (522)
Q Consensus         6 r~Lf-VgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl~-~~~~i~Gr~I~V~~a~~k   83 (522)
                      .++| |.+|+.++++++|+++|..++.|..++++.++.++.+++|++|+|.+...+.++++ ..+.+.++++.+....++
T Consensus       185 ~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  264 (285)
T KOG4210|consen  185 DTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALNDQTRSIGGRPLRLEEDEPR  264 (285)
T ss_pred             ccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhcccCcccCcccccccCCCC
Confidence            4455 99999999999999999999999999999999999999999999999999999994 667888898988877765


Q ss_pred             cc
Q 009920           84 DD   85 (522)
Q Consensus        84 ~~   85 (522)
                      ..
T Consensus       265 ~~  266 (285)
T KOG4210|consen  265 PK  266 (285)
T ss_pred             cc
Confidence            43

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.21  E-value=0.00071  Score=51.54  Aligned_cols=52  Identities=19%  Similarity=0.388  Sum_probs=42.6

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI   64 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl   64 (522)
                      +.|-|.+.|.+..+ +|.++|..||+|+++.+....      -+.+|+|++..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~~~------~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPEST------NWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCCCC------cEEEEEECCHHHHHhhC
Confidence            56888999877654 566699999999998886333      38999999999999986

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.16  E-value=0.00032  Score=71.49  Aligned_cols=77  Identities=19%  Similarity=0.357  Sum_probs=67.5

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcC--CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFG--TITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG--~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      +.-++||+||-|.+|++||.+.++..|  .+.++++..++.++++||||+|...++.++++.++.+. ++|.|+.-.|.-
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            445799999999999999999998766  46788889999999999999999999999999999999 799997766643

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.13  E-value=0.00026  Score=72.21  Aligned_cols=73  Identities=16%  Similarity=0.465  Sum_probs=63.5

Q ss_pred             EEEECCCCCCCCHHHHHHHHhccC--CeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            7 KLFIGGISWDTDEERLKEYFSRYG--EVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         7 ~LfVgnLP~~~teedL~e~F~~~G--~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      .+||+||-|.+|++||.+.+...|  .+.++++..++.++.+||||.|...+.+..++.+  +-.++|+|+.-.|..
T Consensus        82 ~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~  158 (498)
T KOG4849|consen   82 CCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLS  158 (498)
T ss_pred             EEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeec
Confidence            479999999999999999998765  6788899999999999999999999999999888  778888887655543

>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=97.10  E-value=0.0017  Score=53.91  Aligned_cols=67  Identities=16%  Similarity=0.332  Sum_probs=45.8

Q ss_pred             ceeEecCCCCCCCHH----HHHHHHhhcC-CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          106 KKIFVGGLASTVTES----DFKKYFDQFG-TITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       106 ~~LfVgnLp~~vtee----dL~~~F~~fG-~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      ..|+|.|||.+.+..    .|+++++.+| .|.+|  .        .+.|+|.|.+++.|++|++.|+ .++-|++|.|+
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--S--------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--e--------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            468999999998875    4667777785 45443  1        2379999999999999999988 89999999999


Q ss_pred             EcC
Q 009920          180 RAV  182 (522)
Q Consensus       180 ~a~  182 (522)
                      +..
T Consensus        73 ~~~   75 (90)
T PF11608_consen   73 FSP   75 (90)
T ss_dssp             SS-
T ss_pred             EcC
Confidence            874

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.05  E-value=0.0012  Score=50.27  Aligned_cols=52  Identities=27%  Similarity=0.494  Sum_probs=41.3

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHH
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL  164 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al  164 (522)
                      +.|-|.+.+.+..+. +.++|..||+|+++.+...++      ..+|+|.++.+|++||
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~~~~------~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPESTN------WMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCCCCc------EEEEEECCHHHHHhhC
Confidence            457788888776655 555888999999988873333      8999999999999986

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=96.97  E-value=0.0056  Score=69.67  Aligned_cols=18  Identities=44%  Similarity=0.765  Sum_probs=8.1

Q ss_pred             CCCCCCCCCCCCCCCCCC
Q 009920          237 ATGRGGISPFGGAGYGVG  254 (522)
Q Consensus       237 gGGrGG~gg~gggGyG~g  254 (522)
                      .+.|.|...+.++|||.+
T Consensus      1180 SgyRRGgssysgGGYGgg 1197 (1282)
T KOG0921|consen 1180 SGYRRGGSSYSGGGYGGG 1197 (1282)
T ss_pred             cccccCCCCCCCCCcCCC
Confidence            344444444444455544

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.93  E-value=0.00055  Score=67.45  Aligned_cols=71  Identities=28%  Similarity=0.476  Sum_probs=59.9

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCC--------CCccc----EEEEEecCHHHHHHHH--Hcccc
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRAT--------GRARG----FGFVVFADPAVAERVI--MDKHM   69 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~t--------g~srG----~aFVeF~~~e~A~kAl--~~~~~   69 (522)
                      ....|||.+||+.++...|+++|+.||+|-.|.|.+...+        +.++.    -+.|+|.++..|+++.  +|+..
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            4578999999999999999999999999999999877655        23333    2779999999999987  89999


Q ss_pred             cCCeE
Q 009920           70 IDGRT   74 (522)
Q Consensus        70 i~Gr~   74 (522)
                      |.+++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            88864

>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=96.93  E-value=0.0025  Score=55.02  Aligned_cols=79  Identities=16%  Similarity=0.330  Sum_probs=53.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEE-EeecC------CCCCcccEEEEEecCHHHHHHHH-HcccccCCe-
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAV-IMRDR------ATGRARGFGFVVFADPAVAERVI-MDKHMIDGR-   73 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~-i~~d~------~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr-   73 (522)
                      .+++-|.|=+.|+. ....|.++|++||+|.+.. +.++.      .......+-.|+|.++.+|++|| .|+..|.+. 
T Consensus         4 ~~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~   82 (100)
T PF05172_consen    4 DSETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSL   82 (100)
T ss_dssp             GGCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCE
T ss_pred             cCCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcE
Confidence            45677888899988 6678999999999998775 10100      00123458999999999999999 899999875 


Q ss_pred             EEEEeecCC
Q 009920           74 TVEAKKAVP   82 (522)
Q Consensus        74 ~I~V~~a~~   82 (522)
                      .+-|++.++
T Consensus        83 mvGV~~~~~   91 (100)
T PF05172_consen   83 MVGVKPCDP   91 (100)
T ss_dssp             EEEEEE-HH
T ss_pred             EEEEEEcHH
Confidence            444666643

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.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.83  E-value=0.0021  Score=65.46  Aligned_cols=82  Identities=22%  Similarity=0.458  Sum_probs=63.8

Q ss_pred             CCcceeEecCCCCCCCHHH------HHHHHhhcCCeeEEEEEecCCCCCc-ceEE--EEEecCHHHHHHHHHhcC-CccC
Q 009920          103 GRTKKIFVGGLASTVTESD------FKKYFDQFGTITDVVVMYDHNTQRP-RGFG--FITYDSEEAVDRVLHKTF-HELN  172 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteed------L~~~F~~fG~I~~v~i~~d~~tg~~-rG~a--FVeF~s~e~A~~Al~~~~-~~l~  172 (522)
                      ....-+||-+||..+..|+      -.++|.+||.|++|.|-+......+ .+.+  +|+|.+.|+|.+||...+ ..++
T Consensus       112 vQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~D  191 (480)
T COG5175         112 VQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLD  191 (480)
T ss_pred             eecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccccc
Confidence            3445689999998887776      3578999999999888765422211 1223  999999999999999999 8999


Q ss_pred             CeEEEEEEcCCC
Q 009920          173 GKMVEVKRAVPK  184 (522)
Q Consensus       173 Gr~I~V~~a~pk  184 (522)
                      ||.|+..+-..|
T Consensus       192 Gr~lkatYGTTK  203 (480)
T COG5175         192 GRVLKATYGTTK  203 (480)
T ss_pred             CceEeeecCchH
Confidence            999999887654

>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]

Probab=96.81  E-value=0.022  Score=65.07  Aligned_cols=12  Identities=33%  Similarity=0.401  Sum_probs=4.6

Q ss_pred             CcccEEEEEecC
Q 009920           45 RARGFGFVVFAD   56 (522)
Q Consensus        45 ~srG~aFVeF~~   56 (522)
                      +.++|+--.|++
T Consensus       900 ~q~~~~g~kfsd  911 (1282)
T KOG0921|consen  900 TQRKFAGNKFSD  911 (1282)
T ss_pred             chhhcccccccc
Confidence            333343333433

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.61  E-value=0.0018  Score=67.84  Aligned_cols=62  Identities=15%  Similarity=0.224  Sum_probs=53.4

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeec---CCCCC----------cccEEEEEecCHHHHHHHH
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRD---RATGR----------ARGFGFVVFADPAVAERVI   64 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d---~~tg~----------srG~aFVeF~~~e~A~kAl   64 (522)
                      ..+++|.+-|||.+-.-+.|.++|..+|.|..|+|++-   +++.+          .+-+|+|+|.+.+.|+||.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~  303 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAR  303 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHH
Confidence            46899999999999888999999999999999999775   33221          2567999999999999998

>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=96.58  E-value=0.0068  Score=52.35  Aligned_cols=79  Identities=27%  Similarity=0.363  Sum_probs=52.3

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEE-EEecC------CCCCcceEEEEEecCHHHHHHHHHhcCCccCCe-E
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVV-VMYDH------NTQRPRGFGFITYDSEEAVDRVLHKTFHELNGK-M  175 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~-i~~d~------~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr-~  175 (522)
                      ...-|.|-+.|+. ....|-+.|++||+|.+.. +.++.      ..........|+|+++.+|++||+++...|.|. +
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~m   83 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSLM   83 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCEE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcEE
Confidence            3456888899987 5567888999999997764 11100      001112388999999999999999999889884 6


Q ss_pred             EEEEEcCC
Q 009920          176 VEVKRAVP  183 (522)
Q Consensus       176 I~V~~a~p  183 (522)
                      |-|.+.++
T Consensus        84 vGV~~~~~   91 (100)
T PF05172_consen   84 VGVKPCDP   91 (100)
T ss_dssp             EEEEE-HH
T ss_pred             EEEEEcHH
Confidence            66777743

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.

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=96.43  E-value=0.0082  Score=64.54  Aligned_cols=61  Identities=23%  Similarity=0.338  Sum_probs=57.0

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHh-ccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFS-RYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI   64 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~-~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl   64 (522)
                      ..+||||+.||.-++.+||..+|+ -||-|.-+-|=.|++-+-+||-+=|.|.+...-.+||
T Consensus       369 prrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AI  430 (520)
T KOG0129|consen  369 PRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAI  430 (520)
T ss_pred             ccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHH
Confidence            468999999999999999999999 5999999999999777889999999999999999998

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.32  E-value=0.0076  Score=61.52  Aligned_cols=77  Identities=22%  Similarity=0.531  Sum_probs=59.0

Q ss_pred             EEEECCCCCCCCHHHH------HHHHhccCCeEEEEEeecCCC-CCcccEE--EEEecCHHHHHHHH--HcccccCCeEE
Q 009920            7 KLFIGGISWDTDEERL------KEYFSRYGEVVEAVIMRDRAT-GRARGFG--FVVFADPAVAERVI--MDKHMIDGRTV   75 (522)
Q Consensus         7 ~LfVgnLP~~~teedL------~e~F~~~G~V~~v~i~~d~~t-g~srG~a--FVeF~~~e~A~kAl--~~~~~i~Gr~I   75 (522)
                      -|||-+||+.+..|++      .++|.+||+|..|.|-+.... ....+.+  ||.|.++|+|.+||  .++..++||.|
T Consensus       116 LvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~l  195 (480)
T COG5175         116 LVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRVL  195 (480)
T ss_pred             eeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCceE
Confidence            4689999999776662      489999999988777554211 1122233  99999999999999  88999999999


Q ss_pred             EEeecCCC
Q 009920           76 EAKKAVPR   83 (522)
Q Consensus        76 ~V~~a~~k   83 (522)
                      ++.+-..+
T Consensus       196 katYGTTK  203 (480)
T COG5175         196 KATYGTTK  203 (480)
T ss_pred             eeecCchH
Confidence            98776554

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.30  E-value=0.009  Score=59.11  Aligned_cols=97  Identities=18%  Similarity=0.346  Sum_probs=78.8

Q ss_pred             HcccccCCeEEEEeecCCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCC
Q 009920           65 MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQ  144 (522)
Q Consensus        65 ~~~~~i~Gr~I~V~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg  144 (522)
                      ++.....++.++|.++..                       +.|+|.||+.-++-+.|++.|+.||+|....++.|.. .
T Consensus        14 Ld~~~~~~~~lr~rfa~~-----------------------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r-~   69 (275)
T KOG0115|consen   14 LDGRFPKGRSLRVRFAMH-----------------------AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDR-G   69 (275)
T ss_pred             cCCCCCCCCceEEEeecc-----------------------ceEEEEecchhhhhHHHHHhhhhcCccchheeeeccc-c
Confidence            788888999999988753                       4699999999999999999999999999888877754 6


Q ss_pred             CcceEEEEEecCHHHHHHHHHhcC-C----ccCCeEEEEEEcCCCC
Q 009920          145 RPRGFGFITYDSEEAVDRVLHKTF-H----ELNGKMVEVKRAVPKE  185 (522)
Q Consensus       145 ~~rG~aFVeF~s~e~A~~Al~~~~-~----~l~Gr~I~V~~a~pk~  185 (522)
                      ++.+-.+|+|...-.+.+|+.... .    ...++++-|.......
T Consensus        70 k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP~eq~~  115 (275)
T KOG0115|consen   70 KPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEPMEQPD  115 (275)
T ss_pred             cccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCChhhccC
Confidence            778899999999988888888774 2    4555666666544333

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=96.28  E-value=0.0024  Score=69.01  Aligned_cols=75  Identities=21%  Similarity=0.318  Sum_probs=58.0

Q ss_pred             CcEEEECCCCCC--CCHH----HHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccC-CeEE
Q 009920            5 LGKLFIGGISWD--TDEE----RLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMID-GRTV   75 (522)
Q Consensus         5 ~r~LfVgnLP~~--~tee----dL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~-Gr~I   75 (522)
                      ...|+|-|+|.-  +..+    -|.++|+++|+|+++.+..+.+ +..+||.|++|++..+|++|+  +|++.|+ .++.
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            456899999964  2222    3457899999999999998877 459999999999999999999  7777765 4455


Q ss_pred             EEeec
Q 009920           76 EAKKA   80 (522)
Q Consensus        76 ~V~~a   80 (522)
                      .|..-
T Consensus       137 ~v~~f  141 (698)
T KOG2314|consen  137 FVRLF  141 (698)
T ss_pred             Eeehh
Confidence            55443

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.13  E-value=0.028  Score=44.21  Aligned_cols=56  Identities=20%  Similarity=0.375  Sum_probs=46.4

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhc---CCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhc
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQF---GTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT  167 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~f---G~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~  167 (522)
                      +..+|+|.++. +++.+||+.+|..|   .....|..+-|.       .|-|.|.+++.|.+||.++
T Consensus         4 rpeavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    4 RPEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eeceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            45689999995 58889999999998   234678888775       5899999999999999764

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.09  E-value=0.024  Score=52.07  Aligned_cols=56  Identities=18%  Similarity=0.340  Sum_probs=45.9

Q ss_pred             HHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcCCC
Q 009920          121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPK  184 (522)
Q Consensus       121 dL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~pk  184 (522)
                      +|-+.|.+||+|.-|+++.+        .-+|+|.+-++|.+|+++...+++|+.|+|+...|.
T Consensus        52 ~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALSLDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHHGCCSEETTEEEEEEE----
T ss_pred             HHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHccCCcEECCEEEEEEeCCcc
Confidence            67778888999998888755        469999999999999999999999999999998765

; PDB: 1UFW_A 2DNR_A.

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=95.88  E-value=0.015  Score=62.83  Aligned_cols=71  Identities=13%  Similarity=0.203  Sum_probs=58.8

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHh--hcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC---CccCCeEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFD--QFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF---HELNGKMVE  177 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~--~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~---~~l~Gr~I~  177 (522)
                      .+.+.|.|+.||+++-+|+|+.+|+  .|-++.+|.+-.+..       =||+|+++.||++|.+.+.   ++|.||+|.
T Consensus       173 ~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n-------WyITfesd~DAQqAykylreevk~fqgKpIm  245 (684)
T KOG2591|consen  173 HKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN-------WYITFESDTDAQQAYKYLREEVKTFQGKPIM  245 (684)
T ss_pred             cceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc-------eEEEeecchhHHHHHHHHHHHHHhhcCcchh
Confidence            4567788999999999999999995  478888888876543       5999999999999998876   588898885


Q ss_pred             EEE
Q 009920          178 VKR  180 (522)
Q Consensus       178 V~~  180 (522)
                      ...
T Consensus       246 ARI  248 (684)
T KOG2591|consen  246 ARI  248 (684)
T ss_pred             hhh
Confidence            443

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=95.79  E-value=0.17  Score=51.20  Aligned_cols=164  Identities=10%  Similarity=0.144  Sum_probs=102.1

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecC-------CCCCcccEEEEEecCHHHHHHHH--------Hccc
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDR-------ATGRARGFGFVVFADPAVAERVI--------MDKH   68 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~-------~tg~srG~aFVeF~~~e~A~kAl--------~~~~   68 (522)
                      ..|.|.+.||..+++-.++.+.|.+|++|++|.++.+.       +.-+......+.|-+.+.+-...        .=++
T Consensus        14 rTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEfK~   93 (309)
T PF10567_consen   14 RTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEFKT   93 (309)
T ss_pred             eeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHHHH
Confidence            46788899999999999999999999999999999876       11234467889999999876554        1234


Q ss_pred             ccCCeEEEEeecCCCcccccc-cccc--------CCCC-CCCCCCCcceeEecCCCCCC-CHHHHHHHHh---hcC----
Q 009920           69 MIDGRTVEAKKAVPRDDQNML-NRNT--------SSIH-SSPGPGRTKKIFVGGLASTV-TESDFKKYFD---QFG----  130 (522)
Q Consensus        69 ~i~Gr~I~V~~a~~k~~~~~~-~~~~--------~~~~-~~~~~~~~~~LfVgnLp~~v-teedL~~~F~---~fG----  130 (522)
                      .++-..|.+....-+...... +...        ...+ .......++.|.|.=- ..+ +++-+.+.+.   .-.    
T Consensus        94 ~L~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~IeF~-~~~~~~dl~~~kL~fL~~~~n~RY  172 (309)
T PF10567_consen   94 KLKSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIEFK-DPVDKDDLIEKKLPFLKNSNNKRY  172 (309)
T ss_pred             hcCCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEEec-CccchhHHHHHhhhhhccCCCceE
Confidence            556666665543211111000 0000        0111 1223456777877544 444 4443444332   111    


Q ss_pred             CeeEEEEEecC--CCCCcceEEEEEecCHHHHHHHHHhcC
Q 009920          131 TITDVVVMYDH--NTQRPRGFGFITYDSEEAVDRVLHKTF  168 (522)
Q Consensus       131 ~I~~v~i~~d~--~tg~~rG~aFVeF~s~e~A~~Al~~~~  168 (522)
                      .|+.|.|+...  ...-++-||.++|-+...|.+.++.+.
T Consensus       173 VlEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk  212 (309)
T PF10567_consen  173 VLESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLK  212 (309)
T ss_pred             EEEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHH
Confidence            46777777543  233467799999999888888887655

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=95.71  E-value=0.0093  Score=58.98  Aligned_cols=72  Identities=13%  Similarity=0.313  Sum_probs=59.0

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCC--------CCc----ceEEEEEecCHHHHHHHHHhcC-Cc
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNT--------QRP----RGFGFITYDSEEAVDRVLHKTF-HE  170 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~t--------g~~----rG~aFVeF~s~e~A~~Al~~~~-~~  170 (522)
                      .+..||+.+||+.+....|+++|..||+|-+|-+.....+        +..    ---+.|||.+...|+++.+.++ ..
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            5678999999999999999999999999999888765543        111    1246899999999999988888 78


Q ss_pred             cCCeE
Q 009920          171 LNGKM  175 (522)
Q Consensus       171 l~Gr~  175 (522)
                      |.|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            88764

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=95.64  E-value=0.011  Score=62.99  Aligned_cols=72  Identities=18%  Similarity=0.286  Sum_probs=58.8

Q ss_pred             eeEecCCCCCC-CHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcCCC
Q 009920          107 KIFVGGLASTV-TESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPK  184 (522)
Q Consensus       107 ~LfVgnLp~~v-teedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~pk  184 (522)
                      .|-+.-.|+.+ |.++|...|.+||+|..|.|-....      .|.|+|.+..+|-+|.......|++|.|+|.|-.|-
T Consensus       374 ~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~~------~a~vTF~t~aeag~a~~s~~avlnnr~iKl~whnps  446 (526)
T KOG2135|consen  374 PLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSL------HAVVTFKTRAEAGEAYASHGAVLNNRFIKLFWHNPS  446 (526)
T ss_pred             hhhhhccCCCCchHhhhhhhhhhcCccccccccCchh------hheeeeeccccccchhccccceecCceeEEEEecCC
Confidence            45555566655 4589999999999999998865533      699999999999888777778999999999998873

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=95.63  E-value=0.026  Score=56.82  Aligned_cols=63  Identities=24%  Similarity=0.296  Sum_probs=51.1

Q ss_pred             HHHHHHHHhccCCeEEEEEeecCCCCCccc-EEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920           19 EERLKEYFSRYGEVVEAVIMRDRATGRARG-FGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus        19 eedL~e~F~~~G~V~~v~i~~d~~tg~srG-~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      |+++++.+++||.|..|.|...+......- --||+|...++|.+|+  +|+..+.||.+....-.
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            568899999999999999877654332222 2799999999999999  99999999999876543

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=95.62  E-value=0.049  Score=59.25  Aligned_cols=77  Identities=18%  Similarity=0.296  Sum_probs=60.2

Q ss_pred             CCcceeEecCCCCCCC------HHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-Ccc-CCe
Q 009920          103 GRTKKIFVGGLASTVT------ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HEL-NGK  174 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vt------eedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l-~Gr  174 (522)
                      .-...|+|-++|.--.      ..-|.++|+++|+|+.+.++.+.+++ .+||.|++|.+..+|+.|++.++ +.| ..+
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknH  134 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNH  134 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccc
Confidence            3456788999985322      23577889999999999999998855 89999999999999999999888 443 445


Q ss_pred             EEEEEE
Q 009920          175 MVEVKR  180 (522)
Q Consensus       175 ~I~V~~  180 (522)
                      +..|..
T Consensus       135 tf~v~~  140 (698)
T KOG2314|consen  135 TFFVRL  140 (698)
T ss_pred             eEEeeh
Confidence            566654

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=95.52  E-value=0.043  Score=45.60  Aligned_cols=57  Identities=19%  Similarity=0.318  Sum_probs=43.4

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF  168 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~  168 (522)
                      .+.+..+|. .|.++...||.++|+.||.| .|..+.|.       .|||...+++.|+.|+..+.
T Consensus         7 ~RdHVFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    7 SRDHVFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             SGCCEEEEE---TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEECCCHHHHHHHHHHT
T ss_pred             CcceEEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEeecHHHHHHHHHHhc
Confidence            455566666 99999999999999999987 56666553       69999999999999887765

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=95.49  E-value=0.036  Score=55.83  Aligned_cols=64  Identities=13%  Similarity=0.205  Sum_probs=51.9

Q ss_pred             HHHHHHHHhhcCCeeEEEEEecCCCCCcc-eEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          119 ESDFKKYFDQFGTITDVVVMYDHNTQRPR-GFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       119 eedL~~~F~~fG~I~~v~i~~d~~tg~~r-G~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      |+++++.+++||.|..|.|..++...... --.||+|+..++|.+|+-.++ ..|.||.+...+-.
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            46788999999999999998775432221 247999999999999999999 89999999877654

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=95.36  E-value=0.0085  Score=59.31  Aligned_cols=60  Identities=22%  Similarity=0.370  Sum_probs=48.9

Q ss_pred             HHHHHHHh-ccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920           20 ERLKEYFS-RYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus        20 edL~e~F~-~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      +||...|+ +||+|++++|..+.. -..+|-+||.|..+|+|++|+  +++..+.+++|.++..
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~-~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLG-DHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccc-hhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            34444445 899999998877653 457889999999999999999  9999999999988754

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=95.34  E-value=0.047  Score=50.15  Aligned_cols=55  Identities=31%  Similarity=0.494  Sum_probs=44.4

Q ss_pred             HHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecCCC
Q 009920           21 RLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAVPR   83 (522)
Q Consensus        21 dL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~~k   83 (522)
                      +|.+.|+.||+|.-++++-+        .-+|+|.+-+.|-+|+ ++..+|.++.|+|+...|.
T Consensus        52 ~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALSLDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHHGCCSEETTEEEEEEE----
T ss_pred             HHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHccCCcEECCEEEEEEeCCcc
Confidence            67788888999987777665        4699999999999999 9999999999999877654

; PDB: 1UFW_A 2DNR_A.

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=95.26  E-value=0.024  Score=59.10  Aligned_cols=78  Identities=13%  Similarity=0.182  Sum_probs=63.5

Q ss_pred             cceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecC---CCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEc
Q 009920          105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDH---NTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRA  181 (522)
Q Consensus       105 ~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~---~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a  181 (522)
                      ...|.|.||.+.+|.++++.+|...|.|.++.++...   ......-.|||.|.+...+..|..+.+..+-++.|.|-..
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~   86 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPY   86 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEec
Confidence            3479999999999999999999999999999987632   1222344899999999999999999997777777776554


Q ss_pred             C
Q 009920          182 V  182 (522)
Q Consensus       182 ~  182 (522)
                      .
T Consensus        87 ~   87 (479)
T KOG4676|consen   87 G   87 (479)
T ss_pred             C
Confidence            3

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=95.24  E-value=0.0092  Score=59.08  Aligned_cols=62  Identities=18%  Similarity=0.296  Sum_probs=49.6

Q ss_pred             HHHHHHHh-hcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          120 SDFKKYFD-QFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       120 edL~~~F~-~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      |||...|+ +||+|+++.|..+.. ...+|-++|.|..+|+|++|++.++ ..+.|++|...+..
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~-~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLG-DHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccc-hhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            34444444 899999997776543 4557889999999999999999999 89999999887753

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=95.19  E-value=0.012  Score=62.56  Aligned_cols=80  Identities=15%  Similarity=0.164  Sum_probs=66.6

Q ss_pred             CCCCCcEEEECCCCCCC-CHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEe
Q 009920            1 MESDLGKLFIGGISWDT-DEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAK   78 (522)
Q Consensus         1 me~d~r~LfVgnLP~~~-teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~   78 (522)
                      |+.|.+.|-+.-+|... |-++|...|.+||+|++|.|-...+      -|.|+|.+..+|-+|. .+...|++|.|+|.
T Consensus       368 ~~~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~~------~a~vTF~t~aeag~a~~s~~avlnnr~iKl~  441 (526)
T KOG2135|consen  368 AVVDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSL------HAVVTFKTRAEAGEAYASHGAVLNNRFIKLF  441 (526)
T ss_pred             hhcccchhhhhccCCCCchHhhhhhhhhhcCccccccccCchh------hheeeeeccccccchhccccceecCceeEEE
Confidence            45678888888888884 6778999999999999999866533      6999999999996665 88999999999999


Q ss_pred             ecCCCccc
Q 009920           79 KAVPRDDQ   86 (522)
Q Consensus        79 ~a~~k~~~   86 (522)
                      |-.+....
T Consensus       442 whnps~~t  449 (526)
T KOG2135|consen  442 WHNPSPVT  449 (526)
T ss_pred             EecCCccc
Confidence            98875433

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=94.98  E-value=0.037  Score=60.02  Aligned_cols=69  Identities=14%  Similarity=0.219  Sum_probs=58.2

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhc--cCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH----HcccccCCeEEEE
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSR--YGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI----MDKHMIDGRTVEA   77 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~--~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl----~~~~~i~Gr~I~V   77 (522)
                      +.|.|+|+-||..+.+|+|+.+|+.  |-++.+|.+-.+..       =||+|++.+||++|.    .+.++|.++.|.+
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n-------WyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN-------WYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc-------eEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            5688999999999999999999964  78899999877643       599999999999997    5667888988866


Q ss_pred             ee
Q 009920           78 KK   79 (522)
Q Consensus        78 ~~   79 (522)
                      ..
T Consensus       247 RI  248 (684)
T KOG2591|consen  247 RI  248 (684)
T ss_pred             hh
Confidence            44

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=94.65  E-value=0.14  Score=40.36  Aligned_cols=50  Identities=30%  Similarity=0.518  Sum_probs=43.0

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhcc----CCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRY----GEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI   64 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~----G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl   64 (522)
                      .+|+|++|. +++.++|+.+|..|    .+ ..|..+-|.       -|-|.|.+++.|.+||
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~-~~IEWIdDt-------ScNvvf~d~~~A~~AL   59 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGP-FRIEWIDDT-------SCNVVFKDEETAARAL   59 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCC-ceEEEecCC-------cEEEEECCHHHHHHHH
Confidence            579999994 68999999999998    54 468888774       5899999999999998

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=94.65  E-value=0.19  Score=45.89  Aligned_cols=75  Identities=16%  Similarity=0.219  Sum_probs=60.1

Q ss_pred             CCCCcceeEecCCCCCCC-HHHHHHH---HhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEE
Q 009920          101 GPGRTKKIFVGGLASTVT-ESDFKKY---FDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMV  176 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vt-eedL~~~---F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I  176 (522)
                      ...+..+|.|+=|..++. .+||+.+   ++.||+|..|...     ++.  .|.|.|.+..+|.+|+.+......|.++
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----Grq--savVvF~d~~SAC~Av~Af~s~~pgtm~  154 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----GRQ--SAVVVFKDITSACKAVSAFQSRAPGTMF  154 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----CCc--eEEEEehhhHHHHHHHHhhcCCCCCceE
Confidence            456778999988887764 3555554   4679999999886     322  7999999999999999999988899999


Q ss_pred             EEEEcC
Q 009920          177 EVKRAV  182 (522)
Q Consensus       177 ~V~~a~  182 (522)
                      .+.|-.
T Consensus       155 qCsWqq  160 (166)
T PF15023_consen  155 QCSWQQ  160 (166)
T ss_pred             Eeeccc
Confidence            998864

>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=94.35  E-value=0.04  Score=46.41  Aligned_cols=71  Identities=14%  Similarity=0.254  Sum_probs=46.1

Q ss_pred             EEEEecCHHHHHHHH-Hcc--cccCCeEEEEeecCCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHH
Q 009920           50 GFVVFADPAVAERVI-MDK--HMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYF  126 (522)
Q Consensus        50 aFVeF~~~e~A~kAl-~~~--~~i~Gr~I~V~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F  126 (522)
                      |.|+|.+++.|++.+ +..  ..++.+.+.|+...-.......-       ........++|.|.+||..+.|++|++.+
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~-------qv~~~vs~rtVlvsgip~~l~ee~l~D~L   73 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKF-------QVFSGVSKRTVLVSGIPDVLDEEELRDKL   73 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEE-------EEEEcccCCEEEEeCCCCCCChhhheeeE
Confidence            689999999999999 444  35566776665432211110000       00112456789999999999999998765


Q ss_pred             h
Q 009920          127 D  127 (522)
Q Consensus       127 ~  127 (522)
                      +
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 [].

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=94.29  E-value=0.036  Score=58.31  Aligned_cols=76  Identities=25%  Similarity=0.445  Sum_probs=60.5

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC--CccCCeEEEEEEcCC
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF--HELNGKMVEVKRAVP  183 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~--~~l~Gr~I~V~~a~p  183 (522)
                      .+|||+||.+.++.+||+.+|...-.-..-.++..      .||+||.+.++.-|.+|++.++  .++.|++++|....|
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 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            47999999999999999999976411111122222      3699999999999999999998  589999999999988


Q ss_pred             CCCC
Q 009920          184 KEFS  187 (522)
Q Consensus       184 k~~~  187 (522)
                      +..+
T Consensus        76 kkqr   79 (584)
T KOG2193|consen   76 KKQR   79 (584)
T ss_pred             HHHH
Confidence            7653

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=94.20  E-value=0.16  Score=42.26  Aligned_cols=51  Identities=16%  Similarity=0.270  Sum_probs=39.2

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI   64 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl   64 (522)
                      .+..+|. .|.++...||.++|+.||.|. |..+.|-       -|||...+.+.|+.|+
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~dT-------SAfV~l~~r~~~~~v~   59 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWINDT-------SAFVALHNRDQAKVVM   59 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECTT-------EEEEEECCCHHHHHHH
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcCC-------cEEEEeecHHHHHHHH
Confidence            4555666 999999999999999999984 6666652       7999999999999988

; 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.

>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=93.97  E-value=0.068  Score=50.91  Aligned_cols=68  Identities=15%  Similarity=0.085  Sum_probs=40.5

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhc-cCCe---EEEEEeec--CCCCCcccEEEEEecCHHHHHHHH--Hccccc
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSR-YGEV---VEAVIMRD--RATGRARGFGFVVFADPAVAERVI--MDKHMI   70 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~-~G~V---~~v~i~~d--~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i   70 (522)
                      .+..+|.|+.||+.+||+++.+.++. +++.   ..+.-...  ......-.-|||.|.+.+++...+  .+++.+
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F   80 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVF   80 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEE
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEE
Confidence            56789999999999999999997776 5554   22321111  111112345999999999988877  555544

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.

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=93.45  E-value=0.066  Score=53.16  Aligned_cols=74  Identities=23%  Similarity=0.373  Sum_probs=60.0

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--H--cc--cccCCeEEEEee
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M--DK--HMIDGRTVEAKK   79 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~--~~--~~i~Gr~I~V~~   79 (522)
                      ..|+|.||+.-+..|.|++.|+.||+|+..+++.|. .++..+-++|+|..+-.|.+|+  .  ..  -++.++++.|.+
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~-r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP  110 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEP  110 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCCh
Confidence            679999999999999999999999999988887775 4889999999999999999988  2  11  234455555544


Q ss_pred             c
Q 009920           80 A   80 (522)
Q Consensus        80 a   80 (522)
                      .
T Consensus       111 ~  111 (275)
T KOG0115|consen  111 M  111 (275)
T ss_pred             h
Confidence            3

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=93.18  E-value=0.12  Score=56.59  Aligned_cols=78  Identities=13%  Similarity=0.171  Sum_probs=61.8

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHh-hcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-C---ccCCeE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFD-QFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-H---ELNGKM  175 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~-~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~---~l~Gr~  175 (522)
                      ....++.|+|.||-..+|.-+|+.++. ..+.|++.  .+|+.    |-.|||.|.+.++|.+.+.+|+ .   .-+.|.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~--WmDkI----KShCyV~yss~eEA~atr~AlhnV~WP~sNPK~  513 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF--WMDKI----KSHCYVSYSSVEEAAATREALHNVQWPPSNPKH  513 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHH--HHHHh----hcceeEecccHHHHHHHHHHHhccccCCCCCce
Confidence            445678999999999999999999998 56667766  44443    4479999999999999998887 3   456788


Q ss_pred             EEEEEcCCC
Q 009920          176 VEVKRAVPK  184 (522)
Q Consensus       176 I~V~~a~pk  184 (522)
                      |.|.+....
T Consensus       514 L~adf~~~d  522 (718)
T KOG2416|consen  514 LIADFVRAD  522 (718)
T ss_pred             eEeeecchh
Confidence            888877643

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=91.96  E-value=0.26  Score=56.44  Aligned_cols=75  Identities=19%  Similarity=0.327  Sum_probs=62.9

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccC--CeEEEEee
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMID--GRTVEAKK   79 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~--Gr~I~V~~   79 (522)
                      ..++|||++|+..+....|...|..||+|..|.+.....      ||+|++++.+.|+.|+  +....|.  .+.|.|..
T Consensus       454 ~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq~------yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvdl  527 (975)
T KOG0112|consen  454 PTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQP------YAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVDL  527 (975)
T ss_pred             cceeeccCCCCCCChHHHHHHHhhccCcceeeecccCCc------ceeeecccCccchhhHHHHhcCcCCCCCccccccc
Confidence            468899999999999999999999999999988866543      9999999999999999  6666664  36677877


Q ss_pred             cCCCc
Q 009920           80 AVPRD   84 (522)
Q Consensus        80 a~~k~   84 (522)
                      +.+..
T Consensus       528 a~~~~  532 (975)
T KOG0112|consen  528 ASPPG  532 (975)
T ss_pred             ccCCC
Confidence            76543

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=91.70  E-value=0.59  Score=47.57  Aligned_cols=73  Identities=19%  Similarity=0.290  Sum_probs=53.9

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeE-EEEeecCCC
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRT-VEAKKAVPR   83 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~-I~V~~a~~k   83 (522)
                      .=|-|-++|+. .-.-|..+|++||+|++.+...+-      -+-+|.|.+.-+|+||| ++++.|++.. |-|+....+
T Consensus       198 ~WVTVfGFppg-~~s~vL~~F~~cG~Vvkhv~~~ng------NwMhirYssr~~A~KALskng~ii~g~vmiGVkpCtDk  270 (350)
T KOG4285|consen  198 TWVTVFGFPPG-QVSIVLNLFSRCGEVVKHVTPSNG------NWMHIRYSSRTHAQKALSKNGTIIDGDVMIGVKPCTDK  270 (350)
T ss_pred             ceEEEeccCcc-chhHHHHHHHhhCeeeeeecCCCC------ceEEEEecchhHHHHhhhhcCeeeccceEEeeeecCCH
Confidence            34556677765 344678899999999876665433      38999999999999999 9999998754 456665554


Q ss_pred             cc
Q 009920           84 DD   85 (522)
Q Consensus        84 ~~   85 (522)
                      ..
T Consensus       271 sv  272 (350)
T KOG4285|consen  271 SV  272 (350)
T ss_pred             HH
Confidence            43

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=91.43  E-value=0.78  Score=50.42  Aligned_cols=121  Identities=17%  Similarity=0.274  Sum_probs=72.8

Q ss_pred             CCCCcEEEECCCCCC-CCHHHHHHHHhcc----CCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHHHcccccCCeEEE
Q 009920            2 ESDLGKLFIGGISWD-TDEERLKEYFSRY----GEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTVE   76 (522)
Q Consensus         2 e~d~r~LfVgnLP~~-~teedL~e~F~~~----G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl~~~~~i~Gr~I~   76 (522)
                      +..+++|-|-||.|+ +..++|.-+|..|    |.|.+|.|.+..- |                 +.-|...+++|-.++
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeF-G-----------------keRM~eEeV~GP~~e  232 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEF-G-----------------KERMKEEEVHGPPKE  232 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhh-h-----------------HHHhhhhcccCChhh
Confidence            456899999999999 8999999999887    5788998876531 1                 111344445554444


Q ss_pred             EeecCCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecC
Q 009920           77 AKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS  156 (522)
Q Consensus        77 V~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s  156 (522)
                      +...........                        .....-++-.++-+.+| .+..++..          ||.|+|++
T Consensus       233 l~~~~e~~~~s~------------------------sD~ee~~~~~~~kLR~Y-q~~rLkYY----------yAVvecDs  277 (650)
T KOG2318|consen  233 LFKPVEEYKESE------------------------SDDEEEEDVDREKLRQY-QLNRLKYY----------YAVVECDS  277 (650)
T ss_pred             hccccccCcccc------------------------cchhhhhhHHHHHHHHH-HhhhheeE----------EEEEEecC
Confidence            322211110000                        01111111223333444 23333333          89999999


Q ss_pred             HHHHHHHHHhcC-CccCCeE
Q 009920          157 EEAVDRVLHKTF-HELNGKM  175 (522)
Q Consensus       157 ~e~A~~Al~~~~-~~l~Gr~  175 (522)
                      .+.|.++.+.++ .++...-
T Consensus       278 i~tA~~vYe~CDG~EfEsS~  297 (650)
T KOG2318|consen  278 IETAKAVYEECDGIEFESSA  297 (650)
T ss_pred             chHHHHHHHhcCcceecccc
Confidence            999999999998 6666543

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=91.29  E-value=0.92  Score=41.58  Aligned_cols=74  Identities=14%  Similarity=0.184  Sum_probs=53.6

Q ss_pred             CCCCcEEEECCCCCCCC-HHH---HHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEE
Q 009920            2 ESDLGKLFIGGISWDTD-EER---LKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVE   76 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~t-eed---L~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~   76 (522)
                      |....+|.|+=|..++. .+|   |...++.||+|.+|.++-.       --|.|+|+|...|-+|+ .-.....+..+.
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGr-------qsavVvF~d~~SAC~Av~Af~s~~pgtm~q  155 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGR-------QSAVVVFKDITSACKAVSAFQSRAPGTMFQ  155 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCC-------ceEEEEehhhHHHHHHHHhhcCCCCCceEE
Confidence            45667888987777743 334   4456678999998877543       26999999999999999 333466777787


Q ss_pred             EeecCC
Q 009920           77 AKKAVP   82 (522)
Q Consensus        77 V~~a~~   82 (522)
                      +.|.+.
T Consensus       156 CsWqqr  161 (166)
T PF15023_consen  156 CSWQQR  161 (166)
T ss_pred             eecccc
Confidence            777543

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=90.27  E-value=1.6  Score=44.46  Aligned_cols=73  Identities=22%  Similarity=0.280  Sum_probs=54.1

Q ss_pred             eEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCe-EEEEEEcCCCCC
Q 009920          108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGK-MVEVKRAVPKEF  186 (522)
Q Consensus       108 LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr-~I~V~~a~pk~~  186 (522)
                      |-|-++|... -.-|-.+|++||.|++......   +   -+-+|.|.++-+|+|||.++...|++. .|-|+....|..
T Consensus       200 VTVfGFppg~-~s~vL~~F~~cG~Vvkhv~~~n---g---NwMhirYssr~~A~KALskng~ii~g~vmiGVkpCtDksv  272 (350)
T KOG4285|consen  200 VTVFGFPPGQ-VSIVLNLFSRCGEVVKHVTPSN---G---NWMHIRYSSRTHAQKALSKNGTIIDGDVMIGVKPCTDKSV  272 (350)
T ss_pred             EEEeccCccc-hhHHHHHHHhhCeeeeeecCCC---C---ceEEEEecchhHHHHhhhhcCeeeccceEEeeeecCCHHH
Confidence            4455666543 3567789999999987665522   2   288999999999999999999888875 567777666654


Q ss_pred             C
Q 009920          187 S  187 (522)
Q Consensus       187 ~  187 (522)
                      .
T Consensus       273 i  273 (350)
T KOG4285|consen  273 I  273 (350)
T ss_pred             h
Confidence            3

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=90.25  E-value=0.21  Score=47.59  Aligned_cols=79  Identities=14%  Similarity=0.110  Sum_probs=45.9

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhh-cCCe---eEEEEEecC--CCCCcceEEEEEecCHHHHHHHHHhcC-CccCC---
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQ-FGTI---TDVVVMYDH--NTQRPRGFGFITYDSEEAVDRVLHKTF-HELNG---  173 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~-fG~I---~~v~i~~d~--~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~G---  173 (522)
                      ...+|.|++||+.+||+++.+.+.. ++..   ..+.-....  .....-.-|+|.|.+.+++..-++..+ +.+..   
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            4569999999999999999987766 5544   233311221  111123468999999999888888776 33221   


Q ss_pred             --eEEEEEEcC
Q 009920          174 --KMVEVKRAV  182 (522)
Q Consensus       174 --r~I~V~~a~  182 (522)
                        .+..|++|-
T Consensus        86 ~~~~~~VE~Ap   96 (176)
T PF03467_consen   86 NEYPAVVEFAP   96 (176)
T ss_dssp             -EEEEEEEE-S
T ss_pred             CCcceeEEEcc
Confidence              345666654

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=90.21  E-value=0.17  Score=56.13  Aligned_cols=117  Identities=16%  Similarity=0.139  Sum_probs=78.1

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      ..-+|||+||...+.++-++.++..+|-|.+++...         |+|++|..+..+.+|+  ++...+++.++.++.-.
T Consensus        39 ~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~d~  109 (668)
T KOG2253|consen   39 PRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENVDE  109 (668)
T ss_pred             CCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhccchh
Confidence            456799999999999999999999999997776654         9999999999988888  77788888888776531


Q ss_pred             CCccccc--cccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhc
Q 009920           82 PRDDQNM--LNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQF  129 (522)
Q Consensus        82 ~k~~~~~--~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~f  129 (522)
                      ..-....  ........+.-.+....+-++|.++|....+...+..+.--
T Consensus       110 q~~~n~~k~~~~~~~~~~~f~p~~srr~e~i~~k~~~l~~~~~~~~~~is  159 (668)
T KOG2253|consen  110 QTIENADKEKSIANKESHKFVPSSSRRQESIQNKPLSLDEQIHKKSLQIS  159 (668)
T ss_pred             hhhcCccccccchhhhhcccCCchhHHHHHhhccccchhHHHHHHHHhcc
Confidence            1110000  00011111111122224567778888777766666665443

>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=89.90  E-value=4.1  Score=35.83  Aligned_cols=63  Identities=13%  Similarity=0.133  Sum_probs=46.8

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcC-CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFG-TITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF  168 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG-~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~  168 (522)
                      .+..+.+...|..++.++|..+.+.+- .|..++|++|..  ..+-.++++|.+.++|++-.+..|
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fN   75 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFN   75 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhC
Confidence            344555556666677778877777764 477889998854  345689999999999999888776

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>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=89.02  E-value=1.4  Score=35.12  Aligned_cols=53  Identities=28%  Similarity=0.437  Sum_probs=39.4

Q ss_pred             CCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEE
Q 009920           16 DTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEA   77 (522)
Q Consensus        16 ~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V   77 (522)
                      .++-++|+..+.+|.-   .+|+.++.     || ||.|.+.++|+++.  .+...+...+|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~---~~I~~d~t-----Gf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRW---DRIRDDRT-----GF-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc---ceEEecCC-----EE-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            3788999999999964   34556653     55 89999999999999  5566665555543

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=88.90  E-value=1.2  Score=47.68  Aligned_cols=66  Identities=17%  Similarity=0.234  Sum_probs=54.5

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhcc-CCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRY-GEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMID   71 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~-G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~   71 (522)
                      .++.|.|--+|..++-.||..|...+ -.|.+++|+||..  -.+=...|+|++.++|....  .|+..+.
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~--pnrymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGM--PNRYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCC--CceEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            47889999999999999999999875 5689999999643  23445899999999999998  6666554

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=88.08  E-value=0.39  Score=52.85  Aligned_cols=72  Identities=15%  Similarity=0.140  Sum_probs=55.9

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHh-ccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hccccc---CCeEEE
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFS-RYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMI---DGRTVE   76 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~-~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i---~Gr~I~   76 (522)
                      +-++.|+|.||=.-.|.-+|++++. ..+.|++.+|-+      .|-.|||.|.+.++|.+..  |++...   +.+.|.
T Consensus       442 ~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDk------IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~  515 (718)
T KOG2416|consen  442 EPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDK------IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLI  515 (718)
T ss_pred             CccceEeeecccccchHHHHHHHHhhccCchHHHHHHH------hhcceeEecccHHHHHHHHHHHhccccCCCCCceeE
Confidence            3468899999999999999999999 477888774422      3458999999999998877  666544   456666


Q ss_pred             Eeec
Q 009920           77 AKKA   80 (522)
Q Consensus        77 V~~a   80 (522)
                      +.+.
T Consensus       516 adf~  519 (718)
T KOG2416|consen  516 ADFV  519 (718)
T ss_pred             eeec
Confidence            6554

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=87.73  E-value=0.26  Score=50.85  Aligned_cols=80  Identities=24%  Similarity=0.471  Sum_probs=58.8

Q ss_pred             cEEEECCCCCCCCHHH-HH--HHHhccCCeEEEEEeecCC--CCC-cccEEEEEecCHHHHHHHH--HcccccCCeEEEE
Q 009920            6 GKLFIGGISWDTDEER-LK--EYFSRYGEVVEAVIMRDRA--TGR-ARGFGFVVFADPAVAERVI--MDKHMIDGRTVEA   77 (522)
Q Consensus         6 r~LfVgnLP~~~teed-L~--e~F~~~G~V~~v~i~~d~~--tg~-srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V   77 (522)
                      +-+||-+||.+...++ |+  +.|.+||.|..|.+.++.-  ... ...-++|.|...|+|..||  .++..++++.|++
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            4568888998854444 43  6888999999888877652  111 1223899999999999999  8888899998877


Q ss_pred             eecCCCcc
Q 009920           78 KKAVPRDD   85 (522)
Q Consensus        78 ~~a~~k~~   85 (522)
                      .....+..
T Consensus       158 ~~gttkyc  165 (327)
T KOG2068|consen  158 SLGTTKYC  165 (327)
T ss_pred             hhCCCcch
Confidence            76665543

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=87.32  E-value=0.18  Score=51.91  Aligned_cols=84  Identities=23%  Similarity=0.372  Sum_probs=62.9

Q ss_pred             CCcceeEecCCCCCCCHHHHH---HHHhhcCCeeEEEEEecCCCC---CcceEEEEEecCHHHHHHHHHhcC-CccCCeE
Q 009920          103 GRTKKIFVGGLASTVTESDFK---KYFDQFGTITDVVVMYDHNTQ---RPRGFGFITYDSEEAVDRVLHKTF-HELNGKM  175 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~---~~F~~fG~I~~v~i~~d~~tg---~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~  175 (522)
                      .....+||-.|+..+.++++-   +.|.+||.|..|.+..++...   -.-..++|+|..+|+|..||...+ ..++++.
T Consensus        75 Vqknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~  154 (327)
T KOG2068|consen   75 VQKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRA  154 (327)
T ss_pred             hhhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhh
Confidence            445678898999877665543   467788999999888776211   122347999999999999999888 7888888


Q ss_pred             EEEEEcCCCCC
Q 009920          176 VEVKRAVPKEF  186 (522)
Q Consensus       176 I~V~~a~pk~~  186 (522)
                      |+..+..++.-
T Consensus       155 lka~~gttkyc  165 (327)
T KOG2068|consen  155 LKASLGTTKYC  165 (327)
T ss_pred             hHHhhCCCcch
Confidence            88887776643

>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=87.27  E-value=3.8  Score=36.01  Aligned_cols=64  Identities=16%  Similarity=0.185  Sum_probs=45.0

Q ss_pred             cEEEECCCCC-CCCHHHHHHHHhcc-CCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccC
Q 009920            6 GKLFIGGISW-DTDEERLKEYFSRY-GEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMID   71 (522)
Q Consensus         6 r~LfVgnLP~-~~teedL~e~F~~~-G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~   71 (522)
                      .+|.|--+|. .++.++|..+.+.+ -.|..++|+++..  .++=.+.++|.+.++|++..  .|++.+.
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            4444444444 46667777777765 4577888988743  36667999999999999998  6665543

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]

Probab=87.21  E-value=6  Score=41.19  Aligned_cols=12  Identities=17%  Similarity=0.202  Sum_probs=5.6

Q ss_pred             CCHHHHHHHHhh
Q 009920          117 VTESDFKKYFDQ  128 (522)
Q Consensus       117 vteedL~~~F~~  128 (522)
                      .++++|+++++.
T Consensus       198 a~w~~iE~~~~~  209 (465)
T KOG3973|consen  198 ATWPEIEKQCES  209 (465)
T ss_pred             hhHHHHHHHHHH
Confidence            344555544443

>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=86.63  E-value=2.1  Score=41.14  Aligned_cols=61  Identities=15%  Similarity=0.236  Sum_probs=43.9

Q ss_pred             CHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC---CccCCeEEEEEEcCCC
Q 009920          118 TESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF---HELNGKMVEVKRAVPK  184 (522)
Q Consensus       118 teedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~---~~l~Gr~I~V~~a~pk  184 (522)
                      ..+.|+++|..+..+..+.+++.-      .-..|.|.+.++|++|.+.++   ..+.++.|+|.++.+.
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sF------rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSF------RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTT------TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCC------CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            457899999999998888777432      258999999999999999987   4799999999988543

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.

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=85.46  E-value=3.9  Score=33.02  Aligned_cols=55  Identities=22%  Similarity=0.403  Sum_probs=32.6

Q ss_pred             CCHHHHHHHHhccC-----CeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920           17 TDEERLKEYFSRYG-----EVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus        17 ~teedL~e~F~~~G-----~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ++..+|..++....     .|-.|+|..+        |+||+-... .|++++  +++..+.+++|.|+.|
T Consensus        13 ~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   13 LTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             --HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             CCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            88999999998764     3666777654        899988765 566666  8899999999999865

; PDB: 2G0C_A 3MOJ_B.

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=84.54  E-value=0.94  Score=41.22  Aligned_cols=110  Identities=12%  Similarity=0.016  Sum_probs=71.9

Q ss_pred             CCCHHHHHHHHhc-cCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecCCCcccccccccc
Q 009920           16 DTDEERLKEYFSR-YGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAVPRDDQNMLNRNT   93 (522)
Q Consensus        16 ~~teedL~e~F~~-~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~~k~~~~~~~~~~   93 (522)
                      +.+-+.|.+.+.+ ......+.+..-.     .++..++|.+++++++++ .....+++..+.++.-.+........   
T Consensus        28 ~~~~~~l~~~l~~~W~~~~~~~i~~l~-----~~~fl~~F~~~~d~~~vl~~~p~~~~~~~~~l~~W~~~~~~~~~~---   99 (153)
T PF14111_consen   28 PISLSALEQELAKIWKLKGGVKIRDLG-----DNLFLFQFESEEDRQRVLKGGPWNFNGHFLILQRWSPDFNPSEVK---   99 (153)
T ss_pred             CCCHHHHHHHHHHHhCCCCcEEEEEeC-----CCeEEEEEEeccceeEEEecccccccccchhhhhhcccccccccc---
Confidence            3566677776655 2333334443321     258999999999999999 66667778778777665443221110   


Q ss_pred             CCCCCCCCCCCcceeEecCCCCC-CCHHHHHHHHhhcCCeeEEEEEec
Q 009920           94 SSIHSSPGPGRTKKIFVGGLAST-VTESDFKKYFDQFGTITDVVVMYD  140 (522)
Q Consensus        94 ~~~~~~~~~~~~~~LfVgnLp~~-vteedL~~~F~~fG~I~~v~i~~d  140 (522)
                             -....-=|.|.+||.. .+++-|+++.+.+|++.+++....
T Consensus       100 -------~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~~t~  140 (153)
T PF14111_consen  100 -------FEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDENTL  140 (153)
T ss_pred             -------eeccchhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEcCCC
Confidence                   0012223667799977 578889999999999988876544

>smart00596 PRE_C2HC PRE_C2HC domain

Probab=83.60  E-value=1.7  Score=34.96  Aligned_cols=64  Identities=19%  Similarity=0.254  Sum_probs=50.0

Q ss_pred             HHHHHHHhccC-CeEEEEEeecCCCCCcccEEEEEecCHHHHHHHHHcccccCCeEEEEeecCCCc
Q 009920           20 ERLKEYFSRYG-EVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTVEAKKAVPRD   84 (522)
Q Consensus        20 edL~e~F~~~G-~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl~~~~~i~Gr~I~V~~a~~k~   84 (522)
                      ++|++.|+++| +|..+..|..+++...--.=+|+.....+... +++-+.|.+++|.|+....+.
T Consensus         2 ~~I~~~L~~~G~~v~~i~~m~~~~~r~P~nmf~vel~~~~~~~~-Il~ik~Lg~~~V~VEr~~k~~   66 (69)
T smart00596        2 SQIEEALKDIGFPVLFIHNMLNRDTKNPQNMFEVELVPAANGKE-ILNIKTLGGQRVTVERPHKRK   66 (69)
T ss_pred             HHHHHHHHHcCCceeEEEcccccCCCCcceeEEEEeeecCCCcc-eEeehhhCCeeEEEecCcccC
Confidence            57889999988 68889888888877777778888877655554 567788899999998776543

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=82.94  E-value=0.91  Score=50.67  Aligned_cols=70  Identities=14%  Similarity=0.165  Sum_probs=60.4

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      .+..++||+++...+.++-++.+...+|.|..+....         |+|++|.......+|+..+. ..++++.+.+...
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~d  108 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENVD  108 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhccch
Confidence            4567899999999999999999999999988776653         89999999999999998888 6888888877653

>COG5594 Uncharacterized integral membrane protein [Function unknown]

Probab=82.54  E-value=0.18  Score=57.54  Aligned_cols=28  Identities=25%  Similarity=0.473  Sum_probs=24.4

Q ss_pred             CCCcEEEECCCCCC-CCHHHHHHHHhccC
Q 009920            3 SDLGKLFIGGISWD-TDEERLKEYFSRYG   30 (522)
Q Consensus         3 ~d~r~LfVgnLP~~-~teedL~e~F~~~G   30 (522)
                      ..+|+|+|..||.+ .++++|+++|.+..
T Consensus       206 ~ssRTvlis~LP~~~~~~e~L~~~~~kl~  234 (827)
T COG5594         206 LSSRTVLISGLPSELRSDEELKELFDKLK  234 (827)
T ss_pred             CCCceEEeecCChhhcCchhHHHHHhhcC
Confidence            36899999999999 67888999999874

>PF07530 PRE_C2HC: Associated with zinc fingers; InterPro: IPR006579 This domain is present in proteins found exclusively in the arthropods, including a number of Drosophila species, the silk moth and the gypsy moth

Probab=82.49  E-value=2.2  Score=34.14  Aligned_cols=64  Identities=22%  Similarity=0.258  Sum_probs=49.8

Q ss_pred             HHHHHHHhccC-CeEEEEEeecCCCCCcccEEEEEecCHHHHHHHHHcccccCCeEEEEeecCCCc
Q 009920           20 ERLKEYFSRYG-EVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTVEAKKAVPRD   84 (522)
Q Consensus        20 edL~e~F~~~G-~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl~~~~~i~Gr~I~V~~a~~k~   84 (522)
                      ++|++.|+..| +|.++.-|..+.+.+.--.-||+.+...+.. -+.+-..|.+.+|+|+....+.
T Consensus         2 ~~I~~~L~~~G~~v~~i~~~~~~~~k~pl~mf~veL~p~~~~k-~i~~Ik~l~~~~V~vE~~~k~~   66 (68)
T PF07530_consen    2 EEIKEELKDQGHPVRNIHNMHSRNTKKPLNMFFVELEPKPNNK-EIYKIKTLCGQRVKVERPRKRR   66 (68)
T ss_pred             HHHHHHHHHcCCceEEEEccccCCCCCCceEEEEeeccCcccc-ceeehHhhCCeEEEEecCCCCC
Confidence            57888898887 6888888888877778888899988877733 3466678889999998776543

These proteins are possibly involved in RNA binding or single strand DNA binding.

>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=81.94  E-value=3.3  Score=39.81  Aligned_cols=61  Identities=23%  Similarity=0.311  Sum_probs=42.7

Q ss_pred             CCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hc--ccccCCeEEEEeecCCC
Q 009920           17 TDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MD--KHMIDGRTVEAKKAVPR   83 (522)
Q Consensus        17 ~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~--~~~i~Gr~I~V~~a~~k   83 (522)
                      -..++|+++|..+.++..+.+++.=      +-..|.|.+.++|.+|.  ++  ...+.+..+++..+...
T Consensus         7 ~~~~~l~~l~~~~~~~~~~~~L~sF------rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    7 DNLAELEELFSTYDPPVQFSPLKSF------RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             --HHHHHHHHHTT-SS-EEEEETTT------TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hhHHHHHHHHHhcCCceEEEEcCCC------CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            3568899999999999888777642      35789999999999998  56  77899999999887443

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.

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=81.88  E-value=9.9  Score=38.66  Aligned_cols=55  Identities=16%  Similarity=0.289  Sum_probs=39.4

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCe-eEEEEEecCCCCCcceEEEEEecC-------HHHHHHHHHh
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTI-TDVVVMYDHNTQRPRGFGFITYDS-------EEAVDRVLHK  166 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I-~~v~i~~d~~tg~~rG~aFVeF~s-------~e~A~~Al~~  166 (522)
                      .-|+|.|||.++.-.||+..+.+-+.+ .++.+      +-+++-||++|-+       .+++++++..
T Consensus       331 ~di~~~nl~rd~rv~dlk~~lr~~~~~pm~isw------kg~~~k~flh~~~~~~~~~~~~~~~~~~~s  393 (396)
T KOG4410|consen  331 TDIKLTNLSRDIRVKDLKSELRKRECTPMSISW------KGHFGKCFLHFGNRKGVPSTQDDMDKVLKS  393 (396)
T ss_pred             cceeeccCccccchHHHHHHHHhcCCCceeEee------ecCCcceeEecCCccCCCCCchHHHHHhcc
Confidence            469999999999999999999887654 23333      2345689999955       3455555543

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=80.79  E-value=1.3  Score=50.61  Aligned_cols=77  Identities=17%  Similarity=0.204  Sum_probs=65.2

Q ss_pred             eeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-C--ccCCeEEEEEEcCC
Q 009920          107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-H--ELNGKMVEVKRAVP  183 (522)
Q Consensus       107 ~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~--~l~Gr~I~V~~a~p  183 (522)
                      +..+.|++-.++...|..+|.+||.|.++..+++-+      .|.|+|.+.+.|..|++++. +  ...|-+.+|.+|++
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N------~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLN------MALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheeccccc------chhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            456677777888899999999999999999988866      79999999999999998877 4  46778899999998


Q ss_pred             CCCCCC
Q 009920          184 KEFSPG  189 (522)
Q Consensus       184 k~~~~~  189 (522)
                      -+....
T Consensus       374 ~~~~ep  379 (1007)
T KOG4574|consen  374 LPMYEP  379 (1007)
T ss_pred             cccccC
Confidence            776543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	522
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		2e-42
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		1e-14
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		9e-33
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		5e-18
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		1e-32
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		5e-18
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-32
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		5e-18
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		2e-32
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		1e-17
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		2e-32
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		8e-18
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		3e-32
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-17
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		2e-20
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		9e-20
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		2e-12
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		9e-19
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		2e-18
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		6e-12
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		9e-17
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		8e-14
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		7e-16
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		6e-13
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		7e-16
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		7e-10
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		8e-16
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		1e-14
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		2e-13
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		7e-13
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		2e-08
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		2e-12
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		4e-12
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		4e-12
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		9e-12
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		2e-11
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		9e-05
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		3e-11
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		3e-11
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		6e-11
1wtb_A	79	Complex Structure Of The C-Terminal Rna-Binding Dom		2e-10
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		2e-10
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		1e-09
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		9e-06
1iqt_A	75	Solution Structure Of The C-Terminal Rna-Binding Do		3e-09
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		3e-09
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		5e-08
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		1e-07
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		2e-07
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		2e-07
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		3e-07
1wf0_A	88	Solution Structure Of Rrm Domain In Tar Dna-Binding		4e-07
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		4e-07
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		5e-07
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		5e-07
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		5e-07
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		6e-07
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		7e-07
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		7e-07
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		7e-07
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		9e-07
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		1e-06
3d2w_A	89	Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Co		2e-06
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		2e-06
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		3e-06
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		3e-06
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		6e-06
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		6e-06
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		6e-06
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		8e-06
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		8e-06
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		3e-05
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		9e-06
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		1e-05
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		1e-05
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		1e-05
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		1e-05
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		3e-05
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		6e-05
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		3e-05
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		8e-04
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		4e-05
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		5e-05
2dgp_A	106	Solution Structure Of The N-Terminal Rna Binding Do		6e-05
2dgp_A	106	Solution Structure Of The N-Terminal Rna Binding Do		9e-04
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		1e-04
3b4d_A	96	Crystal Structure Of Human Pabpn1 Rrm Length = 96		1e-04
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		1e-04
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		1e-04
2div_A	99	Solution Structure Of The Rrm Domain Of Trna Seleno		2e-04
2ytc_A	85	Solution Structure Of Rna Binding Domain In Pre-Mrn		2e-04
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		2e-04
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		3e-04
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		4e-04
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		4e-04
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		4e-04
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		4e-04
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		4e-04
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		4e-04
3ucg_A	89	Crystal Structure Of A Rna Binding Domain Of Hypoth		5e-04
2dgq_A	108	Solution Structure Of The N-Terminal Rna Binding Do		6e-04
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		7e-04
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		7e-04
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		8e-04
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		8e-04

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score =  170 bits (430), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 78/178 (43%), Positives = 118/178 (66%), Gaps = 16/178 (8%)
Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
           K+FIGG++WDT E+ L+EYF +YG V +  IM+D ATGR+RGFGF+ F  P+  + V+  
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 67  KHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYF 126
           +H++DG+ ++ K+A+PRD+Q+                +T KIFVGG+   V   +F+++F
Sbjct: 65  QHILDGKVIDPKRAIPRDEQD----------------KTGKIFVGGIGPDVRPKEFEEFF 108
Query: 127 DQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPK 184
            Q+GTI D  +M D +T + RGFGF+TYDS +AVDRV    F +   + +E+KRA P+
Sbjct: 109 SQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPR 166

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 77.8 bits (190), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 35/79 (44%), Positives = 58/79 (73%), Gaps = 1/79 (1%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+F+GGL    TE + ++YF ++GT+TD+ +M D  T R RGFGF++++   +VD V+ K
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV-K 63
Query: 167 TFHELNGKMVEVKRAVPKE 185
           T H L+GK+++ KRA+P++
Sbjct: 64  TQHILDGKVIDPKRAIPRD 82

>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 =  138 bits (347), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 73/187 (39%), Positives = 112/187 (59%), Gaps = 21/187 (11%)
Query: 5   LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFA-----DPAV 59
           L KLFIGG+S++T +E L+ +F ++G + + V+MRD  T R+RGFGFV +A     D A+
Sbjct: 14  LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 73
Query: 60  AERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRT-KKIFVGGLASTVT 118
             R     H +DGR VE K+AV R+D              PG   T KKIFVGG+     
Sbjct: 74  NAR----PHKVDGRVVEPKRAVSREDSQ-----------RPGAHLTVKKIFVGGIKEDTE 118
Query: 119 ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEV 178
           E   + YF+Q+G I  + +M D  + + RGF F+T+D  ++VD+++ + +H +NG   EV
Sbjct: 119 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV 178
Query: 179 KRAVPKE 185
           ++A+ K+
Sbjct: 179 RKALSKQ 185

>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 = 89.4 bits (220), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 43/97 (44%), Positives = 65/97 (67%)
Query: 94  SSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFIT 153
           S   S   P + +K+F+GGL+   T+   + +F+Q+GT+TD VVM D NT+R RGFGF+T
Sbjct: 3   SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 62
Query: 154 YDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGP 190
           Y + E VD  ++   H+++G++VE KRAV +E S  P
Sbjct: 63  YATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP 99

>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 =  137 bits (346), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 73/187 (39%), Positives = 112/187 (59%), Gaps = 21/187 (11%)
Query: 5   LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFA-----DPAV 59
           L KLFIGG+S++T +E L+ +F ++G + + V+MRD  T R+RGFGFV +A     D A+
Sbjct: 12  LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 71
Query: 60  AERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRT-KKIFVGGLASTVT 118
             R     H +DGR VE K+AV R+D              PG   T KKIFVGG+     
Sbjct: 72  NAR----PHKVDGRVVEPKRAVSREDSQ-----------RPGAHLTVKKIFVGGIKEDTE 116
Query: 119 ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEV 178
           E   + YF+Q+G I  + +M D  + + RGF F+T+D  ++VD+++ + +H +NG   EV
Sbjct: 117 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV 176
Query: 179 KRAVPKE 185
           ++A+ K+
Sbjct: 177 RKALSKQ 183

>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 = 89.4 bits (220), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 43/97 (44%), Positives = 65/97 (67%)
Query: 94  SSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFIT 153
           S   S   P + +K+F+GGL+   T+   + +F+Q+GT+TD VVM D NT+R RGFGF+T
Sbjct: 1   SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 60
Query: 154 YDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGP 190
           Y + E VD  ++   H+++G++VE KRAV +E S  P
Sbjct: 61  YATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP 97

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score =  137 bits (346), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 73/187 (39%), Positives = 112/187 (59%), Gaps = 21/187 (11%)
Query: 5   LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFA-----DPAV 59
           L KLFIGG+S++T +E L+ +F ++G + + V+MRD  T R+RGFGFV +A     D A+
Sbjct: 13  LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 72
Query: 60  AERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRT-KKIFVGGLASTVT 118
             R     H +DGR VE K+AV R+D              PG   T KKIFVGG+     
Sbjct: 73  NAR----PHKVDGRVVEPKRAVSREDSQ-----------RPGAHLTVKKIFVGGIKEDTE 117
Query: 119 ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEV 178
           E   + YF+Q+G I  + +M D  + + RGF F+T+D  ++VD+++ + +H +NG   EV
Sbjct: 118 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV 177
Query: 179 KRAVPKE 185
           ++A+ K+
Sbjct: 178 RKALSKQ 184

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 89.4 bits (220), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 43/97 (44%), Positives = 65/97 (67%)
Query: 94  SSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFIT 153
           S   S   P + +K+F+GGL+   T+   + +F+Q+GT+TD VVM D NT+R RGFGF+T
Sbjct: 2   SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 61
Query: 154 YDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGP 190
           Y + E VD  ++   H+++G++VE KRAV +E S  P
Sbjct: 62  YATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP 98

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score =  137 bits (344), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 73/187 (39%), Positives = 112/187 (59%), Gaps = 21/187 (11%)
Query: 5   LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFA-----DPAV 59
           L KLFIGG+S++T +E L+ +F ++G + + V+MRD  T R+RGFGFV +A     D A+
Sbjct: 6   LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 65
Query: 60  AERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRT-KKIFVGGLASTVT 118
             R     H +DGR VE K+AV R+D              PG   T KKIFVGG+     
Sbjct: 66  NAR----PHKVDGRVVEPKRAVSREDSQ-----------RPGAHLTVKKIFVGGIKEDTE 110
Query: 119 ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEV 178
           E   + YF+Q+G I  + +M D  + + RGF F+T+D  ++VD+++ + +H +NG   EV
Sbjct: 111 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV 170
Query: 179 KRAVPKE 185
           ++A+ K+
Sbjct: 171 RKALSKQ 177

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 88.2 bits (217), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 41/89 (46%), Positives = 63/89 (70%)
Query: 102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD 161
           P + +K+F+GGL+   T+   + +F+Q+GT+TD VVM D NT+R RGFGF+TY + E VD
Sbjct: 3   PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 62
Query: 162 RVLHKTFHELNGKMVEVKRAVPKEFSPGP 190
             ++   H+++G++VE KRAV +E S  P
Sbjct: 63  AAMNARPHKVDGRVVEPKRAVSREDSQRP 91

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score =  137 bits (344), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 73/187 (39%), Positives = 112/187 (59%), Gaps = 21/187 (11%)
Query: 5   LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFA-----DPAV 59
           L KLFIGG+S++T +E L+ +F ++G + + V+MRD  T R+RGFGFV +A     D A+
Sbjct: 13  LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 72
Query: 60  AERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRT-KKIFVGGLASTVT 118
             R     H +DGR VE K+AV R+D              PG   T KKIFVGG+     
Sbjct: 73  NAR----PHKVDGRVVEPKRAVSREDSQ-----------RPGAHLTVKKIFVGGIKEDTE 117
Query: 119 ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEV 178
           E   + YF+Q+G I  + +M D  + + RGF F+T+D  ++VD+++ + +H +NG   EV
Sbjct: 118 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV 177
Query: 179 KRAVPKE 185
           ++A+ K+
Sbjct: 178 RKALSKQ 184

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 88.6 bits (218), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 43/97 (44%), Positives = 65/97 (67%)
Query: 94  SSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFIT 153
           S   S   P + +K+F+GGL+   T+   + +F+Q+GT+TD VVM D NT+R RGFGF+T
Sbjct: 2   SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 61
Query: 154 YDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGP 190
           Y + E VD  ++   H+++G++VE KRAV +E S  P
Sbjct: 62  YATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP 98

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score =  136 bits (343), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 73/187 (39%), Positives = 112/187 (59%), Gaps = 21/187 (11%)
Query: 5   LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFA-----DPAV 59
           L KLFIGG+S++T +E L+ +F ++G + + V+MRD  T R+RGFGFV +A     D A+
Sbjct: 11  LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM 70
Query: 60  AERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRT-KKIFVGGLASTVT 118
             R     H +DGR VE K+AV R+D              PG   T KKIFVGG+     
Sbjct: 71  NAR----PHKVDGRVVEPKRAVSREDSQ-----------RPGAHLTVKKIFVGGIKEDTE 115
Query: 119 ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEV 178
           E   + YF+Q+G I  + +M D  + + RGF F+T+D  ++VD+++ + +H +NG   EV
Sbjct: 116 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV 175
Query: 179 KRAVPKE 185
           ++A+ K+
Sbjct: 176 RKALSKQ 182

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 88.2 bits (217), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 42/93 (45%), Positives = 64/93 (68%)
Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE 157
           S   P + +K+F+GGL+   T+   + +F+Q+GT+TD VVM D NT+R RGFGF+TY + 
Sbjct: 4   SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 63
Query: 158 EAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGP 190
           E VD  ++   H+++G++VE KRAV +E S  P
Sbjct: 64  EEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP 96

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 97.1 bits (240), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 44/86 (51%), Positives = 65/86 (75%), Gaps = 1/86 (1%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           KIFVGG+     E++ ++YF +FG +T+VV++YD   QRPRGFGFIT++ E++VD+ ++ 
Sbjct: 12  KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 167 TFHELNGKMVEVKRAVPKE-FSPGPS 191
            FH++ GK VEVKRA P++  S GPS
Sbjct: 72  HFHDIMGKKVEVKRAEPRDSKSSGPS 97

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 95.1 bits (235), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 40/81 (49%), Positives = 57/81 (70%), Gaps = 1/81 (1%)
Query: 4  DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV 63
          ++GKLF+GG+ W T +E L+ YFS+YGEVV+ VIM+D+ T ++RGFGFV F DP     V
Sbjct: 15 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV 74
Query: 64 IMDK-HMIDGRTVEAKKAVPR 83
          +  + H +DGR ++ K   PR
Sbjct: 75 LASRPHTLDGRNIDPKPCTPR 95

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 70.5 bits (171), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 33/86 (38%), Positives = 48/86 (55%), Gaps = 1/86 (1%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+FVGGL  + T+   + YF Q+G + D V+M D  T + RGFGF+ +     V  VL  
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 167 TFHELNGKMVEVKRAVPKEFSP-GPS 191
             H L+G+ ++ K   P+   P GPS
Sbjct: 78  RPHTLDGRNIDPKPCTPRGMQPSGPS 103

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 91.7 bits (226), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 39/74 (52%), Positives = 53/74 (71%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           IFVGGL+   T  D K YF+QFG + D ++M+D  T R RGFGF+T++SE+ V++V    
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 168 FHELNGKMVEVKRA 181
           FHE+N KMVE K+A
Sbjct: 62  FHEINNKMVECKKA 75

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 90.9 bits (224), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 42/80 (52%), Positives = 59/80 (73%), Gaps = 1/80 (1%)
Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
          E D GK F+GG+SWDT ++ LK+YF+++GEVV+  I  D  TGR+RGFGF++F D A  E
Sbjct: 8  EEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVE 67
Query: 62 RVIMDK-HMIDGRTVEAKKA 80
          +V+  K H +DGR ++ KKA
Sbjct: 68 KVLDQKEHRLDGRVIDPKKA 87

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 68.9 bits (167), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 33/86 (38%), Positives = 52/86 (60%)
Query: 96  IHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD 155
           I++S       K FVGGL+   ++ D K YF +FG + D  +  D NT R RGFGFI + 
Sbjct: 2   INASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFK 61
Query: 156 SEEAVDRVLHKTFHELNGKMVEVKRA 181
              +V++VL +  H L+G++++ K+A
Sbjct: 62  DAASVEKVLDQKEHRLDGRVIDPKKA 87

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 85.1 bits (209), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 42/87 (48%), Positives = 59/87 (67%), Gaps = 1/87 (1%)
Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
           M S   K+FIGG+SW T +E L+EYF ++GEV E ++MRD  T R+RGFGFV F D A  
Sbjct: 21  MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGV 80
Query: 61  ERVI-MDKHMIDGRTVEAKKAVPRDDQ 86
           ++V+   +H +D +T++ K A PR  Q
Sbjct: 81  DKVLAQSRHELDSKTIDPKVAFPRRAQ 107

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 75.1 bits (183), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 34/82 (41%), Positives = 54/82 (65%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+F+GGL+   T+   ++YF QFG + + +VM D  T+R RGFGF+T+  +  VD+VL +
Sbjct: 27  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 167 TFHELNGKMVEVKRAVPKEFSP 188
           + HEL+ K ++ K A P+   P
Sbjct: 87  SRHELDSKTIDPKVAFPRRAQP 108

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 82.0 bits (201), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 37/75 (49%), Positives = 54/75 (72%), Gaps = 1/75 (1%)
Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
          K+FIGG+SW T +E L+EYF ++GEV E ++MRD  T R+RGFGFV F D A  ++V+  
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 66 DKHMIDGRTVEAKKA 80
           +H +D +T++ K A
Sbjct: 62 SRHELDSKTIDPKVA 76

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 72.4 bits (176), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 32/75 (42%), Positives = 51/75 (68%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+F+GGL+   T+   ++YF QFG + + +VM D  T+R RGFGF+T+  +  VD+VL +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 167 TFHELNGKMVEVKRA 181
           + HEL+ K ++ K A
Sbjct: 62  SRHELDSKTIDPKVA 76

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 82.0 bits (201), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 38/82 (46%), Positives = 57/82 (69%), Gaps = 2/82 (2%)
Query: 1  MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFA--DPA 58
          M SD GKLF+GG+S+DT+E+ L++ FS+YG++ E V+++DR T R+RGFGFV F   D A
Sbjct: 8  MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 67
Query: 59 VAERVIMDKHMIDGRTVEAKKA 80
              + M+   +DGR +   +A
Sbjct: 68 KDAMMAMNGKSVDGRQIRVDQA 89

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 62.0 bits (149), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 50/76 (65%), Gaps = 1/76 (1%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS-EEAVDRVLH 165
           K+FVGGL+    E   ++ F ++G I++VVV+ D  TQR RGFGF+T+++ ++A D ++ 
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 166 KTFHELNGKMVEVKRA 181
                ++G+ + V +A
Sbjct: 74  MNGKSVDGRQIRVDQA 89

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 82.0 bits (201), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 39/87 (44%), Positives = 58/87 (66%), Gaps = 1/87 (1%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           +K+F+GGL+   TE   + Y++Q+G +TD VVM D  ++R RGFGF+T+ S   VD  + 
Sbjct: 28  RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 166 KTFHELNGKMVEVKRAVPKEFS-PGPS 191
              H ++G++VE KRAV +E S  GPS
Sbjct: 88  ARPHSIDGRVVEPKRAVAREESGSGPS 114

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 77.8 bits (190), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 34/74 (45%), Positives = 55/74 (74%), Gaps = 1/74 (1%)
Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          +FIGG+SWDT ++ LK+YFS++GEVV+  +  D  TGR+RGFGFV+F +    ++V+  K
Sbjct: 2  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 68 -HMIDGRTVEAKKA 80
           H ++G+ ++ K+A
Sbjct: 62 EHKLNGKVIDPKRA 75

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 73.6 bits (179), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 32/74 (43%), Positives = 49/74 (66%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           +F+GGL+   T+ D K YF +FG + D  +  D  T R RGFGF+ +   E+VD+V+ + 
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 168 FHELNGKMVEVKRA 181
            H+LNGK+++ KRA
Sbjct: 62  EHKLNGKVIDPKRA 75

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 72.0 bits (175), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 32/68 (47%), Positives = 49/68 (72%), Gaps = 1/68 (1%)
Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          K+F+GG+ + T +  L++YF  +G++ EAV++ DR TG++RG+GFV  AD A AER   D
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 67 KH-MIDGR 73
           + +IDGR
Sbjct: 79 PNPIIDGR 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 = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/75 (37%), Positives = 41/75 (54%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           KIFVGGL    T++  +KYF+ FG I + VV+ D  T + RG+GF+T     A +R    
Sbjct: 19  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 167 TFHELNGKMVEVKRA 181
               ++G+   V  A
Sbjct: 79  PNPIIDGRKANVNLA 93

>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 = 70.5 bits (171), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/195 (26%), Positives = 89/195 (45%), Gaps = 22/195 (11%)
Query: 5   LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
           +  L++G +  D  E  L E FS  G ++   + RD  T R+ G+ +V F  PA AER +
Sbjct: 15  MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 74
Query: 65  --MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDF 122
             M+  +I G+ V            M ++   S+  S G G    IF+  L  ++     
Sbjct: 75  DTMNFDVIKGKPVRI----------MWSQRDPSLRKS-GVG---NIFIKNLDKSIDNKAL 120
Query: 123 KKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAV 182
              F  FG I    V+ D N    +G+GF+ ++++EA +R + K    +NG ++  ++  
Sbjct: 121 YDTFSAFGNILSCKVVCDENGS--KGYGFVHFETQEAAERAIEK----MNGMLLNDRKVF 174
Query: 183 PKEFSPGPSRSSMIG 197
              F     R + +G
Sbjct: 175 VGRFKSRKEREAELG 189

>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 = 69.7 bits (169), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 52/195 (26%), Positives = 89/195 (45%), Gaps = 22/195 (11%)
Query: 5   LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
           +  L++G +  D  E  L E FS  G ++   + RD  T R+ G+ +V F  PA AER +
Sbjct: 10  MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 69
Query: 65  --MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDF 122
             M+  +I G+ V            M ++   S+  S G G    IF+  L  ++     
Sbjct: 70  DTMNFDVIKGKPVRI----------MWSQRDPSLRKS-GVG---NIFIKNLDKSIDNKAL 115
Query: 123 KKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAV 182
              F  FG I    V+ D N    +G+GF+ ++++EA +R + K    +NG ++  ++  
Sbjct: 116 YDTFSAFGNILSCKVVCDENGS--KGYGFVHFETQEAAERAIEK----MNGMLLNDRKVF 169
Query: 183 PKEFSPGPSRSSMIG 197
              F     R + +G
Sbjct: 170 VGRFKSRKEREAELG 184

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 69.7 bits (169), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 44/159 (27%), Positives = 80/159 (50%), Gaps = 22/159 (13%)
Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
           L +  +  +  +E  +  F   GE+    ++RD+ TG++ G+GFV + DP  AE+ I  +
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 66  DKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKY 125
           +   +  +T++   A P         +++SI       R   ++V GL  T+T+ + ++ 
Sbjct: 65  NGLRLQTKTIKVSYARP---------SSASI-------RDANLYVSGLPKTMTQKELEQL 108
Query: 126 FDQFGTITDVVVMYDHNTQRPRGFGFITYD----SEEAV 160
           F Q+G I    ++ D  T   RG GFI +D    +EEA+
Sbjct: 109 FSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 68.6 bits (166), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 41/159 (25%), Positives = 81/159 (50%), Gaps = 22/159 (13%)
Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
           L +  +  +  ++  K  F   G++    ++RD+ TG++ G+GFV ++DP  A++ I  +
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 66  DKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKY 125
           +   +  +T++   A P         +++SI       R   ++V GL  T+++ + ++ 
Sbjct: 67  NGLKLQTKTIKVSYARP---------SSASI-------RDANLYVSGLPKTMSQKEMEQL 110
Query: 126 FDQFGTITDVVVMYDHNTQRPRGFGFITYD----SEEAV 160
           F Q+G I    ++ D  T   RG GFI +D    +EEA+
Sbjct: 111 FSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 149

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 67.4 bits (163), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 32/80 (40%), Positives = 48/80 (60%)
Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          L + G+ W T E+ LKEYFS +GEV+   + +D  TG ++GFGFV F +     +V+  +
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77
Query: 68 HMIDGRTVEAKKAVPRDDQN 87
          HMIDGR  + K    +  Q+
Sbjct: 78 HMIDGRWCDCKLPNSKQSQD 97

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 45.1 bits (105), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 29/89 (32%), Positives = 44/89 (49%), Gaps = 2/89 (2%)
Query: 104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV 163
           +T  + V GL    TE D K+YF  FG +  V V  D  T   +GFGF+ +   E   +V
Sbjct: 14  KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 73
Query: 164 LHKTFHELNGKMVEVKRAVPKEFS-PGPS 191
           + +  H ++G+  + K    K+    GPS
Sbjct: 74  MSQR-HMIDGRWCDCKLPNSKQSQDSGPS 101

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 66.6 bits (161), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 43/159 (27%), Positives = 74/159 (46%), Gaps = 22/159 (13%)
Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
           L +  +  +  ++ L+  FS  GEV  A ++RD+  G + G+GFV +     AER I  +
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 66  DKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKY 125
           +   +  +T++   A P                S    +   +++ GL  T+T+ D +  
Sbjct: 65  NGLRLQSKTIKVSYARP----------------SSEVIKDANLYISGLPRTMTQKDVEDM 108
Query: 126 FDQFGTITDVVVMYDHNTQRPRGFGFITYD----SEEAV 160
           F +FG I +  V+ D  T   RG  FI +D    +EEA+
Sbjct: 109 FSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 66.6 bits (161), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 43/159 (27%), Positives = 74/159 (46%), Gaps = 22/159 (13%)
Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
           L +  +  +  ++ L+  FS  GEV  A ++RD+  G + G+GFV +     AER I  +
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 66  DKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKY 125
           +   +  +T++   A P                S    +   +++ GL  T+T+ D +  
Sbjct: 65  NGLRLQSKTIKVSYARP----------------SSEVIKDANLYISGLPRTMTQKDVEDM 108
Query: 126 FDQFGTITDVVVMYDHNTQRPRGFGFITYD----SEEAV 160
           F +FG I +  V+ D  T   RG  FI +D    +EEA+
Sbjct: 109 FSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147

>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 = 65.5 bits (158), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 44/187 (23%), Positives = 90/187 (48%), Gaps = 20/187 (10%)
Query: 5   LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
           + ++++G I ++  E+ +++ F+ +G +    +  D  T + +GF FV +  P  A+  +
Sbjct: 28  MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 87
Query: 65  --MDKHMIDGRTVEAKK------AVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLAST 116
             M+  M+ GR ++  +      A P  DQ  L     + +         +I+V  +   
Sbjct: 88  EQMNSVMLGGRNIKVGRPSNIGQAQPIIDQ--LAEEARAFN---------RIYVASVHQD 136
Query: 117 VTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD-SEEAVDRVLHKTFHELNGKM 175
           +++ D K  F+ FG I    +  D  T + +G+GFI Y+ ++ + D V      +L G+ 
Sbjct: 137 LSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQY 196
Query: 176 VEVKRAV 182
           + V +AV
Sbjct: 197 LRVGKAV 203

>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 = 64.3 bits (155), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 29/77 (37%), Positives = 45/77 (58%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           KKIFVGGL+    E   ++YF  FG +  + +  D+ T + RGF FIT+  EE V +++ 
Sbjct: 2   KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
Query: 166 KTFHELNGKMVEVKRAV 182
           K +H +     E+K A+
Sbjct: 62  KKYHNVGLSKCEIKVAM 78

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 63.9 bits (154), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 44/187 (23%), Positives = 90/187 (48%), Gaps = 20/187 (10%)
Query: 5   LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
           + ++++G I ++  E+ +++ F+ +G +    +  D  T + +GF FV +  P  A+  +
Sbjct: 13  MCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 72
Query: 65  --MDKHMIDGRTVEAKK------AVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLAST 116
             M+  M+ GR ++  +      A P  DQ  L     + +         +I+V  +   
Sbjct: 73  EQMNSVMLGGRNIKVGRPSNIGQAQPIIDQ--LAEEARAFN---------RIYVASVHQD 121
Query: 117 VTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD-SEEAVDRVLHKTFHELNGKM 175
           +++ D K  F+ FG I    +  D  T + +G+GFI Y+ ++ + D V      +L G+ 
Sbjct: 122 LSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQY 181
Query: 176 VEVKRAV 182
           + V +AV
Sbjct: 182 LRVGKAV 188

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 61.2 bits (147), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/73 (38%), Positives = 50/73 (68%), Gaps = 4/73 (5%)
Query: 6  GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIM 65
          GKLFIGG++ +T+E+ LK  F ++G + E ++++DR T ++RGF F+ F +PA A+    
Sbjct: 8  GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAK 66
Query: 66 DKHMIDGRTVEAK 78
          D   ++G+++  K
Sbjct: 67 D---MNGKSLHGK 76

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 48.5 bits (114), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 48/90 (53%), Gaps = 8/90 (8%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY----DSEEAVDR 162
           K+F+GGL     E   K  F + G I++V+++ D  T + RGF FIT+    D++ A   
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKD 67
Query: 163 VLHKTFHELNGKMVEVKRAVPKEFSPGPSR 192
           +  K+ H   GK ++V++A    F  G  R
Sbjct: 68  MNGKSLH---GKAIKVEQAKKPSFQSGGRR 94

>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 = 60.1 bits (144), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 27/74 (36%), Positives = 42/74 (56%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           IFVGGL+    E   ++YF  FG +  + +  D+ T + RGF FIT+  EE V +++ K 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 168 FHELNGKMVEVKRA 181
           +H +     E+K A
Sbjct: 62  YHNVGLSKCEIKVA 75

>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 = 60.1 bits (144), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 42/185 (22%), Positives = 84/185 (45%), Gaps = 20/185 (10%)
Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
           ++++G I ++  E+ +++ F+ +G +       D  T + +GF FV +  P  A+  +  
Sbjct: 14  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 67  KHMID--------GRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVT 118
            + +         GR     +A P  DQ  L     + +         +I+V  +   ++
Sbjct: 74  XNSVXLGGRNIKVGRPSNIGQAQPIIDQ--LAEEARAFN---------RIYVASVHQDLS 122
Query: 119 ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD-SEEAVDRVLHKTFHELNGKMVE 177
           + D K  F+ FG I    +  D  T + +G+GFI Y+ ++ + D V      +L G+ + 
Sbjct: 123 DDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLR 182
Query: 178 VKRAV 182
           V +AV
Sbjct: 183 VGKAV 187

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 56.2 bits (134), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 40/153 (26%), Positives = 65/153 (42%), Gaps = 18/153 (11%)
Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
           L +  +  D  +  L   F   G +    IMRD  TG + G+ FV F     ++R I   
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI--- 62
Query: 68  HMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTK--KIFVGGLASTVTESDFKKY 125
            +++G TV              N+     ++ PG    K   ++V  L  T+T+      
Sbjct: 63  KVLNGITVR-------------NKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTI 109
Query: 126 FDQFGTITDVVVMYDHNTQRPRGFGFITYDSEE 158
           F ++G+I    ++ D  T RPRG  F+ Y+  E
Sbjct: 110 FGKYGSIVQKNILRDKLTGRPRGVAFVRYNKRE 142

>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 = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 43/80 (53%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           + I+VG L  + T    K+ F QFG + +V ++YD  T++P+GFGF+    E   + +  
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61
Query: 166 KTFHELNGKMVEVKRAVPKE 185
               +  G+ + V  A PK+
Sbjct: 62  LDNTDFMGRTIRVTEANPKK 81

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 44/176 (25%), Positives = 78/176 (44%), Gaps = 26/176 (14%)
Query: 3   SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATG--RARGFGFVVFADPAVA 60
           SD  K+F+G +     E+ L+E F +YG V E  ++RDR+    +++G  FV F     A
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 61  ERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRT------KKIFVGGLA 114
                         +EA+ A+   +  +L      I   P           +K+F+G ++
Sbjct: 61  --------------LEAQNAL--HNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMIS 104
Query: 115 STVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHE 170
              TE+D +  F  FG I +  ++   +    RG  F+T+ +  A+ +   K  H+
Sbjct: 105 KKCTENDIRVMFSSFGQIEECRILRGPDG-LSRGCAFVTFTT-RAMAQTAIKAMHQ 158

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/95 (30%), Positives = 52/95 (54%), Gaps = 8/95 (8%)
Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
           +F+GGI    DE  ++ +F+RYG V E  I+ DR TG ++G+GFV F +    ++++  +
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 68  HMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGP 102
               G+ ++   A+ +       +N S+ H  P P
Sbjct: 71  INFHGKKLKLGPAIRK-------QNLSTYHVQPRP 98

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 53.1 bits (126), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 39/159 (24%), Positives = 65/159 (40%), Gaps = 18/159 (11%)
Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
           L +  +  D  +  L   F   G +    I RD  TG + G+ FV F     ++R I   
Sbjct: 17  LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAI--- 73
Query: 68  HMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTK--KIFVGGLASTVTESDFKKY 125
            +++G TV              N+     ++ PG    K   ++V  L  T+T+      
Sbjct: 74  KVLNGITVR-------------NKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTI 120
Query: 126 FDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
           F ++G+I    ++ D  T RPRG  F+ Y+  E     +
Sbjct: 121 FGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 159

>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding Protein- 43 Length = 88

Iteration: 1
 Score = 52.8 bits (125), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 45/80 (56%), Gaps = 5/80 (6%)
Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          +F+G  + D  E+ L+E+FS+YG+V++  I +       R F FV FAD  +A+ +  + 
Sbjct: 8  VFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCGED 62
Query: 68 HMIDGRTVEAKKAVPRDDQN 87
           +I G +V    A P+ + N
Sbjct: 63 LIIKGISVHISNAEPKHNSN 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 = 52.8 bits (125), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 33/96 (34%), Positives = 51/96 (53%), Gaps = 3/96 (3%)
Query: 99  SPGPGRTKKI-FVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD-S 156
           S G   TK++ +VGGLA  V +      F  FG ITD+ +  D+ T++ RGF F+ ++ +
Sbjct: 5   SSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 64
Query: 157 EEAVDRVLHKTFHELNGKMVEVKRAVPKEFSP-GPS 191
           E+A   + +    EL G+ + V  A P      GPS
Sbjct: 65  EDAAAAIDNMNESELFGRTIRVNLAKPMRIKESGPS 100

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 29/90 (32%), Positives = 50/90 (55%), Gaps = 9/90 (10%)
Query: 93  TSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFI 152
           +S   ++P P     +F  GL+   TE D ++ F ++G I DV ++YD  ++R RGF F+
Sbjct: 5   SSGNRANPDPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 62
Query: 153 TY----DSEEAVDRVLHKTFHELNGKMVEV 178
            +    D++EA +R       EL+G+ + V
Sbjct: 63  YFENVDDAKEAKERA---NGMELDGRRIRV 89

>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 = 52.8 bits (125), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 43/175 (24%), Positives = 77/175 (44%), Gaps = 26/175 (14%)
Query: 4   DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATG--RARGFGFVVFADPAVAE 61
           D  K+F+G +     E+ L+E F +YG V E  ++RDR+    +++G  FV F     A 
Sbjct: 14  DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA- 72
Query: 62  RVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRT------KKIFVGGLAS 115
                        +EA+ A+   +  +L      I   P           +K+F+G ++ 
Sbjct: 73  -------------LEAQNAL--HNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISK 117
Query: 116 TVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHE 170
             TE+D +  F  FG I +  ++   +    RG  F+T+ +  A+ +   K  H+
Sbjct: 118 KCTENDIRVMFSSFGQIEECRILRGPDG-LSRGCAFVTF-TTRAMAQTAIKAMHQ 170

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 41/160 (25%), Positives = 70/160 (43%), Gaps = 25/160 (15%)
Query: 3   SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATG--RARGFGFVVFADPAVA 60
           SD  K F+G +     E+ L+E F +YG V E  ++RDR+    +++G  FV F     A
Sbjct: 1   SDAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 61  ERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRT------KKIFVGGLA 114
                         +EA+ A+   +  +L      I   P           +K+F+G ++
Sbjct: 61  --------------LEAQNAL--HNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXIS 104
Query: 115 STVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY 154
              TE+D +  F  FG I +  ++   +    RG  F+T+
Sbjct: 105 KKCTENDIRVXFSSFGQIEECRILRGPDG-LSRGCAFVTF 143

>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 = 52.4 bits (124), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 29/92 (31%), Positives = 51/92 (55%), Gaps = 9/92 (9%)
Query: 97  HSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-- 154
            ++P P     +F  GL+   TE D ++ F ++G I DV ++YD  ++R RGF F+ +  
Sbjct: 9   RANPDPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66
Query: 155 --DSEEAVDRVLHKTFHELNGKMVEVKRAVPK 184
             D++EA +R       EL+G+ + V  ++ K
Sbjct: 67  VDDAKEAKERA---NGMELDGRRIRVDFSITK 95

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 29/91 (31%), Positives = 51/91 (56%), Gaps = 9/91 (9%)
Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY--- 154
           ++P P     +F  GL+   TE D ++ F ++G I DV ++YD  ++R RGF F+ +   
Sbjct: 41  ANPDPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 98
Query: 155 -DSEEAVDRVLHKTFHELNGKMVEVKRAVPK 184
            D++EA +R       EL+G+ + V  ++ K
Sbjct: 99  DDAKEAKERA---NGMELDGRRIRVDFSITK 126

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 34/78 (43%), Positives = 43/78 (55%), Gaps = 5/78 (6%)
Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVF--ADPAVAERVIM 65
          LF+ G+S DT EE LKE F      V A I+ DR TG ++GFGFV F   + A A +  M
Sbjct: 18 LFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 66 DKHMIDGRTVEAKKAVPR 83
          +   IDG  V    A P+
Sbjct: 75 EDGEIDGNKVTLDWAKPK 92

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 52.0 bits (123), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 29/86 (33%), Positives = 46/86 (53%), Gaps = 2/86 (2%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK- 166
           ++VG L   +TE   +  F+ FG I ++V+M D +T R +G+GFIT+   E   R L + 
Sbjct: 8   LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQL 67
Query: 167 TFHELNGKMVEVKRAVPK-EFSPGPS 191
              EL G+ + V     + +   GPS
Sbjct: 68  NGFELAGRPMRVGHVTERLDGGSGPS 93

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 52.0 bits (123), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 29/92 (31%), Positives = 51/92 (55%), Gaps = 9/92 (9%)
Query: 97  HSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-- 154
            ++P P     +F  GL+   TE D ++ F ++G I DV ++YD  ++R RGF F+ +  
Sbjct: 6   RANPDPNCCLGVF--GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 63
Query: 155 --DSEEAVDRVLHKTFHELNGKMVEVKRAVPK 184
             D++EA +R       EL+G+ + V  ++ K
Sbjct: 64  VDDAKEAKERA---NGMELDGRRIRVDFSITK 92

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 51.6 bits (122), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 29/86 (33%), Positives = 47/86 (54%), Gaps = 2/86 (2%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFIT-YDSEEAVDRVLHK 166
           +FVG L+  +T  D K  F  FG I+D  V+ D  T + +G+GF++ Y+  +A + ++H 
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 167 TFHELNGKMVEVKRAVPKEFSP-GPS 191
               L G+ +    A  K  +P GPS
Sbjct: 78  GGQWLGGRQIRTNWATRKPPAPSGPS 103

>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex Wit Length = 89

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/84 (35%), Positives = 45/84 (53%), Gaps = 7/84 (8%)
Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          K+F+G  + D   E L+++F +YGEVV+  I +       R F FV FAD  VA+ +  +
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCGE 67
Query: 67 KHMIDGRTVEAKKAVPRDDQNMLN 90
            +I G +V    A P+   N LN
Sbjct: 68 DLIIKGISVHISNAEPK--HNKLN 89

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 43/161 (26%), Positives = 70/161 (43%), Gaps = 27/161 (16%)
Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
           +LF+G +  D  EE  K  F RYGE  E  I RD      RGFGF+      +AE   + 
Sbjct: 24  RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAE---IA 74
Query: 67  KHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYF 126
           K  +DG  ++++            R   + H +        + V  L+  V+    ++ F
Sbjct: 75  KAELDGTILKSRPL----------RIRFATHGA-------ALTVKNLSPVVSNELLEQAF 117
Query: 127 DQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
            QFG +   VV+ D +  R  G GF+ + ++    + L + 
Sbjct: 118 SQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERC 157

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 50.4 bits (119), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           K +FV  +    TES  ++ F+ +G I  + ++Y   + +PRG+ FI Y+ E    R +H
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHE----RDMH 158
Query: 166 KTFHELNGKMVEVKRAV 182
             +   +GK ++ +R +
Sbjct: 159 SAYKHADGKKIDGRRVL 175

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          +F+GGI    DE  ++ +F+RYG V E  I+ DR TG ++G+GFV F +    ++++  +
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 68 HMIDGRTVEAKKAVPRDD 85
              G+ ++   A+ + +
Sbjct: 72 INFHGKKLKLGPAIRKQN 89

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 49.3 bits (116), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 27/79 (34%), Positives = 45/79 (56%), Gaps = 2/79 (2%)
Query: 105 TKKI-FVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD-SEEAVDR 162
           TK++ +VGGLA  V +      F  FG ITD+ +  D+ T++ RGF F+ ++ +E+A   
Sbjct: 62  TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 121
Query: 163 VLHKTFHELNGKMVEVKRA 181
           + +    EL G+ + V  A
Sbjct: 122 IDNMNESELFGRTIRVNLA 140

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 48.9 bits (115), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 2/75 (2%)
Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
           L +  +++ T  + L+  F +YG V +  I RDR T  +RGF FV F D   AE  +  M
Sbjct: 50  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 66  DKHMIDGRTVEAKKA 80
           D  ++DGR +  + A
Sbjct: 110 DGAVLDGRELRVQMA 124

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 48.9 bits (115), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 39/75 (52%), Gaps = 7/75 (9%)
Query: 99  SPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEE 158
           S GP R   ++VG L   +TE   +  F+ FG I  + +M D  T R +G+GFIT+   E
Sbjct: 23  SAGPMR---LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSE 79
Query: 159 AVDRVLHKTFHELNG 173
              + L     +LNG
Sbjct: 80  CAKKAL----EQLNG 90

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 48.9 bits (115), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          +F+GGI    DE  ++ +F+RYG V E  I+ DR TG ++G+GFV F +    ++++  +
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 68 HMIDGRTVEAKKAVPRD 84
              G+ ++   A+ + 
Sbjct: 71 INFHGKKLKLGPAIRKQ 87

>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 = 48.5 bits (114), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 22/60 (36%), Positives = 36/60 (60%)
Query: 1  MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
          ++  L  +F+G I ++  EE+LK+ FS  G VV   ++ DR TG+ +G+GF  + D   A
Sbjct: 4  VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63

>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 = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEAVDRVL 164
           + +FVG +    TE   K  F + G +    ++YD  T +P+G+GF  Y D E A+  + 
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 165 HKTFHELNGKMVEVKRA 181
           +    E +G+ + V  A
Sbjct: 69  NLNGREFSGRALRVDNA 85

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 48.5 bits (114), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 27/79 (34%), Positives = 45/79 (56%), Gaps = 2/79 (2%)
Query: 105 TKKI-FVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD-SEEAVDR 162
           TK++ +VGGLA  V +      F  FG ITD+ +  D+ T++ RGF F+ ++ +E+A   
Sbjct: 6   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65
Query: 163 VLHKTFHELNGKMVEVKRA 181
           + +    EL G+ + V  A
Sbjct: 66  IDNMNESELFGRTIRVNLA 84

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 48.5 bits (114), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD-SEEAVDRVLHK 166
           ++VGGLA  V +      F  FG ITD+ +  D+ T++ RGF F+ ++ +E+A   + + 
Sbjct: 5   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 167 TFHELNGKMVEVKRA 181
              EL G+ + V  A
Sbjct: 65  NESELFGRTIRVNLA 79

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/82 (31%), Positives = 44/82 (53%), Gaps = 1/82 (1%)
Query: 101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD-SEEA 159
           G    + ++VGGLA  V +      F  FG ITD+ +  D+ T++ RGF F+ ++ +E+A
Sbjct: 1   GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60
Query: 160 VDRVLHKTFHELNGKMVEVKRA 181
              + +    EL G+ + V  A
Sbjct: 61  AAAIDNMNESELFGRTIRVNLA 82

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           K +FV  +    TES  ++ F+ +G I  + ++Y   + +PRG+ FI Y+ E    R +H
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHE----RDMH 158
Query: 166 KTFHELNGKMVEVKRAV 182
             +   +GK ++ +R +
Sbjct: 159 SAYKHADGKKIDGRRVL 175

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 27/78 (34%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 5   LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
           +  L +  +++ T  + L+  F +YG V +  I RDR T  +RGF FV F D   AE  +
Sbjct: 70  MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 129
Query: 65  --MDKHMIDGRTVEAKKA 80
             MD  ++DGR +  + A
Sbjct: 130 DAMDGAVLDGRELRVQMA 147

>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 = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 27/98 (27%), Positives = 50/98 (51%), Gaps = 2/98 (2%)
Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
           +F+G +S +   E +K  F+ +G + +A +++D ATG+++G+GFV F +   AE  I  M
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 66  DKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPG 103
               + GR +    A  +         +++  S P  G
Sbjct: 78  GGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPSSG 115

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 26/85 (30%), Positives = 45/85 (52%), Gaps = 7/85 (8%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFIT----YDSEEAVDRV 163
           +FVG L+  +T  D K  F  FG I+D  V+ D  T + +G+GF++    +D+E A+ ++
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 164 LHKTFHELNGKMVEVKRAVPKEFSP 188
             +    L G+ +    A  K  +P
Sbjct: 78  GGQW---LGGRQIRTNWATRKPPAP 99

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 42/71 (59%), Gaps = 5/71 (7%)
Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          L++  +    D+ERL++ FS +G +  A +M +   GR++GFGFV F+ P  A + + + 
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE- 74
Query: 68 HMIDGRTVEAK 78
            ++GR V  K
Sbjct: 75 --MNGRIVATK 83

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 38/73 (52%), Gaps = 8/73 (10%)
Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS-EEAVDRVLHK 166
           ++V  L   + +   +K F  FGTIT   VM +    R +GFGF+ + S EEA      K
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGG--RSKGFGFVCFSSPEEAT-----K 70
Query: 167 TFHELNGKMVEVK 179
              E+NG++V  K
Sbjct: 71  AVTEMNGRIVATK 83

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 46.6 bits (109), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 39/175 (22%), Positives = 73/175 (41%), Gaps = 14/175 (8%)
Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
           L++G +     E+ LK+YF   G +    IM D+   +   + FV +     A   +   
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIAL--- 58
Query: 68  HMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFD 127
             ++G+ +E          N++  N +          T  +FVG L   V +   +  F 
Sbjct: 59  QTLNGKQIE---------NNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFK 109
Query: 128 QFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT-FHELNGKMVEVKRA 181
            F +     VM+D  T   RG+GF+++ S++     +      +LNG+ + +  A
Sbjct: 110 DFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA 164

>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 = 46.2 bits (108), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 23/77 (29%), Positives = 44/77 (57%), Gaps = 4/77 (5%)
Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE---RVI 64
          +++  + +      L   FS+YG+VV+  IM+D+ T +++G  F++F D   A+   R I
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 65 MDKHMIDGRTVEAKKAV 81
           +K +  GR ++A  A+
Sbjct: 79 NNKQLF-GRVIKASIAI 94

>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 = 45.8 bits (107), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 20/55 (36%), Positives = 33/55 (60%)
Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFAD 56
          + D  KLFIG I  + DE+ LK  F  +G++ E  +++DR TG  +G  F+ + +
Sbjct: 10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCE 64

>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 = 42.0 bits (97), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 6/80 (7%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEA---VDRV 163
           K+F+G +   + E D K  F++FG I ++ V+ D  T   +G  F+TY   E+       
Sbjct: 15  KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 164 LH--KTFHELNGKMVEVKRA 181
           LH  KT   +N + ++VK A
Sbjct: 75  LHEQKTLPGMN-RPIQVKPA 93

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 45.1 bits (105), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 39/163 (23%), Positives = 70/163 (42%), Gaps = 31/163 (19%)
Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE--RVI 64
           +LF+G +  D  EE +++ F +YG+  E  I +D      +GFGF+      +AE  +V 
Sbjct: 24  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 77
Query: 65  MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKK 124
           +D   + G+ +  + A                HS+        + V  L   V+    ++
Sbjct: 78  LDNMPLRGKQLRVRFAC---------------HSA-------SLTVRNLPQYVSNELLEE 115
Query: 125 YFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
            F  FG +   VV+ D +  RP G G + +  + A  + L + 
Sbjct: 116 AFSVFGQVERAVVIVD-DRGRPSGKGIVEFSGKPAARKALDRC 157

>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm Length = 96

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/84 (26%), Positives = 45/84 (53%), Gaps = 4/84 (4%)
Query: 1  MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADP-AV 59
          ME+D   +++G + +    E L+ +F   G V    I+ D+ +G  +GF ++ F+D  +V
Sbjct: 1  MEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 60
Query: 60 AERVIMDKHMIDGRTVEAKKAVPR 83
             + +D+ +  GR +   K +P+
Sbjct: 61 RTSLALDESLFRGRQI---KVIPK 81

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/82 (30%), Positives = 44/82 (53%), Gaps = 3/82 (3%)
Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEA-VIMRDRATGRARGFGFVVFA--DPAVAERVI 64
          +FIG +  + DE+ L + FS +G +++   IMRD  TG ++G+ F+ FA  D + A    
Sbjct: 8  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 65 MDKHMIDGRTVEAKKAVPRDDQ 86
          M+   +  R +    A  +D +
Sbjct: 68 MNGQYLCNRPITVSYAFKKDSK 89

>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: Compositional matrix adjust.
 Identities = 29/90 (32%), Positives = 48/90 (53%), Gaps = 8/90 (8%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV-- 163
           K++ V  +     + D ++ F QFG I DV +++  N +  +GFGF+T+++    DR   
Sbjct: 16  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF--NERGSKGFGFVTFENSADADRARE 73
Query: 164 -LHKTFHELNGKMVEVKRAVPKEFS-PGPS 191
            LH T  E  G+ +EV  A  +  +  GPS
Sbjct: 74  KLHGTVVE--GRKIEVNNATARVMTNSGPS 101

>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna Selenocysteine Associated Protein Length = 99

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 40/69 (57%), Gaps = 4/69 (5%)
Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAV-IMRDRATGRARGFGFVVFADPAVAERVIMD 66
          L++G +    DE  +   F+  GE V +V I+R+R TG   G+ FV FAD A AE+ +  
Sbjct: 12 LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCL-- 69
Query: 67 KHMIDGRTV 75
           H I+G+ +
Sbjct: 70 -HKINGKPL 77

>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna- Splicing Factor Rbm22 Length = 85

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 31/87 (35%), Positives = 48/87 (55%), Gaps = 11/87 (12%)
Query: 98  SSPGPGRTKKI---FVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY 154
           SS   G  K I   +VGGL  T+TE+D + +F QFG I  + V+     QR +   FI +
Sbjct: 2   SSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVV-----QRQQ-CAFIQF 55
Query: 155 DSEEAVDRVLHKTFHEL--NGKMVEVK 179
            + +A +    K+F++L  NG+ + VK
Sbjct: 56  ATRQAAEVAAEKSFNKLIVNGRRLNVK 82

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 19/57 (33%), Positives = 35/57 (61%)
Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          L++ G+     ++ +++ FS+YG ++ + I+ D+ATG +RG GF+ F     AE  I
Sbjct: 4  LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60

>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 = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 44/82 (53%), Gaps = 7/82 (8%)
Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV-- 163
           K++ V  +     + D ++ F QFG I DV +++  N +  +GFGF+T+++    DR   
Sbjct: 30  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF--NERGSKGFGFVTFENSADADRARE 87
Query: 164 -LHKTFHELNGKMVEVKRAVPK 184
            LH T  E  G+ +EV  A  +
Sbjct: 88  KLHGTVVE--GRKIEVNNATAR 107

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 22/60 (36%), Positives = 34/60 (56%)
Query: 5   LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
           L  L +  I    DE +L++ F RYG +    I+ DR T ++RG+GFV F   + A++ I
Sbjct: 42  LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 25/93 (26%), Positives = 48/93 (51%), Gaps = 3/93 (3%)
Query: 99  SPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEE 158
           +P P   + + V  + +TV E   ++ F+++G I  V ++ D  T++ RG+GF+ + S  
Sbjct: 36  NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGS 95
Query: 159 AVDRVLH--KTFHELNGKMVEVKRAVPKEFSPG 189
           +  + +     F+ LN K ++V  A      PG
Sbjct: 96  SAQQAIAGLNGFNILN-KRLKVALAASGHQRPG 127

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 43/72 (59%), Gaps = 6/72 (8%)
Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD-SEEAVDRVLH 165
           ++FV  L+ T +E D +K F  +G ++++    D  T++P+GF F+T+   E AV     
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAV----- 64
Query: 166 KTFHELNGKMVE 177
           K + E++G++ +
Sbjct: 65  KAYAEVDGQVFQ 76

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/97 (24%), Positives = 45/97 (46%), Gaps = 6/97 (6%)
Query: 101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
           GP  +  IF+  L  ++        F  FG I    V+ D N    +G+GF+ ++++EA 
Sbjct: 1   GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS--KGYGFVHFETQEAA 58
Query: 161 DRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRSSMIG 197
           +R + K    +NG ++  ++     F     R + +G
Sbjct: 59  ERAIEK----MNGMLLNDRKVFVGRFKSRKEREAELG 91

>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 = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          L +  +  +  ++ L+  FS  GEV  A ++RD+  G + G+GFV +     AER I  +
Sbjct: 7  LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 66 DKHMIDGRTVEAKKAVP 82
          +   +  +T++   A P
Sbjct: 67 NGLRLQSKTIKVSYARP 83

>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 = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 17/49 (34%), Positives = 30/49 (61%)
Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFAD 56
          +++G I +D  EE++ +  S  G V+   +M D  TGR++G+ F+ F D
Sbjct: 7  VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRD 55

>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens At 1.95 A Resolution Length = 89

Iteration: 1
 Score = 42.7 bits (99), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/83 (25%), Positives = 44/83 (53%), Gaps = 4/83 (4%)
Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADP-AVA 60
          E+D   +++G + +    E L+ +F   G V    I+ D+ +G  +GF ++ F+D  +V 
Sbjct: 3  EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62
Query: 61 ERVIMDKHMIDGRTVEAKKAVPR 83
            + +D+ +  GR +   K +P+
Sbjct: 63 TSLALDESLFRGRQI---KVIPK 82

>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 6 Rna-Binding Protein Length = 108

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 26/84 (30%), Positives = 45/84 (53%), Gaps = 5/84 (5%)
Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFA--DPAV 59
          + D  KLF+G I    DE+ LK  F  +G + E  +++DR TG  +G  F+ +   D A+
Sbjct: 12 DHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSAL 71
Query: 60 -AERVIMDKHMIDG--RTVEAKKA 80
           A+  + ++  + G  R ++ K A
Sbjct: 72 KAQSALHEQKTLPGMNRPIQVKPA 95

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 17/49 (34%), Positives = 30/49 (61%)
Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFAD 56
          +++G I +D  EE++ +  S  G V+   +M D  TGR++G+ F+ F D
Sbjct: 6  VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRD 54

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 46/83 (55%), Gaps = 9/83 (10%)
Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIM- 65
           KLFIGG+    +++++KE  + +G +    +++D ATG ++G+ F  + D  V ++ I  
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175
Query: 66  -------DKHMIDGR-TVEAKKA 80
                  DK ++  R +V AK A
Sbjct: 176 LNGMQLGDKKLLVQRASVGAKNA 198

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 17/49 (34%), Positives = 30/49 (61%)
Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFAD 56
          +++G I +D  EE++ +  S  G V+   +M D  TGR++G+ F+ F D
Sbjct: 5  VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRD 53

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 18/58 (31%), Positives = 36/58 (62%)
Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
           KLFIGG+    +++++KE  + +G +    +++D ATG ++G+ F  + D  V ++ I
Sbjct: 98  KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 155

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	522
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-91
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-34
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	6e-90
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	9e-35
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-63
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-22
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-49
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-25
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	6e-20
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-48
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-47
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-20
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	6e-46
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-45
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-24
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-16
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	7e-44
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	7e-20
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-43
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	3e-37
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-43
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-40
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	5e-43
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-37
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-42
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-34
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-10
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	3e-42
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	1e-39
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-41
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-18
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	6e-41
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	6e-40
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	8e-40
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-34
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	2e-39
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	1e-37
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	4e-39
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	8e-36
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	6e-39
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-34
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-38
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	6e-37
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	8e-38
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	5e-36
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	9e-38
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-34
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-37
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-18
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-13
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-36
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-32
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-35
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-31
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-35
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-17
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	5e-13
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	9e-33
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-24
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-31
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-22
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-30
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-21
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	7e-26
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-19
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-25
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-18
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	6e-25
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	9e-24
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-24
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	8e-19
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-24
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-18
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-24
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-15
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-24
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-18
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	6e-24
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	7e-16
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	7e-24
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	4e-16
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	9e-24
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	5e-17
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-23
1x4e_A	85	RNA binding motif, single-stranded interacting pro	9e-18
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-23
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	5e-17
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-23
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	9e-21
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-23
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	2e-17
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-23
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	7e-16
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-23
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-17
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-23
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-17
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-23
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-18
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	4e-23
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	1e-18
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	4e-23
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	7e-17
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	4e-23
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-15
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	5e-23
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-18
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	5e-23
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	9e-16
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	7e-23
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-18
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	9e-23
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-16
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-22
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-22
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-17
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-22
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	9e-18
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-22
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	3e-21
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-22
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-10
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-22
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	5e-16
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-22
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	9e-16
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-22
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-16
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	3e-22
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-19
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-22
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	6e-15
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	5e-22
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-17
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	8e-22
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	9e-18
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	3e-21
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	9e-15
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	3e-21
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-14
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-21
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-15
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	4e-21
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-15
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-21
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	8e-17
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	5e-21
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-15
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	5e-21
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	8e-13
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	6e-21
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-17
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-21
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	6e-21
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-16
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-20
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-14
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-20
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	5e-14
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-20
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	5e-18
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-20
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	7e-17
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-20
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-15
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-20
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	3e-14
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	3e-20
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	6e-14
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-20
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-14
1x5o_A	114	RNA binding motif, single-stranded interacting pro	4e-20
1x5o_A	114	RNA binding motif, single-stranded interacting pro	7e-15
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-20
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-13
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	8e-20
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	6e-17
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-19
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-12
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-19
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	5e-15
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-19
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-15
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	4e-19
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	4e-14
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	4e-19
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	2e-17
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	8e-19
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-14
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	1e-18
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	1e-13
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-18
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	9e-15
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-18
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-15
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-18
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-14
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-18
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-14
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-17
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-16
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-17
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-16
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	4e-17
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	7e-14
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-17
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-13
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	4e-17
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-13
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	6e-17
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	9e-13
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	7e-17
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	5e-16
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	7e-17
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-14
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	8e-17
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	7e-14
2div_A	99	TRNA selenocysteine associated protein; structural	1e-16
2div_A	99	TRNA selenocysteine associated protein; structural	2e-13
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-16
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	9e-15
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-16
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-16
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-16
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	3e-13
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-16
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-14
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	4e-16
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	7e-11
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	5e-16
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	8e-13
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	6e-16
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-12
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	9e-16
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-15
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-15
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	8e-13
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-15
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-11
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	3e-15
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	5e-15
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	3e-15
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-11
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	4e-15
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	7e-11
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	7e-15
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	9e-12
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	7e-15
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	4e-13
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-14
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-13
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-14
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-11
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	8e-14
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	6e-10
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	8e-14
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-12
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-13
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	7e-09
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	1e-13
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-10
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-13
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	5e-13
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-13
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-10
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-13
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-12
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	3e-13
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-11
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	6e-13
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	3e-10
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	7e-13
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	4e-12
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	9e-13
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-11
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	1e-12
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	5e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-12
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	9e-05
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	3e-12
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	4e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-12
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-11
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-12
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	9e-10
1x5p_A	97	Negative elongation factor E; structure genomics,	4e-12
1x5p_A	97	Negative elongation factor E; structure genomics,	2e-11
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	5e-12
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-07
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	7e-12
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	4e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	7e-12
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	4e-11
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	1e-11
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	1e-09
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-11
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-09
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-11
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	4e-11
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-11
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	7e-11
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-11
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	9e-11
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	4e-11
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	3e-07
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	1e-10
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-09
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-10
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-07
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	3e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	7e-09
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	5e-10
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	9e-07
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	7e-10
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	2e-06
3h0g_A	1752	DNA-directed RNA polymerase II subunit RPB1; trans	6e-05
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	7e-10
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	4e-09
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	8e-10
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-09
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-09
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-09
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-09
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-07
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-09
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-08
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-09
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-08
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	8e-09
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-04
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-08
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	3e-07
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	5e-08
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	6e-05
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	2e-04
1twf_A	1733	B220, DNA-directed RNA polymerase II largest subun	5e-04
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	9e-08
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	4e-07
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	2e-05
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	7e-05
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-04
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	9e-04
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	2e-04
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	4e-04
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	6e-04
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	6e-04

>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 =  275 bits (705), Expect = 3e-91
 Identities = 78/181 (43%), Positives = 119/181 (65%), Gaps = 16/181 (8%)

Query: 4   DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV 63
           +  K+FIGG++WDT E+ L+EYF +YG V +  IM+D ATGR+RGFGF+ F  P+  + V
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61

Query: 64  IMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFK 123
           +  +H++DG+ ++ K+A+PRD+Q+                +T KIFVGG+   V   +F+
Sbjct: 62  VKTQHILDGKVIDPKRAIPRDEQD----------------KTGKIFVGGIGPDVRPKEFE 105

Query: 124 KYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVP 183
           ++F Q+GTI D  +M D +T + RGFGF+TYDS +AVDRV    F +   + +E+KRA P
Sbjct: 106 EFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEP 165

Query: 184 K 184
           +
Sbjct: 166 R 166

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score =  126 bits (318), Expect = 3e-34
 Identities = 35/89 (39%), Positives = 60/89 (67%), Gaps = 1/89 (1%)

Query: 104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV 163
            + K+F+GGL    TE + ++YF ++GT+TD+ +M D  T R RGFGF++++   +VD V
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61

Query: 164 LHKTFHELNGKMVEVKRAVPKEFSPGPSR 192
           + KT H L+GK+++ KRA+P++      +
Sbjct: 62  V-KTQHILDGKVIDPKRAIPRDEQDKTGK 89

>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 =  273 bits (699), Expect = 6e-90
 Identities = 69/194 (35%), Positives = 109/194 (56%), Gaps = 11/194 (5%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
               L KLFIGG+S++T +E L+ +F ++G + + V+MRD  T R+RGFGFV +A     
Sbjct: 9   EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEV 68

Query: 61  ERVI-MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTE 119
           +  +    H +DGR VE K+AV R+D                    KKIFVGG+     E
Sbjct: 69  DAAMNARPHKVDGRVVEPKRAVSREDSQ----------RPGAHLTVKKIFVGGIKEDTEE 118

Query: 120 SDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVK 179
              + YF+Q+G I  + +M D  + + RGF F+T+D  ++VD+++ + +H +NG   EV+
Sbjct: 119 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR 178

Query: 180 RAVPKEFSPGPSRS 193
           +A+ K+     S S
Sbjct: 179 KALSKQEMASASSS 192

>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 =  128 bits (324), Expect = 9e-35
 Identities = 43/101 (42%), Positives = 65/101 (64%)

Query: 94  SSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFIT 153
           S   S   P + +K+F+GGL+   T+   + +F+Q+GT+TD VVM D NT+R RGFGF+T
Sbjct: 2   SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 61

Query: 154 YDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRSS 194
           Y + E VD  ++   H+++G++VE KRAV +E S  P    
Sbjct: 62  YATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHL 102

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  204 bits (522), Expect = 2e-63
 Identities = 39/195 (20%), Positives = 86/195 (44%), Gaps = 11/195 (5%)

Query: 2   ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
            + + ++++G I ++  E+ +++ F+ +G +    +  D  T + +GF FV +  P  A+
Sbjct: 25  LAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQ 84

Query: 62  RVI--MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTE 119
             +  M+  M+ GR ++  +                   +       +I+V  +   +++
Sbjct: 85  LALEQMNSVMLGGRNIKVGRPSNIG-----QAQPIIDQLAEEARAFNRIYVASVHQDLSD 139

Query: 120 SDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK-TFHELNGKMVEV 178
            D K  F+ FG I    +  D  T + +G+GFI Y+  ++    +      +L G+ + V
Sbjct: 140 DDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199

Query: 179 KRAVPKEFSPGPSRS 193
            +AV     P P  +
Sbjct: 200 GKAVTP---PMPLLT 211

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 94.3 bits (235), Expect = 3e-22
 Identities = 21/95 (22%), Positives = 40/95 (42%), Gaps = 1/95 (1%)

Query: 91  RNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFG 150
              S+           +++VG +   + E   ++ F  FG I  + + +D  T + +GF 
Sbjct: 14  GRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFA 73

Query: 151 FITYDSEEAVDRVLHKT-FHELNGKMVEVKRAVPK 184
           F+ Y+  EA    L +     L G+ ++V R    
Sbjct: 74  FVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNI 108

>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 =  167 bits (425), Expect = 1e-49
 Identities = 30/182 (16%), Positives = 68/182 (37%), Gaps = 23/182 (12%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAV-----IMRDRATGRARGFGFVVFADPAVAE 61
           +L++G I +   EE + ++F+    +          +      + + F F+ F       
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 62  RVI-MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTES 120
           + +  D  +  G++++ ++                           K+F+GGL + + + 
Sbjct: 66  QAMAFDGIIFQGQSLKIRRPHDYQP----------------LPGAHKLFIGGLPNYLNDD 109

Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK-TFHELNGKMVEVK 179
             K+    FG +    ++ D  T   +G+ F  Y      D+ +      +L  K + V+
Sbjct: 110 QVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQ 169

Query: 180 RA 181
           RA
Sbjct: 170 RA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score =  100 bits (252), Expect = 4e-25
 Identities = 19/77 (24%), Positives = 44/77 (57%), Gaps = 2/77 (2%)

Query: 6   GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI- 64
            KLFIGG+    +++++KE  + +G +    +++D ATG ++G+ F  + D  V ++ I 
Sbjct: 95  HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 154

Query: 65  -MDKHMIDGRTVEAKKA 80
            ++   +  + +  ++A
Sbjct: 155 GLNGMQLGDKKLLVQRA 171

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 86.1 bits (214), Expect = 6e-20
 Identities = 12/92 (13%), Positives = 37/92 (40%), Gaps = 5/92 (5%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVV-----VMYDHNTQRPRGFGFITYDSEEAV 160
           ++++VG +   +TE     +F+    +  +       +      + + F F+ + S +  
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 161 DRVLHKTFHELNGKMVEVKRAVPKEFSPGPSR 192
            + +        G+ ++++R    +  PG  +
Sbjct: 65  TQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHK 96

>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 =  164 bits (417), Expect = 2e-48
 Identities = 41/187 (21%), Positives = 72/187 (38%), Gaps = 21/187 (11%)

Query: 3   SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATG--RARGFGFVVFADPAVA 60
           SD  K+F+G +     E+ L+E F +YG V E  ++RDR+    +++G  FV F     A
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60

Query: 61  ERVI--MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVT 118
                 +    +        +  P D +                   +K+F+G ++   T
Sbjct: 61  LEAQNALHNMKVLPGMHHPIQMKPADSEKN------------NAVEDRKLFIGMISKKCT 108

Query: 119 ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL----HKTFHELNGK 174
           E+D +  F  FG I +  ++        RG  F+T+ +       +         E    
Sbjct: 109 ENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSS 167

Query: 175 MVEVKRA 181
            + VK A
Sbjct: 168 PMVVKFA 174

>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 =  160 bits (407), Expect = 4e-47
 Identities = 43/180 (23%), Positives = 78/180 (43%), Gaps = 21/180 (11%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            L +  +  +  +E  +  F   GE+    ++RD+ TG++ G+GFV + DP  AE+ I  
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 65  MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKK 124
           ++   +  +T++   A P                     R   ++V GL  T+T+ + ++
Sbjct: 64  LNGLRLQTKTIKVSYARPSSASI----------------RDANLYVSGLPKTMTQKELEQ 107

Query: 125 YFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV---LHKTFHELNGKMVEVKRA 181
            F Q+G I    ++ D  T   RG GFI +D     +     L+        + + VK A
Sbjct: 108 LFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 87.2 bits (217), Expect = 2e-20
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 2   ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
                 L++ G+     ++ L++ FS+YG ++ + I+ D+ TG +RG GF+ F     AE
Sbjct: 85  SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE 144

Query: 62  RVI--MDKHMIDGRT 74
             I  ++     G T
Sbjct: 145 EAIKGLNGQKPSGAT 159

>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 =  160 bits (407), Expect = 6e-46
 Identities = 49/236 (20%), Positives = 77/236 (32%), Gaps = 36/236 (15%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
             +   +LF+G +  D  EE  K  F RYGE  E  I RD      RGFGF+      +A
Sbjct: 18  TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLA 71

Query: 61  ERVI--MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVT 118
           E     +D  ++  R +  + A                           + V  L+  V+
Sbjct: 72  EIAKAELDGTILKSRPLRIRFAT----------------------HGAALTVKNLSPVVS 109

Query: 119 ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEV 178
               ++ F QFG +   VV+ D +  R  G GF+ + ++    + L             +
Sbjct: 110 NELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKAL----ERCGDGAFLL 164

Query: 179 KRAV-PKEFSPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRF 233
                P    P        G       +         Q    +  G F     SR+
Sbjct: 165 TTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYHKEREQPPRFAQPGTFEFEYASRW 220

>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 =  157 bits (398), Expect = 2e-45
 Identities = 32/190 (16%), Positives = 72/190 (37%), Gaps = 11/190 (5%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAV-----IMRDRATGRARGFGFVVFADPAVAE 61
           +L++G I +   EE + ++F+    +          +      + + F F+ F       
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 62  RVI-MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTK----KIFVGGLAST 116
           + +  D  +  G++++ ++         ++ N S                K+F+GGL + 
Sbjct: 66  QAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNY 125

Query: 117 VTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK-TFHELNGKM 175
           + +   K+    FG +    ++ D  T   +G+ F  Y      D+ +      +L  K 
Sbjct: 126 LNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKK 185

Query: 176 VEVKRAVPKE 185
           + V+RA    
Sbjct: 186 LLVQRASVGA 195

>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 = 99.0 bits (247), Expect = 4e-24
 Identities = 19/82 (23%), Positives = 44/82 (53%), Gaps = 2/82 (2%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           KLFIGG+    +++++KE  + +G +    +++D ATG ++G+ F  + D  V ++ I  
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175

Query: 65  MDKHMIDGRTVEAKKAVPRDDQ 86
           ++   +  + +  ++A      
Sbjct: 176 LNGMQLGDKKLLVQRASVGAKN 197

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 76.2 bits (188), Expect = 3e-16
 Identities = 13/94 (13%), Positives = 38/94 (40%), Gaps = 5/94 (5%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVV-----VMYDHNTQRPRGFGFITYDSEEAV 160
           ++++VG +   +TE     +F+    +  +       +      + + F F+ + S +  
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 161 DRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRSS 194
            + +        G+ ++++R    +  PG S + 
Sbjct: 65  TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENP 98

>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 =  151 bits (385), Expect = 7e-44
 Identities = 40/184 (21%), Positives = 70/184 (38%), Gaps = 29/184 (15%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            L +  +  D  +  L   F   G +    IMRD  TG + G+ FV F     ++R I  
Sbjct: 5   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64

Query: 65  MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKK 124
           ++   +  + ++   A P  +                  +   ++V  L  T+T+     
Sbjct: 65  LNGITVRNKRLKVSYARPGGESI----------------KDTNLYVTNLPRTITDDQLDT 108

Query: 125 YFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVE------- 177
            F ++G+I    ++ D  T RPRG  F+ Y+  E     +      LN  + E       
Sbjct: 109 IFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI----SALNNVIPEGGSQPLS 164

Query: 178 VKRA 181
           V+ A
Sbjct: 165 VRLA 168

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 85.7 bits (213), Expect = 7e-20
 Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 3   SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
                L++  +     +++L   F +YG +V+  I+RD+ TGR RG  FV +     A+ 
Sbjct: 87  IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE 146

Query: 63  VI--MDKHMIDGRT 74
            I  ++  + +G +
Sbjct: 147 AISALNNVIPEGGS 160

>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 =  148 bits (376), Expect = 2e-43
 Identities = 32/85 (37%), Positives = 48/85 (56%)

Query: 3  SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
               L + G+ W T E+ LKEYFS +GEV+   + +D  TG ++GFGFV F +     +
Sbjct: 13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVK 72

Query: 63 VIMDKHMIDGRTVEAKKAVPRDDQN 87
          V+  +HMIDGR  + K    +  Q+
Sbjct: 73 VMSQRHMIDGRWCDCKLPNSKQSQD 97

>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 =  131 bits (333), Expect = 3e-37
 Identities = 28/102 (27%), Positives = 44/102 (43%), Gaps = 1/102 (0%)

Query: 92  NTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGF 151
           ++ S        +T  + V GL    TE D K+YF  FG +  V V  D  T   +GFGF
Sbjct: 2   SSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGF 61

Query: 152 ITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRS 193
           + +   E   +V+    H ++G+  + K    K+       S
Sbjct: 62  VRFTEYETQVKVM-SQRHMIDGRWCDCKLPNSKQSQDSGPSS 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 =  148 bits (376), Expect = 3e-43
 Identities = 42/87 (48%), Positives = 59/87 (67%), Gaps = 1/87 (1%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
           M S   K+FIGG+SW T +E L+EYF ++GEV E ++MRD  T R+RGFGFV F D A  
Sbjct: 21  MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGV 80

Query: 61  ERVI-MDKHMIDGRTVEAKKAVPRDDQ 86
           ++V+   +H +D +T++ K A PR  Q
Sbjct: 81  DKVLAQSRHELDSKTIDPKVAFPRRAQ 107

>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 =  140 bits (355), Expect = 3e-40
 Identities = 35/100 (35%), Positives = 57/100 (57%)

Query: 89  LNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRG 148
            + +      S       K+F+GGL+   T+   ++YF QFG + + +VM D  T+R RG
Sbjct: 9   HHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRG 68

Query: 149 FGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSP 188
           FGF+T+  +  VD+VL ++ HEL+ K ++ K A P+   P
Sbjct: 69  FGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRAQP 108

>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 =  147 bits (373), Expect = 5e-43
 Identities = 42/97 (43%), Positives = 65/97 (67%)

Query: 97  HSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
            S     ++ KIFVGG+     E++ ++YF +FG +T+VV++YD   QRPRGFGFIT++ 
Sbjct: 2   SSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFED 61

Query: 157 EEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRS 193
           E++VD+ ++  FH++ GK VEVKRA P++       S
Sbjct: 62  EQSVDQAVNMHFHDIMGKKVEVKRAEPRDSKSSGPSS 98

>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 =  133 bits (336), Expect = 1e-37
 Identities = 35/86 (40%), Positives = 51/86 (59%), Gaps = 1/86 (1%)

Query: 3  SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
          S   K+F+GGI  +  E  L+EYF ++G V E V++ D    R RGFGF+ F D    ++
Sbjct: 8  SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQ 67

Query: 63 VI-MDKHMIDGRTVEAKKAVPRDDQN 87
           + M  H I G+ VE K+A PRD ++
Sbjct: 68 AVNMHFHDIMGKKVEVKRAEPRDSKS 93

>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 =  152 bits (386), Expect = 1e-42
 Identities = 25/185 (13%), Positives = 57/185 (30%), Gaps = 22/185 (11%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            L +  +     +++ +E    +G +    ++    TG+++G+GF  +     A R    
Sbjct: 97  LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156

Query: 65  MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESD-FK 123
           +    +  RT+                        P    ++ + V  L     + D   
Sbjct: 157 LLGKPLGPRTLYVHWTDAGQLT-------------PALLHSRCLCVDRLPPGFNDVDALC 203

Query: 124 KYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV---LHKTFHELNGKMVEVKR 180
           +      + T   +       + +GF  + Y++ E  +            L G  + V  
Sbjct: 204 RALSAVHSPTFCQLACG-QDGQLKGFAVLEYETAEMAEEAQQQADGL--SLGGSHLRVSF 260

Query: 181 AVPKE 185
             P  
Sbjct: 261 CAPGP 265

>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 =  130 bits (328), Expect = 2e-34
 Identities = 30/194 (15%), Positives = 65/194 (33%), Gaps = 32/194 (16%)

Query: 3   SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
            +  K+ I G+  D   + + +  S Y        ++     + +G  FV   +   AE 
Sbjct: 20  RNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEA 72

Query: 63  VI--MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTES 120
            I    +  +  R +  +                             + V  L  ++T+ 
Sbjct: 73  AINAFHQSRLRERELSVQLQPTD----------------------ALLCVANLPPSLTQQ 110

Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK-TFHELNGKMVEVK 179
            F++    FG++    ++Y   T + +G+GF  Y  +++  R         L  + + V 
Sbjct: 111 QFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVH 170

Query: 180 RAVPKEFSPGPSRS 193
                + +P    S
Sbjct: 171 WTDAGQLTPALLHS 184

>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 = 59.6 bits (145), Expect = 5e-10
 Identities = 19/119 (15%), Positives = 37/119 (31%), Gaps = 26/119 (21%)

Query: 68  HMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFD 127
           HM+D   +  +                  H+       +KI + GL   VT  +      
Sbjct: 1   HMLDPEEIRKRLE----------------HTERQFRNRRKILIRGLPGDVTNQEVHDLLS 44

Query: 128 QFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFH--ELNGKMVEVKRAVPK 184
            +  +    V       + +G  F+T  + E  +  +   FH   L  + + V+     
Sbjct: 45  DYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAI-NAFHQSRLRERELSVQLQPTD 95

>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 =  145 bits (368), Expect = 3e-42
 Identities = 39/123 (31%), Positives = 62/123 (50%), Gaps = 12/123 (9%)

Query: 71  DGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFG 130
                +  + VP +                   + +K+F+GGL+   TE   + Y++Q+G
Sbjct: 5   SSGMEKTLETVPLER------------KKREKEQFRKLFIGGLSFETTEESLRNYYEQWG 52

Query: 131 TITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGP 190
            +TD VVM D  ++R RGFGF+T+ S   VD  +    H ++G++VE KRAV +E S   
Sbjct: 53  KLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREESGSG 112

Query: 191 SRS 193
             S
Sbjct: 113 PSS 115

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score =  138 bits (351), Expect = 1e-39
 Identities = 38/88 (43%), Positives = 59/88 (67%), Gaps = 1/88 (1%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
            +    KLFIGG+S++T EE L+ Y+ ++G++ + V+MRD A+ R+RGFGFV F+  A  
Sbjct: 23  EKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEV 82

Query: 61  ERVIMDK-HMIDGRTVEAKKAVPRDDQN 87
           +  +  + H IDGR VE K+AV R++  
Sbjct: 83  DAAMAARPHSIDGRVVEPKRAVAREESG 110

>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 =  145 bits (369), Expect = 2e-41
 Identities = 35/185 (18%), Positives = 69/185 (37%), Gaps = 22/185 (11%)

Query: 2   ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
            +    LFIG ++ +     LK   S      +  ++ D  TG  R FG+V F      E
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLE 68

Query: 62  RVI-MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTES 120
           + + +    + G  ++ +K   RD +                   + +    L+  +TE 
Sbjct: 69  KALELTGLKVFGNEIKLEKPKGRDSKK--------------VRAARTLLAKNLSFNITED 114

Query: 121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT-FHELNGKMVEVK 179
           + K+ F+    I            + +G  +I + SE   ++ L +    E++G+ V + 
Sbjct: 115 ELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY 169

Query: 180 RAVPK 184
               K
Sbjct: 170 YTGEK 174

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 82.7 bits (205), Expect = 1e-18
 Identities = 15/83 (18%), Positives = 39/83 (46%), Gaps = 1/83 (1%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
             +F+G L    + ++ K    +     D+ V+    T   R FG++ ++S E +++ L 
Sbjct: 14  FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE 72

Query: 166 KTFHELNGKMVEVKRAVPKEFSP 188
            T  ++ G  +++++   ++   
Sbjct: 73  LTGLKVFGNEIKLEKPKGRDSKK 95

>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 =  141 bits (359), Expect = 6e-41
 Identities = 34/102 (33%), Positives = 52/102 (50%)

Query: 92  NTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGF 151
           + SS  ++ G     K+FVGGL  + T+   + YF Q+G + D V+M D  T + RGFGF
Sbjct: 3   SGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGF 62

Query: 152 ITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRS 193
           + +     V  VL    H L+G+ ++ K   P+   P    S
Sbjct: 63  VKFKDPNCVGTVLASRPHTLDGRNIDPKPCTPRGMQPSGPSS 104

>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 =  139 bits (352), Expect = 6e-40
 Identities = 41/85 (48%), Positives = 58/85 (68%), Gaps = 1/85 (1%)

Query: 3  SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
           ++GKLF+GG+ W T +E L+ YFS+YGEVV+ VIM+D+ T ++RGFGFV F DP     
Sbjct: 14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGT 73

Query: 63 VIMDK-HMIDGRTVEAKKAVPRDDQ 86
          V+  + H +DGR ++ K   PR  Q
Sbjct: 74 VLASRPHTLDGRNIDPKPCTPRGMQ 98

>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 =  145 bits (367), Expect = 8e-40
 Identities = 25/182 (13%), Positives = 68/182 (37%), Gaps = 13/182 (7%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            L++        +  +++       V  ++ +       +R F ++       A   +  
Sbjct: 119 TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 178

Query: 65  MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVT-ESDFK 123
           ++   I+G T+  K + P +     +  T            ++I +  L++ +  E+  +
Sbjct: 179 LNGLKIEGYTLVTKVSNPLEKSKRTDSATLE---------GREIMIRNLSTELLDENLLR 229

Query: 124 KYFDQFGTITDVVVMYD-HNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAV 182
           + F+ FG+I  + +              F+ ++++++ +R L      L  + + V  A 
Sbjct: 230 ESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLAD 289

Query: 183 PK 184
            K
Sbjct: 290 KK 291

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score =  130 bits (328), Expect = 2e-34
 Identities = 22/203 (10%), Positives = 59/203 (29%), Gaps = 31/203 (15%)

Query: 3   SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
            +L  + +  +    ++ ++ +YF   G ++   +       +   F  + FA    A  
Sbjct: 39  RELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALA 96

Query: 63  VI-MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESD 121
            I     ++    +                                +++     + T+ +
Sbjct: 97  AITKTHKVVGQNEIIV-----------------------SHLTECTLWMTNFPPSYTQRN 133

Query: 122 FKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD---RVLHKTFHELNGKMVEV 178
            +        +   + +        R F +I   S+E        L+    ++ G  +  
Sbjct: 134 IRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGL--KIEGYTLVT 191

Query: 179 KRAVPKEFSPGPSRSSMIGYNNF 201
           K + P E S     +++ G    
Sbjct: 192 KVSNPLEKSKRTDSATLEGREIM 214

>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 =  138 bits (349), Expect = 2e-39
 Identities = 37/115 (32%), Positives = 56/115 (48%), Gaps = 14/115 (12%)

Query: 2   ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
           ++   K+F+GG+ + T +  L++YF  +G++ EAV++ DR TG++RG+GFV  AD A AE
Sbjct: 14  DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 73

Query: 62  RVIMDK-HMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLAS 115
           R   D   +IDGR      A                           I V G +S
Sbjct: 74  RACKDPNPIIDGRKANVNLAYLGAKPRS-------------LQTGFAIGVSGPSS 115

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score =  133 bits (336), Expect = 1e-37
 Identities = 33/108 (30%), Positives = 49/108 (45%)

Query: 90  NRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGF 149
           +  +S +H S       KIFVGGL    T++  +KYF+ FG I + VV+ D  T + RG+
Sbjct: 2   SSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGY 61

Query: 150 GFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRSSMIG 197
           GF+T     A +R        ++G+   V  A              IG
Sbjct: 62  GFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTGFAIG 109

>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 =  136 bits (345), Expect = 4e-39
 Identities = 42/80 (52%), Positives = 60/80 (75%), Gaps = 1/80 (1%)

Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
          E D GK+F+GG+SWDT ++ LK+YF+++GEVV+  I  D  TGR+RGFGF++F D A  E
Sbjct: 8  EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVE 67

Query: 62 RVIMDK-HMIDGRTVEAKKA 80
          +V+  K H +DGR ++ KKA
Sbjct: 68 KVLDQKEHRLDGRVIDPKKA 87

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score =  127 bits (321), Expect = 8e-36
 Identities = 33/86 (38%), Positives = 53/86 (61%)

Query: 96  IHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD 155
           I++S       K+FVGGL+   ++ D K YF +FG + D  +  D NT R RGFGFI + 
Sbjct: 2   INASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFK 61

Query: 156 SEEAVDRVLHKTFHELNGKMVEVKRA 181
              +V++VL +  H L+G++++ K+A
Sbjct: 62  DAASVEKVLDQKEHRLDGRVIDPKKA 87

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score =  135 bits (342), Expect = 6e-39
 Identities = 37/75 (49%), Positives = 54/75 (72%), Gaps = 1/75 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
          K+FIGG+SW T +E L+EYF ++GEV E ++MRD  T R+RGFGFV F D A  ++V+  
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 66 DKHMIDGRTVEAKKA 80
           +H +D +T++ K A
Sbjct: 62 SRHELDSKTIDPKVA 76

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score =  124 bits (313), Expect = 1e-34
 Identities = 32/75 (42%), Positives = 51/75 (68%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+F+GGL+   T+   ++YF QFG + + +VM D  T+R RGFGF+T+  +  VD+VL +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 167 TFHELNGKMVEVKRA 181
           + HEL+ K ++ K A
Sbjct: 62  SRHELDSKTIDPKVA 76

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score =  134 bits (339), Expect = 2e-38
 Identities = 40/75 (53%), Positives = 54/75 (72%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           KIFVGGL+   T  D K YF+QFG + D ++M+D  T R RGFGF+T++SE+ V++V   
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 167 TFHELNGKMVEVKRA 181
            FHE+N KMVE K+A
Sbjct: 61  HFHEINNKMVECKKA 75

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score =  129 bits (328), Expect = 6e-37
 Identities = 33/75 (44%), Positives = 50/75 (66%), Gaps = 1/75 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
          K+F+GG+S +T  E +K YF ++G+V +A++M D+ T R RGFGFV F    + E+V  +
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 66 DKHMIDGRTVEAKKA 80
            H I+ + VE KKA
Sbjct: 61 HFHEINNKMVECKKA 75

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score =  132 bits (335), Expect = 8e-38
 Identities = 28/75 (37%), Positives = 43/75 (57%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           KIFVGGL+    E   ++YF  FG +  + +  D+ T + RGF FIT+  EE V +++ K
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 167 TFHELNGKMVEVKRA 181
            +H +     E+K A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score =  127 bits (322), Expect = 5e-36
 Identities = 27/75 (36%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          K+F+GG+S DT EE+++EYF  +GEV    +  D  T + RGF F+ F +    ++++  
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 67 K-HMIDGRTVEAKKA 80
          K H +     E K A
Sbjct: 61 KYHNVGLSKCEIKVA 75

>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 =  132 bits (335), Expect = 9e-38
 Identities = 27/84 (32%), Positives = 44/84 (52%), Gaps = 5/84 (5%)

Query: 3  SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
              K+F+G  + D   E L+++F +YGEVV+  I +       R F FV FAD  VA+ 
Sbjct: 9  HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFADDKVAQS 63

Query: 63 VIMDKHMIDGRTVEAKKAVPRDDQ 86
          +  +  +I G +V    A P+ ++
Sbjct: 64 LCGEDLIIKGISVHISNAEPKHNK 87

>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 =  123 bits (312), Expect = 2e-34
 Identities = 20/89 (22%), Positives = 37/89 (41%), Gaps = 6/89 (6%)

Query: 97  HSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
            S        K+FVG     +T  + +++F Q+G + DV +         R F F+T+  
Sbjct: 3   GSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFAD 57

Query: 157 EEAVDRVLHKTFHELNGKMVEVKRAVPKE 185
           ++    +  +    + G  V +  A PK 
Sbjct: 58  DKVAQSLCGED-LIIKGISVHISNAEPKH 85

>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 =  133 bits (338), Expect = 4e-37
 Identities = 35/172 (20%), Positives = 69/172 (40%), Gaps = 21/172 (12%)

Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
           L++G +     E+ LK+YF   G +    IM D+   +   + FV +     A   +  +
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61

Query: 66  DKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKY 125
           +   I+   V+   A          +++S    +        +FVG L   V +   +  
Sbjct: 62  NGKQIENNIVKINWAFQS------QQSSSDDTFN--------LFVGDLNVNVDDETLRNA 107

Query: 126 FDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVE 177
           F  F +     VM+D  T   RG+GF+++ S++     +      + G+ + 
Sbjct: 108 FKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM----DSMQGQDLN 155

>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 = 81.8 bits (203), Expect = 2e-18
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 3   SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
            D   LF+G ++ + D+E L+  F  +   +   +M D  TG +RG+GFV F     A+ 
Sbjct: 85  DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 144

Query: 63  VI--MDKHMIDGRTV 75
            +  M    ++GR +
Sbjct: 145 AMDSMQGQDLNGRPL 159

>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 = 67.9 bits (167), Expect = 1e-13
 Identities = 21/97 (21%), Positives = 39/97 (40%), Gaps = 7/97 (7%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           + ++VG L   +TE   K+YF   G I ++ +M D    +   + F+ Y      +  L 
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59

Query: 166 K-TFHELNGKMVEVKRAVPKEFSPGPSRSSMIGYNNF 201
                ++   +V++  A           SS   +N F
Sbjct: 60  TLNGKQIENNIVKINWA-----FQSQQSSSDDTFNLF 91

>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 =  129 bits (326), Expect = 2e-36
 Identities = 27/85 (31%), Positives = 46/85 (54%), Gaps = 5/85 (5%)

Query: 3  SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
          S    +F+G  + D  E+ L+E+FS+YG+V++  I +       R F FV FAD  +A+ 
Sbjct: 3  SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQS 57

Query: 63 VIMDKHMIDGRTVEAKKAVPRDDQN 87
          +  +  +I G +V    A P+ + N
Sbjct: 58 LCGEDLIIKGISVHISNAEPKHNSN 82

>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 =  118 bits (297), Expect = 2e-32
 Identities = 22/93 (23%), Positives = 39/93 (41%), Gaps = 6/93 (6%)

Query: 101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
           G   +  +FVG     +TE + +++F Q+G + DV +         R F F+T+  ++  
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIA 55

Query: 161 DRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRS 193
             +       + G  V +  A PK  S     S
Sbjct: 56  QSLC-GEDLIIKGISVHISNAEPKHNSNSGPSS 87

>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 =  126 bits (320), Expect = 2e-35
 Identities = 28/102 (27%), Positives = 52/102 (50%), Gaps = 8/102 (7%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
            +     +F+GGI    DE  ++ +F+RYG V E  I+ DR TG ++G+GFV F +    
Sbjct: 5   GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDV 63

Query: 61  ERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGP 102
           ++++  +    G+ ++   A+ + +        S+ H  P P
Sbjct: 64  QKIVESQINFHGKKLKLGPAIRKQNL-------STYHVQPRP 98

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score =  115 bits (291), Expect = 2e-31
 Identities = 19/94 (20%), Positives = 49/94 (52%), Gaps = 2/94 (2%)

Query: 101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
           G      +FVGG+   + E++ + +F ++G++ +V ++ D  T   +G+GF+++ ++  V
Sbjct: 5   GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDV 63

Query: 161 DRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRSS 194
            +++       +GK +++  A+ K+         
Sbjct: 64  QKIVES-QINFHGKKLKLGPAIRKQNLSTYHVQP 96

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score =  130 bits (328), Expect = 3e-35
 Identities = 54/214 (25%), Positives = 86/214 (40%), Gaps = 30/214 (14%)

Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
           L++G +  D  E  L E FS  G ++   + RD  T R+ G+ +V F  PA AER +  M
Sbjct: 18  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77

Query: 66  DKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKY 125
           +  +I G+ V    +          R+ S   S  G      IF+  L  ++        
Sbjct: 78  NFDVIKGKPVRIMWS---------QRDPSLRKSGVG-----NIFIKNLDKSIDNKALYDT 123

Query: 126 FDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK-TFHELNGKMVEVKRAVPK 184
           F  FG I    V+ D      +G+GF+ ++++EA +R + K     LN + V V R   +
Sbjct: 124 FSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR 181

Query: 185 EFSPGPSRSSMIGYNNFGFNRPTNLLNSFAQRYN 218
                  R + +G       R           Y 
Sbjct: 182 -----KEREAELG------ARAKEFYPYDVPDYA 204

>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 = 80.4 bits (199), Expect = 2e-17
 Identities = 29/134 (21%), Positives = 52/134 (38%), Gaps = 24/134 (17%)

Query: 2   ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
           +S +G +FI  +    D + L + FS +G ++   ++ D     ++G+GFV F     AE
Sbjct: 100 KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAE 157

Query: 62  RVI--MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTE 119
           R I  M+  +++ R V   +   R +                    ++  +G  A     
Sbjct: 158 RAIEKMNGMLLNDRKVFVGRFKSRKE--------------------REAELGARAKEFYP 197

Query: 120 SDFKKYFDQFGTIT 133
            D   Y    G I 
Sbjct: 198 YDVPDYAGSSGRIV 211

>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 = 67.3 bits (165), Expect = 5e-13
 Identities = 26/110 (23%), Positives = 42/110 (38%), Gaps = 6/110 (5%)

Query: 93  TSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFI 152
             S++ S        ++VG L   VTE+   + F   G I  + V  D  T+R  G+ ++
Sbjct: 3   LGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 62

Query: 153 TYDSEEAVDRVLHK-TFHELNGKMVEVKRAVPKEFSPGPSRSSMIGYNNF 201
            +      +R L    F  + GK V +  +        PS       N F
Sbjct: 63  NFQQPADAERALDTMNFDVIKGKPVRIMWS-----QRDPSLRKSGVGNIF 107

>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 =  119 bits (301), Expect = 9e-33
 Identities = 38/89 (42%), Positives = 59/89 (66%), Gaps = 2/89 (2%)

Query: 1  MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
          M SD GKLF+GG+S+DT+E+ L++ FS+YG++ E V+++DR T R+RGFGFV F +   A
Sbjct: 8  MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 67

Query: 61 ERVI--MDKHMIDGRTVEAKKAVPRDDQN 87
          +  +  M+   +DGR +   +A    D  
Sbjct: 68 KDAMMAMNGKSVDGRQIRVDQAGKSSDNR 96

>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 = 96.9 bits (242), Expect = 2e-24
 Identities = 30/100 (30%), Positives = 51/100 (51%), Gaps = 1/100 (1%)

Query: 95  SIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY 154
           S  SS       K+FVGGL+    E   ++ F ++G I++VVV+ D  TQR RGFGF+T+
Sbjct: 2   SSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTF 61

Query: 155 DSEEAVDRVLHKT-FHELNGKMVEVKRAVPKEFSPGPSRS 193
           ++ +     +       ++G+ + V +A     +     S
Sbjct: 62  ENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDNRSGPSS 101

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score =  116 bits (293), Expect = 1e-31
 Identities = 26/95 (27%), Positives = 39/95 (41%), Gaps = 5/95 (5%)

Query: 99  SPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEE 158
           S G    + +FV G    V  +   +YF  FG +  VV+  D        F  +      
Sbjct: 2   SSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-----FAIVEMGDVG 56

Query: 159 AVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRS 193
           A + VL ++ H L G  + V+    KEF    S+S
Sbjct: 57  AREAVLSQSQHSLGGHRLRVRPREQKEFQSPASKS 91

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 91.2 bits (227), Expect = 1e-22
 Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 6/86 (6%)

Query: 3  SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
          S L  +F+ G     D  +L EYF  +G V   V+ +D+       F  V   D    E 
Sbjct: 6  SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDK-----GVFAIVEMGDVGAREA 60

Query: 63 VI-MDKHMIDGRTVEAKKAVPRDDQN 87
          V+   +H + G  +  +    ++ Q+
Sbjct: 61 VLSQSQHSLGGHRLRVRPREQKEFQS 86

>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 =  114 bits (288), Expect = 1e-30
 Identities = 33/108 (30%), Positives = 63/108 (58%), Gaps = 4/108 (3%)

Query: 1   MESDL-GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAV 59
           +E+D  GKLFIGG++ +T+E+ LK  F ++G + E ++++DR T ++RGF F+ F +PA 
Sbjct: 2   VEADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPAD 60

Query: 60  AERVI--MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRT 105
           A+     M+   + G+ ++ ++A     Q+   R   +   +  P  +
Sbjct: 61  AKNAAKDMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGS 108

>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 = 87.8 bits (218), Expect = 3e-21
 Identities = 28/101 (27%), Positives = 46/101 (45%), Gaps = 2/101 (1%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+F+GGL     E   K  F + G I++V+++ D  T + RGF FIT+++          
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKD 67

Query: 167 T-FHELNGKMVEVKRAVPKEFSPGPSRSSMIGYNNFGFNRP 206
                L+GK ++V++A    F  G  R       N   +  
Sbjct: 68  MNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGS 108

>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 =  100 bits (252), Expect = 7e-26
 Identities = 21/93 (22%), Positives = 43/93 (46%), Gaps = 8/93 (8%)

Query: 3   SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
           ++   +FI  +S+D++EE L E   ++G++    ++    T  ++G  F  F     A++
Sbjct: 13  TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72

Query: 63  VI--------MDKHMIDGRTVEAKKAVPRDDQN 87
            +             +DGR ++   AV RD+  
Sbjct: 73  CLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA 105

>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 = 82.4 bits (204), Expect = 2e-19
 Identities = 24/94 (25%), Positives = 44/94 (46%), Gaps = 8/94 (8%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL- 164
           K +F+  L+    E    +   QFG +  V V+   +T+  +G  F  + ++EA  + L 
Sbjct: 16  KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75

Query: 165 ------HKTFHELNGKMVEVKRAVPK-EFSPGPS 191
                      +L+G+ ++V  AV + E + GPS
Sbjct: 76  AASLEAEGGGLKLDGRQLKVDLAVTRDEAASGPS 109

>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 = 98.3 bits (246), Expect = 2e-25
 Identities = 22/80 (27%), Positives = 39/80 (48%), Gaps = 2/80 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           LF+G ++ + D+E L+  F  +   +   +M D  TG +RG+GFV F     A+  +  
Sbjct: 3  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62

Query: 65 MDKHMIDGRTVEAKKAVPRD 84
          M    ++GR +    A   +
Sbjct: 63 MQGQDLNGRPLRINWAAKLE 82

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 78.3 bits (194), Expect = 3e-18
 Identities = 20/86 (23%), Positives = 36/86 (41%), Gaps = 9/86 (10%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
           T  +FVG L   V +   +  F  F +     VM+D  T   RG+GF+++ S++     +
Sbjct: 1   TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60

Query: 165 HKTFHELNGKMVE-----VKRAVPKE 185
                 + G+ +      +  A   E
Sbjct: 61  ----DSMQGQDLNGRPLRINWAAKLE 82

>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 = 98.5 bits (246), Expect = 6e-25
 Identities = 17/83 (20%), Positives = 36/83 (43%), Gaps = 1/83 (1%)

Query: 2   ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
           E D   +F   ++       L+++FS  G+V +  I+ DR + R++G  +V F +     
Sbjct: 22  ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP 81

Query: 62  RVI-MDKHMIDGRTVEAKKAVPR 83
             I +    + G  +  + +   
Sbjct: 82  LAIGLTGQRLLGVPIIVQASQAE 104

>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 = 95.1 bits (237), Expect = 9e-24
 Identities = 21/88 (23%), Positives = 42/88 (47%), Gaps = 1/88 (1%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           + +F   LA+ +   D + +F   G + DV ++ D N++R +G  ++ +   ++V   + 
Sbjct: 26  RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG 85

Query: 166 KTFHELNGKMVEVKRAVP-KEFSPGPSR 192
            T   L G  + V+ +   K    GPS 
Sbjct: 86  LTGQRLLGVPIIVQASQAEKNRLSGPSS 113

>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 = 98.8 bits (246), Expect = 1e-24
 Identities = 27/83 (32%), Positives = 42/83 (50%), Gaps = 2/83 (2%)

Query: 3   SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
             +  L +  +++ T  + L+  F +YG V +  I RDR T  +RGF FV F D   AE 
Sbjct: 68  EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 127

Query: 63  VI--MDKHMIDGRTVEAKKAVPR 83
            +  MD  ++DGR +  + A   
Sbjct: 128 AMDAMDGAVLDGRELRVQMARYG 150

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 82.6 bits (204), Expect = 8e-19
 Identities = 24/145 (16%), Positives = 48/145 (33%), Gaps = 7/145 (4%)

Query: 51  FVVFADPAVAERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFV 110
            V  A      +   + + +DG                    +   H          + V
Sbjct: 20  AVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTV----TEGSHHHHHHMDVEGMTSLKV 75

Query: 111 GGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-H 169
             L    +    ++ F+++G + DV +  D  T+  RGF F+ +  +   +  +      
Sbjct: 76  DNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGA 135

Query: 170 ELNGKMVEVKRAVPKEFSPGPSRSS 194
            L+G+ + V+ A      P  S  S
Sbjct: 136 VLDGRELRVQMARYGR--PPDSHHS 158

>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 = 96.5 bits (241), Expect = 2e-24
 Identities = 25/87 (28%), Positives = 43/87 (49%), Gaps = 2/87 (2%)

Query: 3  SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
          S  G+LF+  +S+ + EE L++ FS YG + E     D  T + +GF FV F  P  A +
Sbjct: 6  SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVK 65

Query: 63 VI--MDKHMIDGRTVEAKKAVPRDDQN 87
              +D  +  GR +    +  + + +
Sbjct: 66 AYAEVDGQVFQGRMLHVLPSTIKKEAS 92

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 78.4 bits (194), Expect = 5e-18
 Identities = 25/97 (25%), Positives = 48/97 (49%), Gaps = 1/97 (1%)

Query: 99  SPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEE 158
           S G   + ++FV  L+ T +E D +K F  +G ++++    D  T++P+GF F+T+   E
Sbjct: 2   SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61

Query: 159 AVDRVLHKT-FHELNGKMVEVKRAVPKEFSPGPSRSS 194
              +   +       G+M+ V  +  K+ +     SS
Sbjct: 62  HAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSS 98

>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 = 95.3 bits (238), Expect = 3e-24
 Identities = 19/85 (22%), Positives = 41/85 (48%), Gaps = 4/85 (4%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYG--EVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
           L+IG ++W T +E L E     G  +++E     +RA G+++GF  V     A +++++
Sbjct: 3  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 65 --MDKHMIDGRTVEAKKAVPRDDQN 87
            + K  + G+      +   +  +
Sbjct: 63 DLLPKRELHGQNPVVTPSNKLEHHH 87

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 70.3 bits (173), Expect = 3e-15
 Identities = 17/91 (18%), Positives = 34/91 (37%), Gaps = 9/91 (9%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGT--ITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV- 163
            +++G L    T+ D  +     G   I ++    +    + +GF  +   SE +  ++ 
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 164 --LHKTFHELNGKMVEVKRAVPKEFSPGPSR 192
             L K   EL+G+   V  +   E       
Sbjct: 63  DLLPKR--ELHGQNPVVTPSNKLE--HHHHH 89

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 95.7 bits (239), Expect = 4e-24
 Identities = 25/89 (28%), Positives = 43/89 (48%), Gaps = 2/89 (2%)

Query: 1  MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
          M +    L++GG++ + D++ L   F  +G++ +  I  D  T + RGF FV F     A
Sbjct: 8  MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 67

Query: 61 ERVI--MDKHMIDGRTVEAKKAVPRDDQN 87
             I  M++  + GRT+    A P   + 
Sbjct: 68 AAAIDNMNESELFGRTIRVNLAKPMRIKE 96

>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 = 80.0 bits (198), Expect = 1e-18
 Identities = 26/89 (29%), Positives = 41/89 (46%), Gaps = 1/89 (1%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           + ++VGGLA  V +      F  FG ITD+ +  D+ T++ RGF F+ ++  E     + 
Sbjct: 13  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72

Query: 166 KT-FHELNGKMVEVKRAVPKEFSPGPSRS 193
                EL G+ + V  A P         S
Sbjct: 73  NMNESELFGRTIRVNLAKPMRIKESGPSS 101

>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 = 95.5 bits (238), Expect = 6e-24
 Identities = 27/99 (27%), Positives = 50/99 (50%), Gaps = 2/99 (2%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            +F+G +S +   E +K  F+ +G + +A +++D ATG+++G+GFV F +   AE  I  
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76

Query: 65  MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPG 103
           M    + GR +    A  +         +++  S P  G
Sbjct: 77  MGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPSSG 115

>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 = 72.8 bits (179), Expect = 7e-16
 Identities = 24/89 (26%), Positives = 44/89 (49%), Gaps = 1/89 (1%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
            +FVG L+  +T  D K  F  FG I+D  V+ D  T + +G+GF+++ ++   +  + +
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76

Query: 167 -TFHELNGKMVEVKRAVPKEFSPGPSRSS 194
                L G+ +    A  K  +P  +  S
Sbjct: 77  MGGQWLGGRQIRTNWATRKPPAPKSTYES 105

>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 = 94.5 bits (236), Expect = 7e-24
 Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           +F+G +S +     +   F+ +G + +A +++D ATG+++G+GFV F +   AE  I  
Sbjct: 8  HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 65 MDKHMIDGRTVEAKKAVPR 83
          M    + GR +    A  +
Sbjct: 68 MGGQWLGGRQIRTNWATRK 86

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 72.6 bits (179), Expect = 4e-16
 Identities = 20/79 (25%), Positives = 39/79 (49%), Gaps = 1/79 (1%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
            +FVG L+  +T +     F  FG I+D  V+ D  T + +G+GF+++ ++   +  + +
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 167 -TFHELNGKMVEVKRAVPK 184
                L G+ +    A  K
Sbjct: 68  MGGQWLGGRQIRTNWATRK 86

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 96.0 bits (239), Expect = 9e-24
 Identities = 29/90 (32%), Positives = 45/90 (50%), Gaps = 5/90 (5%)

Query: 3   SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
             +  L +  +++ T  + L+  F +YG V +  I RDR T  +RGF FV F D   AE 
Sbjct: 45  EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 104

Query: 63  VI--MDKHMIDGRTV---EAKKAVPRDDQN 87
            +  MD  ++DGR +    A+   P D  +
Sbjct: 105 AMDAMDGAVLDGRELRVQMARYGRPPDSHH 134

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 76.7 bits (189), Expect = 5e-17
 Identities = 23/114 (20%), Positives = 43/114 (37%), Gaps = 3/114 (2%)

Query: 82  PRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDH 141
               Q M   + S     P       + V  L    +    ++ F+++G + DV +  D 
Sbjct: 24  MTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDR 83

Query: 142 NTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPKEFSPGPSRSS 194
            T+  RGF F+ +  +   +  +       L+G+ + V+ A      P  S  S
Sbjct: 84  YTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR--PPDSHHS 135

>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 = 94.1 bits (235), Expect = 1e-23
 Identities = 20/83 (24%), Positives = 41/83 (49%), Gaps = 4/83 (4%)

Query: 3  SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
          S    L+I G+   T ++ L +    YG++V    + D+ T + +G+GFV F  P+ A++
Sbjct: 3  SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQK 62

Query: 63 VI--MDKHMIDGRTVEAKKAVPR 83
           +  +    +  +    K++ P 
Sbjct: 63 AVTALKASGVQAQMA--KQSGPS 83

>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 = 77.2 bits (191), Expect = 9e-18
 Identities = 20/81 (24%), Positives = 34/81 (41%), Gaps = 4/81 (4%)

Query: 101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
           G   +  +++ GL    T+ D  K    +G I     + D  T + +G+GF+ +DS  A 
Sbjct: 1   GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60

Query: 161 DRVLHKTFHELNGKMVEVKRA 181
                K    L    V+ + A
Sbjct: 61  Q----KAVTALKASGVQAQMA 77

>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 = 94.7 bits (236), Expect = 1e-23
 Identities = 21/81 (25%), Positives = 45/81 (55%), Gaps = 2/81 (2%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           +L++G + ++  E+ L+  F  +G +    +M D  TGR++G+GF+ F+D   A++ +  
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87

Query: 65  MDKHMIDGRTVEAKKAVPRDD 85
           ++   + GR ++      R D
Sbjct: 88  LNGFELAGRPMKVGHVTERTD 108

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 75.8 bits (187), Expect = 5e-17
 Identities = 25/102 (24%), Positives = 46/102 (45%), Gaps = 3/102 (2%)

Query: 85  DQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQ 144
             +M     +++          +++VG L   +TE   +  F+ FG I  + +M D  T 
Sbjct: 8   HSHMAAAMANNLQKGSAG--PMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETG 65

Query: 145 RPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPKE 185
           R +G+GFIT+   E   + L +    EL G+ ++V     + 
Sbjct: 66  RSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERT 107

>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 = 95.2 bits (237), Expect = 2e-23
 Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            L + G+S  T E  L+E FS+YG + +  I+ D+ + R+RGF FV F +   A+     
Sbjct: 48  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107

Query: 65  MDKHMIDGRTVEAKKAVPR 83
            +   +DGR +    ++ +
Sbjct: 108 ANGMELDGRRIRVDFSITK 126

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 87.1 bits (216), Expect = 9e-21
 Identities = 27/119 (22%), Positives = 52/119 (43%), Gaps = 1/119 (0%)

Query: 67  KHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYF 126
            H   G                + R +  + +   P     + V GL+   TE D ++ F
Sbjct: 8   HHHSSGLVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVF 67

Query: 127 DQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK-TFHELNGKMVEVKRAVPK 184
            ++G I DV ++YD  ++R RGF F+ +++ +       +    EL+G+ + V  ++ K
Sbjct: 68  SKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK 126

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 95.8 bits (238), Expect = 2e-23
 Identities = 19/86 (22%), Positives = 43/86 (50%), Gaps = 4/86 (4%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYG--EVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
            +++G  SW T +++L +     G  +VVE     +RA G+++G+  VV A      +++
Sbjct: 57  AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLL 116

Query: 65  --MDKHMIDGRTVEAKKAVPRDDQNM 88
             +   +++G  V+ + A  ++    
Sbjct: 117 ELLPGKVLNGEKVDVRPATRQNLSQF 142

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 78.4 bits (193), Expect = 2e-17
 Identities = 18/99 (18%), Positives = 41/99 (41%), Gaps = 3/99 (3%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGT--ITDVVVMYDHNTQRPRGFGFITYD 155
            S    R   ++VG  +   T+    +     G   + ++    +    + +G+  +   
Sbjct: 48  YSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVA 107

Query: 156 SEEAVDRVLHKT-FHELNGKMVEVKRAVPKEFSPGPSRS 193
           SE +V ++L       LNG+ V+V+ A  +  S   +++
Sbjct: 108 SENSVHKLLELLPGKVLNGEKVDVRPATRQNLSQFEAQA 146

>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 = 93.4 bits (233), Expect = 2e-23
 Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 3/80 (3%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRA-TGRARGFGFVVFADPAVAERVI- 64
          K+ IG ++ +  ++ + E FS YG++    +  +R     ++G+ +V F +P  AE+ + 
Sbjct: 6  KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 65 -MDKHMIDGRTVEAKKAVPR 83
           MD   IDG+ + A   +  
Sbjct: 66 HMDGGQIDGQEITATAVLAP 85

>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 = 71.8 bits (177), Expect = 7e-16
 Identities = 13/84 (15%), Positives = 36/84 (42%), Gaps = 2/84 (2%)

Query: 104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHN-TQRPRGFGFITY-DSEEAVD 161
           +  K+ +G L   VT+    + F  +G I  + +  +       +G+ ++ + + +EA  
Sbjct: 3   KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62

Query: 162 RVLHKTFHELNGKMVEVKRAVPKE 185
            + H    +++G+ +     +   
Sbjct: 63  ALKHMDGGQIDGQEITATAVLAPW 86

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 93.3 bits (233), Expect = 2e-23
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 1/84 (1%)

Query: 1  MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
          ME+D   +++G + +    E L+ +F   G V    I+ D+ +G  +GF ++ F+D    
Sbjct: 2  MEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 61

Query: 61 ERVI-MDKHMIDGRTVEAKKAVPR 83
             + +D+ +  GR ++       
Sbjct: 62 RTSLALDESLFRGRQIKVIPKRTN 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 = 76.8 bits (190), Expect = 1e-17
 Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 2/85 (2%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
            + I+VG +    T  + + +F   G++  V ++ D  +  P+GF +I +  +E+V   L
Sbjct: 6   ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65

Query: 165 HKTFHELNGKMVEVKRAVPKEFSPG 189
                   G+ ++V         PG
Sbjct: 66  ALDESLFRGRQIKVIPKRTNR--PG 88

>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 = 93.0 bits (232), Expect = 2e-23
 Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 5/83 (6%)

Query: 1  MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
          M +    L++GG++ + D++ L   F  +G++ +  I  D  T + RGF FV F     A
Sbjct: 3  MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 62

Query: 61 ERVI--MDKHMIDGRTV---EAK 78
             I  M++  + GRT+    AK
Sbjct: 63 AAAIDNMNESELFGRTIRVNLAK 85

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 75.6 bits (187), Expect = 3e-17
 Identities = 24/79 (30%), Positives = 42/79 (53%), Gaps = 5/79 (6%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD---R 162
           + ++VGGLA  V +      F  FG ITD+ +  D+ T++ RGF F+ ++  E       
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67

Query: 163 VLHKTFHELNGKMVEVKRA 181
            ++++  EL G+ + V  A
Sbjct: 68  NMNES--ELFGRTIRVNLA 84

>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 = 93.1 bits (232), Expect = 3e-23
 Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 3  SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
            +  L +  +++ T  + L+  F +YG V +  I R+  T   RGF FV F D   A+ 
Sbjct: 11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQD 70

Query: 63 VI--MDKHMIDGRTVEAKKAVPR 83
              MD   +DGR +  + A   
Sbjct: 71 AEAAMDGAELDGRELRVQVARYG 93

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 79.2 bits (196), Expect = 3e-18
 Identities = 22/101 (21%), Positives = 40/101 (39%), Gaps = 1/101 (0%)

Query: 94  SSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFIT 153
           SS  S P       + V  L    +    ++ F+++G + DV +  + +T+ PRGF F+ 
Sbjct: 2   SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR 61

Query: 154 YDSEEAVDRVLHKTF-HELNGKMVEVKRAVPKEFSPGPSRS 193
           +                EL+G+ + V+ A           S
Sbjct: 62  FHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLSGPSS 102

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 93.5 bits (232), Expect = 4e-23
 Identities = 18/95 (18%), Positives = 38/95 (40%), Gaps = 9/95 (9%)

Query: 99  SPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYD--HNTQRPRGFGFITYDS 156
           S G   ++K+FVGGL   + E +    F +FG +           +   P+G+ F+ +  
Sbjct: 2   SSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQE 61

Query: 157 EEAVDRVLHKTFH-------ELNGKMVEVKRAVPK 184
           E +V  ++             ++   ++ K    +
Sbjct: 62  ESSVQALIDACLEEDGKLYLCVSSPTIKDKPVQIR 96

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 80.8 bits (199), Expect = 1e-18
 Identities = 18/87 (20%), Positives = 39/87 (44%), Gaps = 10/87 (11%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRD--RATGRARGFGFVVFADPAVAERVI 64
          K+F+GG+  D DE+ +   F R+G +V     +   ++    +G+ F++F + +  + +I
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69

Query: 65 MDKHM--------IDGRTVEAKKAVPR 83
                       +   T++ K    R
Sbjct: 70 DACLEEDGKLYLCVSSPTIKDKPVQIR 96

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 92.6 bits (231), Expect = 4e-23
 Identities = 23/83 (27%), Positives = 45/83 (54%), Gaps = 2/83 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L++G + ++  E+ L+  F  +G++   V+M+D  TGR++G+GF+ F+D   A R +  
Sbjct: 7  GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

Query: 65 MDKHMIDGRTVEAKKAVPRDDQN 87
          ++   + GR +       R D  
Sbjct: 67 LNGFELAGRPMRVGHVTERLDGG 89

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 74.9 bits (185), Expect = 7e-17
 Identities = 30/95 (31%), Positives = 47/95 (49%), Gaps = 3/95 (3%)

Query: 101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
           G   +  ++VG L   +TE   +  F+ FG I ++V+M D +T R +G+GFIT+   E  
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60

Query: 161 DRVLHKTF-HELNGKMVEVKRAVPKEFSPGPSRSS 194
            R L +    EL G+ + V     +    G S  S
Sbjct: 61  RRALEQLNGFELAGRPMRVGHVTERL--DGGSGPS 93

>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 = 92.7 bits (231), Expect = 4e-23
 Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 5/89 (5%)

Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATG---RARGFGFVVFADPA 58
           S    LFI  +++ T EE LK  FS+ G +    I + +       + GFGFV +  P 
Sbjct: 2  SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61

Query: 59 VAERVI--MDKHMIDGRTVEAKKAVPRDD 85
           A++ +  +  H +DG  +E + +     
Sbjct: 62 QAQKALKQLQGHTVDGHKLEVRISERATK 90

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 71.1 bits (175), Expect = 2e-15
 Identities = 21/89 (23%), Positives = 35/89 (39%), Gaps = 4/89 (4%)

Query: 101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQ---RPRGFGFITYDSE 157
           G   +  +F+  L  + TE   K  F + G I    +    N        GFGF+ Y   
Sbjct: 1   GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60

Query: 158 EAVDRVLHKT-FHELNGKMVEVKRAVPKE 185
           E   + L +   H ++G  +EV+ +    
Sbjct: 61  EQAQKALKQLQGHTVDGHKLEVRISERAT 89

>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 = 92.2 bits (230), Expect = 5e-23
 Identities = 23/88 (26%), Positives = 45/88 (51%), Gaps = 3/88 (3%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           +++G + +    E++KE FS++G+V    ++ DR T + +GFGFV   + +     I  
Sbjct: 3  NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAK 61

Query: 65 MDKHMIDGRTVEAKKAVPRDDQNMLNRN 92
          +D     GRT+   +A P+      + +
Sbjct: 62 LDNTDFMGRTIRVTEANPKKSLEHHHHH 89

>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 = 78.8 bits (195), Expect = 3e-18
 Identities = 25/87 (28%), Positives = 43/87 (49%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           + I+VG L  + T    K+ F QFG + +V ++YD  T++P+GFGF+    E   + +  
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61

Query: 166 KTFHELNGKMVEVKRAVPKEFSPGPSR 192
               +  G+ + V  A PK+       
Sbjct: 62  LDNTDFMGRTIRVTEANPKKSLEHHHH 88

>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 = 92.7 bits (231), Expect = 5e-23
 Identities = 25/87 (28%), Positives = 44/87 (50%), Gaps = 2/87 (2%)

Query: 1  MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
          ++  L  +F+G I ++  EE+LK+ FS  G VV   ++ DR TG+ +G+GF  + D   A
Sbjct: 4  VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63

Query: 61 ERVI--MDKHMIDGRTVEAKKAVPRDD 85
             +  ++     GR +    A    +
Sbjct: 64 LSAMRNLNGREFSGRALRVDNAASEKN 90

>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 = 71.9 bits (177), Expect = 9e-16
 Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 5/84 (5%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD--- 161
            + +FVG +    TE   K  F + G +    ++YD  T +P+G+GF  Y  +E      
Sbjct: 8   LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67

Query: 162 RVLHKTFHELNGKMVEVKRAVPKE 185
           R L+    E +G+ + V  A  ++
Sbjct: 68  RNLNGR--EFSGRALRVDNAASEK 89

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 93.7 bits (233), Expect = 7e-23
 Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            L++GG++ + D++ L   F  +G++ +  I  D  T + RGF FV F     A   I  
Sbjct: 65  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 124

Query: 65  MDKHMIDGRTVEAKKA 80
           M++  + GRT+    A
Sbjct: 125 MNESELFGRTIRVNLA 140

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 79.8 bits (197), Expect = 4e-18
 Identities = 26/93 (27%), Positives = 45/93 (48%), Gaps = 5/93 (5%)

Query: 92  NTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGF 151
           +  S  S       + ++VGGLA  V +      F  FG ITD+ +  D+ T++ RGF F
Sbjct: 50  SGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAF 109

Query: 152 ITYDSEEAVD---RVLHKTFHELNGKMVEVKRA 181
           + ++  E        ++++  EL G+ + V  A
Sbjct: 110 VEFELAEDAAAAIDNMNES--ELFGRTIRVNLA 140

>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 = 92.3 bits (230), Expect = 9e-23
 Identities = 23/122 (18%), Positives = 47/122 (38%), Gaps = 12/122 (9%)

Query: 3   SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
              G +FI  +    D + L + FS +G ++   ++ D     ++G+GFV F     AER
Sbjct: 3   LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAER 60

Query: 63  VI--MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTES 120
            I  M+  +++ R V   +   R ++       +             +++       T +
Sbjct: 61  AIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAK--------EFTNVYIKNFGPGSTRA 112

Query: 121 DF 122
             
Sbjct: 113 AA 114

>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 = 74.2 bits (183), Expect = 2e-16
 Identities = 25/101 (24%), Positives = 44/101 (43%), Gaps = 3/101 (2%)

Query: 101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
           GP  +  IF+  L  ++        F  FG I    V+ D N    +G+GF+ ++++EA 
Sbjct: 1   GPLGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAA 58

Query: 161 DRVLHKT-FHELNGKMVEVKRAVPKEFSPGPSRSSMIGYNN 200
           +R + K     LN + V V R   ++       +    + N
Sbjct: 59  ERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTN 99

>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 = 95.0 bits (236), Expect = 1e-22
 Identities = 34/202 (16%), Positives = 66/202 (32%), Gaps = 35/202 (17%)

Query: 8   LFIGGIS-WDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L +  ++      + L   F  YG+V    I+ ++     +    V  AD   A+  +  
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSH 60

Query: 65  MDKHMIDGRT----------VEAKKAVPRDDQNMLNRNTSSIHSSPGPGR---------T 105
           ++ H + G+           V+  +    D     +   S +H    PG          +
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
             + +  +  +V+E D K  F   G +           Q+ R    I   S E   + L 
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF----FQKDRKMALIQMGSVEEAVQAL- 175

Query: 166 KTFHELNGKMVEVKRAVPKEFS 187
               +L+   +     +   FS
Sbjct: 176 ---IDLHNHDLGENHHLRVSFS 194

>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 = 91.1 bits (227), Expect = 1e-22
 Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L + G+S  T E  L+E FS+YG + +  I+ D+ + R+RGF FV F +   A+     
Sbjct: 17 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76

Query: 65 MDKHMIDGRTVEAKKA 80
           +   +DGR +     
Sbjct: 77 ANGMELDGRRIRVSGP 92

>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 = 76.9 bits (190), Expect = 2e-17
 Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 4/80 (5%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE 157
           +   P     + V GL+   TE D ++ F ++G I DV ++YD  ++R RGF F+ +++ 
Sbjct: 8   NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENV 67

Query: 158 EAVDRVLHKTFHELNGKMVE 177
           +             NG  ++
Sbjct: 68  DDAKEAK----ERANGMELD 83

>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 = 92.9 bits (231), Expect = 1e-22
 Identities = 23/81 (28%), Positives = 40/81 (49%), Gaps = 2/81 (2%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            L +  I    DE +L++ F RYG +    I+ DR T ++RG+GFV F   + A++ I  
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103

Query: 65  MDKHMIDGRTVEAKKAVPRDD 85
           ++   I  + ++   A     
Sbjct: 104 LNGFNILNKRLKVALAASGHQ 124

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 79.0 bits (195), Expect = 9e-18
 Identities = 24/117 (20%), Positives = 52/117 (44%), Gaps = 5/117 (4%)

Query: 86  QNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQR 145
           Q    ++      +P P   + + V  + +TV E   ++ F+++G I  V ++ D  T++
Sbjct: 23  QQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQ 82

Query: 146 PRGFGFITYDSEEAVDRVLHKTFH--ELNGKMVEVKRAVPKEFSPGPSRSSMIGYNN 200
            RG+GF+ + S  +  + +    +   +  K ++V  A        P  +  +G  N
Sbjct: 83  SRGYGFVKFQSGSSAQQAI-AGLNGFNILNKRLKVALAASGH--QRPGIAGAVGDGN 136

>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 = 91.6 bits (228), Expect = 1e-22
 Identities = 25/87 (28%), Positives = 44/87 (50%), Gaps = 5/87 (5%)

Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
          + D  KLFIG I  + DE+ LK  F  +G++ E  +++DR TG  +G  F+ + +   A 
Sbjct: 10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESAL 69

Query: 62 RVIM---DKHMIDG--RTVEAKKAVPR 83
          +      ++  + G  R ++ K A   
Sbjct: 70 KAQSALHEQKTLPGMNRPIQVKPADSE 96

>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 = 87.8 bits (218), Expect = 3e-21
 Identities = 27/104 (25%), Positives = 45/104 (43%), Gaps = 4/104 (3%)

Query: 94  SSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFIT 153
           SS  S        K+F+G +   + E D K  F++FG I ++ V+ D  T   +G  F+T
Sbjct: 2   SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61

Query: 154 YDSEEAVDR---VLH-KTFHELNGKMVEVKRAVPKEFSPGPSRS 193
           Y   E+  +    LH +       + ++VK A  +        S
Sbjct: 62  YCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRGGSGPSS 105

>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 = 94.8 bits (235), Expect = 1e-22
 Identities = 29/196 (14%), Positives = 57/196 (29%), Gaps = 33/196 (16%)

Query: 8   LFIGGISWD-TDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L + G+     + +R+   F  YG V +   M+ +      G   V  AD    +R I  
Sbjct: 7   LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITH 61

Query: 65  MDKHMIDGRTVE---------------------AKKAVPRDDQNMLNRNTSSIHSSPGPG 103
           ++ + + G+ +                             + +N           +    
Sbjct: 62  LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQH 121

Query: 104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV 163
            +  +        VTE +F +  D+ G      V            G + +DS+      
Sbjct: 122 PSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALET 181

Query: 164 LHKTFHELNGKMVEVK 179
           L      LN   ++  
Sbjct: 182 L----GFLNHYQMKNP 193

>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 = 58.6 bits (141), Expect = 4e-10
 Identities = 7/70 (10%), Positives = 17/70 (24%), Gaps = 2/70 (2%)

Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
           L       +  EE   E     G      +            G + +   + A   +  +
Sbjct: 126 LHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFL 185

Query: 66  DKHMIDGRTV 75
           + + +     
Sbjct: 186 NHYQMKNPNG 195

>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 = 90.7 bits (226), Expect = 2e-22
 Identities = 20/83 (24%), Positives = 43/83 (51%), Gaps = 2/83 (2%)

Query: 1  MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
          +      +++  + +      L   FS+YG+VV+  IM+D+ T +++G  F++F D   A
Sbjct: 12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSA 71

Query: 61 ERVI--MDKHMIDGRTVEAKKAV 81
          +     ++   + GR ++A  A+
Sbjct: 72 QNCTRAINNKQLFGRVIKASIAI 94

>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 = 72.3 bits (178), Expect = 5e-16
 Identities = 18/84 (21%), Positives = 38/84 (45%), Gaps = 4/84 (4%)

Query: 94  SSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFIT 153
           SS  S         ++V  L  ++T +D  + F ++G +  V +M D +T++ +G  FI 
Sbjct: 5   SSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFIL 64

Query: 154 YDSEEAVDRVLHKTFHELNGKMVE 177
           +  +++           +N K + 
Sbjct: 65  FLDKDSAQNCT----RAINNKQLF 84

>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 = 91.1 bits (227), Expect = 2e-22
 Identities = 22/85 (25%), Positives = 39/85 (45%), Gaps = 2/85 (2%)

Query: 3  SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
           D   + +  +S DT E  L+E F  +G +    + +D+ TG+++GF F+ F     A R
Sbjct: 13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 72

Query: 63 VI--MDKHMIDGRTVEAKKAVPRDD 85
           I  +     D   +  + A P  +
Sbjct: 73 AIAGVSGFGYDHLILNVEWAKPSTN 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 = 71.9 bits (177), Expect = 9e-16
 Identities = 26/101 (25%), Positives = 43/101 (42%), Gaps = 3/101 (2%)

Query: 94  SSIHSSPGPGR--TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGF 151
           SS  S P         I V  L+    E+D ++ F  FG+I+ + +  D  T + +GF F
Sbjct: 2   SSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61

Query: 152 ITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPKEFSPGPS 191
           I++   E   R +        +  ++ V+ A P   S   S
Sbjct: 62  ISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNSGPSS 102

>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 = 90.8 bits (226), Expect = 2e-22
 Identities = 19/84 (22%), Positives = 42/84 (50%), Gaps = 2/84 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           +++G I +D  EE++ +  S  G V+   +M D  TGR++G+ F+ F D   +   +  
Sbjct: 4  VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 65 MDKHMIDGRTVEAKKAVPRDDQNM 88
          ++ + +  R ++   +   D   +
Sbjct: 64 LNGYQLGSRFLKCGYSSNSDISGV 87

>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 = 73.0 bits (180), Expect = 3e-16
 Identities = 16/91 (17%), Positives = 39/91 (42%), Gaps = 1/91 (1%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEAVDRV 163
           ++ +++G +    TE          G + ++ +M+D  T R +G+ FI + D E +   V
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61

Query: 164 LHKTFHELNGKMVEVKRAVPKEFSPGPSRSS 194
            +   ++L  + ++   +   + S       
Sbjct: 62  RNLNGYQLGSRFLKCGYSSNSDISGVSLEHH 92

>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 = 91.3 bits (227), Expect = 3e-22
 Identities = 18/83 (21%), Positives = 42/83 (50%), Gaps = 1/83 (1%)

Query: 2   ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
           E D   +++G + + +  + L+ +FS  G +    I+ D+ +G  +G+ ++ FA+    +
Sbjct: 33  EIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVD 92

Query: 62  RVI-MDKHMIDGRTVEAKKAVPR 83
             + MD+ +  GRT++       
Sbjct: 93  AAVAMDETVFRGRTIKVLPKRTN 115

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 83.6 bits (207), Expect = 2e-19
 Identities = 19/124 (15%), Positives = 44/124 (35%), Gaps = 9/124 (7%)

Query: 77  AKKAVPRDDQNMLNRNTSSIHSSPGPGR-------TKKIFVGGLASTVTESDFKKYFDQF 129
           A     +   + +     +                 + ++VG +    T  D + +F   
Sbjct: 1   AIAPCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC 60

Query: 130 GTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPG 189
           G+I  + ++ D  +  P+G+ +I +    +VD  +        G+ ++V         PG
Sbjct: 61  GSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRTNM--PG 118

Query: 190 PSRS 193
            S +
Sbjct: 119 ISST 122

>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 = 91.3 bits (227), Expect = 3e-22
 Identities = 21/104 (20%), Positives = 43/104 (41%), Gaps = 4/104 (3%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            LF+ G+  +  EE + + F+ YGE+    +  DR TG  +G+  V +     A+  +  
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 83

Query: 65  MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKI 108
           ++   + G+ +       R       +       S  P R +++
Sbjct: 84  LNGQDLMGQPISVDWCFVRGPPK--GKRRGGRRRSRSPDRRRRL 125

>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 = 70.5 bits (173), Expect = 6e-15
 Identities = 27/130 (20%), Positives = 53/130 (40%), Gaps = 14/130 (10%)

Query: 83  RDDQNMLNRNTSSIHSSPGPGR---TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMY 139
           R+D + + ++       PGP R      +FV G+    TE D    F ++G I ++ +  
Sbjct: 1   REDYDSVEQD----GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNL 56

Query: 140 DHNTQRPRGFGFITYDSEE----AVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRSSM 195
           D  T   +G+  + Y++ +    A++  L+    +L G+ + V     +    G  R   
Sbjct: 57  DRRTGYLKGYTLVEYETYKEAQAAMEG-LNGQ--DLMGQPISVDWCFVRGPPKGKRRGGR 113

Query: 196 IGYNNFGFNR 205
               +    R
Sbjct: 114 RRSRSPDRRR 123

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 90.1 bits (224), Expect = 5e-22
 Identities = 21/84 (25%), Positives = 45/84 (53%), Gaps = 4/84 (4%)

Query: 2   ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
           +S   +L +  I +   +  L++ F ++G++++  I+ +     ++GFGFV F + A A+
Sbjct: 26  KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADAD 83

Query: 62  RVI--MDKHMIDGRTVEAKKAVPR 83
           R    +   +++GR +E   A  R
Sbjct: 84  RAREKLHGTVVEGRKIEVNNATAR 107

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 77.7 bits (192), Expect = 1e-17
 Identities = 24/90 (26%), Positives = 46/90 (51%), Gaps = 7/90 (7%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE 157
           ++    + K++ V  +     + D ++ F QFG I DV ++++      +GFGF+T+++ 
Sbjct: 22  NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENS 79

Query: 158 EAVDRV---LHKTFHELNGKMVEVKRAVPK 184
              DR    LH T   + G+ +EV  A  +
Sbjct: 80  ADADRAREKLHGT--VVEGRKIEVNNATAR 107

>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 = 89.2 bits (222), Expect = 8e-22
 Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 2/83 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           +++GG+     E  L E F + G VV   + +DR TG+ +G+GFV F     A+  I  
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76

Query: 65 MDKHMIDGRTVEAKKAVPRDDQN 87
          MD   + G+ +   KA   +   
Sbjct: 77 MDMIKLYGKPIRVNKASAHNKNL 99

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 77.7 bits (192), Expect = 9e-18
 Identities = 29/103 (28%), Positives = 46/103 (44%), Gaps = 3/103 (2%)

Query: 94  SSIHSSPGPGR--TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGF 151
           SS  S P   R     ++VGGL   V+E    + F Q G + +  +  D  T + +G+GF
Sbjct: 2   SSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGF 61

Query: 152 ITYDSEEAVDRVLHKT-FHELNGKMVEVKRAVPKEFSPGPSRS 193
           + + SEE  D  +      +L GK + V +A     +     S
Sbjct: 62  VEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGPSS 104

>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 = 88.6 bits (220), Expect = 3e-21
 Identities = 19/81 (23%), Positives = 39/81 (48%), Gaps = 3/81 (3%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           KL +  + +   +  ++E F+ +G + +A +  DR +GR+ G   V F   A A + +  
Sbjct: 37  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQ 95

Query: 65  MDKHMIDGRTVEAKKAVPRDD 85
                +DGR ++ +    + D
Sbjct: 96  YKGVPLDGRPMDIQLVASQID 116

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 70.1 bits (172), Expect = 9e-15
 Identities = 18/90 (20%), Positives = 40/90 (44%), Gaps = 4/90 (4%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE 157
              G     K+ V  L   V+++D ++ F +FGT+    V YD  + R  G   + ++  
Sbjct: 28  GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERR 86

Query: 158 EAVDRVLHKTFH--ELNGKMVEVKRAVPKE 185
               + + K +    L+G+ ++++    + 
Sbjct: 87  ADALKAM-KQYKGVPLDGRPMDIQLVASQI 115

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 87.7 bits (218), Expect = 3e-21
 Identities = 18/79 (22%), Positives = 36/79 (45%), Gaps = 2/79 (2%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            LF+ G+  +  EE + + F+ YGE+    +  DR TG  +G+  V +     A+  +  
Sbjct: 25  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEG 84

Query: 65  MDKHMIDGRTVEAKKAVPR 83
           ++   + G+ +       R
Sbjct: 85  LNGQDLMGQPISVDWCFVR 103

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 68.8 bits (169), Expect = 1e-14
 Identities = 22/94 (23%), Positives = 43/94 (45%), Gaps = 10/94 (10%)

Query: 98  SSPGPGRTK---KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY 154
             PGP R+     +FV G+    TE D    F ++G I ++ +  D  T   +G+  + Y
Sbjct: 13  DEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEY 72

Query: 155 DSEE----AVDRVLHKTFHELNGKMVEVKRAVPK 184
           ++ +    A++  L+    +L G+ + V     +
Sbjct: 73  ETYKEAQAAMEG-LNGQ--DLMGQPISVDWCFVR 103

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 87.3 bits (217), Expect = 3e-21
 Identities = 18/80 (22%), Positives = 38/80 (47%), Gaps = 3/80 (3%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          KLFI G+ +   +E L+E    +G V +  ++ +R  G+ +G  +V + + + A + +  
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMK 77

Query: 65 MDKHMIDGRTVEAKKAVPRD 84
          MD   I    ++   +    
Sbjct: 78 MDGMTIKENIIKVAISNSGP 97

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 71.2 bits (175), Expect = 2e-15
 Identities = 15/96 (15%), Positives = 42/96 (43%), Gaps = 2/96 (2%)

Query: 91  RNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFG 150
             +S +          K+F+ GL  + T+ + ++     GT+ D+ ++ +    +P+G  
Sbjct: 3   SGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLA 61

Query: 151 FITYDSEEAVDRVLHKT-FHELNGKMVEVKRAVPKE 185
           ++ Y++E    + + K     +   +++V  +    
Sbjct: 62  YVEYENESQASQAVMKMDGMTIKENIIKVAISNSGP 97

>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 = 89.1 bits (221), Expect = 4e-21
 Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            LF+  I  +  E+ ++E F  YGE+    +  DR TG ++G+  V +     A      
Sbjct: 74  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 133

Query: 65  MDKHMIDGRTVEAKKAVPRDDQN 87
           ++   I G+T++      +  + 
Sbjct: 134 LNGAEIMGQTIQVDWCFVKGPKR 156

>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 = 72.6 bits (178), Expect = 3e-15
 Identities = 21/100 (21%), Positives = 40/100 (40%), Gaps = 4/100 (4%)

Query: 90  NRNTSSIHSSPGPGR---TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRP 146
            RN       PGP R      +FV  +     E + ++ F  +G I ++ +  D  T   
Sbjct: 54  VRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFS 113

Query: 147 RGFGFITY-DSEEAVDRVLHKTFHELNGKMVEVKRAVPKE 185
           +G+  + Y   ++A+         E+ G+ ++V     K 
Sbjct: 114 KGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKG 153

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 87.0 bits (216), Expect = 4e-21
 Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 8/82 (9%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYG--EVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
           + +  I+  T  + +    S Y    V    +++D+ T + RGF FV  +    A +++
Sbjct: 11 TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70

Query: 65 ------MDKHMIDGRTVEAKKA 80
                     IDG+T+    A
Sbjct: 71 QILQSLHPPLKIDGKTIGVDFA 92

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 74.7 bits (184), Expect = 8e-17
 Identities = 16/92 (17%), Positives = 33/92 (35%), Gaps = 9/92 (9%)

Query: 97  HSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGT--ITDVVVMYDHNTQRPRGFGFITY 154
           H          I +  +A              + +  + ++ ++ D  TQ+ RGF F+  
Sbjct: 3   HHHHHH--MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQL 60

Query: 155 DSEEAVDRVL-----HKTFHELNGKMVEVKRA 181
            S     ++L          +++GK + V  A
Sbjct: 61  SSAMDASQLLQILQSLHPPLKIDGKTIGVDFA 92

>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 = 87.0 bits (216), Expect = 5e-21
 Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 2/79 (2%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            LF+  I  +  E+ ++E F  YGE+    +  DR TG ++G+  V +     A      
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 65  MDKHMIDGRTVEAKKAVPR 83
           ++   I G+T++      +
Sbjct: 88  LNGAEIMGQTIQVDWCFVK 106

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 71.9 bits (177), Expect = 1e-15
 Identities = 22/103 (21%), Positives = 44/103 (42%), Gaps = 10/103 (9%)

Query: 90  NRNTSSIHSSPGPGRT---KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRP 146
            RN       PGP R+     +FV  +     E + ++ F  +G I ++ +  D  T   
Sbjct: 8   VRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFS 67

Query: 147 RGFGFITYDSEE----AVDRVLHKTFHELNGKMVEVKRAVPKE 185
           +G+  + Y++ +    A +  L+    E+ G+ ++V     K 
Sbjct: 68  KGYALVEYETHKQALAAKEA-LNGA--EIMGQTIQVDWCFVKG 107

>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 = 86.6 bits (215), Expect = 5e-21
 Identities = 19/83 (22%), Positives = 33/83 (39%), Gaps = 7/83 (8%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L    +S++  E+ LKE F    E+           G+++G  ++ F   A AE+ +  
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 65 MDKHMIDGRTVEAKKAVPRDDQN 87
               IDGR+V       +    
Sbjct: 73 KQGAEIDGRSVSLYYTGEKGGTR 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 = 63.4 bits (155), Expect = 8e-13
 Identities = 16/85 (18%), Positives = 35/85 (41%), Gaps = 6/85 (7%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL- 164
           + +    L+  +TE + K+ F+         +       + +G  +I + SE   ++ L 
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALE-----IRLVSQDGKSKGIAYIEFKSEADAEKNLE 71

Query: 165 HKTFHELNGKMVEVKRAVPKEFSPG 189
            K   E++G+ V +     K  + G
Sbjct: 72  EKQGAEIDGRSVSLYYTGEKGGTRG 96

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 86.9 bits (216), Expect = 6e-21
 Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 2/80 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
           LFIG ++ +     LK   S      +  ++ D  TG  R FG+V F      E+ + +
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKALEL 77

Query: 66 DKHMIDGRTVEAKKAVPRDD 85
              + G  ++ +K   RD 
Sbjct: 78 TGLKVFGNEIKLEKPKGRDG 97

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 76.5 bits (189), Expect = 2e-17
 Identities = 17/83 (20%), Positives = 42/83 (50%), Gaps = 1/83 (1%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
            +F+G L    + ++ K    +     D+ V+ D  T   R FG++ ++S E +++ L  
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKALEL 77

Query: 167 TFHELNGKMVEVKRAVPKEFSPG 189
           T  ++ G  +++++   ++ + G
Sbjct: 78  TGLKVFGNEIKLEKPKGRDGTRG 100

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 90.8 bits (225), Expect = 6e-21
 Identities = 33/202 (16%), Positives = 65/202 (32%), Gaps = 35/202 (17%)

Query: 8   LFIGGIS-WDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L +  ++      + L   F  YG+V    I+ ++     +    V  AD   A+  +  
Sbjct: 37  LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSH 91

Query: 65  MDKHMIDGRTVE----------AKKAVPRDDQNMLNRNTSSIHSSPGPGR---------T 105
           ++ H + G+ +             +    D     +   S +H    PG          +
Sbjct: 92  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 151

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
             + +  +  +V+E D K  F   G +           Q+ R    I   S E   + L 
Sbjct: 152 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF----FQKDRKMALIQMGSVEEAVQAL- 206

Query: 166 KTFHELNGKMVEVKRAVPKEFS 187
               +L+   +     +   FS
Sbjct: 207 ---IDLHNHDLGENHHLRVSFS 225

>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 = 87.0 bits (216), Expect = 6e-21
 Identities = 21/83 (25%), Positives = 44/83 (53%), Gaps = 4/83 (4%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          +L +  I +   +  L++ F ++G++++  I+ +     ++GFGFV F + A A+R    
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREK 74

Query: 65 MDKHMIDGRTVEAKKAVPRDDQN 87
          +   +++GR +E   A  R   N
Sbjct: 75 LHGTVVEGRKIEVNNATARVMTN 97

>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 = 74.6 bits (184), Expect = 1e-16
 Identities = 24/97 (24%), Positives = 46/97 (47%), Gaps = 3/97 (3%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE 157
           +S      K++ V  +     + D ++ F QFG I DV ++++   +  +GFGF+T+++ 
Sbjct: 8   NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENS 65

Query: 158 EAVDRVLHKT-FHELNGKMVEVKRAVPKEFSPGPSRS 193
              DR   K     + G+ +EV  A  +  +     S
Sbjct: 66  ADADRAREKLHGTVVEGRKIEVNNATARVMTNSGPSS 102

>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 = 86.1 bits (214), Expect = 1e-20
 Identities = 22/81 (27%), Positives = 45/81 (55%), Gaps = 4/81 (4%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L++  +    D+ERL++ FS +G +  A +M +   GR++GFGFV F+ P  A + +  
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE 74

Query: 65 MDKHMIDGRTVEAKKAVPRDD 85
          M+  ++  + +    A  +++
Sbjct: 75 MNGRIVATKPLYVALAQRKEE 95

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 67.6 bits (166), Expect = 3e-14
 Identities = 27/92 (29%), Positives = 41/92 (44%), Gaps = 11/92 (11%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
            ++V  L   + +   +K F  FGTIT   VM +    R +GFGF+ + S E   + +  
Sbjct: 17  NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAV-- 72

Query: 167 TFHELNGKMVE-----VKRAVPKEFSPGPSRS 193
              E+NG++V      V  A  KE       S
Sbjct: 73  --TEMNGRIVATKPLYVALAQRKEERQSGPSS 102

>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 = 86.2 bits (214), Expect = 1e-20
 Identities = 33/87 (37%), Positives = 42/87 (48%), Gaps = 5/87 (5%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            LF+ G+S DT EE LKE F      V A I+ DR TG ++GFGFV F     A+     
Sbjct: 17  TLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEA 73

Query: 65  MDKHMIDGRTVEAKKAVPRDDQNMLNR 91
           M+   IDG  V    A P+ +      
Sbjct: 74  MEDGEIDGNKVTLDWAKPKGEGGSGPS 100

>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 = 67.3 bits (165), Expect = 5e-14
 Identities = 27/90 (30%), Positives = 40/90 (44%), Gaps = 5/90 (5%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
           +K +FV GL+   TE   K   + F       ++ D  T   +GFGF+ ++SEE      
Sbjct: 15  SKTLFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAK 71

Query: 165 HKTF-HELNGKMVEVKRAVPKE-FSPGPSR 192
                 E++G  V +  A PK     GPS 
Sbjct: 72  EAMEDGEIDGNKVTLDWAKPKGEGGSGPSS 101

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 86.3 bits (214), Expect = 1e-20
 Identities = 16/80 (20%), Positives = 33/80 (41%), Gaps = 2/80 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          ++    ++ +  E  LK+   +YGEV E  I+    T +  G   V+F     A+  +  
Sbjct: 8  EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 65 MDKHMIDGRTVEAKKAVPRD 84
          +    + G  + A+  +   
Sbjct: 68 LHLTSVMGNIIHAQLDIKGQ 87

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 78.6 bits (194), Expect = 5e-18
 Identities = 12/86 (13%), Positives = 32/86 (37%), Gaps = 1/86 (1%)

Query: 101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
           G    K++    L   V E+  K    ++G + +V ++    T++  G   + + S    
Sbjct: 2   GQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGA 61

Query: 161 DRVLHKT-FHELNGKMVEVKRAVPKE 185
              +       + G ++  +  +  +
Sbjct: 62  KETVKNLHLTSVMGNIIHAQLDIKGQ 87

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 85.8 bits (213), Expect = 1e-20
 Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 4/85 (4%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDR-ATGRARGFGFVVFADPAVAERVI- 64
           K+ +  I +  ++  ++E FS +GE+    + +    TG  RGFGFV F     A++   
Sbjct: 17  KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76

Query: 65  --MDKHMIDGRTVEAKKAVPRDDQN 87
                  + GR +  + A       
Sbjct: 77  ALCHSTHLYGRRLVLEWADSEVTVQ 101

>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 = 75.4 bits (186), Expect = 7e-17
 Identities = 25/106 (23%), Positives = 46/106 (43%), Gaps = 8/106 (7%)

Query: 92  NTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDH-NTQRPRGFG 150
           ++ S    P    T KI V  +     + + ++ F  FG +  V +      T   RGFG
Sbjct: 2   SSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFG 61

Query: 151 FITYDSEE----AVDRVLHKTFHELNGKMVEVKRAVPKE-FSPGPS 191
           F+ + +++    A + + H T   L G+ + ++ A  +     GPS
Sbjct: 62  FVDFITKQDAKKAFNALCHST--HLYGRRLVLEWADSEVTVQSGPS 105

>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 = 89.8 bits (222), Expect = 1e-20
 Identities = 21/102 (20%), Positives = 44/102 (43%), Gaps = 4/102 (3%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYG--EVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
            L+IG ++W T +E L E     G  +++E     +RA G+++GF  V     A +++++
Sbjct: 70  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129

Query: 65  --MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGR 104
             + K  + G+         +       ++  +  S    G 
Sbjct: 130 DLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMSGE 171

>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 = 75.1 bits (184), Expect = 1e-15
 Identities = 23/169 (13%), Positives = 50/169 (29%), Gaps = 3/169 (1%)

Query: 80  AVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGT--ITDVVV 137
            +P    + + +  +        G+   +++G L    T+ D  +     G   I ++  
Sbjct: 43  TLPPTVGDDVGKGAAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKF 102

Query: 138 MYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPKEFSPGPSRSSMI 196
             +    + +GF  +   SE +  +++      EL+G+   V     +  S    +S   
Sbjct: 103 FENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKT 162

Query: 197 GYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATGRGGISP 245
             +              + R      G    R            G   P
Sbjct: 163 TQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGP 211

>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 = 84.9 bits (211), Expect = 2e-20
 Identities = 25/93 (26%), Positives = 46/93 (49%), Gaps = 3/93 (3%)

Query: 3  SDLGKLFIGGISWDTDEERLKEYFSRYGEVVE-AVIMRDRATGRARGFGFVVFADPAVAE 61
          S    +FIG +  + DE+ L + FS +G +++   IMRD  TG ++G+ F+ FA    ++
Sbjct: 3  SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASD 62

Query: 62 RVI--MDKHMIDGRTVEAKKAVPRDDQNMLNRN 92
            I  M+   +  R +    A  +D +     +
Sbjct: 63 AAIEAMNGQYLCNRPITVSYAFKKDSKGSGPSS 95

>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 = 67.2 bits (165), Expect = 3e-14
 Identities = 23/89 (25%), Positives = 35/89 (39%), Gaps = 2/89 (2%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDV-VVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
            IF+G L   + E      F  FG I     +M D +T   +G+ FI + S +A D  + 
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 166 K-TFHELNGKMVEVKRAVPKEFSPGPSRS 193
                 L  + + V  A  K+       S
Sbjct: 67  AMNGQYLCNRPITVSYAFKKDSKGSGPSS 95

>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 = 85.0 bits (211), Expect = 3e-20
 Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           KL +  + +   +  ++E F+ +G + +A +  DR +GR+ G   V F   A A + +  
Sbjct: 31  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQ 89

Query: 65  MDKHMIDGRTV 75
            +   +DGR +
Sbjct: 90  YNGVPLDGRPM 100

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 66.9 bits (164), Expect = 6e-14
 Identities = 19/94 (20%), Positives = 39/94 (41%), Gaps = 5/94 (5%)

Query: 84  DDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNT 143
            D+   +   S      G     K+ V  L   V+++D ++ F +FGT+    V YD  +
Sbjct: 8   PDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-S 66

Query: 144 QRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVE 177
            R  G   + ++ +    + +     + NG  ++
Sbjct: 67  GRSLGTADVHFERKADALKAM----KQYNGVPLD 96

>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 = 85.1 bits (211), Expect = 3e-20
 Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 2/81 (2%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            LFI  +  +  ++ L + F  +G VV A +  D+ T  ++ FGFV + +P  A+  I  
Sbjct: 27  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86

Query: 65  MDKHMIDGRTVEAKKAVPRDD 85
           M+   I  + ++ +    ++D
Sbjct: 87  MNGFQIGMKRLKVQLKRSKND 107

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 69.3 bits (170), Expect = 1e-14
 Identities = 20/92 (21%), Positives = 34/92 (36%), Gaps = 9/92 (9%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
            +F+  L     + D  + F  FG +    V  D  T   + FGF++YD+  +    +  
Sbjct: 27  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI-- 84

Query: 167 TFHELNGKMVE-----VKRAVPKEFSPGPSRS 193
               +NG  +      V+    K  S     S
Sbjct: 85  --QSMNGFQIGMKRLKVQLKRSKNDSKSGPSS 114

>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 = 84.6 bits (210), Expect = 4e-20
 Identities = 22/85 (25%), Positives = 34/85 (40%), Gaps = 3/85 (3%)

Query: 2   ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
           E D   L+I  +    DE+ L+     +G+V+   I+RD  +G +RG GF         E
Sbjct: 22  EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCE 80

Query: 62  RVI--MDKHMIDGRTVEAKKAVPRD 84
            VI   +   I      +    P  
Sbjct: 81  AVIGHFNGKFIKTPPGVSAPTEPLL 105

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 70.0 bits (172), Expect = 7e-15
 Identities = 19/92 (20%), Positives = 36/92 (39%), Gaps = 12/92 (13%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
            +++  L  ++ E + +     FG +    ++ D ++   RG GF   +S E  + V+  
Sbjct: 27  NLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVI-- 83

Query: 167 TFHELNGKMVE-----VKRAVPKE--FSPGPS 191
                NGK ++          P    FS   S
Sbjct: 84  --GHFNGKFIKTPPGVSAPTEPLLCKFSGPSS 113

>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 = 84.3 bits (209), Expect = 6e-20
 Identities = 25/99 (25%), Positives = 41/99 (41%), Gaps = 3/99 (3%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            +F+  + +    ++LKE FS  G VV A I+ D+  G++RG G V F     A + I  
Sbjct: 17  TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISM 75

Query: 65  MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPG 103
            +  ++  R +  K       +           S P  G
Sbjct: 76  FNGQLLFDRPMHVKMDERALPKGDFFPPERPQQSGPSSG 114

>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 = 66.6 bits (163), Expect = 1e-13
 Identities = 19/96 (19%), Positives = 36/96 (37%), Gaps = 5/96 (5%)

Query: 93  TSSIHSSPGPGRT-KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGF 151
           +S    +   GR    +FV  L   V     K+ F   G +    ++ D +  + RG G 
Sbjct: 2   SSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDG-KSRGIGT 60

Query: 152 ITYDSEEAVDRVLHKTFH--ELNGKMVEVKRAVPKE 185
           +T++      + +   F+   L  + + VK      
Sbjct: 61  VTFEQSIEAVQAI-SMFNGQLLFDRPMHVKMDERAL 95

>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 = 83.9 bits (208), Expect = 8e-20
 Identities = 17/82 (20%), Positives = 36/82 (43%), Gaps = 2/82 (2%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            L++  +S    E  L   F+R+ E     I     TGR RG  F+ F +  +A + +  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 65  MDKHMIDGRTVEAKKAVPRDDQ 86
           ++ + + G+ +  +    +  +
Sbjct: 87  VNGYKLYGKILVIEFGKNKKQR 108

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 75.8 bits (187), Expect = 6e-17
 Identities = 26/89 (29%), Positives = 44/89 (49%), Gaps = 2/89 (2%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
            K +++  L+  VTE D    F +F       + +   T R RG  FIT+ ++E   + L
Sbjct: 25  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 84

Query: 165 HKTF-HELNGKMVEVKRAVPKEF-SPGPS 191
           H    ++L GK++ ++    K+  S GPS
Sbjct: 85  HLVNGYKLYGKILVIEFGKNKKQRSSGPS 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 = 84.9 bits (210), Expect = 1e-19
 Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 2/81 (2%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            L++G +S+ T EE++ E FS+ G++ + ++  D+    A GF FV +   A AE  +  
Sbjct: 41  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100

Query: 65  MDKHMIDGRTVEAKKAVPRDD 85
           ++   +D R +         +
Sbjct: 101 INGTRLDDRIIRTDWDAGFKE 121

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 64.1 bits (156), Expect = 2e-12
 Identities = 17/109 (15%), Positives = 37/109 (33%), Gaps = 5/109 (4%)

Query: 78  KKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVV 137
           + +  RD     +                 ++VG L+   TE    + F + G I  +++
Sbjct: 16  ELSQYRDQHFRGDNEEQEKLLKKS----CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIM 71

Query: 138 MYDHNTQRPRGFGFITYDSEEAVDRVLHK-TFHELNGKMVEVKRAVPKE 185
             D   +   GF F+ Y S    +  +       L+ +++        +
Sbjct: 72  GLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK 120

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 82.8 bits (205), Expect = 2e-19
 Identities = 25/96 (26%), Positives = 39/96 (40%), Gaps = 10/96 (10%)

Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAV--------IMRDRATGRARGFGFVV 53
           SD   +F+ G+  +   E + +YF + G +            +  DR TG+ +G   V 
Sbjct: 4  NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63

Query: 54 FADPAVAERVI--MDKHMIDGRTVEAKKAVPRDDQN 87
          F DP  A+  I   D     G  ++   A  R D N
Sbjct: 64 FDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFN 99

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 70.1 bits (172), Expect = 5e-15
 Identities = 21/110 (19%), Positives = 35/110 (31%), Gaps = 13/110 (11%)

Query: 104 RTKKIFVGGLASTVTESDFKKYFDQFGTIT--------DVVVMYDHNTQRPRGFGFITYD 155
               IFV GL   VT      YF Q G I          + +  D  T + +G   +++D
Sbjct: 6   DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65

Query: 156 SEEAVD---RVLHKTFHELNGKMVEVKRAVPKEFSPGPSRSSMIGYNNFG 202
              +             E +G  ++V  A  +        +   G  +  
Sbjct: 66  DPPSAKAAIDWFDGK--EFSGNPIKVSFATRRADFNRGGGNGRGGLEHHH 113

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 83.2 bits (206), Expect = 2e-19
 Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 2/71 (2%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            LFI  +  +  +  L   F  +G V+ A +  D+ T  ++ FGFV F +P  A+  I  
Sbjct: 42  NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101

Query: 65  MDKHMIDGRTV 75
           M+   +  + +
Sbjct: 102 MNGFQVGTKRL 112

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 71.6 bits (176), Expect = 2e-15
 Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 4/74 (5%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
            +F+  L    T++D    F  FG +    V  D  T   + FGF+++D+ ++    +  
Sbjct: 42  NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAI-- 99

Query: 167 TFHELNGKMVEVKR 180
               +NG  V  KR
Sbjct: 100 --KAMNGFQVGTKR 111

>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 = 81.6 bits (202), Expect = 4e-19
 Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 6/83 (7%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L +  +S+   EE L+E F +   +     +     G+++G+ F+ FA    A+  +  
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFEDAKEALNS 72

Query: 65 MDKHMIDGRTVEAKKAVPRDDQN 87
           +K  I+GR +  +   PR   N
Sbjct: 73 CNKREIEGRAIRLELQGPRGSPN 95

>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 = 67.3 bits (165), Expect = 4e-14
 Identities = 20/103 (19%), Positives = 47/103 (45%), Gaps = 6/103 (5%)

Query: 92  NTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGF 151
           ++ S  +S   G +K + +  L+ + TE   ++ F++       + +  +   + +G+ F
Sbjct: 2   SSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATF----IKVPQNQNGKSKGYAF 57

Query: 152 ITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPK-EFSPGPSR 192
           I + S E     L+     E+ G+ + ++   P+   + GPS 
Sbjct: 58  IEFASFEDAKEALNSCNKREIEGRAIRLELQGPRGSPNSGPSS 100

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 81.9 bits (202), Expect = 4e-19
 Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 3/87 (3%)

Query: 99  SPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEE 158
           S G      + V GL   V +     YF+         V+   + QR    G +T+    
Sbjct: 2   SSGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVL---SWQRLGCGGVLTFREPA 58

Query: 159 AVDRVLHKTFHELNGKMVEVKRAVPKE 185
             +RVL +  HEL+G  + ++ A P+ 
Sbjct: 59  DAERVLAQADHELHGAQLSLRPAPPRA 85

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 76.5 bits (188), Expect = 2e-17
 Identities = 27/108 (25%), Positives = 40/108 (37%), Gaps = 14/108 (12%)

Query: 2   ESDLGKLFIGGISWDTDEERLKEYF-----SRYGEVVEAVIMRDRATGRARGFGFVVFAD 56
            S    + + G+     +E L  YF     S  G V+           R    G + F +
Sbjct: 5   SSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ--------RLGCGGVLTFRE 56

Query: 57  PAVAERVIMDK-HMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPG 103
           PA AERV+    H + G  +  + A PR    +L +      S P  G
Sbjct: 57  PADAERVLAQADHELHGAQLSLRPAPPRAPARLLLQGLPPGTSGPSSG 104

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 83.0 bits (205), Expect = 8e-19
 Identities = 19/81 (23%), Positives = 39/81 (48%), Gaps = 3/81 (3%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           KL +  + +   +  ++E F+ +G + +A +  DR +GR+ G   V F   A A + +  
Sbjct: 90  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQ 148

Query: 65  MDKHMIDGRTVEAKKAVPRDD 85
                +DGR ++ +    + D
Sbjct: 149 YKGVPLDGRPMDIQLVASQID 169

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 70.3 bits (172), Expect = 2e-14
 Identities = 22/116 (18%), Positives = 47/116 (40%), Gaps = 4/116 (3%)

Query: 72  GRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGT 131
            R     +  P  D+   +   S      G     K+ V  L   V+++D ++ F +FGT
Sbjct: 55  NRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGT 114

Query: 132 ITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFH--ELNGKMVEVKRAVPKE 185
           +    V YD  + R  G   + ++      + + K +    L+G+ ++++    + 
Sbjct: 115 LKKAAVDYDR-SGRSLGTADVHFERRADALKAM-KQYKGVPLDGRPMDIQLVASQI 168

>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 = 81.0 bits (200), Expect = 1e-18
 Identities = 16/99 (16%), Positives = 43/99 (43%), Gaps = 1/99 (1%)

Query: 6   GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI- 64
             +++ G+ ++ + + + ++F +   V +++ +     G+A G GFV F + A  +  + 
Sbjct: 26  FCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC 85

Query: 65  MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPG 103
             K  +  R ++      +     ++     + S P  G
Sbjct: 86  RHKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQSGPSSG 124

>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 = 66.8 bits (163), Expect = 1e-13
 Identities = 12/89 (13%), Positives = 29/89 (32%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE 157
           S         +++ GL           +F +   + D + +      +  G GF+ + +E
Sbjct: 18  SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNE 77

Query: 158 EAVDRVLHKTFHELNGKMVEVKRAVPKEF 186
                 L +    +  + ++V     K  
Sbjct: 78  ADYKAALCRHKQYMGNRFIQVHPITKKGM 106

>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 = 80.0 bits (198), Expect = 1e-18
 Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 10/89 (11%)

Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAV--------IMRDRATGRARGFGFVV 53
           SD   +F+ G+  +   E + +YF + G +            +  DR TG+ +G   V 
Sbjct: 10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 69

Query: 54 FADPAVAERVI--MDKHMIDGRTVEAKKA 80
          F DP  A+  I   D     G  ++   A
Sbjct: 70 FDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 69.3 bits (170), Expect = 9e-15
 Identities = 21/96 (21%), Positives = 32/96 (33%), Gaps = 13/96 (13%)

Query: 97  HSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITD--------VVVMYDHNTQRPRG 148
           H          IFV GL   VT      YF Q G I          + +  D  T + +G
Sbjct: 5   HHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKG 64

Query: 149 FGFITYDSEEAVD---RVLHKTFHELNGKMVEVKRA 181
              +++D   +             E +G  ++V  A
Sbjct: 65  EATVSFDDPPSAKAAIDWFDGK--EFSGNPIKVSFA 98

>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 = 79.6 bits (197), Expect = 1e-18
 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 3/76 (3%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           +F+G +     EE L E F + G + +  I +DR  G+ + FGFV F  P      I  
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIAL 76

Query: 65 MDKHMIDGRTVEAKKA 80
          ++   + GR +     
Sbjct: 77 LNGIRLYGRPINVSGP 92

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 70.0 bits (172), Expect = 4e-15
 Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 5/71 (7%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           + +FVG L + V E    + F Q G +T V +  D    +P+ FGF+ +   E+V   + 
Sbjct: 17  RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREG-KPKSFGFVCFKHPESVSYAI- 74

Query: 166 KTFHELNGKMV 176
                LNG  +
Sbjct: 75  ---ALLNGIRL 82

>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 = 79.2 bits (196), Expect = 2e-18
 Identities = 21/99 (21%), Positives = 43/99 (43%), Gaps = 10/99 (10%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            LF+  ++    EE L++ FS++G++     ++D        + F+ F +   A + +  
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEE 64

Query: 65  MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPG 103
           M+   ++G  +E   A P D +    +      S P  G
Sbjct: 65  MNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGPSSG 103

>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 = 68.8 bits (169), Expect = 1e-14
 Identities = 27/91 (29%), Positives = 44/91 (48%), Gaps = 13/91 (14%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS- 156
            S G  + K +FV  LA+TVTE   +K F QFG +  V  +        + + FI +D  
Sbjct: 4   GSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDER 55

Query: 157 EEAVD--RVLHKTFHELNGKMVEVKRAVPKE 185
           + AV     ++    +L G+ +E+  A P +
Sbjct: 56  DGAVKAMEEMNGK--DLEGENIEIVFAKPPD 84

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 78.8 bits (195), Expect = 3e-18
 Identities = 23/80 (28%), Positives = 41/80 (51%), Gaps = 4/80 (5%)

Query: 3  SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
          S   ++F+  + +D   + LK+ F+  G V+ A I  +   G+++G G V F  P VAER
Sbjct: 6  SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAER 63

Query: 63 VI--MDKHMIDGRTVEAKKA 80
              M+   + GR ++ +  
Sbjct: 64 ACRMMNGMKLSGREIDVRID 83

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 67.2 bits (165), Expect = 3e-14
 Identities = 18/89 (20%), Positives = 38/89 (42%), Gaps = 5/89 (5%)

Query: 99  SPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEE 158
           S G     +IFV  L    T    K  F++ G +    +  +    + +G G + ++S E
Sbjct: 2   SSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPE 59

Query: 159 AVDRVLHKTFH--ELNGKMVEVKRAVPKE 185
             +R   +  +  +L+G+ ++V+      
Sbjct: 60  VAERAC-RMMNGMKLSGREIDVRIDRNAS 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 = 77.5 bits (191), Expect = 1e-17
 Identities = 22/87 (25%), Positives = 33/87 (37%), Gaps = 6/87 (6%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIM--RDRATGRARGFGFVVFADPAVAERVI 64
          +LFIGGI      E + E  ++  E V  VI+        + RGF FV +     A    
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69

Query: 65 ----MDKHMIDGRTVEAKKAVPRDDQN 87
                +  + G  +    A P  D +
Sbjct: 70 RKLMPGRIQLWGHQIAVDWAEPEIDVD 96

>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 = 73.7 bits (181), Expect = 3e-16
 Identities = 20/84 (23%), Positives = 36/84 (42%), Gaps = 5/84 (5%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGT-ITDVVVMYD-HNTQRPRGFGFITYDSEEAVD--- 161
           ++F+GG+       +  +   +    + DV+V     +  + RGF F+ Y+S  A     
Sbjct: 10  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69

Query: 162 RVLHKTFHELNGKMVEVKRAVPKE 185
           R L     +L G  + V  A P+ 
Sbjct: 70  RKLMPGRIQLWGHQIAVDWAEPEI 93

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 77.1 bits (190), Expect = 1e-17
 Identities = 14/86 (16%), Positives = 29/86 (33%), Gaps = 2/86 (2%)

Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
          +     ++I G   D   + +KE+    G+V+   + R       +G  FVVF     A+
Sbjct: 8  DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAK 66

Query: 62 RVI-MDKHMIDGRTVEAKKAVPRDDQ 86
          + +           +          +
Sbjct: 67 KFVETPGQKYKETDLLILFKDDYFAK 92

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 74.0 bits (182), Expect = 2e-16
 Identities = 10/76 (13%), Positives = 33/76 (43%), Gaps = 1/76 (1%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           + +++ G  +  T  D K++ +  G + ++ +    + +  +G  F+ +DS E+  + + 
Sbjct: 12  RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE 70

Query: 166 KTFHELNGKMVEVKRA 181
               +     + +   
Sbjct: 71  TPGQKYKETDLLILFK 86

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 76.3 bits (188), Expect = 4e-17
 Identities = 20/97 (20%), Positives = 39/97 (40%), Gaps = 10/97 (10%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAV--------IMRDRATGRARGFGFV 52
            +SD   +++ G++     + L ++F + G V            I  D+ TG+ +G   V
Sbjct: 11  EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 70

Query: 53  VFADPAVAERVI--MDKHMIDGRTVEAKKAVPRDDQN 87
            + DP  A+  +   D     G  ++   A  +   N
Sbjct: 71  SYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMN 107

>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 = 67.0 bits (164), Expect = 7e-14
 Identities = 23/113 (20%), Positives = 38/113 (33%), Gaps = 15/113 (13%)

Query: 93  TSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTIT--------DVVVMYDHNTQ 144
           + S            I+V GL  +VT  D   +F Q G +          + +  D  T 
Sbjct: 3   SGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETG 62

Query: 145 RPRGFGFITYDSEEAVD---RVLHKTFHELNGKMVEVKRAVPKEFSPGPSRSS 194
           +P+G   ++Y+                 +  G  ++V  A  K   P  S  S
Sbjct: 63  KPKGDATVSYEDPPTAKAAVEWFDGK--DFQGSKLKVSLARKKP--PMNSGPS 111

>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 = 75.8 bits (187), Expect = 4e-17
 Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 8/87 (9%)

Query: 1  MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
            +   +LF+G +  D  EE +++ F +YG+  E  I +D      +GFGF+      +A
Sbjct: 11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLA 64

Query: 61 ERVI--MDKHMIDGRTVEAKKAVPRDD 85
          E     +D   + G+ +  + A     
Sbjct: 65 EIAKVELDNMPLRGKQLRVRFACHSAS 91

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 65.0 bits (159), Expect = 3e-13
 Identities = 26/103 (25%), Positives = 47/103 (45%), Gaps = 9/103 (8%)

Query: 92  NTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGF 151
           + SS        R++ +FVG L   +TE + +K F+++G   +V +       + +GFGF
Sbjct: 3   SGSSGGEKTFTQRSR-LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGF 55

Query: 152 ITYDSEEAVDRVLHKT-FHELNGKMVEVKRAVPK-EFSPGPSR 192
           I  ++    +    +     L GK + V+ A      + GPS 
Sbjct: 56  IRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLTSGPSS 98

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 75.8 bits (187), Expect = 4e-17
 Identities = 14/82 (17%), Positives = 35/82 (42%), Gaps = 2/82 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
            ++G + ++T +  +   F     +    ++RD+ T + +GF +V F +    +  +  
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY 75

Query: 66 DKHMIDGRTVEAKKAVPRDDQN 87
          D  ++  R++    A  R    
Sbjct: 76 DGALLGDRSLRVDIAEGRKQDK 97

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 65.4 bits (160), Expect = 2e-13
 Identities = 17/88 (19%), Positives = 34/88 (38%), Gaps = 1/88 (1%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
              +VG L     + D    F     I  V ++ D +T + +GF ++ +D  +++   L 
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 74

Query: 166 KTFHELNGKMVEVKRAVPKEFSPGPSRS 193
                L  + + V  A  ++       S
Sbjct: 75  YDGALLGDRSLRVDIAEGRKQDKSGPSS 102

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 75.4 bits (186), Expect = 6e-17
 Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 3/81 (3%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRAT-GRARGFGFVVFADPAVAERVI- 64
             F+G + +D  EE +KE+F     +    + R+ +   R +GFG+  F D       + 
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79

Query: 65  MDKHMIDGRTVEAKKAVPRDD 85
           +++  +  R +    A    D
Sbjct: 80  LNEESLGNRRIRVDVADQAQD 100

>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 = 63.4 bits (155), Expect = 9e-13
 Identities = 21/94 (22%), Positives = 38/94 (40%), Gaps = 3/94 (3%)

Query: 94  SSIHSSPGPGR-TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQ-RPRGFGF 151
              H S  P       F+G L   VTE   K++F     I+ V +  + +   R +GFG+
Sbjct: 7   HHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGY 65

Query: 152 ITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKE 185
             ++  +++   L      L  + + V  A   +
Sbjct: 66  AEFEDLDSLLSALSLNEESLGNRRIRVDVADQAQ 99

>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 = 75.2 bits (185), Expect = 7e-17
 Identities = 16/102 (15%), Positives = 41/102 (40%)

Query: 92  NTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGF 151
           ++ S  +SP       + + GL    ++ +  ++F     + + + +      R  G  F
Sbjct: 2   SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61

Query: 152 ITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRS 193
           + + S+E  ++ L K    +  + +E+ ++   E       S
Sbjct: 62  VQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTSGPSS 103

>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 = 72.9 bits (179), Expect = 5e-16
 Identities = 20/86 (23%), Positives = 40/86 (46%), Gaps = 1/86 (1%)

Query: 3  SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
          ++ G + + G+ +   +E + ++FS    V   + +     GR+ G  FV FA   +AE+
Sbjct: 13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEK 72

Query: 63 VI-MDKHMIDGRTVEAKKAVPRDDQN 87
           +   K  I  R +E  K+   + + 
Sbjct: 73 ALKKHKERIGHRYIEIFKSSRAEVRT 98

>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 = 76.1 bits (187), Expect = 7e-17
 Identities = 19/87 (21%), Positives = 40/87 (45%), Gaps = 1/87 (1%)

Query: 2   ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
            ++ G + + G+ +   +E + ++FS    V   + +     G+  G  FV FA   +AE
Sbjct: 39  SANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAE 98

Query: 62  RVI-MDKHMIDGRTVEAKKAVPRDDQN 87
           + +   K  I  R +E  K+   + ++
Sbjct: 99  KALGKHKERIGHRYIEVFKSSQEEVRS 125

>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 = 69.1 bits (169), Expect = 2e-14
 Identities = 14/90 (15%), Positives = 37/90 (41%)

Query: 97  HSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
            +S        + + GL    T+ +  ++F     + + + +      +  G  F+ + S
Sbjct: 34  SNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFAS 93

Query: 157 EEAVDRVLHKTFHELNGKMVEVKRAVPKEF 186
           +E  ++ L K    +  + +EV ++  +E 
Sbjct: 94  QELAEKALGKHKERIGHRYIEVFKSSQEEV 123

>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 = 75.5 bits (186), Expect = 8e-17
 Identities = 16/104 (15%), Positives = 33/104 (31%), Gaps = 1/104 (0%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
           + S      I  I +   +  + ++         AV +     G+  G   V F +   A
Sbjct: 11  VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 70

Query: 61  ERVI-MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPG 103
            +   + +  ++GR          D + +     +   S P  G
Sbjct: 71  RKSERLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSGPSSG 114

>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 = 67.1 bits (164), Expect = 7e-14
 Identities = 15/94 (15%), Positives = 36/94 (38%), Gaps = 2/94 (2%)

Query: 94  SSIHSSPGPGRTKK--IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGF 151
           SS  S  G   + K    +  +  ++T+ D  ++ +      + V +   N  +  G   
Sbjct: 2   SSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQAL 61

Query: 152 ITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKE 185
           + + +E+   +       +LNG+   V     ++
Sbjct: 62  VQFKNEDDARKSERLHRKKLNGREAFVHVVTLED 95

>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 = 74.3 bits (183), Expect = 1e-16
 Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 3/73 (4%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAV-IMRDRATGRARGFGFVVFADPAVAERVI- 64
           L++G +    DE  +   F+  GE V +V I+R+R TG   G+ FV FAD A AE+ + 
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLH 70

Query: 65 -MDKHMIDGRTVE 76
           ++   + G T  
Sbjct: 71 KINGKPLPGATPA 83

>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 = 65.4 bits (160), Expect = 2e-13
 Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 5/80 (6%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFG-TITDVVVMYDHNTQRPRGFGFITYDS 156
           SS   G    +++G L   + E+   + F   G T+  V ++ +  T  P G+ F+ +  
Sbjct: 2   SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFAD 61

Query: 157 EEAVDRVLHKTFHELNGKMV 176
               ++ LHK    +NGK +
Sbjct: 62  LATAEKCLHK----INGKPL 77

>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 = 74.2 bits (183), Expect = 1e-16
 Identities = 26/96 (27%), Positives = 42/96 (43%), Gaps = 9/96 (9%)

Query: 99  SPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEE 158
           S G     K+++G L+  VT  D ++ F          V+         G+ F+ Y  + 
Sbjct: 2   SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL------LKSGYAFVDYPDQN 55

Query: 159 AVDRVLHKT--FHELNGKMVEVKRAVPKEF-SPGPS 191
              R +       EL+GK++EV  +V K+  S GPS
Sbjct: 56  WAIRAIETLSGKVELHGKIMEVDYSVSKKLRSSGPS 91

>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 = 68.8 bits (169), Expect = 9e-15
 Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 9/84 (10%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          KL+IG +S     + L++ F      +              G+ FV + D   A R I  
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIET 63

Query: 67 ---KHMIDGRTVEAKKAVPRDDQN 87
             K  + G+ +E   +V +  ++
Sbjct: 64 LSGKVELHGKIMEVDYSVSKKLRS 87

>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 = 73.9 bits (182), Expect = 2e-16
 Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          KLF+G ++    EE +   F  +G + E  ++R    G ++G  FV F+    A+  I  
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHA 75

Query: 67 KH 68
           H
Sbjct: 76 LH 77

>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 = 73.5 bits (181), Expect = 3e-16
 Identities = 26/105 (24%), Positives = 42/105 (40%), Gaps = 6/105 (5%)

Query: 92  NTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGF 151
           ++ S  S    GR +K+FVG L    +E D  + F  FG I +  V+   +    +G  F
Sbjct: 2   SSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAF 60

Query: 152 ITYDSEE----AVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSR 192
           + + S      A+  +            + VK A   +   GPS 
Sbjct: 61  VKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDK-ESGPSS 104

>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 = 16/87 (18%), Positives = 34/87 (39%), Gaps = 1/87 (1%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
             F+G + +D  EE +KE+F         +        R +GFG+  F D       + +
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 76

Query: 66  DKHMIDGRTVEAKKAVPRDDQNMLNRN 92
           ++  +  + +    A    D++    +
Sbjct: 77  NEESLGNKRIRVDVADQAQDKDSGPSS 103

>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 = 65.0 bits (159), Expect = 3e-13
 Identities = 22/101 (21%), Positives = 36/101 (35%), Gaps = 1/101 (0%)

Query: 94  SSIHSSPGPGR-TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFI 152
           S    S  P       F+G L   VTE   K++F         +     N +R +GFG+ 
Sbjct: 3   SGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYA 62

Query: 153 TYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRS 193
            ++  +++   L      L  K + V  A   +       S
Sbjct: 63  EFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDKDSGPSS 103

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 73.5 bits (181), Expect = 3e-16
 Identities = 19/87 (21%), Positives = 30/87 (34%), Gaps = 10/87 (11%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
            E    +LF+     D  E  L E F  +G + E  I+         GF FV F +   A
Sbjct: 27  GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESA 78

Query: 61  ERVI--MDKHMIDGRTVEAKKAVPRDD 85
            + I  +       + +E   +     
Sbjct: 79  AKAIEEVHGKSFANQPLEVVYSKLPAK 105

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 69.2 bits (170), Expect = 1e-14
 Identities = 21/100 (21%), Positives = 40/100 (40%), Gaps = 17/100 (17%)

Query: 91  RNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFG 150
           R +   H   G     ++FV      V ES+  + F  FG + +V ++         GF 
Sbjct: 17  RGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFA 68

Query: 151 FITYDSEEAVDRVLHKTFHELNGKM-----VEVKRAVPKE 185
           F+ ++  E+  + +     E++GK      +EV  +    
Sbjct: 69  FVEFEEAESAAKAI----EEVHGKSFANQPLEVVYSKLPA 104

>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 = 73.1 bits (180), Expect = 4e-16
 Identities = 18/88 (20%), Positives = 35/88 (39%), Gaps = 4/88 (4%)

Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
          +     L++G +S D  E  + + FS+ G      ++ +  +     + FV F +   A 
Sbjct: 12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAA 69

Query: 62 RVI--MDKHMIDGRTVEAKKAVPRDDQN 87
            +  M+   I G+ V+   A     Q 
Sbjct: 70 AALAAMNGRKILGKEVKVNWATTPSSQK 97

>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 = 58.0 bits (141), Expect = 7e-11
 Identities = 21/95 (22%), Positives = 36/95 (37%), Gaps = 5/95 (5%)

Query: 94  SSIHSSPGPGRT--KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGF 151
           SS  S         + ++VG L+  VTE    + F Q G      ++ +H +  P  + F
Sbjct: 2   SSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCF 59

Query: 152 ITYDSEEAVDRVLHKT-FHELNGKMVEVKRAVPKE 185
           + +         L      ++ GK V+V  A    
Sbjct: 60  VEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPS 94

>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 = 72.7 bits (179), Expect = 5e-16
 Identities = 16/84 (19%), Positives = 35/84 (41%), Gaps = 8/84 (9%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L++  +   T EE +++ F+         + +       R + FV F++   A   +  
Sbjct: 17 ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI------RDYAFVHFSNREDAVEAMKA 70

Query: 65 MDKHMIDGRTVEAKKAVPRDDQNM 88
          ++  ++DG  +E   A P D  + 
Sbjct: 71 LNGKVLDGSPIEVTLAKPVDKDSS 94

>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 = 63.4 bits (155), Expect = 8e-13
 Identities = 19/89 (21%), Positives = 34/89 (38%), Gaps = 8/89 (8%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
            K ++V  L  + +E   +K F+         V       + R + F+ + + E     +
Sbjct: 15  VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAM 68

Query: 165 HKT-FHELNGKMVEVKRAVPKEFSP-GPS 191
                  L+G  +EV  A P +    GPS
Sbjct: 69  KALNGKVLDGSPIEVTLAKPVDKDSSGPS 97

>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 = 11/78 (14%), Positives = 27/78 (34%), Gaps = 2/78 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           + +  + +    + + ++F  Y  +  +V ++    G   G   V F     A   +  
Sbjct: 17 IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76

Query: 65 MDKHMIDGRTVEAKKAVP 82
          ++   I  R V+      
Sbjct: 77 LNDRPIGSRKVKLVLGSG 94

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 62.7 bits (153), Expect = 1e-12
 Identities = 14/95 (14%), Positives = 33/95 (34%), Gaps = 1/95 (1%)

Query: 92  NTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGF 151
           ++ S  +S G      I V  +  TV+  +   +F  +  I   V +  +    P G   
Sbjct: 2   SSGSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAM 61

Query: 152 ITYDSEEAVDRVLHK-TFHELNGKMVEVKRAVPKE 185
           + ++S +     +       +  + V++       
Sbjct: 62  VAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPS 96

>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 = 71.5 bits (176), Expect = 9e-16
 Identities = 16/83 (19%), Positives = 36/83 (43%), Gaps = 10/83 (12%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          K+F+G +S     + L+  F R G V+E  ++        + + FV     A A+  I  
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQ 62

Query: 65 MDKHMIDGRTVEAKKAVPRDDQN 87
          ++   + G+ +  + +     ++
Sbjct: 63 LNGKEVKGKRINVELSTKGQKKS 85

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 71.1 bits (175), Expect = 1e-15
 Identities = 22/96 (22%), Positives = 42/96 (43%), Gaps = 9/96 (9%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DS 156
           SS   G T KIFVG +++  T  + +  F++ G + +  V+        + + F+     
Sbjct: 2   SSGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKE 53

Query: 157 EEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSR 192
            +A   +      E+ GK + V+ +   +   GPS 
Sbjct: 54  ADAKAAIAQLNGKEVKGKRINVELSTKGQKKSGPSS 89

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 71.6 bits (176), Expect = 2e-15
 Identities = 14/82 (17%), Positives = 30/82 (36%), Gaps = 5/82 (6%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          L+I  + +    E + + F +YG + +  +     T   RG  +VV+ D   A+  +  +
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNAVDHL 67

Query: 66 DKHMIDGRTVEAKKAVPRDDQN 87
              +  R +            
Sbjct: 68 SGFNVSNRYLVVLYYNANRAFQ 89

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 63.9 bits (156), Expect = 8e-13
 Identities = 18/87 (20%), Positives = 35/87 (40%), Gaps = 6/87 (6%)

Query: 99  SPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSE 157
            P   R   +++  L   +T  +    F ++G I  + V    NT   RG  ++ Y D  
Sbjct: 4   PPEVNRI--LYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIF 58

Query: 158 EAVDRVLHKTFHELNGKMVEVKRAVPK 184
           +A + V H +   ++ + + V      
Sbjct: 59  DAKNAVDHLSGFNVSNRYLVVLYYNAN 85

>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 = 70.4 bits (173), Expect = 2e-15
 Identities = 11/71 (15%), Positives = 27/71 (38%), Gaps = 2/71 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          + +  + +    + + ++F  Y  +  +V ++    G   G   V F     A   +  +
Sbjct: 18 IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 77

Query: 66 DKHMIDGRTVE 76
          +   I  R V+
Sbjct: 78 NDRPIGSRKVK 88

>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 = 59.2 bits (144), Expect = 2e-11
 Identities = 14/85 (16%), Positives = 30/85 (35%), Gaps = 1/85 (1%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE 157
           SS G      I V  +  TV+  +   +F  +  I   V +  +    P G   + ++S 
Sbjct: 8   SSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 67

Query: 158 EAVDRVLHKT-FHELNGKMVEVKRA 181
           +     +       +  + V++   
Sbjct: 68  DEATAAVIDLNDRPIGSRKVKLSGP 92

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 72.2 bits (177), Expect = 3e-15
 Identities = 36/152 (23%), Positives = 62/152 (40%), Gaps = 20/152 (13%)

Query: 47  RGFGFVVFADPAVAERVIMD---KHMIDG--RTVEAKKAVPRDDQNMLNRNTSSIHSSPG 101
           +G       D A AE+V       + +DG     +A K     + +  + +     S P 
Sbjct: 13  KGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCP- 71

Query: 102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEAV 160
                K++VG L +   +++ ++ F  +G +  V V  +     P GF F+ + D  +A 
Sbjct: 72  --LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAA 124

Query: 161 DRVLHKTFHELNGKMVEVKRAVPKEFSPGPSR 192
           D V      EL+G+ +     V  E S G  R
Sbjct: 125 DAV-----RELDGRTLC-GCRVRVELSNGEKR 150

>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 = 71.4 bits (175), Expect = 5e-15
 Identities = 20/81 (24%), Positives = 34/81 (41%), Gaps = 9/81 (11%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           K+++G +  + ++  L+  F  YG +    + R+       GF FV F DP  A   +  
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDAADAVRE 129

Query: 65  MDKHMIDGR--TVEAKKAVPR 83
           +D   + G    VE      R
Sbjct: 130 LDGRTLCGCRVRVELSNGEKR 150

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 70.4 bits (173), Expect = 3e-15
 Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 5/83 (6%)

Query: 8  LFIGGISWDTDEERLKEYFS-RYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          LF+G ++ D D+  L E+F   Y       ++ D+ TG ++G+GFV F D    +R +  
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTE 70

Query: 65 MD-KHMIDGRTVEAKKAVPRDDQ 86
                +  + V    A+P+  +
Sbjct: 71 CQGAVGLGSKPVRLSVAIPKASR 93

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 60.4 bits (147), Expect = 1e-11
 Identities = 26/104 (25%), Positives = 41/104 (39%), Gaps = 12/104 (11%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQ-FGTITDVVVMYDHNTQRPRGFGFITYDS 156
           SS   G    +FVG L   V +    ++F + + +     V+ D  T   +G+GF+ +  
Sbjct: 2   SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTD 60

Query: 157 EEAVDRVLHKTFHELNGKM------VEVKRAVPKEFSPGPSRSS 194
           E    R L     E  G +      V +  A+PK     P  S 
Sbjct: 61  ELEQKRAL----TECQGAVGLGSKPVRLSVAIPKASRVKPVESG 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 = 71.4 bits (175), Expect = 4e-15
 Identities = 20/95 (21%), Positives = 41/95 (43%), Gaps = 10/95 (10%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEV--VEAVIMRD---RATGRARGFGFVVFADPAVAE 61
           ++++  ++    E+ LK  F RY +       IM D      GR +G  F+   +   A 
Sbjct: 47  RIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAA 106

Query: 62  RVI--MDKHMIDGRTV---EAKKAVPRDDQNMLNR 91
           + +   + +++ G+ +    A+ A P+ D     R
Sbjct: 107 KALKEANGYVLFGKPMVVQFARSARPKQDPKEGKR 141

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 59.5 bits (144), Expect = 7e-11
 Identities = 32/143 (22%), Positives = 52/143 (36%), Gaps = 24/143 (16%)

Query: 54  FADPAVAERVIMDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGR-TKKIFVGG 112
                  E   M    I  R +E  +    + + +      S+  S  PG    +I+V  
Sbjct: 2   PLGSDSDE---MPSECISRRELEKGRISREEMETL------SVFRSYEPGEPNCRIYVKN 52

Query: 113 LASTVTESDFKKYFDQFGTIT--DVVVMYD---HNTQRPRGFGFITYDSEEAVDRVLHKT 167
           LA  V E D K  F ++   +     +M+D       R +G  FI   +E+A  + L   
Sbjct: 53  LAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKAL--- 109

Query: 168 FHELNGKMVE-----VKRAVPKE 185
             E NG ++      V+ A    
Sbjct: 110 -KEANGYVLFGKPMVVQFARSAR 131

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 69.6 bits (171), Expect = 7e-15
 Identities = 25/108 (23%), Positives = 41/108 (37%), Gaps = 14/108 (12%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           K+++G +     +  L+  FS YG +    I R+       GF FV F DP  AE  +  
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRG 56

Query: 65  MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGG 112
           +D  +I G  V  + +             S     P   +  ++   G
Sbjct: 57  LDGKVICGSRVRVELSTGM-------PRRSRFDRPPARRKLLEVLFNG 97

>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 = 19/89 (21%), Positives = 36/89 (40%), Gaps = 6/89 (6%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSEEAVDRVLH 165
           K++VG L +   + + ++ F  +G +  V +  +     P GF F+ + D  +A D V  
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56

Query: 166 KTFHELNGKMVEVKRAVPKEFSPGPSRSS 194
                + G  V V+ +          R  
Sbjct: 57  LDGKVICGSRVRVELSTGMPRRSRFDRPP 85

>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 = 21/87 (24%), Positives = 40/87 (45%), Gaps = 10/87 (11%)

Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
           S + KLFIG +  +  E+ ++  F +YG+V+E  I+        + +GFV   D   AE
Sbjct: 5  SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAE 56

Query: 62 RVI--MDKHMIDGRTVEAKKAVPRDDQ 86
            I  +  + + G  +  + +  +   
Sbjct: 57 DAIRNLHHYKLHGVNINVEASKNKSKA 83

>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 = 64.1 bits (157), Expect = 4e-13
 Identities = 23/96 (23%), Positives = 45/96 (46%), Gaps = 10/96 (10%)

Query: 99  SPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DSE 157
           S G     K+F+G L    TE + +  F+Q+G + +  ++        + +GF+   D  
Sbjct: 2   SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKT 53

Query: 158 EAVDRVLHKTFHELNGKMVEVKRAVPKEFSP-GPSR 192
            A D + +   ++L+G  + V+ +  K  +  GPS 
Sbjct: 54  AAEDAIRNLHHYKLHGVNINVEASKNKSKASSGPSS 89

>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 = 68.8 bits (169), Expect = 1e-14
 Identities = 19/79 (24%), Positives = 31/79 (39%), Gaps = 10/79 (12%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          KL +G IS     + L+  F  YG V+E  I+        + + FV       A   I  
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRG 63

Query: 65 MDKHMIDGRTVEAKKAVPR 83
          +D     G+ +  + +  R
Sbjct: 64 LDNTEFQGKRMHVQLSTSR 82

>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 = 64.9 bits (159), Expect = 2e-13
 Identities = 19/96 (19%), Positives = 44/96 (45%), Gaps = 10/96 (10%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-DS 156
           S      + K+ VG ++ T T  + +  F+++G + +  ++        + + F+    +
Sbjct: 3   SGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERA 54

Query: 157 EEAVDRVLHKTFHELNGKMVEVKRAVPK-EFSPGPS 191
           E+AV+ +      E  GK + V+ +  +   + GPS
Sbjct: 55  EDAVEAIRGLDNTEFQGKRMHVQLSTSRLRTASGPS 90

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 67.7 bits (166), Expect = 3e-14
 Identities = 13/70 (18%), Positives = 24/70 (34%), Gaps = 8/70 (11%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
           +IG I     E  L   F  +G +++     +      +G  F+ +     A   I  +
Sbjct: 30 AYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQAAVCIVAL 83

Query: 66 DKHMIDGRTV 75
                GR +
Sbjct: 84 ANFPFQGRNL 93

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 57.7 bits (140), Expect = 8e-11
 Identities = 16/69 (23%), Positives = 23/69 (33%), Gaps = 10/69 (14%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
            ++G +    TE+D    F  FG I D            +G  FI YD+ E     +   
Sbjct: 30  AYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCI--- 80

Query: 168 FHELNGKMV 176
              L     
Sbjct: 81  -VALANFPF 88

>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 = 72.6 bits (177), Expect = 8e-14
 Identities = 21/87 (24%), Positives = 37/87 (42%), Gaps = 2/87 (2%)

Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
           LF+  +++DT E +L+  F  YG +    ++  + +G+ RG+ F+ +             
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 66  DKHMIDGRTVEAKKAVPRDDQNMLNRN 92
           D   IDGR V       R  +    R 
Sbjct: 165 DGKKIDGRRVLVDVERGRTVKGWRPRR 191

>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 = 60.2 bits (145), Expect = 6e-10
 Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 6/80 (7%)

Query: 97  HSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
           ++     +T  +FV  +    TES  ++ F+ +G I  + ++Y   + +PRG+ FI Y+ 
Sbjct: 96  NAQGDAFKT--LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEH 153

Query: 157 EEAVDRVLHKTFHELNGKMV 176
           E  +    H  +   +GK +
Sbjct: 154 ERDM----HSAYKHADGKKI 169

>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 = 65.8 bits (161), Expect = 8e-14
 Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 9/86 (10%)

Query: 97  HSSPGPGRT-KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD 155
             S G  +T   ++VGGL  T+TE+D + +F QFG I  + V+        +   FI + 
Sbjct: 3   SGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFA 56

Query: 156 SEEAVDRVLHKTFH--ELNGKMVEVK 179
           + +A +    K+F+   +NG+ + VK
Sbjct: 57  TRQAAEVAAEKSFNKLIVNGRRLNVK 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 = 62.7 bits (153), Expect = 1e-12
 Identities = 16/72 (22%), Positives = 34/72 (47%), Gaps = 9/72 (12%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L++GG+     E  L+ +F ++GE+    +++       +   F+ FA    AE     
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEK 67

Query: 65 -MDKHMIDGRTV 75
            +K +++GR +
Sbjct: 68 SFNKLIVNGRRL 79

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 65.9 bits (161), Expect = 1e-13
 Identities = 19/70 (27%), Positives = 30/70 (42%), Gaps = 2/70 (2%)

Query: 6  GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI- 64
          G   I        ++ L   FS+ G+VV      D ATG+ +GF FV       A+++I 
Sbjct: 13 GAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72

Query: 65 -MDKHMIDGR 73
                +D +
Sbjct: 73 SFHGKRLDLK 82

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 52.4 bits (126), Expect = 7e-09
 Identities = 11/66 (16%), Positives = 24/66 (36%), Gaps = 4/66 (6%)

Query: 109 FVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF 168
            +      V +      F + G + ++    D  T + +GF F+   S     +++    
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKII---- 71

Query: 169 HELNGK 174
              +GK
Sbjct: 72  KSFHGK 77

>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 = 66.4 bits (162), Expect = 1e-13
 Identities = 16/102 (15%), Positives = 33/102 (32%), Gaps = 5/102 (4%)

Query: 2   ESDLGKLFIGGISWDTDEERLKEYFSRYG--EVVEAVIMRDRATGRARGFGFVVFADPAV 59
             D+  +   G+ W    E +  +FS          +       G+ RG   +       
Sbjct: 8   VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQD 67

Query: 60  AERVI-MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSP 100
            ++ +   +  +  R VE  +    D   ++      + SSP
Sbjct: 68  VQKALEKHRMYMGQRYVEVYEINNEDVDALMKSL--QVKSSP 107

>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 = 57.2 bits (138), Expect = 2e-10
 Identities = 17/91 (18%), Positives = 29/91 (31%), Gaps = 2/91 (2%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDV--VVMYDHNTQRPRGFGFITYD 155
                     I   GL  + T  D   +F           +    +   + RG   I  +
Sbjct: 4   LEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEME 63

Query: 156 SEEAVDRVLHKTFHELNGKMVEVKRAVPKEF 186
           SE+ V + L K    +  + VEV     ++ 
Sbjct: 64  SEQDVQKALEKHRMYMGQRYVEVYEINNEDV 94

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 66.5 bits (162), Expect = 2e-13
 Identities = 14/86 (16%), Positives = 33/86 (38%), Gaps = 9/86 (10%)

Query: 7   KLFIGGISWDTDEERLKE----YFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
            + I  I+ +  +E+L+       S  G++++ V+     +    G  ++VFA    A+ 
Sbjct: 31  VVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQA 87

Query: 63  VI--MDKHMIDGRTVEAKKAVPRDDQ 86
            +     +   G  +    +     Q
Sbjct: 88  FVEAFQGYPFQGNPLVITFSETPQSQ 113

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 64.9 bits (158), Expect = 5e-13
 Identities = 17/116 (14%), Positives = 39/116 (33%), Gaps = 10/116 (8%)

Query: 75  VEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKK----YFDQFG 130
           ++   A   + Q+M + +  S      P +   + +  +   V +   +          G
Sbjct: 1   MKETAAAKFERQHMDSPDLGSTPPHTEPSQV--VLITNINPEVPKEKLQALLYALASSQG 58

Query: 131 TITDVVVMYDHNTQRPRGFGFITYDS-EEAVDRVLHKTFHELNGKMVEVKRAVPKE 185
            I D+VV     +    G  +I + + E A   V     +   G  + +  +   +
Sbjct: 59  DILDIVVD---LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQ 111

>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 = 65.8 bits (161), Expect = 2e-13
 Identities = 16/70 (22%), Positives = 36/70 (51%), Gaps = 8/70 (11%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          ++ GGI+    ++ +++ FS +G+++E  +  +      +G+ FV F+    A   I  +
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81

Query: 66 DKHMIDGRTV 75
          +   I+G  V
Sbjct: 82 NGTTIEGHVV 91

>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 = 57.7 bits (140), Expect = 1e-10
 Identities = 17/92 (18%), Positives = 38/92 (41%), Gaps = 11/92 (11%)

Query: 85  DQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQ 144
             N        + +   P     ++ GG+AS +T+   ++ F  FG I ++ V  +    
Sbjct: 6   SGNTKQLRFEDVVNQSSPKNCT-VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE---- 60

Query: 145 RPRGFGFITYDSEEAVDRVLHKTFHELNGKMV 176
             +G+ F+ + + E+    +      +NG  +
Sbjct: 61  --KGYSFVRFSTHESAAHAI----VSVNGTTI 86

>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 = 64.6 bits (158), Expect = 3e-13
 Identities = 17/84 (20%), Positives = 40/84 (47%), Gaps = 9/84 (10%)

Query: 8  LFIGGISWDTDEERLKE----YFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV 63
          ++I  ++    ++ LK+     FSR+G++++ ++ R   + + RG  FV+F + + A   
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA 67

Query: 64 I--MDKHMIDGRTVEAKKAVPRDD 85
          +  M       + +  + A    D
Sbjct: 68 LRSMQGFPFYDKPMRIQYAKTDSD 91

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 62.2 bits (152), Expect = 2e-12
 Identities = 17/79 (21%), Positives = 31/79 (39%), Gaps = 13/79 (16%)

Query: 102 PGRTKKIFVGGLASTVTESDFKK----YFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE 157
           P  T  I++  L   + + + KK     F +FG I D++V     + + RG  F+ +   
Sbjct: 7   PNHT--IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS---RSLKMRGQAFVIFKEV 61

Query: 158 EAVDRVLHKTFHELNGKMV 176
            +    L      + G   
Sbjct: 62  SSATNAL----RSMQGFPF 76

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 64.9 bits (158), Expect = 6e-13
 Identities = 23/106 (21%), Positives = 48/106 (45%), Gaps = 6/106 (5%)

Query: 2   ESDLGKLFIGGISWDTDEERLKEYFSRYGEV---VEAVIMRDRATGRARGFGFVVFADPA 58
           + +   + + G+ +    E +  +F ++  +    E ++      GR  G  FV+FA   
Sbjct: 20  KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEE 79

Query: 59  VAERVI-MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPG 103
            A+  +   K ++  R +E  ++   + Q +LNR +S+  S P  G
Sbjct: 80  YAQNALRKHKDLLGKRYIELFRSTAAEVQQVLNRFSSA--SGPSSG 123

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 56.8 bits (137), Expect = 3e-10
 Identities = 22/107 (20%), Positives = 39/107 (36%), Gaps = 3/107 (2%)

Query: 91  RNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDV---VVMYDHNTQRPR 147
             ++ +           + + GL  T T  +   +F Q   IT     ++   +   RP 
Sbjct: 9   GTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPT 68

Query: 148 GFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRSS 194
           G  F+ +  EE     L K    L  + +E+ R+   E     +R S
Sbjct: 69  GDAFVLFACEEYAQNALRKHKDLLGKRYIELFRSTAAEVQQVLNRFS 115

>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 = 20/94 (21%), Positives = 36/94 (38%), Gaps = 3/94 (3%)

Query: 2   ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
             D   + + G+ +   E  ++++F     V    +++D   GR  G G V F  P    
Sbjct: 13  NPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTF 70

Query: 62  RVI-MDKHMIDGRTVEAKKAVPRDDQNMLNRNTS 94
             +  ++ ++  R VE   A  R         TS
Sbjct: 71  EALKRNRMLMIQRYVEVSPATERQWVAAGGHITS 104

>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 = 61.7 bits (150), Expect = 4e-12
 Identities = 20/93 (21%), Positives = 38/93 (40%), Gaps = 2/93 (2%)

Query: 94  SSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFIT 153
           SS    P       + V G+  +  E+D + +F     +  V ++ DH   R  G G + 
Sbjct: 5   SSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVG-RNNGNGLVK 62

Query: 154 YDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEF 186
           + S +     L +    +  + VEV  A  +++
Sbjct: 63  FLSPQDTFEALKRNRMLMIQRYVEVSPATERQW 95

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 63.9 bits (156), Expect = 9e-13
 Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          ++++G +  D   + +++ F +YG + +  +   R       F FV F DP  AE  +  
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPRDAEDAVYG 80

Query: 65 MDKHMIDGRTV 75
           D +  DG  +
Sbjct: 81 RDGYDYDGYRL 91

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 59.3 bits (144), Expect = 3e-11
 Identities = 19/104 (18%), Positives = 39/104 (37%), Gaps = 4/104 (3%)

Query: 91  RNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFG 150
            +   +   P      +I+VG L   +   D +  F ++G I D+ +           F 
Sbjct: 8   MSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFA 64

Query: 151 FITY-DSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRS 193
           F+ + D  +A D V  +  ++ +G  + V+       +     S
Sbjct: 65  FVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGRGTGSGPSS 108

>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 = 63.8 bits (155), Expect = 1e-12
 Identities = 19/99 (19%), Positives = 36/99 (36%), Gaps = 3/99 (3%)

Query: 8   LFIGGISWDTDEERLKEYFSRYG--EVVEAVIMRDRATGRARGFGFVVFADPAVAERVI- 64
           + + G+ W    E ++ + S     + V  V       GR  G  FV        +  + 
Sbjct: 20  VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK 79

Query: 65  MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPG 103
            D+  +  R +E  K+   +   +L  +  +  S P  G
Sbjct: 80  KDRESMGHRYIEVFKSHRTEMDWVLKHSGPNSASGPSSG 118

>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 = 56.1 bits (135), Expect = 5e-10
 Identities = 20/107 (18%), Positives = 37/107 (34%), Gaps = 2/107 (1%)

Query: 90  NRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDV--VVMYDHNTQRPR 147
           +  +S +   P  G    + + GL  + +  D + +         V  V        R  
Sbjct: 2   SSGSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQS 61

Query: 148 GFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRSS 194
           G  F+  +SE+ V   L K    +  + +EV ++   E       S 
Sbjct: 62  GEAFVELESEDDVKLALKKDRESMGHRYIEVFKSHRTEMDWVLKHSG 108

>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 = 67.2 bits (163), Expect = 1e-12
 Identities = 16/85 (18%), Positives = 40/85 (47%), Gaps = 9/85 (10%)

Query: 8  LFIGGISWDTDEERLKE----YFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV 63
          ++I  ++    ++ LK+     FS++G++++ ++ R   + + RG  FV+F + + A   
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA 68

Query: 64 I--MDKHMIDGRTVEAKKAVPRDDQ 86
          +  M       + +  + A    D 
Sbjct: 69 LRSMQGFPFYDKPMRIQYAKTDSDI 93

>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 = 62.6 bits (151), Expect = 5e-11
 Identities = 24/160 (15%), Positives = 48/160 (30%), Gaps = 18/160 (11%)

Query: 102 PGRTKKIFVGGLASTVTESDFKK----YFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE 157
           P  T  I++  L   + + + KK     F QFG I D++V     + + RG  F+ +   
Sbjct: 8   PNHT--IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS---RSLKMRGQAFVIFKEV 62

Query: 158 EAVDRVLHKTFHELNGKMV-----EVKRAVPKEFSPGPSRSSMIGYNNFGFNRPTNLLNS 212
            +    L      + G         ++ A          + + +  +     R      +
Sbjct: 63  SSATNAL----RSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQET 118

Query: 213 FAQRYNLSPAGGFGVRMDSRFSPLATGRGGISPFGGAGYG 252
            A +  +   G   V    +           +P       
Sbjct: 119 PATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMP 158

>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 = 48.3 bits (114), Expect = 2e-06
 Identities = 11/56 (19%), Positives = 21/56 (37%), Gaps = 5/56 (8%)

Query: 9   FIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
           F+  +  +T+E  L   F+++    E  ++  R         FV F +   A    
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAAR 261

>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 = 43.3 bits (101), Expect = 9e-05
 Identities = 13/95 (13%), Positives = 25/95 (26%), Gaps = 9/95 (9%)

Query: 82  PRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDH 141
               Q ++                  +F+  L     E      F+QF    +V ++   
Sbjct: 184 AMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR 243

Query: 142 NTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMV 176
                    F+ +D+E             L G  +
Sbjct: 244 -----HDIAFVEFDNEVQAGAAR----DALQGFKI 269

>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 = 62.2 bits (151), Expect = 3e-12
 Identities = 18/78 (23%), Positives = 39/78 (50%), Gaps = 8/78 (10%)

Query: 8  LFIGGISWDTDEE---RLKEYFSRYGEVVEAVIMRDRATGRAR---GFGFVVFADPAVAE 61
          +F+ G+S    +    +  EYF ++G++ + VI    +   ++      +V +     A 
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 62 RVI--MDKHMIDGRTVEA 77
          R I  ++  ++DGRT++A
Sbjct: 78 RAIQCVNNVVVDGRTLKA 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 = 59.1 bits (143), Expect = 4e-11
 Identities = 23/94 (24%), Positives = 41/94 (43%), Gaps = 12/94 (12%)

Query: 108 IFVGGLASTVTESDF---KKYFDQFGTITDVVVMYDH---NTQRPRGFGFITYDSEEAVD 161
           +FV GL+  + + +     +YF +FG I  VV+        +Q P    ++TY   E   
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 162 R---VLHKTFHELNGKMVEVKRAVPKEFS-PGPS 191
           R    ++     ++G+ ++      K  S  GPS
Sbjct: 78  RAIQCVNNV--VVDGRTLKASLGTTKYCSYSGPS 109

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 61.7 bits (150), Expect = 3e-12
 Identities = 12/75 (16%), Positives = 24/75 (32%), Gaps = 5/75 (6%)

Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
             + KL I  I      E L     +YG V     +   +         V ++    A 
Sbjct: 12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKDQAR 68

Query: 62 RVI--MDKHMIDGRT 74
          + +  ++   ++  T
Sbjct: 69 QALDKLNGFQLENFT 83

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 60.2 bits (146), Expect = 1e-11
 Identities = 15/89 (16%), Positives = 31/89 (34%), Gaps = 4/89 (4%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE 157
           S P   R +K+ +  +   +          Q+G +     +   NT        +TY S+
Sbjct: 8   SVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQV---NTDSETAVVNVTYSSK 64

Query: 158 EAVDRVLHKT-FHELNGKMVEVKRAVPKE 185
           +   + L K    +L    ++V     + 
Sbjct: 65  DQARQALDKLNGFQLENFTLKVAYIPDEM 93

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 61.5 bits (150), Expect = 3e-12
 Identities = 21/93 (22%), Positives = 36/93 (38%), Gaps = 13/93 (13%)

Query: 7  KLFIGGISWDTDEER-LKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI- 64
          +LFIG +      +  L   FS YG +++  I           FGF+ F +P      I 
Sbjct: 12 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN--------AFGFIQFDNPQSVRDAIE 63

Query: 65 -MDKHMIDGR--TVEAKKAVPRDDQNMLNRNTS 94
             + M  G+   +E   +  R   +  +  T+
Sbjct: 64 CESQEMNFGKKLILEVSSSNARPQFDHGDHGTN 96

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 54.9 bits (133), Expect = 9e-10
 Identities = 19/89 (21%), Positives = 38/89 (42%), Gaps = 14/89 (15%)

Query: 105 TKKIFVGGL-ASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV 163
             ++F+G L    V++ D  + F  +G I  + +           FGFI +D+ ++V   
Sbjct: 10  KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDA 61

Query: 164 LHKTFHELNGKMVEVKRAVPKEFSPGPSR 192
           +       + +M   K+ +  E S   +R
Sbjct: 62  I----ECESQEMNFGKK-LILEVSSSNAR 85

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 61.5 bits (150), Expect = 4e-12
 Identities = 12/82 (14%), Positives = 32/82 (39%), Gaps = 10/82 (12%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          L++ G   D     L+  FS +G +++  +         R   FV +     A++ +  +
Sbjct: 18 LYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAEL 69

Query: 66 DKHMIDGRTVEAKKAVPRDDQN 87
          +   ++   ++   A  +   +
Sbjct: 70 NGTQVESVQLKVNIARKQPMLD 91

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 59.6 bits (145), Expect = 2e-11
 Identities = 24/104 (23%), Positives = 44/104 (42%), Gaps = 14/104 (13%)

Query: 92  NTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGF 151
           ++ S      P +   ++V G    +T +  +  F  FG I D+      +   PR   F
Sbjct: 2   SSGSSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDL------SMDPPRNCAF 53

Query: 152 ITYDSEEAVDR---VLHKTFHELNGKMVEVKRAVPK-EFSPGPS 191
           +TY+  E+ D+    L+ T  ++    ++V  A  +     GPS
Sbjct: 54  VTYEKMESADQAVAELNGT--QVESVQLKVNIARKQPMLDSGPS 95

>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 = 61.8 bits (150), Expect = 5e-12
 Identities = 18/102 (17%), Positives = 32/102 (31%), Gaps = 9/102 (8%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           ++ + G+      + LK++    G+V  A + RD       G G V F         +  
Sbjct: 18  RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRK 70

Query: 65  MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTK 106
           +D         E      + D         S   S    R++
Sbjct: 71  LDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSRSRSRSRSR 112

>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 = 49.4 bits (118), Expect = 1e-07
 Identities = 17/99 (17%), Positives = 32/99 (32%), Gaps = 9/99 (9%)

Query: 98  SSPGPGRTK-KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
             P   R++ ++ V GL  + +  D K +  + G +    V  D       G G + +  
Sbjct: 8   YGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVR 60

Query: 157 EEAVDRVLHK-TFHELNGKMVEVKRAVPKEFSPGPSRSS 194
           +E +   + K    +      E      K   P      
Sbjct: 61  KEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSPSYG 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 = 61.4 bits (149), Expect = 7e-12
 Identities = 18/100 (18%), Positives = 31/100 (31%), Gaps = 11/100 (11%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           ++ + G+      + LK++    G+V  A + RD       G G V F         +  
Sbjct: 17  RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRK 69

Query: 65  MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGR 104
           +D         E      + D       +     S GP  
Sbjct: 70  LDNTKFRSHEGETAYIRVKVDGP--RSPSYGRSRSSGPSS 107

>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 = 50.6 bits (121), Expect = 4e-08
 Identities = 19/104 (18%), Positives = 35/104 (33%), Gaps = 12/104 (11%)

Query: 94  SSIHSSPGPGRTK-KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFI 152
           S     P   R++ ++ V GL  + +  D K +  + G +    V  D       G G +
Sbjct: 3   SGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVV 55

Query: 153 TYDSEEAVDRVLHKTFH--ELNGKMVEVKRA-VPKEFSPGPSRS 193
            +  +E +   + K     +      E     V  +    PS  
Sbjct: 56  EFVRKEDMTYAVRK-LDNTKFRSHEGETAYIRVKVDGPRSPSYG 98

>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 = 62.2 bits (151), Expect = 7e-12
 Identities = 18/133 (13%), Positives = 38/133 (28%), Gaps = 3/133 (2%)

Query: 66  DKHMIDGRTVEAKKAVPR-DDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKK 124
             H      V     +        + R +     +        + + GL    TE+D   
Sbjct: 6   HHHHHSSGLVPRGSHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYN 65

Query: 125 YFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPK 184
           +F        V +    +  R  G   + + + E     + K    +  + +E+      
Sbjct: 66  FFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTT 123

Query: 185 EFSPGPSRSSMIG 197
             S G   S ++ 
Sbjct: 124 GASNGAYSSQVMQ 136

>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 = 59.9 bits (145), Expect = 4e-11
 Identities = 17/86 (19%), Positives = 29/86 (33%), Gaps = 3/86 (3%)

Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MD 66
           + + G+ +   E  +  +FS    V   V +     GR  G   V FA    A   +  D
Sbjct: 49  VHMRGLPYKATENDIYNFFSPLNPV--RVHIEIGPDGRVTGEADVEFATHEEAVAAMSKD 106

Query: 67  KHMIDGRTVEAKKAVPRDDQNMLNRN 92
           +  +  R +E          N    +
Sbjct: 107 RANMQHRYIELFLNSTTGASNGAYSS 132

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 60.6 bits (147), Expect = 1e-11
 Identities = 7/81 (8%), Positives = 21/81 (25%), Gaps = 5/81 (6%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           ++ +  +      + LK+                  T    G G + F    +    +  
Sbjct: 30  RITMKNLPEGCSWQDLKDLARENSLE---TTFSSVNTRDFDGTGALEFPSEEILVEALER 86

Query: 65  MDKHMIDGRTVEAKKAVPRDD 85
           ++     G  +  ++      
Sbjct: 87  LNNIEFRGSVITVERDDNPPP 107

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 54.8 bits (132), Expect = 1e-09
 Identities = 23/99 (23%), Positives = 37/99 (37%), Gaps = 8/99 (8%)

Query: 97  HSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
           H S  P +  +I +  L    +  D K    +             NT+   G G + + S
Sbjct: 20  HMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSL---ETTFSSVNTRDFDGTGALEFPS 76

Query: 157 EEAVDRVLHK-TFHELNGKMVEVKRAVPKEFSPGPSRSS 194
           EE +   L +    E  G ++ V+R      +P P R S
Sbjct: 77  EEILVEALERLNNIEFRGSVITVERDD----NPPPIRRS 111

>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 = 60.8 bits (147), Expect = 2e-11
 Identities = 15/94 (15%), Positives = 32/94 (34%), Gaps = 3/94 (3%)

Query: 2   ESDLGKLFIGGISWDTDEERLKEYFSRYG--EVVEAVIMRDRATGRARGFGFVVFADPAV 59
             +   + + G+ W    E ++ + S     +    V       GR  G  FV       
Sbjct: 41  GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDD 100

Query: 60  AERVI-MDKHMIDGRTVEAKKAVPRDDQNMLNRN 92
            +  +  D+  +  R +E  K+   +   +L  +
Sbjct: 101 VKMALKKDRESMGHRYIEVFKSHRTEMDWVLKHS 134

>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 = 55.0 bits (132), Expect = 2e-09
 Identities = 19/122 (15%), Positives = 36/122 (29%), Gaps = 3/122 (2%)

Query: 66  DKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKY 125
             H      +  + +              S+   P  G    + + GL  + +  D + +
Sbjct: 6   HHHHHSSG-LVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNF 64

Query: 126 FDQFGTITDV--VVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVP 183
                       V        R  G  F+   SE+ V   L K    +  + +EV ++  
Sbjct: 65  LSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVFKSHR 124

Query: 184 KE 185
            E
Sbjct: 125 TE 126

>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 = 59.7 bits (145), Expect = 2e-11
 Identities = 17/86 (19%), Positives = 27/86 (31%), Gaps = 3/86 (3%)

Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MD 66
           + + G+ +   E  +  +FS        V +     GR  G   V FA    A   +  D
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLN--PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKD 75

Query: 67  KHMIDGRTVEAKKAVPRDDQNMLNRN 92
           K  +  R VE               +
Sbjct: 76  KANMQHRYVELFLNSTAGTSGSGPSS 101

>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 = 58.9 bits (143), Expect = 4e-11
 Identities = 18/102 (17%), Positives = 33/102 (32%), Gaps = 2/102 (1%)

Query: 92  NTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGF 151
           ++ S  SS        + + GL    TE+D   +F        V +    +  R  G   
Sbjct: 2   SSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDG-RVTGEAD 59

Query: 152 ITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRS 193
           + + + E     + K    +  + VE+        S     S
Sbjct: 60  VEFATHEDAVAAMAKDKANMQHRYVELFLNSTAGTSGSGPSS 101

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 59.2 bits (144), Expect = 3e-11
 Identities = 12/71 (16%), Positives = 26/71 (36%), Gaps = 8/71 (11%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          +L++GG+  +T    L   F R+G +     ++         F ++ +     A+     
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAK 72

Query: 65 MDKHMIDGRTV 75
          M    + G   
Sbjct: 73 MRGFPLGGPDR 83

>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 = 58.0 bits (141), Expect = 7e-11
 Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 13/80 (16%)

Query: 100 PGPGR---TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
            G G+   T +++VGGL    + +   + FD+FG+I  +         +   F +I Y+S
Sbjct: 9   IGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDH------VKGDSFAYIQYES 62

Query: 157 EEAVDRVLHKTFHELNGKMV 176
            +A      K    + G  +
Sbjct: 63  LDAAQAACAK----MRGFPL 78

>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 = 58.9 bits (143), Expect = 3e-11
 Identities = 20/82 (24%), Positives = 32/82 (39%), Gaps = 13/82 (15%)

Query: 7  KLFIGGISWDTDEER-LKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI- 64
          +LFIG +      +  L   FS YG +++  I           FGF+ F +P      I 
Sbjct: 24 RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIE 75

Query: 65 -MDKHMIDGR--TVEAKKAVPR 83
             + M  G+   +E   +  R
Sbjct: 76 XESQEMNFGKKLILEVSSSNAR 97

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 57.7 bits (140), Expect = 9e-11
 Identities = 22/104 (21%), Positives = 43/104 (41%), Gaps = 14/104 (13%)

Query: 90  NRNTSSIHSSPGPGRTKKIFVGGL-ASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRG 148
           + + SS     G     ++F+G L    V++ D  + F  +G I  + +           
Sbjct: 7   HHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NA 58

Query: 149 FGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSR 192
           FGFI +D+ ++V   +       + +M   K+ +  E S   +R
Sbjct: 59  FGFIQFDNPQSVRDAI----EXESQEMNFGKK-LILEVSSSNAR 97

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 59.0 bits (143), Expect = 4e-11
 Identities = 12/75 (16%), Positives = 32/75 (42%), Gaps = 10/75 (13%)

Query: 7  KLFIGGISWDTDE------ERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
           + +  +     +        + + FS++G++       +   G+ +G+ F+ +A PA A
Sbjct: 17 VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHA 74

Query: 61 ERVI--MDKHMIDGR 73
             +   D + +D +
Sbjct: 75 VDAVKNADGYKLDKQ 89

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 47.8 bits (114), Expect = 3e-07
 Identities = 15/78 (19%), Positives = 26/78 (33%), Gaps = 12/78 (15%)

Query: 103 GRTKKIFVGGLASTVTE------SDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
           G    I V  +     +      +   K F +FG IT+    Y     + +G+ F+ Y S
Sbjct: 13  GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITND--FYPEEDGKTKGYIFLEYAS 70

Query: 157 EEAVDRVLHKTFHELNGK 174
                  +       +G 
Sbjct: 71  PAHAVDAV----KNADGY 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 = 57.1 bits (138), Expect = 1e-10
 Identities = 12/86 (13%), Positives = 35/86 (40%), Gaps = 6/86 (6%)

Query: 101 GPGRT-KKIFVGGLASTVTESDFKKYFDQFGTITDVVVM-----YDHNTQRPRGFGFITY 154
           GP  + ++++VG +   +TE     +F+    +  +              + + F F+ +
Sbjct: 1   GPLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF 60

Query: 155 DSEEAVDRVLHKTFHELNGKMVEVKR 180
            S +   + +        G+ ++++R
Sbjct: 61  RSVDETTQAMAFDGIIFQGQSLKIRR 86

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 53.6 bits (129), Expect = 2e-09
 Identities = 11/75 (14%), Positives = 29/75 (38%), Gaps = 6/75 (8%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMR-----DRATGRARGFGFVVFADPAVAE 61
          +L++G I +   EE + ++F+    +                 + + F F+ F       
Sbjct: 8  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 62 RVI-MDKHMIDGRTV 75
          + +  D  +  G+++
Sbjct: 68 QAMAFDGIIFQGQSL 82

>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 = 57.3 bits (139), Expect = 1e-10
 Identities = 14/75 (18%), Positives = 35/75 (46%), Gaps = 3/75 (4%)

Query: 3  SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
          +    + + G  ++  E+ + E+ +     V   I+R+   G   G+ FV F++    ++
Sbjct: 8  TTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNA-HGNKTGYIFVDFSNEEEVKQ 65

Query: 63 VI-MDKHMIDGRTVE 76
           +  ++  + GR +E
Sbjct: 66 ALKCNREYMGGRYIE 80

>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 = 57.3 bits (139), Expect = 1e-10
 Identities = 16/90 (17%), Positives = 34/90 (37%), Gaps = 2/90 (2%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE 157
           S         + + G    VTE +  ++         + ++ + +     G+ F+ + +E
Sbjct: 3   SGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHG-NKTGYIFVDFSNE 60

Query: 158 EAVDRVLHKTFHELNGKMVEVKRAVPKEFS 187
           E V + L      + G+ +EV R      S
Sbjct: 61  EEVKQALKCNREYMGGRYIEVFREKSGPSS 90

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 56.8 bits (137), Expect = 2e-10
 Identities = 14/81 (17%), Positives = 29/81 (35%), Gaps = 7/81 (8%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           +++G +  D     LK      G V   +  +       R   F+ + D A A++ +  
Sbjct: 21 DVYVGNLPRDARVSDLKRALRELGSVPLRLTWQ-----GPRRRAFLHYPDSAAAQQAVSC 75

Query: 65 MDKHMIDGRTVEAKKAVPRDD 85
          +    +   T+    A  + D
Sbjct: 76 LQGLRLGTDTLRVALARQQRD 96

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 48.7 bits (116), Expect = 1e-07
 Identities = 16/81 (19%), Positives = 28/81 (34%), Gaps = 8/81 (9%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
            ++VG L      SD K+   + G++   +       Q PR   F+ Y    A  + +  
Sbjct: 21  DVYVGNLPRDARVSDLKRALRELGSVPLRLT-----WQGPRRRAFLHYPDSAAAQQAV-S 74

Query: 167 TFH--ELNGKMVEVKRAVPKE 185
                 L    + V  A  + 
Sbjct: 75  CLQGLRLGTDTLRVALARQQR 95

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 56.3 bits (136), Expect = 3e-10
 Identities = 14/72 (19%), Positives = 23/72 (31%), Gaps = 10/72 (13%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--- 64
          + I G+     E  L E    +G +   V+M        +    V F D   A   +   
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYA 77

Query: 65 -MDKHMIDGRTV 75
            ++  I G   
Sbjct: 78 ADNQIYIAGHPA 89

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 52.5 bits (126), Expect = 7e-09
 Identities = 14/85 (16%), Positives = 27/85 (31%), Gaps = 11/85 (12%)

Query: 97  HSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
                      + + GL   V E+D  +   +FG I+ VVVM        +    + ++ 
Sbjct: 15  PHKTPASPV--VHIRGLIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFED 66

Query: 157 EEAVDRVLHKTFH---ELNGKMVEV 178
                  ++        + G    V
Sbjct: 67  VLGACNAVNYAADNQIYIAGHPAFV 91

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 55.1 bits (133), Expect = 5e-10
 Identities = 12/74 (16%), Positives = 33/74 (44%), Gaps = 10/74 (13%)

Query: 8  LFIGGI------SWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
          + +  +        +  +  + + FS++G++       +   G+ +G+ F+ +A PA A 
Sbjct: 4  IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAV 61

Query: 62 RVI--MDKHMIDGR 73
            +   D + +D +
Sbjct: 62 DAVKNADGYKLDKQ 75

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 45.8 bits (109), Expect = 9e-07
 Identities = 14/74 (18%), Positives = 24/74 (32%), Gaps = 14/74 (18%)

Query: 108 IFVGGLASTVTESDF-------KKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
           I V  +   V             K F +FG IT+     +    + +G+ F+ Y S    
Sbjct: 4   IVVDNVPQ-VGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHA 60

Query: 161 DRVLHKTFHELNGK 174
              +       +G 
Sbjct: 61  VDAV----KNADGY 70

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 60.9 bits (147), Expect = 7e-10
 Identities = 47/252 (18%), Positives = 76/252 (30%), Gaps = 8/252 (3%)

Query: 223  GGFGVRMDSRFSPLATGRGGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLG 282
            G F + +D       +    +    G+G G     +G  +P Y  S    +         
Sbjct: 1445 GAFDIYLDQDMLMNYSLGTAVPTLAGSGMGTSQLPEGAGTP-YERSPMVDSGFVGSPDAA 1503

Query: 283  PFPGGNSNRFSTPVGFSGGNGRGD----SVLSSTTWNVWGNGSLNSATNPASPGAFLGSG 338
             F            GF      G       + S  +    + +++      SP     S 
Sbjct: 1504 AFSPLVQGGSEGREGFGDYGLLGAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSP 1563

Query: 339  SGNFEVSFGNNSVNWGPVSAPGGGSASGYSAGSMGYGSGDGNYGLGGGGFGRTSSAGVGP 398
              +   ++  +S ++ P S     ++  YS  S  Y     +Y      +  TS +   P
Sbjct: 1564 GYSTSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSY-SP 1622

Query: 399  TSSFAGSTSGYEGSYGDSYRSGSGYGDPTWRSATPELDGSGSFSYGLGTVSTNVAAKSSE 458
            TS     TS        SY   S    PT  S +P        S      S + +  S  
Sbjct: 1623 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1682

Query: 459  GFIGS--YNVTS 468
                S  Y+ TS
Sbjct: 1683 YSPTSPSYSPTS 1694

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 50.1 bits (119), Expect = 2e-06
 Identities = 55/239 (23%), Positives = 77/239 (32%), Gaps = 31/239 (12%)

Query: 220  SPAGGFGVRMDSRFSPLAT-GRGGISPFGGAGYGVGMN-LDGGLSPSYGGSSNFSNSLGY 277
              +G  G    + FSPL   G  G   FG  G     +   G  SP Y    + + S GY
Sbjct: 1492 VDSGFVGSPDAAAFSPLVQGGSEGREGFGDYGLLGAASPYKGVQSPGYTSPFSSAMSPGY 1551

Query: 278  GRMLGPFPGGNSNRFSTPVGFSGGNGRGDSVLSSTTWNVWGNGSLNSATNPASPGAFLGS 337
            G    P    +S  +ST   +           SS ++            +P SP     S
Sbjct: 1552 GLT-SPSYSPSSPGYSTSPAYMP---------SSPSY------------SPTSPSYSPTS 1589

Query: 338  GSGNFEVSFGNNSVNWGPVSAPGGGSASGYSAGSMGYGSGDGNYGLGGGGFGRTSSAGVG 397
                   S+   S ++ P S     ++  YS  S  Y     +Y      +  TS +   
Sbjct: 1590 P------SYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY-S 1642

Query: 398  PTSSFAGSTSGYEGSYGDSYRSGSGYGDPTWRSATPELDGSGSFSYGLGTVSTNVAAKS 456
            PTS     TS        SY   S    PT  S +P        S      S + +  S
Sbjct: 1643 PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1701

>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 1752

 Score = 45.1 bits (106), Expect = 6e-05
 Identities = 47/216 (21%), Positives = 63/216 (29%), Gaps = 15/216 (6%)

Query: 220  SPAGGFGVRMDSRFSPLATGRGGISPFGGAGYGVGM-NLDGGLSPSYGGSSNFSNSLGYG 278
            SP    G      F       G  SP+ G             +SP YG +S   +    G
Sbjct: 1506 SPLVQGGSEGREGFGD-YGLLGAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPG 1564

Query: 279  RMLGPFPGGNSNRFSTPVGFSGGNGRGDSVLSSTTWNVWGNGSLNSATN-PASPGAFLGS 337
                P    +S  +S             S  S +      + S  S +  P SP     S
Sbjct: 1565 YSTSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTS 1624

Query: 338  GSGNFEVSFGNNSVNWGPVSAPGGGSASGYSAGSMGYGSGDGNYGLGGGGFGRTS----- 392
                   S+   S ++ P S     ++  YS  S  Y     +Y      +  TS     
Sbjct: 1625 P------SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1678

Query: 393  -SAGVGPTSSFAGSTSGYEGSYGDSYRSGSGYGDPT 427
             S    PTS     TS        SY   S    PT
Sbjct: 1679 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1714

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 54.7 bits (132), Expect = 7e-10
 Identities = 9/78 (11%), Positives = 27/78 (34%), Gaps = 11/78 (14%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           + +  +  D++ + + +    Y        ++     R +   FV   +   A+  I  
Sbjct: 7  GILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQM 59

Query: 65 MDKHMIDGRT--VEAKKA 80
            ++   G+   V+ +  
Sbjct: 60 FHQYSFRGKDLIVQLQPT 77

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 52.8 bits (127), Expect = 4e-09
 Identities = 14/93 (15%), Positives = 24/93 (25%), Gaps = 9/93 (9%)

Query: 101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
           G   +  I V  L       +       +               R +   F+T  + E  
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYDLK-------YCYVDRNKRTAFVTLLNGEQA 53

Query: 161 DRVLHK-TFHELNGKMVEVKRAVPKE-FSPGPS 191
              +     +   GK + V+          GPS
Sbjct: 54  QNAIQMFHQYSFRGKDLIVQLQPTDALLCSGPS 86

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 55.2 bits (133), Expect = 8e-10
 Identities = 9/89 (10%), Positives = 32/89 (35%), Gaps = 10/89 (11%)

Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--- 64
           + I  +  D  E  +      +G+V   ++++       +   F+       A  ++   
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYY 72

Query: 65  -MDKHMIDGRTVEAKKAVPRDDQNMLNRN 92
                ++ G+ +  + +  ++ +   + N
Sbjct: 73  TSVTPVLRGQPIYIQFSNHKELKTDSSPN 101

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 54.5 bits (131), Expect = 1e-09
 Identities = 21/92 (22%), Positives = 41/92 (44%), Gaps = 11/92 (11%)

Query: 97  HSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
           H S  P R   I +  L   VTE +       FG +T+++++      + +   FI  ++
Sbjct: 10  HGSGVPSRV--IHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNT 61

Query: 157 EEAVDRVL---HKTFHELNGKMVEVKRAVPKE 185
           EEA + ++         L G+ + ++ +  KE
Sbjct: 62  EEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE 93

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 54.5 bits (131), Expect = 2e-09
 Identities = 19/105 (18%), Positives = 44/105 (41%), Gaps = 9/105 (8%)

Query: 84  DDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNT 143
               ++ R +    S      ++ I +  L   VTE +       FG +T+++++     
Sbjct: 10  HSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLML----- 64

Query: 144 QRPRGFGFITYDSEEAVDRVL---HKTFHELNGKMVEVKRAVPKE 185
            + +   FI  ++EEA + ++         L G+ + ++ +  KE
Sbjct: 65  -KGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKE 108

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 54.2 bits (130), Expect = 2e-09
 Identities = 9/91 (9%), Positives = 33/91 (36%), Gaps = 10/91 (10%)

Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--- 64
           + I  +  D  E  +      +G+V   ++++       +   F+       A  ++   
Sbjct: 34  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYY 87

Query: 65  -MDKHMIDGRTVEAKKAVPRDDQNMLNRNTS 94
                ++ G+ +  + +  ++ +   + N +
Sbjct: 88  TSVTPVLRGQPIYIQFSNHKELKTDSSPNQA 118

>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 = 54.4 bits (131), Expect = 2e-09
 Identities = 11/75 (14%), Positives = 24/75 (32%), Gaps = 8/75 (10%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          +    +   T    ++E FSR+G +   ++              V F +P  A +    +
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKAFRHL 66

Query: 66 DKHMIDGRTVEAKKA 80
                   +  + A
Sbjct: 67 AYSKFHHVPLYLEWA 81

>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 = 48.3 bits (115), Expect = 3e-07
 Identities = 19/104 (18%), Positives = 36/104 (34%), Gaps = 18/104 (17%)

Query: 98  SSPGPGRTKK-IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITY-D 155
           SS   GR+K  I    L +    ++ ++ F +FG++  V++              + + +
Sbjct: 2   SSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLE 55

Query: 156 SEEAVDRVLHKTFHELNGKMVE-----VKRAVPKEFSPGPSRSS 194
             EA      K F  L           ++ A    F   P +  
Sbjct: 56  PLEA-----RKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKD 94

>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 = 54.3 bits (131), Expect = 2e-09
 Identities = 15/83 (18%), Positives = 36/83 (43%), Gaps = 11/83 (13%)

Query: 7   KLFIGGISWD-TDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI- 64
           ++FIG ++     +  ++  FS+YG V    +         +G+ FV +++   A   + 
Sbjct: 29  RVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARAAVL 80

Query: 65  -MDKHMIDGRTVEAKKAVPRDDQ 86
             +  ++ G+T++   A      
Sbjct: 81  GENGRVLAGQTLDINMAGEPKPD 103

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 51.2 bits (123), Expect = 2e-08
 Identities = 23/109 (21%), Positives = 45/109 (41%), Gaps = 16/109 (14%)

Query: 89  LNRNTSSIHSSPGPGRTKKIFVGGL-ASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPR 147
           L  +  +  + P    ++ +F+G L  + V +SD +  F ++G +    V         +
Sbjct: 12  LQASNVTNKNDPKSINSR-VFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HK 62

Query: 148 GFGFITYDSEEAVD---RVLHKTFHELNGKMVEVKRA-VPKEFSPGPSR 192
           G+ F+ Y +E          +     L G+ +++  A  PK    GPS 
Sbjct: 63  GYAFVQYSNERHARAAVLGENGR--VLAGQTLDINMAGEPKPDRSGPSS 109

>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 = 54.0 bits (130), Expect = 2e-09
 Identities = 17/111 (15%), Positives = 40/111 (36%), Gaps = 11/111 (9%)

Query: 90  NRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGF 149
           +  +S  H          + V GL  +V E+D  +  ++FGTI  V++M        +  
Sbjct: 2   SSGSSGSHHKVSVSPV--VHVRGLCESVVEADLVEALEKFGTICYVMMM------PFKRQ 53

Query: 150 GFITYDSEEAVDRVLHK---TFHELNGKMVEVKRAVPKEFSPGPSRSSMIG 197
             + +++ ++    +         + G+      +  K  +   +     G
Sbjct: 54  ALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGPSSG 104

>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 = 50.6 bits (121), Expect = 3e-08
 Identities = 14/92 (15%), Positives = 29/92 (31%), Gaps = 10/92 (10%)

Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--- 64
           + + G+     E  L E   ++G +   ++M        +    V F +   A+  +   
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFA 71

Query: 65  -MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSS 95
                 I G+      +  +      N   SS
Sbjct: 72  ADVPVYIAGQQAFFNYSTSKRITRPGNSGPSS 103

>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 = 52.6 bits (126), Expect = 8e-09
 Identities = 17/95 (17%), Positives = 38/95 (40%), Gaps = 11/95 (11%)

Query: 82  PRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDH 141
               ++ L R+   I +     ++  +  GGL + V+ +      ++ G +  +++  + 
Sbjct: 5   SSGAKHTLLRHEG-IETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN- 62

Query: 142 NTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMV 176
                + + F  Y + E   R     +  LNGK V
Sbjct: 63  -----KPYSFARYRTTEESKRA----YVTLNGKEV 88

>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 = 39.9 bits (93), Expect = 2e-04
 Identities = 7/57 (12%), Positives = 19/57 (33%), Gaps = 6/57 (10%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          +  GG+       +L     + G V   ++  +      + + F  +     ++R  
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAY 80

>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 = 10/83 (12%), Positives = 33/83 (39%), Gaps = 1/83 (1%)

Query: 97  HSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
                  + + +++ G  +  T  D K++ +  G + ++ +    +    +G  F+ +DS
Sbjct: 101 DEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHK-AFKGSIFVVFDS 159

Query: 157 EEAVDRVLHKTFHELNGKMVEVK 179
            E+  + +     +     + + 
Sbjct: 160 IESAKKFVETPGQKYKETDLLIL 182

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 49.8 bits (118), Expect = 3e-07
 Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
           ++I G   D   + +KE+    G+V   + MR       +G  FVVF     A++ +
Sbjct: 112 VYIKGFPTDATLDDIKEWLEDKGQV-LNIQMRRTLHKAFKGSIFVVFDSIESAKKFV 167

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 55.1 bits (132), Expect = 5e-08
 Identities = 49/224 (21%), Positives = 68/224 (30%), Gaps = 19/224 (8%)

Query: 220  SPAGGFGVRMDSRFSPLAT------GRGGISPFGGAGYG-----VGMNLDGGLSPSYGGS 268
                   V+ +  FSPL          GG + +GGA YG      G   +   SP +G S
Sbjct: 1479 LVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVS 1538

Query: 269  S-NFS----NSLGYGRMLGPFPGGNSNRFSTPVGFSGGNGRGDSVLSSTTWNVWGNGSLN 323
            S  FS              P     S    +    S          S T+ +        
Sbjct: 1539 SPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1598

Query: 324  SATNPASPGAFLGSGSGNFEVSFGNNSVNWGPVSAPGGGSASGYSAGSMGYGSGDGNYGL 383
            S T+P+           +   S+   S ++ P S     ++  YS  S  Y     +Y  
Sbjct: 1599 SPTSPSYSPTSPSYSPTS--PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1656

Query: 384  GGGGFGRTSSAGVGPTSSFAGSTSGYEGSYGDSYRSGSGYGDPT 427
                +  TS     PTS     TS        SY   S    PT
Sbjct: 1657 TSPAYSPTSP-SYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPT 1699

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 45.1 bits (106), Expect = 6e-05
 Identities = 47/248 (18%), Positives = 71/248 (28%), Gaps = 22/248 (8%)

Query: 186  FSP---GPSRSSMIGYNNFGFNRPTNLLNSFAQRYNLSPAGGFGVRMDSRFSPLATGRGG 242
            FSP     S  +M G              S    Y  +P           FSP +     
Sbjct: 1492 FSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSP 1551

Query: 243  ISPFGGAGYGVGMNLDGGLSPSYG-GSSNFSNSLGYGRMLGPFPGGNSNRFSTPVGFSGG 301
             SP                SPSY   S ++S +        P     S  +S        
Sbjct: 1552 TSPAYSPTSPSY----SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1607

Query: 302  NGRGDSVLSSTTWNVWGNGSLNSAT-NPASPGAFLGSGSGNFEVSFGNNSVNWGPVSAPG 360
                 S  S +      + S  S + +P SP     S S      +   S ++ P S   
Sbjct: 1608 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS------YSPTSPSYSPTSPAY 1661

Query: 361  GGSASGYSAGSMGYGSGDGNYGLGGGGFGRTS------SAGVGPTS-SFAGSTSGYEGSY 413
              ++  YS  S  Y     +Y      +  TS      S    PTS  ++  +  Y    
Sbjct: 1662 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQ 1721

Query: 414  GDSYRSGS 421
             +   + +
Sbjct: 1722 DEQKHNEN 1729

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 43.2 bits (101), Expect = 2e-04
 Identities = 32/136 (23%), Positives = 44/136 (32%), Gaps = 2/136 (1%)

Query: 323  NSATNPASPGAFLGSGSGNFEVSFGN-NSVNWGPVSAPGGGSASGYSAGSMGYGSGDGNY 381
            +S +N A  G F   G  ++  +     +    P S   G S+ G+S  S  Y      Y
Sbjct: 1497 DSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAY 1556

Query: 382  GLGGGGFGRTSSAGVGPTSSFAGSTSGYEGSYGDSYRSGSGYGDPTWRSATPELDGSGSF 441
                  +  TS     PTS     TS        SY   S    PT  S +P        
Sbjct: 1557 SPTSPSYSPTSP-SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1615

Query: 442  SYGLGTVSTNVAAKSS 457
            S      S + +  S 
Sbjct: 1616 SPSYSPTSPSYSPTSP 1631

>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ... Length = 1733

 Score = 42.0 bits (98), Expect = 5e-04
 Identities = 51/254 (20%), Positives = 73/254 (28%), Gaps = 35/254 (13%)

Query: 223  GGFGVRMDSRFSPLATGRGGISPFGGAGYGVGMNLDGGLSPSYGGSSNFSNSLGYGRMLG 282
            G F V +D            I+             DGG++P    S   +  L       
Sbjct: 1439 GAFDVMIDEESLVKYMPEQKITEIEDG-------QDGGVTPYSNESGLVNADLD------ 1485

Query: 283  PFPGGNSNRFSTPVGFSGGNGRGDSVLSSTTWNVWGNGSLNSATNPASPGAFLGSGSGNF 342
                         + FS     G +   +  +  +G      AT+P        +  G  
Sbjct: 1486 ---------VKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPG-- 1534

Query: 343  EVSFGNNSVNWGPVSAPGGGSASGYSAGSMGYGSGDGNYGLGGGGFGRTS------SAGV 396
               FG +S  + P S     ++  YS  S  Y     +Y      +  TS      S   
Sbjct: 1535 ---FGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1591

Query: 397  GPTSSFAGSTSGYEGSYGDSYRSGSGYGDPTWRSATPELDGSGSFSYGLGTVSTNVAAKS 456
             PTS     TS        SY   S    PT  S +P        S      S + +  S
Sbjct: 1592 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1651

Query: 457  SEGFIGS--YNVTS 468
                  S  Y+ TS
Sbjct: 1652 PSYSPTSPAYSPTS 1665

>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 = 49.4 bits (118), Expect = 9e-08
 Identities = 8/72 (11%), Positives = 24/72 (33%), Gaps = 10/72 (13%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--- 64
          L I  +  +  E  +      +G+V   ++++       +   F+  A    A  ++   
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYY 71

Query: 65 -MDKHMIDGRTV 75
                +  + +
Sbjct: 72 SAVTPHLRNQPI 83

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 47.5 bits (113), Expect = 4e-07
 Identities = 17/98 (17%), Positives = 39/98 (39%), Gaps = 11/98 (11%)

Query: 91  RNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFG 150
             +S       P R   + +  L   VTE++       FG +T+++++      + +   
Sbjct: 3   SGSSGDKMDGAPSRV--LHIRKLPGEVTETEVIALGLPFGKVTNILML------KGKNQA 54

Query: 151 FITYDSEEAVDRVL---HKTFHELNGKMVEVKRAVPKE 185
           F+   +EEA   ++         L  + + ++ +  KE
Sbjct: 55  FLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE 92

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 43.0 bits (101), Expect = 2e-05
 Identities = 22/107 (20%), Positives = 40/107 (37%), Gaps = 13/107 (12%)

Query: 90  NRNTSSIHSSPGPGRTKKIFVGGL-ASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRG 148
            +           GR   I +  L  S  ++S   K  + +G I + ++M      R + 
Sbjct: 12  GKPDQKFDQKQELGRV--IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM------RMKS 63

Query: 149 FGFITYDSEEAVDRVL---HKTFHELNGKMVEVKRAVP-KEFSPGPS 191
             FI  ++ E    ++    K      G+ V+V  +   K+   GPS
Sbjct: 64  QAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKKLVSGPS 110

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 41.9 bits (98), Expect = 7e-05
 Identities = 10/62 (16%), Positives = 26/62 (41%), Gaps = 4/62 (6%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          + +  + +    + L + FS++G V++ +        +A     + +ADP  A+   +  
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQA----LLQYADPVSAQHAKLSL 86

Query: 68 HM 69
            
Sbjct: 87 DG 88

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 42.9 bits (100), Expect = 1e-04
 Identities = 21/94 (22%), Positives = 33/94 (35%), Gaps = 19/94 (20%)

Query: 8   LFIGGIS---------WDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPA 58
           L++GGI              E R++  FSR G++     +        +  GFV F   A
Sbjct: 137 LYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQA 190

Query: 59  VAERVI--MDKHMIDGRTVEAKKAVPRDDQNMLN 90
            AE     M    +   +   K+   R +   L 
Sbjct: 191 NAEFAKEAMSNQTLLLPSD--KEWDDRREGTGLL 222

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 40.2 bits (93), Expect = 9e-04
 Identities = 11/69 (15%), Positives = 24/69 (34%), Gaps = 15/69 (21%)

Query: 100 PGPGRTKKIFVGGLASTVT---------ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFG 150
               + K ++VGG+   +          ES  +  F + G I  +  +        +  G
Sbjct: 129 SFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV------ESKNCG 182

Query: 151 FITYDSEEA 159
           F+ +  +  
Sbjct: 183 FVKFKYQAN 191

>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 = 41.6 bits (97), Expect = 2e-04
 Identities = 10/62 (16%), Positives = 26/62 (41%), Gaps = 4/62 (6%)

Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
           + +  + +    + L + FS++G V++ +        +A     + +ADP  A+   +  
Sbjct: 49  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQA----LLQYADPVSAQHAKLSL 104

Query: 68  HM 69
             
Sbjct: 105 DG 106

>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 = 39.1 bits (91), Expect = 4e-04
 Identities = 13/70 (18%), Positives = 30/70 (42%), Gaps = 6/70 (8%)

Query: 119 ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEV 178
           E  F +  +++G + ++ V  D+      G  ++ +  EE  ++ +      LN +    
Sbjct: 41  EEVFTEMEEKYGEVEEMNV-CDNLGDHLVGNVYVKFRREEDAEKAVID----LNNRWFN- 94

Query: 179 KRAVPKEFSP 188
            + +  E SP
Sbjct: 95  GQPIHAELSP 104

>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 = 38.5 bits (90), Expect = 6e-04
 Identities = 17/75 (22%), Positives = 30/75 (40%), Gaps = 7/75 (9%)

Query: 14  SWDTD-EERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMI 70
               +  E L+   S++G++ + ++      G A     V F DP  A+  I  +D    
Sbjct: 34  LVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVA----SVSFRDPEEADYCIQTLDGRWF 89

Query: 71  DGRTVEAKKAVPRDD 85
            GR + A+      D
Sbjct: 90  GGRQITAQAWDGTTD 104

>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 = 38.5 bits (90), Expect = 6e-04
 Identities = 14/67 (20%), Positives = 29/67 (43%), Gaps = 7/67 (10%)

Query: 15 WDTD-EERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKH--MID 71
          WDT+ ++ + E  +++G V+   + ++ A G      +V     A A   +   H     
Sbjct: 26 WDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNV----YVKCPSIAAAIAAVNALHGRWFA 81

Query: 72 GRTVEAK 78
          G+ + A 
Sbjct: 82 GKMITAA 88

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	522
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.98
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.97
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.97
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.97
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.97
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.96
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.96
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.96
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.96
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.96
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.96
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.95
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.95
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.89
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.85
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.84
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.79
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.78
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.77
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.76
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.76
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.76
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.76
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.75
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.75
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.75
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.75
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.74
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.74
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.74
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.74
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.74
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.74
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.74
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.74
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.74
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.74
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.74
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.74
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.74
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.74
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.73
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.73
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.73
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.73
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.73
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.73
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.73
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.73
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.73
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.73
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.73
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.73
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.73
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.73
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.72
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.72
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.72
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.72
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.72
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.72
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.72
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.72
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.72
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.72
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.72
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.72
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.72
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.72
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.72
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.72
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.72
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.72
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.72
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.71
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.71
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.71
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.71
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.71
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.71
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.71
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.71
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.71
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.71
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.71
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.71
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.71
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.71
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.71
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.71
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.71
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.71
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.71
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.71
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.71
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.7
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.7
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.7
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.7
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.7
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.7
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.7
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.7
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.7
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.7
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.7
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.7
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.7
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.7
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.7
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.7
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.7
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.7
2div_A	99	TRNA selenocysteine associated protein; structural	99.7
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.7
2div_A	99	TRNA selenocysteine associated protein; structural	99.7
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.7
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.69
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.69
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.69
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.69
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.69
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.69
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.69
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.69
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.69
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.69
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.69
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.69
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.69
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.69
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.69
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.69
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.69
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.69
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.69
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.68
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.68
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.68
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.68
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.68
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.68
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.68
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.68
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.68
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.68
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.68
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.68
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.68
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.68
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.68
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.68
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.68
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.68
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.68
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.68
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.68
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.67
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.67
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.67
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.67
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.67
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.67
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.67
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.67
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.67
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.67
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.67
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.67
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.67
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.67
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.66
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.66
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.66
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.66
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.66
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.66
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.66
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.66
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.66
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.66
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.66
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.66
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.66
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.66
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.65
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.65
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.65
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.65
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.65
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.65
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.65
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.65
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.65
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.65
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.65
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.65
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.65
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.65
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.65
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.65
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.64
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.64
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.64
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.64
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.64
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.64
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.64
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.64
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.64
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.64
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.64
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.63
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.63
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.63
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.63
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.63
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.63
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.63
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.63
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.63
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.63
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.63
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.63
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.63
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.63
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.63
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.63
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.63
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.63
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.63
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.62
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.62
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.62
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.62
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.62
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.62
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.62
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.62
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.61
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.61
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.61
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.61
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.61
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.61
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.61
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.61
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.4
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.4
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.61
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.61
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.61
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.61
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.6
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.6
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.6
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.6
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.6
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.6
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.6
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.6
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.6
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.59
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.59
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.59
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.59
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.59
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.59
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.59
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.59
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.59
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.59
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.58
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.58
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.58
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.58
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.58
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.58
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.58
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.58
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.58
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.58
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.58
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.57
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.57
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.57
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.57
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.57
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.57
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.57
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.57
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.57
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.57
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.57
1x5p_A	97	Negative elongation factor E; structure genomics,	99.57
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.57
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.57
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.56
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.56
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.56
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.56
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.56
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.56
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.56
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.55
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.55
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.55
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.55
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.55
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.54
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.54
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.54
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.54
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.54
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.53
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.53
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.52
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.52
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.52
1x5p_A	97	Negative elongation factor E; structure genomics,	99.52
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.52
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.51
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.51
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.51
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.5
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.5
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.5
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.49
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.48
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.48
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.48
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.48
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.48
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.47
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.47
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.46
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.45
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.44
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.44
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.44
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.43
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.43
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.42
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.41
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.41
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.4
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.39
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.38
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.34
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.34
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.34
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.3
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.3
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.29
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.29
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.29
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.28
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.27
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.24
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.23
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.22
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.08
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.04
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.04
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.98
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.86
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.84
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.83
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.68
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.64
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.57
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.47
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.47
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.4
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.19
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.13
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.88
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.12
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.04
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.0
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.93
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.91
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.86
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.59
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.38
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.13
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	95.97
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.82
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.71
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.04
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	94.52
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	94.3
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	93.84
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	84.18
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	84.08

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=100.00  E-value=3.8e-35  Score=276.66  Aligned_cols=177  Identities=38%  Similarity=0.738  Sum_probs=153.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      .+.++|||+|||+++||++|+++|++||+|++|+|++++.+++++|||||+|.++++|++|| ++.+.|+++.|.|.++.
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~~~   90 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV   90 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeeccc
Confidence            56799999999999999999999999999999999999999999999999999999999999 88899999999999987


Q ss_pred             CCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHH
Q 009920           82 PRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD  161 (522)
Q Consensus        82 ~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~  161 (522)
                      ++......          ......++|||.|||+++|+++|+++|++||.|+.|.|+.++.+++++|||||+|.++++|+
T Consensus        91 ~~~~~~~~----------~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~  160 (196)
T 1l3k_A           91 SREDSQRP----------GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD  160 (196)
T ss_dssp             C---------------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             Cccccccc----------ccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHH
Confidence            65443211          12245689999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcCCccCCeEEEEEEcCCCCCCCC
Q 009920          162 RVLHKTFHELNGKMVEVKRAVPKEFSPG  189 (522)
Q Consensus       162 ~Al~~~~~~l~Gr~I~V~~a~pk~~~~~  189 (522)
                      +||+++.+.|+|++|+|+++.+++....
T Consensus       161 ~A~~~~~~~~~G~~i~v~~a~~k~~~~~  188 (196)
T 1l3k_A          161 KIVIQKYHTVNGHNCEVRKALSKQEMAS  188 (196)
T ss_dssp             HHHHCSCCEETTEECEEEECC-------
T ss_pred             HHHHhCCcEECCEEEEEEecCChhHhcc
Confidence            9999877999999999999999887543

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=100.00  E-value=9.2e-35  Score=267.17  Aligned_cols=167  Identities=47%  Similarity=0.960  Sum_probs=154.5

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHHHcccccCCeEEEEeecCC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl~~~~~i~Gr~I~V~~a~~   82 (522)
                      +++++|||+|||+++||++|+++|++||+|.+|+|++++.+++++|||||+|.++++|++|+.+.+.++++.|.|.++.+
T Consensus         1 k~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~~~~   80 (167)
T 2cjk_A            1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIP   80 (167)
T ss_dssp             CGGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHSCCEETTEECCCEECCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhcccccCCeEcccccccc
Confidence            47899999999999999999999999999999999999999999999999999999999999778899999999998876


Q ss_pred             CccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHH
Q 009920           83 RDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDR  162 (522)
Q Consensus        83 k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~  162 (522)
                      +...                ...++|||+|||.++|+++|+++|++||.|+++.|+.++.+++++|||||+|.++++|++
T Consensus        81 ~~~~----------------~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~  144 (167)
T 2cjk_A           81 RDEQ----------------DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR  144 (167)
T ss_dssp             HHHH----------------HHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHH
T ss_pred             hhhc----------------cCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHH
Confidence            5432                235689999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhcCCccCCeEEEEEEcCCCC
Q 009920          163 VLHKTFHELNGKMVEVKRAVPKE  185 (522)
Q Consensus       163 Al~~~~~~l~Gr~I~V~~a~pk~  185 (522)
                      |+++....|+|++|+|+++.||+
T Consensus       145 A~~~~~~~~~g~~i~V~~a~pk~  167 (167)
T 2cjk_A          145 VCQNKFIDFKDRKIEIKRAEPRH  167 (167)
T ss_dssp             HHHCSEECSSSSCEEEEECCCCC
T ss_pred             HHhCCCEEeCCeEEEEeecCCCC
Confidence            99843389999999999999874

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=1.2e-33  Score=272.66  Aligned_cols=167  Identities=28%  Similarity=0.479  Sum_probs=152.0

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      ..++|||+|||+++||++|+++|++||+|++|+|++++.+++++|||||+|.++++|++||  ++...+.++.|.+.++.
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~   93 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   93 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccc
Confidence            4689999999999999999999999999999999999999999999999999999999999  89999999999999886


Q ss_pred             CCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHH
Q 009920           82 PRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD  161 (522)
Q Consensus        82 ~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~  161 (522)
                      .......              ...++|||+|||+++|+++|+++|++||.|++|+|++|+.  .+||||||+|.++++|+
T Consensus        94 ~~~~~~~--------------~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~--~~~g~~fV~f~~~~~a~  157 (213)
T 4f02_A           94 RDPSLRK--------------SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAE  157 (213)
T ss_dssp             CCTHHHH--------------HCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT--EEEEEEEEEESSHHHHH
T ss_pred             ccccccc--------------cccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCC--CCceEEEEEeCCHHHHH
Confidence            6543321              1346899999999999999999999999999999999864  47999999999999999


Q ss_pred             HHHHhcC-CccCCeEEEEEEcCCCCC
Q 009920          162 RVLHKTF-HELNGKMVEVKRAVPKEF  186 (522)
Q Consensus       162 ~Al~~~~-~~l~Gr~I~V~~a~pk~~  186 (522)
                      +||++++ .+|+|++|+|++++++.+
T Consensus       158 ~Ai~~lng~~~~g~~i~V~~a~~~~~  183 (213)
T 4f02_A          158 RAIEKMNGMLLNDRKVFVGRFKSRKE  183 (213)
T ss_dssp             HHHHHHTTCEETTEECEEEECCCHHH
T ss_pred             HHHHHhCCCEECCEEEEEEEcCCCcc
Confidence            9999887 899999999999988653

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=100.00  E-value=1.4e-33  Score=270.02  Aligned_cols=180  Identities=21%  Similarity=0.475  Sum_probs=156.3

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      +.++|||+|||+++||++|+++|++||+|++|+|++++.++++++||||+|.++++|++||  ++++.|.+++|.|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            4689999999999999999999999999999999999989999999999999999999999  89999999999998877


Q ss_pred             CCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHH
Q 009920           82 PRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD  161 (522)
Q Consensus        82 ~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~  161 (522)
                      .+..........     .......++|||.|||.++|+++|+++|++||.|++|+|++++.+++++|||||+|.++++|+
T Consensus       107 ~~~~~~~~~~~~-----~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~  181 (216)
T 2qfj_A          107 NIGQAQPIIDQL-----AEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQ  181 (216)
T ss_dssp             CCGGGHHHHHHH-----HHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             Cccccchhhhhh-----hcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHH
Confidence            654332111000     001235679999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcC-CccCCeEEEEEEcCCCCCCC
Q 009920          162 RVLHKTF-HELNGKMVEVKRAVPKEFSP  188 (522)
Q Consensus       162 ~Al~~~~-~~l~Gr~I~V~~a~pk~~~~  188 (522)
                      +|++.++ ..|+|++|+|+++.++....
T Consensus       182 ~A~~~l~g~~~~g~~i~V~~a~~~~~~~  209 (216)
T 2qfj_A          182 DAVSSMNLFDLGGQYLRVGKAVTPPMPL  209 (216)
T ss_dssp             HHHHHHTTCBCSSSBCEEEECSSCSSTT
T ss_pred             HHHHHccCCEeCCcEEEEEEecCCCCCC
Confidence            9999887 89999999999999876543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1e-32  Score=252.22  Aligned_cols=163  Identities=23%  Similarity=0.464  Sum_probs=150.6

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCCC
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVPR   83 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~k   83 (522)
                      |+|||+|||+++||++|+++|++||+|.+|+|++++. +++++||||+|.++++|++|+  +++..+.+++|.|.++.+.
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            6899999999999999999999999999999999975 789999999999999999999  8999999999999998665


Q ss_pred             ccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHH
Q 009920           84 DDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV  163 (522)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~A  163 (522)
                      ...              .....++|||.|||..+|+++|+++|++||.|+++.++.++.+++++|+|||+|.++++|++|
T Consensus        80 ~~~--------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A  145 (166)
T 3md3_A           80 QQS--------------SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA  145 (166)
T ss_dssp             CCC--------------CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHH
T ss_pred             CCC--------------CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHH
Confidence            431              224678999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhcC-CccCCeEEEEEEcCC
Q 009920          164 LHKTF-HELNGKMVEVKRAVP  183 (522)
Q Consensus       164 l~~~~-~~l~Gr~I~V~~a~p  183 (522)
                      ++.++ ..|+|++|+|++|++
T Consensus       146 ~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          146 MDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             HHHHTTCEETTEECEEEESCC
T ss_pred             HHHhCCCccCCcEEEEEecCC
Confidence            99877 899999999999864

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=100.00  E-value=1.2e-32  Score=253.05  Aligned_cols=162  Identities=23%  Similarity=0.437  Sum_probs=151.6

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      ..++|||+|||+++|+++|+++|++||+|.+|+|++++.+++++|||||+|.++++|++|+  +++..+.+++|.|.++.
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            4689999999999999999999999999999999999989999999999999999999999  89999999999999987


Q ss_pred             CCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHH
Q 009920           82 PRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD  161 (522)
Q Consensus        82 ~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~  161 (522)
                      ++...                ...++|||.|||..+++++|+++|++||.|+++.+++++.+++++|+|||+|.++++|+
T Consensus        82 ~~~~~----------------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~  145 (168)
T 1b7f_A           82 PGGES----------------IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ  145 (168)
T ss_dssp             CCSST----------------TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             CCccc----------------CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHH
Confidence            65421                34679999999999999999999999999999999999989999999999999999999


Q ss_pred             HHHHhcC-CccCC--eEEEEEEc
Q 009920          162 RVLHKTF-HELNG--KMVEVKRA  181 (522)
Q Consensus       162 ~Al~~~~-~~l~G--r~I~V~~a  181 (522)
                      +|++.++ ..|.+  ++|+|++|
T Consensus       146 ~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          146 EAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHhcCCEecCCCeEEEEEeC
Confidence            9999888 88988  99999986

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=100.00  E-value=2.4e-32  Score=250.00  Aligned_cols=161  Identities=27%  Similarity=0.520  Sum_probs=149.7

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCC
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~   82 (522)
                      .++|||+|||+++||++|+++|++||+|.+|+|++++.+++++|||||+|.++++|++|+  +++..+.+++|.|.++.+
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            689999999999999999999999999999999999989999999999999999999999  899999999999999876


Q ss_pred             CccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHH
Q 009920           83 RDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDR  162 (522)
Q Consensus        83 k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~  162 (522)
                      ....                ...++|||.|||..+++++|+++|++||.|++++++.++.+++++|+|||+|.++++|++
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            5432                245689999999999999999999999999999999999899999999999999999999


Q ss_pred             HHHhcC-CccCCeE--EEEEEc
Q 009920          163 VLHKTF-HELNGKM--VEVKRA  181 (522)
Q Consensus       163 Al~~~~-~~l~Gr~--I~V~~a  181 (522)
                      |++.++ ..|.|+.  |+|++|
T Consensus       146 A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          146 AIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHhcCCccCCCccceEEEeC
Confidence            999888 8999975  888775

>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=99.98  E-value=1.1e-31  Score=247.86  Aligned_cols=164  Identities=24%  Similarity=0.432  Sum_probs=144.6

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCC--CcccEEEEEecCHHHHHHHH--HcccccC---CeEE
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATG--RARGFGFVVFADPAVAERVI--MDKHMID---GRTV   75 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg--~srG~aFVeF~~~e~A~kAl--~~~~~i~---Gr~I   75 (522)
                      ++.++|||+|||+++||++|+++|++||+|.+|+|++++.++  +++|||||+|.++++|++|+  ++...+.   .+.+
T Consensus         1 s~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~   80 (175)
T 3nmr_A            1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPI   80 (175)
T ss_dssp             CCCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccce
Confidence            478999999999999999999999999999999999999876  89999999999999999999  7776665   5677


Q ss_pred             EEeecCCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEec
Q 009920           76 EAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD  155 (522)
Q Consensus        76 ~V~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~  155 (522)
                      .+.++.++...               ....++|||+|||+++|+++|+++|++||.|++|+|++++. ++++|||||+|.
T Consensus        81 ~~~~~~~~~~~---------------~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~-g~~~g~afV~f~  144 (175)
T 3nmr_A           81 QMKPADSEKNN---------------AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCAFVTFT  144 (175)
T ss_dssp             EEEECGGGCCS---------------CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEES
T ss_pred             EEccccccccc---------------cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCC-CCEEEEEEEEEC
Confidence            77766543321               23567899999999999999999999999999999999965 889999999999


Q ss_pred             CHHHHHHHHHhcC-CccC---CeEEEEEEcC
Q 009920          156 SEEAVDRVLHKTF-HELN---GKMVEVKRAV  182 (522)
Q Consensus       156 s~e~A~~Al~~~~-~~l~---Gr~I~V~~a~  182 (522)
                      ++++|++|++.++ ..+.   +++|+|++|.
T Consensus       145 ~~~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          145 TRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             SHHHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             CHHHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            9999999999888 5555   4999999974

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.97  E-value=5e-31  Score=248.80  Aligned_cols=178  Identities=20%  Similarity=0.416  Sum_probs=149.8

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhcc----C-------CeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-Hccccc
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRY----G-------EVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMI   70 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~----G-------~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i   70 (522)
                      +.+++|||+|||+++||++|+++|++|    +       +|.++++      ++++|||||+|.++++|++|| ++++.|
T Consensus         2 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al~l~g~~~   75 (198)
T 2yh0_A            2 AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAMAFDGIIF   75 (198)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHGGGTTEEE
T ss_pred             CceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHHHhcCCEE
Confidence            468999999999999999999999999    5       5666555      345799999999999999999 999999


Q ss_pred             CCeEEEEeecCCCcccccccccc----CCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCc
Q 009920           71 DGRTVEAKKAVPRDDQNMLNRNT----SSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRP  146 (522)
Q Consensus        71 ~Gr~I~V~~a~~k~~~~~~~~~~----~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~  146 (522)
                      .+++|.|.++.+...........    ............++|||+|||+.+++++|+++|++||.|++|.|++++.++++
T Consensus        76 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~  155 (198)
T 2yh0_A           76 QGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLS  155 (198)
T ss_dssp             TTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSE
T ss_pred             cCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCc
Confidence            99999999987654332211111    01111223356789999999999999999999999999999999999989999


Q ss_pred             ceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCCCC
Q 009920          147 RGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPKEF  186 (522)
Q Consensus       147 rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk~~  186 (522)
                      +|||||+|.++++|++|++.++ ..|+|++|+|++++|+..
T Consensus       156 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          156 KGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             EEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             ceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            9999999999999999999877 899999999999998764

>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=99.97  E-value=9.1e-31  Score=241.61  Aligned_cols=158  Identities=21%  Similarity=0.451  Sum_probs=143.3

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhcc----C-------CeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-Hccccc
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRY----G-------EVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMI   70 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~----G-------~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i   70 (522)
                      ++.++|||+|||+++||++|+++|++|    |       +|.++++.+      ++|||||+|.++++|++|+ ++++.|
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~------~~g~afV~f~~~~~A~~A~~~~~~~~   75 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ------DKNFAFLEFRSVDETTQAMAFDGIIF   75 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET------TTTEEEEEESSHHHHHHHGGGTTCEE
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC------CCCEEEEEeCCHHHHHHHHHhCCcEe
Confidence            468999999999999999999999999    6       777777754      4789999999999999999 999999


Q ss_pred             CCeEEEEeecCCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEE
Q 009920           71 DGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFG  150 (522)
Q Consensus        71 ~Gr~I~V~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~a  150 (522)
                      ++++|.|+++.+...                ....++|||+|||.++|+++|+++|++||+|++|.|++++.+++++|+|
T Consensus        76 ~g~~i~v~~~~~~~~----------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~a  139 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQP----------------LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYA  139 (172)
T ss_dssp             TTEECEEECCSSCCC----------------CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEE
T ss_pred             cCceeeecCCcccCC----------------CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEE
Confidence            999999988654322                1246899999999999999999999999999999999999899999999


Q ss_pred             EEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          151 FITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       151 FVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      ||+|.++++|++|++.++ ..|+|++|+|++|.
T Consensus       140 fV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A          140 FCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             EEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             EEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            999999999999999877 89999999999974

>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=99.97  E-value=2.5e-31  Score=246.63  Aligned_cols=163  Identities=22%  Similarity=0.350  Sum_probs=144.7

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      .+.++|||+|||+++|+++|+++|++|++|.. .++++..+++++|||||+|.++++|++|| ++++.|.+++|.|.++.
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~~~   89 (175)
T 1fje_B           11 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPK   89 (175)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEecCC
Confidence            57899999999999999999999999998766 44555567889999999999999999999 99999999999999987


Q ss_pred             CCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHH
Q 009920           82 PRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD  161 (522)
Q Consensus        82 ~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~  161 (522)
                      ++...              .....++|||+|||.++|+++|+++|++||.|..+     ..+++++|||||+|.++++|+
T Consensus        90 ~~~~~--------------~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~  150 (175)
T 1fje_B           90 GRDSK--------------KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAE  150 (175)
T ss_dssp             CSSCS--------------TTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHH
T ss_pred             Ccccc--------------ccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHH
Confidence            65432              12357899999999999999999999999987655     566889999999999999999


Q ss_pred             HHHHhcC-CccCCeEEEEEEcCCCC
Q 009920          162 RVLHKTF-HELNGKMVEVKRAVPKE  185 (522)
Q Consensus       162 ~Al~~~~-~~l~Gr~I~V~~a~pk~  185 (522)
                      +|++.++ ..|+|++|+|+++.||.
T Consensus       151 ~A~~~l~g~~~~g~~i~v~~a~~k~  175 (175)
T 1fje_B          151 KNLEEKQGAEIDGRSVSLYYTGEKG  175 (175)
T ss_dssp             HHHHHHTEEEETTEEEEEEECSSCC
T ss_pred             HHHHHhCCCEECCeEEEEEecCCCC
Confidence            9999888 89999999999999863

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.97  E-value=2.2e-29  Score=251.99  Aligned_cols=170  Identities=14%  Similarity=0.222  Sum_probs=156.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++|+++|+++|++||+|.+|+|++++.+++++|||||+|.++++|++|+  +++..|++++|.|.++
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a  172 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT  172 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            45789999999999999999999999999999999999999999999999999999999999  8999999999999998


Q ss_pred             CCCccccccccccCCCCCCCCCCCcceeEecCCCCCC-CHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHH
Q 009920           81 VPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTV-TESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEA  159 (522)
Q Consensus        81 ~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~v-teedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~  159 (522)
                      .++....             .....++|||.|||+++ |+++|+++|++||.|++|+|++++ +++++|+|||+|.++++
T Consensus       173 ~~~~~~~-------------~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~  238 (284)
T 3smz_A          173 DAGQLTP-------------ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEM  238 (284)
T ss_dssp             CGGGCCT-------------TTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHH
T ss_pred             CCCCCCc-------------ccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHH
Confidence            7654321             22467899999999995 999999999999999999999987 58999999999999999


Q ss_pred             HHHHHHhcC-CccCCeEEEEEEcCCCCC
Q 009920          160 VDRVLHKTF-HELNGKMVEVKRAVPKEF  186 (522)
Q Consensus       160 A~~Al~~~~-~~l~Gr~I~V~~a~pk~~  186 (522)
                      |++|++.++ ..|.|++|+|+++.++..
T Consensus       239 A~~A~~~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          239 AEEAQQQADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             HHHHHHHHTTCEETTEECEEEECCSSSC
T ss_pred             HHHHHHHhCCCccCCeEEEEEEecCCCc
Confidence            999999888 899999999999998765

>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=99.96  E-value=5.1e-29  Score=249.08  Aligned_cols=172  Identities=16%  Similarity=0.297  Sum_probs=144.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHH----HHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEE
Q 009920            3 SDLGKLFIGGISWDTDEERLK----EYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVE   76 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~----e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~   76 (522)
                      +.+++|||+|||+++||++|+    ++|++||+|++|+|++   ++++||||||+|.++++|++||  +++..|.+++|.
T Consensus         7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   83 (282)
T 3pgw_A            7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   83 (282)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEE
Confidence            568999999999999999977    8999999999999987   5789999999999999999999  899999999999


Q ss_pred             EeecCCCccccccccccC--------------------------------------------------------------
Q 009920           77 AKKAVPRDDQNMLNRNTS--------------------------------------------------------------   94 (522)
Q Consensus        77 V~~a~~k~~~~~~~~~~~--------------------------------------------------------------   94 (522)
                      |+++..+...........                                                              
T Consensus        84 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  163 (282)
T 3pgw_A           84 IQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPY  163 (282)
T ss_pred             EEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCC
Confidence            999866543100000000                                                              


Q ss_pred             ---------------------------------CCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecC
Q 009920           95 ---------------------------------SIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDH  141 (522)
Q Consensus        95 ---------------------------------~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~  141 (522)
                                                       ...........++|||+|||..+|+++|+++|++||.|++|+|+.++
T Consensus       164 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~  243 (282)
T 3pgw_A          164 MPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR  243 (282)
T ss_pred             CCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC
Confidence                                             00000122356889999999999999999999999999999999654


Q ss_pred             CCCCcceEEEEEecCHHHHHHHHHhcC-CccC-CeEEEEEEcC
Q 009920          142 NTQRPRGFGFITYDSEEAVDRVLHKTF-HELN-GKMVEVKRAV  182 (522)
Q Consensus       142 ~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~-Gr~I~V~~a~  182 (522)
                           +|||||+|.+.++|++||+.++ ..|. +++|+|++++
T Consensus       244 -----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          244 -----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             -----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence                 5899999999999999999888 7898 9999999986

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.96  E-value=2e-29  Score=253.25  Aligned_cols=171  Identities=14%  Similarity=0.266  Sum_probs=145.1

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccC-CeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYG-EVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G-~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      +.++|||+|||+++++++|+++|++|| +|.+|+|++++. +++++||||+|.++++|++|+  ++++.|.+++|.|+++
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            578999999999999999999999999 999999999876 789999999999999999999  8999999999999999


Q ss_pred             CCCccccccccccCCCCCCCCCCCcceeEecCCCCC-CCHHHHHHHHhhcCCeeEEEEEecCC-CCCcceEEEEEecCHH
Q 009920           81 VPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLAST-VTESDFKKYFDQFGTITDVVVMYDHN-TQRPRGFGFITYDSEE  158 (522)
Q Consensus        81 ~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~-vteedL~~~F~~fG~I~~v~i~~d~~-tg~~rG~aFVeF~s~e  158 (522)
                      .++......         .......++|||.|||.. +|+++|+++|++||.|+.|+|++++. |++++|||||+|.+++
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            876543321         122346789999999999 99999999999999999999999887 6899999999999999


Q ss_pred             HHHHHHHhcC-CccCCeEEEEEEcCCCC
Q 009920          159 AVDRVLHKTF-HELNGKMVEVKRAVPKE  185 (522)
Q Consensus       159 ~A~~Al~~~~-~~l~Gr~I~V~~a~pk~  185 (522)
                      +|++|+ .++ ..|.|++|+|+++.+|+
T Consensus       266 ~A~~A~-~l~g~~~~g~~i~V~~a~~k~  292 (292)
T 2ghp_A          266 SAERAL-QMNRSLLGNREISVSLADKKP  292 (292)
T ss_dssp             HHHHHG-GGTTEEETTEEEEEEECCCCC
T ss_pred             HHHHHH-HhcCCEECCcEEEEEEecCCC
Confidence            999999 777 89999999999999874

>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=99.96  E-value=3.8e-29  Score=240.95  Aligned_cols=171  Identities=18%  Similarity=0.215  Sum_probs=139.7

Q ss_pred             CCcEEEECCCC-CCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            4 DLGKLFIGGIS-WDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         4 d~r~LfVgnLP-~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      +.++|||+||| +++|+++|+++|++||+|.+|+|+++     .||||||+|.++++|++||  ++++.|.+++|.|.++
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            57899999999 89999999999999999999999875     3799999999999999999  9999999999999988


Q ss_pred             CCCcccccc----ccc--------cCCCC---------CCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCe--eEEEE
Q 009920           81 VPRDDQNML----NRN--------TSSIH---------SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTI--TDVVV  137 (522)
Q Consensus        81 ~~k~~~~~~----~~~--------~~~~~---------~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I--~~v~i  137 (522)
                      ..+......    ...        ....+         ......+.++|||.|||+++||++|+++|++||.|  ++|+|
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            644321100    000        00000         00112356789999999999999999999999999  89999


Q ss_pred             EecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCe----EEEEEEc
Q 009920          138 MYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGK----MVEVKRA  181 (522)
Q Consensus       138 ~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr----~I~V~~a  181 (522)
                      +.++  ++++|+|||+|+++++|++||+.++ .+|.++    ++.|+++
T Consensus       158 ~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          158 FSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             EcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            8775  4567999999999999999999988 788886    5777764

>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=99.96  E-value=1.2e-28  Score=240.18  Aligned_cols=172  Identities=17%  Similarity=0.243  Sum_probs=143.8

Q ss_pred             CCCcEEEECCCCC-CCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            3 SDLGKLFIGGISW-DTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         3 ~d~r~LfVgnLP~-~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      .++++|||+|||+ ++++++|+++|++||+|++|+|++++     ++||||+|.++++|++|+  +++..|.+++|.|++
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~  106 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL  106 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEEC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            4679999999999 99999999999999999999999875     689999999999999999  899999999999999


Q ss_pred             cCCCcccccccccc----------CC---------CCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcC-CeeEEEEEe
Q 009920           80 AVPRDDQNMLNRNT----------SS---------IHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFG-TITDVVVMY  139 (522)
Q Consensus        80 a~~k~~~~~~~~~~----------~~---------~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG-~I~~v~i~~  139 (522)
                      +.++..........          ..         ........+.++|||.|||..+++++|+++|++|| .|++|+|+.
T Consensus       107 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~  186 (229)
T 2adc_A          107 SKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ  186 (229)
T ss_dssp             CSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS
T ss_pred             ecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEE
Confidence            87653221110000          00         00011123568999999999999999999999999 999999975


Q ss_pred             cCCCCCcceEEEEEecCHHHHHHHHHhcC-CccC-CeEEEEEEcCCC
Q 009920          140 DHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELN-GKMVEVKRAVPK  184 (522)
Q Consensus       140 d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~-Gr~I~V~~a~pk  184 (522)
                      +     .+|+|||+|++.++|++|++.++ ..|. +++|+|++++++
T Consensus       187 ~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          187 K-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             S-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             C-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            3     36899999999999999999887 8899 999999999875

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.96  E-value=5.9e-29  Score=235.71  Aligned_cols=171  Identities=17%  Similarity=0.242  Sum_probs=143.5

Q ss_pred             CCcEEEECCCCC-CCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            4 DLGKLFIGGISW-DTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         4 d~r~LfVgnLP~-~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ++++|||+|||+ ++++++|+++|++||+|.+|+|++++     ++||||+|.++++|++|+  +++..|.+++|.|.++
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a   76 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS   76 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEEC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEe
Confidence            579999999999 99999999999999999999999875     689999999999999999  8999999999999988


Q ss_pred             CCCcccccccccc-------------------CCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcC-CeeEEEEEec
Q 009920           81 VPRDDQNMLNRNT-------------------SSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFG-TITDVVVMYD  140 (522)
Q Consensus        81 ~~k~~~~~~~~~~-------------------~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG-~I~~v~i~~d  140 (522)
                      .++..........                   ..........+.++|||.|||..+++++|+++|++|| .|++|+|+.+
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~  156 (198)
T 1qm9_A           77 KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK  156 (198)
T ss_dssp             CCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST
T ss_pred             cCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC
Confidence            7653221110000                   0000011124578999999999999999999999999 9999999764


Q ss_pred             CCCCCcceEEEEEecCHHHHHHHHHhcC-CccC-CeEEEEEEcCCC
Q 009920          141 HNTQRPRGFGFITYDSEEAVDRVLHKTF-HELN-GKMVEVKRAVPK  184 (522)
Q Consensus       141 ~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~-Gr~I~V~~a~pk  184 (522)
                           .+|+|||+|.++++|++|++.++ ..|. +++|+|++++++
T Consensus       157 -----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          157 -----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             -----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             -----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence                 27899999999999999999888 8899 999999999875

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A

Probab=99.96  E-value=2.8e-28  Score=244.92  Aligned_cols=160  Identities=13%  Similarity=0.228  Sum_probs=138.3

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeec
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a   80 (522)
                      +++.++|||+|||+++|+++|+++|++||+|.+|+|++++.+  +++||||+|.++++|++|| ++...|.+++|.|.++
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            356899999999999999999999999999999999998753  5899999999999999999 9999999999999874


Q ss_pred             CCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcC-CeeEEEEEecCCCCCcceEEEEEecCHHH
Q 009920           81 VPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFG-TITDVVVMYDHNTQRPRGFGFITYDSEEA  159 (522)
Q Consensus        81 ~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG-~I~~v~i~~d~~tg~~rG~aFVeF~s~e~  159 (522)
                                             ..++|||+|||..+++++|+++|++|| .|.+|.|+.++. ++++|||||+|.++++
T Consensus       116 -----------------------~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~  171 (292)
T 2ghp_A          116 -----------------------TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKED  171 (292)
T ss_dssp             -----------------------CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHH
T ss_pred             -----------------------CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHH
Confidence                                   356899999999999999999999999 999999999877 7789999999999999


Q ss_pred             HHHHHHhcC-CccCCeEEEEEEcCCCCCC
Q 009920          160 VDRVLHKTF-HELNGKMVEVKRAVPKEFS  187 (522)
Q Consensus       160 A~~Al~~~~-~~l~Gr~I~V~~a~pk~~~  187 (522)
                      |++|++.++ ..|.+++|.|+++.|+...
T Consensus       172 a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  200 (292)
T 2ghp_A          172 ARYCVEKLNGLKIEGYTLVTKVSNPLEKS  200 (292)
T ss_dssp             HHHHHHHHTTCEETTEECEEEECCCC---
T ss_pred             HHHHHHHhCCCEeCCcEEEEEECCCCccc
Confidence            999999777 8999999999999887654

>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=1.1e-27  Score=239.65  Aligned_cols=156  Identities=18%  Similarity=0.395  Sum_probs=143.9

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++|+++|+++|++|| |.+|++      ++++|||||+|.++++|++|+  +++..|.+++|.|.++
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~------~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~   92 (284)
T 3smz_A           20 RNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQ   92 (284)
T ss_dssp             HCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE------ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEec
Confidence            3678999999999999999999999999 999888      356789999999999999999  7999999999999874


Q ss_pred             CCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHH
Q 009920           81 VPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV  160 (522)
Q Consensus        81 ~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A  160 (522)
                      .                      ..++|||+|||+++|+++|+++|++||.|.++.|+.++.+++++|||||+|.++++|
T Consensus        93 ~----------------------~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a  150 (284)
T 3smz_A           93 P----------------------TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSA  150 (284)
T ss_dssp             C----------------------CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHH
T ss_pred             C----------------------CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHH
Confidence            2                      236899999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhcC-CccCCeEEEEEEcCCCCCC
Q 009920          161 DRVLHKTF-HELNGKMVEVKRAVPKEFS  187 (522)
Q Consensus       161 ~~Al~~~~-~~l~Gr~I~V~~a~pk~~~  187 (522)
                      ++|++.++ ..|.+++|.|.++.++...
T Consensus       151 ~~A~~~l~~~~~~g~~i~v~~a~~~~~~  178 (284)
T 3smz_A          151 ARAKSDLLGKPLGPRTLYVHWTDAGQLT  178 (284)
T ss_dssp             HHHHHHHTTCEETTEECEEEECCGGGCC
T ss_pred             HHHHHHhCCCEeCCcEEEEEECCCCCCC
Confidence            99998777 8999999999999887643

>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=99.95  E-value=6e-28  Score=240.02  Aligned_cols=157  Identities=28%  Similarity=0.460  Sum_probs=142.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++|+++|+++|++||+|.+|+|+++      +|||||+|.++++|++|+  ++++.|.+++|.|.++
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a   93 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA   93 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeec
Confidence            35689999999999999999999999999999999653      689999999999999999  8999999999999987


Q ss_pred             CCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHH
Q 009920           81 VPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV  160 (522)
Q Consensus        81 ~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A  160 (522)
                      .+                      .++|||+|||..+|+++|+++|++||.|++|.|+.| .+++++|||||+|.+.++|
T Consensus        94 ~~----------------------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A  150 (261)
T 3sde_A           94 TH----------------------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPA  150 (261)
T ss_dssp             CC----------------------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHH
T ss_pred             cc----------------------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHH
Confidence            53                      458999999999999999999999999999999999 5799999999999999999


Q ss_pred             HHHHHhcC-C-ccC---CeEEEEEEcCCCCCCC
Q 009920          161 DRVLHKTF-H-ELN---GKMVEVKRAVPKEFSP  188 (522)
Q Consensus       161 ~~Al~~~~-~-~l~---Gr~I~V~~a~pk~~~~  188 (522)
                      ++||+.++ . .+.   +++|.|+++.+.....
T Consensus       151 ~~A~~~l~~~~~~~~~~~r~i~v~~~~~~~~~~  183 (261)
T 3sde_A          151 RKALERCGDGAFLLTTTPRPVIVEPMEQFDDED  183 (261)
T ss_dssp             HHHHHHHHHSCEESSSSCCBCEEEECCCEESSS
T ss_pred             HHHHHHhcCCeEEecCCCceEEEeeccccCccC
Confidence            99999984 3 443   9999999998775443

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.89  E-value=1.7e-22  Score=185.34  Aligned_cols=148  Identities=18%  Similarity=0.269  Sum_probs=114.9

Q ss_pred             EEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hcc-cccCCeEEEEeecCCCccccccccccCCCCCCCCCCCcceeEe
Q 009920           34 EAVIMRDRATGRARGFGFVVFADPAVAERVI--MDK-HMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFV  110 (522)
Q Consensus        34 ~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~-~~i~Gr~I~V~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~LfV  110 (522)
                      +++|+.+..  +++|||||+|.++++|++|+  ++. ..+++ .+.+...........   ..............++|||
T Consensus         2 ~~kl~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~-~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~l~v   75 (158)
T 2kn4_A            2 QYKLILNGK--TLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTE---GSHHHHHHMDVEGMTSLKV   75 (158)
T ss_dssp             EEEEEEECS--SCEEEEEEECSSHHHHHHHHHHHHHHHTCCC-EEEEETTTTEEEEEC---CCCCSSCCCCCCBCCEEEE
T ss_pred             cEEEEecCc--cccchhHHHHHHHHhHHHHHHhhcccCCCCC-cccccCccccccccc---cccccccccCCCCCCEEEE
Confidence            567888764  69999999999999999999  343 33333 333332222211111   0111112223356789999


Q ss_pred             cCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCCCCC
Q 009920          111 GGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPKEFS  187 (522)
Q Consensus       111 gnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk~~~  187 (522)
                      +|||+++|+++|+++|++||.|++|.|++|+.+++++|||||+|.++++|++||+.++ +.|.|++|+|++++++...
T Consensus        76 ~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  153 (158)
T 2kn4_A           76 DNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  153 (158)
T ss_dssp             ESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSCC
T ss_pred             eCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            9999999999999999999999999999999999999999999999999999999887 8999999999999987543

>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=99.85  E-value=5.9e-21  Score=174.00  Aligned_cols=136  Identities=18%  Similarity=0.270  Sum_probs=113.9

Q ss_pred             CCcccEEEEEecCHHHHHHHH--H-cccccCCeEEEEeecCCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHH
Q 009920           44 GRARGFGFVVFADPAVAERVI--M-DKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTES  120 (522)
Q Consensus        44 g~srG~aFVeF~~~e~A~kAl--~-~~~~i~Gr~I~V~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vtee  120 (522)
                      .+.+|+++|+|.++++|++|+  + +...+++ .|.+.++..+......................++|||+|||+++|++
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            468999999999999999999  6 8999999 99999887654332222222222233344577899999999999999


Q ss_pred             HHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCCC
Q 009920          121 DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPKE  185 (522)
Q Consensus       121 dL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk~  185 (522)
                      +|+++|++||.|++|+|+++     ++|||||+|.++++|++||+.++ ..|.|++|+|++++++.
T Consensus        89 ~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           89 ELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             HHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             HHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            99999999999999999876     58899999999999999999777 89999999999998864

>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=99.84  E-value=4.3e-21  Score=167.62  Aligned_cols=108  Identities=21%  Similarity=0.437  Sum_probs=74.0

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      ..++|||+|||+++||++|+++|++||+|++|+|++++  .++||||||+|.++++|++||  ++++.|++++|.|+++.
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            46799999999999999999999999999999999986  458999999999999999999  89999999999999988


Q ss_pred             CCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHH
Q 009920           82 PRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESD  121 (522)
Q Consensus        82 ~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteed  121 (522)
                      ++........        .......+|||.|||+++|++.
T Consensus        82 ~~~~~~~~~~--------~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           82 SRKEREAELG--------ARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             CCCC------------------------------------
T ss_pred             Cccccccccc--------cccCCCCceEeCCCCCCccccc
Confidence            7654332111        1123456799999999999874

>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=99.79  E-value=3.4e-19  Score=151.78  Aligned_cols=80  Identities=28%  Similarity=0.502  Sum_probs=76.7

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++||++|+++|++||+|++|+|++++.++++||||||+|.++++|++|+  +++..|++++|.|++|
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~A   96 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA   96 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            45689999999999999999999999999999999999999999999999999999999999  8999999999999998


Q ss_pred             CC
Q 009920           81 VP   82 (522)
Q Consensus        81 ~~   82 (522)
                      +|
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            75

>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=99.78  E-value=9.7e-20  Score=194.26  Aligned_cols=168  Identities=18%  Similarity=0.276  Sum_probs=112.3

Q ss_pred             HHHHHhccCCeEEEEEeec----C-CCCCcccEE--EEEecCHHHHHHHH--HcccccCCeEEEEeecC-CCcccccccc
Q 009920           22 LKEYFSRYGEVVEAVIMRD----R-ATGRARGFG--FVVFADPAVAERVI--MDKHMIDGRTVEAKKAV-PRDDQNMLNR   91 (522)
Q Consensus        22 L~e~F~~~G~V~~v~i~~d----~-~tg~srG~a--FVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~-~k~~~~~~~~   91 (522)
                      |.++|.++++|..|..+..    + .+....+++  |++|.+++++..++  ++..++..+....+... .+........
T Consensus         9 L~~lF~p~pPl~~~~P~~~~p~~~~~~~~~~gia~~~~~f~~~~~~~~~~~~e~~~~~~~~~~~~k~~~~~~~~~~~~~~   88 (437)
T 3pgw_S            9 LLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELKM   88 (437)
T ss_pred             HHHhcCCCCCCcCCCCcccccccccCCCCcccHHHHHHhhcCcccccccccccCHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            7899999999988743322    1 112223333  78887766555444  11111111100000000 0000000000


Q ss_pred             ccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-Cc
Q 009920           92 NTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HE  170 (522)
Q Consensus        92 ~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~  170 (522)
                      ............+.++|||+|||+.||+++|+++|++||.|+.|.|+.++.+++++|||||+|.++++|++||++|+ +.
T Consensus        89 ~~p~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~  168 (437)
T 3pgw_S           89 WDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKK  168 (437)
T ss_pred             cCCcccccccCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCE
Confidence            11111112223467899999999999999999999999999999999999999999999999999999999999888 89


Q ss_pred             cCCeEEEEEEcCCCCCCCC
Q 009920          171 LNGKMVEVKRAVPKEFSPG  189 (522)
Q Consensus       171 l~Gr~I~V~~a~pk~~~~~  189 (522)
                      |+|++|.|+++.++....+
T Consensus       169 i~gr~i~V~~a~~~~~~~~  187 (437)
T 3pgw_S          169 IDGRRVLVDVERGRTVKGW  187 (437)
T ss_pred             ECCEEEEEEEeCCCCCCCC
Confidence            9999999999998765443

>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=99.77  E-value=1.1e-18  Score=148.52  Aligned_cols=80  Identities=20%  Similarity=0.453  Sum_probs=76.7

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      +.++|||+|||+++||++|+++|++||+|++|+|++|+.++++||||||+|.++++|++||+.++ ..|+|++|+|++|+
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            45789999999999999999999999999999999999999999999999999999999999877 89999999999998


Q ss_pred             C
Q 009920          183 P  183 (522)
Q Consensus       183 p  183 (522)
                      |
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            6

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.76  E-value=4.5e-19  Score=148.51  Aligned_cols=82  Identities=22%  Similarity=0.374  Sum_probs=75.7

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccC-CeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--H-cccccCCeEEEEeec
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYG-EVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M-DKHMIDGRTVEAKKA   80 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G-~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~-~~~~i~Gr~I~V~~a   80 (522)
                      +++|||+|||+++||++|+++|++|| +|++|+|++++.|+++||||||+|.++++|++||  + +...|++++|.|+++
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            57899999999999999999999999 8999999999999999999999999999999999  3 456799999999999


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      .++...
T Consensus        81 ~~~~~~   86 (91)
T 2lxi_A           81 DPKPKI   86 (91)
T ss_dssp             CSCCCC
T ss_pred             CCCCCC
Confidence            877544

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.76  E-value=8.2e-18  Score=150.89  Aligned_cols=90  Identities=23%  Similarity=0.518  Sum_probs=83.2

Q ss_pred             CCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEE
Q 009920           99 SPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVE  177 (522)
Q Consensus        99 ~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~  177 (522)
                      .+.....++|||+|||.++|+++|+++|++||+|++|+|++++.+++++|||||+|+++++|++||+.++ ..|.+++|+
T Consensus        36 ~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  115 (139)
T 1u6f_A           36 NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLK  115 (139)
T ss_dssp             SCCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            3445677899999999999999999999999999999999999999999999999999999999999888 899999999


Q ss_pred             EEEcCCCCCCC
Q 009920          178 VKRAVPKEFSP  188 (522)
Q Consensus       178 V~~a~pk~~~~  188 (522)
                      |++++++..++
T Consensus       116 v~~a~~~~~~~  126 (139)
T 1u6f_A          116 VALAASGHQRP  126 (139)
T ss_dssp             EEESSCCCCCC
T ss_pred             EEECCCCCCCC
Confidence            99999876554

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.76  E-value=3.7e-18  Score=156.38  Aligned_cols=85  Identities=18%  Similarity=0.332  Sum_probs=80.1

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+.++|||+|||+++|+++|+++|++||+|++|.|++++.+++++|||||+|+++++|++||+.++ +.|++++|+|++
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            3467899999999999999999999999999999999999999999999999999999999999877 899999999999


Q ss_pred             cCCCCC
Q 009920          181 AVPKEF  186 (522)
Q Consensus       181 a~pk~~  186 (522)
                      ++++..
T Consensus       116 a~~~~~  121 (156)
T 1h2v_Z          116 DAGFKE  121 (156)
T ss_dssp             ESCCCT
T ss_pred             CCCCCC
Confidence            987654

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.76  E-value=1e-18  Score=146.34  Aligned_cols=83  Identities=19%  Similarity=0.368  Sum_probs=77.3

Q ss_pred             cceeEecCCCCCCCHHHHHHHHhhcC-CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC--CccCCeEEEEEEc
Q 009920          105 TKKIFVGGLASTVTESDFKKYFDQFG-TITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF--HELNGKMVEVKRA  181 (522)
Q Consensus       105 ~~~LfVgnLp~~vteedL~~~F~~fG-~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~--~~l~Gr~I~V~~a  181 (522)
                      +++|||+|||+++||+||+++|++|| +|++|+|++|+.++++||||||+|.++++|++||+.+.  ..|+|++|+|+++
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 89999999999999999999999999999999999764  5799999999999


Q ss_pred             CCCCCC
Q 009920          182 VPKEFS  187 (522)
Q Consensus       182 ~pk~~~  187 (522)
                      .|+++.
T Consensus        81 ~~~~~~   86 (91)
T 2lxi_A           81 DPKPKI   86 (91)
T ss_dssp             CSCCCC
T ss_pred             CCCCCC
Confidence            987653

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.75  E-value=2.9e-18  Score=148.86  Aligned_cols=84  Identities=20%  Similarity=0.311  Sum_probs=79.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++||++|+++|++||+|++|+|++++.|+++||||||+|.++++|++||  +|++.|++++|.|+++
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            56789999999999999999999999999999999999999999999999999999999999  8999999999999998


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      ......
T Consensus        84 ~~~~~~   89 (110)
T 3s8s_A           84 IKGQQR   89 (110)
T ss_dssp             STTHHH
T ss_pred             CCCcHH
Confidence            765443

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=9.6e-18  Score=141.69  Aligned_cols=87  Identities=46%  Similarity=0.943  Sum_probs=80.7

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEc
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRA  181 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a  181 (522)
                      ..+.++|||+|||.++++++|+++|++||.|++|.|++++.+++++|||||+|+++++|++||++..+.|++++|+|+++
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            35678999999999999999999999999999999999999999999999999999999999995448999999999999


Q ss_pred             CCCCCCC
Q 009920          182 VPKEFSP  188 (522)
Q Consensus       182 ~pk~~~~  188 (522)
                      +++....
T Consensus        87 ~~~~~~~   93 (99)
T 2dgs_A           87 EPRDSKS   93 (99)
T ss_dssp             CCCCCCC
T ss_pred             CCCcccC
Confidence            9887654

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.7e-17  Score=144.28  Aligned_cols=88  Identities=32%  Similarity=0.556  Sum_probs=81.7

Q ss_pred             CCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEE
Q 009920          100 PGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVK  179 (522)
Q Consensus       100 ~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~  179 (522)
                      ....+.++|||+|||+++|+++|+++|++||+|++|+|++++.+++++|||||+|+++++|++||+.++..|++++|+|+
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~   91 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVN   91 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCCcCCCEEEEEE
Confidence            34457789999999999999999999999999999999999999999999999999999999999999989999999999


Q ss_pred             EcCCCCCC
Q 009920          180 RAVPKEFS  187 (522)
Q Consensus       180 ~a~pk~~~  187 (522)
                      ++.++...
T Consensus        92 ~a~~~~~~   99 (116)
T 2cqd_A           92 LAYLGAKP   99 (116)
T ss_dssp             ESTTTCCC
T ss_pred             EcccCCCc
Confidence            99876543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=6.9e-18  Score=142.59  Aligned_cols=85  Identities=41%  Similarity=0.777  Sum_probs=80.1

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeec
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a   80 (522)
                      +.+.++|||+|||+++++++|+++|++||+|++|+|++++.++++++||||+|.++++|++|| ++++.|++++|.|+++
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            357899999999999999999999999999999999999999999999999999999999999 8999999999999999


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      .++...
T Consensus        87 ~~~~~~   92 (99)
T 2dgs_A           87 EPRDSK   92 (99)
T ss_dssp             CCCCCC
T ss_pred             CCCccc
Confidence            876554

>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=99.74  E-value=1.1e-17  Score=145.31  Aligned_cols=87  Identities=21%  Similarity=0.363  Sum_probs=81.2

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+.++|||+|||+++++++|+++|++||.|++|+|++++.+++++|||||+|.++++|++||+.++ .+|++++|+|++
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            3466899999999999999999999999999999999999999999999999999999999998877 899999999999


Q ss_pred             cCCCCCCC
Q 009920          181 AVPKEFSP  188 (522)
Q Consensus       181 a~pk~~~~  188 (522)
                      ++++...+
T Consensus       102 a~~~~~~~  109 (115)
T 2cpz_A          102 KRSKNDSK  109 (115)
T ss_dssp             CCCSCCCC
T ss_pred             cCCCCcCC
Confidence            99887644

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.74  E-value=2e-18  Score=155.24  Aligned_cols=123  Identities=16%  Similarity=0.242  Sum_probs=82.0

Q ss_pred             EEEEEecCHHHHHHHH--HcccccCCeEEEEeecCCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHH
Q 009920           49 FGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYF  126 (522)
Q Consensus        49 ~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F  126 (522)
                      ++|+++++...+.+|+  ++.....++.. +..                ....+...+.++|||+|||+++|+++|+++|
T Consensus         6 ~~~~~~~~~~~~~~a~~~~~g~~~~g~~~-~~~----------------~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F   68 (135)
T 2lea_A            6 HHHHHSSGLVPRGSHMASMTGGQQMGRGS-MSY----------------GRPPPDVEGMTSLKVDNLTYRTSPDTLRRVF   68 (135)
T ss_dssp             ------------------------------CCS----------------CCSCSSGGGCCCEEEECCCSSCHHHHHHHHH
T ss_pred             cccccccCCCchhhhhhhccCCCCCCCCC-CCc----------------CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            5667777777777777  44443333221 111                1112233467899999999999999999999


Q ss_pred             hhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCCCCCC
Q 009920          127 DQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPKEFSP  188 (522)
Q Consensus       127 ~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk~~~~  188 (522)
                      ++||+|++|+|+.++.+++++|||||+|.++++|++||+.++ ..|++++|+|++++++...+
T Consensus        69 ~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~~~  131 (135)
T 2lea_A           69 EKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPD  131 (135)
T ss_dssp             GGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCCCT
T ss_pred             HhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCCc
Confidence            999999999999999999999999999999999999999877 89999999999999866543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=1.1e-17  Score=140.06  Aligned_cols=85  Identities=31%  Similarity=0.578  Sum_probs=80.1

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      .+.++|||+|||.++|+++|+++|++||+|++|+|++++.+++++|||||+|+++++|++||+.++ ..|++++|+|+++
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            467899999999999999999999999999999999999999999999999999999999999877 8999999999999


Q ss_pred             CCCCCC
Q 009920          182 VPKEFS  187 (522)
Q Consensus       182 ~pk~~~  187 (522)
                      +++...
T Consensus        83 ~~~~~~   88 (95)
T 2dnz_A           83 TERLDG   88 (95)
T ss_dssp             SCCCCC
T ss_pred             ccccCC
Confidence            987653

>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=99.74  E-value=1.2e-17  Score=142.54  Aligned_cols=88  Identities=26%  Similarity=0.403  Sum_probs=82.1

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      ...+.++|||+|||+++|+++|+++|++||+|++|.|++++.+++++|||||+|.++++|++||+.++ ..|++++|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   90 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   90 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            44577899999999999999999999999999999999999999999999999999999999999888 89999999999


Q ss_pred             EcCCCCCCC
Q 009920          180 RAVPKEFSP  188 (522)
Q Consensus       180 ~a~pk~~~~  188 (522)
                      +++++....
T Consensus        91 ~a~~~~~~~   99 (105)
T 1x5u_A           91 KASAHNKNL   99 (105)
T ss_dssp             ETTTTSCCC
T ss_pred             ECCCCCcCC
Confidence            999877543

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.74  E-value=6.5e-18  Score=156.55  Aligned_cols=137  Identities=13%  Similarity=0.216  Sum_probs=79.9

Q ss_pred             EEecCHHHHHHHH--HcccccC--CeEEEEeecCCCcccc--ccc--cccCCCCCCCCCCCcceeEecCCCCCCCHHHHH
Q 009920           52 VVFADPAVAERVI--MDKHMID--GRTVEAKKAVPRDDQN--MLN--RNTSSIHSSPGPGRTKKIFVGGLASTVTESDFK  123 (522)
Q Consensus        52 VeF~~~e~A~kAl--~~~~~i~--Gr~I~V~~a~~k~~~~--~~~--~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~  123 (522)
                      .+|.+.++|+.++  ++.....  ++.+....+.......  ...  .............+.++|||+|||+.+|+++|+
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            6789999999988  4444333  4544444322111000  000  000011122234567899999999999999999


Q ss_pred             HHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCCCCCC
Q 009920          124 KYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPKEFSP  188 (522)
Q Consensus       124 ~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk~~~~  188 (522)
                      ++|++||+|+.|.|+.++.+++++|||||+|.+.++|++||+.++ ..|.|++|.|.++.++...+
T Consensus        91 ~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~~  156 (165)
T 1rk8_A           91 EKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKR  156 (165)
T ss_dssp             HHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC---
T ss_pred             HHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCCCC
Confidence            999999999999999999999999999999999999999999877 89999999999999876544

>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=99.74  E-value=8e-18  Score=142.03  Aligned_cols=85  Identities=29%  Similarity=0.530  Sum_probs=80.1

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      ..+.++|||+|||+++|+++|+++|++||+|++|+|++++.++++++||||+|.++++|++||  ++++.|++++|.|++
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            357899999999999999999999999999999999999989999999999999999999999  899999999999999


Q ss_pred             cCCCccc
Q 009920           80 AVPRDDQ   86 (522)
Q Consensus        80 a~~k~~~   86 (522)
                      +.++...
T Consensus        85 a~~~~~~   91 (99)
T 1whw_A           85 STIKKEA   91 (99)
T ss_dssp             CCCCSTT
T ss_pred             cCCCccc
Confidence            9887654

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.74  E-value=8.7e-18  Score=145.87  Aligned_cols=83  Identities=13%  Similarity=0.299  Sum_probs=78.5

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      .+.++|||+|||++++|++|+++|++||+|++|+|++|+.|+++||||||+|+++++|++||+.++ .+|+|++|+|+++
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            457899999999999999999999999999999999999999999999999999999999999888 8999999999999


Q ss_pred             CCCC
Q 009920          182 VPKE  185 (522)
Q Consensus       182 ~pk~  185 (522)
                      ..++
T Consensus        84 ~~~~   87 (110)
T 3s8s_A           84 IKGQ   87 (110)
T ss_dssp             STTH
T ss_pred             CCCc
Confidence            7554

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.74  E-value=1.6e-17  Score=144.12  Aligned_cols=85  Identities=29%  Similarity=0.539  Sum_probs=80.0

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++|+++|+++|++||+|++|+|++++.++++++||||+|.++++|++||  ++++.|++++|.|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (115)
T 2dgo_A           13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   92 (115)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            57899999999999999999999999999999999999989999999999999999999999  7999999999999999


Q ss_pred             CCCcccc
Q 009920           81 VPRDDQN   87 (522)
Q Consensus        81 ~~k~~~~   87 (522)
                      .++....
T Consensus        93 ~~~~~~~   99 (115)
T 2dgo_A           93 TRKPPAP   99 (115)
T ss_dssp             SCCCCCS
T ss_pred             cCCCCCC
Confidence            8776543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=7.8e-18  Score=143.30  Aligned_cols=88  Identities=19%  Similarity=0.355  Sum_probs=81.5

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      ...+.++|||+|||+++++++|+++|++||.|++|.|+.++.+++++|||||+|.++++|++||+.++ +.|++++|+|+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999877 89999999999


Q ss_pred             EcCCCCCCC
Q 009920          180 RAVPKEFSP  188 (522)
Q Consensus       180 ~a~pk~~~~  188 (522)
                      +++++....
T Consensus        89 ~a~~~~~~~   97 (103)
T 2dnm_A           89 VARYGRRDL   97 (103)
T ss_dssp             ECSSCCSCC
T ss_pred             ECCcCCCCC
Confidence            999776543

>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=99.74  E-value=1.5e-17  Score=140.32  Aligned_cols=86  Identities=24%  Similarity=0.463  Sum_probs=80.8

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+.++|||+|||+++|+++|+++|++||+|++|.|++++.+++++|||||+|.++++|++||+.++ +.|++++|+|++
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            3567899999999999999999999999999999999999999999999999999999999998888 899999999999


Q ss_pred             cCCCCCC
Q 009920          181 AVPKEFS  187 (522)
Q Consensus       181 a~pk~~~  187 (522)
                      ++++...
T Consensus        85 a~~~~~~   91 (99)
T 1whw_A           85 STIKKEA   91 (99)
T ss_dssp             CCCCSTT
T ss_pred             cCCCccc
Confidence            9988654

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.3e-17  Score=141.85  Aligned_cols=87  Identities=24%  Similarity=0.437  Sum_probs=81.6

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      ...+.++|||+|||.++++++|+++|++||+|++|.|++++.+++++|||||+|.++++|++||+.++ +.|++++|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            34578999999999999999999999999999999999999999999999999999999999999888 89999999999


Q ss_pred             EcCCCCCC
Q 009920          180 RAVPKEFS  187 (522)
Q Consensus       180 ~a~pk~~~  187 (522)
                      +++++...
T Consensus        91 ~a~~~~~~   98 (103)
T 2cq0_A           91 WAKPSTNS   98 (103)
T ss_dssp             ESSCCCCS
T ss_pred             ECCCCCCC
Confidence            99987654

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=4.8e-18  Score=144.18  Aligned_cols=86  Identities=44%  Similarity=0.828  Sum_probs=80.7

Q ss_pred             CCCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEe
Q 009920            1 MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAK   78 (522)
Q Consensus         1 me~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~   78 (522)
                      |..+.++|||+|||+++||++|+++|++||+|++|+|++++.++++++||||+|.++++|++||  ++++.|++++|.|+
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            4578899999999999999999999999999999999999999999999999999999999999  89999999999999


Q ss_pred             ecCCCccc
Q 009920           79 KAVPRDDQ   86 (522)
Q Consensus        79 ~a~~k~~~   86 (522)
                      ++.++...
T Consensus        88 ~a~~~~~~   95 (102)
T 1x5s_A           88 QAGKSSDN   95 (102)
T ss_dssp             EEECCCCC
T ss_pred             ECCCCCCC
Confidence            99876543

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.1e-17  Score=141.96  Aligned_cols=87  Identities=30%  Similarity=0.593  Sum_probs=81.3

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+.++|||+|||+++|+++|+++|++||+|++|+|++++.+++++|||||+|.++++|++||+.++ ..|++++|+|++
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 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3567899999999999999999999999999999999999999999999999999999999998877 899999999999


Q ss_pred             cCCCCCCC
Q 009920          181 AVPKEFSP  188 (522)
Q Consensus       181 a~pk~~~~  188 (522)
                      ++++...+
T Consensus        89 a~~~~~~~   96 (102)
T 1x5s_A           89 AGKSSDNR   96 (102)
T ss_dssp             EECCCCCC
T ss_pred             CCCCCCCC
Confidence            99877644

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=8.9e-18  Score=142.53  Aligned_cols=88  Identities=28%  Similarity=0.523  Sum_probs=81.8

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+.++|||+|||.++|+++|+++|++||+|++|.|++++.+++++|||||+|.++++|++||+.++ ..|++++|+|++
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            3467899999999999999999999999999999999999999999999999999999999998877 899999999999


Q ss_pred             cCCCCCCCC
Q 009920          181 AVPKEFSPG  189 (522)
Q Consensus       181 a~pk~~~~~  189 (522)
                      ++++..++.
T Consensus        89 a~~~~~~~~   97 (102)
T 2cqb_A           89 AKPMRIKES   97 (102)
T ss_dssp             CCCCCCCCC
T ss_pred             CCCCCCCCC
Confidence            998876543

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.4e-17  Score=141.63  Aligned_cols=85  Identities=38%  Similarity=0.721  Sum_probs=79.6

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHHHcccccCCeEEEEeecCC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl~~~~~i~Gr~I~V~~a~~   82 (522)
                      .+.++|||+|||+++++++|+++|++||+|++|+|++++.+++++|||||+|.++++|++||.+.+.|++++|.|+++.+
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~l~v~~a~~   92 (103)
T 2cqg_A           13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNS   92 (103)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCEEETTEEEEEECCCT
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHcCCeeCCeEEEEEecCC
Confidence            56789999999999999999999999999999999999999999999999999999999999778899999999999988


Q ss_pred             Ccccc
Q 009920           83 RDDQN   87 (522)
Q Consensus        83 k~~~~   87 (522)
                      +.+..
T Consensus        93 ~~~~~   97 (103)
T 2cqg_A           93 KQSQD   97 (103)
T ss_dssp             TCCCC
T ss_pred             CCcCC
Confidence            76543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=5.1e-18  Score=144.06  Aligned_cols=87  Identities=29%  Similarity=0.477  Sum_probs=81.2

Q ss_pred             CCCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEe
Q 009920            1 MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAK   78 (522)
Q Consensus         1 me~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~   78 (522)
                      |..+.++|||+|||+++|+++|+++|++||+|++|+|++++.++++++||||+|.++++|++||  ++++.|++++|.|+
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            4567899999999999999999999999999999999999999999999999999999999999  89999999999999


Q ss_pred             ecCCCcccc
Q 009920           79 KAVPRDDQN   87 (522)
Q Consensus        79 ~a~~k~~~~   87 (522)
                      ++.++....
T Consensus        88 ~a~~~~~~~   96 (102)
T 2cqb_A           88 LAKPMRIKE   96 (102)
T ss_dssp             ECCCCCCCC
T ss_pred             eCCCCCCCC
Confidence            998765443

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.73  E-value=3e-18  Score=145.12  Aligned_cols=81  Identities=22%  Similarity=0.400  Sum_probs=74.2

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCC--eEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hccc----ccCCe
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGE--VVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKH----MIDGR   73 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~--V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~----~i~Gr   73 (522)
                      +....+|||+|||+++||++|+++|++||+  |.+|+|++|+.|+++||||||+|.++++|++||  +++.    .|+||
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr   85 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGK   85 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTE
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCE
Confidence            356789999999999999999999999995  679999999999999999999999999999999  6665    58999


Q ss_pred             EEEEeecCC
Q 009920           74 TVEAKKAVP   82 (522)
Q Consensus        74 ~I~V~~a~~   82 (522)
                      +|.|++|+.
T Consensus        86 ~i~V~~Aks   94 (95)
T 2lkz_A           86 TIGVDFAKS   94 (95)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEEccC
Confidence            999999864

>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=99.73  E-value=1.1e-17  Score=137.84  Aligned_cols=79  Identities=52%  Similarity=1.040  Sum_probs=75.1

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeec
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a   80 (522)
                      +.+.++|||+|||+++++++|+++|++||+|++|+|++++.+++++|||||+|.++++|++|+ ++++.|++++|.|++|
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            467899999999999999999999999999999999999999999999999999999999999 7788899999999875

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=1.4e-17  Score=139.42  Aligned_cols=84  Identities=29%  Similarity=0.652  Sum_probs=79.4

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++|+++|+++|++||+|++|+|++++.++++++||||+|.++++|++|+  ++++.|++++|.|+++
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            56899999999999999999999999999999999999999999999999999999999999  8999999999999999


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      .++...
T Consensus        83 ~~~~~~   88 (95)
T 2dnz_A           83 TERLDG   88 (95)
T ss_dssp             SCCCCC
T ss_pred             ccccCC
Confidence            876543

>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=99.73  E-value=1.2e-17  Score=137.29  Aligned_cols=81  Identities=27%  Similarity=0.530  Sum_probs=75.0

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++++++|+++|++||+|.+|+|++++.++++++||||+|.++++|++|+  ++++.|++++|.|+++
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            46789999999999999999999999999999999999989999999999999999999999  8999999999999998


Q ss_pred             CCC
Q 009920           81 VPR   83 (522)
Q Consensus        81 ~~k   83 (522)
                      .++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            765

>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=99.73  E-value=1.1e-17  Score=136.98  Aligned_cols=81  Identities=30%  Similarity=0.495  Sum_probs=77.2

Q ss_pred             CCCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEe
Q 009920            1 MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAK   78 (522)
Q Consensus         1 me~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~   78 (522)
                      ++.+.++|||+|||+++++++|+++|++||+|++|+|++++.++++++||||+|.++++|++|+  ++++.|++++|.|+
T Consensus         3 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   82 (85)
T 3mdf_A            3 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   82 (85)
T ss_dssp             CCCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            4678899999999999999999999999999999999999889999999999999999999999  89999999999999


Q ss_pred             ecC
Q 009920           79 KAV   81 (522)
Q Consensus        79 ~a~   81 (522)
                      +++
T Consensus        83 ~ak   85 (85)
T 3mdf_A           83 LAK   85 (85)
T ss_dssp             ECC
T ss_pred             EcC
Confidence            874

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.3e-17  Score=139.71  Aligned_cols=86  Identities=26%  Similarity=0.424  Sum_probs=80.3

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEE-EEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDV-VVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v-~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      .+.++|||+|||.++|+++|+++|++||.|++| +|++++.+++++|||||+|+++++|++||+.++ ..|++++|+|++
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            357899999999999999999999999999999 999999999999999999999999999999877 899999999999


Q ss_pred             cCCCCCCC
Q 009920          181 AVPKEFSP  188 (522)
Q Consensus       181 a~pk~~~~  188 (522)
                      +.++....
T Consensus        83 a~~~~~~~   90 (96)
T 1x5t_A           83 AFKKDSKG   90 (96)
T ss_dssp             SCCCCCCC
T ss_pred             ecccCCCC
Confidence            99876543

>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=99.73  E-value=9.8e-18  Score=145.65  Aligned_cols=84  Identities=25%  Similarity=0.466  Sum_probs=79.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++++++|+++|++||+|++|+|++++.++++++||||+|.++++|++||  ++++.|++++|.|+++
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  102 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK  102 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            46789999999999999999999999999999999999989999999999999999999999  8999999999999999


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      .++...
T Consensus       103 ~~~~~~  108 (115)
T 2cpz_A          103 RSKNDS  108 (115)
T ss_dssp             CCSCCC
T ss_pred             CCCCcC
Confidence            877553

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.73  E-value=3.7e-17  Score=141.88  Aligned_cols=88  Identities=26%  Similarity=0.491  Sum_probs=82.0

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      ...+.++|||+|||+++|+++|+++|++||.|++|+|++++.+++++|||||+|.++++|++||+.++ +.|++++|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34577899999999999999999999999999999999999999999999999999999999999887 89999999999


Q ss_pred             EcCCCCCCC
Q 009920          180 RAVPKEFSP  188 (522)
Q Consensus       180 ~a~pk~~~~  188 (522)
                      +++++...+
T Consensus        91 ~a~~~~~~~   99 (115)
T 2dgo_A           91 WATRKPPAP   99 (115)
T ss_dssp             ESSCCCCCS
T ss_pred             EccCCCCCC
Confidence            999876544

>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=99.73  E-value=1.7e-17  Score=135.20  Aligned_cols=80  Identities=28%  Similarity=0.530  Sum_probs=76.3

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCC
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~   82 (522)
                      +.+|||+|||+++++++|+++|++||+|.+|+|++++.++++++||||+|.++++|++|+  ++++.|++++|.|+++.+
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            468999999999999999999999999999999999989999999999999999999999  899999999999999987


Q ss_pred             Cc
Q 009920           83 RD   84 (522)
Q Consensus        83 k~   84 (522)
                      ++
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.73  E-value=4.2e-18  Score=140.64  Aligned_cols=83  Identities=23%  Similarity=0.550  Sum_probs=78.4

Q ss_pred             CCCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEee
Q 009920            1 MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKK   79 (522)
Q Consensus         1 me~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~   79 (522)
                      ||.+.++|||+|||+++|+++|+++|++||+|.+|+|++++.++++++||||+|.++++|++|+ ++++.|++++|.|++
T Consensus         2 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l~V~~   81 (89)
T 3ucg_A            2 MEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIP   81 (89)
T ss_dssp             HHHHHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEE
T ss_pred             CCCcCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEE
Confidence            3567899999999999999999999999999999999999989999999999999999999999 999999999999999


Q ss_pred             cCCC
Q 009920           80 AVPR   83 (522)
Q Consensus        80 a~~k   83 (522)
                      +.+.
T Consensus        82 a~~~   85 (89)
T 3ucg_A           82 KRTN   85 (89)
T ss_dssp             TTTT
T ss_pred             ccCC
Confidence            8754

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.4e-17  Score=142.15  Aligned_cols=88  Identities=35%  Similarity=0.744  Sum_probs=81.7

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR  180 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~  180 (522)
                      ...+.++|||+|||+++++++|+++|++||+|++|.|++++.+++++|||||+|+++++|++||+...+.|++++|+|++
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKP   91 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEEE
Confidence            34577899999999999999999999999999999999999999999999999999999999999944899999999999


Q ss_pred             cCCCCCCC
Q 009920          181 AVPKEFSP  188 (522)
Q Consensus       181 a~pk~~~~  188 (522)
                      +.++...+
T Consensus        92 a~~~~~~~   99 (105)
T 2dh8_A           92 CTPRGMQP   99 (105)
T ss_dssp             SCCSSCCT
T ss_pred             ccCCCCCC
Confidence            99887654

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=4.7e-17  Score=138.45  Aligned_cols=88  Identities=30%  Similarity=0.496  Sum_probs=80.8

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR  180 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~  180 (522)
                      ...+.++|||+|||+++++++|+++|++||+|++|.|+.++.+++++|||||+|.++++|++||+. .+.|+|++|+|++
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 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ-RHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS-CEEETTEEEEEEC
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc-CCeeCCeEEEEEe
Confidence            345678999999999999999999999999999999999999999999999999999999999984 5789999999999


Q ss_pred             cCCCCCCCC
Q 009920          181 AVPKEFSPG  189 (522)
Q Consensus       181 a~pk~~~~~  189 (522)
                      +.++.....
T Consensus        90 a~~~~~~~~   98 (103)
T 2cqg_A           90 PNSKQSQDS   98 (103)
T ss_dssp             CCTTCCCCC
T ss_pred             cCCCCcCCC
Confidence            998876543

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.72  E-value=1e-17  Score=142.03  Aligned_cols=98  Identities=27%  Similarity=0.446  Sum_probs=83.0

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCCC
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVPR   83 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~k   83 (522)
                      ++|||+|||+++|+++|+++|++||+|++|+|+++     +++||||+|.++++|++|+  ++++.|++++|.|+++.++
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            58999999999999999999999999999999886     6899999999999999999  7999999999999999887


Q ss_pred             ccccccccccCCCCCCCCCCCcceeEecCCC
Q 009920           84 DDQNMLNRNTSSIHSSPGPGRTKKIFVGGLA  114 (522)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp  114 (522)
                      ..........      .......+|||++|+
T Consensus        76 ~~~~~~~~~~------~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           76 PRRSRFDRPP------ARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CCSSCCCSCC------CSCCCCSCCCSCCCC
T ss_pred             CCcccCCCCC------ccccCCCceecCCCC
Confidence            6443222111      122446789999997

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=3.6e-17  Score=138.40  Aligned_cols=84  Identities=17%  Similarity=0.414  Sum_probs=78.8

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+.++|||+|||.++|+++|+++|++||+|++|.|+.++ +++++|||||+|.++++|++||+.++ ..|++++|+|++
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            3567899999999999999999999999999999999998 89999999999999999999998877 899999999999


Q ss_pred             cCCCCC
Q 009920          181 AVPKEF  186 (522)
Q Consensus       181 a~pk~~  186 (522)
                      ++++..
T Consensus        93 a~~~~~   98 (100)
T 2do4_A           93 SNSGPS   98 (100)
T ss_dssp             CCCCSC
T ss_pred             CCCCCC
Confidence            998764

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.2e-17  Score=142.02  Aligned_cols=84  Identities=26%  Similarity=0.457  Sum_probs=79.3

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++++++|+++|++||+|++|+|++++.++++++||||+|.++++|++||  ++++.|++++|.|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   92 (103)
T 2cq0_A           13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   92 (103)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEC
Confidence            56899999999999999999999999999999999999989999999999999999999999  8999999999999999


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      .++...
T Consensus        93 ~~~~~~   98 (103)
T 2cq0_A           93 KPSTNS   98 (103)
T ss_dssp             SCCCCS
T ss_pred             CCCCCC
Confidence            876543

>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=99.72  E-value=2.3e-17  Score=134.37  Aligned_cols=81  Identities=27%  Similarity=0.547  Sum_probs=77.3

Q ss_pred             cceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCC
Q 009920          105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVP  183 (522)
Q Consensus       105 ~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~p  183 (522)
                      +.+|||+|||+++++++|+++|++||+|+++.|+.++.+++++|||||+|.++++|++|++.++ ..|+|++|+|+++++
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            3689999999999999999999999999999999999999999999999999999999999877 899999999999998


Q ss_pred             CC
Q 009920          184 KE  185 (522)
Q Consensus       184 k~  185 (522)
                      ++
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=2.7e-17  Score=140.63  Aligned_cols=88  Identities=19%  Similarity=0.370  Sum_probs=81.4

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEec-CCCCCcceEEEEEecCHHHHHHHHHhc-C-CccCCeEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYD-HNTQRPRGFGFITYDSEEAVDRVLHKT-F-HELNGKMVE  177 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d-~~tg~~rG~aFVeF~s~e~A~~Al~~~-~-~~l~Gr~I~  177 (522)
                      .....++|||+|||+++|+++|+++|++||+|++|.|+++ +.+++++|||||+|.++++|++||+.+ + ..|.+++|+
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            3456789999999999999999999999999999999999 788999999999999999999999998 6 899999999


Q ss_pred             EEEcCCCCCCC
Q 009920          178 VKRAVPKEFSP  188 (522)
Q Consensus       178 V~~a~pk~~~~  188 (522)
                      |++++++....
T Consensus        91 v~~a~~~~~~~  101 (107)
T 2cph_A           91 LEWADSEVTVQ  101 (107)
T ss_dssp             EEECCCCCCCC
T ss_pred             EEeCCCCCCCC
Confidence            99999876543

>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=99.72  E-value=2e-17  Score=135.96  Aligned_cols=82  Identities=26%  Similarity=0.500  Sum_probs=75.7

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      .+.++|||+|||.++++++|+++|++||.|++|.|+.++.+++++|||||+|.++++|++|++.++ ..|+|++|+|+++
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            356899999999999999999999999999999999999999999999999999999999999877 8999999999999


Q ss_pred             CCC
Q 009920          182 VPK  184 (522)
Q Consensus       182 ~pk  184 (522)
                      +++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            876

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=9.4e-18  Score=143.27  Aligned_cols=85  Identities=48%  Similarity=0.984  Sum_probs=79.9

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeec
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a   80 (522)
                      +.+.++|||+|||+++++++|+++|++||+|++|+|++++.++++++||||+|.++++|++|| .+.+.|++++|.|+++
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            357899999999999999999999999999999999999999999999999999999999999 7889999999999999


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      .++...
T Consensus        93 ~~~~~~   98 (105)
T 2dh8_A           93 TPRGMQ   98 (105)
T ss_dssp             CCSSCC
T ss_pred             cCCCCC
Confidence            877654

>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=99.72  E-value=2.5e-17  Score=140.71  Aligned_cols=88  Identities=24%  Similarity=0.399  Sum_probs=80.7

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-Ccc---CCeEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HEL---NGKMV  176 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l---~Gr~I  176 (522)
                      ...+.++|||+|||.++|+++|+++|++||+|++|+|+.++.+++++|||||+|.++++|++||+.++ ..+   .+++|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            34567899999999999999999999999999999999999999999999999999999999999887 676   88999


Q ss_pred             EEEEcCCCCCCC
Q 009920          177 EVKRAVPKEFSP  188 (522)
Q Consensus       177 ~V~~a~pk~~~~  188 (522)
                      +|+++.++....
T Consensus        89 ~v~~a~~~~~~~  100 (106)
T 2dgp_A           89 QVKPADSESRGG  100 (106)
T ss_dssp             EEEECCCCSCCC
T ss_pred             EEEECCcccccC
Confidence            999999876543

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=2.5e-17  Score=138.75  Aligned_cols=86  Identities=23%  Similarity=0.434  Sum_probs=79.5

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCC---CCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHN---TQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEV  178 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~---tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V  178 (522)
                      .+.++|||+|||+++|+++|+++|++||+|++|.|+.++.   |++++|||||+|.++++|++||+.++ +.|++++|+|
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            3578999999999999999999999999999999999887   66899999999999999999999887 8999999999


Q ss_pred             EEcCCCCCCC
Q 009920          179 KRAVPKEFSP  188 (522)
Q Consensus       179 ~~a~pk~~~~  188 (522)
                      ++++++...+
T Consensus        83 ~~a~~~~~~~   92 (98)
T 2cpf_A           83 RISERATKPA   92 (98)
T ss_dssp             ECSSCSSCCC
T ss_pred             EEccCCCCCC
Confidence            9999876543

>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=99.72  E-value=1.6e-17  Score=141.64  Aligned_cols=84  Identities=30%  Similarity=0.519  Sum_probs=79.3

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++|+++|+++|++||+|++|+|++++.+++++|||||+|.++++|++||  ++.+.|++++|.|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   92 (105)
T 1x5u_A           13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   92 (105)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            56799999999999999999999999999999999999989999999999999999999999  7999999999999999


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      .++...
T Consensus        93 ~~~~~~   98 (105)
T 1x5u_A           93 SAHNKN   98 (105)
T ss_dssp             TTTSCC
T ss_pred             CCCCcC
Confidence            876554

>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=99.72  E-value=2e-17  Score=142.37  Aligned_cols=85  Identities=25%  Similarity=0.483  Sum_probs=79.4

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hc------ccccCCeE
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MD------KHMIDGRT   74 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~------~~~i~Gr~   74 (522)
                      .+.++|||+|||+++|+++|+++|++||+|++|+|++++.++++++||||+|.++++|++||  ++      .+.|++++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~   92 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   92 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEE
Confidence            46789999999999999999999999999999999999999999999999999999999999  77      89999999


Q ss_pred             EEEeecCCCcccc
Q 009920           75 VEAKKAVPRDDQN   87 (522)
Q Consensus        75 I~V~~a~~k~~~~   87 (522)
                      |.|+++.++....
T Consensus        93 l~v~~a~~~~~~~  105 (111)
T 1x4h_A           93 LKVDLAVTRDEAA  105 (111)
T ss_dssp             EEEECCCCCCCCC
T ss_pred             EEEEECCCCccCC
Confidence            9999998775543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.72  E-value=2.4e-17  Score=139.49  Aligned_cols=82  Identities=22%  Similarity=0.446  Sum_probs=77.3

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++|+++|+++|++||+|++|+|++++ ++++++||||+|.++++|++|+  ++++.|++++|.|+++
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   93 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS   93 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            467899999999999999999999999999999999998 8999999999999999999999  8999999999999999


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      .++..
T Consensus        94 ~~~~~   98 (100)
T 2do4_A           94 NSGPS   98 (100)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            87653

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.72  E-value=4.1e-17  Score=138.91  Aligned_cols=85  Identities=19%  Similarity=0.351  Sum_probs=78.4

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+.++|||+|||+++++++|+++|++|+ |++|.|++++.+++++|||||+|+++++|++|| .++ ..|++++|+|++
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 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDI   89 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEE
Confidence            35678999999999999999999999996 999999999999999999999999999999999 666 899999999999


Q ss_pred             cCCCCCCC
Q 009920          181 AVPKEFSP  188 (522)
Q Consensus       181 a~pk~~~~  188 (522)
                      +.++....
T Consensus        90 a~~~~~~~   97 (103)
T 2dng_A           90 AEGRKQDK   97 (103)
T ss_dssp             CCCCCCCC
T ss_pred             ecCCCCCC
Confidence            99876543

>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=99.72  E-value=2.5e-17  Score=135.66  Aligned_cols=80  Identities=39%  Similarity=0.780  Sum_probs=76.1

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEc
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRA  181 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a  181 (522)
                      ..+.++|||+|||+++++++|+++|++||.|++|+|+.++.+++++|||||+|.++++|++||+++++.|+|++|+|++|
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            35678999999999999999999999999999999999999999999999999999999999988778999999999986

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=3.8e-17  Score=142.14  Aligned_cols=85  Identities=38%  Similarity=0.764  Sum_probs=78.0

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      +.+.++|||+|||+++||++|+++|++||+|++|+|++++.++++++||||+|.++++|++||  ++. .|++++|.|++
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~   92 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   92 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEE
Confidence            457899999999999999999999999999999999999999999999999999999999999  565 89999999999


Q ss_pred             cCCCcccc
Q 009920           80 AVPRDDQN   87 (522)
Q Consensus        80 a~~k~~~~   87 (522)
                      +.++....
T Consensus        93 a~~~~~~~  100 (116)
T 2cqd_A           93 AYLGAKPR  100 (116)
T ss_dssp             STTTCCCC
T ss_pred             cccCCCcc
Confidence            97664443

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=3.6e-17  Score=139.14  Aligned_cols=87  Identities=26%  Similarity=0.418  Sum_probs=80.0

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      ...+.++|||+|||+++|+++|+++|++||.|++|+|+.+  ++++++||||+|.++++|++||+.++ ..|++++|+|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVA   88 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            3457889999999999999999999999999999999998  78999999999999999999999877 89999999999


Q ss_pred             EcCCCCCCCC
Q 009920          180 RAVPKEFSPG  189 (522)
Q Consensus       180 ~a~pk~~~~~  189 (522)
                      +++++..++.
T Consensus        89 ~a~~~~~~~~   98 (103)
T 2d9p_A           89 LAQRKEERQS   98 (103)
T ss_dssp             ECSSCCCCCC
T ss_pred             EecccccCCC
Confidence            9998876543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.3e-17  Score=139.81  Aligned_cols=84  Identities=30%  Similarity=0.561  Sum_probs=79.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEE-EEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEA-VIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v-~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      .+.++|||+|||+++|+++|+++|++||+|++| +|++++.++++++||||+|.++++|++|+  ++++.|++++|.|++
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            578999999999999999999999999999999 99999889999999999999999999999  899999999999999


Q ss_pred             cCCCccc
Q 009920           80 AVPRDDQ   86 (522)
Q Consensus        80 a~~k~~~   86 (522)
                      +.++...
T Consensus        83 a~~~~~~   89 (96)
T 1x5t_A           83 AFKKDSK   89 (96)
T ss_dssp             SCCCCCC
T ss_pred             ecccCCC
Confidence            9876543

>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=99.72  E-value=3.8e-17  Score=140.61  Aligned_cols=88  Identities=23%  Similarity=0.413  Sum_probs=81.3

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-------CccCC
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-------HELNG  173 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-------~~l~G  173 (522)
                      ...+.++|||+|||+++|+++|+++|++||+|++|+|++|+.+++++|||||+|.++++|++||+.++       ..|+|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            34567899999999999999999999999999999999999999999999999999999999999874       68999


Q ss_pred             eEEEEEEcCCCCCCC
Q 009920          174 KMVEVKRAVPKEFSP  188 (522)
Q Consensus       174 r~I~V~~a~pk~~~~  188 (522)
                      ++|+|+++.++....
T Consensus        91 ~~l~v~~a~~~~~~~  105 (111)
T 1x4h_A           91 RQLKVDLAVTRDEAA  105 (111)
T ss_dssp             CEEEEECCCCCCCCC
T ss_pred             EEEEEEECCCCccCC
Confidence            999999999886654

>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=99.72  E-value=3e-17  Score=139.98  Aligned_cols=84  Identities=23%  Similarity=0.385  Sum_probs=78.1

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCC-CCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNT-QRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~t-g~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      .+.++|||+|||+++|+++|+++|++|| |++|.|++++.+ ++++|||||+|.++++|++|| .++ ..|++++|+|++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEE
Confidence            4678999999999999999999999999 999999999988 899999999999999999999 665 899999999999


Q ss_pred             cCCCCCCC
Q 009920          181 AVPKEFSP  188 (522)
Q Consensus       181 a~pk~~~~  188 (522)
                      ++++....
T Consensus        91 a~~~~~~~   98 (104)
T 1wi8_A           91 ADQAQDKD   98 (104)
T ss_dssp             CCCCCCCC
T ss_pred             ccCCCCCC
Confidence            99887644

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.71  E-value=9.6e-18  Score=141.98  Aligned_cols=82  Identities=18%  Similarity=0.353  Sum_probs=75.4

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCC--eeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-C----ccCCe
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGT--ITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-H----ELNGK  174 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~--I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~----~l~Gr  174 (522)
                      .....+|||+|||+++|+++|+++|++||.  |++|+|++|+.|+++||||||+|.++++|++||+.++ .    .|+||
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr   85 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGK   85 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTE
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCE
Confidence            346789999999999999999999999995  6799999999999999999999999999999999877 3    49999


Q ss_pred             EEEEEEcCC
Q 009920          175 MVEVKRAVP  183 (522)
Q Consensus       175 ~I~V~~a~p  183 (522)
                      +|.|++|+.
T Consensus        86 ~i~V~~Aks   94 (95)
T 2lkz_A           86 TIGVDFAKS   94 (95)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEEccC
Confidence            999999974

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=1.9e-17  Score=139.42  Aligned_cols=84  Identities=29%  Similarity=0.532  Sum_probs=78.0

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCC---CCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEE
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRA---TGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEA   77 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~---tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V   77 (522)
                      .+.++|||+|||+++||++|+++|++||+|++|+|++++.   |+++++||||+|.++++|++||  ++++.|++++|.|
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            5789999999999999999999999999999999999876   6689999999999999999999  7999999999999


Q ss_pred             eecCCCccc
Q 009920           78 KKAVPRDDQ   86 (522)
Q Consensus        78 ~~a~~k~~~   86 (522)
                      +++.++...
T Consensus        83 ~~a~~~~~~   91 (98)
T 2cpf_A           83 RISERATKP   91 (98)
T ss_dssp             ECSSCSSCC
T ss_pred             EEccCCCCC
Confidence            999876543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=1.6e-17  Score=141.39  Aligned_cols=83  Identities=29%  Similarity=0.458  Sum_probs=78.6

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++++++|+++|++||+|++|+|++++.++++++||||+|.++++|++||  ++++.|++++|.|+++
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2dnm_A           11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVA   90 (103)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEC
Confidence            46799999999999999999999999999999999999999999999999999999999999  8999999999999999


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      .++..
T Consensus        91 ~~~~~   95 (103)
T 2dnm_A           91 RYGRR   95 (103)
T ss_dssp             SSCCS
T ss_pred             CcCCC
Confidence            87544

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=2.5e-17  Score=140.83  Aligned_cols=85  Identities=24%  Similarity=0.455  Sum_probs=79.3

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeec-CCCCCcccEEEEEecCHHHHHHHH--H-cccccCCeEEEE
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRD-RATGRARGFGFVVFADPAVAERVI--M-DKHMIDGRTVEA   77 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d-~~tg~srG~aFVeF~~~e~A~kAl--~-~~~~i~Gr~I~V   77 (522)
                      +.+.++|||+|||+++|+++|+++|++||+|++|+|+++ +.++++++||||+|.++++|++||  + +.+.|++++|.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v   91 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   91 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEE
Confidence            357799999999999999999999999999999999999 788999999999999999999999  6 899999999999


Q ss_pred             eecCCCccc
Q 009920           78 KKAVPRDDQ   86 (522)
Q Consensus        78 ~~a~~k~~~   86 (522)
                      +++.++...
T Consensus        92 ~~a~~~~~~  100 (107)
T 2cph_A           92 EWADSEVTV  100 (107)
T ss_dssp             EECCCCCCC
T ss_pred             EeCCCCCCC
Confidence            999876544

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=4.8e-17  Score=135.89  Aligned_cols=83  Identities=28%  Similarity=0.556  Sum_probs=78.3

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      .+.+.++|||+|||+++++++|+++|++||+|++|.|++++.+++++|||||+|+++++|++||+.++ ..|++++|+|+
T Consensus        11 ~~~~~~~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           11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS   90 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34577899999999999999999999999999999999999999999999999999999999999877 89999999999


Q ss_pred             EcCC
Q 009920          180 RAVP  183 (522)
Q Consensus       180 ~a~p  183 (522)
                      ++++
T Consensus        91 ~a~~   94 (95)
T 2cqc_A           91 GPSS   94 (95)
T ss_dssp             CCSC
T ss_pred             ecCC
Confidence            9874

>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=99.71  E-value=1.5e-17  Score=144.26  Aligned_cols=102  Identities=16%  Similarity=0.287  Sum_probs=91.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++|+++|+++|++||+|.+|.|+++   ++++|||||+|.++++|++|+  +++..|+++.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            45789999999999999999999999999999999976   456999999999999999999  8999999999999998


Q ss_pred             CCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCC
Q 009920           81 VPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGT  131 (522)
Q Consensus        81 ~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~  131 (522)
                      .++...                        .+++...++++|+++|++||.
T Consensus        83 ~~~~~~------------------------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           83 NANRAF------------------------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             CHHHHT------------------------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             cCChhh------------------------hhhhHhHhHHHHHHHHHHhCC
Confidence            765432                        356778899999999999985

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=3.2e-17  Score=137.00  Aligned_cols=80  Identities=30%  Similarity=0.465  Sum_probs=76.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++++++|+++|++||+|++|+|++++.++++++||||+|.++++|++|+  ++++.|++++|.|+++
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   92 (95)
T 2cqc_A           13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGP   92 (95)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            46789999999999999999999999999999999999999999999999999999999999  8999999999999988


Q ss_pred             CC
Q 009920           81 VP   82 (522)
Q Consensus        81 ~~   82 (522)
                      ++
T Consensus        93 ~~   94 (95)
T 2cqc_A           93 SS   94 (95)
T ss_dssp             SC
T ss_pred             CC
Confidence            64

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.71  E-value=2.3e-17  Score=142.58  Aligned_cols=85  Identities=48%  Similarity=0.882  Sum_probs=76.4

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeec
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a   80 (522)
                      +.+.++|||+|||+++||++|+++|++||+|++|+|++++.+++++|||||+|.++++|++|| ..++.|++++|.|+++
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~~a  101 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA  101 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEc
Confidence            467899999999999999999999999999999999999999999999999999999999999 5568999999999999


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      .++..+
T Consensus       102 ~~~~~~  107 (109)
T 2rs2_A          102 FPRRAQ  107 (109)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            877543

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=2.4e-17  Score=143.39  Aligned_cols=86  Identities=42%  Similarity=0.764  Sum_probs=80.2

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcC
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAV  182 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~  182 (522)
                      .+.++|||+|||+++|+++|+++|++||.|++|.|+.++.+++++|||||+|.++++|++||+.+.+.|+|++|+|+++.
T Consensus        25 ~~~~~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           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEECC
Confidence            35689999999999999999999999999999999999999999999999999999999999994489999999999999


Q ss_pred             CCCCCC
Q 009920          183 PKEFSP  188 (522)
Q Consensus       183 pk~~~~  188 (522)
                      ++....
T Consensus       105 ~~~~~~  110 (116)
T 1x4b_A          105 AREESG  110 (116)
T ss_dssp             SCCCCC
T ss_pred             CCccCC
Confidence            887644

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.71  E-value=3.4e-17  Score=139.42  Aligned_cols=83  Identities=17%  Similarity=0.389  Sum_probs=78.0

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      .+.++|||+|||+++||++|+++|++|+ |++|+|++++.+++++|||||+|.++++|++|| ++++.|++++|.|+++.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~   91 (103)
T 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAE   91 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEEEECC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEEEEec
Confidence            5679999999999999999999999996 999999999999999999999999999999999 99999999999999998


Q ss_pred             CCccc
Q 009920           82 PRDDQ   86 (522)
Q Consensus        82 ~k~~~   86 (522)
                      ++...
T Consensus        92 ~~~~~   96 (103)
T 2dng_A           92 GRKQD   96 (103)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=9.6e-18  Score=143.96  Aligned_cols=81  Identities=17%  Similarity=0.223  Sum_probs=76.2

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeec
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a   80 (522)
                      +.+.++|||+|||+++|+++|+++|++||+|++|+|++++. +++||||||+|.++++|++|| ++.+.|++++|.|+++
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFK   86 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEEH
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            45679999999999999999999999999999999999987 999999999999999999999 8899999999999987


Q ss_pred             CCC
Q 009920           81 VPR   83 (522)
Q Consensus        81 ~~k   83 (522)
                      .+.
T Consensus        87 ~~~   89 (103)
T 1s79_A           87 DDY   89 (103)
T ss_dssp             HHH
T ss_pred             hHH
Confidence            664

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.71  E-value=2.9e-17  Score=141.92  Aligned_cols=86  Identities=38%  Similarity=0.717  Sum_probs=79.0

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEc
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRA  181 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a  181 (522)
                      ..+.++|||+|||+++|+++|+++|++||.|++|+|++++.+++++|||||+|.++++|++||+.+++.|+|++|+|+++
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~~a  101 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA  101 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEc
Confidence            35678999999999999999999999999999999999999999999999999999999999999989999999999999


Q ss_pred             CCCCCC
Q 009920          182 VPKEFS  187 (522)
Q Consensus       182 ~pk~~~  187 (522)
                      .++..+
T Consensus       102 ~~~~~~  107 (109)
T 2rs2_A          102 FPRRAQ  107 (109)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            987654

>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=99.71  E-value=9.1e-18  Score=139.75  Aligned_cols=80  Identities=24%  Similarity=0.503  Sum_probs=70.8

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccC--CeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYG--EVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G--~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      .+|||+|||+++||++|+++|++||  +|.+|+|++++.++++||||||+|.++++|++|+  ++++.|++++|.|+++.
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            5799999999999999999999999  9999999999999999999999999999999999  99999999999999988


Q ss_pred             CCcc
Q 009920           82 PRDD   85 (522)
Q Consensus        82 ~k~~   85 (522)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7643

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=3.4e-17  Score=139.88  Aligned_cols=82  Identities=22%  Similarity=0.406  Sum_probs=77.7

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++++++|+++|++||+|++|+|++++.+++++|||||+|.++++|++|+  ++++.|++++|.|+++
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            45789999999999999999999999999999999999999999999999999999999999  8999999999999998


Q ss_pred             CCCc
Q 009920           81 VPRD   84 (522)
Q Consensus        81 ~~k~   84 (522)
                      .++.
T Consensus       101 ~~~~  104 (106)
T 1p27_B          101 FVRG  104 (106)
T ss_dssp             EESS
T ss_pred             cCCC
Confidence            7654

>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=99.71  E-value=7.4e-17  Score=137.55  Aligned_cols=85  Identities=26%  Similarity=0.426  Sum_probs=78.6

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCC---eEEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNG---KMVEV  178 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~G---r~I~V  178 (522)
                      ...++|||+|||.++++++|+++|++||.|++|.|+.++ +++++|||||+|.++++|++||+.++ ..|.+   ++|+|
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            467899999999999999999999999999999999998 68999999999999999999999887 78888   99999


Q ss_pred             EEcCCCCCCC
Q 009920          179 KRAVPKEFSP  188 (522)
Q Consensus       179 ~~a~pk~~~~  188 (522)
                      ++++++..++
T Consensus        92 ~~a~~~~~~~  101 (105)
T 2dnh_A           92 KFADTDKESG  101 (105)
T ss_dssp             EESCSSCCCS
T ss_pred             EECccCcccC
Confidence            9999877543

>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=99.71  E-value=2.2e-17  Score=141.08  Aligned_cols=85  Identities=28%  Similarity=0.509  Sum_probs=79.2

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hccccc---CCeEEE
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMI---DGRTVE   76 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i---~Gr~I~   76 (522)
                      +.+.++|||+|||+++||++|+++|++||+|++|+|++++.++++|+||||+|.++++|++||  +++..+   .+++|.
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~   89 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQ   89 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEE
Confidence            467899999999999999999999999999999999999999999999999999999999999  888887   899999


Q ss_pred             EeecCCCccc
Q 009920           77 AKKAVPRDDQ   86 (522)
Q Consensus        77 V~~a~~k~~~   86 (522)
                      |+++.++...
T Consensus        90 v~~a~~~~~~   99 (106)
T 2dgp_A           90 VKPADSESRG   99 (106)
T ss_dssp             EEECCCCSCC
T ss_pred             EEECCccccc
Confidence            9999876543

>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=99.71  E-value=9.7e-17  Score=136.47  Aligned_cols=87  Identities=25%  Similarity=0.581  Sum_probs=78.9

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      ...+.++|||+|||+++|+++|+++|++||.|++|+|+.++.+  +++||||+|.++++|++||+.++ +.|++++|+|+
T Consensus        11 ~~~~~~~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           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT--TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC--CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3456789999999999999999999999999999999998753  89999999999999999999877 89999999999


Q ss_pred             EcCCCCCCCC
Q 009920          180 RAVPKEFSPG  189 (522)
Q Consensus       180 ~a~pk~~~~~  189 (522)
                      +++++.....
T Consensus        89 ~a~~~~~~~~   98 (103)
T 2cq3_A           89 NATARVMTNS   98 (103)
T ss_dssp             ECCSSCCCCC
T ss_pred             EcccCCCCCC
Confidence            9998876543

>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=99.71  E-value=1.3e-16  Score=135.73  Aligned_cols=86  Identities=21%  Similarity=0.367  Sum_probs=77.7

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      .....++|||+|||+++++++|+++|++||+|++|+|++++.+  ++|||||+|.++++|++||+.++ ..|.+++|+|+
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            3456789999999999999999999999999999999998654  68999999999999999999777 89999999999


Q ss_pred             EcCCCCCCC
Q 009920          180 RAVPKEFSP  188 (522)
Q Consensus       180 ~a~pk~~~~  188 (522)
                      +++++...+
T Consensus        89 ~a~~~~~~~   97 (103)
T 2cqi_A           89 WATTPSSQK   97 (103)
T ss_dssp             ECCCTTCCC
T ss_pred             ECCCCcccc
Confidence            999876543

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=4.5e-17  Score=140.87  Aligned_cols=87  Identities=22%  Similarity=0.383  Sum_probs=80.8

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCee--------EEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-Ccc
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTIT--------DVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HEL  171 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~--------~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l  171 (522)
                      ...+.++|||+|||+++|+++|+++|++||.|+        +|+|+.++.+++++|||||+|.++++|++||+.++ +.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            345678999999999999999999999999999        79999999999999999999999999999999877 899


Q ss_pred             CCeEEEEEEcCCCCCC
Q 009920          172 NGKMVEVKRAVPKEFS  187 (522)
Q Consensus       172 ~Gr~I~V~~a~pk~~~  187 (522)
                      .+++|+|++++++...
T Consensus        91 ~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           91 QGSKLKVSLARKKPPM  106 (113)
T ss_dssp             TTEECEEECSSCCCCS
T ss_pred             CCCEEEEEECCCCCCC
Confidence            9999999999987654

>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=99.71  E-value=3.1e-17  Score=139.92  Aligned_cols=83  Identities=22%  Similarity=0.460  Sum_probs=78.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCC-CCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRAT-GRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~t-g~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++|+++|+++|++|| |++|+|++++.+ ++++|||||+|.++++|++|| ++++.|++++|.|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a   91 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEEEEEc
Confidence            4678999999999999999999999999 999999999987 999999999999999999999 9999999999999999


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      .++...
T Consensus        92 ~~~~~~   97 (104)
T 1wi8_A           92 DQAQDK   97 (104)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            876554

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=2.8e-17  Score=137.25  Aligned_cols=79  Identities=25%  Similarity=0.580  Sum_probs=75.6

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++++++|+++|++||+|++|+|++++.++++++||||+|.++++|++|+  ++++.|++++|+|+++
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA   93 (94)
T ss_dssp             CCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEec
Confidence            56789999999999999999999999999999999999999999999999999999999999  8999999999999987


Q ss_pred             C
Q 009920           81 V   81 (522)
Q Consensus        81 ~   81 (522)
                      +
T Consensus        94 k   94 (94)
T 2e5h_A           94 I   94 (94)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.70  E-value=1e-17  Score=139.38  Aligned_cols=82  Identities=18%  Similarity=0.342  Sum_probs=71.4

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcC--CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFG--TITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG--~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      .+|||+|||+++|+++|+++|++||  .|++|+|+.|+.++++||||||+|.++++|++||+.++ .+|+|++|+|+++.
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  99999999999999999999999999999999999888 89999999999999


Q ss_pred             CCCCC
Q 009920          183 PKEFS  187 (522)
Q Consensus       183 pk~~~  187 (522)
                      |+...
T Consensus        82 ~~~~~   86 (90)
T 3p5t_L           82 KLEHH   86 (90)
T ss_dssp             -----
T ss_pred             CCccc
Confidence            87654

>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=99.70  E-value=4.2e-17  Score=140.40  Aligned_cols=85  Identities=16%  Similarity=0.313  Sum_probs=79.9

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+.++|||+|||.++|+++|+++|++||.|++|.|+.++.+++++|||||+|.++++|++||+.++ ..|+|++|+|++
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            3567899999999999999999999999999999999999999999999999999999999999777 899999999999


Q ss_pred             cCCCCC
Q 009920          181 AVPKEF  186 (522)
Q Consensus       181 a~pk~~  186 (522)
                      +.++..
T Consensus       103 a~~~~~  108 (110)
T 1oo0_B          103 CFVKGP  108 (110)
T ss_dssp             SEESSC
T ss_pred             cccCCC
Confidence            998764

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.70  E-value=3.6e-17  Score=137.47  Aligned_cols=83  Identities=23%  Similarity=0.454  Sum_probs=78.8

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCC
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~   82 (522)
                      +++|||+|||+++++++|+++|++||+|++|+|++++.++++++||||+|.+.++|++|+  +++..|++++|.|+++.+
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            689999999999999999999999999999999999999999999999999999999999  899999999999999988


Q ss_pred             Ccccc
Q 009920           83 RDDQN   87 (522)
Q Consensus        83 k~~~~   87 (522)
                      +....
T Consensus        82 ~~~~~   86 (96)
T 2x1f_A           82 SDISG   86 (96)
T ss_dssp             SSGGG
T ss_pred             CCCCC
Confidence            76543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=9.7e-17  Score=138.86  Aligned_cols=83  Identities=27%  Similarity=0.412  Sum_probs=76.8

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++++++|+++|++||+|++|+|++++ ++++++||||+|.++++|++||  ++++.|++++|.|+++
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   91 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD   91 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEc
Confidence            467899999999999999999999999999999999998 4999999999999999999999  8999999999999998


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      ......
T Consensus        92 ~~~~~~   97 (114)
T 2do0_A           92 ERALPK   97 (114)
T ss_dssp             SCCCCC
T ss_pred             ccCCCC
Confidence            765433

>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=99.70  E-value=7.8e-17  Score=140.89  Aligned_cols=85  Identities=29%  Similarity=0.586  Sum_probs=79.4

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      .+.++|||+|||.++|+++|+++|++||.|++|.|+.++ +++++|||||+|+++++|++||+.++ ..|++++|+|+++
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            567899999999999999999999999999999999998 89999999999999999999999888 8999999999999


Q ss_pred             CCCCCCC
Q 009920          182 VPKEFSP  188 (522)
Q Consensus       182 ~pk~~~~  188 (522)
                      +++....
T Consensus        84 ~~~~~~~   90 (116)
T 2fy1_A           84 KKPSFQS   90 (116)
T ss_dssp             CCSSCSS
T ss_pred             CCCCCCC
Confidence            9876543

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=5.2e-17  Score=138.24  Aligned_cols=86  Identities=26%  Similarity=0.447  Sum_probs=79.8

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhh-cCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-Cc-cCCeEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQ-FGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HE-LNGKMVEV  178 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~-fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~-l~Gr~I~V  178 (522)
                      ..+.++|||+|||+++|+++|+++|++ ||.|++|.|+.++ +++++|||||+|.++++|++||+.++ .. |++++|+|
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            356789999999999999999999999 9999999999999 89999999999999999999999888 78 99999999


Q ss_pred             EEcCCCCCCC
Q 009920          179 KRAVPKEFSP  188 (522)
Q Consensus       179 ~~a~pk~~~~  188 (522)
                      +++.++....
T Consensus        85 ~~a~~~~~~~   94 (104)
T 2dhg_A           85 SVAIPKASRV   94 (104)
T ss_dssp             CBCCCCCSCC
T ss_pred             EEccCCCcCC
Confidence            9998876544

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=5.2e-17  Score=138.74  Aligned_cols=83  Identities=19%  Similarity=0.387  Sum_probs=78.9

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      .+.++|||+|||.++++++|+++|++||+|++|.|+.++.+++++|||||+|.++++|++||+.++ +.|+|++|+|+++
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            467899999999999999999999999999999999999999999999999999999999999877 8999999999999


Q ss_pred             CCCC
Q 009920          182 VPKE  185 (522)
Q Consensus       182 ~pk~  185 (522)
                      .++.
T Consensus       101 ~~~~  104 (106)
T 1p27_B          101 FVRG  104 (106)
T ss_dssp             EESS
T ss_pred             cCCC
Confidence            8865

>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=99.70  E-value=1e-17  Score=145.71  Aligned_cols=85  Identities=14%  Similarity=0.197  Sum_probs=79.0

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCe-EEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEV-VEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V-~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~   79 (522)
                      +.+.++|||+|||+++||++|+++|++||+| .+|+|++++ ++++||||||+|.++++|++|| ++++.|++++|.|++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHV   90 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEEEE
Confidence            4578999999999999999999999999999 899999998 8999999999999999999999 888999999999999


Q ss_pred             cCCCcccc
Q 009920           80 AVPRDDQN   87 (522)
Q Consensus        80 a~~k~~~~   87 (522)
                      +.+++...
T Consensus        91 a~~~~~~~   98 (114)
T 2cpy_A           91 VTLEDMRE   98 (114)
T ss_dssp             ECHHHHHH
T ss_pred             CCHHHHHH
Confidence            98776444

>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=99.70  E-value=3.4e-17  Score=140.18  Aligned_cols=83  Identities=25%  Similarity=0.394  Sum_probs=76.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEE-EEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVE-AVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~-v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++||++|+++|++||+|.+ |+|+++ .+++++|||||+|.++++|++|| ++++.|.+|+|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v~~~   91 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEEEEC
Confidence            46799999999999999999999999999998 888888 67999999999999999999999 8889999999999998


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      .+++..
T Consensus        92 ~~~~~~   97 (104)
T 1wg5_A           92 SRAEVR   97 (104)
T ss_dssp             CTTTSC
T ss_pred             CHHHHH
Confidence            766543

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=1.8e-17  Score=141.86  Aligned_cols=80  Identities=21%  Similarity=0.229  Sum_probs=74.5

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      .+.++|||+|||+++||+||+++|++||+| +|+|++++ ++++||||||+|.++++|++|| ++.+.|++|.|+|.++.
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~~~   90 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECC
Confidence            467899999999999999999999999965 99999998 7999999999999999999999 99999999999999887


Q ss_pred             CCc
Q 009920           82 PRD   84 (522)
Q Consensus        82 ~k~   84 (522)
                      +.+
T Consensus        91 ~~~   93 (102)
T 1wez_A           91 TAG   93 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.70  E-value=1.3e-17  Score=146.35  Aligned_cols=85  Identities=18%  Similarity=0.277  Sum_probs=78.5

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCC---eEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEe
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGE---VVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAK   78 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~---V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~   78 (522)
                      .+.++|||+|||+++||++|+++|++||+   |++|+|++++. +++||||||+|.++++|++|| ++++.|++|.|+|.
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~   93 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVF   93 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEE
Confidence            46789999999999999999999999999   89999999987 999999999999999999999 99999999999999


Q ss_pred             ecCCCccccc
Q 009920           79 KAVPRDDQNM   88 (522)
Q Consensus        79 ~a~~k~~~~~   88 (522)
                      ++.+++.+..
T Consensus        94 ~a~~~~~~~~  103 (118)
T 2db1_A           94 KSHRTEMDWV  103 (118)
T ss_dssp             EECHHHHHHH
T ss_pred             ECCHHHHHHH
Confidence            9977665443

>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=99.70  E-value=6.7e-17  Score=137.83  Aligned_cols=83  Identities=23%  Similarity=0.374  Sum_probs=77.5

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCC---eEEEE
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDG---RTVEA   77 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~G---r~I~V   77 (522)
                      .+.++|||+|||+++++++|+++|++||+|++|+|++++ ++++++||||+|.++++|++||  +++..|.+   ++|.|
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            457999999999999999999999999999999999998 6999999999999999999999  89999998   99999


Q ss_pred             eecCCCccc
Q 009920           78 KKAVPRDDQ   86 (522)
Q Consensus        78 ~~a~~k~~~   86 (522)
                      +++.++...
T Consensus        92 ~~a~~~~~~  100 (105)
T 2dnh_A           92 KFADTDKES  100 (105)
T ss_dssp             EESCSSCCC
T ss_pred             EECccCccc
Confidence            999877654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=5e-17  Score=138.24  Aligned_cols=83  Identities=27%  Similarity=0.596  Sum_probs=77.7

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++|+++|+++|++||+|++|+|+++  ++++++||||+|.++++|++||  ++++.|++++|.|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2d9p_A           13 YQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA   90 (103)
T ss_dssp             SSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            57899999999999999999999999999999999998  7899999999999999999999  8999999999999999


Q ss_pred             CCCcccc
Q 009920           81 VPRDDQN   87 (522)
Q Consensus        81 ~~k~~~~   87 (522)
                      .++....
T Consensus        91 ~~~~~~~   97 (103)
T 2d9p_A           91 QRKEERQ   97 (103)
T ss_dssp             SSCCCCC
T ss_pred             cccccCC
Confidence            8876543

>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=99.70  E-value=5.1e-17  Score=141.66  Aligned_cols=82  Identities=27%  Similarity=0.500  Sum_probs=74.6

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      ...+|||+|||+++||++|+++|++||.|++|+|++|+.  .+||||||+|+++++|++||+.++ +.|+|++|+|++++
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~--~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT--EEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCC--CCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            356899999999999999999999999999999999964  479999999999999999999877 89999999999998


Q ss_pred             CCCCC
Q 009920          183 PKEFS  187 (522)
Q Consensus       183 pk~~~  187 (522)
                      ++..+
T Consensus        82 ~~~~~   86 (115)
T 4f25_A           82 SRKER   86 (115)
T ss_dssp             CCCC-
T ss_pred             Ccccc
Confidence            87654

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.70  E-value=4.4e-18  Score=166.43  Aligned_cols=82  Identities=17%  Similarity=0.334  Sum_probs=76.8

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcC--CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFG--TITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG--~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..++|||+|||+++||++|+++|++||  .|++|+|++|+.++++||||||+|+++++|++||+.++ ++|++++|+|++
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            567999999999999999999999999  99999999999999999999999999999999999888 899999999999


Q ss_pred             cCCCC
Q 009920          181 AVPKE  185 (522)
Q Consensus       181 a~pk~  185 (522)
                      ++++.
T Consensus       147 a~~~~  151 (229)
T 3q2s_C          147 VNKQF  151 (229)
T ss_dssp             CCHHH
T ss_pred             CCCCc
Confidence            98654

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=6.7e-17  Score=134.89  Aligned_cols=81  Identities=20%  Similarity=0.491  Sum_probs=76.8

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+.++|||+|||.++++++|+++|++||+|++|.|++++.+++++|||||+|+++++|++|++.++ ..|++++|+|++
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            4567899999999999999999999999999999999999999999999999999999999999888 899999999999


Q ss_pred             cC
Q 009920          181 AV  182 (522)
Q Consensus       181 a~  182 (522)
                      |+
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            85

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.70  E-value=9.7e-18  Score=142.65  Aligned_cols=83  Identities=22%  Similarity=0.273  Sum_probs=78.3

Q ss_pred             CCCcEEEECCCCC------CCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCC-e
Q 009920            3 SDLGKLFIGGISW------DTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDG-R   73 (522)
Q Consensus         3 ~d~r~LfVgnLP~------~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~G-r   73 (522)
                      ...++|||+|||+      ++++++|+++|++||+|++|+|++++.|+++||||||+|.++++|++||  ++++.|++ +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            4578999999999      9999999999999999999999999999999999999999999999999  99999999 9


Q ss_pred             EEEEeecCCCcc
Q 009920           74 TVEAKKAVPRDD   85 (522)
Q Consensus        74 ~I~V~~a~~k~~   85 (522)
                      +|.|.++.+++.
T Consensus        84 ~l~V~~a~~~~~   95 (100)
T 3ns6_A           84 RLFLYTMKDVER   95 (100)
T ss_dssp             BCEEEESHHHHH
T ss_pred             EEEEEECchhhh
Confidence            999999977543

>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=99.70  E-value=5.7e-17  Score=139.98  Aligned_cols=82  Identities=24%  Similarity=0.623  Sum_probs=78.3

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++++++|+++|++||+|++|+|++++.+++++|||||+|.++++|++|+  +++..|++++|.|+++
T Consensus        24 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a  103 (108)
T 2jrs_A           24 AGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHV  103 (108)
T ss_dssp             SSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            56799999999999999999999999999999999999999999999999999999999999  8999999999999999


Q ss_pred             CCCc
Q 009920           81 VPRD   84 (522)
Q Consensus        81 ~~k~   84 (522)
                      .++.
T Consensus       104 ~~k~  107 (108)
T 2jrs_A          104 TERT  107 (108)
T ss_dssp             CSSC
T ss_pred             ccCC
Confidence            8764

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=6.7e-17  Score=136.34  Aligned_cols=85  Identities=20%  Similarity=0.376  Sum_probs=79.4

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCee-EEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeE----
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTIT-DVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKM----  175 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~-~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~----  175 (522)
                      ....++|||+|||+++++++|+++|++||+|+ +|+|++++.+++++|||||+|.++++|++|++.++ ..|.++.    
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            35678999999999999999999999999999 99999999999999999999999999999999888 8999999    


Q ss_pred             EEEEEcCCCCC
Q 009920          176 VEVKRAVPKEF  186 (522)
Q Consensus       176 I~V~~a~pk~~  186 (522)
                      |+|+++++...
T Consensus        86 l~v~~a~~~~~   96 (99)
T 2div_A           86 FKLNYATYSGP   96 (99)
T ss_dssp             CCEEETTCCSS
T ss_pred             EEEeecCCCCC
Confidence            99999987643

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.70  E-value=5.8e-17  Score=132.61  Aligned_cols=80  Identities=30%  Similarity=0.542  Sum_probs=76.1

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      .+.++|||+|||+++++++|+++|++||+|++|.|++++.+++++|||||+|+++++|++|++.++ ..|+|++|+|+++
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            467899999999999999999999999999999999999999999999999999999999998877 8999999999997


Q ss_pred             C
Q 009920          182 V  182 (522)
Q Consensus       182 ~  182 (522)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=4.2e-17  Score=137.58  Aligned_cols=82  Identities=30%  Similarity=0.460  Sum_probs=77.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeE-EEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeE----E
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVV-EAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRT----V   75 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~-~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~----I   75 (522)
                      ...++|||+|||++++|++|+++|++||+|+ +|+|++++.++++++||||+|.++++|++|+  ++++.|+++.    |
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l   86 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRF   86 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEEC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeE
Confidence            5689999999999999999999999999999 9999999999999999999999999999999  8999999999    9


Q ss_pred             EEeecCCCc
Q 009920           76 EAKKAVPRD   84 (522)
Q Consensus        76 ~V~~a~~k~   84 (522)
                      +|.++.+..
T Consensus        87 ~v~~a~~~~   95 (99)
T 2div_A           87 KLNYATYSG   95 (99)
T ss_dssp             CEEETTCCS
T ss_pred             EEeecCCCC
Confidence            999887653

>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=99.70  E-value=5.9e-17  Score=135.52  Aligned_cols=79  Identities=28%  Similarity=0.515  Sum_probs=74.8

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      +.+.++|||+|||+++++++|+++|++||+|++|+|++++. +++++||||+|.++++|++|+  ++++.|++++|.|++
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            35679999999999999999999999999999999999986 899999999999999999999  899999999999998


Q ss_pred             cC
Q 009920           80 AV   81 (522)
Q Consensus        80 a~   81 (522)
                      +.
T Consensus        92 a~   93 (95)
T 2ywk_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=4.2e-17  Score=141.04  Aligned_cols=84  Identities=23%  Similarity=0.410  Sum_probs=78.9

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeE--------EEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVV--------EAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDG   72 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~--------~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~G   72 (522)
                      .+.++|||+|||+++|+++|+++|++||+|+        .|+|++++.++++++||||+|.++++|++||  ++++.|++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   92 (113)
T 2cpe_A           13 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   92 (113)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccCC
Confidence            5789999999999999999999999999999        6999999889999999999999999999999  79999999


Q ss_pred             eEEEEeecCCCccc
Q 009920           73 RTVEAKKAVPRDDQ   86 (522)
Q Consensus        73 r~I~V~~a~~k~~~   86 (522)
                      ++|.|+++.++...
T Consensus        93 ~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           93 SKLKVSLARKKPPM  106 (113)
T ss_dssp             EECEEECSSCCCCS
T ss_pred             CEEEEEECCCCCCC
Confidence            99999999876543

>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=99.69  E-value=9.7e-17  Score=136.46  Aligned_cols=82  Identities=22%  Similarity=0.356  Sum_probs=75.7

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++++++|+++|++||+|++|+|++++.  .+++||||+|.++++|++||  ++++.|++++|.|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2cqi_A           13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   90 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEEC
Confidence            5679999999999999999999999999999999999864  37999999999999999999  8999999999999999


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      .++...
T Consensus        91 ~~~~~~   96 (103)
T 2cqi_A           91 TTPSSQ   96 (103)
T ss_dssp             CCTTCC
T ss_pred             CCCccc
Confidence            876543

>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=99.69  E-value=8.5e-17  Score=138.88  Aligned_cols=85  Identities=29%  Similarity=0.609  Sum_probs=80.0

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      .....++|||+|||..+++++|+++|++||+|++|.|++++.+++++|||||+|.++++|++|++.++ ..|+|++|+|+
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            34567899999999999999999999999999999999999999999999999999999999999877 89999999999


Q ss_pred             EcCCCC
Q 009920          180 RAVPKE  185 (522)
Q Consensus       180 ~a~pk~  185 (522)
                      +++++.
T Consensus       102 ~a~~k~  107 (108)
T 2jrs_A          102 HVTERT  107 (108)
T ss_dssp             CSCSSC
T ss_pred             EcccCC
Confidence            999875

>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=99.69  E-value=9.7e-17  Score=140.28  Aligned_cols=84  Identities=35%  Similarity=0.687  Sum_probs=78.4

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++|+++|+++|++||+|++|+|++++ ++++++||||+|.+.++|++|+  +++..|++++|.|+++
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            467999999999999999999999999999999999998 8999999999999999999999  8999999999999999


Q ss_pred             CCCcccc
Q 009920           81 VPRDDQN   87 (522)
Q Consensus        81 ~~k~~~~   87 (522)
                      .++....
T Consensus        84 ~~~~~~~   90 (116)
T 2fy1_A           84 KKPSFQS   90 (116)
T ss_dssp             CCSSCSS
T ss_pred             CCCCCCC
Confidence            8765443

>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=99.69  E-value=1.2e-16  Score=135.85  Aligned_cols=84  Identities=26%  Similarity=0.568  Sum_probs=77.0

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      +.+.++|||+|||+++|+++|+++|++||+|++|+|++++.  .+++||||+|.++++|++||  ++++.|++++|.|++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   89 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45789999999999999999999999999999999999864  48999999999999999999  899999999999999


Q ss_pred             cCCCcccc
Q 009920           80 AVPRDDQN   87 (522)
Q Consensus        80 a~~k~~~~   87 (522)
                      +.++....
T Consensus        90 a~~~~~~~   97 (103)
T 2cq3_A           90 ATARVMTN   97 (103)
T ss_dssp             CCSSCCCC
T ss_pred             cccCCCCC
Confidence            98775443

>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=99.69  E-value=5e-17  Score=143.29  Aligned_cols=87  Identities=18%  Similarity=0.355  Sum_probs=80.9

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+.++|||+|||+++|+++|+++|++||.|++|.|+.++.+++++|||||+|.++++|++||+.++ ..|++++|+|++
T Consensus        19 ~~~~~~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           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   98 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            3467899999999999999999999999999999999999999999999999999999999999877 899999999999


Q ss_pred             cCCCCCCC
Q 009920          181 AVPKEFSP  188 (522)
Q Consensus       181 a~pk~~~~  188 (522)
                      +.++....
T Consensus        99 a~~~~~~~  106 (126)
T 3ex7_B           99 CFVRGPPK  106 (126)
T ss_dssp             SEESSSCC
T ss_pred             ecCCCCCC
Confidence            99876543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.69  E-value=6.4e-17  Score=145.02  Aligned_cols=84  Identities=29%  Similarity=0.490  Sum_probs=79.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++||++|+++|++||+|++|+|++++.+++++|||||+|.++++|++||  +++..|++++|.|+++
T Consensus        40 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  119 (139)
T 1u6f_A           40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45689999999999999999999999999999999999999999999999999999999999  7999999999999999


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      .++...
T Consensus       120 ~~~~~~  125 (139)
T 1u6f_A          120 ASGHQR  125 (139)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            876544

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=6.3e-17  Score=137.73  Aligned_cols=83  Identities=27%  Similarity=0.533  Sum_probs=77.6

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhc-cCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hcccc-cCCeEEEEe
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSR-YGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHM-IDGRTVEAK   78 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~-~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~-i~Gr~I~V~   78 (522)
                      ...++|||+|||+++|+++|+++|++ ||+|++|+|++++ ++++++||||+|.++++|++||  ++.+. |++++|.|+
T Consensus         7 ~~~~~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            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            46789999999999999999999999 9999999999998 8999999999999999999999  88888 999999999


Q ss_pred             ecCCCccc
Q 009920           79 KAVPRDDQ   86 (522)
Q Consensus        79 ~a~~k~~~   86 (522)
                      ++.++...
T Consensus        86 ~a~~~~~~   93 (104)
T 2dhg_A           86 VAIPKASR   93 (104)
T ss_dssp             BCCCCCSC
T ss_pred             EccCCCcC
Confidence            99776544

>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=99.69  E-value=7.6e-17  Score=135.49  Aligned_cols=82  Identities=16%  Similarity=0.415  Sum_probs=78.1

Q ss_pred             cceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCC
Q 009920          105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVP  183 (522)
Q Consensus       105 ~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~p  183 (522)
                      +++|||+|||.++++++|+++|++||.|++|+|+.++.+++++|||||+|+++++|++|++.++ ..|+|++|+|+++.+
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            5799999999999999999999999999999999999999999999999999999999998877 899999999999998


Q ss_pred             CCC
Q 009920          184 KEF  186 (522)
Q Consensus       184 k~~  186 (522)
                      +..
T Consensus        82 ~~~   84 (96)
T 2x1f_A           82 SDI   84 (96)
T ss_dssp             SSG
T ss_pred             CCC
Confidence            764

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.69  E-value=2.4e-17  Score=131.99  Aligned_cols=74  Identities=45%  Similarity=0.815  Sum_probs=71.4

Q ss_pred             EEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeec
Q 009920            7 KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         7 ~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a   80 (522)
                      +|||+|||+++++++|+++|++||+|.+|+|++++.+++++|||||+|.++++|++|+ ++++.|++++|.|++|
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            5999999999999999999999999999999999989999999999999999999999 9999999999999875

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=8.4e-17  Score=138.14  Aligned_cols=84  Identities=25%  Similarity=0.368  Sum_probs=77.6

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCC-eEEEEEe-ecCCCCCcccEEEEEecCHHHHHHHH--Hc--ccccCCeEEE
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGE-VVEAVIM-RDRATGRARGFGFVVFADPAVAERVI--MD--KHMIDGRTVE   76 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~-V~~v~i~-~d~~tg~srG~aFVeF~~~e~A~kAl--~~--~~~i~Gr~I~   76 (522)
                      .+.++|||+|||+++|+++|+++|++||+ |++|+|+ +++.+++++|||||+|.++++|++|+  ++  .+.|++++|.
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            56799999999999999999999999998 9999998 78888999999999999999999999  65  5899999999


Q ss_pred             EeecCCCccc
Q 009920           77 AKKAVPRDDQ   86 (522)
Q Consensus        77 V~~a~~k~~~   86 (522)
                      |+++.++...
T Consensus        86 V~~a~~~~~~   95 (109)
T 2dis_A           86 VDWAEPEIDV   95 (109)
T ss_dssp             EEESCSSCST
T ss_pred             EEEcCCCCCc
Confidence            9999877654

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.69  E-value=5.9e-17  Score=139.45  Aligned_cols=82  Identities=23%  Similarity=0.379  Sum_probs=77.8

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++|+++|+++|++||+|++|+|++++.++++++||||+|.++++|++|+  ++++.|++++|.|+++
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  103 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  103 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEc
Confidence            46789999999999999999999999999999999999999999999999999999999999  8999999999999998


Q ss_pred             CCCc
Q 009920           81 VPRD   84 (522)
Q Consensus        81 ~~k~   84 (522)
                      .++.
T Consensus       104 ~~~~  107 (110)
T 1oo0_B          104 FVKG  107 (110)
T ss_dssp             EESS
T ss_pred             ccCC
Confidence            7654

>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=99.69  E-value=1.6e-17  Score=141.26  Aligned_cols=86  Identities=29%  Similarity=0.626  Sum_probs=80.4

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      +.+.++|||+|||+++++++|+++|++||+|.+|+|++++.++++++||||+|.++++|++|+  ++++.|++++|.|++
T Consensus         5 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   84 (104)
T 1p1t_A            5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN   84 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEE
T ss_pred             CCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Confidence            356789999999999999999999999999999999999989999999999999999999999  899999999999999


Q ss_pred             cCCCcccc
Q 009920           80 AVPRDDQN   87 (522)
Q Consensus        80 a~~k~~~~   87 (522)
                      +.++....
T Consensus        85 a~~~~~~~   92 (104)
T 1p1t_A           85 AASEKNKE   92 (104)
T ss_dssp             TTCTTHHH
T ss_pred             CCCccchh
Confidence            98876544

>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=99.69  E-value=4.9e-17  Score=139.08  Aligned_cols=83  Identities=16%  Similarity=0.215  Sum_probs=75.3

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEc
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRA  181 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a  181 (522)
                      ....++|||+|||+++||+||+++|++||+| +|+|++|+ ++++||||||+|+++++|++||+++.+.|++|.|+|.++
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 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEEC
Confidence            3567899999999999999999999999954 99999998 799999999999999999999976448999999999998


Q ss_pred             CCCCC
Q 009920          182 VPKEF  186 (522)
Q Consensus       182 ~pk~~  186 (522)
                      .+++.
T Consensus        90 ~~~~~   94 (102)
T 1wez_A           90 STAGT   94 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=8.7e-17  Score=133.66  Aligned_cols=80  Identities=19%  Similarity=0.401  Sum_probs=75.7

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      .+.++|||+|||+++|+++|+++|++| +|.+|+|+++ .+++++|||||+|.++++|++|| ++++.|++++|+|.++.
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~~a~   85 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFREK   85 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEEEES
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEEECC
Confidence            567999999999999999999999999 9999999999 67999999999999999999999 99999999999999998


Q ss_pred             CCc
Q 009920           82 PRD   84 (522)
Q Consensus        82 ~k~   84 (522)
                      ++.
T Consensus        86 ~~~   88 (91)
T 2dgw_A           86 SGP   88 (91)
T ss_dssp             SCC
T ss_pred             cCC
Confidence            764

>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=99.69  E-value=1.8e-16  Score=136.35  Aligned_cols=84  Identities=15%  Similarity=0.319  Sum_probs=75.5

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      ...+.++|||+|||+++|+++|+++|++||.|++|.|+.+   .++++||||+|+++++|++||+.++ .+|++++|+|+
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   94 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   94 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            3456789999999999999999999999999999999654   4579999999999999999998877 89999999999


Q ss_pred             EcCCCCCC
Q 009920          180 RAVPKEFS  187 (522)
Q Consensus       180 ~a~pk~~~  187 (522)
                      +++++...
T Consensus        95 ~a~~~~~~  102 (109)
T 1x4a_A           95 FPRSGRGT  102 (109)
T ss_dssp             CCCCCCCC
T ss_pred             EcccCCCC
Confidence            99887643

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=7.1e-17  Score=140.41  Aligned_cols=83  Identities=46%  Similarity=0.885  Sum_probs=78.2

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecCC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~~   82 (522)
                      +.++|||+|||+++|+++|+++|++||+|++|+|++++.+++++|||||+|.++++|++|| .+.+.|++++|.|+++.+
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~~  105 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVA  105 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEECCC
Confidence            3589999999999999999999999999999999999999999999999999999999999 888899999999999988


Q ss_pred             Cccc
Q 009920           83 RDDQ   86 (522)
Q Consensus        83 k~~~   86 (522)
                      +...
T Consensus       106 ~~~~  109 (116)
T 1x4b_A          106 REES  109 (116)
T ss_dssp             CCCC
T ss_pred             CccC
Confidence            7653

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=2e-17  Score=143.53  Aligned_cols=80  Identities=23%  Similarity=0.404  Sum_probs=74.5

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      .+.++|||+|||+++||+||+++|++| .|++|+|+++++ +++||||||+|.++++|++|| ++++.|.+|.|+|..+.
T Consensus        14 ~~~~~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           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECC
Confidence            356799999999999999999999999 899999999986 999999999999999999999 99999999999999887


Q ss_pred             CCc
Q 009920           82 PRD   84 (522)
Q Consensus        82 ~k~   84 (522)
                      +++
T Consensus        92 ~~~   94 (109)
T 2dnn_A           92 ERQ   94 (109)
T ss_dssp             HHH
T ss_pred             ccc
Confidence            654

>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=99.69  E-value=7.4e-17  Score=135.82  Aligned_cols=84  Identities=13%  Similarity=0.207  Sum_probs=78.5

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ....++|||+|||+++++++|+++|++||.|+++.++.++.+++++|||||+|.++++|++||+.++ ..|++++|+|++
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            3567899999999999999999999999999999999999999999999999999999999999888 899999999999


Q ss_pred             cCCCC
Q 009920          181 AVPKE  185 (522)
Q Consensus       181 a~pk~  185 (522)
                      +.++.
T Consensus        92 a~~~~   96 (98)
T 2cqp_A           92 GSGPS   96 (98)
T ss_dssp             SSCSS
T ss_pred             cCCCC
Confidence            98653

>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=99.68  E-value=6.7e-17  Score=144.16  Aligned_cols=85  Identities=28%  Similarity=0.568  Sum_probs=80.2

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      ...+.++|||+|||+++|+++|+++|++||+|++|+|++++.+++++|||||+|+++++|++||+.++ ..|+|++|+|+
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~  121 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD  121 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEES
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999877 89999999999


Q ss_pred             EcCCCC
Q 009920          180 RAVPKE  185 (522)
Q Consensus       180 ~a~pk~  185 (522)
                      ++++++
T Consensus       122 ~a~~~~  127 (129)
T 2kxn_B          122 FSITKR  127 (129)
T ss_dssp             CCSSSS
T ss_pred             EecCCC
Confidence            998865

>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=99.68  E-value=2.3e-16  Score=135.79  Aligned_cols=84  Identities=23%  Similarity=0.319  Sum_probs=75.6

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCC-----eE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNG-----KM  175 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~G-----r~  175 (522)
                      ....++|||+|||+++|+++|+++|++||+|++|.|+.+       |||||+|+++++|++||+.++ ++|++     ++
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            346789999999999999999999999999999999876       799999999999999999888 89999     99


Q ss_pred             EEEEEcCCCCCCCCCCC
Q 009920          176 VEVKRAVPKEFSPGPSR  192 (522)
Q Consensus       176 I~V~~a~pk~~~~~~~r  192 (522)
                      |+|++++++...+.+.+
T Consensus        85 i~V~~a~~~~~~~~rsr  101 (108)
T 1x4c_A           85 IRVKVDGPRSPSYGRSR  101 (108)
T ss_dssp             EEEEESSCCSCCCCCSS
T ss_pred             EEEEeCCCCCCCCCCCC
Confidence            99999999876554443

>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=99.68  E-value=7.2e-17  Score=132.76  Aligned_cols=82  Identities=26%  Similarity=0.488  Sum_probs=76.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCC-cccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGR-ARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~-srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      .+.++|||+|||+++|+++|+++|++||+|.+|+|++++.++. +++||||+|.++++|++|+  +++..|++++|.|++
T Consensus         2 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   81 (88)
T 4a8x_A            2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATA   81 (88)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEE
Confidence            4678999999999999999999999999999999999987766 9999999999999999999  899999999999999


Q ss_pred             cCCCc
Q 009920           80 AVPRD   84 (522)
Q Consensus        80 a~~k~   84 (522)
                      +.+..
T Consensus        82 a~~~~   86 (88)
T 4a8x_A           82 VLAPW   86 (88)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            87643

>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=99.68  E-value=5.6e-17  Score=144.64  Aligned_cols=82  Identities=29%  Similarity=0.475  Sum_probs=78.0

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++||++|+++|++||+|++|+|++++.+++++|||||+|.++++|++||  +++..|++++|.|+++
T Consensus        44 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a  123 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS  123 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            46789999999999999999999999999999999999999999999999999999999999  8999999999999999


Q ss_pred             CCCc
Q 009920           81 VPRD   84 (522)
Q Consensus        81 ~~k~   84 (522)
                      .++.
T Consensus       124 ~~~~  127 (129)
T 2kxn_B          124 ITKR  127 (129)
T ss_dssp             SSSS
T ss_pred             cCCC
Confidence            8764

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.68  E-value=1.4e-16  Score=134.67  Aligned_cols=82  Identities=24%  Similarity=0.403  Sum_probs=77.2

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeE--------EEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-Ccc
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITD--------VVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HEL  171 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~--------v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l  171 (522)
                      .+...++|||+|||+++|+++|+++|++||.|++        |+|+.++.+++++|||||+|.++++|++|++.++ ..|
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            4457789999999999999999999999999999        9999999999999999999999999999999777 899


Q ss_pred             CCeEEEEEEcC
Q 009920          172 NGKMVEVKRAV  182 (522)
Q Consensus       172 ~Gr~I~V~~a~  182 (522)
                      .|++|+|++|+
T Consensus        89 ~g~~l~V~~A~   99 (99)
T 2la6_A           89 SGNPIKVSFAT   99 (99)
T ss_dssp             SSSBCEEEECC
T ss_pred             CCcEEEEEecC
Confidence            99999999974

>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=99.68  E-value=3.1e-17  Score=137.19  Aligned_cols=79  Identities=14%  Similarity=0.283  Sum_probs=74.0

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++|+++|+++|++||+|+++++++++.++++++||||+|.++++|++||  ++++.|++++|+|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            34689999999999999999999999999999999999999999999999999999999999  8999999999999987


Q ss_pred             C
Q 009920           81 V   81 (522)
Q Consensus        81 ~   81 (522)
                      .
T Consensus        93 ~   93 (95)
T 2ek1_A           93 S   93 (95)
T ss_dssp             C
T ss_pred             c
Confidence            5

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.68  E-value=1.3e-16  Score=132.60  Aligned_cols=82  Identities=28%  Similarity=0.498  Sum_probs=76.1

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      +.+.++|||+|||+++++++|+++|++||+|++|+|+++  ++++++||||+|.++++|++|+  ++++.|++++|.|++
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            357899999999999999999999999999999999984  6899999999999999999999  899999999999999


Q ss_pred             cCCCcc
Q 009920           80 AVPRDD   85 (522)
Q Consensus        80 a~~k~~   85 (522)
                      +.+...
T Consensus        83 a~~~~~   88 (92)
T 2dgv_A           83 DRNASG   88 (92)
T ss_dssp             CSCCSS
T ss_pred             cCCCCC
Confidence            887654

>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=99.68  E-value=3.9e-17  Score=137.54  Aligned_cols=81  Identities=14%  Similarity=0.253  Sum_probs=76.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++++++|+++|++||+|+++++++++.++++++||||+|.++++|++||  ++++.|++++|+|+++
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            45689999999999999999999999999999999999999999999999999999999999  8899999999999998


Q ss_pred             CCC
Q 009920           81 VPR   83 (522)
Q Consensus        81 ~~k   83 (522)
                      ..+
T Consensus        93 ~~~   95 (98)
T 2cqp_A           93 SGP   95 (98)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            754

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.68  E-value=1.4e-16  Score=138.82  Aligned_cols=82  Identities=20%  Similarity=0.376  Sum_probs=76.8

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      ...+.++|||+|||+++++++|+++|++||+|++|+|++++.+++++|||||+|.++++|++||+.++ .+|++++|+|+
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999887 89999999999


Q ss_pred             EcC
Q 009920          180 RAV  182 (522)
Q Consensus       180 ~a~  182 (522)
                      +++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            874

>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=99.68  E-value=1.5e-17  Score=144.34  Aligned_cols=83  Identities=19%  Similarity=0.367  Sum_probs=78.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      .+.++|||+|||+++++++|+++|++||+|++|+|++++.+++++|||||+|.++++|++|| ++++.|++++|.|+++.
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~  102 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeEEEEEecC
Confidence            34689999999999999999999999999999999999999999999999999999999999 99999999999999987


Q ss_pred             CCcc
Q 009920           82 PRDD   85 (522)
Q Consensus        82 ~k~~   85 (522)
                      ++..
T Consensus       103 ~~~~  106 (114)
T 2cq4_A          103 AEKN  106 (114)
T ss_dssp             HHHH
T ss_pred             CCcc
Confidence            6544

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.68  E-value=1.2e-16  Score=135.05  Aligned_cols=79  Identities=28%  Similarity=0.492  Sum_probs=75.4

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEE--------EEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVE--------AVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDG   72 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~--------v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~G   72 (522)
                      ...++|||+|||+++++++|+++|++||+|.+        |+|++++.+++++|||||+|.++++|++|+  +++..|++
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g   90 (99)
T 2la6_A           11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   90 (99)
T ss_dssp             CCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            46789999999999999999999999999999        999999999999999999999999999999  89999999


Q ss_pred             eEEEEeecC
Q 009920           73 RTVEAKKAV   81 (522)
Q Consensus        73 r~I~V~~a~   81 (522)
                      ++|.|++|+
T Consensus        91 ~~l~V~~A~   99 (99)
T 2la6_A           91 NPIKVSFAT   99 (99)
T ss_dssp             SBCEEEECC
T ss_pred             cEEEEEecC
Confidence            999999874

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.68  E-value=6.6e-17  Score=148.99  Aligned_cols=81  Identities=23%  Similarity=0.535  Sum_probs=76.0

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccC--CeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYG--EVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G--~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      +.++|||+|||+++||++|+++|++||  +|++|+|++|+.++++||||||+|.++++|++||  ++++.|++++|.|++
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            568999999999999999999999999  9999999999999999999999999999999999  799999999999999


Q ss_pred             cCCCc
Q 009920           80 AVPRD   84 (522)
Q Consensus        80 a~~k~   84 (522)
                      +.++.
T Consensus       134 a~~~~  138 (156)
T 3n9u_C          134 ATRQN  138 (156)
T ss_dssp             CCHHH
T ss_pred             cCCCc
Confidence            97654

>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=99.68  E-value=1.4e-16  Score=145.81  Aligned_cols=83  Identities=25%  Similarity=0.432  Sum_probs=78.5

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++||++|+++|++||+|++|+|++++.++++++||||+|.++++|++||  ++.+.|++++|.|+++
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            46799999999999999999999999999999999999999999999999999999999999  7999999999999999


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      .++..
T Consensus       117 ~~~~~  121 (156)
T 1h2v_Z          117 AGFKE  121 (156)
T ss_dssp             SCCCT
T ss_pred             CCCCC
Confidence            87543

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=9.2e-17  Score=138.43  Aligned_cols=80  Identities=10%  Similarity=0.219  Sum_probs=71.7

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hc--ccccCCeEEEE
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MD--KHMIDGRTVEA   77 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~--~~~i~Gr~I~V   77 (522)
                      +.+.++|||+|||+++||++|+++|++||+|++|+|+++      ||||||+|.++++|++|+  ++  ..+|++++|.|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   86 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI   86 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            357899999999999999999999999999999999875      689999999999999999  44  47899999999


Q ss_pred             eecCCCcccc
Q 009920           78 KKAVPRDDQN   87 (522)
Q Consensus        78 ~~a~~k~~~~   87 (522)
                      +++.++....
T Consensus        87 ~~A~~~~~~~   96 (105)
T 1sjq_A           87 QFSNHKELKT   96 (105)
T ss_dssp             CCCSSSSCCC
T ss_pred             EEcCCCCCCc
Confidence            9998765544

>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=99.68  E-value=2.2e-16  Score=133.05  Aligned_cols=81  Identities=10%  Similarity=0.149  Sum_probs=75.3

Q ss_pred             CCcceeEecCCCCCCCHHHHH----HHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFK----KYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVE  177 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~----~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~  177 (522)
                      ...++|||+|||+++++++|+    ++|++||+|++|+|++|+.+   |+||||+|+++++|++||+.++ .+|+|++|+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~   83 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKIL   83 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            456899999999999999999    99999999999999999876   7899999999999999999888 899999999


Q ss_pred             EEEcCCCCC
Q 009920          178 VKRAVPKEF  186 (522)
Q Consensus       178 V~~a~pk~~  186 (522)
                      |++++++..
T Consensus        84 V~~a~~~~~   92 (96)
T 2dgx_A           84 VSLATGASG   92 (96)
T ss_dssp             EEECCCSSC
T ss_pred             EEEcCCCCC
Confidence            999987654

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.68  E-value=9e-17  Score=141.65  Aligned_cols=84  Identities=21%  Similarity=0.393  Sum_probs=79.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++|+++|+++|++||+|++|+|++++.++++++||||+|.++++|++||  ++++.|++++|.|+++
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   99 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC   99 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEe
Confidence            46789999999999999999999999999999999999989999999999999999999999  8999999999999999


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      .++...
T Consensus       100 ~~~~~~  105 (126)
T 3ex7_B          100 FVRGPP  105 (126)
T ss_dssp             EESSSC
T ss_pred             cCCCCC
Confidence            776544

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.68  E-value=4.8e-17  Score=141.76  Aligned_cols=79  Identities=24%  Similarity=0.431  Sum_probs=74.8

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++++++|+++|++||+|++|+|++++.++++++||||+|.++++|++|+  +++..|++++|+|+++
T Consensus        38 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a  117 (118)
T 2khc_A           38 PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK  117 (118)
T ss_dssp             CCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            46799999999999999999999999999999999999989999999999999999999999  7999999999999886


Q ss_pred             C
Q 009920           81 V   81 (522)
Q Consensus        81 ~   81 (522)
                      +
T Consensus       118 k  118 (118)
T 2khc_A          118 K  118 (118)
T ss_dssp             -
T ss_pred             C
Confidence            3

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.68  E-value=2.4e-17  Score=140.24  Aligned_cols=83  Identities=18%  Similarity=0.307  Sum_probs=78.4

Q ss_pred             CCcceeEecCCCC------CCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCC-e
Q 009920          103 GRTKKIFVGGLAS------TVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNG-K  174 (522)
Q Consensus       103 ~~~~~LfVgnLp~------~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~G-r  174 (522)
                      ...++|||+|||.      ++++++|+++|++||.|++|+|++|+.|+++||||||+|.++++|++||+.++ ..|.+ +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            3467999999999      99999999999999999999999999999999999999999999999999887 89999 9


Q ss_pred             EEEEEEcCCCC
Q 009920          175 MVEVKRAVPKE  185 (522)
Q Consensus       175 ~I~V~~a~pk~  185 (522)
                      +|+|+++.|++
T Consensus        84 ~l~V~~a~~~~   94 (100)
T 3ns6_A           84 RLFLYTMKDVE   94 (100)
T ss_dssp             BCEEEESHHHH
T ss_pred             EEEEEECchhh
Confidence            99999998764

>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=99.68  E-value=2.1e-16  Score=130.41  Aligned_cols=80  Identities=21%  Similarity=0.468  Sum_probs=75.6

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      ..++|||+|||+++|+++|+++|++||+|++|.|+.++.+++++|||||+|.++++|++|+ .++ ..|+|++|+|++++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            3579999999999999999999999999999999999999999999999999999999999 666 89999999999998


Q ss_pred             CC
Q 009920          183 PK  184 (522)
Q Consensus       183 pk  184 (522)
                      ++
T Consensus        84 ~~   85 (89)
T 3ucg_A           84 TN   85 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            75

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=1.2e-16  Score=136.72  Aligned_cols=85  Identities=15%  Similarity=0.334  Sum_probs=77.5

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeE-EEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITD-VVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~-v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~  180 (522)
                      ....++|||+|||+++|++||+++|++||.|++ |.|+.+ .+++++|||||+|+++++|++||+++.+.|++|+|+|.+
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            356789999999999999999999999999988 888888 789999999999999999999999955899999999999


Q ss_pred             cCCCCCC
Q 009920          181 AVPKEFS  187 (522)
Q Consensus       181 a~pk~~~  187 (522)
                      +.+++..
T Consensus        91 ~~~~~~~   97 (104)
T 1wg5_A           91 SSRAEVR   97 (104)
T ss_dssp             ECTTTSC
T ss_pred             CCHHHHH
Confidence            9876643

>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=99.68  E-value=1e-16  Score=131.78  Aligned_cols=82  Identities=13%  Similarity=0.416  Sum_probs=76.5

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCC-cceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQR-PRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~-~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ..++|||+|||.++|+++|+++|++||.|++|.|+.++.+.. ++|||||+|.++++|++|++.++ ..|+|++|+|+++
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            467999999999999999999999999999999999988766 89999999999999999999877 8999999999999


Q ss_pred             CCCC
Q 009920          182 VPKE  185 (522)
Q Consensus       182 ~pk~  185 (522)
                      .++.
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8764

>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=99.67  E-value=3.5e-17  Score=147.56  Aligned_cols=84  Identities=17%  Similarity=0.263  Sum_probs=77.9

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCC---eEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEe
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGE---VVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAK   78 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~---V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~   78 (522)
                      .+.++|||+|||+++||++|+++|++||+   |++|+|++++. +++||||||+|.++++|++|| ++++.|++|+|+|.
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i~V~  120 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVF  120 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHTTTEEESSSSEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCEECCEEEEEE
Confidence            56789999999999999999999999999   89999999987 999999999999999999999 99999999999999


Q ss_pred             ecCCCcccc
Q 009920           79 KAVPRDDQN   87 (522)
Q Consensus        79 ~a~~k~~~~   87 (522)
                      ++.+++.+.
T Consensus       121 ~a~~~e~~~  129 (136)
T 2hgl_A          121 KSHRTEMDW  129 (136)
T ss_dssp             ECCHHHHHH
T ss_pred             ECChHHHHH
Confidence            987665433

>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=99.67  E-value=1.8e-16  Score=135.60  Aligned_cols=78  Identities=24%  Similarity=0.459  Sum_probs=74.4

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++|+++|+++|++||+|++|+|++++ ++++++||||+|.++++|++||  ++++.|++++|.|+++
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  105 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV  105 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            457899999999999999999999999999999999998 8999999999999999999999  7999999999999987


Q ss_pred             C
Q 009920           81 V   81 (522)
Q Consensus        81 ~   81 (522)
                      .
T Consensus       106 ~  106 (107)
T 3ulh_A          106 T  106 (107)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=2.8e-16  Score=130.57  Aligned_cols=82  Identities=17%  Similarity=0.311  Sum_probs=76.3

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ....++|||+|||+++|+++|+++|++| .|++|+|+++ .+++++|||||+|+++++|++||+ ++ ..|++++|+|.+
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            3467899999999999999999999999 9999999999 779999999999999999999999 66 899999999999


Q ss_pred             cCCCCC
Q 009920          181 AVPKEF  186 (522)
Q Consensus       181 a~pk~~  186 (522)
                      +.++..
T Consensus        84 a~~~~~   89 (91)
T 2dgw_A           84 EKSGPS   89 (91)
T ss_dssp             ESSCCC
T ss_pred             CCcCCC
Confidence            988754

>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=99.67  E-value=1.9e-16  Score=132.45  Aligned_cols=81  Identities=26%  Similarity=0.466  Sum_probs=75.7

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+.++|||+|||+++++++|+++|++||+|++|+|++++. ++++|||||+|.++++|++||+.++ +.|++++|+|++
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            35678999999999999999999999999999999999987 8999999999999999999999777 899999999999


Q ss_pred             cCC
Q 009920          181 AVP  183 (522)
Q Consensus       181 a~p  183 (522)
                      ++.
T Consensus        92 a~~   94 (95)
T 2ywk_A           92 PSS   94 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            863

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=5e-16  Score=134.33  Aligned_cols=84  Identities=18%  Similarity=0.228  Sum_probs=77.3

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+.++|||+|||+++++++|+++|++||.|++|+|+.++. ++++|||||+|+++++|++||+.++ +.|++++|+|++
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   90 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKM   90 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTT-CSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC-CCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEE
Confidence            34678999999999999999999999999999999999984 8999999999999999999999877 899999999999


Q ss_pred             cCCCCC
Q 009920          181 AVPKEF  186 (522)
Q Consensus       181 a~pk~~  186 (522)
                      +++...
T Consensus        91 a~~~~~   96 (114)
T 2do0_A           91 DERALP   96 (114)
T ss_dssp             CSCCCC
T ss_pred             cccCCC
Confidence            986543

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.67  E-value=2.3e-16  Score=131.14  Aligned_cols=83  Identities=19%  Similarity=0.319  Sum_probs=76.8

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      .+.++|||+|||.++++++|+++|++||+|++|+|+++  +++++|||||+|.++++|++|++.++ ..|++++|+|+++
T Consensus         6 ~~~~~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            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            46789999999999999999999999999999999984  68899999999999999999999877 8999999999999


Q ss_pred             CCCCCC
Q 009920          182 VPKEFS  187 (522)
Q Consensus       182 ~pk~~~  187 (522)
                      +++...
T Consensus        84 ~~~~~~   89 (92)
T 2dgv_A           84 RNASGP   89 (92)
T ss_dssp             SCCSSC
T ss_pred             CCCCCC
Confidence            987653

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=4.4e-17  Score=133.62  Aligned_cols=78  Identities=23%  Similarity=0.510  Sum_probs=73.8

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++++++|+++|++||+|.+|+|++++.+++++|||||+|.++++|++|+  ++++.|+++.|++.++
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            57899999999999999999999999999999999999999999999999999999999999  8999999998887654

>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=99.67  E-value=1.8e-16  Score=133.57  Aligned_cols=80  Identities=14%  Similarity=0.173  Sum_probs=74.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHH----HHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEE
Q 009920            3 SDLGKLFIGGISWDTDEERLK----EYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVE   76 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~----e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~   76 (522)
                      .+.++|||+|||++++|++|+    ++|++||+|++|+|++++.+   |+||||+|.++++|++|+  +++..|++++|.
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~   83 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKIL   83 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            467899999999999999999    99999999999999999865   899999999999999999  999999999999


Q ss_pred             EeecCCCcc
Q 009920           77 AKKAVPRDD   85 (522)
Q Consensus        77 V~~a~~k~~   85 (522)
                      |+++.++..
T Consensus        84 V~~a~~~~~   92 (96)
T 2dgx_A           84 VSLATGASG   92 (96)
T ss_dssp             EEECCCSSC
T ss_pred             EEEcCCCCC
Confidence            999976543

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.67  E-value=8.3e-17  Score=143.43  Aligned_cols=85  Identities=21%  Similarity=0.309  Sum_probs=78.8

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeE--EEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-C----ccCCe
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITD--VVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-H----ELNGK  174 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~--v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~----~l~Gr  174 (522)
                      ....++|||+|||+++||++|+++|++||.|+.  |+|++|+.++++||||||+|+++ +|++||+.++ .    +|+||
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            356789999999999999999999999999966  99999999999999999999999 9999999988 7    99999


Q ss_pred             EEEEEEcCCCCCC
Q 009920          175 MVEVKRAVPKEFS  187 (522)
Q Consensus       175 ~I~V~~a~pk~~~  187 (522)
                      +|+|++++++...
T Consensus        99 ~l~V~~a~~~~~~  111 (131)
T 2m2b_A           99 TINVEFAKGSKRD  111 (131)
T ss_dssp             CCCCEECCCSCCC
T ss_pred             EEEEEECCCCCCC
Confidence            9999999987543

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=3.6e-17  Score=145.04  Aligned_cols=85  Identities=18%  Similarity=0.321  Sum_probs=76.9

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCe----EEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEE
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEV----VEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEA   77 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V----~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V   77 (522)
                      .+.++|||+|||+++||+||+++|++||+|    .+|+|++++ ++++||||||+|.++++|++|| ++++.|.+|.|+|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~V   99 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIEL   99 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEE
Confidence            567899999999999999999999999986    689999985 7999999999999999999999 8889999999999


Q ss_pred             eecCCCccccc
Q 009920           78 KKAVPRDDQNM   88 (522)
Q Consensus        78 ~~a~~k~~~~~   88 (522)
                      ..+.+++....
T Consensus       100 ~~a~~~e~~~~  110 (123)
T 2dha_A          100 FRSTAAEVQQV  110 (123)
T ss_dssp             EEECHHHHHHH
T ss_pred             EECCHHHHHHH
Confidence            99877655443

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.67  E-value=4e-17  Score=131.06  Aligned_cols=74  Identities=50%  Similarity=0.942  Sum_probs=70.9

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ++|||+|||+++++++|+++|++||+|.+|+|++++.+++++|||||+|.++++|++|+  ++ +.|++++|.|++|
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            58999999999999999999999999999999999989999999999999999999999  66 9999999999886

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.5e-16  Score=137.10  Aligned_cols=82  Identities=21%  Similarity=0.303  Sum_probs=74.0

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC---CccCCeEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF---HELNGKMVEV  178 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~---~~l~Gr~I~V  178 (522)
                      +.+.++|||+|||+++||+||+++|++||.|++|+|+++      ||||||+|+++++|++|++.++   .+|+|++|.|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   86 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI   86 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCB
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            456789999999999999999999999999999999965      6899999999999999999654   5899999999


Q ss_pred             EEcCCCCCCCC
Q 009920          179 KRAVPKEFSPG  189 (522)
Q Consensus       179 ~~a~pk~~~~~  189 (522)
                      +++++++..+.
T Consensus        87 ~~A~~~~~~~~   97 (105)
T 1sjq_A           87 QFSNHKELKTD   97 (105)
T ss_dssp             CCCSSSSCCCT
T ss_pred             EEcCCCCCCcc
Confidence            99998876543

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.67  E-value=4.2e-17  Score=145.33  Aligned_cols=83  Identities=16%  Similarity=0.333  Sum_probs=77.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEE--EEEeecCCCCCcccEEEEEecCHHHHHHHH--Hccc----ccCCeE
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVE--AVIMRDRATGRARGFGFVVFADPAVAERVI--MDKH----MIDGRT   74 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~--v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~----~i~Gr~   74 (522)
                      ...++|||+|||+++||++|+++|++||+|+.  |+|++++.++++||||||+|.++ +|++|+  ++++    .|++++
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~   99 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKT   99 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEE
Confidence            46789999999999999999999999999977  99999999999999999999999 999999  8998    999999


Q ss_pred             EEEeecCCCccc
Q 009920           75 VEAKKAVPRDDQ   86 (522)
Q Consensus        75 I~V~~a~~k~~~   86 (522)
                      |.|+++.++...
T Consensus       100 l~V~~a~~~~~~  111 (131)
T 2m2b_A          100 INVEFAKGSKRD  111 (131)
T ss_dssp             CCCEECCCSCCC
T ss_pred             EEEEECCCCCCC
Confidence            999999876543

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=3.3e-16  Score=132.75  Aligned_cols=84  Identities=30%  Similarity=0.480  Sum_probs=76.4

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      ...+.++|||+|||+++|+++|+++|++|   .+|.++.++.+++++|||||+|.++++|++||+.++ ++|++++|+|+
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 RSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLD   87 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            34577899999999999999999999977   478899999999999999999999999999999877 89999999999


Q ss_pred             EcCCCCCC
Q 009920          180 RAVPKEFS  187 (522)
Q Consensus       180 ~a~pk~~~  187 (522)
                      +++++...
T Consensus        88 ~a~~~~~~   95 (102)
T 2fc8_A           88 WAKPKGEG   95 (102)
T ss_dssp             ECCCCCSS
T ss_pred             EecCCCCC
Confidence            99987653

>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=4.4e-17  Score=141.27  Aligned_cols=83  Identities=19%  Similarity=0.417  Sum_probs=77.4

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ...++|||+|||+++++++|+++|++||.|++|+|+.++.+++++|||||+|.++++|++|| .++ +.|+|++|+|+++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  101 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS  101 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEec
Confidence            45689999999999999999999999999999999999999999999999999999999999 555 8999999999999


Q ss_pred             CCCCC
Q 009920          182 VPKEF  186 (522)
Q Consensus       182 ~pk~~  186 (522)
                      +++..
T Consensus       102 ~~~~~  106 (114)
T 2cq4_A          102 QAEKN  106 (114)
T ss_dssp             HHHHH
T ss_pred             CCCcc
Confidence            87653

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.66  E-value=8.3e-17  Score=134.60  Aligned_cols=81  Identities=14%  Similarity=0.240  Sum_probs=74.8

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ...++|||+|||+++|++||+++|++||.|+++.++.++.+++++|||||+|.++++|++||+.++ +.|++++|+|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            456899999999999999999999999999999999999999999999999999999999999877 8999999999987


Q ss_pred             CC
Q 009920          182 VP  183 (522)
Q Consensus       182 ~p  183 (522)
                      .+
T Consensus        93 ~s   94 (95)
T 2ek1_A           93 SS   94 (95)
T ss_dssp             C-
T ss_pred             cC
Confidence            63

>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=99.66  E-value=5.9e-17  Score=137.55  Aligned_cols=81  Identities=22%  Similarity=0.447  Sum_probs=74.6

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecC-CCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDR-ATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~-~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++++++|+++|++|| |++|+|++++ .+++++|||||+|.+.++|++|| ++++.|++++|.|+++
T Consensus        17 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~l~V~~a   95 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVA   95 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBCCCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeEEEEEec
Confidence            4679999999999999999999999999 9999999998 68999999999999999999999 9999999999999998


Q ss_pred             CCCc
Q 009920           81 VPRD   84 (522)
Q Consensus        81 ~~k~   84 (522)
                      .++.
T Consensus        96 ~~~~   99 (100)
T 2j76_E           96 DQAQ   99 (100)
T ss_dssp             CCSC
T ss_pred             cCCC
Confidence            7754

>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=99.66  E-value=4.3e-17  Score=130.36  Aligned_cols=74  Identities=35%  Similarity=0.635  Sum_probs=71.0

Q ss_pred             EEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeec
Q 009920            7 KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         7 ~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a   80 (522)
                      +|||+|||+++++++|+++|++||+|.+|+|++++.+++++|||||+|.++++|++|+ ++.+.|++++|.|++|
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            6999999999999999999999999999999999999999999999999999999999 8889999999999875

>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=99.66  E-value=3.4e-16  Score=133.88  Aligned_cols=81  Identities=21%  Similarity=0.427  Sum_probs=76.3

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      ...+.++|||+|||+.+|+++|+++|++||+|++|+|+.++ +++++|||||+|.++++|++||+.++ ..|++++|+|+
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  103 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            44578899999999999999999999999999999999999 89999999999999999999999877 89999999999


Q ss_pred             EcC
Q 009920          180 RAV  182 (522)
Q Consensus       180 ~a~  182 (522)
                      ++.
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            985

>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=99.66  E-value=1.1e-16  Score=136.16  Aligned_cols=84  Identities=25%  Similarity=0.568  Sum_probs=79.2

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ...++|||+|||..+++++|+++|++||.|++|.|+.++.+++++|||||+|.++++|++|++.++ ..|+|++|+|+++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            356799999999999999999999999999999999999999999999999999999999999888 8999999999999


Q ss_pred             CCCCC
Q 009920          182 VPKEF  186 (522)
Q Consensus       182 ~pk~~  186 (522)
                      .++..
T Consensus        86 ~~~~~   90 (104)
T 1p1t_A           86 ASEKN   90 (104)
T ss_dssp             TCTTH
T ss_pred             CCccc
Confidence            98764

>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=99.66  E-value=1.2e-16  Score=138.87  Aligned_cols=84  Identities=13%  Similarity=0.223  Sum_probs=77.9

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCe-eEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTI-TDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I-~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~  180 (522)
                      +.+.++|||+|||+++|+++|+++|++||.| ..|+|++|+ +++++|||||+|.++++|++||+++.+.|++++|+|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHV   90 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEEEE
Confidence            3567899999999999999999999999999 899999998 89999999999999999999999944899999999999


Q ss_pred             cCCCCC
Q 009920          181 AVPKEF  186 (522)
Q Consensus       181 a~pk~~  186 (522)
                      +.+++.
T Consensus        91 a~~~~~   96 (114)
T 2cpy_A           91 VTLEDM   96 (114)
T ss_dssp             ECHHHH
T ss_pred             CCHHHH
Confidence            987763

>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=99.66  E-value=2.4e-16  Score=136.44  Aligned_cols=85  Identities=21%  Similarity=0.377  Sum_probs=77.6

Q ss_pred             CCCcceeEecCCCCCCCHHHHH---HHHhhcCCeeEEEEEecCCCC---CcceEEEEEecCHHHHHHHHHhcC-CccCCe
Q 009920          102 PGRTKKIFVGGLASTVTESDFK---KYFDQFGTITDVVVMYDHNTQ---RPRGFGFITYDSEEAVDRVLHKTF-HELNGK  174 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~---~~F~~fG~I~~v~i~~d~~tg---~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr  174 (522)
                      ..+.++|||+|||+++++++|+   ++|++||+|++|.|++++.++   +++|||||+|+++++|++||+.++ +.|+|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            3467899999999999999999   999999999999999988754   566999999999999999999877 899999


Q ss_pred             EEEEEEcCCCCC
Q 009920          175 MVEVKRAVPKEF  186 (522)
Q Consensus       175 ~I~V~~a~pk~~  186 (522)
                      +|+|++++++..
T Consensus        92 ~l~V~~a~~k~~  103 (111)
T 2cpi_A           92 TLKASLGTTKYC  103 (111)
T ss_dssp             EEEEESCCCCSC
T ss_pred             EEEEEecccccc
Confidence            999999998864

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.66  E-value=8.2e-17  Score=129.23  Aligned_cols=76  Identities=42%  Similarity=0.784  Sum_probs=73.6

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEc
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRA  181 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a  181 (522)
                      ++|||+|||+++++++|+++|++||+|++|.|++++.+++++|||||+|.++++|++|++.+++.|+|++|+|++|
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 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCCCccCCEEEEEEec
Confidence            4799999999999999999999999999999999999999999999999999999999999999999999999987

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.66  E-value=1.2e-16  Score=140.56  Aligned_cols=81  Identities=21%  Similarity=0.520  Sum_probs=76.8

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecCC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~~   82 (522)
                      +.++|||+|||+++|+++|+++|++||+|++|+|++++.+++++|||||+|.++++|++|| ++++.|++++|.|+++.+
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETTEECEEEESSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCC
Confidence            4689999999999999999999999999999999999989999999999999999999999 899999999999999875


Q ss_pred             Cc
Q 009920           83 RD   84 (522)
Q Consensus        83 k~   84 (522)
                      ..
T Consensus       115 ~~  116 (124)
T 2jwn_A          115 NM  116 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=1.7e-16  Score=137.60  Aligned_cols=88  Identities=25%  Similarity=0.349  Sum_probs=76.1

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+.++|||+|||+++|+++|+++|++||.|+.+.+..+..+++++|||||+|.++++|++||+.++ ..|++++|+|++
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3467899999999999999999999999999655444443478899999999999999999999888 899999999999


Q ss_pred             cCCCCCCCC
Q 009920          181 AVPKEFSPG  189 (522)
Q Consensus       181 a~pk~~~~~  189 (522)
                      ++++.....
T Consensus       102 a~~~~~~~~  110 (115)
T 2cpx_A          102 GKNKKQRSS  110 (115)
T ss_dssp             CCCCSCCCC
T ss_pred             ccCCCCCCC
Confidence            998876543

>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=99.66  E-value=5.8e-16  Score=132.87  Aligned_cols=86  Identities=22%  Similarity=0.395  Sum_probs=79.2

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCC-eeEEEEE-ecCCCCCcceEEEEEecCHHHHHHHHHhcC---CccCCeEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGT-ITDVVVM-YDHNTQRPRGFGFITYDSEEAVDRVLHKTF---HELNGKMVE  177 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~-I~~v~i~-~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~---~~l~Gr~I~  177 (522)
                      .+.++|||+|||+++|+++|+++|++||. |++|.|+ .++.+++++|||||+|.++++|++|++.++   ..|+|++|+
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            45789999999999999999999999998 9999999 888889999999999999999999999874   689999999


Q ss_pred             EEEcCCCCCCC
Q 009920          178 VKRAVPKEFSP  188 (522)
Q Consensus       178 V~~a~pk~~~~  188 (522)
                      |++++++....
T Consensus        86 V~~a~~~~~~~   96 (109)
T 2dis_A           86 VDWAEPEIDVD   96 (109)
T ss_dssp             EEESCSSCSTT
T ss_pred             EEEcCCCCCcC
Confidence            99999876543

>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=99.66  E-value=3.9e-16  Score=134.20  Aligned_cols=80  Identities=20%  Similarity=0.375  Sum_probs=73.6

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++||++|+++|++||+|++|+|+.+   +++++||||+|.++++|++||  ++.+.|++++|.|+++
T Consensus        20 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   96 (109)
T 1x4a_A           20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   96 (109)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            56789999999999999999999999999999999664   568999999999999999999  8999999999999999


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      .++..
T Consensus        97 ~~~~~  101 (109)
T 1x4a_A           97 RSGRG  101 (109)
T ss_dssp             CCCCC
T ss_pred             ccCCC
Confidence            87644

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.66  E-value=9.7e-16  Score=134.88  Aligned_cols=87  Identities=20%  Similarity=0.367  Sum_probs=80.2

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      .....++|||+|||..+++++|+++|++||+|++|+|+.++ +++++|||||+|.++++|++|++.++ ..|+|++|+|+
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            44577899999999999999999999999999999999998 89999999999999999999999777 89999999999


Q ss_pred             EcCCCCCCC
Q 009920          180 RAVPKEFSP  188 (522)
Q Consensus       180 ~a~pk~~~~  188 (522)
                      ++.++...+
T Consensus       110 ~a~~~~~~~  118 (124)
T 2kt5_A          110 LVASQIDLE  118 (124)
T ss_dssp             EECCTTCCC
T ss_pred             EeCCCCCCC
Confidence            999876543

>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=99.65  E-value=3.2e-17  Score=141.01  Aligned_cols=84  Identities=17%  Similarity=0.273  Sum_probs=77.8

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCC---eEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEe
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGE---VVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAK   78 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~---V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~   78 (522)
                      .+.++|||+|||+++|+++|+++|++||+   |.+|+|++++. ++++|||||+|.++++|++|| ++++.|.+|.|+|.
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~   87 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVY   87 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCCCCE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHHhCcceeCCeEEEEE
Confidence            56789999999999999999999999988   89999999987 999999999999999999999 99999999999999


Q ss_pred             ecCCCcccc
Q 009920           79 KAVPRDDQN   87 (522)
Q Consensus        79 ~a~~k~~~~   87 (522)
                      ++.+++...
T Consensus        88 ~a~~~~~~~   96 (107)
T 2lmi_A           88 EINNEDVDA   96 (107)
T ss_dssp             ECCHHHHHH
T ss_pred             ECCHHHHHH
Confidence            988765443

>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=99.65  E-value=3.7e-17  Score=144.26  Aligned_cols=83  Identities=16%  Similarity=0.360  Sum_probs=77.0

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      .+.++|||+|||+++||++|+++|++||+|.++.++.+..+++++|||||+|.++++|++|| ++++.|++++|+|.++.
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a~  102 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPIT  102 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECC
Confidence            45689999999999999999999999999999777777778999999999999999999999 99999999999999998


Q ss_pred             CCcc
Q 009920           82 PRDD   85 (522)
Q Consensus        82 ~k~~   85 (522)
                      +++.
T Consensus       103 ~~~~  106 (124)
T 1wel_A          103 KKGM  106 (124)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7654

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.65  E-value=2.7e-16  Score=144.88  Aligned_cols=82  Identities=20%  Similarity=0.385  Sum_probs=77.0

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcC--CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFG--TITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG--~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..++|||+|||+++||++|+++|++||  .|++|+|+.|+.++++||||||+|.++++|++||+.++ ..|+|++|+|++
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            567999999999999999999999999  99999999999999999999999999999999999988 899999999999


Q ss_pred             cCCCC
Q 009920          181 AVPKE  185 (522)
Q Consensus       181 a~pk~  185 (522)
                      +.++.
T Consensus       134 a~~~~  138 (156)
T 3n9u_C          134 ATRQN  138 (156)
T ss_dssp             CCHHH
T ss_pred             cCCCc
Confidence            98653

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.65  E-value=4.7e-16  Score=136.91  Aligned_cols=82  Identities=23%  Similarity=0.416  Sum_probs=77.0

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++++++|+++|++||+|++|+|++++ ++++++||||+|.++++|++|+  ++++.|++++|.|+++
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  111 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  111 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEe
Confidence            456899999999999999999999999999999999998 8999999999999999999999  8999999999999999


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      .+...
T Consensus       112 ~~~~~  116 (124)
T 2kt5_A          112 ASQID  116 (124)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            87544

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.65  E-value=3.4e-17  Score=148.20  Aligned_cols=82  Identities=15%  Similarity=0.209  Sum_probs=74.2

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcC
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAV  182 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~  182 (522)
                      ...++|||+|||+++||+||+++|++|| |++|+|++|++ +++||||||+|+++++|++||+++.++|++|.|+|..+.
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a~  121 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNS  121 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEECC
Confidence            4567999999999999999999999999 67999999987 999999999999999999999544489999999999998


Q ss_pred             CCCC
Q 009920          183 PKEF  186 (522)
Q Consensus       183 pk~~  186 (522)
                      +++.
T Consensus       122 ~~~~  125 (139)
T 2hgn_A          122 TTGA  125 (139)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            7654

>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=99.65  E-value=1.3e-16  Score=143.77  Aligned_cols=83  Identities=19%  Similarity=0.314  Sum_probs=76.8

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCC---eeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGT---ITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMV  176 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~---I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I  176 (522)
                      .....++|||+|||+++||+||+++|++||.   |++|+|++|+. +++||||||+|+++++|++||+ ++ ++|++|+|
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i  117 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYI  117 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEE
Confidence            3456789999999999999999999999999   89999999988 9999999999999999999999 66 89999999


Q ss_pred             EEEEcCCCC
Q 009920          177 EVKRAVPKE  185 (522)
Q Consensus       177 ~V~~a~pk~  185 (522)
                      +|.++.+++
T Consensus       118 ~V~~a~~~e  126 (136)
T 2hgl_A          118 EVFKSHRTE  126 (136)
T ss_dssp             EEEECCHHH
T ss_pred             EEEECChHH
Confidence            999998765

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=1.8e-16  Score=135.94  Aligned_cols=80  Identities=13%  Similarity=0.276  Sum_probs=74.8

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcC
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAV  182 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~  182 (522)
                      ...++|||+|||+++|+++|+++|++||+|++|.|++|+. +++||||||+|+++++|++||++..+.|+|++|.|.++.
T Consensus         9 ~~~~~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            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   87 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEEHH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEch
Confidence            4568999999999999999999999999999999999988 999999999999999999999954489999999999877


Q ss_pred             C
Q 009920          183 P  183 (522)
Q Consensus       183 p  183 (522)
                      +
T Consensus        88 ~   88 (103)
T 1s79_A           88 D   88 (103)
T ss_dssp             H
T ss_pred             H
Confidence            5

>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=99.65  E-value=6.9e-16  Score=132.01  Aligned_cols=81  Identities=17%  Similarity=0.290  Sum_probs=73.0

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC---CccCCeEEEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF---HELNGKMVEVK  179 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~---~~l~Gr~I~V~  179 (522)
                      .+.++|||+|||+++||++|+++|++||.|++|.|+++      ||||||+|+++++|++|++.++   .+|.|++|.|+
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   86 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   86 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEE
Confidence            46789999999999999999999999999999998864      7899999999999999999753   57999999999


Q ss_pred             EcCCCCCCCC
Q 009920          180 RAVPKEFSPG  189 (522)
Q Consensus       180 ~a~pk~~~~~  189 (522)
                      +++++.....
T Consensus        87 ~a~~~~~~~~   96 (101)
T 2cq1_A           87 YSNHKELKTS   96 (101)
T ss_dssp             ECSCSSCCCC
T ss_pred             EcCcccCcCC
Confidence            9998876553

>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=1.2e-16  Score=127.86  Aligned_cols=75  Identities=53%  Similarity=0.977  Sum_probs=71.1

Q ss_pred             eeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEc
Q 009920          107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRA  181 (522)
Q Consensus       107 ~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a  181 (522)
                      +|||+|||+++++++|+++|++||+|++|.|+.++.+++++|||||+|.++++|++|+++..+.|+|++|+|++|
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            589999999999999999999999999999999999999999999999999999999985558999999999875

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=5.7e-16  Score=131.21  Aligned_cols=82  Identities=21%  Similarity=0.426  Sum_probs=73.5

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+.++|||+|||+++|+++|+++|++||.|   +|+.+ .+++++|||||+|+++++|++||+.++ ..|++++|+|++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            3567899999999999999999999999977   56666 678899999999999999999999887 899999999999


Q ss_pred             cCCCCCC
Q 009920          181 AVPKEFS  187 (522)
Q Consensus       181 a~pk~~~  187 (522)
                      ++++...
T Consensus        88 a~~~~~~   94 (101)
T 2fc9_A           88 QGPRGSP   94 (101)
T ss_dssp             CSSCCCC
T ss_pred             cCCCCCC
Confidence            9987543

>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=99.65  E-value=1.4e-15  Score=129.48  Aligned_cols=80  Identities=29%  Similarity=0.509  Sum_probs=72.6

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+.++|||+|||+++|+++|+++|++||.|++|+|+        ++||||+|+++++|++||+.++ ++|++++|+|++
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            3567899999999999999999999999999999987        4499999999999999999877 899999999999


Q ss_pred             cCCCCCCCC
Q 009920          181 AVPKEFSPG  189 (522)
Q Consensus       181 a~pk~~~~~  189 (522)
                      ++++...+.
T Consensus        80 a~~~~~~~~   88 (103)
T 2dgu_A           80 AKPPDQKRK   88 (103)
T ss_dssp             CCCCCCCCC
T ss_pred             cCCCcccch
Confidence            998876543

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.65  E-value=1.3e-16  Score=143.24  Aligned_cols=83  Identities=33%  Similarity=0.546  Sum_probs=78.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++|+++|+++|++||+|++|+|++++.+++++|||||+|.++++|++||  ++++.|++++|.|+++
T Consensus        45 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a  124 (135)
T 2lea_A           45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  124 (135)
T ss_dssp             GGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45789999999999999999999999999999999999989999999999999999999999  8999999999999999


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      .++..
T Consensus       125 ~~~~~  129 (135)
T 2lea_A          125 RYGRP  129 (135)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87544

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.65  E-value=9.9e-17  Score=142.77  Aligned_cols=80  Identities=26%  Similarity=0.449  Sum_probs=73.6

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeE--EEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEee
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVV--EAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKK   79 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~--~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~   79 (522)
                      .+.++|||+|||+++||++|+++|++| .|+  +|+|+++++ +++||||||+|.++++|++|| ++++.|.+|.|+|.+
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V~~  117 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFK  117 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEEEE
Confidence            457899999999999999999999999 677  899999987 999999999999999999999 778999999999998


Q ss_pred             cCCCc
Q 009920           80 AVPRD   84 (522)
Q Consensus        80 a~~k~   84 (522)
                      +.+++
T Consensus       118 a~~~e  122 (126)
T 2hgm_A          118 SSQEE  122 (126)
T ss_dssp             ECHHH
T ss_pred             CCHHH
Confidence            86544

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=7.8e-16  Score=127.72  Aligned_cols=79  Identities=20%  Similarity=0.507  Sum_probs=72.3

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+.++|||+|||.++|+++|+++|++||+|++|.|+        |+||||+|+++++|++|++.++ ..|++++|+|++
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            3567899999999999999999999999999999997        5799999999999999998887 799999999999


Q ss_pred             cCCCCCCC
Q 009920          181 AVPKEFSP  188 (522)
Q Consensus       181 a~pk~~~~  188 (522)
                      ++++....
T Consensus        77 a~~~~~~~   84 (90)
T 2dnq_A           77 SKNKSKAS   84 (90)
T ss_dssp             SSCCCCCC
T ss_pred             CCCCCCCC
Confidence            99876543

>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=99.65  E-value=4.9e-17  Score=134.76  Aligned_cols=80  Identities=29%  Similarity=0.646  Sum_probs=72.0

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCCC
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVPR   83 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~k   83 (522)
                      ++|||+|||+++++++|+++|++||+|++|+|++++.+++++|||||+|.+++ |++|+  ++++.|++++|.|+++.++
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            78999999999999999999999999999999999999999999999999999 99999  8999999999999999876


Q ss_pred             ccc
Q 009920           84 DDQ   86 (522)
Q Consensus        84 ~~~   86 (522)
                      ...
T Consensus        81 ~~~   83 (90)
T 2ki2_A           81 KSL   83 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            543

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.65  E-value=6.8e-16  Score=135.61  Aligned_cols=82  Identities=18%  Similarity=0.435  Sum_probs=76.4

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      ..++|||+|||.++|+++|+++|++||.|++|.|+.++.+++++|||||+|.++++|++|| .++ +.|+|++|+|++++
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~  113 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR  113 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            4579999999999999999999999999999999999999999999999999999999999 555 89999999999998


Q ss_pred             CCCC
Q 009920          183 PKEF  186 (522)
Q Consensus       183 pk~~  186 (522)
                      ++..
T Consensus       114 ~~~~  117 (124)
T 2jwn_A          114 TNMP  117 (124)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            6543

>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=99.64  E-value=1.2e-16  Score=127.85  Aligned_cols=75  Identities=37%  Similarity=0.741  Sum_probs=72.1

Q ss_pred             eeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEc
Q 009920          107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRA  181 (522)
Q Consensus       107 ~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a  181 (522)
                      +|||+|||.++|+++|+++|++||+|++|.+++++.+++++|||||+|.++++|++|++++++.|+|++|+|++|
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            699999999999999999999999999999999999999999999999999999999998778999999999875

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.64  E-value=1.1e-16  Score=135.77  Aligned_cols=82  Identities=29%  Similarity=0.632  Sum_probs=76.3

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHHHcccccCCeEEEEeecCC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl~~~~~i~Gr~I~V~~a~~   82 (522)
                      .+.++|||+|||+++++++|+++|++||+|++|+|++++ +++++|||||+|.++++|++|+.+++.|++++|.|.++.+
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~~~~~~~g~~l~v~~a~~   85 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQINFHGKKLKLGPAIR   85 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTTCCCEETTEECEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHhCCCeECCEEEEEEECCc
Confidence            457899999999999999999999999999999999998 8999999999999999999999888899999999999876


Q ss_pred             Ccc
Q 009920           83 RDD   85 (522)
Q Consensus        83 k~~   85 (522)
                      +..
T Consensus        86 ~~~   88 (102)
T 2xs2_A           86 KQN   88 (102)
T ss_dssp             CC-
T ss_pred             Ccc
Confidence            654

>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=99.64  E-value=4e-16  Score=142.72  Aligned_cols=83  Identities=33%  Similarity=0.546  Sum_probs=78.0

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++|+++|+++|++||+|++|+|++++.+++++|||||+|.++++|++||  ++++.|.+++|.|+++
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  147 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  147 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            34689999999999999999999999999999999999989999999999999999999999  7999999999999999


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      .++..
T Consensus       148 ~~~~~  152 (158)
T 2kn4_A          148 RYGRP  152 (158)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            87643

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=2.4e-16  Score=136.79  Aligned_cols=81  Identities=21%  Similarity=0.337  Sum_probs=74.3

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcC
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAV  182 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~  182 (522)
                      ....+|||+|||+++|++||+++|++| .|++|+|++|+. ++++|||||+|+++++|++||+++.+.|++|.|+|..+.
T Consensus        14 ~~~~~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           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECC
Confidence            456799999999999999999999999 899999999987 999999999999999999999655589999999999987


Q ss_pred             CCC
Q 009920          183 PKE  185 (522)
Q Consensus       183 pk~  185 (522)
                      +++
T Consensus        92 ~~~   94 (109)
T 2dnn_A           92 ERQ   94 (109)
T ss_dssp             HHH
T ss_pred             ccc
Confidence            654

>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=99.64  E-value=2.1e-16  Score=136.77  Aligned_cols=81  Identities=22%  Similarity=0.424  Sum_probs=75.1

Q ss_pred             CCcEEEECCCCCCCCHHHHH---HHHhccCCeEEEEEeecCCCC---CcccEEEEEecCHHHHHHHH--HcccccCCeEE
Q 009920            4 DLGKLFIGGISWDTDEERLK---EYFSRYGEVVEAVIMRDRATG---RARGFGFVVFADPAVAERVI--MDKHMIDGRTV   75 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~---e~F~~~G~V~~v~i~~d~~tg---~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I   75 (522)
                      ..++|||+|||++++|++|+   ++|++||+|++|+|++++.++   +++|||||+|.++++|++||  ++++.|++++|
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l   93 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   93 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEE
Confidence            56899999999999999999   999999999999999987754   56699999999999999999  79999999999


Q ss_pred             EEeecCCCc
Q 009920           76 EAKKAVPRD   84 (522)
Q Consensus        76 ~V~~a~~k~   84 (522)
                      .|+++.++.
T Consensus        94 ~V~~a~~k~  102 (111)
T 2cpi_A           94 KASLGTTKY  102 (111)
T ss_dssp             EEESCCCCS
T ss_pred             EEEeccccc
Confidence            999998775

>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=99.64  E-value=6e-16  Score=133.98  Aligned_cols=80  Identities=28%  Similarity=0.528  Sum_probs=73.6

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hccccc--------CC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMI--------DG   72 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i--------~G   72 (522)
                      .+.++|||+|||+++|+++|+++|++||+|++|+|++++ ++++++||||+|.++++|++||  +++..|        .+
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~  101 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT  101 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCC
Confidence            567999999999999999999999999999999999998 8999999999999999999999  899988        46


Q ss_pred             eEEEEeecCCC
Q 009920           73 RTVEAKKAVPR   83 (522)
Q Consensus        73 r~I~V~~a~~k   83 (522)
                      ++|.|+++.++
T Consensus       102 ~~l~v~~a~p~  112 (114)
T 1x5o_A          102 EPLLCKFSGPS  112 (114)
T ss_dssp             SCBEEEECCCS
T ss_pred             CceeEEccCCC
Confidence            77888887654

>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=99.64  E-value=9.7e-16  Score=131.82  Aligned_cols=77  Identities=21%  Similarity=0.315  Sum_probs=71.4

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCC-----eEE
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDG-----RTV   75 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~G-----r~I   75 (522)
                      ...++|||+|||+++|+++|+++|++||+|++|+|+++       +||||+|.++++|++||  +++++|++     ++|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            46789999999999999999999999999999999886       79999999999999999  89999999     999


Q ss_pred             EEeecCCCccc
Q 009920           76 EAKKAVPRDDQ   86 (522)
Q Consensus        76 ~V~~a~~k~~~   86 (522)
                      +|+++.++...
T Consensus        86 ~V~~a~~~~~~   96 (108)
T 1x4c_A           86 RVKVDGPRSPS   96 (108)
T ss_dssp             EEEESSCCSCC
T ss_pred             EEEeCCCCCCC
Confidence            99999886543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.64  E-value=1.2e-16  Score=135.33  Aligned_cols=84  Identities=17%  Similarity=0.364  Sum_probs=76.6

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ...++|||+|||+++|+++|+++|++||.|.. .++.++.+++++|||||+|.++++|++||+ ++ ..|.+++|+|+++
T Consensus        15 ~~~~~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           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            45789999999999999999999999999988 777888889999999999999999999999 66 8999999999999


Q ss_pred             CCCCCCC
Q 009920          182 VPKEFSP  188 (522)
Q Consensus       182 ~pk~~~~  188 (522)
                      +++...+
T Consensus        93 ~~~~~~~   99 (101)
T 1fj7_A           93 KGRDGTR   99 (101)
T ss_dssp             SCCCCSS
T ss_pred             CCCCCCC
Confidence            9876543

>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=99.64  E-value=1.2e-15  Score=131.24  Aligned_cols=80  Identities=18%  Similarity=0.302  Sum_probs=71.7

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC---CccCCeEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF---HELNGKMVEV  178 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~---~~l~Gr~I~V  178 (522)
                      ..+.++|||+|||++++|++|+++|++||.|++|.|+++      ||||||+|+++++|++|++.++   ..|+|++|.|
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            346789999999999999999999999999999998854      6899999999999999999764   3699999999


Q ss_pred             EEcCCCCCC
Q 009920          179 KRAVPKEFS  187 (522)
Q Consensus       179 ~~a~pk~~~  187 (522)
                      ++++++...
T Consensus        86 ~~a~~~~~~   94 (104)
T 1wex_A           86 NYSTSKRIT   94 (104)
T ss_dssp             EECSSSSCC
T ss_pred             EEccCcccc
Confidence            999987654

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.64  E-value=5e-16  Score=138.76  Aligned_cols=78  Identities=29%  Similarity=0.503  Sum_probs=74.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++|+++|+++|++||+|++|+|++++.++++++||||+|.++++|++|+  ++++.|++++|+|++|
T Consensus        61 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A           61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            46899999999999999999999999999999999999999999999999999999999999  8999999999999875

>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=99.64  E-value=8.2e-16  Score=135.46  Aligned_cols=80  Identities=21%  Similarity=0.316  Sum_probs=73.3

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC---CccCCeEEEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF---HELNGKMVEVK  179 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~---~~l~Gr~I~V~  179 (522)
                      .+.++|||+|||+++||++|+++|++||.|++|.|+++      ||||||+|+++++|++|++.++   .+|.|++|+|+
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~  102 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ  102 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEE
Confidence            46789999999999999999999999999999999975      6899999999999999999775   47999999999


Q ss_pred             EcCCCCCCC
Q 009920          180 RAVPKEFSP  188 (522)
Q Consensus       180 ~a~pk~~~~  188 (522)
                      ++++++..+
T Consensus       103 ~a~~k~~~~  111 (119)
T 2ad9_A          103 FSNHKELKT  111 (119)
T ss_dssp             ECSSSSCCC
T ss_pred             EccCCCCCc
Confidence            999887654

>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=99.63  E-value=1.4e-16  Score=135.31  Aligned_cols=83  Identities=23%  Similarity=0.409  Sum_probs=74.0

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecC-CCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDH-NTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEV  178 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~-~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V  178 (522)
                      .....++|||+|||+++++++|+++|++|| |++|+|++++ .+++++|||||+|.++++|++|| .++ ..|+|++|+|
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V   92 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRV   92 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEE
Confidence            345678999999999999999999999999 9999999998 68999999999999999999999 566 8999999999


Q ss_pred             EEcCCCC
Q 009920          179 KRAVPKE  185 (522)
Q Consensus       179 ~~a~pk~  185 (522)
                      ++++++.
T Consensus        93 ~~a~~~~   99 (100)
T 2j76_E           93 DVADQAQ   99 (100)
T ss_dssp             EECCCSC
T ss_pred             EeccCCC
Confidence            9998764

>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=99.63  E-value=2.6e-16  Score=153.83  Aligned_cols=80  Identities=24%  Similarity=0.494  Sum_probs=74.7

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccC--CeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYG--EVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G--~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      +.++|||+|||+++||++|+++|++||  +|++|+|++++.++++||||||+|.++++|++||  ++.+.|++++|+|++
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  899999999999998


Q ss_pred             cCCC
Q 009920           80 AVPR   83 (522)
Q Consensus        80 a~~k   83 (522)
                      +.++
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
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=99.63  E-value=3.3e-16  Score=137.33  Aligned_cols=83  Identities=20%  Similarity=0.361  Sum_probs=76.5

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCC---eeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGT---ITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEV  178 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~---I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V  178 (522)
                      ....++|||+|||+++|++||+++|++||.   |++|+|++++. +++||||||+|.++++|++||+++.+.|++|.|+|
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            346789999999999999999999999999   89999999988 99999999999999999999995448999999999


Q ss_pred             EEcCCCC
Q 009920          179 KRAVPKE  185 (522)
Q Consensus       179 ~~a~pk~  185 (522)
                      .++.+++
T Consensus        93 ~~a~~~~   99 (118)
T 2db1_A           93 FKSHRTE   99 (118)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9998665

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=5.1e-16  Score=131.53  Aligned_cols=80  Identities=24%  Similarity=0.493  Sum_probs=72.6

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      +.+.++|||+|||+++|+++|+++|++||+|   +|+++ .++++++||||+|.++++|++||  ++++.|++++|.|++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            4578999999999999999999999999977   56666 57899999999999999999999  899999999999999


Q ss_pred             cCCCcc
Q 009920           80 AVPRDD   85 (522)
Q Consensus        80 a~~k~~   85 (522)
                      +.++..
T Consensus        88 a~~~~~   93 (101)
T 2fc9_A           88 QGPRGS   93 (101)
T ss_dssp             CSSCCC
T ss_pred             cCCCCC
Confidence            987654

>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=1.2e-16  Score=131.04  Aligned_cols=80  Identities=20%  Similarity=0.461  Sum_probs=74.4

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      .+.++|||+|||+++++++|+++|++||+|++|.|+.++.+++++|||||+|.++++|++|++.++ ..|+++.|+|.++
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            467899999999999999999999999999999999999999999999999999999999999887 8999999887664


Q ss_pred             C
Q 009920          182 V  182 (522)
Q Consensus       182 ~  182 (522)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.63  E-value=8.4e-16  Score=131.49  Aligned_cols=78  Identities=10%  Similarity=0.172  Sum_probs=70.0

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--H--cccccCCeEEEEe
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M--DKHMIDGRTVEAK   78 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~--~~~~i~Gr~I~V~   78 (522)
                      ...++|||+|||+++||++|+++|++||+|++|+|+++      |+||||+|.++++|++|+  +  +...|.+++|.|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   86 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   86 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEE
Confidence            46789999999999999999999999999999998875      689999999999999999  3  4578999999999


Q ss_pred             ecCCCccc
Q 009920           79 KAVPRDDQ   86 (522)
Q Consensus        79 ~a~~k~~~   86 (522)
                      ++.++...
T Consensus        87 ~a~~~~~~   94 (101)
T 2cq1_A           87 YSNHKELK   94 (101)
T ss_dssp             ECSCSSCC
T ss_pred             EcCcccCc
Confidence            99876544

>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=99.63  E-value=1.5e-16  Score=131.90  Aligned_cols=81  Identities=33%  Similarity=0.673  Sum_probs=72.8

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCC
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPK  184 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk  184 (522)
                      ++|||+|||.++++++|+++|++||+|++|.|++++.+++++|||||+|++++ |++|++.++ ..|+|++|+|++|.++
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            58999999999999999999999999999999999999999999999999999 999999888 8999999999999987


Q ss_pred             CCC
Q 009920          185 EFS  187 (522)
Q Consensus       185 ~~~  187 (522)
                      ...
T Consensus        81 ~~~   83 (90)
T 2ki2_A           81 KSL   83 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            643

>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=99.63  E-value=7.7e-16  Score=135.64  Aligned_cols=79  Identities=10%  Similarity=0.225  Sum_probs=71.0

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hc--ccccCCeEEEEe
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MD--KHMIDGRTVEAK   78 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~--~~~i~Gr~I~V~   78 (522)
                      ...++|||+|||+++||++|+++|++||+|++|+|+++      ||||||+|.++++|++|+  ++  ...|.+++|.|.
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~  102 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ  102 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEE
Confidence            45789999999999999999999999999999999875      689999999999999999  44  468999999999


Q ss_pred             ecCCCcccc
Q 009920           79 KAVPRDDQN   87 (522)
Q Consensus        79 ~a~~k~~~~   87 (522)
                      ++.++....
T Consensus       103 ~a~~k~~~~  111 (119)
T 2ad9_A          103 FSNHKELKT  111 (119)
T ss_dssp             ECSSSSCCC
T ss_pred             EccCCCCCc
Confidence            998766544

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=6.8e-16  Score=133.20  Aligned_cols=83  Identities=27%  Similarity=0.605  Sum_probs=76.2

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      .....++|||+|||.++|+++|+++|++||.|++|+|+.++.  +++|||||+|+++++|++|++.++ ..|+|++|+|+
T Consensus        25 ~~~~~~~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           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT--BCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC--CCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            345678999999999999999999999999999999999864  489999999999999999999877 89999999999


Q ss_pred             EcCCCC
Q 009920          180 RAVPKE  185 (522)
Q Consensus       180 ~a~pk~  185 (522)
                      +++++.
T Consensus       103 ~a~~~~  108 (109)
T 2err_A          103 NATARV  108 (109)
T ss_dssp             ECCCSC
T ss_pred             ECCCCc
Confidence            998864

>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=99.63  E-value=1.1e-15  Score=132.31  Aligned_cols=82  Identities=17%  Similarity=0.357  Sum_probs=75.8

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-Ccc--------C
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HEL--------N  172 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l--------~  172 (522)
                      ..+.++|||+|||+++|+++|+++|++||.|++|+|+.++ +++++|||||+|.++++|++||+.++ ..|        .
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            3467899999999999999999999999999999999998 89999999999999999999999877 777        5


Q ss_pred             CeEEEEEEcCCC
Q 009920          173 GKMVEVKRAVPK  184 (522)
Q Consensus       173 Gr~I~V~~a~pk  184 (522)
                      +++|.|+++.|+
T Consensus       101 ~~~l~v~~a~p~  112 (114)
T 1x5o_A          101 TEPLLCKFSGPS  112 (114)
T ss_dssp             SSCBEEEECCCS
T ss_pred             CCceeEEccCCC
Confidence            788999999865

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=1.1e-15  Score=126.72  Aligned_cols=77  Identities=27%  Similarity=0.585  Sum_probs=71.1

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      ..+.++|||+|||+++|+++|+++|++||+|++|+|+        |+||||+|.++++|++|+  +++..|++++|.|++
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            3578999999999999999999999999999999997        479999999999999999  899999999999999


Q ss_pred             cCCCccc
Q 009920           80 AVPRDDQ   86 (522)
Q Consensus        80 a~~k~~~   86 (522)
                      +.++...
T Consensus        77 a~~~~~~   83 (90)
T 2dnq_A           77 SKNKSKA   83 (90)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            9876543

>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=99.63  E-value=1.1e-15  Score=131.36  Aligned_cols=78  Identities=15%  Similarity=0.193  Sum_probs=69.3

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hcc--cccCCeEEEEe
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDK--HMIDGRTVEAK   78 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~--~~i~Gr~I~V~   78 (522)
                      ..+++|||+|||++++|++|+++|++||+|++|+|+++      |+||||+|.++++|++|+  ++.  ..|++++|.|+
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~   86 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            45789999999999999999999999999999998864      689999999999999999  443  56999999999


Q ss_pred             ecCCCccc
Q 009920           79 KAVPRDDQ   86 (522)
Q Consensus        79 ~a~~k~~~   86 (522)
                      ++.++...
T Consensus        87 ~a~~~~~~   94 (104)
T 1wex_A           87 YSTSKRIT   94 (104)
T ss_dssp             ECSSSSCC
T ss_pred             EccCcccc
Confidence            99876544

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A

Probab=99.63  E-value=9.5e-17  Score=145.27  Aligned_cols=81  Identities=20%  Similarity=0.232  Sum_probs=74.4

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      .+.++|||+|||+++||+||+++|++|| |++|+|+++++ +++||||||+|.++++|++|| ++++.|++|.|+|..+.
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a~  121 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNS  121 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEECC
Confidence            4568999999999999999999999999 66999999986 999999999999999999999 89999999999999887


Q ss_pred             CCcc
Q 009920           82 PRDD   85 (522)
Q Consensus        82 ~k~~   85 (522)
                      +++.
T Consensus       122 ~~~~  125 (139)
T 2hgn_A          122 TTGA  125 (139)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            6654

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=5.1e-16  Score=133.99  Aligned_cols=80  Identities=26%  Similarity=0.607  Sum_probs=74.6

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      +.+.++|||+|||+++|+++|+++|++||+|++|+|++++  ++++|||||+|.++++|++|+  ++++.|++++|.|++
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  103 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN  103 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3568999999999999999999999999999999999986  359999999999999999999  899999999999999


Q ss_pred             cCCC
Q 009920           80 AVPR   83 (522)
Q Consensus        80 a~~k   83 (522)
                      +.++
T Consensus       104 a~~~  107 (109)
T 2err_A          104 ATAR  107 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            9775

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.63  E-value=7.6e-17  Score=136.65  Aligned_cols=82  Identities=24%  Similarity=0.334  Sum_probs=75.7

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      .+.++|||+|||+++|+++|+++|++||+|.+ ++++++.+++++|||||+|.++++|++|| ++++.|++++|.|+++.
T Consensus        15 ~~~~~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           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPK   93 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEECCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEEEcC
Confidence            36789999999999999999999999999988 77777778999999999999999999999 99999999999999998


Q ss_pred             CCcc
Q 009920           82 PRDD   85 (522)
Q Consensus        82 ~k~~   85 (522)
                      ++..
T Consensus        94 ~~~~   97 (101)
T 1fj7_A           94 GRDG   97 (101)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.63  E-value=7.4e-16  Score=132.14  Aligned_cols=78  Identities=13%  Similarity=0.170  Sum_probs=70.4

Q ss_pred             CCcceeEecCCCC-CCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC---CccCCeEEEE
Q 009920          103 GRTKKIFVGGLAS-TVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF---HELNGKMVEV  178 (522)
Q Consensus       103 ~~~~~LfVgnLp~-~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~---~~l~Gr~I~V  178 (522)
                      .+.++|||+|||+ ++||+||+++|++||.|++|.|+++      |+||||+|+++++|++||+.++   .+|.||+|.|
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            4678999999999 9999999999999999999999865      4699999999999999999876   3599999999


Q ss_pred             EEcCCCCC
Q 009920          179 KRAVPKEF  186 (522)
Q Consensus       179 ~~a~pk~~  186 (522)
                      .+++++..
T Consensus        87 ~~a~~~~~   94 (102)
T 1x4d_A           87 HLSQKYKR   94 (102)
T ss_dssp             EEECCCTT
T ss_pred             EECCCCCC
Confidence            99986543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=2.2e-15  Score=125.46  Aligned_cols=78  Identities=18%  Similarity=0.413  Sum_probs=71.5

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ....++|||+|||+++|+++|+++|++||.|++|.|+++        ||||+|+++++|++|++.++ +.|++++|+|++
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 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS--------EEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            457789999999999999999999999999999999843        99999999999999999877 899999999999


Q ss_pred             cCCCCCC
Q 009920          181 AVPKEFS  187 (522)
Q Consensus       181 a~pk~~~  187 (522)
                      ++++...
T Consensus        79 a~~~~~~   85 (92)
T 2dgt_A           79 STSRLRT   85 (92)
T ss_dssp             SSCCCSC
T ss_pred             ccCCCCC
Confidence            9987653

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=7.1e-16  Score=130.70  Aligned_cols=81  Identities=41%  Similarity=0.578  Sum_probs=74.5

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++|+++|+++|++|   .+|++++++.++++++||||+|.++++|++||  ++++.|++++|.|+++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2fc8_A           13 QPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWA   89 (102)
T ss_dssp             CCCSSEEEECCCTTCCHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCccCHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEe
Confidence            567999999999999999999999977   47889999889999999999999999999999  8999999999999999


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      .++...
T Consensus        90 ~~~~~~   95 (102)
T 2fc8_A           90 KPKGEG   95 (102)
T ss_dssp             CCCCSS
T ss_pred             cCCCCC
Confidence            876543

>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=99.63  E-value=2.5e-16  Score=138.89  Aligned_cols=83  Identities=13%  Similarity=0.298  Sum_probs=76.6

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ....++|||+|||+++|+++|+++|++||.|+++.++.+..+++++|||||+|.++++|++||+ ++ +.|++++|+|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            3466899999999999999999999999999998888888899999999999999999999999 55 899999999999


Q ss_pred             cCCCC
Q 009920          181 AVPKE  185 (522)
Q Consensus       181 a~pk~  185 (522)
                      +.+++
T Consensus       101 a~~~~  105 (124)
T 1wel_A          101 ITKKG  105 (124)
T ss_dssp             ECHHH
T ss_pred             CCHHH
Confidence            98765

>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=99.62  E-value=1.1e-15  Score=131.69  Aligned_cols=76  Identities=21%  Similarity=0.481  Sum_probs=69.4

Q ss_pred             CCcceeEecCCCCC-CCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          103 GRTKKIFVGGLAST-VTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       103 ~~~~~LfVgnLp~~-vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ...++|||+|||++ +|+++|+++|++||+|++|.|        +++||||+|+++++|++||+.++ ..|++++|+|++
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   96 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINM   96 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34689999999999 999999999999999999998        47899999999999999998877 899999999999


Q ss_pred             cCCCCC
Q 009920          181 AVPKEF  186 (522)
Q Consensus       181 a~pk~~  186 (522)
                      ++++..
T Consensus        97 a~~~~~  102 (110)
T 1wf1_A           97 AGEPKP  102 (110)
T ss_dssp             SCCCCS
T ss_pred             CCCCCC
Confidence            986543

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.62  E-value=1.8e-15  Score=135.10  Aligned_cols=81  Identities=30%  Similarity=0.546  Sum_probs=75.9

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      ...+.++|||+|||..+|+++|+++|++||+|++|+|++++.+++++|||||+|+++++|++||+.++ ..|+|++|+|+
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            34567899999999999999999999999999999999999999999999999999999999999888 89999999998


Q ss_pred             Ec
Q 009920          180 RA  181 (522)
Q Consensus       180 ~a  181 (522)
                      +|
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            75

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.62  E-value=1.6e-15  Score=129.54  Aligned_cols=77  Identities=18%  Similarity=0.300  Sum_probs=70.4

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-C--ccCCeEEEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-H--ELNGKMVEVK  179 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~--~l~Gr~I~V~  179 (522)
                      .++++|||+|||+++|+++|+++|++||.|++|.+++      .||||||+|+++++|++|++.++ .  .|.||+|.|.
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~   92 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN   92 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEE
Confidence            4678999999999999999999999999999999984      36899999999999999999877 4  4899999999


Q ss_pred             EcCCCC
Q 009920          180 RAVPKE  185 (522)
Q Consensus       180 ~a~pk~  185 (522)
                      ++++++
T Consensus        93 ~S~~k~   98 (100)
T 3r27_A           93 YSTSQK   98 (100)
T ss_dssp             ECSCSC
T ss_pred             eccccc
Confidence            998875

>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=99.62  E-value=1.9e-15  Score=128.60  Aligned_cols=78  Identities=22%  Similarity=0.445  Sum_probs=71.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++|+++|+++|++||+|++|+|++        +||||+|.++++|++||  ++++.|++++|.|+++
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK--------DYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC--------CEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            4578999999999999999999999999999999874        49999999999999999  7999999999999999


Q ss_pred             CCCccccc
Q 009920           81 VPRDDQNM   88 (522)
Q Consensus        81 ~~k~~~~~   88 (522)
                      .++.....
T Consensus        81 ~~~~~~~~   88 (103)
T 2dgu_A           81 KPPDQKRK   88 (103)
T ss_dssp             CCCCCCCC
T ss_pred             CCCcccch
Confidence            88765543

>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=99.62  E-value=1.3e-15  Score=128.16  Aligned_cols=79  Identities=24%  Similarity=0.416  Sum_probs=72.0

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccC--CeEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELN--GKMVEV  178 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~--Gr~I~V  178 (522)
                      ..+.++|||+|||+++|+++|+++|++||+|++|.|+++      ++||||+|+++++|++|++.++ ..|+  +++|+|
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            346789999999999999999999999999999999754      6799999999999999999877 8899  999999


Q ss_pred             EEcCCCCC
Q 009920          179 KRAVPKEF  186 (522)
Q Consensus       179 ~~a~pk~~  186 (522)
                      ++++++..
T Consensus        88 ~~a~~~~~   95 (97)
T 1why_A           88 DFAKSGPS   95 (97)
T ss_dssp             EECCCCCC
T ss_pred             EECCCCCC
Confidence            99998753

>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=99.62  E-value=1.3e-15  Score=141.03  Aligned_cols=84  Identities=23%  Similarity=0.374  Sum_probs=77.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++|+++|+++|++||+|.+|.|++++.+++++|||||+|.++++|++||  ++++.|.+++|.|.++
T Consensus        70 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  149 (165)
T 1rk8_A           70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  149 (165)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            35678999999999999999999999999999999999999999999999999999999999  8999999999999999


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      .++...
T Consensus       150 ~~~~~~  155 (165)
T 1rk8_A          150 FVKGPK  155 (165)
T ss_dssp             EECC--
T ss_pred             cCCCCC
Confidence            776543

>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=99.62  E-value=2.4e-16  Score=140.30  Aligned_cols=83  Identities=18%  Similarity=0.346  Sum_probs=75.7

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCee--EEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTIT--DVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVK  179 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~--~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~  179 (522)
                      ....++|||+|||+++||+||+++|++| .|+  +|+|++|+. +++||||||+|+++++|++||++++.+|++|.|+|.
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            3467889999999999999999999999 676  899999988 999999999999999999999987799999999999


Q ss_pred             EcCCCCC
Q 009920          180 RAVPKEF  186 (522)
Q Consensus       180 ~a~pk~~  186 (522)
                      .+.+++.
T Consensus       117 ~a~~~e~  123 (126)
T 2hgm_A          117 KSSQEEV  123 (126)
T ss_dssp             EECHHHH
T ss_pred             ECCHHHh
Confidence            9876653

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=3.7e-15  Score=125.80  Aligned_cols=78  Identities=22%  Similarity=0.390  Sum_probs=70.7

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhc--CCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQF--GTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEV  178 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~f--G~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V  178 (522)
                      ..+.++|||+|||+++|+++|+++|++|  |.|++|+++        ++||||+|.++++|++||+.++ ..|++++|+|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            3467899999999999999999999999  999998875        5699999999999999999777 8999999999


Q ss_pred             EEcCCCCCC
Q 009920          179 KRAVPKEFS  187 (522)
Q Consensus       179 ~~a~pk~~~  187 (522)
                      ++++++...
T Consensus        84 ~~a~~~~~~   92 (99)
T 2cpd_A           84 TLAKPVDKD   92 (99)
T ss_dssp             ECCCCCCCC
T ss_pred             EECCCCCCC
Confidence            999987653

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.61  E-value=2.1e-15  Score=128.81  Aligned_cols=76  Identities=18%  Similarity=0.219  Sum_probs=68.3

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hcccc--cCCeEEEEe
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHM--IDGRTVEAK   78 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~--i~Gr~I~V~   78 (522)
                      ..+++|||+|||.++||++|+++|++||+|++|+|++      .|+||||+|.+.++|++|+  ++...  |.+++|.|.
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~   92 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN   92 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEE
Confidence            4678999999999999999999999999999999985      3689999999999999999  66554  889999999


Q ss_pred             ecCCCc
Q 009920           79 KAVPRD   84 (522)
Q Consensus        79 ~a~~k~   84 (522)
                      ++++++
T Consensus        93 ~S~~k~   98 (100)
T 3r27_A           93 YSTSQK   98 (100)
T ss_dssp             ECSCSC
T ss_pred             eccccc
Confidence            998754

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=2.7e-15  Score=124.42  Aligned_cols=78  Identities=23%  Similarity=0.471  Sum_probs=71.2

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ....++|||+|||+++|+++|+++|++||.|++|+|+++        ||||+|.++++|++||+.++ ..|++++|+|++
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   77 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS--------CEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            356789999999999999999999999999999999843        99999999999999999877 899999999999


Q ss_pred             cCCCCCC
Q 009920          181 AVPKEFS  187 (522)
Q Consensus       181 a~pk~~~  187 (522)
                      ++++...
T Consensus        78 a~~~~~~   84 (90)
T 2dnp_A           78 STKGQKK   84 (90)
T ss_dssp             SCCCCCC
T ss_pred             CCCCCCC
Confidence            9987544

>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=99.61  E-value=2.2e-15  Score=127.17  Aligned_cols=79  Identities=27%  Similarity=0.504  Sum_probs=72.5

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+.++|||+|||+++|+++|+++|++||+|++|+|+++      |+||||+|+++++|++|++.++ +.|++++|+|++
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 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   85 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEE
Confidence            356789999999999999999999999999999999854      6799999999999999998887 899999999999


Q ss_pred             cCCCCC
Q 009920          181 AVPKEF  186 (522)
Q Consensus       181 a~pk~~  186 (522)
                      ++++..
T Consensus        86 a~~~~~   91 (99)
T 2cpj_A           86 ACHSAS   91 (99)
T ss_dssp             SSCCSC
T ss_pred             cCCCCC
Confidence            998764

>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=99.61  E-value=2.4e-15  Score=129.40  Aligned_cols=80  Identities=19%  Similarity=0.446  Sum_probs=73.4

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ...++|||+|||..+++++|+++|++||.|++|+|+.+      ++||||+|.++++|++||+.++ ..|+|++|+|+++
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            46789999999999999999999999999999999876      6799999999999999998877 8999999999999


Q ss_pred             CCCCCCC
Q 009920          182 VPKEFSP  188 (522)
Q Consensus       182 ~pk~~~~  188 (522)
                      +++....
T Consensus        97 ~~~~~~~  103 (109)
T 1x4g_A           97 KESPDMT  103 (109)
T ss_dssp             CCCCSSC
T ss_pred             CCCCCCC
Confidence            9876543

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.61  E-value=1.4e-15  Score=128.71  Aligned_cols=77  Identities=18%  Similarity=0.425  Sum_probs=71.8

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCC
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPK  184 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk  184 (522)
                      ++|||+|||+++|+++|+++|++||+|++|.|+.+     ++|||||+|.++++|++|++.++ ..|+|++|+|++++++
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            47999999999999999999999999999999977     68899999999999999999877 8999999999999987


Q ss_pred             CCC
Q 009920          185 EFS  187 (522)
Q Consensus       185 ~~~  187 (522)
                      ...
T Consensus        76 ~~~   78 (101)
T 2hvz_A           76 PRR   78 (101)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            643

>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=99.61  E-value=2.2e-15  Score=129.61  Aligned_cols=78  Identities=22%  Similarity=0.469  Sum_probs=72.3

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++++++|+++|++||+|++|+|+++      ++||||+|.++++|++|+  ++++.|++++|.|+++
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            46789999999999999999999999999999999886      689999999999999999  8999999999999999


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      .++...
T Consensus        97 ~~~~~~  102 (109)
T 1x4g_A           97 KESPDM  102 (109)
T ss_dssp             CCCCSS
T ss_pred             CCCCCC
Confidence            876543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.61  E-value=1.3e-15  Score=126.65  Aligned_cols=72  Identities=13%  Similarity=0.202  Sum_probs=67.4

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      .+.-|||+||++++||++|+++|.+||+|.+++|+.      +||||||+|.++++|++|+  +|..++.+|+|.|+.|.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            357899999999999999999999999999999965      6899999999999999999  99999999999999874

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.61  E-value=9.1e-16  Score=131.43  Aligned_cols=79  Identities=18%  Similarity=0.312  Sum_probs=72.7

Q ss_pred             CCcEEEECCCCCCC------CHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCe-E
Q 009920            4 DLGKLFIGGISWDT------DEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGR-T   74 (522)
Q Consensus         4 d~r~LfVgnLP~~~------teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr-~   74 (522)
                      ..++|||+|||+++      |+++|+++|++||+|.+|+|+  +.+++++|||||+|.++++|++||  ++++.|+++ +
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~   91 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT   91 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCE
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCce
Confidence            46899999999999      789999999999999999988  357899999999999999999999  799999998 9


Q ss_pred             EEEeecCCCc
Q 009920           75 VEAKKAVPRD   84 (522)
Q Consensus        75 I~V~~a~~k~   84 (522)
                      |.|+++.+.+
T Consensus        92 l~V~~a~~~~  101 (105)
T 2nlw_A           92 FRVNLFTDFD  101 (105)
T ss_dssp             EEEECSCCCC
T ss_pred             EEEEEcchHh
Confidence            9999987654

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.40  E-value=4.6e-17  Score=141.75  Aligned_cols=85  Identities=28%  Similarity=0.483  Sum_probs=79.8

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEE--------EEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccC
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVE--------AVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMID   71 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~--------v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~   71 (522)
                      +.+.++|||+|||+++++++|+++|++||+|.+        |+|++++.++++++||||+|.++++|++||  +++..|+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            567899999999999999999999999999999        999999889999999999999999999999  8999999


Q ss_pred             CeEEEEeecCCCccc
Q 009920           72 GRTVEAKKAVPRDDQ   86 (522)
Q Consensus        72 Gr~I~V~~a~~k~~~   86 (522)
                      +++|.|+++.++...
T Consensus        84 g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           84 GNPIKVSFATRRADF   98 (116)
Confidence            999999999877554

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.40  E-value=4.7e-17  Score=141.65  Aligned_cols=85  Identities=24%  Similarity=0.370  Sum_probs=79.6

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeE--------EEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCC
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITD--------VVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNG  173 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~--------v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~G  173 (522)
                      .+.++|||+|||.++++++|+++|++||.|+.        |.|+.++.+++++|||||+|.++++|++||+.++ ..|++
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            46789999999999999999999999999998        9999999999999999999999999999999877 89999


Q ss_pred             eEEEEEEcCCCCCC
Q 009920          174 KMVEVKRAVPKEFS  187 (522)
Q Consensus       174 r~I~V~~a~pk~~~  187 (522)
                      ++|+|++++++...
T Consensus        85 ~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           85 NPIKVSFATRRADF   98 (116)
Confidence            99999999987653

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.61  E-value=7.8e-16  Score=130.61  Aligned_cols=83  Identities=22%  Similarity=0.579  Sum_probs=76.3

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcC
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAV  182 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~  182 (522)
                      ...++|||+|||+++++++|+++|++||.|++|.|+.++ +++++|||||+|+++++|++|++ ..+.|+|++|.|.++.
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            456899999999999999999999999999999999998 89999999999999999999998 5589999999999998


Q ss_pred             CCCCC
Q 009920          183 PKEFS  187 (522)
Q Consensus       183 pk~~~  187 (522)
                      ++...
T Consensus        85 ~~~~~   89 (102)
T 2xs2_A           85 RKQNL   89 (102)
T ss_dssp             ECC--
T ss_pred             cCcch
Confidence            77653

>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=99.61  E-value=1.7e-15  Score=127.38  Aligned_cols=76  Identities=17%  Similarity=0.335  Sum_probs=70.3

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccC--CeEEEEe
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMID--GRTVEAK   78 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~--Gr~I~V~   78 (522)
                      ...++|||+|||+++||++|+++|++||+|++|+|+++      ++||||+|.++++|++|+  ++++.|+  +++|.|+
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            45689999999999999999999999999999999764      679999999999999999  8999999  9999999


Q ss_pred             ecCCCc
Q 009920           79 KAVPRD   84 (522)
Q Consensus        79 ~a~~k~   84 (522)
                      ++.++.
T Consensus        89 ~a~~~~   94 (97)
T 1why_A           89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             ECCCCC
Confidence            998764

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=2.5e-15  Score=125.75  Aligned_cols=81  Identities=26%  Similarity=0.490  Sum_probs=71.4

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ...++|||+|||+++|+++|+++|++||+|++|  +.++.+++   ||||+|.++++|++||+ ++ +.|+|++|+|+++
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            356799999999999999999999999999987  66666655   99999999999999999 66 8999999999999


Q ss_pred             CCCCCCCC
Q 009920          182 VPKEFSPG  189 (522)
Q Consensus       182 ~pk~~~~~  189 (522)
                      .++.....
T Consensus        80 ~~~~~~~~   87 (94)
T 2e5g_A           80 EQKEFQSP   87 (94)
T ss_dssp             CCSCCCCC
T ss_pred             CcCCCCCC
Confidence            87765443

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=2.5e-15  Score=126.57  Aligned_cols=80  Identities=19%  Similarity=0.336  Sum_probs=71.7

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ....++|||+|||+++|+++|+++|++||.|+ +.++.+    +++|||||+|.++++|++||+.++ ..|+|++|+|++
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   90 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVAL   90 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            34578999999999999999999999999997 677754    568999999999999999999887 899999999999


Q ss_pred             cCCCCC
Q 009920          181 AVPKEF  186 (522)
Q Consensus       181 a~pk~~  186 (522)
                      ++++..
T Consensus        91 a~~~~~   96 (97)
T 2e5j_A           91 ARQQRD   96 (97)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            998753

>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=99.60  E-value=1.2e-15  Score=130.74  Aligned_cols=77  Identities=12%  Similarity=0.167  Sum_probs=68.8

Q ss_pred             CCCcEEEECCCCC-CCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hcc--cccCCeEEEE
Q 009920            3 SDLGKLFIGGISW-DTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDK--HMIDGRTVEA   77 (522)
Q Consensus         3 ~d~r~LfVgnLP~-~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~--~~i~Gr~I~V   77 (522)
                      ..+++|||+|||+ ++||+||+++|++||+|++|+|+++      |+||||+|.++++|++|+  ++.  ..|++++|.|
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            4678999999999 9999999999999999999999875      379999999999999999  554  4699999999


Q ss_pred             eecCCCcc
Q 009920           78 KKAVPRDD   85 (522)
Q Consensus        78 ~~a~~k~~   85 (522)
                      .++.++..
T Consensus        87 ~~a~~~~~   94 (102)
T 1x4d_A           87 HLSQKYKR   94 (102)
T ss_dssp             EEECCCTT
T ss_pred             EECCCCCC
Confidence            99986543

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=4.8e-16  Score=137.77  Aligned_cols=83  Identities=23%  Similarity=0.339  Sum_probs=75.3

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCe----eEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTI----TDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEV  178 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I----~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V  178 (522)
                      ....+|||+|||+++|++||+++|++||+|    ++|.|++|+ ++++||||||+|+++++|++||+++.+.|.+|.|+|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~V   99 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIEL   99 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEE
Confidence            356799999999999999999999999875    689999985 799999999999999999999998668999999999


Q ss_pred             EEcCCCCC
Q 009920          179 KRAVPKEF  186 (522)
Q Consensus       179 ~~a~pk~~  186 (522)
                      ..+.+++.
T Consensus       100 ~~a~~~e~  107 (123)
T 2dha_A          100 FRSTAAEV  107 (123)
T ss_dssp             EEECHHHH
T ss_pred             EECCHHHH
Confidence            99987653

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.60  E-value=1.4e-15  Score=126.64  Aligned_cols=78  Identities=35%  Similarity=0.611  Sum_probs=65.6

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHHHcccccCCeEEEEeecCC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl~~~~~i~Gr~I~V~~a~~   82 (522)
                      ...++|||+|||+++||++|+++|++||+|++|+|+++     +||||||+|.++++|+++....+.+.+++|.|.++.+
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~~~~~~~~~~g~~v~v~~a~~   83 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCGEDLIIKGISVHISNAEP   83 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHHHTTCEEEETTEEEEEEECC-
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHHHcCCCcccCCEEEEEEEcCC
Confidence            46789999999999999999999999999999999874     7899999999999999655445667899999999987


Q ss_pred             Ccc
Q 009920           83 RDD   85 (522)
Q Consensus        83 k~~   85 (522)
                      +..
T Consensus        84 k~~   86 (89)
T 3d2w_A           84 KHN   86 (89)
T ss_dssp             ---
T ss_pred             CCc
Confidence            654

>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=2.2e-15  Score=129.08  Aligned_cols=82  Identities=18%  Similarity=0.265  Sum_probs=74.8

Q ss_pred             CCcceeEecCCCCCC------CHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCe-
Q 009920          103 GRTKKIFVGGLASTV------TESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGK-  174 (522)
Q Consensus       103 ~~~~~LfVgnLp~~v------teedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr-  174 (522)
                      ...++|||+|||+.+      |+++|+++|++||.|++|.|+  +.+++++|||||+|.++++|++||+.++ ..|.|+ 
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~   90 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   90 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTC
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCc
Confidence            346899999999999      789999999999999999988  4678999999999999999999999888 899998 


Q ss_pred             EEEEEEcCCCCC
Q 009920          175 MVEVKRAVPKEF  186 (522)
Q Consensus       175 ~I~V~~a~pk~~  186 (522)
                      +|+|+++.+.++
T Consensus        91 ~l~V~~a~~~~k  102 (105)
T 2nlw_A           91 TFRVNLFTDFDK  102 (105)
T ss_dssp             EEEEECSCCCCC
T ss_pred             eEEEEEcchHhh
Confidence            999999987654

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.60  E-value=8.5e-16  Score=125.11  Aligned_cols=71  Identities=18%  Similarity=0.378  Sum_probs=65.7

Q ss_pred             CcEEEECCCCCCC------CHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCe-EE
Q 009920            5 LGKLFIGGISWDT------DEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGR-TV   75 (522)
Q Consensus         5 ~r~LfVgnLP~~~------teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr-~I   75 (522)
                      +++|||+|||+++      ++++|+++|++||+|.+|+|+  +.+++++|||||+|.++++|++|+  +++..|+++ +|
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            4799999999999      789999999999999999987  357899999999999999999999  899999999 88


Q ss_pred             EE
Q 009920           76 EA   77 (522)
Q Consensus        76 ~V   77 (522)
                      .|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            76

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=3e-15  Score=124.70  Aligned_cols=77  Identities=26%  Similarity=0.441  Sum_probs=70.7

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      +.+.++|||+|||+++|+++|+++|++||+|++|+|+++        ||||+|.++++|++|+  ++++.|++++|.|++
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 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS--------EEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            357899999999999999999999999999999999853        9999999999999999  899999999999999


Q ss_pred             cCCCccc
Q 009920           80 AVPRDDQ   86 (522)
Q Consensus        80 a~~k~~~   86 (522)
                      +.++...
T Consensus        79 a~~~~~~   85 (92)
T 2dgt_A           79 STSRLRT   85 (92)
T ss_dssp             SSCCCSC
T ss_pred             ccCCCCC
Confidence            9876543

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=3e-15  Score=125.31  Aligned_cols=78  Identities=26%  Similarity=0.511  Sum_probs=69.9

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      +..++|||+|||+++||++|+++|++||+|.+|  +.++.+++   ||||+|.++++|++|| ++++.|++++|.|+++.
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            467899999999999999999999999999986  66665555   9999999999999999 99999999999999887


Q ss_pred             CCcc
Q 009920           82 PRDD   85 (522)
Q Consensus        82 ~k~~   85 (522)
                      ++..
T Consensus        81 ~~~~   84 (94)
T 2e5g_A           81 QKEF   84 (94)
T ss_dssp             CSCC
T ss_pred             cCCC
Confidence            6544

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.60  E-value=1.7e-15  Score=128.31  Aligned_cols=75  Identities=19%  Similarity=0.326  Sum_probs=69.4

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++++++|+++|++||+|++|+|+      ++++||||+|.+.++|++|+  ++++.|++++|.|+++
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   98 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            357899999999999999999999999999999998      35789999999999999999  8999999999999998


Q ss_pred             CCC
Q 009920           81 VPR   83 (522)
Q Consensus        81 ~~k   83 (522)
                      .++
T Consensus        99 ~~~  101 (101)
T 2la4_A           99 KER  101 (101)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            764

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.60  E-value=2.3e-15  Score=126.16  Aligned_cols=81  Identities=20%  Similarity=0.348  Sum_probs=72.5

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+.++|||+|||+.+|+++|+++|++||.|..+     ..+++++|||||+|.++++|++|++.++ ..|+|++|+|++
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   87 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3467899999999999999999999999988766     3457899999999999999999999888 899999999999


Q ss_pred             cCCCCCC
Q 009920          181 AVPKEFS  187 (522)
Q Consensus       181 a~pk~~~  187 (522)
                      +.++...
T Consensus        88 a~~~~~~   94 (96)
T 1fjc_A           88 TGEKGGT   94 (96)
T ss_dssp             CSSSCCC
T ss_pred             cCCCCCC
Confidence            9887643

>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=99.59  E-value=1.8e-15  Score=127.72  Aligned_cols=77  Identities=27%  Similarity=0.575  Sum_probs=71.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++|+++|+++|++||+|++|+|+++      |+||||+|.++++|++|+  ++++.|++++|.|+++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   86 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA   86 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEc
Confidence            46789999999999999999999999999999999864      689999999999999999  8999999999999999


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      .++..
T Consensus        87 ~~~~~   91 (99)
T 2cpj_A           87 CHSAS   91 (99)
T ss_dssp             SCCSC
T ss_pred             CCCCC
Confidence            87654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.59  E-value=2.1e-15  Score=131.24  Aligned_cols=79  Identities=20%  Similarity=0.210  Sum_probs=70.5

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcC-CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFG-TITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG-~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ....+|||+|||+++|+++|+++|++|| +|+.+.|+.+    +++|||||+|+++++|++||++++ .+|+|++|+|++
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            3567999999999999999999999999 8999988643    478999999999999999999888 899999999999


Q ss_pred             cCCCC
Q 009920          181 AVPKE  185 (522)
Q Consensus       181 a~pk~  185 (522)
                      ++.+.
T Consensus       102 a~~~p  106 (111)
T 2jvr_A          102 DDNPP  106 (111)
T ss_dssp             SCC--
T ss_pred             CCCCC
Confidence            97543

>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=99.59  E-value=4.6e-16  Score=134.77  Aligned_cols=84  Identities=20%  Similarity=0.311  Sum_probs=72.3

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++|+++|+++|++||+|.++.+..+..++++++||||+|.++++|++||  ++++.|++++|.|+++
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            35689999999999999999999999999854433333336889999999999999999999  7999999999999999


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      .++...
T Consensus       103 ~~~~~~  108 (115)
T 2cpx_A          103 KNKKQR  108 (115)
T ss_dssp             CCCSCC
T ss_pred             cCCCCC
Confidence            876543

>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=4.2e-16  Score=134.01  Aligned_cols=83  Identities=20%  Similarity=0.275  Sum_probs=76.6

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCC---eeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGT---ITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEV  178 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~---I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V  178 (522)
                      ....++|||+|||+++|+++|+++|++||.   |++|+|++|+. ++++|||||+|.++++|++||++..+.|++|.|+|
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            356789999999999999999999999998   89999999988 99999999999999999999994448999999999


Q ss_pred             EEcCCCC
Q 009920          179 KRAVPKE  185 (522)
Q Consensus       179 ~~a~pk~  185 (522)
                      .++.+++
T Consensus        87 ~~a~~~~   93 (107)
T 2lmi_A           87 YEINNED   93 (107)
T ss_dssp             EECCHHH
T ss_pred             EECCHHH
Confidence            9998765

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=2.7e-15  Score=130.43  Aligned_cols=81  Identities=22%  Similarity=0.386  Sum_probs=71.3

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCC---CCcccEEEEEecCHHHHHHHHHcccccCCeEEEEee
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRAT---GRARGFGFVVFADPAVAERVIMDKHMIDGRTVEAKK   79 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~t---g~srG~aFVeF~~~e~A~kAl~~~~~i~Gr~I~V~~   79 (522)
                      ++.++|||+|||+++||++|+++|++||+|. ++++.++.+   +++||||||+|.++++|++||..-+.++++.|.+..
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~~~G~~~~~~~   84 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLYLCVS   84 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEEETTEEEEEEC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhhcCCcEEEecc
Confidence            5689999999999999999999999999999 888888777   799999999999999999999444568999998876


Q ss_pred             cCCCc
Q 009920           80 AVPRD   84 (522)
Q Consensus        80 a~~k~   84 (522)
                      +.+..
T Consensus        85 ~~~~~   89 (114)
T 2dnl_A           85 SPTIK   89 (114)
T ss_dssp             CSSSC
T ss_pred             CCCcC
Confidence            65443

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.59  E-value=2.8e-15  Score=129.37  Aligned_cols=79  Identities=20%  Similarity=0.459  Sum_probs=71.3

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      .....++|||+|||+++|+++|+++|++||.|++|.|+        +|||||+|.++++|++|++.++ ..|+|++|+|+
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            44577899999999999999999999999999999998        6799999999999999999877 89999999999


Q ss_pred             EcCCCCCC
Q 009920          180 RAVPKEFS  187 (522)
Q Consensus       180 ~a~pk~~~  187 (522)
                      +++++..+
T Consensus        99 ~a~~~~~r  106 (108)
T 2jvo_A           99 YSKLPAKR  106 (108)
T ss_dssp             SCSCCC--
T ss_pred             EecCCCCC
Confidence            99987643

>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=99.59  E-value=3.1e-15  Score=124.71  Aligned_cols=79  Identities=25%  Similarity=0.519  Sum_probs=69.2

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCC-eeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC--CccCCeEEEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGT-ITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF--HELNGKMVEVK  179 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~-I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~--~~l~Gr~I~V~  179 (522)
                      ...++|||+|||+++|+++|+++|++||. |..+.+.       ++|||||+|+++++|++||+.++  ..|++++|+|+
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            46789999999999999999999999999 6655553       47899999999999999999766  68999999999


Q ss_pred             EcCCCCCCC
Q 009920          180 RAVPKEFSP  188 (522)
Q Consensus       180 ~a~pk~~~~  188 (522)
                      +++++..+.
T Consensus        79 ~a~~~~~~~   87 (93)
T 2cqh_A           79 YSVSKKLRS   87 (93)
T ss_dssp             ECCCCCCCC
T ss_pred             EccCccccC
Confidence            999876543

>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=99.59  E-value=5.6e-15  Score=120.81  Aligned_cols=76  Identities=29%  Similarity=0.511  Sum_probs=69.5

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhc-C-CccCCeEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT-F-HELNGKMVEV  178 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~-~-~~l~Gr~I~V  178 (522)
                      ...+.++|||+|||.++++++|+++|++||+|++|+|+++      |+||||+|+++++|++|++.+ + ..|+|++|+|
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v   81 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNV   81 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCE
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEE
Confidence            3456789999999999999999999999999999999864      689999999999999999977 6 7999999999


Q ss_pred             EEcC
Q 009920          179 KRAV  182 (522)
Q Consensus       179 ~~a~  182 (522)
                      ++++
T Consensus        82 ~~ak   85 (85)
T 2ytc_A           82 KWGR   85 (85)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9974

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=2.7e-15  Score=126.27  Aligned_cols=77  Identities=17%  Similarity=0.284  Sum_probs=70.0

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++|+++|+++|++||+|. ++++.+    ++++||||+|.++++|++|+  ++++.|++++|.|+++
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            3478999999999999999999999999997 677654    57899999999999999999  8999999999999999


Q ss_pred             CCCc
Q 009920           81 VPRD   84 (522)
Q Consensus        81 ~~k~   84 (522)
                      .++.
T Consensus        92 ~~~~   95 (97)
T 2e5j_A           92 RQQR   95 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8764

>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=99.59  E-value=1.3e-15  Score=125.89  Aligned_cols=79  Identities=33%  Similarity=0.627  Sum_probs=70.7

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHHHcccccCCeEEEEeecCC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl~~~~~i~Gr~I~V~~a~~   82 (522)
                      ...++|||+|||+++||++|+++|++||+|++|+|+++     +||||||+|.++++|++|+...+.+.+++|+|.++.+
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~~~~~~g~~l~v~~a~~   77 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEP   77 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTCEEEETTEEEEEECCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcCCceeCCEEEEEEecCC
Confidence            56799999999999999999999999999999999864     6899999999999999877556778999999999987


Q ss_pred             Cccc
Q 009920           83 RDDQ   86 (522)
Q Consensus        83 k~~~   86 (522)
                      +...
T Consensus        78 ~~~~   81 (88)
T 1wf0_A           78 KHNS   81 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=4.2e-15  Score=123.28  Aligned_cols=76  Identities=22%  Similarity=0.479  Sum_probs=70.0

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      +.+.++|||+|||+++|+++|+++|++||+|++|+|+++        ||||+|.++++|++|+  ++++.|++++|.|++
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   77 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS--------CEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            357899999999999999999999999999999999853        9999999999999999  899999999999999


Q ss_pred             cCCCcc
Q 009920           80 AVPRDD   85 (522)
Q Consensus        80 a~~k~~   85 (522)
                      +.++..
T Consensus        78 a~~~~~   83 (90)
T 2dnp_A           78 STKGQK   83 (90)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            987643

>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=99.58  E-value=3.9e-15  Score=121.80  Aligned_cols=74  Identities=23%  Similarity=0.481  Sum_probs=68.3

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--H-cccccCCeEEEEe
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M-DKHMIDGRTVEAK   78 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~-~~~~i~Gr~I~V~   78 (522)
                      +.+.++|||+|||+++++++|+++|++||+|.+|+|+++      |+||||+|.++++|++|+  + +++.|++++|.|+
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 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK   82 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEE
Confidence            356789999999999999999999999999999999874      689999999999999999  5 8899999999999


Q ss_pred             ecC
Q 009920           79 KAV   81 (522)
Q Consensus        79 ~a~   81 (522)
                      +++
T Consensus        83 ~ak   85 (85)
T 2ytc_A           83 WGR   85 (85)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            874

>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=131.91  Aligned_cols=81  Identities=12%  Similarity=0.256  Sum_probs=72.8

Q ss_pred             CCcceeEecCCCCCCCHHHHH----HHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFK----KYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVE  177 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~----~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~  177 (522)
                      .+.++|||+|||+.+++++|+    ++|++||.|++|.+.+   ++++||||||+|.+.++|++|++.++ ..|.|++|+
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            457899999999999999876    6999999999988753   57889999999999999999999988 899999999


Q ss_pred             EEEcCCCCC
Q 009920          178 VKRAVPKEF  186 (522)
Q Consensus       178 V~~a~pk~~  186 (522)
                      |++++++..
T Consensus       104 V~~a~~~~~  112 (127)
T 2a3j_A          104 ITFSETPQS  112 (127)
T ss_dssp             EEECCCCCH
T ss_pred             EEEccCcch
Confidence            999987654

>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=99.58  E-value=2.3e-15  Score=131.24  Aligned_cols=79  Identities=20%  Similarity=0.286  Sum_probs=66.8

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeE-----E
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKM-----V  176 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~-----I  176 (522)
                      ...++|||+|||+++|+++|+++|++||+|++|.|+.+       |||||+|+++++|++||++++ .+|+|++     |
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            35689999999999999999999999999999999866       799999999999999999888 8999998     8


Q ss_pred             EEEEcCCCCCCC
Q 009920          177 EVKRAVPKEFSP  188 (522)
Q Consensus       177 ~V~~a~pk~~~~  188 (522)
                      +|+.+.++...+
T Consensus        87 ~v~~~~~~~~~~   98 (115)
T 3beg_B           87 RVKVDGPRSPSY   98 (115)
T ss_dssp             EEEECC----CC
T ss_pred             EeccCCCCCCCC
Confidence            888887765544

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=4.6e-15  Score=124.28  Aligned_cols=82  Identities=17%  Similarity=0.212  Sum_probs=73.2

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEE-EEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDV-VVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEV  178 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v-~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V  178 (522)
                      .....++|||+|||+++|+++|+++|++||+|++| .|+.++.++    .|||+|.++++|++||+.++ ..|+|++|+|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V   86 (96)
T 2e44_A           11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKV   86 (96)
T ss_dssp             CCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEE
T ss_pred             CCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            34567899999999999999999999999999999 588876644    39999999999999999877 8999999999


Q ss_pred             EEcCCCCC
Q 009920          179 KRAVPKEF  186 (522)
Q Consensus       179 ~~a~pk~~  186 (522)
                      +++.+++.
T Consensus        87 ~~a~~~~~   94 (96)
T 2e44_A           87 AYIPDEMA   94 (96)
T ss_dssp             EECCCCCS
T ss_pred             EEcCcccc
Confidence            99998853

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.58  E-value=3.4e-15  Score=124.03  Aligned_cols=72  Identities=10%  Similarity=0.199  Sum_probs=68.0

Q ss_pred             cceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       105 ~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      +.-|+|+||++.+||++|+++|.+||+|++++++.      +||||||+|.++++|++|++.++ .+|.+|+|+|++|.
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------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            56799999999999999999999999999999975      58999999999999999999998 89999999999985

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.58  E-value=2.3e-15  Score=131.00  Aligned_cols=77  Identities=9%  Similarity=0.135  Sum_probs=69.5

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccC-CeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYG-EVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G-~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      ...++|||+|||+++|+++|+++|++|| +|..++|+.+    +++|||||+|.++++|++||  +++.+|++++|.|++
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            3567999999999999999999999999 8999988643    47899999999999999999  899999999999998


Q ss_pred             cCCC
Q 009920           80 AVPR   83 (522)
Q Consensus        80 a~~k   83 (522)
                      +...
T Consensus       102 a~~~  105 (111)
T 2jvr_A          102 DDNP  105 (111)
T ss_dssp             SCC-
T ss_pred             CCCC
Confidence            8643

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.58  E-value=6.5e-15  Score=141.46  Aligned_cols=83  Identities=23%  Similarity=0.376  Sum_probs=77.3

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      .+.++|||+|||+++||++|+++|++||+|++|+|++|+.+++++|||||+|.++++|++||+.++ ..+.++.|+|.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            456899999999999999999999999999999999999999999999999999999999999988 8999999999998


Q ss_pred             CCCC
Q 009920          182 VPKE  185 (522)
Q Consensus       182 ~pk~  185 (522)
                      .+..
T Consensus        93 ~~~~   96 (213)
T 4f02_A           93 QRDP   96 (213)
T ss_dssp             CCCT
T ss_pred             cccc
Confidence            7654

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.58  E-value=3.3e-15  Score=126.44  Aligned_cols=76  Identities=22%  Similarity=0.403  Sum_probs=70.2

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ...++|||+|||.++++++|+++|++||.|++|+|+      +++|||||+|++.++|++|++.++ ..|+|++|+|+++
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   98 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            456899999999999999999999999999999998      357899999999999999999877 8999999999999


Q ss_pred             CCC
Q 009920          182 VPK  184 (522)
Q Consensus       182 ~pk  184 (522)
                      +++
T Consensus        99 ~~~  101 (101)
T 2la4_A           99 KER  101 (101)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            874

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.58  E-value=5.7e-15  Score=127.41  Aligned_cols=76  Identities=25%  Similarity=0.434  Sum_probs=70.2

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      +.+.++|||+|||+++|+++|+++|++||+|++|+|+        +|||||+|.+.++|++|+  +++..|++++|.|++
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   99 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY   99 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEES
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3578999999999999999999999999999999998        689999999999999999  899999999999999


Q ss_pred             cCCCcc
Q 009920           80 AVPRDD   85 (522)
Q Consensus        80 a~~k~~   85 (522)
                      +.++..
T Consensus       100 a~~~~~  105 (108)
T 2jvo_A          100 SKLPAK  105 (108)
T ss_dssp             CSCCC-
T ss_pred             ecCCCC
Confidence            987643

>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=99.58  E-value=7.2e-15  Score=137.66  Aligned_cols=86  Identities=47%  Similarity=0.819  Sum_probs=78.2

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEc
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRA  181 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a  181 (522)
                      +...++|||+|||+++|+++|+++|++||+|++|.|++++.+++++|||||+|.++++|++||+.+++.|.|+.|.|.++
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            35678999999999999999999999999999999999999999999999999999999999999779999999999999


Q ss_pred             CCCCCC
Q 009920          182 VPKEFS  187 (522)
Q Consensus       182 ~pk~~~  187 (522)
                      .++...
T Consensus        90 ~~~~~~   95 (196)
T 1l3k_A           90 VSREDS   95 (196)
T ss_dssp             CC----
T ss_pred             cCcccc
Confidence            876543

>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=99.57  E-value=2.5e-15  Score=130.92  Aligned_cols=78  Identities=12%  Similarity=0.183  Sum_probs=69.2

Q ss_pred             CCCcEEEECCCCCC-CCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hc--ccccCCeEEEE
Q 009920            3 SDLGKLFIGGISWD-TDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MD--KHMIDGRTVEA   77 (522)
Q Consensus         3 ~d~r~LfVgnLP~~-~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~--~~~i~Gr~I~V   77 (522)
                      ..+++|||+|||++ +||++|+++|++||+|++|+|++      +|+||||+|.++++|++|+  ++  ...|++|+|.|
T Consensus        23 ~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   96 (112)
T 1x4f_A           23 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   96 (112)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            45789999999998 99999999999999999999975      4689999999999999999  44  45799999999


Q ss_pred             eecCCCccc
Q 009920           78 KKAVPRDDQ   86 (522)
Q Consensus        78 ~~a~~k~~~   86 (522)
                      .++.++...
T Consensus        97 ~~a~~~~~~  105 (112)
T 1x4f_A           97 DLSEKYKKL  105 (112)
T ss_dssp             EEECSCSSS
T ss_pred             EECcccccc
Confidence            999766543

>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=99.57  E-value=1.6e-15  Score=131.42  Aligned_cols=77  Identities=14%  Similarity=0.140  Sum_probs=70.2

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      +++.++|||+|||+++|+++|+++|++||+|++|.|++      +++||||+|.++++|++||  +++..|++++|.|++
T Consensus         7 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   80 (111)
T 1whx_A            7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEW   80 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            45678999999999999999999999999999998874      5689999999999999999  899999999999999


Q ss_pred             cCCCc
Q 009920           80 AVPRD   84 (522)
Q Consensus        80 a~~k~   84 (522)
                      +....
T Consensus        81 a~~~~   85 (111)
T 1whx_A           81 APIGV   85 (111)
T ss_dssp             EETTT
T ss_pred             CCCCc
Confidence            86543

>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=99.57  E-value=4.4e-15  Score=129.40  Aligned_cols=80  Identities=16%  Similarity=0.263  Sum_probs=71.4

Q ss_pred             CCCcceeEecCCCCC-CCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC---CccCCeEEE
Q 009920          102 PGRTKKIFVGGLAST-VTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF---HELNGKMVE  177 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~-vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~---~~l~Gr~I~  177 (522)
                      ..+.++|||+|||++ +|++||+++|++||.|++|.|++      .||||||+|+++++|++|++.++   .+|.||+|.
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            346789999999998 99999999999999999999974      37899999999999999999764   469999999


Q ss_pred             EEEcCCCCCC
Q 009920          178 VKRAVPKEFS  187 (522)
Q Consensus       178 V~~a~pk~~~  187 (522)
                      |.+++++...
T Consensus        96 V~~a~~~~~~  105 (112)
T 1x4f_A           96 VDLSEKYKKL  105 (112)
T ss_dssp             EEEECSCSSS
T ss_pred             EEECcccccc
Confidence            9999877654

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.57  E-value=2.9e-15  Score=126.01  Aligned_cols=78  Identities=21%  Similarity=0.411  Sum_probs=69.9

Q ss_pred             CCCcceeEecCCCC-CCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          102 PGRTKKIFVGGLAS-TVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       102 ~~~~~~LfVgnLp~-~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      ..+.++|||+|||+ ++|+++|+++|++||.|++|.|.        +|||||+|+++++|++|++.++ ..|.+++|+|+
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            35688999999998 99999999999999999999994        6799999999999999999877 89999999999


Q ss_pred             EcCCCCCC
Q 009920          180 RAVPKEFS  187 (522)
Q Consensus       180 ~a~pk~~~  187 (522)
                      +++++...
T Consensus        79 ~a~~~~~~   86 (96)
T 2kvi_A           79 VSSSNARP   86 (96)
T ss_dssp             EEECCCC-
T ss_pred             EcCcCCCC
Confidence            99876543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.57  E-value=2e-15  Score=126.48  Aligned_cols=79  Identities=24%  Similarity=0.366  Sum_probs=70.5

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      +++.++|||+|||+++++++|+++|++||+|..+     ..+++++|||||+|.++++|++|+  ++++.|++++|.|++
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   87 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3567999999999999999999999999887655     346889999999999999999999  899999999999999


Q ss_pred             cCCCcc
Q 009920           80 AVPRDD   85 (522)
Q Consensus        80 a~~k~~   85 (522)
                      +.++..
T Consensus        88 a~~~~~   93 (96)
T 1fjc_A           88 TGEKGG   93 (96)
T ss_dssp             CSSSCC
T ss_pred             cCCCCC
Confidence            977643

>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=99.57  E-value=2.7e-15  Score=125.79  Aligned_cols=80  Identities=21%  Similarity=0.436  Sum_probs=73.9

Q ss_pred             CCCcEEEECCCCCCCCHHHHH----HHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEE
Q 009920            3 SDLGKLFIGGISWDTDEERLK----EYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVE   76 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~----e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~   76 (522)
                      ...++|||+|||+++++++|+    ++|++||+|.+|+|++   ++++++||||+|.++++|++|+  +++..|++++|.
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            568999999999999999999    9999999999999874   4678999999999999999999  899999999999


Q ss_pred             EeecCCCcc
Q 009920           77 AKKAVPRDD   85 (522)
Q Consensus        77 V~~a~~k~~   85 (522)
                      |+++.++..
T Consensus        83 v~~a~~~~~   91 (97)
T 1nu4_A           83 IQYAKTDSD   91 (97)
T ss_dssp             EEECSSCCT
T ss_pred             EEEccCCCc
Confidence            999987654

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=2.9e-15  Score=124.89  Aligned_cols=77  Identities=25%  Similarity=0.454  Sum_probs=68.3

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCC-eEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hcc-cccCCeEEEEe
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGE-VVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDK-HMIDGRTVEAK   78 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~-V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~-~~i~Gr~I~V~   78 (522)
                      .+.++|||+|||+++||++|+++|++||+ |..+.++       +++||||+|.++++|++|+  +++ +.|++++|.|+
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            56789999999999999999999999999 6555553       4689999999999999999  888 99999999999


Q ss_pred             ecCCCccc
Q 009920           79 KAVPRDDQ   86 (522)
Q Consensus        79 ~a~~k~~~   86 (522)
                      ++.++...
T Consensus        79 ~a~~~~~~   86 (93)
T 2cqh_A           79 YSVSKKLR   86 (93)
T ss_dssp             ECCCCCCC
T ss_pred             EccCcccc
Confidence            99876543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=1.2e-14  Score=122.63  Aligned_cols=75  Identities=25%  Similarity=0.468  Sum_probs=68.9

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhcc--CCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEe
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRY--GEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAK   78 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~--G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~   78 (522)
                      .+.++|||+|||+++|+++|+++|++|  |+|.+|+++        ++||||+|.++++|++||  ++++.|++++|.|+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   84 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVT   84 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            467899999999999999999999999  999988875        469999999999999999  89999999999999


Q ss_pred             ecCCCcc
Q 009920           79 KAVPRDD   85 (522)
Q Consensus        79 ~a~~k~~   85 (522)
                      ++.++..
T Consensus        85 ~a~~~~~   91 (99)
T 2cpd_A           85 LAKPVDK   91 (99)
T ss_dssp             CCCCCCC
T ss_pred             ECCCCCC
Confidence            9987654

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=3.6e-15  Score=124.93  Aligned_cols=77  Identities=18%  Similarity=0.192  Sum_probs=70.6

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEE-EEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEA-VIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v-~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ..++|||+|||+++++++|+++|++||+|++| .|++++.+++    |||+|.++++|++|+  ++++.|++++|.|+++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~----afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   89 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV----VNVTYSSKDQARQALDKLNGFQLENFTLKVAYI   89 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEE----EEEEESSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCE----EEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            47899999999999999999999999999999 5888776543    999999999999999  8999999999999999


Q ss_pred             CCCc
Q 009920           81 VPRD   84 (522)
Q Consensus        81 ~~k~   84 (522)
                      .+++
T Consensus        90 ~~~~   93 (96)
T 2e44_A           90 PDEM   93 (96)
T ss_dssp             CCCC
T ss_pred             Cccc
Confidence            8874

>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=99.57  E-value=3.1e-15  Score=124.59  Aligned_cols=79  Identities=24%  Similarity=0.454  Sum_probs=64.2

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEc
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRA  181 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a  181 (522)
                      ..+..+|||+|||+++||++|+++|++||+|++|+|+++     +||||||+|+++++|+++. .....+.+++|.|+++
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~~~-~~~~~~~g~~v~v~~a   81 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLC-GEDLIIKGISVHISNA   81 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHHHT-TCEEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHHHc-CCCcccCCEEEEEEEc
Confidence            356789999999999999999999999999999999874     7899999999999998543 2235678999999999


Q ss_pred             CCCCC
Q 009920          182 VPKEF  186 (522)
Q Consensus       182 ~pk~~  186 (522)
                      .|+..
T Consensus        82 ~~k~~   86 (89)
T 3d2w_A           82 EPKHN   86 (89)
T ss_dssp             C----
T ss_pred             CCCCc
Confidence            98764

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.57  E-value=4e-15  Score=132.53  Aligned_cols=82  Identities=17%  Similarity=0.266  Sum_probs=73.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHH----HHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEE
Q 009920            3 SDLGKLFIGGISWDTDEERLK----EYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVE   76 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~----e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~   76 (522)
                      ...++|||+|||+++++++|+    ++|++||+|++|.|++   ++++||||||+|.+.++|++|+  +++..|.+++|.
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~  103 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLV  103 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEE
Confidence            356899999999999999876    6999999999988864   5789999999999999999999  899999999999


Q ss_pred             EeecCCCcccc
Q 009920           77 AKKAVPRDDQN   87 (522)
Q Consensus        77 V~~a~~k~~~~   87 (522)
                      |+++.++....
T Consensus       104 V~~a~~~~~~~  114 (127)
T 2a3j_A          104 ITFSETPQSQV  114 (127)
T ss_dssp             EEECCCCCHHH
T ss_pred             EEEccCcchhc
Confidence            99998765543

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.57  E-value=2.4e-14  Score=120.41  Aligned_cols=78  Identities=23%  Similarity=0.429  Sum_probs=70.3

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ..+.++|||+||  ++|+++|+++|++||+|++|.|.      +++|||||+|+++++|++||+.++ ..|++++|+|++
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            346789999996  89999999999999999999984      467899999999999999999888 899999999999


Q ss_pred             cCCCCCC
Q 009920          181 AVPKEFS  187 (522)
Q Consensus       181 a~pk~~~  187 (522)
                      ++++...
T Consensus        84 a~~~~~~   90 (97)
T 1x5p_A           84 ARKQPML   90 (97)
T ss_dssp             CSSCCCC
T ss_pred             CCCCCCC
Confidence            9887654

>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=99.57  E-value=1.2e-14  Score=122.85  Aligned_cols=76  Identities=21%  Similarity=0.453  Sum_probs=69.9

Q ss_pred             CCCcceeEecCCCC-CCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          102 PGRTKKIFVGGLAS-TVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       102 ~~~~~~LfVgnLp~-~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      ..+.++|||+|||+ ++++++|+++|++||.|++|+|.        +|||||+|+++++|++|++.++ ..|+|++|+|+
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   90 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE   90 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45678999999998 99999999999999999999983        7899999999999999999887 89999999999


Q ss_pred             EcCCCC
Q 009920          180 RAVPKE  185 (522)
Q Consensus       180 ~a~pk~  185 (522)
                      +++++.
T Consensus        91 ~a~~~~   96 (97)
T 2xnq_A           91 VSSSNA   96 (97)
T ss_dssp             ECCCCC
T ss_pred             ecCCCC
Confidence            998754

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.57  E-value=4.4e-15  Score=139.50  Aligned_cols=81  Identities=23%  Similarity=0.420  Sum_probs=76.2

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      ..++|||+|||+++++++|+++|++||+|++|.|++++ ++++++||||+|.++++|++||  +++..|++++|.|+++.
T Consensus        87 ~~~~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           87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  165 (177)
T ss_dssp             TCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            46899999999999999999999999999999999998 8999999999999999999999  79999999999999987


Q ss_pred             CCcc
Q 009920           82 PRDD   85 (522)
Q Consensus        82 ~k~~   85 (522)
                      +...
T Consensus       166 ~~~~  169 (177)
T 2f3j_A          166 SQID  169 (177)
T ss_dssp             SGGG
T ss_pred             CCCC
Confidence            6543

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=2.4e-15  Score=124.21  Aligned_cols=80  Identities=25%  Similarity=0.488  Sum_probs=69.7

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcC
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAV  182 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~  182 (522)
                      .+.++|||+|||+++|+++|+++|++||+|++|+|+++     +||||||+|+++++|++|+.. ...+++++|+|+++.
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~-~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE-DLIIKGISVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC-EEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC-CceeCCEEEEEEecC
Confidence            35689999999999999999999999999999999864     689999999999999876543 357799999999999


Q ss_pred             CCCCCC
Q 009920          183 PKEFSP  188 (522)
Q Consensus       183 pk~~~~  188 (522)
                      ++....
T Consensus        77 ~~~~~~   82 (88)
T 1wf0_A           77 PKHNSN   82 (88)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876543

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.56  E-value=1.1e-14  Score=136.86  Aligned_cols=85  Identities=20%  Similarity=0.386  Sum_probs=78.7

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      .....++|||.|||+.+++++|+++|++||+|++|.|+.++ +++++|||||+|+++++|++||+.++ ..|++++|+|+
T Consensus        84 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~  162 (177)
T 2f3j_A           84 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  162 (177)
T ss_dssp             SCTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999998 89999999999999999999999888 89999999999


Q ss_pred             EcCCCCC
Q 009920          180 RAVPKEF  186 (522)
Q Consensus       180 ~a~pk~~  186 (522)
                      ++.+...
T Consensus       163 ~a~~~~~  169 (177)
T 2f3j_A          163 LVASQID  169 (177)
T ss_dssp             EESSGGG
T ss_pred             EecCCCC
Confidence            9987543

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.56  E-value=5.3e-15  Score=122.35  Aligned_cols=74  Identities=12%  Similarity=0.265  Sum_probs=68.8

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      +..++|||+|||++++|++|+++|++| +|.+|+|.      ++||||||+|.++++|++|+  +++..+++++|.|+++
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            567899999999999999999999999 99999884      57899999999999999999  9999999999999998


Q ss_pred             CCC
Q 009920           81 VPR   83 (522)
Q Consensus        81 ~~k   83 (522)
                      ...
T Consensus        76 ~~~   78 (88)
T 1wg1_A           76 PTD   78 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.56  E-value=3.5e-15  Score=125.09  Aligned_cols=82  Identities=18%  Similarity=0.375  Sum_probs=74.0

Q ss_pred             CCCcceeEecCCCCCCCHHHHH----HHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFK----KYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMV  176 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~----~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I  176 (522)
                      ..+.++|||+|||.++++++|+    ++|++||.|++|.|+.   +++++|||||+|.++++|++|++.++ ..|+|++|
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            3567899999999999999999    9999999999999874   46778999999999999999999877 89999999


Q ss_pred             EEEEcCCCCC
Q 009920          177 EVKRAVPKEF  186 (522)
Q Consensus       177 ~V~~a~pk~~  186 (522)
                      +|++++++..
T Consensus        82 ~v~~a~~~~~   91 (97)
T 1nu4_A           82 RIQYAKTDSD   91 (97)
T ss_dssp             EEEECSSCCT
T ss_pred             EEEEccCCCc
Confidence            9999998754

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.56  E-value=1.3e-14  Score=131.68  Aligned_cols=80  Identities=29%  Similarity=0.549  Sum_probs=76.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||.++|+++|+++|++||+|.+++|++++.+++++|+|||+|.++++|++|+  +++..|++++|.|.++
T Consensus        85 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  164 (166)
T 3md3_A           85 DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA  164 (166)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEec
Confidence            45789999999999999999999999999999999999999999999999999999999999  8999999999999998


Q ss_pred             CC
Q 009920           81 VP   82 (522)
Q Consensus        81 ~~   82 (522)
                      .+
T Consensus       165 ~~  166 (166)
T 3md3_A          165 AK  166 (166)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.56  E-value=1.4e-14  Score=137.70  Aligned_cols=83  Identities=20%  Similarity=0.532  Sum_probs=78.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||.++|+++|+++|++||+|++|+|++++.++++++||||+|.++++|++|+  +++..|++++|.|.++
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            35689999999999999999999999999999999999989999999999999999999999  8999999999999999


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      .++..
T Consensus       203 ~~~~~  207 (216)
T 2qfj_A          203 VTPPM  207 (216)
T ss_dssp             SSCSS
T ss_pred             cCCCC
Confidence            87643

>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=99.56  E-value=3.8e-15  Score=136.00  Aligned_cols=81  Identities=37%  Similarity=0.734  Sum_probs=76.8

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecCC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~~   82 (522)
                      ..++|||+|||+++|+++|+++|++||+|++|+|++++.+++++|||||+|.++++|++|+ ++.+.|++++|+|+++.+
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~V~~a~p  165 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEP  165 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHHCSEECSSSSCEEEEECCC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHhCCCEEeCCeEEEEeecCC
Confidence            3578999999999999999999999999999999999989999999999999999999999 888999999999999987


Q ss_pred             Cc
Q 009920           83 RD   84 (522)
Q Consensus        83 k~   84 (522)
                      ++
T Consensus       166 k~  167 (167)
T 2cjk_A          166 RH  167 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>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=99.55  E-value=8.5e-15  Score=126.09  Aligned_cols=73  Identities=21%  Similarity=0.463  Sum_probs=67.8

Q ss_pred             CCcEEEECCCCCC-CCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            4 DLGKLFIGGISWD-TDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         4 d~r~LfVgnLP~~-~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ..++|||+|||++ +|+++|+++|++||+|++|+|        +++||||+|.++++|++||  ++.+.|++++|.|+++
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   97 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA   97 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEES
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            3489999999999 999999999999999999998        4689999999999999999  8999999999999999


Q ss_pred             CCCc
Q 009920           81 VPRD   84 (522)
Q Consensus        81 ~~k~   84 (522)
                      .+..
T Consensus        98 ~~~~  101 (110)
T 1wf1_A           98 GEPK  101 (110)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.55  E-value=6.9e-15  Score=123.68  Aligned_cols=76  Identities=25%  Similarity=0.478  Sum_probs=68.9

Q ss_pred             CCCcEEEECCCCC-CCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            3 SDLGKLFIGGISW-DTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         3 ~d~r~LfVgnLP~-~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      .+.++|||+|||+ ++++++|+++|++||+|++|+|.        ++||||+|.++++|++|+  +++..+.+++|.|++
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   79 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEV   79 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            5789999999998 99999999999999999999984        689999999999999999  899999999999999


Q ss_pred             cCCCccc
Q 009920           80 AVPRDDQ   86 (522)
Q Consensus        80 a~~k~~~   86 (522)
                      +.++...
T Consensus        80 a~~~~~~   86 (96)
T 2kvi_A           80 SSSNARP   86 (96)
T ss_dssp             EECCCC-
T ss_pred             cCcCCCC
Confidence            9776543

>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=99.55  E-value=1.7e-14  Score=121.84  Aligned_cols=73  Identities=26%  Similarity=0.488  Sum_probs=68.3

Q ss_pred             CCCcEEEECCCCC-CCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            3 SDLGKLFIGGISW-DTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         3 ~d~r~LfVgnLP~-~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      .+.++|||+|||+ ++++++|+++|++||+|.+|+|.        +|||||+|.+.++|++|+  +++..+++++|.|++
T Consensus        20 ~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   91 (97)
T 2xnq_A           20 HMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEV   91 (97)
T ss_dssp             CTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            5789999999998 99999999999999999999983        689999999999999999  899999999999999


Q ss_pred             cCCC
Q 009920           80 AVPR   83 (522)
Q Consensus        80 a~~k   83 (522)
                      +.++
T Consensus        92 a~~~   95 (97)
T 2xnq_A           92 SSSN   95 (97)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8764

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.55  E-value=3.4e-15  Score=121.52  Aligned_cols=71  Identities=20%  Similarity=0.324  Sum_probs=65.9

Q ss_pred             ceeEecCCCCCC------CHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCe-EEE
Q 009920          106 KKIFVGGLASTV------TESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGK-MVE  177 (522)
Q Consensus       106 ~~LfVgnLp~~v------teedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr-~I~  177 (522)
                      ++|||+|||..+      |+++|+++|++||+|++|.|+  +.+++++|||||+|.++++|++|++.++ ..|+|+ +|+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            689999999999      789999999999999999987  4678999999999999999999999888 899999 887


Q ss_pred             E
Q 009920          178 V  178 (522)
Q Consensus       178 V  178 (522)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=6e-15  Score=128.19  Aligned_cols=80  Identities=24%  Similarity=0.495  Sum_probs=71.5

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCC---CCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNT---QRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVK  179 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~t---g~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~  179 (522)
                      ...++|||+|||+++|+++|+++|++||+|+ +.++.++.+   +++||||||+|+++++|++||+.+ +.|+|+.|.|.
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~-~~~~G~~~~~~   83 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDAC-LEEDGKLYLCV   83 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHS-EEETTEEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhh-hhcCCcEEEec
Confidence            4578999999999999999999999999999 888888877   699999999999999999999988 46888888887


Q ss_pred             EcCCC
Q 009920          180 RAVPK  184 (522)
Q Consensus       180 ~a~pk  184 (522)
                      .+.+.
T Consensus        84 ~~~~~   88 (114)
T 2dnl_A           84 SSPTI   88 (114)
T ss_dssp             CCSSS
T ss_pred             cCCCc
Confidence            65543

>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=99.54  E-value=1.1e-14  Score=126.21  Aligned_cols=81  Identities=12%  Similarity=0.270  Sum_probs=73.9

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ...++|||+|||..+|+++|+++|++||.|++|.|+.+.   +++|||||+|.++++|++|++.++ ..|+|++|.|+++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~---~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECST---TTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCC---CCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            467899999999999999999999999999999999764   458999999999999999999777 8999999999999


Q ss_pred             CCCCC
Q 009920          182 VPKEF  186 (522)
Q Consensus       182 ~pk~~  186 (522)
                      .++..
T Consensus        83 ~~~~~   87 (115)
T 3lqv_A           83 NANRA   87 (115)
T ss_dssp             CHHHH
T ss_pred             cCChh
Confidence            87654

>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=99.54  E-value=2.3e-14  Score=130.17  Aligned_cols=82  Identities=22%  Similarity=0.435  Sum_probs=77.5

Q ss_pred             cceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCC
Q 009920          105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVP  183 (522)
Q Consensus       105 ~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~p  183 (522)
                      .++|||+|||+++|+++|+++|++||+|.+|.+++++.+++++|||||+|.++++|++|++.++ ..|.+++|+|.++.+
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            5789999999999999999999999999999999999899999999999999999999999777 899999999999987


Q ss_pred             CCC
Q 009920          184 KEF  186 (522)
Q Consensus       184 k~~  186 (522)
                      +..
T Consensus        82 ~~~   84 (167)
T 1fxl_A           82 SSA   84 (167)
T ss_dssp             CCG
T ss_pred             Ccc
Confidence            654

>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=99.54  E-value=1.1e-14  Score=132.32  Aligned_cols=77  Identities=23%  Similarity=0.431  Sum_probs=71.7

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++|+++|+++|++||+|++|+|+++     ++|||||+|.++++|++|+  ++++.|++++|.|+++
T Consensus        71 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  145 (150)
T 2i2y_A           71 PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS  145 (150)
T ss_dssp             TTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            45689999999999999999999999999999999886     5799999999999999999  8999999999999999


Q ss_pred             CCCc
Q 009920           81 VPRD   84 (522)
Q Consensus        81 ~~k~   84 (522)
                      .++.
T Consensus       146 ~~~~  149 (150)
T 2i2y_A          146 NGEK  149 (150)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8753

>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=99.54  E-value=8.3e-15  Score=127.67  Aligned_cols=74  Identities=22%  Similarity=0.341  Sum_probs=64.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeE-----E
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRT-----V   75 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~-----I   75 (522)
                      ...++|||+|||+++||++|+++|++||+|++|+|+++       +||||+|.++++|++||  +++++|++++     |
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            45689999999999999999999999999999999875       79999999999999999  8999999998     6


Q ss_pred             EEeecCCC
Q 009920           76 EAKKAVPR   83 (522)
Q Consensus        76 ~V~~a~~k   83 (522)
                      +|+.+.++
T Consensus        87 ~v~~~~~~   94 (115)
T 3beg_B           87 RVKVDGPR   94 (115)
T ss_dssp             EEEECC--
T ss_pred             EeccCCCC
Confidence            66665543

>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=99.54  E-value=2e-14  Score=131.15  Aligned_cols=84  Identities=23%  Similarity=0.341  Sum_probs=78.6

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      +.++|||+|||.++++++|+++|++||+|++|.|++++.+++++|||||+|.++++|++|++.++ ..|.+++|+|.++.
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            45799999999999999999999999999999999999999999999999999999999999777 89999999999998


Q ss_pred             CCCCC
Q 009920          183 PKEFS  187 (522)
Q Consensus       183 pk~~~  187 (522)
                      ++...
T Consensus        82 ~~~~~   86 (168)
T 1b7f_A           82 PGGES   86 (168)
T ss_dssp             CCSST
T ss_pred             CCccc
Confidence            77643

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.53  E-value=2.1e-14  Score=134.71  Aligned_cols=83  Identities=23%  Similarity=0.498  Sum_probs=78.4

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++++++|+++|++||+|.+|+|++++.+++++|||||+|.++++|++|+  +++..|++++|.|+++
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            45699999999999999999999999999999999999989999999999999999999999  8999999999999999


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      .++..
T Consensus       192 ~~~~~  196 (198)
T 2yh0_A          192 SVGAK  196 (198)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87653

>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=99.53  E-value=1.5e-14  Score=118.59  Aligned_cols=72  Identities=21%  Similarity=0.529  Sum_probs=66.7

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhcc----C-------CeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-Hcccc
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRY----G-------EVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHM   69 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~----G-------~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~   69 (522)
                      +++.++|||+|||+++++++|+++|++|    |       +|.+++++++      |+||||+|.++++|++|+ ++++.
T Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~~l~g~~   76 (87)
T 2hzc_A            3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAMAFDGII   76 (87)
T ss_dssp             SGGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHGGGTTCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHHhcCCCE
Confidence            3578999999999999999999999999    8       9999999764      689999999999999999 99999


Q ss_pred             cCCeEEEEee
Q 009920           70 IDGRTVEAKK   79 (522)
Q Consensus        70 i~Gr~I~V~~   79 (522)
                      |++++|.|++
T Consensus        77 ~~g~~l~V~r   86 (87)
T 2hzc_A           77 FQGQSLKIRR   86 (87)
T ss_dssp             ETTEECEEEC
T ss_pred             ECCeEEEEeC
Confidence            9999999975

>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=99.52  E-value=2.3e-14  Score=136.44  Aligned_cols=81  Identities=12%  Similarity=0.261  Sum_probs=75.1

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcCC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVP  183 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~p  183 (522)
                      ..++|||+|||+++|+++|+++|++||+|+.|+|++++. ++++|||||+|+++++|++||+.+++.|+|++|.|.+++.
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~-~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDD  186 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTT-CCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCC-CCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHH
Confidence            457999999999999999999999999999999999875 8899999999999999999999888999999999999876


Q ss_pred             CC
Q 009920          184 KE  185 (522)
Q Consensus       184 k~  185 (522)
                      -.
T Consensus       187 y~  188 (193)
T 2voo_A          187 YF  188 (193)
T ss_dssp             C-
T ss_pred             HH
Confidence            43

>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=99.52  E-value=2.5e-14  Score=131.18  Aligned_cols=78  Identities=24%  Similarity=0.537  Sum_probs=74.4

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      ..++|||+|||+++|+++|+++|++||+|.+|+|++++.+++++|||||+|.++++|++|+  ++++.|++++|.|++|.
T Consensus        93 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A           93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             TTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            3589999999999999999999999999999999999989999999999999999999999  89999999999999873

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=99.52  E-value=8.2e-14  Score=129.04  Aligned_cols=81  Identities=12%  Similarity=0.188  Sum_probs=72.5

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCC--eEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNG--KMVEV  178 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~G--r~I~V  178 (522)
                      +....+|||+||++.+|+++|+++|++||+|++|.|+.+    ++++||||+|+++++|++|++.++ .+|.+  ++|+|
T Consensus        43 ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V  118 (164)
T 1sjr_A           43 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI  118 (164)
T ss_dssp             CCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEE
T ss_pred             CCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEE
Confidence            445678999999999999999999999999999999754    257899999999999999999998 88865  99999


Q ss_pred             EEcCCCCC
Q 009920          179 KRAVPKEF  186 (522)
Q Consensus       179 ~~a~pk~~  186 (522)
                      ++++++..
T Consensus       119 ~~Ak~~~l  126 (164)
T 1sjr_A          119 DFSKLTSL  126 (164)
T ss_dssp             EECSSSSC
T ss_pred             EEecCCcc
Confidence            99998754

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.52  E-value=5.8e-14  Score=118.09  Aligned_cols=75  Identities=16%  Similarity=0.328  Sum_probs=68.4

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+||  ++|+++|+++|++||+|++|+|.      ++++||||+|.++++|++||  ++++.|++++|.|+++
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a   84 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   84 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECC
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            46789999996  99999999999999999999984      46789999999999999999  7999999999999999


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      .++..
T Consensus        85 ~~~~~   89 (97)
T 1x5p_A           85 RKQPM   89 (97)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            87654

>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=99.52  E-value=2.3e-14  Score=118.48  Aligned_cols=75  Identities=15%  Similarity=0.208  Sum_probs=68.9

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      ..++|||+|||+++++++|+++|++| .|++++|.      ++||||||+|.++++|++|++.++ .+|+|++|+|+++.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            46789999999999999999999999 99999884      578999999999999999999888 89999999999987


Q ss_pred             CCC
Q 009920          183 PKE  185 (522)
Q Consensus       183 pk~  185 (522)
                      .+.
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            654

>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=99.51  E-value=5.7e-15  Score=133.13  Aligned_cols=83  Identities=18%  Similarity=0.331  Sum_probs=71.0

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEE--E---eecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEE
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAV--I---MRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTV   75 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~--i---~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I   75 (522)
                      ...++|||+|||+++|+++|+++|++||+|..|.  +   ++...+++++|||||+|.++++|++||  +++..|++++|
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l  122 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM  122 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            4578999999999999999999999999987741  1   111236889999999999999999999  89999999999


Q ss_pred             EEeecCCCcc
Q 009920           76 EAKKAVPRDD   85 (522)
Q Consensus        76 ~V~~a~~k~~   85 (522)
                      .|+++.+...
T Consensus       123 ~V~~a~~~~~  132 (143)
T 3egn_A          123 VVQFARSARP  132 (143)
T ss_dssp             EEEECCCSCC
T ss_pred             EEEECCCCCC
Confidence            9999976543

>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=3e-14  Score=123.42  Aligned_cols=77  Identities=10%  Similarity=0.159  Sum_probs=70.1

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      ..++|||+|||+.+|+++|+++|++||.|++|.|++      .++||||+|.++++|++||+.++ ..|.+++|.|+++.
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            457999999999999999999999999999998874      47799999999999999999888 89999999999998


Q ss_pred             CCCC
Q 009920          183 PKEF  186 (522)
Q Consensus       183 pk~~  186 (522)
                      ....
T Consensus        83 ~~~~   86 (111)
T 1whx_A           83 IGVF   86 (111)
T ss_dssp             TTTT
T ss_pred             CCcc
Confidence            6543

>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=99.51  E-value=1.1e-14  Score=131.15  Aligned_cols=86  Identities=24%  Similarity=0.290  Sum_probs=72.4

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEE--E---EecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVV--V---MYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKM  175 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~--i---~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~  175 (522)
                      ..+.++|||+|||+++|+++|+++|++||.|+.+.  +   +....+++++|||||+|.+.++|++||+.++ ..|.|++
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            34678999999999999999999999999987641  1   1112358899999999999999999999877 8999999


Q ss_pred             EEEEEcCCCCCC
Q 009920          176 VEVKRAVPKEFS  187 (522)
Q Consensus       176 I~V~~a~pk~~~  187 (522)
                      |.|++++++..+
T Consensus       122 l~V~~a~~~~~~  133 (143)
T 3egn_A          122 MVVQFARSARPK  133 (143)
T ss_dssp             CEEEECCCSCC-
T ss_pred             EEEEECCCCCCc
Confidence            999999876543

>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=3.9e-14  Score=150.97  Aligned_cols=82  Identities=24%  Similarity=0.487  Sum_probs=77.5

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      ..++|||+|||++||+++|+++|++||+|+.|+|+.++.+++++|||||+|.++++|++||  ++++.|++++|.|+++.
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~  180 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  180 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            4579999999999999999999999999999999999999999999999999999999999  89999999999999998


Q ss_pred             CCcc
Q 009920           82 PRDD   85 (522)
Q Consensus        82 ~k~~   85 (522)
                      ++..
T Consensus       181 ~~~~  184 (437)
T 3pgw_S          181 GRTV  184 (437)
T ss_pred             CCCC
Confidence            7543

>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=99.50  E-value=4.5e-14  Score=123.34  Aligned_cols=79  Identities=16%  Similarity=0.305  Sum_probs=69.9

Q ss_pred             CCcceeEe--cCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-Ccc-----CCe
Q 009920          103 GRTKKIFV--GGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HEL-----NGK  174 (522)
Q Consensus       103 ~~~~~LfV--gnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l-----~Gr  174 (522)
                      .++++|||  +||++++||++|+++|++||+|++|.|+.+      ||||||+|+++++|++|++.++ ++|     .++
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~   96 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            46789999  779999999999999999999999988642      7899999999999999999988 777     789


Q ss_pred             EEEEEEcCCCCCC
Q 009920          175 MVEVKRAVPKEFS  187 (522)
Q Consensus       175 ~I~V~~a~pk~~~  187 (522)
                      +|.|.+++..+..
T Consensus        97 ~l~v~~a~~~p~~  109 (114)
T 2cq2_A           97 TLYLNFVEKVQWS  109 (114)
T ss_dssp             ECEEEEESCCCCS
T ss_pred             EEEEEecccCccc
Confidence            9999999865543

>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=99.50  E-value=8.2e-14  Score=129.04  Aligned_cols=77  Identities=16%  Similarity=0.280  Sum_probs=69.4

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCC--eEEEEeec
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDG--RTVEAKKA   80 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~G--r~I~V~~a   80 (522)
                      ..+|||+|||+++||++|+++|++||+|++|+|+.+    ++++||||+|.+.++|++|+  +++..|.+  ++|+|+++
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~A  121 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            457899999999999999999999999999999754    25789999999999999999  89999966  99999999


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      +++..
T Consensus       122 k~~~l  126 (164)
T 1sjr_A          122 KLTSL  126 (164)
T ss_dssp             SSSSC
T ss_pred             cCCcc
Confidence            88753

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.49  E-value=3.3e-14  Score=125.93  Aligned_cols=76  Identities=16%  Similarity=0.198  Sum_probs=68.2

Q ss_pred             cEEEECCC----CCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecC----HHH----HHHHH----Hcccc
Q 009920            6 GKLFIGGI----SWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFAD----PAV----AERVI----MDKHM   69 (522)
Q Consensus         6 r~LfVgnL----P~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~----~e~----A~kAl----~~~~~   69 (522)
                      ++|||+||    |++++|++|+++|++||+|.+|+++.|++|++++|||||+|.+    +++    |.+|+    ++...
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    433    77887    38899


Q ss_pred             cCCeEEEEeecC
Q 009920           70 IDGRTVEAKKAV   81 (522)
Q Consensus        70 i~Gr~I~V~~a~   81 (522)
                      |+|++|+|+.-.
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            999999998653

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.48  E-value=6.1e-14  Score=124.28  Aligned_cols=77  Identities=21%  Similarity=0.262  Sum_probs=69.2

Q ss_pred             ceeEecCC----CCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecC----HHH----HHHHHH--hcC-Cc
Q 009920          106 KKIFVGGL----ASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS----EEA----VDRVLH--KTF-HE  170 (522)
Q Consensus       106 ~~LfVgnL----p~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s----~e~----A~~Al~--~~~-~~  170 (522)
                      ++|||+||    |+.++|++|+++|++||+|.+|.++.|++|++++|||||+|.+    +++    |.+|++  .++ ..
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    9999999999999999999999999999999999999999995    322    788888  556 79


Q ss_pred             cCCeEEEEEEcC
Q 009920          171 LNGKMVEVKRAV  182 (522)
Q Consensus       171 l~Gr~I~V~~a~  182 (522)
                      |+|++|+|.+.+
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            999999999865

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.48  E-value=1.3e-13  Score=123.17  Aligned_cols=79  Identities=14%  Similarity=0.246  Sum_probs=71.3

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceE-EEEEecCHHHHHHHHHhcC-CccCC--eEEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGF-GFITYDSEEAVDRVLHKTF-HELNG--KMVEV  178 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~-aFVeF~s~e~A~~Al~~~~-~~l~G--r~I~V  178 (522)
                      .+..+|||+||++.+|+++|+++|++||+|++|+|+.+     .++| |||+|+++++|++|++.++ .+|.+  ++|+|
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI  100 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI  100 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEE
Confidence            45678899999999999999999999999999998864     2677 9999999999999999999 89988  99999


Q ss_pred             EEcCCCCC
Q 009920          179 KRAVPKEF  186 (522)
Q Consensus       179 ~~a~pk~~  186 (522)
                      ++++++..
T Consensus       101 ~~ak~~~l  108 (130)
T 3zzy_A          101 DFSKLTSL  108 (130)
T ss_dssp             EECSCSSC
T ss_pred             EecCCCce
Confidence            99998754

>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=99.48  E-value=9.4e-14  Score=132.16  Aligned_cols=80  Identities=18%  Similarity=0.200  Sum_probs=72.8

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecCC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~~   82 (522)
                      +.++|||+|||+++|+++|+++|++||+|.+|+|++++. ++++|||||+|.++++|++|+ +.++.|+|++|.|.++..
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~-~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDD  186 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTT-CCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCC-CCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHH
Confidence            358999999999999999999999999999999999874 899999999999999999999 556799999999998776


Q ss_pred             Cc
Q 009920           83 RD   84 (522)
Q Consensus        83 k~   84 (522)
                      ..
T Consensus       187 y~  188 (193)
T 2voo_A          187 YF  188 (193)
T ss_dssp             C-
T ss_pred             HH
Confidence            43

>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=99.48  E-value=5.7e-14  Score=122.67  Aligned_cols=76  Identities=12%  Similarity=0.202  Sum_probs=66.6

Q ss_pred             CCCcEEEE--CCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hccccc-----CCe
Q 009920            3 SDLGKLFI--GGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMI-----DGR   73 (522)
Q Consensus         3 ~d~r~LfV--gnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i-----~Gr   73 (522)
                      ...++|||  +|||+++||++|+++|++||+|++|+|++      .|+||||+|.++++|++|+  +|+++|     .++
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~   96 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            45789999  77999999999999999999999988864      3689999999999999999  899887     688


Q ss_pred             EEEEeecCCCc
Q 009920           74 TVEAKKAVPRD   84 (522)
Q Consensus        74 ~I~V~~a~~k~   84 (522)
                      +|.|..+....
T Consensus        97 ~l~v~~a~~~p  107 (114)
T 2cq2_A           97 TLYLNFVEKVQ  107 (114)
T ss_dssp             ECEEEEESCCC
T ss_pred             EEEEEecccCc
Confidence            88888876543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.47  E-value=2.5e-13  Score=120.42  Aligned_cols=79  Identities=9%  Similarity=0.194  Sum_probs=69.4

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceE-EEEEecCHHHHHHHHHhcC-CccCC--eEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGF-GFITYDSEEAVDRVLHKTF-HELNG--KMVE  177 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~-aFVeF~s~e~A~~Al~~~~-~~l~G--r~I~  177 (522)
                      +.....|||+||++.+|+++|+++|++||.|++|+|+..      +|| |||+|+++++|++|++.|+ .+|.+  ++|+
T Consensus        22 ps~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~   95 (124)
T 2e5i_A           22 GNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLK   95 (124)
T ss_dssp             CCSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEE
T ss_pred             CCcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEE
Confidence            344566889999999999999999999999999999752      276 9999999999999999988 88887  6999


Q ss_pred             EEEcCCCCC
Q 009920          178 VKRAVPKEF  186 (522)
Q Consensus       178 V~~a~pk~~  186 (522)
                      |++|+++..
T Consensus        96 V~~Ak~~~l  104 (124)
T 2e5i_A           96 IEYARPTRL  104 (124)
T ss_dssp             EECCSCSCC
T ss_pred             EEEecCCcc
Confidence            999998764

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.47  E-value=2.2e-13  Score=121.62  Aligned_cols=75  Identities=17%  Similarity=0.334  Sum_probs=68.0

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccE-EEEEecCHHHHHHHH--HcccccCC--eEEEEeec
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGF-GFVVFADPAVAERVI--MDKHMIDG--RTVEAKKA   80 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~-aFVeF~~~e~A~kAl--~~~~~i~G--r~I~V~~a   80 (522)
                      -+|||+|||+.+||++|+++|++||+|.+|+|+++     .++| |||+|.++++|++|+  +++..|.+  ++|+|+++
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~a  103 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  103 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEEC
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEec
Confidence            46789999999999999999999999999998764     3578 999999999999999  99999998  99999999


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      +++..
T Consensus       104 k~~~l  108 (130)
T 3zzy_A          104 KLTSL  108 (130)
T ss_dssp             SCSSC
T ss_pred             CCCce
Confidence            87654

>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=1.3e-13  Score=112.90  Aligned_cols=71  Identities=20%  Similarity=0.511  Sum_probs=64.7

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhc----C-------CeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-Cc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQF----G-------TITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HE  170 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~f----G-------~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~  170 (522)
                      .+.++|||+|||+++++++|+++|++|    |       +|.++.++++      ||||||+|.++++|++|+ .++ ..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~   76 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGII   76 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCE
Confidence            356899999999999999999999999    8       8999998754      789999999999999999 666 89


Q ss_pred             cCCeEEEEEE
Q 009920          171 LNGKMVEVKR  180 (522)
Q Consensus       171 l~Gr~I~V~~  180 (522)
                      |+|++|+|++
T Consensus        77 ~~g~~l~V~r   86 (87)
T 2hzc_A           77 FQGQSLKIRR   86 (87)
T ss_dssp             ETTEECEEEC
T ss_pred             ECCeEEEEeC
Confidence            9999999974

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.45  E-value=2.3e-13  Score=117.01  Aligned_cols=82  Identities=18%  Similarity=0.181  Sum_probs=72.7

Q ss_pred             CCCCcEEEECCCCC-----CCCHHHHHHHHhccCCeEEEEEeecCCC-CCcccEEEEEecCHHHHHHHH--HcccccCCe
Q 009920            2 ESDLGKLFIGGISW-----DTDEERLKEYFSRYGEVVEAVIMRDRAT-GRARGFGFVVFADPAVAERVI--MDKHMIDGR   73 (522)
Q Consensus         2 e~d~r~LfVgnLP~-----~~teedL~e~F~~~G~V~~v~i~~d~~t-g~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr   73 (522)
                      ...+++|+|+||..     +.++++|+++|++||+|++|+|++++.+ ++++|||||+|.++++|++|+  +|+..+++|
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            45789999999963     2478999999999999999999998754 689999999999999999999  999999999


Q ss_pred             EEEEeecCCC
Q 009920           74 TVEAKKAVPR   83 (522)
Q Consensus        74 ~I~V~~a~~k   83 (522)
                      +|.|.++.+.
T Consensus        85 ~i~v~~a~~~   94 (105)
T 2pe8_A           85 VVKACFYNLD   94 (105)
T ss_dssp             ECEEEECCHH
T ss_pred             EEEEEEcCHH
Confidence            9999998653

>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=99.44  E-value=2.2e-13  Score=124.76  Aligned_cols=83  Identities=22%  Similarity=0.422  Sum_probs=74.5

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCC--CcceEEEEEecCHHHHHHHHHhcC-CccC---CeEEE
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQ--RPRGFGFITYDSEEAVDRVLHKTF-HELN---GKMVE  177 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg--~~rG~aFVeF~s~e~A~~Al~~~~-~~l~---Gr~I~  177 (522)
                      +.++|||+|||+++|+++|+++|++||+|++|+|++++.++  +++|||||+|.++++|++|++.++ ..+.   .+.|.
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            46799999999999999999999999999999999999887  899999999999999999999887 4554   68888


Q ss_pred             EEEcCCCCC
Q 009920          178 VKRAVPKEF  186 (522)
Q Consensus       178 V~~a~pk~~  186 (522)
                      |.++.++..
T Consensus        82 ~~~~~~~~~   90 (175)
T 3nmr_A           82 MKPADSEKN   90 (175)
T ss_dssp             EEECGGGCC
T ss_pred             Ecccccccc
Confidence            888876654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.44  E-value=5.3e-13  Score=118.29  Aligned_cols=73  Identities=21%  Similarity=0.215  Sum_probs=65.7

Q ss_pred             EEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccE-EEEEecCHHHHHHHH--HcccccCC--eEEEEeecC
Q 009920            7 KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGF-GFVVFADPAVAERVI--MDKHMIDG--RTVEAKKAV   81 (522)
Q Consensus         7 ~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~-aFVeF~~~e~A~kAl--~~~~~i~G--r~I~V~~a~   81 (522)
                      .|||+|||+.+|+++|+++|++||+|++|+|++.      +|| |||+|.+.++|++|+  +++..|.+  ++|+|++++
T Consensus        27 ~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak  100 (124)
T 2e5i_A           27 LLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYAR  100 (124)
T ss_dssp             EEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCS
T ss_pred             EEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEec
Confidence            4689999999999999999999999999999752      276 999999999999999  99999987  699999998


Q ss_pred             CCcc
Q 009920           82 PRDD   85 (522)
Q Consensus        82 ~k~~   85 (522)
                      ++..
T Consensus       101 ~~~l  104 (124)
T 2e5i_A          101 PTRL  104 (124)
T ss_dssp             CSCC
T ss_pred             CCcc
Confidence            7753

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.44  E-value=4.2e-13  Score=115.44  Aligned_cols=82  Identities=12%  Similarity=0.155  Sum_probs=72.4

Q ss_pred             CCcceeEecCCCC-----CCCHHHHHHHHhhcCCeeEEEEEecCCC-CCcceEEEEEecCHHHHHHHHHhcC-CccCCeE
Q 009920          103 GRTKKIFVGGLAS-----TVTESDFKKYFDQFGTITDVVVMYDHNT-QRPRGFGFITYDSEEAVDRVLHKTF-HELNGKM  175 (522)
Q Consensus       103 ~~~~~LfVgnLp~-----~vteedL~~~F~~fG~I~~v~i~~d~~t-g~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~  175 (522)
                      .++++|+|.||..     +.+++||+++|++||.|++|.|++++.+ ++++|++||+|.++++|++|++.|+ ..|+||+
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4678999999963     2378999999999999999999998764 6889999999999999999999988 8999999


Q ss_pred             EEEEEcCCC
Q 009920          176 VEVKRAVPK  184 (522)
Q Consensus       176 I~V~~a~pk  184 (522)
                      |.|.++.+.
T Consensus        86 i~v~~a~~~   94 (105)
T 2pe8_A           86 VKACFYNLD   94 (105)
T ss_dssp             CEEEECCHH
T ss_pred             EEEEEcCHH
Confidence            999999753

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.43  E-value=2.6e-13  Score=113.86  Aligned_cols=74  Identities=11%  Similarity=0.214  Sum_probs=65.3

Q ss_pred             Ccce-eEecCCCCCCCHHH----HHHHHhhc-CCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEE
Q 009920          104 RTKK-IFVGGLASTVTESD----FKKYFDQF-GTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMV  176 (522)
Q Consensus       104 ~~~~-LfVgnLp~~vteed----L~~~F~~f-G~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I  176 (522)
                      ++.+ |||.|||+.+++++    |+++|++| |+|.+|       ++   |+|||+|.+.++|++|++.|+ .+|.||+|
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            4555 99999999999988    55899999 599888       22   899999999999999999888 89999999


Q ss_pred             EEEEcCCCCCC
Q 009920          177 EVKRAVPKEFS  187 (522)
Q Consensus       177 ~V~~a~pk~~~  187 (522)
                      +|++|+++.+.
T Consensus        77 ~v~~A~~~sd~   87 (96)
T 2diu_A           77 IVSFTPKNREL   87 (96)
T ss_dssp             EEESSCCSCCC
T ss_pred             EEEecCCCcce
Confidence            99999987754

>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=99.42  E-value=3.1e-13  Score=124.47  Aligned_cols=76  Identities=25%  Similarity=0.388  Sum_probs=69.4

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++|+++|+++|++||+|..+     ..+++++|||||+|.++++|++|+  ++++.|++++|.|+++
T Consensus        97 ~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  171 (175)
T 1fje_B           97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT  171 (175)
T ss_dssp             GGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEEC
T ss_pred             ccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEec
Confidence            356899999999999999999999999988655     457899999999999999999999  8999999999999999


Q ss_pred             CCC
Q 009920           81 VPR   83 (522)
Q Consensus        81 ~~k   83 (522)
                      .++
T Consensus       172 ~~k  174 (175)
T 1fje_B          172 GEK  174 (175)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            875

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.41  E-value=1.4e-12  Score=112.85  Aligned_cols=84  Identities=12%  Similarity=0.275  Sum_probs=71.3

Q ss_pred             CCCCcceeEecCCCCCCC-----------HHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-
Q 009920          101 GPGRTKKIFVGGLASTVT-----------ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-  168 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vt-----------eedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-  168 (522)
                      .+.++++|+|.||.....           +++|+++|++||+|++|.| .++   .++|||||+|.++++|++|++.++ 
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng   86 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDG   86 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCC
Confidence            345788999999944332           6899999999999999966 554   379999999999999999999988 


Q ss_pred             CccCCeEEEEEEcCCCCCCC
Q 009920          169 HELNGKMVEVKRAVPKEFSP  188 (522)
Q Consensus       169 ~~l~Gr~I~V~~a~pk~~~~  188 (522)
                      ..|++|+|+|+++.++....
T Consensus        87 ~~~~gr~l~v~~a~~~~~~~  106 (112)
T 2dit_A           87 RWFGGRQITAQAWDGTTDYQ  106 (112)
T ss_dssp             CEETTEECEEEECCSCCCSS
T ss_pred             CEECCcEEEEEEeCCCCCcc
Confidence            89999999999999876543

>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=99.41  E-value=4.5e-13  Score=128.52  Aligned_cols=78  Identities=19%  Similarity=0.242  Sum_probs=71.2

Q ss_pred             CcceeEecCCC-CCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          104 RTKKIFVGGLA-STVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       104 ~~~~LfVgnLp-~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      +.++|||+||| +.+|+++|+++|++||.|.+|+|+++     .||||||+|+++++|++||+.++ .+|.|++|+|.++
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            46799999999 89999999999999999999999865     37899999999999999999888 8999999999999


Q ss_pred             CCCCC
Q 009920          182 VPKEF  186 (522)
Q Consensus       182 ~pk~~  186 (522)
                      +.+..
T Consensus        78 ~~~~~   82 (205)
T 3tyt_A           78 KQPAI   82 (205)
T ss_dssp             SCSCC
T ss_pred             cCCcc
Confidence            76543

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=9.7e-13  Score=110.41  Aligned_cols=74  Identities=18%  Similarity=0.256  Sum_probs=64.5

Q ss_pred             CCcE-EEECCCCCCCCHHH----HHHHHhcc-CCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEE
Q 009920            4 DLGK-LFIGGISWDTDEER----LKEYFSRY-GEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTV   75 (522)
Q Consensus         4 d~r~-LfVgnLP~~~teed----L~e~F~~~-G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I   75 (522)
                      ++.+ |||+|||+++++++    |+++|++| |+|.+|       ++   |+|||+|.+.++|++|+  |++..+.+|+|
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 99999999999998    55899999 599887       23   99999999999999999  99999999999


Q ss_pred             EEeecCCCcccc
Q 009920           76 EAKKAVPRDDQN   87 (522)
Q Consensus        76 ~V~~a~~k~~~~   87 (522)
                      +|..|+.+.+..
T Consensus        77 ~v~~A~~~sd~~   88 (96)
T 2diu_A           77 IVSFTPKNRELC   88 (96)
T ss_dssp             EEESSCCSCCCC
T ss_pred             EEEecCCCccee
Confidence            999998776543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.39  E-value=4.6e-13  Score=131.53  Aligned_cols=79  Identities=28%  Similarity=0.386  Sum_probs=68.9

Q ss_pred             CCCCcEEEECCCCCCC---------CHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hccccc
Q 009920            2 ESDLGKLFIGGISWDT---------DEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMI   70 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~---------teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i   70 (522)
                      +.+.++|||+|||.++         +|++|+++|++||+|++|+|++      +||||||+|.+.++|++|+  |+++.|
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            3568999999999998         7999999999999999999986      4789999999999999999  999999


Q ss_pred             ------------CCeEEEEeecCCCccc
Q 009920           71 ------------DGRTVEAKKAVPRDDQ   86 (522)
Q Consensus        71 ------------~Gr~I~V~~a~~k~~~   86 (522)
                                  +++.|.|++|.+....
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~pnp  232 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDPDP  232 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC-----
T ss_pred             eccccccccccCCCCEEEEEEccCCCCH
Confidence                        8999999999865443

>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=99.38  E-value=1.2e-12  Score=130.23  Aligned_cols=83  Identities=19%  Similarity=0.372  Sum_probs=74.8

Q ss_pred             CCCCcceeEecCCCCCCCHHHHH----HHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFK----KYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKM  175 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~----~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~  175 (522)
                      +..+.++|||+|||+++|+++|+    ++|++||.|++|+|++   ++++||||||+|.++++|++||+.++ ..|.+++
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            34568899999999999999977    8999999999999886   57789999999999999999998887 8999999


Q ss_pred             EEEEEcCCCCC
Q 009920          176 VEVKRAVPKEF  186 (522)
Q Consensus       176 I~V~~a~pk~~  186 (522)
                      |+|++++++..
T Consensus        82 l~v~~a~~~~~   92 (282)
T 3pgw_A           82 MRIQYAKTDSD   92 (282)
T ss_pred             EEEEEeccCcc
Confidence            99999976653

>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=99.34  E-value=1.8e-12  Score=125.75  Aligned_cols=79  Identities=14%  Similarity=0.325  Sum_probs=72.6

Q ss_pred             CCcceeEecCCCC-CCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          103 GRTKKIFVGGLAS-TVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       103 ~~~~~LfVgnLp~-~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      .+.++|||+|||+ ++++++|+++|++||.|++|+|++++     +|||||+|.++++|++||+.++ ..|.+++|.|++
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~  106 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL  106 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEEC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            4678999999999 99999999999999999999999875     7899999999999999999777 899999999999


Q ss_pred             cCCCCC
Q 009920          181 AVPKEF  186 (522)
Q Consensus       181 a~pk~~  186 (522)
                      ++++..
T Consensus       107 a~~~~~  112 (229)
T 2adc_A          107 SKHQNV  112 (229)
T ss_dssp             CSCCCC
T ss_pred             ecCccc
Confidence            987643

>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=99.34  E-value=3.2e-12  Score=110.54  Aligned_cols=80  Identities=25%  Similarity=0.374  Sum_probs=68.5

Q ss_pred             CCCcEEEECCCCCCCC-----------HHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hcccc
Q 009920            3 SDLGKLFIGGISWDTD-----------EERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHM   69 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~t-----------eedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~   69 (522)
                      ..+++|+|+||....+           +++|+++|++||+|++|.| .++   .++|||||+|.++++|++|+  ++++.
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~~   88 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGRW   88 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCCE
Confidence            4688999999944332           6899999999999999966 554   38999999999999999999  89999


Q ss_pred             cCCeEEEEeecCCCccc
Q 009920           70 IDGRTVEAKKAVPRDDQ   86 (522)
Q Consensus        70 i~Gr~I~V~~a~~k~~~   86 (522)
                      |++++|.|+++.++...
T Consensus        89 ~~gr~l~v~~a~~~~~~  105 (112)
T 2dit_A           89 FGGRQITAQAWDGTTDY  105 (112)
T ss_dssp             ETTEECEEEECCSCCCS
T ss_pred             ECCcEEEEEEeCCCCCc
Confidence            99999999999876543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.34  E-value=1.3e-12  Score=128.30  Aligned_cols=79  Identities=20%  Similarity=0.364  Sum_probs=69.1

Q ss_pred             CCCcceeEecCCCCCC---------CHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-Ccc
Q 009920          102 PGRTKKIFVGGLASTV---------TESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HEL  171 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~v---------teedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l  171 (522)
                      ....++|||+||+..+         +|++|+++|++||+|++|+|+.      .||||||+|.++++|++|++.|+ ..|
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            3467899999999998         7999999999999999999985      37899999999999999999888 777


Q ss_pred             ------------CCeEEEEEEcCCCCC
Q 009920          172 ------------NGKMVEVKRAVPKEF  186 (522)
Q Consensus       172 ------------~Gr~I~V~~a~pk~~  186 (522)
                                  .++.|.|++|+++..
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                        899999999987654

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.30  E-value=1.9e-11  Score=104.21  Aligned_cols=68  Identities=7%  Similarity=0.223  Sum_probs=60.2

Q ss_pred             CCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcCCCCCCC
Q 009920          115 STVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSP  188 (522)
Q Consensus       115 ~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~pk~~~~  188 (522)
                      ..+++++|+++|++||+|++|.|+     .++||||||+|+++++|++||+.+ ..+.+++|+|++++++....
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~-~~~~g~~l~V~~a~~~~~~~   94 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNE-VGLVDNPLKISWLEGQPQDA   94 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTC-CBCSSSBCEEECSSCCCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhc-CCCCCCeEEEEEccCCCCCC
Confidence            568999999999999999999998     367999999999999999999984 45789999999998876543

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.30  E-value=2.8e-12  Score=120.69  Aligned_cols=77  Identities=14%  Similarity=0.336  Sum_probs=71.0

Q ss_pred             cceeEecCCCC-CCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          105 TKKIFVGGLAS-TVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       105 ~~~LfVgnLp~-~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      .++|||+|||+ ++++++|+++|++||.|++|+|++++     +|||||+|.++++|++|++.++ ..|.+++|+|.++.
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            57999999999 99999999999999999999999775     7899999999999999999777 89999999999998


Q ss_pred             CCCC
Q 009920          183 PKEF  186 (522)
Q Consensus       183 pk~~  186 (522)
                      ++..
T Consensus        78 ~~~~   81 (198)
T 1qm9_A           78 HQNV   81 (198)
T ss_dssp             CCSC
T ss_pred             CCCc
Confidence            7653

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.29  E-value=1.4e-11  Score=105.00  Aligned_cols=78  Identities=18%  Similarity=0.191  Sum_probs=66.1

Q ss_pred             CCCcEEEECCCC-------CCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHHHcccccCCeEE
Q 009920            3 SDLGKLFIGGIS-------WDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTV   75 (522)
Q Consensus         3 ~d~r~LfVgnLP-------~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl~~~~~i~Gr~I   75 (522)
                      ...++|-|.-.+       .+++|++|+++|++||+|++|+|+     +++||||||+|.++++|++||.....+.+++|
T Consensus         8 ~~~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~~~g~~l   82 (100)
T 2d9o_A            8 QGTPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVGLVDNPL   82 (100)
T ss_dssp             CSSCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCBCSSSBC
T ss_pred             CccceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCCCCCCeE
Confidence            346677777655       348999999999999999999998     36889999999999999999966677889999


Q ss_pred             EEeecCCCcc
Q 009920           76 EAKKAVPRDD   85 (522)
Q Consensus        76 ~V~~a~~k~~   85 (522)
                      .|+++.++..
T Consensus        83 ~V~~a~~~~~   92 (100)
T 2d9o_A           83 KISWLEGQPQ   92 (100)
T ss_dssp             EEECSSCCCC
T ss_pred             EEEEccCCCC
Confidence            9999876643

>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=99.29  E-value=6.2e-12  Score=124.41  Aligned_cols=82  Identities=32%  Similarity=0.413  Sum_probs=72.8

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--H-cccccC---CeEEE
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M-DKHMID---GRTVE   76 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~-~~~~i~---Gr~I~   76 (522)
                      .+.++|||+|||+++|+++|+++|++||+|++|+|++++ +++++|||||+|.++++|++|+  + +...+.   +++|.
T Consensus        94 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~  172 (261)
T 3sde_A           94 THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVI  172 (261)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCE
T ss_pred             ccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCC-CCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEE
Confidence            356899999999999999999999999999999999994 7999999999999999999999  5 444444   99999


Q ss_pred             EeecCCCcc
Q 009920           77 AKKAVPRDD   85 (522)
Q Consensus        77 V~~a~~k~~   85 (522)
                      |+++.+...
T Consensus       173 v~~~~~~~~  181 (261)
T 3sde_A          173 VEPMEQFDD  181 (261)
T ss_dssp             EEECCCEES
T ss_pred             EeeccccCc
Confidence            999877543

>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=99.29  E-value=4.9e-12  Score=108.68  Aligned_cols=82  Identities=11%  Similarity=0.186  Sum_probs=71.0

Q ss_pred             CCcceeEecCC--CCCCC--------HHHHHHHHhhcCCeeEEEEEecCCC--CCcceEEEEEecCHHHHHHHHHhcC-C
Q 009920          103 GRTKKIFVGGL--ASTVT--------ESDFKKYFDQFGTITDVVVMYDHNT--QRPRGFGFITYDSEEAVDRVLHKTF-H  169 (522)
Q Consensus       103 ~~~~~LfVgnL--p~~vt--------eedL~~~F~~fG~I~~v~i~~d~~t--g~~rG~aFVeF~s~e~A~~Al~~~~-~  169 (522)
                      .+++.|.|.|+  |..+.        ++||+++|++||+|++|.|++++.+  .+++|++||+|.++++|++|++.|+ .
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            36778999998  44443        3799999999999999999998765  4689999999999999999999999 8


Q ss_pred             ccCCeEEEEEEcCCC
Q 009920          170 ELNGKMVEVKRAVPK  184 (522)
Q Consensus       170 ~l~Gr~I~V~~a~pk  184 (522)
                      .++||+|.|.++.+.
T Consensus        83 ~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           83 KFANRVVVTKYCDPD   97 (105)
T ss_dssp             EETTEECEEEEECHH
T ss_pred             EeCCCEEEEEEeCHH
Confidence            999999999998654

>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=99.28  E-value=5.1e-12  Score=108.56  Aligned_cols=81  Identities=20%  Similarity=0.175  Sum_probs=70.5

Q ss_pred             CCCcEEEECCC--CCCCC--------HHHHHHHHhccCCeEEEEEeecCCC--CCcccEEEEEecCHHHHHHHH--Hccc
Q 009920            3 SDLGKLFIGGI--SWDTD--------EERLKEYFSRYGEVVEAVIMRDRAT--GRARGFGFVVFADPAVAERVI--MDKH   68 (522)
Q Consensus         3 ~d~r~LfVgnL--P~~~t--------eedL~e~F~~~G~V~~v~i~~d~~t--g~srG~aFVeF~~~e~A~kAl--~~~~   68 (522)
                      ..++.|.|.|+  |.++.        ++||+++|++||+|++|+|++++.+  .+++|++||+|.++++|++|+  +|+.
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            45788999998  44443        4799999999999999999998764  468999999999999999999  9999


Q ss_pred             ccCCeEEEEeecCCC
Q 009920           69 MIDGRTVEAKKAVPR   83 (522)
Q Consensus        69 ~i~Gr~I~V~~a~~k   83 (522)
                      .+++|+|.|..+.+.
T Consensus        83 ~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           83 KFANRVVVTKYCDPD   97 (105)
T ss_dssp             EETTEECEEEEECHH
T ss_pred             EeCCCEEEEEEeCHH
Confidence            999999999987654

>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=99.27  E-value=8e-12  Score=109.73  Aligned_cols=79  Identities=18%  Similarity=0.236  Sum_probs=69.7

Q ss_pred             CCcEEEECCCCC--C---CCHHHHHHHHhccCCeEEEEEeecCC----CCCcccEEEEEecCHHHHHHHH--HcccccCC
Q 009920            4 DLGKLFIGGISW--D---TDEERLKEYFSRYGEVVEAVIMRDRA----TGRARGFGFVVFADPAVAERVI--MDKHMIDG   72 (522)
Q Consensus         4 d~r~LfVgnLP~--~---~teedL~e~F~~~G~V~~v~i~~d~~----tg~srG~aFVeF~~~e~A~kAl--~~~~~i~G   72 (522)
                      .++.|+|+|+-.  +   -.++||++.|++||+|++|+|++++.    +++++|++||+|.++++|++|+  +|+..+++
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            678999999842  2   24789999999999999999999864    4678999999999999999999  99999999


Q ss_pred             eEEEEeecCC
Q 009920           73 RTVEAKKAVP   82 (522)
Q Consensus        73 r~I~V~~a~~   82 (522)
                      |+|.|..+..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999998754

>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=99.24  E-value=3.1e-12  Score=109.70  Aligned_cols=70  Identities=20%  Similarity=0.405  Sum_probs=61.1

Q ss_pred             ECCCCCCCCHHHHHHHH------------hccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEE
Q 009920           10 IGGISWDTDEERLKEYF------------SRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTV   75 (522)
Q Consensus        10 VgnLP~~~teedL~e~F------------~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I   75 (522)
                      +.+||+++++++|+++|            ++||+|++|+|++++. ++++|||||+|.++++|++|+  ++++.+++|+|
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            45666677777777666            9999999999999875 789999999999999999999  99999999999


Q ss_pred             EEeec
Q 009920           76 EAKKA   80 (522)
Q Consensus        76 ~V~~a   80 (522)
                      .|+++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99875

>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=99.23  E-value=4.5e-12  Score=108.68  Aligned_cols=71  Identities=15%  Similarity=0.381  Sum_probs=62.5

Q ss_pred             ecCCCCCCCHHHHHHHH------------hhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEE
Q 009920          110 VGGLASTVTESDFKKYF------------DQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMV  176 (522)
Q Consensus       110 VgnLp~~vteedL~~~F------------~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I  176 (522)
                      +.+||..+++++|+++|            ++||+|++|.|++++. ++++|||||+|+++++|++|++.++ ..|+||+|
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            55677778887777666            9999999999998875 6899999999999999999999888 89999999


Q ss_pred             EEEEc
Q 009920          177 EVKRA  181 (522)
Q Consensus       177 ~V~~a  181 (522)
                      +|+++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>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=99.22  E-value=2.4e-11  Score=106.73  Aligned_cols=80  Identities=9%  Similarity=0.196  Sum_probs=69.7

Q ss_pred             CcceeEecCCCC--CC---CHHHHHHHHhhcCCeeEEEEEecCC----CCCcceEEEEEecCHHHHHHHHHhcC-CccCC
Q 009920          104 RTKKIFVGGLAS--TV---TESDFKKYFDQFGTITDVVVMYDHN----TQRPRGFGFITYDSEEAVDRVLHKTF-HELNG  173 (522)
Q Consensus       104 ~~~~LfVgnLp~--~v---teedL~~~F~~fG~I~~v~i~~d~~----tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~G  173 (522)
                      ++++|+|.|+-.  ++   .++||+++|++||+|++|.|++++.    +.+++|++||+|.++++|++|++.++ ..++|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            577889998832  22   3689999999999999999999865    45778999999999999999999999 89999


Q ss_pred             eEEEEEEcCC
Q 009920          174 KMVEVKRAVP  183 (522)
Q Consensus       174 r~I~V~~a~p  183 (522)
                      |+|.|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999864

>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=99.08  E-value=3.1e-10  Score=116.97  Aligned_cols=109  Identities=9%  Similarity=0.126  Sum_probs=76.0

Q ss_pred             CCCCcEEEECC--CCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccC---Ce-
Q 009920            2 ESDLGKLFIGG--ISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMID---GR-   73 (522)
Q Consensus         2 e~d~r~LfVgn--LP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~---Gr-   73 (522)
                      +..+++|||+|  |++++||++|+++|++||+|++|+|.+      +|+||||+|.+.++|++|+  +|++++.   ++ 
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            35678999999  578999999999999999999887743      4789999999999999999  8888772   45 


Q ss_pred             -EEEEeecCCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhc
Q 009920           74 -TVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQF  129 (522)
Q Consensus        74 -~I~V~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~f  129 (522)
                       .|.|..+....  .....    ..    ..+....+   +|.-++++|-.++.+..
T Consensus        89 ~~ly~~~~~~~~--~~~~~----~~----~lp~Gl~~---~p~fis~~Ee~~Ll~~i  132 (345)
T 3tht_A           89 ITLYLNFVEKVQ--WKELR----PQ----ALPPGLMV---VEEIISSEEEKMLLESV  132 (345)
T ss_dssp             EECEEEECSSEE--EEEEE----CC----SCCTTEEE---ETTCSCHHHHHHHHTTC
T ss_pred             eEEEEEEeeccc--ccccc----cc----cCCCceEE---EcCcCCHHHHHHHHHhc
Confidence             45555553221  11000    00    01112333   36668887767776654

>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=99.04  E-value=4.4e-10  Score=97.97  Aligned_cols=78  Identities=13%  Similarity=0.128  Sum_probs=65.1

Q ss_pred             CCcceeEecCCCCCC----------CHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-Ccc
Q 009920          103 GRTKKIFVGGLASTV----------TESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HEL  171 (522)
Q Consensus       103 ~~~~~LfVgnLp~~v----------teedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l  171 (522)
                      .++++|.|.|+=...          .++||+++|++||.|++|.|.++.    ++|++||+|.++++|++|++.|+ ..+
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f   80 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            457788888873221          236899999999999999997653    58999999999999999999988 899


Q ss_pred             CCeEEEEEEcCCC
Q 009920          172 NGKMVEVKRAVPK  184 (522)
Q Consensus       172 ~Gr~I~V~~a~pk  184 (522)
                      +||+|.|.++...
T Consensus        81 ~GR~i~v~~~~~~   93 (114)
T 3s6e_A           81 AGKMITAAYVPLP   93 (114)
T ss_dssp             TTEECEEEEECHH
T ss_pred             CCEEEEEEEEcHH
Confidence            9999999998643

>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=99.04  E-value=4e-10  Score=116.20  Aligned_cols=75  Identities=15%  Similarity=0.265  Sum_probs=63.4

Q ss_pred             CCCcceeEecC--CCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-Ccc---CCe-
Q 009920          102 PGRTKKIFVGG--LASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HEL---NGK-  174 (522)
Q Consensus       102 ~~~~~~LfVgn--Lp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l---~Gr-  174 (522)
                      ..++++|||+|  |++.+||++|+++|++||+|++|.|..      .||||||+|++.++|++||+.++ +++   .|+ 
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            35788999999  578999999999999999999887753      47899999999999999999998 655   345 


Q ss_pred             -EEEEEEcC
Q 009920          175 -MVEVKRAV  182 (522)
Q Consensus       175 -~I~V~~a~  182 (522)
                       .|.|.++.
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             56777764

>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=98.98  E-value=9.9e-10  Score=95.76  Aligned_cols=78  Identities=13%  Similarity=0.126  Sum_probs=64.9

Q ss_pred             CCcEEEECCCCCCC----------CHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccC
Q 009920            4 DLGKLFIGGISWDT----------DEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMID   71 (522)
Q Consensus         4 d~r~LfVgnLP~~~----------teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~   71 (522)
                      .++.|.|.|+=...          .++||+++|++||+|++|+|.++.    .+|++||+|.++++|++|+  ||+..++
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            46778888873321          245889999999999999997653    5899999999999999999  9999999


Q ss_pred             CeEEEEeecCCCcc
Q 009920           72 GRTVEAKKAVPRDD   85 (522)
Q Consensus        72 Gr~I~V~~a~~k~~   85 (522)
                      ||+|.|.++.....
T Consensus        82 GR~i~v~~~~~~~y   95 (114)
T 3s6e_A           82 GKMITAAYVPLPTY   95 (114)
T ss_dssp             TEECEEEEECHHHH
T ss_pred             CEEEEEEEEcHHHH
Confidence            99999999865543

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.86  E-value=2.7e-09  Score=93.87  Aligned_cols=76  Identities=20%  Similarity=0.097  Sum_probs=66.0

Q ss_pred             CCcEEEECCCCCC-CCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecC-HHHHHHHH--H--cccccCCeEEEE
Q 009920            4 DLGKLFIGGISWD-TDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFAD-PAVAERVI--M--DKHMIDGRTVEA   77 (522)
Q Consensus         4 d~r~LfVgnLP~~-~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~-~e~A~kAl--~--~~~~i~Gr~I~V   77 (522)
                      ..+.|+|+||+++ +++++|+++|++||+|..|.++++..      .|||+|.+ +++|++|+  +  .+.+|++..+++
T Consensus        17 ~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~   90 (121)
T 1owx_A           17 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEVTW   90 (121)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEE
T ss_pred             CCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEE
Confidence            4678999999999 99999999999999999999999876      59999999 78999888  3  477889988888


Q ss_pred             eecCCCcc
Q 009920           78 KKAVPRDD   85 (522)
Q Consensus        78 ~~a~~k~~   85 (522)
                      +...-.++
T Consensus        91 evL~GeeE   98 (121)
T 1owx_A           91 EVLEGEVE   98 (121)
T ss_dssp             EECCHHHH
T ss_pred             EECCCHHH
Confidence            77654443

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.84  E-value=8.3e-09  Score=90.71  Aligned_cols=78  Identities=14%  Similarity=0.074  Sum_probs=68.6

Q ss_pred             CCCCCCcceeEecCCCCC-CCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecC-HHHHHHHHHhcC---CccCC
Q 009920           99 SPGPGRTKKIFVGGLAST-VTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS-EEAVDRVLHKTF---HELNG  173 (522)
Q Consensus        99 ~~~~~~~~~LfVgnLp~~-vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s-~e~A~~Al~~~~---~~l~G  173 (522)
                      +....+...|+|+||+.. +++++|+++|++||+|+.|.++++..      .|||+|.+ +++|++|+++++   .+|++
T Consensus        12 ~~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g   85 (121)
T 1owx_A           12 SLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRN   85 (121)
T ss_dssp             CCSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTS
T ss_pred             cccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeC
Confidence            344567789999999999 99999999999999999999998876      59999999 899999999874   58999


Q ss_pred             eEEEEEEcC
Q 009920          174 KMVEVKRAV  182 (522)
Q Consensus       174 r~I~V~~a~  182 (522)
                      ..++|+...
T Consensus        86 ~~~~~evL~   94 (121)
T 1owx_A           86 KEVTWEVLE   94 (121)
T ss_dssp             SSEEEEECC
T ss_pred             cEEEEEECC
Confidence            999887654

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.83  E-value=7.2e-09  Score=86.17  Aligned_cols=73  Identities=15%  Similarity=0.240  Sum_probs=60.7

Q ss_pred             CcceeEecCCC----CCCCH----HHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeE
Q 009920          104 RTKKIFVGGLA----STVTE----SDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKM  175 (522)
Q Consensus       104 ~~~~LfVgnLp----~~vte----edL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~  175 (522)
                      +..+|+|.-++    .+..+    .+|.+.|++||+|..++|+.|+        +||+|++.++|.+||+++..++.||.
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~mnG~~v~Gr~   77 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLSLNGKELLNRT   77 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGGGTTCEETTEE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHhcCCeEeCCeE
Confidence            45577777666    23333    6799999999999999999874        89999999999999994449999999


Q ss_pred             EEEEEcCCC
Q 009920          176 VEVKRAVPK  184 (522)
Q Consensus       176 I~V~~a~pk  184 (522)
                      |+|++++|.
T Consensus        78 LkV~lkt~d   86 (91)
T 2dnr_A           78 ITIALKSPS   86 (91)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEeCCCC
Confidence            999999875

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.68  E-value=4.7e-08  Score=81.23  Aligned_cols=72  Identities=21%  Similarity=0.331  Sum_probs=61.4

Q ss_pred             CCcEEEECCCCC----CCCH----HHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeE
Q 009920            4 DLGKLFIGGISW----DTDE----ERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRT   74 (522)
Q Consensus         4 d~r~LfVgnLP~----~~te----edL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~   74 (522)
                      ...||+|.-+|.    ++.+    .+|++.|++||+|..++|+.++        +||+|.+.++|.+|+ |++..+.+|.
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~mnG~~v~Gr~   77 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLSLNGKELLNRT   77 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGGGTTCEETTEE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHhcCCeEeCCeE
Confidence            456788877762    3333    5789999999999999999874        899999999999999 9999999999


Q ss_pred             EEEeecCCC
Q 009920           75 VEAKKAVPR   83 (522)
Q Consensus        75 I~V~~a~~k   83 (522)
                      |+|+.+.+.
T Consensus        78 LkV~lkt~d   86 (91)
T 2dnr_A           78 ITIALKSPS   86 (91)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEeCCCC
Confidence            999988764

>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=98.64  E-value=3.1e-08  Score=82.77  Aligned_cols=73  Identities=15%  Similarity=0.205  Sum_probs=60.7

Q ss_pred             CCcceeEecCCCCC-----CCH----HHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCC
Q 009920          103 GRTKKIFVGGLAST-----VTE----SDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNG  173 (522)
Q Consensus       103 ~~~~~LfVgnLp~~-----vte----edL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~G  173 (522)
                      .+..+|+|.-++..     +.+    .+|.+.|++||+|..++|+.|+        +||+|.+.++|.+||++...+++|
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~ldG~~v~G   84 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLDVDGMKVKG   84 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHHGGGSEETT
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHhcCCeeeCC
Confidence            35668888887643     222    5799999999999999999874        999999999999999944499999


Q ss_pred             eEEEEEEcCC
Q 009920          174 KMVEVKRAVP  183 (522)
Q Consensus       174 r~I~V~~a~p  183 (522)
                      |.|+|++..|
T Consensus        85 r~L~V~~k~~   94 (95)
T 1ufw_A           85 RAVKISGPSS   94 (95)
T ss_dssp             EEEEEECCCC
T ss_pred             eEEEEeccCC
Confidence            9999998764

>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=98.57  E-value=2.7e-07  Score=88.58  Aligned_cols=67  Identities=10%  Similarity=0.167  Sum_probs=60.1

Q ss_pred             CCHHHHHHHHhhcCCeeEEEEEecCC----CCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCC
Q 009920          117 VTESDFKKYFDQFGTITDVVVMYDHN----TQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVP  183 (522)
Q Consensus       117 vteedL~~~F~~fG~I~~v~i~~d~~----tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~p  183 (522)
                      -.+++|++.|++||.|+++.|+++..    +++++|++||+|.++++|++|++.++ ..++||+|.|.+...
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            45689999999999999999996654    44899999999999999999999999 899999999999764

>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=98.47  E-value=2.6e-07  Score=88.76  Aligned_cols=66  Identities=20%  Similarity=0.263  Sum_probs=59.2

Q ss_pred             CCHHHHHHHHhccCCeEEEEEeecCC----CCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCC
Q 009920           17 TDEERLKEYFSRYGEVVEAVIMRDRA----TGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus        17 ~teedL~e~F~~~G~V~~v~i~~d~~----tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~   82 (522)
                      -.+++|++.|++||+|.+++|+++..    +++++|++||+|.+.++|++|+  +++..+.||+|.+.....
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            45789999999999999999986644    4589999999999999999999  999999999999998754

>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=98.47  E-value=1.4e-07  Score=78.75  Aligned_cols=71  Identities=23%  Similarity=0.238  Sum_probs=60.3

Q ss_pred             CCcEEEECCCCCC-----CCH----HHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCe
Q 009920            4 DLGKLFIGGISWD-----TDE----ERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGR   73 (522)
Q Consensus         4 d~r~LfVgnLP~~-----~te----edL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr   73 (522)
                      ...||+|.-++.+     +.+    .+|++.|++||+|..++|+.++        +||+|.+.++|.+|| ++..++.+|
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            4568889887743     222    5689999999999999999874        999999999999999 999999999


Q ss_pred             EEEEeecCC
Q 009920           74 TVEAKKAVP   82 (522)
Q Consensus        74 ~I~V~~a~~   82 (522)
                      .|+|+...+
T Consensus        86 ~L~V~~k~~   94 (95)
T 1ufw_A           86 AVKISGPSS   94 (95)
T ss_dssp             EEEEECCCC
T ss_pred             EEEEeccCC
Confidence            999987643

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.40  E-value=1.9e-06  Score=72.85  Aligned_cols=88  Identities=26%  Similarity=0.398  Sum_probs=72.7

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhcc-----CCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHHH-cccccCCeEEE
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRY-----GEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIM-DKHMIDGRTVE   76 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~-----G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl~-~~~~i~Gr~I~   76 (522)
                      +-.++|.|.|||.+++++.|+-+|++-     |+|++++...        .-|+|+|.++++|+++|. ..|.|++.+|.
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~~H~L~~~~Ls   77 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQADHELHGAQLS   77 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCSCCBSSSSBCE
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCCcceecCeEEE
Confidence            346789999999999999999999983     6898887755        368999999999999994 49999999999


Q ss_pred             EeecCCCccccccccccCCCCCCCCCCCcceeEecCCCCCCC
Q 009920           77 AKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVT  118 (522)
Q Consensus        77 V~~a~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vt  118 (522)
                      |....++                    ...+|++.+|++.++
T Consensus        78 V~P~~~~--------------------~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           78 LRPAPPR--------------------APARLLLQGLPPGTS   99 (104)
T ss_dssp             EEECCCC--------------------CCCCCCCCSCCCCCC
T ss_pred             EEcCCCC--------------------CcceEeeecCCCCCC
Confidence            9775443                    345788888887764

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.19  E-value=6.9e-06  Score=70.16  Aligned_cols=71  Identities=15%  Similarity=0.222  Sum_probs=63.3

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhc-----CCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEE
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQF-----GTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVE  177 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~f-----G~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~  177 (522)
                      ..++|-|-+||.+++++.|+.+.+++     +.|++|.+..|..      =|+|+|.+..+|-+|.-.++ .+|++|+|+
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~------GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN------GAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT------EEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC------ceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            46788999999999999999999999     9999999998876      69999999888888776666 899999999


Q ss_pred             EEE
Q 009920          178 VKR  180 (522)
Q Consensus       178 V~~  180 (522)
                      |.-
T Consensus        94 ~gT   96 (117)
T 2l9w_A           94 SGT   96 (117)
T ss_dssp             EEC
T ss_pred             ecC
Confidence            864

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.13  E-value=7.2e-06  Score=70.05  Aligned_cols=72  Identities=8%  Similarity=0.203  Sum_probs=65.7

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhcc-----CCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEE
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRY-----GEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTV   75 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~-----G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I   75 (522)
                      ++.++|-|-+||..++++.|+.+++++     ++++.+.+..|..      =|+|+|+|...|-||.  +++.+|++|+|
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~------GAivef~d~~~AgKasLaL~G~ef~gr~L   92 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN------GAIIIFRDSKFAAKMLMILNGSQFQGKVI   92 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT------EEEEECSCHHHHHHHHHHHSSEEETTEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC------ceEEEEccchhhHHHHhhcCCeeecCeEE
Confidence            457899999999999999999999999     9999999999864      6999999999999987  99999999999


Q ss_pred             EEeec
Q 009920           76 EAKKA   80 (522)
Q Consensus        76 ~V~~a   80 (522)
                      .+-..
T Consensus        93 r~gTv   97 (117)
T 2l9w_A           93 RSGTI   97 (117)
T ss_dssp             EEECH
T ss_pred             EecCH
Confidence            98644

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.88  E-value=8e-05  Score=62.97  Aligned_cols=75  Identities=24%  Similarity=0.365  Sum_probs=65.1

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhc-----CCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEE
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQF-----GTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEV  178 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~f-----G~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V  178 (522)
                      -.++|.|.|||..+.++.|+-+|++-     |+|++++...        .-|+|+|.+.+.|+++|++..|.|++.+|.|
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            45789999999999999999999872     6888887753        2699999999999999999899999999999


Q ss_pred             EEcCCCCC
Q 009920          179 KRAVPKEF  186 (522)
Q Consensus       179 ~~a~pk~~  186 (522)
                      ....++..
T Consensus        79 ~P~~~~~~   86 (104)
T 2dhx_A           79 RPAPPRAP   86 (104)
T ss_dssp             EECCCCCC
T ss_pred             EcCCCCCc
Confidence            88766553

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.12  E-value=0.00085  Score=55.73  Aligned_cols=66  Identities=12%  Similarity=0.051  Sum_probs=52.7

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCC--cccEEEEEecCHHHHHHHH--HcccccC
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGR--ARGFGFVVFADPAVAERVI--MDKHMID   71 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~--srG~aFVeF~~~e~A~kAl--~~~~~i~   71 (522)
                      ++|.|+.||+.+||+++.+.+..+.++.....+..+.+.+  .-.-|||.|++.|++....  .+++.+.
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            6899999999999999999999998887777766554322  2345999999999998887  6666543

>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=97.04  E-value=0.0027  Score=53.76  Aligned_cols=76  Identities=12%  Similarity=0.099  Sum_probs=63.1

Q ss_pred             CcceeEecCCCCCCC-----HHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEE
Q 009920          104 RTKKIFVGGLASTVT-----ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVE  177 (522)
Q Consensus       104 ~~~~LfVgnLp~~vt-----eedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~  177 (522)
                      -.++|+|.||+.++-     .++++++|..|.++......+.-.      -..|.|.++++|.+|..+++ ..+.|++|+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR------Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK------RVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT------EEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce------EEEEEeCChHHHHHHHHHhccceecCceeE
Confidence            456899999988762     257899999999998887775422      47899999999999999999 789999999


Q ss_pred             EEEcCCCC
Q 009920          178 VKRAVPKE  185 (522)
Q Consensus       178 V~~a~pk~  185 (522)
                      |-++.+-.
T Consensus        78 ~YFgq~~~   85 (104)
T 1wey_A           78 LYFAQTLH   85 (104)
T ss_dssp             EECCCCSS
T ss_pred             EEecCCCC
Confidence            99998554

>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=97.00  E-value=0.0019  Score=54.70  Aligned_cols=73  Identities=14%  Similarity=0.109  Sum_probs=61.0

Q ss_pred             CcEEEECCCCCCC-C----HHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEE
Q 009920            5 LGKLFIGGISWDT-D----EERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEA   77 (522)
Q Consensus         5 ~r~LfVgnLP~~~-t----eedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V   77 (522)
                      -++|+|.||+.++ +    .++++++|..|.++.....++.=      .=..|.|.++++|.+|-  +++..+.|++|+|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            3689999999875 2    25778999999999888877642      24689999999999998  9999999999999


Q ss_pred             eecCCC
Q 009920           78 KKAVPR   83 (522)
Q Consensus        78 ~~a~~k   83 (522)
                      ..+++.
T Consensus        79 YFgq~~   84 (104)
T 1wey_A           79 YFAQTL   84 (104)
T ss_dssp             ECCCCS
T ss_pred             EecCCC
Confidence            998844

>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=96.93  E-value=0.0024  Score=55.44  Aligned_cols=73  Identities=12%  Similarity=0.251  Sum_probs=58.9

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCC-eEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDG-RTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~G-r~I~V~~a~   81 (522)
                      +.+-|.|-+.|.+. ...|.+.|++||+|++.....      ...+-.|+|.++.+|++|| +|+..|.+ ..|-|++..
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV~p~~   95 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC------CCCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEEEECC
Confidence            46778899999884 678889999999998877622      2349999999999999999 88888874 777787754


Q ss_pred             CC
Q 009920           82 PR   83 (522)
Q Consensus        82 ~k   83 (522)
                      .+
T Consensus        96 d~   97 (119)
T 1wwh_A           96 DK   97 (119)
T ss_dssp             CH
T ss_pred             CH
Confidence            43

>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=96.91  E-value=0.0021  Score=53.76  Aligned_cols=58  Identities=22%  Similarity=0.412  Sum_probs=48.7

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhc
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT  167 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~  167 (522)
                      .+...+.++| .+|.++...||.++|+.||.| .|+.+.|.       .|||.|.+++.|..|+..+
T Consensus        12 ~p~r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           12 QPKRDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CCCCCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHH
T ss_pred             CCCCCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhc
Confidence            3456667777 999999999999999999954 57777663       7999999999999999865

>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=96.86  E-value=0.0022  Score=53.69  Aligned_cols=52  Identities=17%  Similarity=0.312  Sum_probs=44.8

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI   64 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl   64 (522)
                      ..+.++| .+|+++..+||.++|++||.| .|+.+-|-       -|||.|.+++.|..|+
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al   66 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAV   66 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHH
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHH
Confidence            3566777 999999999999999999966 47777763       7999999999999998

>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=96.59  E-value=0.0063  Score=52.85  Aligned_cols=73  Identities=22%  Similarity=0.226  Sum_probs=59.2

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCC-eEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNG-KMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~G-r~I~V~~a  181 (522)
                      ...+.|.|-+.|... .+.|-+.|++||+|.+......      .-...|+|+++.+|++||.++...|.+ -+|-|+..
T Consensus        22 ~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~~------~NWihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           22 LDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEEC
T ss_pred             CCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCCC------CCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEEEEC
Confidence            356778898999885 5678888999999998876221      238999999999999999998888874 78888875


Q ss_pred             C
Q 009920          182 V  182 (522)
Q Consensus       182 ~  182 (522)
                      .
T Consensus        95 ~   95 (119)
T 1wwh_A           95 I   95 (119)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=96.38  E-value=0.01  Score=49.14  Aligned_cols=63  Identities=10%  Similarity=0.144  Sum_probs=51.0

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCC--cceEEEEEecCHHHHHHHHHhcC
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQR--PRGFGFITYDSEEAVDRVLHKTF  168 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~--~rG~aFVeF~s~e~A~~Al~~~~  168 (522)
                      .+|.|++||+.+||+++.+.+.....+.....+.-+.+.+  .-.-|+|.|.+.|++..-.+..+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~   66 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFD   66 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHT
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhC
Confidence            5899999999999999999999988777666665543332  23579999999999999888776

>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=96.13  E-value=0.0059  Score=51.17  Aligned_cols=55  Identities=18%  Similarity=0.341  Sum_probs=46.1

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhc
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT  167 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~  167 (522)
                      +.+.++| .+|.++...||.++|++||. ..|+.+.|.       .|||.|.+++.|+.|+..+
T Consensus         5 R~HV~~l-~FP~ewKt~Di~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~~i   59 (101)
T 3ctr_A            5 SDHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVKIAVNTS   59 (101)
T ss_dssp             EEEEEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEETT-------EEEEEEEEECHHHHHHHHH
T ss_pred             CCeEEEE-eCChhhhhHHHHHHHhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHHhc
Confidence            3455666 99999999999999999984 467777663       7999999999999999865

>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=95.97  E-value=0.0067  Score=50.87  Aligned_cols=51  Identities=18%  Similarity=0.317  Sum_probs=43.7

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI   64 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl   64 (522)
                      .+.++| .+|+++..+||.++|++||.| .|+.+-|-       -|||.|.+++.|..|+
T Consensus         6 ~HV~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al   56 (101)
T 3ctr_A            6 DHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVKIAV   56 (101)
T ss_dssp             EEEEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEETT-------EEEEEEEEECHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHH
Confidence            345666 999999999999999999954 57777763       7999999999999998

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.82  E-value=0.0056  Score=53.94  Aligned_cols=81  Identities=11%  Similarity=0.221  Sum_probs=57.2

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeec---------CCCC-----CcccEEEEEecCHHHHHHHH-Hc
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRD---------RATG-----RARGFGFVVFADPAVAERVI-MD   66 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d---------~~tg-----~srG~aFVeF~~~e~A~kAl-~~   66 (522)
                      +.....|.|-+.|++ ....|.+.|++||.|.+-.-+.+         ++..     ....+-.|+|.++.+|++|| .|
T Consensus         4 ~~~e~~VtVFGFp~~-~~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~N   82 (132)
T 3p3d_A            4 SNGELAILVFGYPET-MANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLEN   82 (132)
T ss_dssp             ----CEEEEECCCGG-GHHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTT
T ss_pred             ccCceEEEEEecCHH-HHHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhC
Confidence            456677888899876 45678889999999876221111         0001     13568899999999999999 99


Q ss_pred             ccccCCeEEEEeecCCC
Q 009920           67 KHMIDGRTVEAKKAVPR   83 (522)
Q Consensus        67 ~~~i~Gr~I~V~~a~~k   83 (522)
                      ++.|.+..|-|++..+.
T Consensus        83 G~ii~G~mIGV~Py~~~   99 (132)
T 3p3d_A           83 GAVFNGVLLGVIPYTKD   99 (132)
T ss_dssp             TCEETTEECEEEECCHH
T ss_pred             CeEeCcEEEEEEECCHH
Confidence            99999998888877543

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.71  E-value=0.0049  Score=51.62  Aligned_cols=67  Identities=10%  Similarity=0.027  Sum_probs=46.9

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCC--cccEEEEEecCHHHHHHHH--Hccccc
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGR--ARGFGFVVFADPAVAERVI--MDKHMI   70 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~--srG~aFVeF~~~e~A~kAl--~~~~~i   70 (522)
                      .+-+|.|+.||+.+||+++.+.+..+=++.....+..+.+-+  .-.-|||.|++.|++....  .+++.+
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F   78 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIF   78 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEE
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEE
Confidence            456899999999999999998888765554433333332221  1234899999999998887  444443

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.04  E-value=0.0092  Score=63.47  Aligned_cols=55  Identities=13%  Similarity=0.243  Sum_probs=42.9

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI   64 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl   64 (522)
                      ..|.|+|. .|.++++++|.++|++||+|.++.+-+++.     -||.|||.+++++.+++
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g-----~~~~vef~~~~~~~~~~  106 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFG-----LYAVVEFCQKESIGSLQ  106 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSS-----EEEEEECC---CCHHHH
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCC-----eEEEEEeCCHHHHHHHH
Confidence            46899997 899999999999999999999988876542     69999999999999887

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=94.52  E-value=0.017  Score=61.37  Aligned_cols=56  Identities=16%  Similarity=0.427  Sum_probs=42.6

Q ss_pred             cceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHh
Q 009920          105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK  166 (522)
Q Consensus       105 ~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~  166 (522)
                      .+.|+|. .|..+++++|.++|++||+|.++.+.+++.     -||+|||.+++++++++..
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g-----~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFG-----LYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSS-----EEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCC-----eEEEEEeCCHHHHHHHHhc
Confidence            4689997 799999999999999999999998876532     4999999999999988754

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=94.30  E-value=0.049  Score=45.54  Aligned_cols=65  Identities=5%  Similarity=0.058  Sum_probs=45.8

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCC--cceEEEEEecCHHHHHHHHHhcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQR--PRGFGFITYDSEEAVDRVLHKTF  168 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~--~rG~aFVeF~s~e~A~~Al~~~~  168 (522)
                      .+-+|.|+.||+.+||+++.+.+...-++.....+.-+.+.+  .-.-|+|.|.+.|++..-.+..+
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~   74 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFD   74 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHST
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcC
Confidence            456899999999999999888887654443322222222211  11358999999999999988777

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=93.84  E-value=0.064  Score=47.22  Aligned_cols=78  Identities=26%  Similarity=0.349  Sum_probs=55.5

Q ss_pred             cceeEecCCCCCCCHHHHHHHHhhcCCeeE-EEEEec--------CCCCC-----cceEEEEEecCHHHHHHHHHhcCCc
Q 009920          105 TKKIFVGGLASTVTESDFKKYFDQFGTITD-VVVMYD--------HNTQR-----PRGFGFITYDSEEAVDRVLHKTFHE  170 (522)
Q Consensus       105 ~~~LfVgnLp~~vteedL~~~F~~fG~I~~-v~i~~d--------~~tg~-----~rG~aFVeF~s~e~A~~Al~~~~~~  170 (522)
                      ...|.|-+.|++.+. .+-+.|++||.|.+ +.+..+        +...+     ......|+|+++.+|++||+++...
T Consensus         7 e~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~i   85 (132)
T 3p3d_A            7 ELAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGAV   85 (132)
T ss_dssp             -CEEEEECCCGGGHH-HHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTCE
T ss_pred             ceEEEEEecCHHHHH-HHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCeE
Confidence            446777788776554 56778899999866 222110        00011     1347799999999999999999999


Q ss_pred             cCCeEEEEEEcCC
Q 009920          171 LNGKMVEVKRAVP  183 (522)
Q Consensus       171 l~Gr~I~V~~a~p  183 (522)
                      |+|.+|-|+...+
T Consensus        86 i~G~mIGV~Py~~   98 (132)
T 3p3d_A           86 FNGVLLGVIPYTK   98 (132)
T ss_dssp             ETTEECEEEECCH
T ss_pred             eCcEEEEEEECCH
Confidence            9999999988764

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=84.18  E-value=1.9  Score=46.29  Aligned_cols=51  Identities=18%  Similarity=0.314  Sum_probs=42.2

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI   64 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl   64 (522)
                      .+.|+|+ +|..+...+|.++|+.|+.| +|+.+.+       ..|||.|.+++.|+.++
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd-------t~a~V~~~~~~~a~~~l  490 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD-------TSAFVSLSQPEQVQIAV  490 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS-------SEEEEECSCHHHHHHHH
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC-------CeEEEEECCHHHHHHHH
Confidence            4567776 99999999999999999965 4555544       27999999999999998

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=84.08  E-value=2.1  Score=46.00  Aligned_cols=58  Identities=21%  Similarity=0.373  Sum_probs=45.9

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF  168 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~  168 (522)
                      ..+.+.++|. +|..+...+|+++|+.|+. .+|+.+.|.       .|||.|.+.++|+.+++...
T Consensus       437 ~~R~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widdt-------~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          437 PKRDHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             CCGGGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSSS-------EEEEECSCHHHHHHHHHHHT
T ss_pred             CCcCcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcCC-------eEEEEECCHHHHHHHHHHHH
Confidence            3455666665 9999999999999999995 356655442       69999999999999998764

---

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	522
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	9e-36
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	9e-17
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	8e-14
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	4e-25
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-22
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-22
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	8e-21
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-22
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-21
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	2e-21
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-20
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-21
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	7e-20
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-20
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-20
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-20
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	3e-20
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-19
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	5e-17
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-19
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-18
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-18
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-17
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-18
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-13
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-18
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-15
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	5e-18
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	7e-16
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	7e-15
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-17
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	4e-14
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-17
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-15
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	5e-17
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	7e-16
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	8e-17
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	7e-14
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-16
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-13
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-16
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-14
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	7e-16
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	6e-13
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-15
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-13
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-15
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-12
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-15
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-14
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-15
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-13
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-15
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	4e-12
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	8e-15
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	9e-14
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-14
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-12
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-14
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-14
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-11
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-14
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	3e-12
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-14
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-11
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-14
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	6e-12
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-14
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	5e-13
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	3e-14
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	1e-13
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	6e-14
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	3e-11
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-13
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-11
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-13
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-12
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-13
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-13
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-13
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	8e-13
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-13
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	8e-13
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-13
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	6e-13
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	6e-13
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	7e-12
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	7e-13
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-12
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	8e-13
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-08
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-12
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-11
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-12
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	5e-10
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	3e-12
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	4e-12
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-12
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-10
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-12
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-11
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	5e-12
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	3e-08
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-12
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-11
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	5e-12
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	2e-11
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-12
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-11
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	6e-12
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-11
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	6e-12
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	9e-10
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	2e-10
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-11
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-10
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	5e-11
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-09
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-10
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	5e-10
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-10
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	3e-09
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	3e-10
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	3e-06
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-09
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-08
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	3e-09
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	3e-08
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	4e-09
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	8e-08
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 4e-09
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	5e-09
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	4e-06
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	8e-09
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	1e-05
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	2e-08
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	3e-07
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-08
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-06
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-07
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	7e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	5e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	3e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	8e-05
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	4e-05
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	8e-04
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	5e-05
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	7e-05
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-05
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	8e-05
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	0.001
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-04
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	3e-04
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	5e-04
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	7e-04
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	0.001
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	8e-04
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	0.002
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	0.004

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  129 bits (325), Expect = 9e-36
 Identities = 66/180 (36%), Positives = 108/180 (60%), Gaps = 11/180 (6%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
           KLFIGG+S++T +E L+ +F ++G + + V+MRD  T R+RGFGFV +A     +  +  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 66  DKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKY 125
             H +DGR VE K+AV R+D      + +           KKIFVGG+     E   + Y
Sbjct: 68  RPHKVDGRVVEPKRAVSREDSQRPGAHLT----------VKKIFVGGIKEDTEEHHLRDY 117

Query: 126 FDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKE 185
           F+Q+G I  + +M D  + + RGF F+T+D  ++VD+++ + +H +NG   EV++A+ K+
Sbjct: 118 FEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQ 177

>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 = 76.2 bits (186), Expect = 9e-17
 Identities = 30/81 (37%), Positives = 50/81 (61%), Gaps = 1/81 (1%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
           K+F+GGI  DT+E  L++YF +YG++    IM DR +G+ RGF FV F D    ++++  
Sbjct: 99  KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 158

Query: 66  DKHMIDGRTVEAKKAVPRDDQ 86
             H ++G   E +KA+ + + 
Sbjct: 159 KYHTVNGHNCEVRKALSKQEM 179

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.7 bits (164), Expect = 8e-14
 Identities = 39/85 (45%), Positives = 61/85 (71%)

Query: 102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD 161
           P + +K+F+GGL+   T+   + +F+Q+GT+TD VVM D NT+R RGFGF+TY + E VD
Sbjct: 3   PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 62

Query: 162 RVLHKTFHELNGKMVEVKRAVPKEF 186
             ++   H+++G++VE KRAV +E 
Sbjct: 63  AAMNARPHKVDGRVVEPKRAVSRED 87

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 97.0 bits (241), Expect = 4e-25
 Identities = 32/81 (39%), Positives = 48/81 (59%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
           L + G+ W T E+ LKEYFS +GEV+   + +D  TG ++GFGFV F +     +V+  
Sbjct: 10 DLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 69

Query: 67 KHMIDGRTVEAKKAVPRDDQN 87
          +HMIDGR  + K    +  Q+
Sbjct: 70 RHMIDGRWCDCKLPNSKQSQD 90

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 89.3 bits (221), Expect = 2e-22
 Identities = 26/82 (31%), Positives = 40/82 (48%), Gaps = 1/82 (1%)

Query: 104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV 163
           +T  + V GL    TE D K+YF  FG +  V V  D  T   +GFGF+ +   E   +V
Sbjct: 7   KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV 66

Query: 164 LHKTFHELNGKMVEVKRAVPKE 185
           +    H ++G+  + K    K+
Sbjct: 67  M-SQRHMIDGRWCDCKLPNSKQ 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 = 89.7 bits (222), Expect = 2e-22
 Identities = 38/85 (44%), Positives = 58/85 (68%), Gaps = 1/85 (1%)

Query: 2   ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
           +    KLFIGG+S++T EE L+ Y+ ++G++ + V+MRD A+ R+RGFGFV F+  A  +
Sbjct: 17  KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVD 76

Query: 62  RVI-MDKHMIDGRTVEAKKAVPRDD 85
             +    H IDGR VE K+AV R++
Sbjct: 77  AAMAARPHSIDGRVVEPKRAVAREE 101

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 85.1 bits (210), Expect = 8e-21
 Identities = 35/84 (41%), Positives = 55/84 (65%)

Query: 102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD 161
             + +K+F+GGL+   TE   + Y++Q+G +TD VVM D  ++R RGFGF+T+ S   VD
Sbjct: 17  KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVD 76

Query: 162 RVLHKTFHELNGKMVEVKRAVPKE 185
             +    H ++G++VE KRAV +E
Sbjct: 77  AAMAARPHSIDGRVVEPKRAVARE 100

>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 = 87.7 bits (217), Expect = 5e-22
 Identities = 28/75 (37%), Positives = 43/75 (57%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           KIFVGGL+    E   ++YF  FG +  + +  D+ T + RGF FIT+  EE V +++ K
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 167 TFHELNGKMVEVKRA 181
            +H +     E+K A
Sbjct: 61  KYHNVGLSKCEIKVA 75

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 84.6 bits (209), Expect = 5e-21
 Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
          K+F+GG+S DT EE+++EYF  +GEV    +  D  T + RGF F+ F +    ++++  
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 66 DKHMIDGRTVEAKKA 80
            H +     E K A
Sbjct: 61 KYHNVGLSKCEIKVA 75

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 86.6 bits (214), Expect = 2e-21
 Identities = 38/81 (46%), Positives = 59/81 (72%)

Query: 102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD 161
           P + +K+F+GGL+   T+   + +F+Q+GT+TD VVM D NT+R RGFGF+TY + E VD
Sbjct: 3   PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 62

Query: 162 RVLHKTFHELNGKMVEVKRAV 182
             ++   H+++G++VE KRAV
Sbjct: 63  AAMNARPHKVDGRVVEPKRAV 83

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 83.9 bits (207), Expect = 1e-20
 Identities = 35/79 (44%), Positives = 52/79 (65%), Gaps = 1/79 (1%)

Query: 4  DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV 63
           L KLFIGG+S++T +E L+ +F ++G + + V+MRD  T R+RGFGFV +A     +  
Sbjct: 5  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64

Query: 64 I-MDKHMIDGRTVEAKKAV 81
          +    H +DGR VE K+AV
Sbjct: 65 MNARPHKVDGRVVEPKRAV 83

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 85.4 bits (211), Expect = 4e-21
 Identities = 37/75 (49%), Positives = 54/75 (72%), Gaps = 1/75 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
          K+FIGG+SW T +E L+EYF ++GEV E ++MRD  T R+RGFGFV F D A  ++V+  
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 66 DKHMIDGRTVEAKKA 80
           +H +D +T++ K A
Sbjct: 62 SRHELDSKTIDPKVA 76

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 81.6 bits (201), Expect = 7e-20
 Identities = 32/75 (42%), Positives = 51/75 (68%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+F+GGL+   T+   ++YF QFG + + +VM D  T+R RGFGF+T+  +  VD+VL +
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 167 TFHELNGKMVEVKRA 181
           + HEL+ K ++ K A
Sbjct: 62  SRHELDSKTIDPKVA 76

>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 = 83.9 bits (207), Expect = 1e-20
 Identities = 33/75 (44%), Positives = 50/75 (66%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+F+GGL+   T+ D K YF +FG + D  +  D  T R RGFGF+ +   E+VD+V+ +
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 167 TFHELNGKMVEVKRA 181
             H+LNGK+++ KRA
Sbjct: 61  KEHKLNGKVIDPKRA 75

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 82.3 bits (203), Expect = 4e-20
 Identities = 34/75 (45%), Positives = 56/75 (74%), Gaps = 1/75 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
          K+FIGG+SWDT ++ LK+YFS++GEVV+  +  D  TGR+RGFGFV+F +    ++V+  
Sbjct: 1  KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 66 DKHMIDGRTVEAKKA 80
           +H ++G+ ++ K+A
Sbjct: 61 KEHKLNGKVIDPKRA 75

>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 = 83.9 bits (207), Expect = 2e-20
 Identities = 19/89 (21%), Positives = 43/89 (48%)

Query: 97  HSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
           + SP     + +F   LA+ +   D + +F   G + DV ++ D N++R +G  ++ +  
Sbjct: 10  NLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCE 69

Query: 157 EEAVDRVLHKTFHELNGKMVEVKRAVPKE 185
            ++V   +  T   L G  + V+ +  ++
Sbjct: 70  IQSVPLAIGLTGQRLLGVPIIVQASQAEK 98

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 83.5 bits (206), Expect = 3e-20
 Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 1/85 (1%)

Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
          E D   +F   ++       L+++FS  G+V +  I+ DR + R++G  +V F +     
Sbjct: 15 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP 74

Query: 62 RVI-MDKHMIDGRTVEAKKAVPRDD 85
            I +    + G  +  + +    +
Sbjct: 75 LAIGLTGQRLLGVPIIVQASQAEKN 99

>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 = 80.5 bits (198), Expect = 2e-19
 Identities = 29/77 (37%), Positives = 50/77 (64%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           KKIFVGG+     E   + YF+Q+G I  + +M D  + + RGF F+T+D  ++VD+++ 
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

Query: 166 KTFHELNGKMVEVKRAV 182
           + +H +NG   EV++A+
Sbjct: 63  QKYHTVNGHNCEVRKAL 79

>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 = 73.6 bits (180), Expect = 5e-17
 Identities = 30/76 (39%), Positives = 48/76 (63%), Gaps = 1/76 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
          K+F+GGI  DT+E  L++YF +YG++    IM DR +G+ RGF FV F D    ++++  
Sbjct: 4  KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 63

Query: 66 DKHMIDGRTVEAKKAV 81
            H ++G   E +KA+
Sbjct: 64 KYHTVNGHNCEVRKAL 79

>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 = 80.4 bits (198), Expect = 4e-19
 Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 4/82 (4%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDR-ATGRARGFGFVVFADPAVAERVI- 64
          K+ +  I +  ++  ++E FS +GE+    + +    TG  RGFGFV F     A++   
Sbjct: 10 KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 69

Query: 65 --MDKHMIDGRTVEAKKAVPRD 84
                 + GR +  + A    
Sbjct: 70 ALCHSTHLYGRRLVLEWADSEV 91

>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 = 77.7 bits (191), Expect = 3e-18
 Identities = 19/89 (21%), Positives = 38/89 (42%), Gaps = 3/89 (3%)

Query: 100 PGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHN-TQRPRGFGFITYDSEE 158
           P    T KI V  +     + + ++ F  FG +  V +      T   RGFGF+ + +++
Sbjct: 3   PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 62

Query: 159 AVDRVLHKTFH--ELNGKMVEVKRAVPKE 185
              +  +   H   L G+ + ++ A  + 
Sbjct: 63  DAKKAFNALCHSTHLYGRRLVLEWADSEV 91

>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 = 77.8 bits (191), Expect = 1e-18
 Identities = 40/75 (53%), Positives = 54/75 (72%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           KIFVGGL+   T  D K YF+QFG + D ++M+D  T R RGFGF+T++SE+ V++V   
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 167 TFHELNGKMVEVKRA 181
            FHE+N KMVE K+A
Sbjct: 61  HFHEINNKMVECKKA 75

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 75.5 bits (185), Expect = 1e-17
 Identities = 33/75 (44%), Positives = 50/75 (66%), Gaps = 1/75 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
          K+F+GG+S +T  E +K YF ++G+V +A++M D+ T R RGFGFV F    + E+V  +
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 66 DKHMIDGRTVEAKKA 80
            H I+ + VE KKA
Sbjct: 61 HFHEINNKMVECKKA 75

>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 = 78.6 bits (193), Expect = 1e-18
 Identities = 40/94 (42%), Positives = 62/94 (65%), Gaps = 6/94 (6%)

Query: 1  MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
          M SD GKLF+GG+S+DT+E+ L++ FS+YG++ E V+++DR T R+RGFGFV F +   A
Sbjct: 1  MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDA 60

Query: 61 ERVI--MDKHMIDGRTVEAKKAVPRDDQNMLNRN 92
          +  +  M+   +DGR +   +A    D    NR+
Sbjct: 61 KDAMMAMNGKSVDGRQIRVDQAGKSSD----NRS 90

>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 = 64.4 bits (156), Expect = 1e-13
 Identities = 26/80 (32%), Positives = 46/80 (57%), Gaps = 1/80 (1%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+FVGGL+    E   ++ F ++G I++VVV+ D  TQR RGFGF+T+++ +     +  
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 66

Query: 167 -TFHELNGKMVEVKRAVPKE 185
                ++G+ + V +A    
Sbjct: 67  MNGKSVDGRQIRVDQAGKSS 86

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 77.1 bits (189), Expect = 5e-18
 Identities = 13/90 (14%), Positives = 38/90 (42%), Gaps = 7/90 (7%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVV-----MYDHNTQRPRGFGFITYDSEEAV 160
           ++++VG +   +TE     +F+    +  +       +      + + F F+ + S +  
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 161 DRVLHKTFHELNGKMVEVKRAVPKEFSPGP 190
            + +        G+ ++++R  P ++ P P
Sbjct: 62  TQAMAFDGIIFQGQSLKIRR--PHDYQPLP 89

>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 = 68.2 bits (166), Expect = 6e-15
 Identities = 14/86 (16%), Positives = 36/86 (41%), Gaps = 8/86 (9%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVI-----MRDRATGRARGFGFVVFADPAVAE 61
          +L++G I +   EE + ++F+    +          +      + + F F+ F       
Sbjct: 3  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 62 RVI-MDKHMIDGRTVEAKKAVPRDDQ 86
          + +  D  +  G++++ ++  P D Q
Sbjct: 63 QAMAFDGIIFQGQSLKIRR--PHDYQ 86

>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 = 76.6 bits (188), Expect = 5e-18
 Identities = 25/85 (29%), Positives = 42/85 (49%), Gaps = 2/85 (2%)

Query: 1  MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
          M +    L++GG++ + D++ L   F  +G++ +  I  D  T + RGF FV F     A
Sbjct: 1  MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDA 60

Query: 61 ERVI--MDKHMIDGRTVEAKKAVPR 83
             I  M++  + GRT+    A P 
Sbjct: 61 AAAIDNMNESELFGRTIRVNLAKPM 85

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.8 bits (173), Expect = 7e-16
 Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 1/81 (1%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           + ++VGGLA  V +      F  FG ITD+ +  D+ T++ RGF F+ ++  E     + 
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65

Query: 166 K-TFHELNGKMVEVKRAVPKE 185
                EL G+ + V  A P  
Sbjct: 66  NMNESELFGRTIRVNLAKPMR 86

>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 = 75.0 bits (184), Expect = 2e-17
 Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L++G +  D  E  L E FS  G ++   + RD  T R+ G+ +V F  PA AER +  
Sbjct: 2  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 65 MDKHMIDGRTVEAKKA 80
          M+  +I G+ V    +
Sbjct: 62 MNFDVIKGKPVRIMWS 77

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.6 bits (165), Expect = 7e-15
 Identities = 20/76 (26%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
            ++VG L   VTE+   + F   G I  + V  D  T+R  G+ ++ +      +R L  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 167 -TFHELNGKMVEVKRA 181
             F  + GK V +  +
Sbjct: 62  MNFDVIKGKPVRIMWS 77

>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 = 74.3 bits (182), Expect = 3e-17
 Identities = 27/85 (31%), Positives = 46/85 (54%), Gaps = 5/85 (5%)

Query: 3  SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
          S    +F+G  + D  E+ L+E+FS+YG+V++  I +       R F FV FAD  +A+ 
Sbjct: 3  SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQS 57

Query: 63 VIMDKHMIDGRTVEAKKAVPRDDQN 87
          +  +  +I G +V    A P+ + N
Sbjct: 58 LCGEDLIIKGISVHISNAEPKHNSN 82

>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 = 65.4 bits (159), Expect = 4e-14
 Identities = 21/93 (22%), Positives = 38/93 (40%), Gaps = 6/93 (6%)

Query: 101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
           G   +  +FVG     +TE + +++F Q+G + DV +           F F+T+  ++  
Sbjct: 1   GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQIA 55

Query: 161 DRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRS 193
             +       + G  V +  A PK  S     S
Sbjct: 56  QSLC-GEDLIIKGISVHISNAEPKHNSNSGPSS 87

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 74.3 bits (182), Expect = 4e-17
 Identities = 19/82 (23%), Positives = 44/82 (53%), Gaps = 2/82 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          KLFIGG+    +++++KE  + +G +    +++D ATG ++G+ F  + D  V ++ I  
Sbjct: 3  KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 65 MDKHMIDGRTVEAKKAVPRDDQ 86
          ++   +  + +  ++A      
Sbjct: 63 LNGMQLGDKKLLVQRASVGAKN 84

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.7 bits (165), Expect = 7e-15
 Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 1/79 (1%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+F+GGL + + +   K+    FG +    ++ D  T   +G+ F  Y      D+ +  
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 167 -TFHELNGKMVEVKRAVPK 184
               +L  K + V+RA   
Sbjct: 63  LNGMQLGDKKLLVQRASVG 81

>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 = 74.0 bits (181), Expect = 5e-17
 Identities = 22/87 (25%), Positives = 33/87 (37%), Gaps = 6/87 (6%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIM--RDRATGRARGFGFVVFADPAVAERVI 64
          +LFIGGI      E + E  ++  E V  VI+        + RGF FV +     A    
Sbjct: 3  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 65 ----MDKHMIDGRTVEAKKAVPRDDQN 87
                +  + G  +    A P  D +
Sbjct: 63 RKLMPGRIQLWGHQIAVDWAEPEIDVD 89

>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 = 70.9 bits (173), Expect = 7e-16
 Identities = 17/84 (20%), Positives = 31/84 (36%), Gaps = 5/84 (5%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVV--VMYDHNTQRPRGFGFITYDSEEAVDRV- 163
           ++F+GG+       +  +   +       V       +  + RGF F+ Y+S  A     
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 164 --LHKTFHELNGKMVEVKRAVPKE 185
             L     +L G  + V  A P+ 
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEI 86

>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 = 73.1 bits (179), Expect = 8e-17
 Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 5/82 (6%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDR---ATGRARGFGFVVFADPAVAERVI 64
          LFI  +++ T EE LK  FS+ G +    I + +       + GFGFV +  P  A++ +
Sbjct: 1  LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 65 --MDKHMIDGRTVEAKKAVPRD 84
            +  H +DG  +E + +    
Sbjct: 61 KQLQGHTVDGHKLEVRISERAT 82

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 65.1 bits (158), Expect = 7e-14
 Identities = 20/82 (24%), Positives = 33/82 (40%), Gaps = 4/82 (4%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHN---TQRPRGFGFITYDSEEAVDRVL 164
           +F+  L  + TE   K  F + G I    +    N        GFGF+ Y   E   + L
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 165 HK-TFHELNGKMVEVKRAVPKE 185
            +   H ++G  +EV+ +    
Sbjct: 61  KQLQGHTVDGHKLEVRISERAT 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 = 71.9 bits (176), Expect = 3e-16
 Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 2/81 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L++G +S+ T EE++ E FS+ G++ + ++  D+    A GF FV +   A AE  +  
Sbjct: 9  TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 65 MDKHMIDGRTVEAKKAVPRDD 85
          ++   +D R +         +
Sbjct: 69 INGTRLDDRIIRTDWDAGFKE 89

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.4 bits (154), Expect = 3e-13
 Identities = 15/83 (18%), Positives = 34/83 (40%), Gaps = 1/83 (1%)

Query: 104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV 163
           ++  ++VG L+   TE    + F + G I  +++  D   +   GF F+ Y S    +  
Sbjct: 6   KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENA 65

Query: 164 LHK-TFHELNGKMVEVKRAVPKE 185
           +       L+ +++        +
Sbjct: 66  MRYINGTRLDDRIIRTDWDAGFK 88

>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 = 72.0 bits (176), Expect = 3e-16
 Identities = 26/84 (30%), Positives = 43/84 (51%), Gaps = 3/84 (3%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           +++GG+     E  L E F + G VV   + +DR TG+ +G+GFV F     A+  I  
Sbjct: 11 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 70

Query: 65 MDKHMIDGRTVEAKKAVPRDDQNM 88
          MD   + G+ +   KA    ++N+
Sbjct: 71 MDMIKLYGKPIRVNKASAH-NKNL 93

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 66.6 bits (162), Expect = 2e-14
 Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 1/83 (1%)

Query: 104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV 163
           +   ++VGGL   V+E    + F Q G + +  +  D  T + +G+GF+ + SEE  D  
Sbjct: 8   QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 67

Query: 164 LHK-TFHELNGKMVEVKRAVPKE 185
           +      +L GK + V +A    
Sbjct: 68  IKIMDMIKLYGKPIRVNKASAHN 90

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.8 bits (173), Expect = 7e-16
 Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 2/86 (2%)

Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
            D   + +  +S DT E  L+E F  +G +    + +D+ TG+++GF F+ F     A 
Sbjct: 5  ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 64

Query: 62 RVI--MDKHMIDGRTVEAKKAVPRDD 85
          R I  +     D   +  + A P  +
Sbjct: 65 RAIAGVSGFGYDHLILNVEWAKPSTN 90

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.4 bits (151), Expect = 6e-13
 Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 1/82 (1%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
              I V  L+    E+D ++ F  FG+I+ + +  D  T + +GF FI++   E   R +
Sbjct: 8   NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 67

Query: 165 HK-TFHELNGKMVEVKRAVPKE 185
              +    +  ++ V+ A P  
Sbjct: 68  AGVSGFGYDHLILNVEWAKPST 89

>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 = 70.8 bits (173), Expect = 1e-15
 Identities = 15/87 (17%), Positives = 32/87 (36%), Gaps = 5/87 (5%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L+I  + +    E + + F +YG + +   +R   T   RG  +VV+ D   A+     
Sbjct: 9  ILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNACDH 65

Query: 65 MDKHMIDGRTVEAKKAVPRDDQNMLNR 91
          +    +  R +             ++ 
Sbjct: 66 LSGFNVCNRYLVVLYYNANRAFQKMDT 92

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.9 bits (155), Expect = 3e-13
 Identities = 12/85 (14%), Positives = 27/85 (31%), Gaps = 4/85 (4%)

Query: 102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVD 161
           P   + +++  L   +T  +    F ++G I     +   NT   RG  ++ Y+      
Sbjct: 4   PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAK 60

Query: 162 RVLHKT-FHELNGKMVEVKRAVPKE 185
                     +  + + V       
Sbjct: 61  NACDHLSGFNVCNRYLVVLYYNANR 85

>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 = 69.6 bits (170), Expect = 1e-15
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 3/77 (3%)

Query: 6  GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI- 64
          GKL +  + +   +  ++E F+ +G + +A +  DR +GR+ G   V F   A A + + 
Sbjct: 1  GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMK 59

Query: 65 -MDKHMIDGRTVEAKKA 80
            +   +DGR +  +  
Sbjct: 60 QYNGVPLDGRPMNIQLV 76

>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 = 60.3 bits (146), Expect = 2e-12
 Identities = 15/76 (19%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+ V  L   V+++D ++ F +FGT+    V Y   + R  G   + ++ +    + + +
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHY-DRSGRSLGTADVHFERKADALKAMKQ 60

Query: 167 -TFHELNGKMVEVKRA 181
                L+G+ + ++  
Sbjct: 61  YNGVPLDGRPMNIQLV 76

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.4 bits (169), Expect = 2e-15
 Identities = 24/82 (29%), Positives = 42/82 (51%), Gaps = 3/82 (3%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEV-VEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          +FIG +  + DE+ L + FS +G +     IMRD  TG ++G+ F+ FA    ++  I  
Sbjct: 1  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 65 MDKHMIDGRTVEAKKAVPRDDQ 86
          M+   +  R +    A  +D +
Sbjct: 61 MNGQYLCNRPITVSYAFKKDSK 82

>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 = 65.9 bits (160), Expect = 3e-14
 Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 2/80 (2%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTI-TDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           IF+G L   + E      F  FG I     +M D +T   +G+ FI + S +A D  +  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 167 -TFHELNGKMVEVKRAVPKE 185
                L  + + V  A  K+
Sbjct: 61  MNGQYLCNRPITVSYAFKKD 80

>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 = 70.2 bits (171), Expect = 2e-15
 Identities = 31/100 (31%), Positives = 47/100 (47%), Gaps = 1/100 (1%)

Query: 96  IHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD 155
           +H S       KIFVGGL    T++  +KYF+ FG I + VV+ D  T + RG+GF+T  
Sbjct: 1   MHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMA 60

Query: 156 SEEAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRSSM 195
              A +R        ++G+   V  A      P   ++  
Sbjct: 61  DRAAAERACKDPNPIIDGRKANVNLAYLGA-KPRSLQTGF 99

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.0 bits (155), Expect = 2e-13
 Identities = 36/91 (39%), Positives = 54/91 (59%), Gaps = 5/91 (5%)

Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
          ++   K+F+GG+ + T +  L++YF  +G++ EAV++ DR TG++RG+GFV  AD A AE
Sbjct: 7  DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAE 66

Query: 62 RVIMDK-HMIDGRTVEAKKAV----PRDDQN 87
          R   D   +IDGR      A     PR  Q 
Sbjct: 67 RACKDPNPIIDGRKANVNLAYLGAKPRSLQT 97

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.3 bits (169), Expect = 2e-15
 Identities = 23/86 (26%), Positives = 42/86 (48%), Gaps = 4/86 (4%)

Query: 3  SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
          S +G +FI  +    D + L + FS +G ++   ++ D      +G+GFV F     AER
Sbjct: 6  SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS--KGYGFVHFETQEAAER 63

Query: 63 VI--MDKHMIDGRTVEAKKAVPRDDQ 86
           I  M+  +++ R V   +   R ++
Sbjct: 64 AIEKMNGMLLNDRKVFVGRFKSRKER 89

>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 = 60.1 bits (145), Expect = 4e-12
 Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 3/82 (3%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
              IF+  L  ++        F  FG I    V+ D N    +G+GF+ ++++EA +R +
Sbjct: 8   VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAI 65

Query: 165 HK-TFHELNGKMVEVKRAVPKE 185
            K     LN + V V R   ++
Sbjct: 66  EKMNGMLLNDRKVFVGRFKSRK 87

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 67.3 bits (164), Expect = 8e-15
 Identities = 20/78 (25%), Positives = 40/78 (51%), Gaps = 4/78 (5%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L++  +     +++L   F +YG +V+  I+RD+ TGR RG  FV +     A+  I  
Sbjct: 8  NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 65 MDKHMIDG--RTVEAKKA 80
          ++  + +G  + +  + A
Sbjct: 68 LNNVIPEGGSQPLSVRLA 85

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 64.6 bits (157), Expect = 9e-14
 Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 3/81 (3%)

Query: 104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV 163
           +   ++V  L  T+T+      F ++G+I    ++ D  T RPRG  F+ Y+  E     
Sbjct: 5   KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 64

Query: 164 ---LHKTFHELNGKMVEVKRA 181
              L+    E   + + V+ A
Sbjct: 65  ISALNNVIPEGGSQPLSVRLA 85

>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 = 67.4 bits (164), Expect = 1e-14
 Identities = 22/88 (25%), Positives = 45/88 (51%), Gaps = 4/88 (4%)

Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
          +S   +L +  I +   +  L++ F ++G++++  I+ +      +GFGFV F + A A+
Sbjct: 8  KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADAD 65

Query: 62 RVI--MDKHMIDGRTVEAKKAVPRDDQN 87
          R    +   +++GR +E   A  R   N
Sbjct: 66 RAREKLHGTVVEGRKIEVNNATARVMTN 93

>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 = 60.8 bits (147), Expect = 2e-12
 Identities = 24/88 (27%), Positives = 41/88 (46%), Gaps = 3/88 (3%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE 157
           +S      K++ V  +     + D ++ F QFG I D  V    N +  +GFGF+T+++ 
Sbjct: 4   NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILD--VEIIFNERGSKGFGFVTFENS 61

Query: 158 EAVDRVLHKT-FHELNGKMVEVKRAVPK 184
              DR   K     + G+ +EV  A  +
Sbjct: 62  ADADRAREKLHGTVVEGRKIEVNNATAR 89

>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 = 66.9 bits (163), Expect = 1e-14
 Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 2/78 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L +  +  D  +  L   F   G +    IMRD  TG + G+ FV F     ++R I  
Sbjct: 4  NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 65 MDKHMIDGRTVEAKKAVP 82
          ++   +  + ++   A P
Sbjct: 64 LNGITVRNKRLKVSYARP 81

>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 = 60.8 bits (147), Expect = 2e-12
 Identities = 18/78 (23%), Positives = 31/78 (39%), Gaps = 1/78 (1%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
            + V  L   +T+ +    F   G I    +M D+ T    G+ F+ + SE    R +  
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 167 -TFHELNGKMVEVKRAVP 183
                +  K ++V  A P
Sbjct: 64  LNGITVRNKRLKVSYARP 81

>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 = 67.0 bits (163), Expect = 1e-14
 Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 2/70 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L++ G+     ++ L++ FS+YG ++ + I+ D+ TG +RG GF+ F     AE  I  
Sbjct: 8  NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 67

Query: 65 MDKHMIDGRT 74
          ++     G T
Sbjct: 68 LNGQKPSGAT 77

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 1e-11
 Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 4/74 (5%)

Query: 104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV 163
           R   ++V GL  T+T+ + ++ F Q+G I    ++ D  T   RG GFI +D     +  
Sbjct: 5   RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 64

Query: 164 LHKTFHELNGKMVE 177
           +      LNG+   
Sbjct: 65  I----KGLNGQKPS 74

>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 = 67.1 bits (163), Expect = 2e-14
 Identities = 19/96 (19%), Positives = 38/96 (39%), Gaps = 10/96 (10%)

Query: 2   ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVI--------MRDRATGRARGFGFVV 53
           +SD   +++ G++     + L ++F + G V               D+ TG+ +G   V 
Sbjct: 5   DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 64

Query: 54  FADPAVAERVI--MDKHMIDGRTVEAKKAVPRDDQN 87
           + DP  A+  +   D     G  ++   A  +   N
Sbjct: 65  YEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMN 100

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.9 bits (147), Expect = 3e-12
 Identities = 21/99 (21%), Positives = 35/99 (35%), Gaps = 14/99 (14%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVV--------MYDHNTQRPRGFGFITYDS 156
              I+V GL  +VT  D   +F Q G +               D  T +P+G   ++Y+ 
Sbjct: 8   NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 67

Query: 157 EEAVDRVLHKT-FHELNGKMVEVKRAVPKEFSPGPSRSS 194
                  +      +  G  ++V  A  K     P  +S
Sbjct: 68  PPTAKAAVEWFDGKDFQGSKLKVSLARKK-----PPMNS 101

>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 = 66.3 bits (161), Expect = 2e-14
 Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L +  +  +  +E  +  F   GE+    ++RD+ TG++ G+GFV + DP  AE+ I  
Sbjct: 4  NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 65 MDKHMIDGRTVEAKKAVP 82
          ++   +  +T++   A P
Sbjct: 64 LNGLRLQTKTIKVSYARP 81

>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 = 58.6 bits (141), Expect = 1e-11
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
            + V  L   +T+ +F+  F   G I    ++ D  T +  G+GF+ Y   +  ++ ++ 
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 167 -TFHELNGKMVEVKRAVP 183
                L  K ++V  A P
Sbjct: 64  LNGLRLQTKTIKVSYARP 81

>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 = 66.6 bits (162), Expect = 2e-14
 Identities = 18/87 (20%), Positives = 34/87 (39%), Gaps = 4/87 (4%)

Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
          +     L++G +S D  E  + + FS+ G      ++ +        + FV F +   A 
Sbjct: 5  DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAA 62

Query: 62 RVI--MDKHMIDGRTVEAKKAVPRDDQ 86
            +  M+   I G+ V+   A     Q
Sbjct: 63 AALAAMNGRKILGKEVKVNWATTPSSQ 89

>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 = 59.7 bits (144), Expect = 6e-12
 Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 3/83 (3%)

Query: 103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDR 162
           G+ + ++VG L+  VTE    + F Q G      ++ +H +  P  + F+ +        
Sbjct: 6   GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAA 63

Query: 163 VLHK-TFHELNGKMVEVKRAVPK 184
            L      ++ GK V+V  A   
Sbjct: 64  ALAAMNGRKILGKEVKVNWATTP 86

>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 = 66.0 bits (160), Expect = 3e-14
 Identities = 10/78 (12%), Positives = 28/78 (35%), Gaps = 2/78 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L++        +  +++       V  ++ +       +R F ++       A   +  
Sbjct: 3  TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 65 MDKHMIDGRTVEAKKAVP 82
          ++   I+G T+  K + P
Sbjct: 63 LNGLKIEGYTLVTKVSNP 80

>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 = 62.5 bits (151), Expect = 5e-13
 Identities = 10/78 (12%), Positives = 27/78 (34%), Gaps = 1/78 (1%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
            +++     + T+ + +        +   + +        R F +I   S+E     + K
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 167 -TFHELNGKMVEVKRAVP 183
               ++ G  +  K + P
Sbjct: 63  LNGLKIEGYTLVTKVSNP 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 = 66.8 bits (162), Expect = 3e-14
 Identities = 12/90 (13%), Positives = 29/90 (32%)

Query: 97  HSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
            S         +++ GL           +F +   + D + +      +  G GF+ + +
Sbjct: 10  RSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRN 69

Query: 157 EEAVDRVLHKTFHELNGKMVEVKRAVPKEF 186
           E      L +    +  + ++V     K  
Sbjct: 70  EADYKAALCRHKQYMGNRFIQVHPITKKGM 99

>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 = 64.9 bits (157), Expect = 1e-13
 Identities = 14/93 (15%), Positives = 41/93 (44%), Gaps = 1/93 (1%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
            +++ G+ ++ + + + ++F +   V +++ +     G+A G GFV F + A  +  +  
Sbjct: 20  CVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCR 79

Query: 66  DKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHS 98
            K  +  R ++      +     ++     + S
Sbjct: 80  HKQYMGNRFIQVHPITKKGMLEKIDMIRKRLQS 112

>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 = 65.5 bits (159), Expect = 6e-14
 Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 2/81 (2%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            LFI  +  +  ++ L + F  +G VV A +  D+ T  ++ FGFV + +P  A+  I  
Sbjct: 20  NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 79

Query: 65  MDKHMIDGRTVEAKKAVPRDD 85
           M+   I  + ++ +    ++D
Sbjct: 80  MNGFQIGMKRLKVQLKRSKND 100

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.2 bits (140), Expect = 3e-11
 Identities = 20/99 (20%), Positives = 38/99 (38%), Gaps = 2/99 (2%)

Query: 89  LNRNTSSIHSSPGPG-RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPR 147
           L + +     S   G     +F+  L     + D  + F  FG +    V  D  T   +
Sbjct: 1   LTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 60

Query: 148 GFGFITYDSEEAVDRVLHKT-FHELNGKMVEVKRAVPKE 185
            FGF++YD+  +    +      ++  K ++V+    K 
Sbjct: 61  CFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKN 99

>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 = 64.8 bits (157), Expect = 1e-13
 Identities = 18/102 (17%), Positives = 44/102 (43%), Gaps = 1/102 (0%)

Query: 92  NTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGF 151
           ++ S  +SP       + + GL    ++ +  ++F     + + + +      R  G  F
Sbjct: 2   SSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAF 61

Query: 152 ITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEF-SPGPSR 192
           + + S+E  ++ L K    +  + +E+ ++   E  + GPS 
Sbjct: 62  VQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEVRTSGPSS 103

>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 = 56.8 bits (136), Expect = 8e-11
 Identities = 20/87 (22%), Positives = 40/87 (45%), Gaps = 1/87 (1%)

Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
           ++ G + + G+ +   +E + ++FS    V   + +     GR+ G  FV FA   +AE
Sbjct: 12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAE 71

Query: 62 RVI-MDKHMIDGRTVEAKKAVPRDDQN 87
          + +   K  I  R +E  K+   + + 
Sbjct: 72 KALKKHKERIGHRYIEIFKSSRAEVRT 98

>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 = 64.8 bits (157), Expect = 1e-13
 Identities = 21/91 (23%), Positives = 43/91 (47%), Gaps = 8/91 (8%)

Query: 3  SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
          ++   +FI  +S+D++EE L E   ++G++    ++    T  ++G  F  F     A++
Sbjct: 6  TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 65

Query: 63 VI--------MDKHMIDGRTVEAKKAVPRDD 85
           +             +DGR ++   AV RD+
Sbjct: 66 CLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 96

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.4 bits (148), Expect = 2e-12
 Identities = 20/87 (22%), Positives = 40/87 (45%), Gaps = 7/87 (8%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
           K +F+  L+    E    +   QFG +  V V+   +T+  +G  F  + ++EA  + L 
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 68

Query: 166 KTFH-------ELNGKMVEVKRAVPKE 185
                      +L+G+ ++V  AV ++
Sbjct: 69  AASLEAEGGGLKLDGRQLKVDLAVTRD 95

>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 = 64.3 bits (156), Expect = 1e-13
 Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L + G+S  T E  L+E FS+YG + +  I+ D+ + R+RGF FV F +   A+     
Sbjct: 11 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 70

Query: 65 MDKHMIDGRTVE 76
           +   +DGR + 
Sbjct: 71 ANGMELDGRRIR 82

>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 = 63.2 bits (153), Expect = 2e-13
 Identities = 24/83 (28%), Positives = 45/83 (54%), Gaps = 3/83 (3%)

Query: 97  HSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
            ++P P     + V GL+   TE D ++ F ++G I DV ++YD  ++R RGF F+ +++
Sbjct: 3   RANPDPNCC--LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60

Query: 157 EEAVDRVLHK-TFHELNGKMVEV 178
            +       +    EL+G+ + V
Sbjct: 61  VDDAKEAKERANGMELDGRRIRV 83

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.5 bits (154), Expect = 2e-13
 Identities = 17/87 (19%), Positives = 36/87 (41%), Gaps = 8/87 (9%)

Query: 3  SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
          S +  L++  +   T EE +++ F+                 + R + FV F++   A  
Sbjct: 6  SSVKILYVRNLMLSTSEEMIEKEFNNIKPG------AVERVKKIRDYAFVHFSNREDAVE 59

Query: 63 VI--MDKHMIDGRTVEAKKAVPRDDQN 87
           +  ++  ++DG  +E   A P D  +
Sbjct: 60 AMKALNGKVLDGSPIEVTLAKPVDKDS 86

>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 = 62.0 bits (150), Expect = 8e-13
 Identities = 15/83 (18%), Positives = 31/83 (37%), Gaps = 7/83 (8%)

Query: 104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV 163
             K ++V  L  + +E   +K F+                ++ R + F+ + + E     
Sbjct: 7   SVKILYVRNLMLSTSEEMIEKEFNNIKPGA------VERVKKIRDYAFVHFSNREDAVEA 60

Query: 164 LHKT-FHELNGKMVEVKRAVPKE 185
           +       L+G  +EV  A P +
Sbjct: 61  MKALNGKVLDGSPIEVTLAKPVD 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 = 63.6 bits (154), Expect = 3e-13
 Identities = 25/87 (28%), Positives = 43/87 (49%), Gaps = 2/87 (2%)

Query: 3  SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
          S  G+LF+  +S+ + EE L++ FS YG + E     D  T + +GF FV F  P  A +
Sbjct: 6  SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVK 65

Query: 63 VI--MDKHMIDGRTVEAKKAVPRDDQN 87
              +D  +  GR +    +  + + +
Sbjct: 66 AYAEVDGQVFQGRMLHVLPSTIKKEAS 92

>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 = 62.4 bits (151), Expect = 8e-13
 Identities = 25/97 (25%), Positives = 48/97 (49%), Gaps = 1/97 (1%)

Query: 99  SPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEE 158
           S G   + ++FV  L+ T +E D +K F  +G ++++    D  T++P+GF F+T+   E
Sbjct: 2   SSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61

Query: 159 AVDRVLHK-TFHELNGKMVEVKRAVPKEFSPGPSRSS 194
              +   +       G+M+ V  +  K+ +     SS
Sbjct: 62  HAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPSS 98

>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 = 62.8 bits (152), Expect = 3e-13
 Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 9/84 (10%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
          KL+IG +S     + L++ F      +              G+ FV + D   A R I  
Sbjct: 3  KLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 67 ---KHMIDGRTVEAKKAVPRDDQN 87
             K  + G+ +E   +V +  ++
Sbjct: 57 LSGKVELHGKIMEVDYSVSKKLRS 80

>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 = 62.0 bits (150), Expect = 6e-13
 Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 8/81 (9%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           K+++G L+  VT  D ++ F                     G+ F+ Y  +    R +  
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 167 T--FHELNGKMVEVKRAVPKE 185
                EL+GK++EV  +V K+
Sbjct: 57  LSGKVELHGKIMEVDYSVSKK 77

>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 = 62.9 bits (152), Expect = 6e-13
 Identities = 10/80 (12%), Positives = 30/80 (37%)

Query: 106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLH 165
               +  +  ++T+ D  ++ +      + V +   N  +  G   + + +E+   +   
Sbjct: 9   VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER 68

Query: 166 KTFHELNGKMVEVKRAVPKE 185
               +LNG+   V     ++
Sbjct: 69  LHRKKLNGREAFVHVVTLED 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 = 59.9 bits (144), Expect = 7e-12
 Identities = 13/96 (13%), Positives = 30/96 (31%), Gaps = 1/96 (1%)

Query: 1  MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
          + S      I  I +   +  + ++         AV +     G+  G   V F +   A
Sbjct: 4  VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 63

Query: 61 ERVI-MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSS 95
           +   + +  ++GR          D + +     + 
Sbjct: 64 RKSERLHRKKLNGREAFVHVVTLEDMREIEKNPPAQ 99

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 62.0 bits (150), Expect = 7e-13
 Identities = 13/85 (15%), Positives = 30/85 (35%), Gaps = 1/85 (1%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE 157
           +S G      I V  +  TV+  +   +F  +  I   V +  +    P G   + ++S 
Sbjct: 2   ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 61

Query: 158 EAVDRVLHKT-FHELNGKMVEVKRA 181
           +     +       +  + V++   
Sbjct: 62  DEATAAVIDLNDRPIGSRKVKLVLG 86

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.5 bits (146), Expect = 3e-12
 Identities = 11/76 (14%), Positives = 27/76 (35%), Gaps = 2/76 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           + +  + +    + + ++F  Y  +  +V ++    G   G   V F     A   +  
Sbjct: 11 IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 70

Query: 65 MDKHMIDGRTVEAKKA 80
          ++   I  R V+    
Sbjct: 71 LNDRPIGSRKVKLVLG 86

>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 = 62.3 bits (151), Expect = 8e-13
 Identities = 17/81 (20%), Positives = 38/81 (46%), Gaps = 8/81 (9%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           ++ GGI+    ++ +++ FS +G+++E  +  +      +G+ FV F+    A   I  
Sbjct: 20 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVS 73

Query: 65 MDKHMIDGRTVEAKKAVPRDD 85
          ++   I+G  V+        D
Sbjct: 74 VNGTTIEGHVVKCYWGKESPD 94

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.4 bits (120), Expect = 1e-08
 Identities = 14/82 (17%), Positives = 34/82 (41%), Gaps = 7/82 (8%)

Query: 104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV 163
           +   ++ GG+AS +T+   ++ F  FG I ++ V  +        + F+ + + E+    
Sbjct: 17  KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESAAHA 70

Query: 164 LHKT-FHELNGKMVEVKRAVPK 184
           +       + G +V+       
Sbjct: 71  IVSVNGTTIEGHVVKCYWGKES 92

>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 = 61.7 bits (149), Expect = 2e-12
 Identities = 24/101 (23%), Positives = 39/101 (38%), Gaps = 2/101 (1%)

Query: 93  TSSIHSSPGPGR-TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGF 151
           +S    S  P       F+G L   VTE   K++F         +     N +R +GFG+
Sbjct: 2   SSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGY 61

Query: 152 ITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPK-EFSPGPS 191
             ++  +++   L      L  K + V  A    +   GPS
Sbjct: 62  AEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDKDSGPS 102

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.2 bits (140), Expect = 2e-11
 Identities = 16/82 (19%), Positives = 33/82 (40%), Gaps = 1/82 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
            F+G + +D  EE +KE+F         +        R +GFG+  F D       + +
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 76

Query: 66 DKHMIDGRTVEAKKAVPRDDQN 87
          ++  +  + +    A    D++
Sbjct: 77 NEESLGNKRIRVDVADQAQDKD 98

>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 = 62.6 bits (151), Expect = 2e-12
 Identities = 24/118 (20%), Positives = 53/118 (44%), Gaps = 1/118 (0%)

Query: 78  KKAVPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVV 137
           + A  +  Q    ++      +P P   + + V  + +TV E   ++ F+++G I  V +
Sbjct: 15  QTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKI 74

Query: 138 MYDHNTQRPRGFGFITYDSEEAVDRVLHK-TFHELNGKMVEVKRAVPKEFSPGPSRSS 194
           + D  T++ RG+GF+ + S  +  + +       +  K ++V  A      PG + + 
Sbjct: 75  VCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQRPGIAGAV 132

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 55.7 bits (133), Expect = 5e-10
 Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 2/82 (2%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            L +  I    DE +L++ F RYG +    I+ DR T ++RG+GFV F   + A++ I  
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103

Query: 65  MDKHMIDGRTVEAKKAVPRDDQ 86
           ++   I  + ++   A     +
Sbjct: 104 LNGFNILNKRLKVALAASGHQR 125

>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 = 60.5 bits (146), Expect = 3e-12
 Identities = 17/80 (21%), Positives = 35/80 (43%), Gaps = 3/80 (3%)

Query: 7  KLFIGGISWD-TDEERLKEYFSRYGEV-VEAVIMRDRATGRARGFGFVVFADPAVAERVI 64
          ++ I  +S +  DE  L+E F  +G +    +    +         F+VF +   AER +
Sbjct: 6  EIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 65

Query: 65 -MDKHMIDGRTVEAKKAVPR 83
           M++ ++  R +    A  +
Sbjct: 66 QMNRSLLGNREISVSLADKK 85

>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 = 60.1 bits (145), Expect = 4e-12
 Identities = 14/81 (17%), Positives = 37/81 (45%), Gaps = 2/81 (2%)

Query: 106 KKIFVGGLASTVT-ESDFKKYFDQFGTITDVVVMYDH-NTQRPRGFGFITYDSEEAVDRV 163
           ++I +  L++ +  E+  ++ F+ FG+I  + +              F+ ++++++ +R 
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 164 LHKTFHELNGKMVEVKRAVPK 184
           L      L  + + V  A  K
Sbjct: 65  LQMNRSLLGNREISVSLADKK 85

>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 = 60.5 bits (146), Expect = 3e-12
 Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 2/78 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          LF+  I  +  E+ ++E F  YGE+    +  DR TG ++G+  V +     A      +
Sbjct: 10 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 69

Query: 66 DKHMIDGRTVEAKKAVPR 83
          +   I G+T++      +
Sbjct: 70 NGAEIMGQTIQVDWCFVK 87

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 55.9 bits (134), Expect = 1e-10
 Identities = 14/78 (17%), Positives = 33/78 (42%), Gaps = 1/78 (1%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK- 166
           +FV  +     E + ++ F  +G I ++ +  D  T   +G+  + Y++ +         
Sbjct: 10  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 69

Query: 167 TFHELNGKMVEVKRAVPK 184
              E+ G+ ++V     K
Sbjct: 70  NGAEIMGQTIQVDWCFVK 87

>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 = 60.5 bits (146), Expect = 4e-12
 Identities = 26/93 (27%), Positives = 46/93 (49%), Gaps = 2/93 (2%)

Query: 1  MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
          ++  L  +F+G I ++  EE+LK+ FS  G VV   ++ DR TG+ +G+GF  + D   A
Sbjct: 4  VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63

Query: 61 ERVI--MDKHMIDGRTVEAKKAVPRDDQNMLNR 91
             +  ++     GR +    A    ++  L  
Sbjct: 64 LSAMRNLNGREFSGRALRVDNAASEKNKEELKS 96

>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 = 57.8 bits (139), Expect = 4e-11
 Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 1/82 (1%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
            + +FVG +    TE   K  F + G +    ++YD  T +P+G+GF  Y  +E     +
Sbjct: 8   LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67

Query: 165 HK-TFHELNGKMVEVKRAVPKE 185
                 E +G+ + V  A  ++
Sbjct: 68  RNLNGREFSGRALRVDNAASEK 89

>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 = 59.6 bits (144), Expect = 5e-12
 Identities = 16/80 (20%), Positives = 24/80 (30%), Gaps = 8/80 (10%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
            + V G             F Q+G I   V+           +  I Y S+    + L K
Sbjct: 6   WVTVFGFPQASAS-YILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALSK 58

Query: 167 TFHELNGK-MVEVKRAVPKE 185
                    M+ VK  + K 
Sbjct: 59  DGRIFGESIMIGVKPCIDKN 78

>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 = 48.8 bits (116), Expect = 3e-08
 Identities = 9/80 (11%), Positives = 29/80 (36%), Gaps = 9/80 (11%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
           + + G    +    L + F++YG +++ V+           +  + +     A + +  
Sbjct: 6  WVTVFGFPQASASYILLQ-FAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALSK 58

Query: 66 DKHMIDGRT-VEAKKAVPRD 84
          D  +      +  K  + ++
Sbjct: 59 DGRIFGESIMIGVKPCIDKN 78

>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 = 60.1 bits (145), Expect = 5e-12
 Identities = 20/79 (25%), Positives = 33/79 (41%), Gaps = 7/79 (8%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L    +S++  E+ LKE F    E     I      G+++G  ++ F   A AE+ +  
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALE-----IRLVSQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 65 MDKHMIDGRTVEAKKAVPR 83
               IDGR+V       +
Sbjct: 73 KQGAEIDGRSVSLYYTGEK 91

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 58.1 bits (140), Expect = 2e-11
 Identities = 17/93 (18%), Positives = 37/93 (39%), Gaps = 6/93 (6%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE 157
           +S      + +    L+  +TE + K+ F+    I            + +G  +I + SE
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSE 63

Query: 158 EAVDRVLHK-TFHELNGKMVEVKRAVPKEFSPG 189
              ++ L +    E++G+ V +     K  + G
Sbjct: 64  ADAEKNLEEKQGAEIDGRSVSLYYTGEKGGTRG 96

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 60.0 bits (144), Expect = 5e-12
 Identities = 16/91 (17%), Positives = 40/91 (43%), Gaps = 1/91 (1%)

Query: 94  SSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFIT 153
           S +           +F+G L    + ++ K    +     D+ V+    T   R FG++ 
Sbjct: 2   SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVD 60

Query: 154 YDSEEAVDRVLHKTFHELNGKMVEVKRAVPK 184
           ++S E +++ L  T  ++ G  +++++   +
Sbjct: 61  FESAEDLEKALELTGLKVFGNEIKLEKPKGR 91

>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 = 58.4 bits (140), Expect = 2e-11
 Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 2/78 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
           LFIG ++ +     LK   S      +  ++  R TG  R FG+V F      E+ + +
Sbjct: 15 NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKALEL 73

Query: 66 DKHMIDGRTVEAKKAVPR 83
              + G  ++ +K   R
Sbjct: 74 TGLKVFGNEIKLEKPKGR 91

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.9 bits (145), Expect = 6e-12
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 11/83 (13%)

Query: 7  KLFIGGISWD-TDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI- 64
          ++FIG ++     +  ++  FS+YG++V   +         +GF FV + +   A   + 
Sbjct: 17 RVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVA 68

Query: 65 -MDKHMIDGRTVEAKKAVPRDDQ 86
            D  MI G+ ++   A      
Sbjct: 69 GEDGRMIAGQVLDINLAAEPKVN 91

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.2 bits (138), Expect = 5e-11
 Identities = 20/97 (20%), Positives = 40/97 (41%), Gaps = 11/97 (11%)

Query: 98  SSPGPGRTKKIFVGGLAS-TVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
            +       ++F+G L +  V +SD +  F ++G I    V          GF F+ Y +
Sbjct: 8   KTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFAFVQYVN 59

Query: 157 EEAVDRVLHK-TFHELNGKMVEVKRAVPKEFS-PGPS 191
           E      +       + G+++++  A   + +  GPS
Sbjct: 60  ERNARAAVAGEDGRMIAGQVLDINLAAEPKVNRSGPS 96

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.2 bits (145), Expect = 6e-12
 Identities = 26/90 (28%), Positives = 44/90 (48%), Gaps = 2/90 (2%)

Query: 98  SSPGPGR-TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
           SS  PG   K +++  L+  VTE D    F +F       + +   T R RG  FIT+ +
Sbjct: 10  SSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPN 69

Query: 157 EEAVDRVLHKT-FHELNGKMVEVKRAVPKE 185
           +E   + LH    ++L GK++ ++    K+
Sbjct: 70  KEIAWQALHLVNGYKLYGKILVIEFGKNKK 99

>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 = 59.4 bits (143), Expect = 1e-11
 Identities = 17/82 (20%), Positives = 36/82 (43%), Gaps = 2/82 (2%)

Query: 7   KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
            L++  +S    E  L   F+R+ E     I     TGR RG  F+ F +  +A + +  
Sbjct: 20  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 79

Query: 65  MDKHMIDGRTVEAKKAVPRDDQ 86
           ++ + + G+ +  +    +  +
Sbjct: 80  VNGYKLYGKILVIEFGKNKKQR 101

>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 = 59.1 bits (142), Expect = 6e-12
 Identities = 14/75 (18%), Positives = 23/75 (30%), Gaps = 2/75 (2%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
            + V  L  +  ++   KYF   G I  V V           F  I +   +     + K
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFR--FARIEFARYDGALAAITK 59

Query: 167 TFHELNGKMVEVKRA 181
           T   +    + V   
Sbjct: 60  THKVVGQNEIIVSHL 74

>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 = 52.9 bits (126), Expect = 9e-10
 Identities = 3/74 (4%), Positives = 18/74 (24%), Gaps = 1/74 (1%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMD 66
           + +  +    ++ ++ +YF   G ++   +                         +   
Sbjct: 2  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFAR-IEFARYDGALAAITKT 60

Query: 67 KHMIDGRTVEAKKA 80
            ++    +     
Sbjct: 61 HKVVGQNEIIVSHL 74

>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 = 21/79 (26%), Positives = 38/79 (48%), Gaps = 8/79 (10%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          +LF+G +  D  EE +++ F +YG+  E  I +D      +GFGF+      +AE     
Sbjct: 10 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 63

Query: 65 MDKHMIDGRTVEAKKAVPR 83
          +D   + G+ +  + A   
Sbjct: 64 LDNMPLRGKQLRVRFACHS 82

>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 = 55.0 bits (132), Expect = 2e-10
 Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 7/79 (8%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           ++FVG L   +TE + +K F+++G   +V +  D        FGFI  ++    +    +
Sbjct: 10  RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKVE 63

Query: 167 T-FHELNGKMVEVKRAVPK 184
                L GK + V+ A   
Sbjct: 64  LDNMPLRGKQLRVRFACHS 82

>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 = 58.9 bits (142), Expect = 1e-11
 Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 9/85 (10%)

Query: 7  KLFIGGISWDTDEERLK----EYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
           ++I  ++    ++ LK      FSR+G++++ ++ R       RG  FV+F + + A  
Sbjct: 5  TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSATN 61

Query: 63 VI--MDKHMIDGRTVEAKKAVPRDD 85
           +  M       + +  + A    D
Sbjct: 62 ALRSMQGFPFYDKPMRIQYAKTDSD 86

>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 = 55.4 bits (133), Expect = 2e-10
 Identities = 11/83 (13%), Positives = 27/83 (32%), Gaps = 2/83 (2%)

Query: 105 TKKIFVGGLASTVTESDFKK-YFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV 163
              I++  L   + + + KK     F     ++ +    + + RG  F+ +    +    
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62

Query: 164 LHKT-FHELNGKMVEVKRAVPKE 185
           L          K + ++ A    
Sbjct: 63  LRSMQGFPFYDKPMRIQYAKTDS 85

>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 = 56.3 bits (135), Expect = 5e-11
 Identities = 17/70 (24%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          L+I G+   T ++ L +    YG++V    + D+ T + +G+GFV F  P+ A++ +  +
Sbjct: 1  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 66 DKHMIDGRTV 75
              +  +  
Sbjct: 61 KASGVQAQMA 70

>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 = 51.7 bits (123), Expect = 2e-09
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 4/74 (5%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           +++ GL    T+ D  K    +G I     + D  T + +G+GF+ +DS  A  + +   
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV--- 57

Query: 168 FHELNGKMVEVKRA 181
              L    V+ + A
Sbjct: 58  -TALKASGVQAQMA 70

>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 = 55.1 bits (132), Expect = 2e-10
 Identities = 11/78 (14%), Positives = 33/78 (42%), Gaps = 1/78 (1%)

Query: 104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV 163
           + + +++ G  +  T  D K++ +  G + + + M     +  +G  F+ +DS E+  + 
Sbjct: 5   KNRSVYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIESAKKF 63

Query: 164 LHKTFHELNGKMVEVKRA 181
           +     +     + +   
Sbjct: 64  VETPGQKYKETDLLILFK 81

>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 = 54.0 bits (129), Expect = 5e-10
 Identities = 14/75 (18%), Positives = 27/75 (36%), Gaps = 2/75 (2%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
           ++I G   D   + +KE+    G+V+   + R       +G  FVVF     A++ +  
Sbjct: 8  SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVET 66

Query: 66 DKHMIDGRTVEAKKA 80
                   +     
Sbjct: 67 PGQKYKETDLLILFK 81

>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 = 55.5 bits (133), Expect = 2e-10
 Identities = 17/79 (21%), Positives = 34/79 (43%), Gaps = 5/79 (6%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          ++++G +  D   + +++ F +YG + +  +   R       F FV F DP  AE  +  
Sbjct: 16 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPRDAEDAVYG 72

Query: 65 MDKHMIDGRTVEAKKAVPR 83
           D +  DG  +  +     
Sbjct: 73 RDGYDYDGYRLRVEFPRSG 91

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.0 bits (124), Expect = 3e-09
 Identities = 14/87 (16%), Positives = 33/87 (37%), Gaps = 4/87 (4%)

Query: 99  SPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEE 158
            P      +I+VG L   +   D +  F ++G I D+ +           F F+ ++   
Sbjct: 8   GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG---GPPFAFVEFEDPR 64

Query: 159 AVDRVLHK-TFHELNGKMVEVKRAVPK 184
             +  ++    ++ +G  + V+     
Sbjct: 65  DAEDAVYGRDGYDYDGYRLRVEFPRSG 91

>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 = 55.3 bits (133), Expect = 3e-10
 Identities = 16/73 (21%), Positives = 29/73 (39%), Gaps = 6/73 (8%)

Query: 15 WDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDG 72
           +   E L+   S++G++ + ++          G   V F DP  A+  I  +D     G
Sbjct: 29 LNEIREDLRVECSKFGQIRKLLLFDRHP----DGVASVSFRDPEEADYCIQTLDGRWFGG 84

Query: 73 RTVEAKKAVPRDD 85
          R + A+      D
Sbjct: 85 RQITAQAWDGTTD 97

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.4 bits (102), Expect = 3e-06
 Identities = 9/68 (13%), Positives = 21/68 (30%), Gaps = 5/68 (7%)

Query: 119 ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK-TFHELNGKMVE 177
             D +    +FG I  +++   H      G   +++   E  D  +         G+ + 
Sbjct: 33  REDLRVECSKFGQIRKLLLFDRHP----DGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 88

Query: 178 VKRAVPKE 185
            +      
Sbjct: 89  AQAWDGTT 96

>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 = 53.1 bits (127), Expect = 2e-09
 Identities = 13/77 (16%), Positives = 26/77 (33%), Gaps = 8/77 (10%)

Query: 100 PGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEA 159
            G     +I V  L   VT     + F +FGT+  ++       +  +    + Y    +
Sbjct: 2   AGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFT----KNNQFQALLQYADPVS 57

Query: 160 VDRVLHKTFHELNGKMV 176
                      L+G+ +
Sbjct: 58  AQHAK----LSLDGQNI 70

>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 = 50.0 bits (119), Expect = 2e-08
 Identities = 15/97 (15%), Positives = 37/97 (38%), Gaps = 8/97 (8%)

Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
          +S + ++ +  + +    + L + FS++G V++ +          +    + +ADP  A+
Sbjct: 4  QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQ 59

Query: 62 RVI--MDKHMI--DGRTVEAKKAVPRDDQNMLNRNTS 94
               +D   I     T+    +         N + S
Sbjct: 60 HAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKS 96

>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 = 51.6 bits (123), Expect = 3e-09
 Identities = 16/85 (18%), Positives = 35/85 (41%), Gaps = 9/85 (10%)

Query: 101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
            P +   ++V G    +T +  +  F  FG I D+ +             F+TY+  E+ 
Sbjct: 1   APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESA 52

Query: 161 DRVLHKT-FHELNGKMVEVKRAVPK 184
           D+ + +    ++    ++V  A  +
Sbjct: 53  DQAVAELNGTQVESVQLKVNIARKQ 77

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 3e-08
 Identities = 12/79 (15%), Positives = 31/79 (39%), Gaps = 10/79 (12%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
           L++ G   D     L+  FS +G +++  +         R   FV +     A++ +  
Sbjct: 7  TLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAE 58

Query: 65 MDKHMIDGRTVEAKKAVPR 83
          ++   ++   ++   A  +
Sbjct: 59 LNGTQVESVQLKVNIARKQ 77

>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 = 51.7 bits (123), Expect = 4e-09
 Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 3/83 (3%)

Query: 2  ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
          E D   L+I  +    DE+ L+     +G+V+   I+RD  +G +RG GF         E
Sbjct: 15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCE 73

Query: 62 RVI--MDKHMIDGRTVEAKKAVP 82
           VI   +   I      +    P
Sbjct: 74 AVIGHFNGKFIKTPPGVSAPTEP 96

>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 = 48.2 bits (114), Expect = 8e-08
 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 5/82 (6%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
            +++  L  ++ E + +     FG +     +   ++   RG GF   +S E  + V+  
Sbjct: 20  NLYISNLPLSMDEQELENMLKPFGQVIS-TRILRDSSGTSRGVGFARMESTEKCEAVI-- 76

Query: 167 TFHELNGKMVEVKRAVPKEFSP 188
                NGK ++    V     P
Sbjct: 77  --GHFNGKFIKTPPGVSAPTEP 96

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.0 bits (124), Expect = 4e-09
 Identities = 16/80 (20%), Positives = 33/80 (41%), Gaps = 3/80 (3%)

Query: 1   MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVA 60
           + S +  + +     +  EE   E   +YGEV E  +  +       G  +V F     A
Sbjct: 23  LRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDA 81

Query: 61  ERVI--MDKHMIDGRTVEAK 78
           E+ +  ++    +G+ + A+
Sbjct: 82  EKAVIDLNNRWFNGQPIHAE 101

>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 = 51.4 bits (122), Expect = 5e-09
 Identities = 16/79 (20%), Positives = 38/79 (48%), Gaps = 8/79 (10%)

Query: 7  KLFIGGISWDTDEE---RLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERV 63
           +F+ G+S    +    +  EYF ++G++ + VI    +   ++G     +     +E  
Sbjct: 10 LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 64 I-----MDKHMIDGRTVEA 77
          +     ++  ++DGRT++A
Sbjct: 70 LRAIQCVNNVVVDGRTLKA 88

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.9 bits (100), Expect = 4e-06
 Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 7/79 (8%)

Query: 107 KIFVGGLASTVTESDFKKYFD---QFGTITDVVVMYDHNTQR---PRGFGFITYDSEEAV 160
            +FV GL+  + + +  K  +   +FG I  VV+    +      P    ++TY   E  
Sbjct: 10  LVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDA 69

Query: 161 DRVLHKT-FHELNGKMVEV 178
            R +       ++G+ ++ 
Sbjct: 70  LRAIQCVNNVVVDGRTLKA 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 = 50.9 bits (121), Expect = 8e-09
 Identities = 17/101 (16%), Positives = 36/101 (35%), Gaps = 11/101 (10%)

Query: 86  QNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQR 145
           ++ L R+   I +     ++  +  GGL + V+ +      ++ G +  +++  +     
Sbjct: 2   KHTLLRHEG-IETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP--- 57

Query: 146 PRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEF 186
              + F  Y + E   R        LNGK V          
Sbjct: 58  ---YSFARYRTTEESKRAY----VTLNGKEVVDDLGQKITL 91

>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 = 42.0 bits (98), Expect = 1e-05
 Identities = 9/70 (12%), Positives = 25/70 (35%), Gaps = 9/70 (12%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M 65
          +  GG+       +L     + G V   ++  +      + + F  +     ++R    +
Sbjct: 23 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTL 76

Query: 66 D-KHMIDGRT 74
          + K ++D   
Sbjct: 77 NGKEVVDDLG 86

>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 = 50.2 bits (119), Expect = 2e-08
 Identities = 16/89 (17%), Positives = 24/89 (26%), Gaps = 8/89 (8%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS- 156
           S          F G L       D    F   G I  +  +           G I +   
Sbjct: 4   SLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGA------KEGIILFKEK 57

Query: 157 -EEAVDRVLHKTFHELNGKMVEVKRAVPK 184
            +EA+ +        L  +  EV   V +
Sbjct: 58  AKEALGKAKDANNGNLQLRNKEVTWEVLE 86

>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 = 46.7 bits (110), Expect = 3e-07
 Identities = 17/87 (19%), Positives = 27/87 (31%), Gaps = 5/87 (5%)

Query: 1  MESDLG--KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPA 58
          +E  +G    F G +   T  E L   FS +GE+     +R    G          A   
Sbjct: 5  LEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGK 64

Query: 59 VAERVIMDKHMIDGRTVEAKKAVPRDD 85
            +    +   +  R  E    V   +
Sbjct: 65 AKD---ANNGNLQLRNKEVTWEVLEGE 88

>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 = 49.4 bits (117), Expect = 3e-08
 Identities = 14/96 (14%), Positives = 28/96 (29%), Gaps = 2/96 (2%)

Query: 98  SSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE 157
           SS        + + GL    TE+D   +F     +   + +             + + + 
Sbjct: 8   SSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTG--EADVEFATH 65

Query: 158 EAVDRVLHKTFHELNGKMVEVKRAVPKEFSPGPSRS 193
           E     + K    +  + VE+        S     S
Sbjct: 66  EDAVAAMAKDKANMQHRYVELFLNSTAGTSGSGPSS 101

>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 = 43.6 bits (102), Expect = 3e-06
 Identities = 16/82 (19%), Positives = 27/82 (32%), Gaps = 3/82 (3%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-M 65
           + + G+ +   E  +  +FS    +   + +     GR  G   V FA    A   +  
Sbjct: 17 CVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPD--GRVTGEADVEFATHEDAVAAMAK 74

Query: 66 DKHMIDGRTVEAKKAVPRDDQN 87
          DK  +  R VE           
Sbjct: 75 DKANMQHRYVELFLNSTAGTSG 96

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.5 bits (110), Expect = 3e-07
 Identities = 15/75 (20%), Positives = 25/75 (33%), Gaps = 4/75 (5%)

Query: 14 SWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGF--VVFADPAVAERVI--MDKHM 69
           ++   E +++  S+YG V    I R        G G   V F      ++ +  +    
Sbjct: 23 EYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK 82

Query: 70 IDGRTVEAKKAVPRD 84
             R V  K   P  
Sbjct: 83 FANRVVVTKYCDPDS 97

>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 = 42.4 bits (99), Expect = 7e-06
 Identities = 15/79 (18%), Positives = 26/79 (32%), Gaps = 7/79 (8%)

Query: 8  LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDK 67
          L +  I     EE LK  FS  G VV+          + R    +       A + ++D 
Sbjct: 13 LHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDL 68

Query: 68 H---MIDGRTVEAKKAVPR 83
          H   + +   +    +   
Sbjct: 69 HNHDLGENHHLRVSFSKST 87

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 5e-05
 Identities = 20/97 (20%), Positives = 32/97 (32%), Gaps = 13/97 (13%)

Query: 91  RNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFG 150
           +N  +I     P  T  + +  +  +V+E D K  F   G     VV      Q+ R   
Sbjct: 1   KNFQNIFP---PSAT--LHLSNIPPSVSEEDLKVLFSSNGG----VVKGFKFFQKDRKMA 51

Query: 151 FITYDSEEAVDRVLHKTFHELNGKMVEVKRAVPKEFS 187
            I   S E   + L       +   +     +   FS
Sbjct: 52  LIQMGSVEEAVQALIDL----HNHDLGENHHLRVSFS 84

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 3e-05
 Identities = 14/93 (15%), Positives = 25/93 (26%), Gaps = 9/93 (9%)

Query: 101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAV 160
           G   +  I V  L       +       +        +      R +   F+T  + E  
Sbjct: 1   GSSGSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQA 53

Query: 161 DRVLHKT-FHELNGKMVEVKRAVPKEF-SPGPS 191
              +     +   GK + V+          GPS
Sbjct: 54  QNAIQMFHQYSFRGKDLIVQLQPTDALLCSGPS 86

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.3 bits (91), Expect = 8e-05
 Identities = 9/83 (10%), Positives = 27/83 (32%), Gaps = 9/83 (10%)

Query: 3  SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAER 62
          S    + +  +  D++ + + +    Y        ++     R +   FV   +   A+ 
Sbjct: 3  SGSSGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQN 55

Query: 63 VI--MDKHMIDGRTVEAKKAVPR 83
           I    ++   G+ +  +     
Sbjct: 56 AIQMFHQYSFRGKDLIVQLQPTD 78

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.5 bits (94), Expect = 4e-05
 Identities = 13/104 (12%), Positives = 26/104 (25%), Gaps = 13/104 (12%)

Query: 7   KLFIGGI-----SWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAE 61
            L          S      + +  F  Y +       +            + F++P  A 
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAA 60

Query: 62  RVI--MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSSIHSSPGPG 103
                + K    G+ ++   A      +      +   S P  G
Sbjct: 61  DARLRLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKSGPSSG 104

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.7 bits (84), Expect = 8e-04
 Identities = 13/105 (12%), Positives = 26/105 (24%), Gaps = 18/105 (17%)

Query: 101 GPGRTKKIFVGGLASTVTES-----DFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYD 155
           G   +  +        V         F+  F  +   T           +      I + 
Sbjct: 1   GSSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF------KSFKRVRINFS 54

Query: 156 SEEAVDRVLHKT-FHELNGKMVEVKRAVPKEFS------PGPSRS 193
           +  +      +    E  GK +++  A            P P +S
Sbjct: 55  NPLSAADARLRLHKTEFLGKEMKLYFAQTLHIGSSHLAPPNPDKS 99

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.1 bits (93), Expect = 5e-05
 Identities = 20/98 (20%), Positives = 34/98 (34%), Gaps = 10/98 (10%)

Query: 98  SSPGPGRTK-KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
             P   R+  ++ V GL  + +  D K +  +            +   +  G G + Y  
Sbjct: 7   GGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREA-------GDVCYADVQKDGMGMVEYLR 59

Query: 157 EEAVDRVLHK-TFHELNGKMVEVKRA-VPKEFSPGPSR 192
           +E ++  L K    +      E     V  E S GPS 
Sbjct: 60  KEDMEYALRKLDDTKFRSHEGETSYIRVYPERSSGPSS 97

>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 = 39.8 bits (92), Expect = 7e-05
 Identities = 12/83 (14%), Positives = 28/83 (33%), Gaps = 9/83 (10%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          ++ + G+      + LK++    G+V  A + +D         G V +      E  +  
Sbjct: 17 RVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG-------MGMVEYLRKEDMEYALRK 69

Query: 65 MDKHMIDGRTVEAKKAVPRDDQN 87
          +D         E        +++
Sbjct: 70 LDDTKFRSHEGETSYIRVYPERS 92

>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 = 40.3 bits (93), Expect = 5e-05
 Identities = 14/98 (14%), Positives = 35/98 (35%), Gaps = 8/98 (8%)

Query: 98  SSPGPGRTK-KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDS 156
           SS   GR+K  I    L +    ++ ++ F +FG++  V++              + +  
Sbjct: 2   SSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG------ITAIVEFLE 55

Query: 157 EEAVDRVLHK-TFHELNGKMVEVKRAVPKEFSPGPSRS 193
                +      + + +   + ++ A    F   P + 
Sbjct: 56  PLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKK 93

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.5 bits (91), Expect = 8e-05
 Identities = 17/93 (18%), Positives = 32/93 (34%), Gaps = 13/93 (13%)

Query: 107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK 166
           ++ V GL  + +  D K +  +            +      G G + +  +E +   + K
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREA-------GDVCYADVYRDGTGVVEFVRKEDMTYAVRK 54

Query: 167 -TFHELNGKM-----VEVKRAVPKEFSPGPSRS 193
               +          + VK   P+  S G SRS
Sbjct: 55  LDNTKFRSHEGETAYIRVKVDGPRSPSYGRSRS 87

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.0 bits (82), Expect = 0.001
 Identities = 14/81 (17%), Positives = 26/81 (32%), Gaps = 9/81 (11%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          ++ + G+      + LK++    G+V  A + RD         G V F         +  
Sbjct: 2  RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-------TGVVEFVRKEDMTYAVRK 54

Query: 65 MDKHMIDGRTVEAKKAVPRDD 85
          +D         E      + D
Sbjct: 55 LDNTKFRSHEGETAYIRVKVD 75

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.0 bits (90), Expect = 2e-04
 Identities = 14/92 (15%), Positives = 29/92 (31%), Gaps = 10/92 (10%)

Query: 8   LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--- 64
           + + G+     E  L E   ++G +   ++M        +    V F +   A+  +   
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFA 71

Query: 65  -MDKHMIDGRTVEAKKAVPRDDQNMLNRNTSS 95
                 I G+      +  +      N   SS
Sbjct: 72  ADVPVYIAGQQAFFNYSTSKRITRPGNSGPSS 103

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.2 bits (88), Expect = 3e-04
 Identities = 16/108 (14%), Positives = 37/108 (34%), Gaps = 11/108 (10%)

Query: 90  NRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGF 149
           +  +S  H          + V GL  +V E+D  +  ++FGTI  V++M           
Sbjct: 2   SSGSSGSHHKVSVSPV--VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------Q 53

Query: 150 GFITYDSEEAVDRV---LHKTFHELNGKMVEVKRAVPKEFSPGPSRSS 194
             + +++ ++              + G+      +  K  +   +   
Sbjct: 54  ALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRITRPGNSGP 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 = 37.2 bits (85), Expect = 3e-04
 Identities = 11/75 (14%), Positives = 25/75 (33%), Gaps = 8/75 (10%)

Query: 108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT 167
           I + GL   VT  +       +        +      + +G  F+T  + E  +  ++  
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDY-------ELKYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 168 F-HELNGKMVEVKRA 181
               L  + + V+  
Sbjct: 54  HQSRLRERELSVQLQ 68

>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 = 37.1 bits (85), Expect = 5e-04
 Identities = 13/84 (15%), Positives = 32/84 (38%), Gaps = 9/84 (10%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
           ++ + +  L   VTE++       FG       + +    + +   F+   +EEA   ++
Sbjct: 8   SRVLHIRKLPGEVTETEVIALGLPFGK------VTNILMLKGKNQAFLELATEEAAITMV 61

Query: 165 ---HKTFHELNGKMVEVKRAVPKE 185
                    L  + + ++ +  KE
Sbjct: 62  NYYSAVTPHLRNQPIYIQYSNHKE 85

>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 = 36.6 bits (84), Expect = 7e-04
 Identities = 9/73 (12%), Positives = 22/73 (30%), Gaps = 11/73 (15%)

Query: 8  LFIGGI-SWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          + I           +L +    +G +   +I+            F+  A    A+  +  
Sbjct: 11 VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDY 64

Query: 65 --MDKHMIDGRTV 75
                ++ G+ V
Sbjct: 65 YTTTPALVFGKPV 77

>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 = 36.2 bits (83), Expect = 0.001
 Identities = 12/81 (14%), Positives = 26/81 (32%), Gaps = 10/81 (12%)

Query: 105 TKKIFVGGLA-STVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRV 163
            + + +              +  + FG I++ +++   N        FI   + E     
Sbjct: 8   RRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN------EAFIEMATTEDAQAA 61

Query: 164 L---HKTFHELNGKMVEVKRA 181
           +     T   + GK V V  +
Sbjct: 62  VDYYTTTPALVFGKPVRVHLS 82

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.6 bits (84), Expect = 8e-04
 Identities = 12/70 (17%), Positives = 26/70 (37%), Gaps = 8/70 (11%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-- 64
          +L++GG+  +T    L   F R+G +     ++         F ++ +     A+     
Sbjct: 19 RLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAK 72

Query: 65 MDKHMIDGRT 74
          M    + G  
Sbjct: 73 MRGFPLGGPD 82

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 16/73 (21%), Positives = 33/73 (45%), Gaps = 10/73 (13%)

Query: 105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVL 164
           T +++VGGL    + +   + FD+FG+I  +  +   +      F +I Y+S +A     
Sbjct: 17  TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYIQYESLDAAQAAC 70

Query: 165 HKTFHELNGKMVE 177
                ++ G  + 
Sbjct: 71  ----AKMRGFPLG 79

>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 = 34.4 bits (78), Expect = 0.004
 Identities = 14/79 (17%), Positives = 28/79 (35%), Gaps = 11/79 (13%)

Query: 7  KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIM- 65
           LF+  +  +T+E  L   F+++    E  ++ +R         FV F     +      
Sbjct: 10 ILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEA 64

Query: 66 --DKHMIDGRTVE---AKK 79
               +     ++   AKK
Sbjct: 65 LQGFKITPTHAMKITFAKK 83

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	522
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	100.0
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.81
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.8
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.8
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.8
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.79
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.78
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.78
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.78
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.78
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.77
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.77
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.77
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.77
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.77
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.77
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.77
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.77
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.77
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.77
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.77
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.76
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.76
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.76
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.76
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.76
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.76
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.76
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.76
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.76
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.76
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.75
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.75
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.75
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.75
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.75
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.75
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.75
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.75
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.75
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.75
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.75
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.74
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.74
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	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
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.73
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.73
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.73
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.73
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.73
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.73
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.72
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.72
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.72
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.72
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.72
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.72
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.72
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.72
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.72
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.72
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.71
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.71
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.71
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.71
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.71
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.71
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.71
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.7
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.7
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.7
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.69
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.69
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.69
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.69
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.68
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.68
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.68
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.68
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.68
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.67
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.66
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.66
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.66
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.66
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.66
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.66
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.66
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.66
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.66
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.65
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.65
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.65
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.65
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.64
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.64
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.64
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.63
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.63
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.63
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.63
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.63
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.63
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.62
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.62
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.62
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.62
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.62
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.61
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.61
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.61
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.6
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.6
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.6
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.59
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.59
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.59
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.59
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.59
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.59
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.58
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.58
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.58
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.58
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.58
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.58
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.58
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.58
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.58
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.58
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.58
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.57
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.57
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.57
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.57
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.56
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.56
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.56
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.56
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.55
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.55
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.55
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.55
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.55
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.55
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.52
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.52
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.52
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.5
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.49
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.49
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.47
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.47
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.44
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.44
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.38
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	99.34
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	99.34
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.25
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.24
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.22
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.21
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.2
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.2
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.19
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.11
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.08
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.06
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.14
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.08
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.68
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.66
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.48
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	95.29
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	93.77
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	91.64

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3.1e-32  Score=253.70  Aligned_cols=173  Identities=39%  Similarity=0.755  Sum_probs=155.7

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecCC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~~   82 (522)
                      +.|+|||+|||+++||++|+++|++||+|+++.|++++.++++++||||+|.++++|++|+ +....+..+.+.+.+..+
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhh
Confidence            3489999999999999999999999999999999999999999999999999999999999 777888899998887765


Q ss_pred             CccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHH
Q 009920           83 RDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDR  162 (522)
Q Consensus        83 k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~  162 (522)
                      +......          ......++|||+|||+.+|+++|+++|+.||.|+.+.|+.|+.+++++|||||+|.++++|++
T Consensus        85 ~~~~~~~----------~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~  154 (183)
T d1u1qa_          85 REDSQRP----------GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK  154 (183)
T ss_dssp             TTGGGST----------TTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHH
T ss_pred             ccccccc----------ccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHH
Confidence            5433221          123456799999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhcCCccCCeEEEEEEcCCCCC
Q 009920          163 VLHKTFHELNGKMVEVKRAVPKEF  186 (522)
Q Consensus       163 Al~~~~~~l~Gr~I~V~~a~pk~~  186 (522)
                      ||+++++.|+|++|+|++|.||++
T Consensus       155 Al~~~~~~~~G~~i~V~~A~~k~e  178 (183)
T d1u1qa_         155 IVIQKYHTVNGHNCEVRKALSKQE  178 (183)
T ss_dssp             HHTSSCEEETTEEEEEEECCCHHH
T ss_pred             HHHhCCCeECCEEEEEEecCCccc
Confidence            998766899999999999988754

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=6.8e-20  Score=151.76  Aligned_cols=84  Identities=38%  Similarity=0.721  Sum_probs=78.8

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHHHcccccCCeEEEEeecCC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl~~~~~i~Gr~I~V~~a~~   82 (522)
                      +..++|||+|||+++||++|+++|++||+|++|+|++|+.++++||||||+|.++++|++||.+.+.|+|+.|.|+++.+
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~~l~Gr~i~v~~a~~   85 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNS   85 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCEEETTEEEEEECCCT
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcCCccCCEEeEEEeCCC
Confidence            46789999999999999999999999999999999999999999999999999999999999777899999999999988


Q ss_pred             Cccc
Q 009920           83 RDDQ   86 (522)
Q Consensus        83 k~~~   86 (522)
                      ++.+
T Consensus        86 k~~~   89 (90)
T d2cqga1          86 KQSQ   89 (90)
T ss_dssp             TCCC
T ss_pred             CCCC
Confidence            7543

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=5.2e-20  Score=151.94  Aligned_cols=85  Identities=45%  Similarity=0.835  Sum_probs=81.4

Q ss_pred             CCCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEe
Q 009920            1 MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAK   78 (522)
Q Consensus         1 me~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~   78 (522)
                      |.++.++|||+|||+++|+++|+++|++||+|..|.+++++.+++++|||||+|.++++|++|+  ++++.|++++|.|+
T Consensus         1 m~~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~   80 (90)
T d1x5sa1           1 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   80 (90)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            8899999999999999999999999999999999999999999999999999999999999999  89999999999999


Q ss_pred             ecCCCcc
Q 009920           79 KAVPRDD   85 (522)
Q Consensus        79 ~a~~k~~   85 (522)
                      ++.++.+
T Consensus        81 ~a~~~~~   87 (90)
T d1x5sa1          81 QAGKSSD   87 (90)
T ss_dssp             EEECCCC
T ss_pred             EcCCCCC
Confidence            9977654

>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=99.80  E-value=4.2e-20  Score=152.45  Aligned_cols=84  Identities=30%  Similarity=0.499  Sum_probs=80.6

Q ss_pred             CCCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEe
Q 009920            1 MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAK   78 (522)
Q Consensus         1 me~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~   78 (522)
                      |....++|||+|||+++||++|+++|++||+|++|+|++++.++++||||||+|.++++|++|+  ++++.|++++|.|+
T Consensus         1 ma~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~   80 (89)
T d2cqba1           1 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   80 (89)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            7888999999999999999999999999999999999999999999999999999999999999  89999999999999


Q ss_pred             ecCCCc
Q 009920           79 KAVPRD   84 (522)
Q Consensus        79 ~a~~k~   84 (522)
                      ++.|+.
T Consensus        81 ~a~p~~   86 (89)
T d2cqba1          81 LAKPMR   86 (89)
T ss_dssp             ECCCCC
T ss_pred             EeCCCC
Confidence            998754

>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=99.80  E-value=3.8e-19  Score=158.37  Aligned_cols=91  Identities=23%  Similarity=0.500  Sum_probs=82.9

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVK  179 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~  179 (522)
                      .....++|||+|||+++||++|+++|++||+|++|+|++|+.|+++||||||+|.+.++|++||+.++ ++|+||+|+|+
T Consensus        38 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~  117 (139)
T d1u6fa1          38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34456789999999999999999999999999999999999999999999999999999999999887 89999999999


Q ss_pred             EcCCCCCCCCCC
Q 009920          180 RAVPKEFSPGPS  191 (522)
Q Consensus       180 ~a~pk~~~~~~~  191 (522)
                      +++++..++...
T Consensus       118 ~a~~~~~~p~~~  129 (139)
T d1u6fa1         118 LAASGHQRPGIA  129 (139)
T ss_dssp             ESSCCCCCCCSS
T ss_pred             EcCCCCCCCCCC
Confidence            999877654333

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=2.9e-19  Score=151.38  Aligned_cols=84  Identities=33%  Similarity=0.589  Sum_probs=79.1

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcC
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAV  182 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~  182 (522)
                      ...++|||+|||+++||+||+++|++||+|++|+|++|+.|+++||||||+|+++++|++||+.+++.|+||+|+|+++.
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            45578999999999999999999999999999999999999999999999999999999999999989999999999998


Q ss_pred             CCCC
Q 009920          183 PKEF  186 (522)
Q Consensus       183 pk~~  186 (522)
                      ++..
T Consensus        88 ~~~~   91 (103)
T d2cqda1          88 LGAK   91 (103)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            7643

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=2.3e-19  Score=146.51  Aligned_cols=79  Identities=44%  Similarity=0.825  Sum_probs=75.4

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      ++.++|||+|||+++||++|+++|++||+|.+++|++|+.++++||||||+|.++++|++|| ++.+.|+|++|+|+.|.
T Consensus         4 e~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            35589999999999999999999999999999999999999999999999999999999999 88899999999999875

>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=99.78  E-value=1.8e-19  Score=145.91  Aligned_cols=78  Identities=24%  Similarity=0.409  Sum_probs=75.3

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCC
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~   82 (522)
                      +++|||+|||+++||++|+++|++||+|++|+|++++.++++|+||||+|.++++|++||  +++..|.+++|.|++|+|
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            578999999999999999999999999999999999999999999999999999999999  899999999999999875

>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=99.78  E-value=3.8e-19  Score=147.88  Aligned_cols=84  Identities=25%  Similarity=0.417  Sum_probs=79.1

Q ss_pred             CCCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEe
Q 009920            1 MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAK   78 (522)
Q Consensus         1 me~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~   78 (522)
                      |.+++++|||+|||+++||++|+++|++||+|++|+|++++.++++||||||+|.++++|++|+  +++..|++++|.|+
T Consensus         3 ~~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~   82 (93)
T d1h2vz_           3 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD   82 (93)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEE
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3468899999999999999999999999999999999999999999999999999999999999  89999999999999


Q ss_pred             ecCCCc
Q 009920           79 KAVPRD   84 (522)
Q Consensus        79 ~a~~k~   84 (522)
                      ++....
T Consensus        83 ~a~~~~   88 (93)
T d1h2vz_          83 WDAGFK   88 (93)
T ss_dssp             EESCCC
T ss_pred             EcCCCC
Confidence            986543

>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=99.78  E-value=3.3e-19  Score=149.83  Aligned_cols=83  Identities=30%  Similarity=0.543  Sum_probs=78.8

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++||++|+++|++||+|++|+|++++.++++||||||+|.++++|++||  ++++.|++++|.|+++
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            56789999999999999999999999999999999999999999999999999999999999  8999999999999999


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      .++.+
T Consensus        86 ~~~~~   90 (99)
T d1whwa_          86 TIKKE   90 (99)
T ss_dssp             CCCST
T ss_pred             CCCCc
Confidence            87654

>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=99.78  E-value=6e-19  Score=148.18  Aligned_cols=85  Identities=25%  Similarity=0.467  Sum_probs=80.1

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ...++|||+|||+++|++||+++|++||+|++|+|++|+.+++++|||||+|+++++|++||+.++ ..|++|+|+|+++
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            457789999999999999999999999999999999999999999999999999999999999888 8999999999999


Q ss_pred             CCCCCC
Q 009920          182 VPKEFS  187 (522)
Q Consensus       182 ~pk~~~  187 (522)
                      ++++..
T Consensus        86 ~~~~~~   91 (99)
T d1whwa_          86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCCcc
Confidence            987653

>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=99.78  E-value=6e-20  Score=147.64  Aligned_cols=75  Identities=49%  Similarity=0.946  Sum_probs=72.9

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeec
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a   80 (522)
                      |+|||+|||+++||++|+++|++||+|++++|++|+.|+++||||||+|.++++|++|| ++.+.|+||+|+|+.|
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            68999999999999999999999999999999999999999999999999999999999 9999999999999876

>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=99.77  E-value=5.9e-19  Score=144.04  Aligned_cols=80  Identities=46%  Similarity=0.831  Sum_probs=76.4

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcC
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAV  182 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~  182 (522)
                      ...++|||+|||+++|+++|+++|++||+|++++|++|+.++++||||||+|.++++|++||+++++.|+||+|+|+.|.
T Consensus         4 e~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            35679999999999999999999999999999999999999999999999999999999999987799999999999986

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=7.9e-19  Score=145.23  Aligned_cols=83  Identities=31%  Similarity=0.543  Sum_probs=77.6

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcC
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAV  182 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~  182 (522)
                      ...++|||+|||+++||++|+++|++||+|++|+|++|+.++++||||||+|.++++|++||+.+ +.|+||+|.|+++.
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 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR-HMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC-EEETTEEEEEECCC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC-CccCCEEeEEEeCC
Confidence            45678999999999999999999999999999999999999999999999999999999999854 58999999999999


Q ss_pred             CCCC
Q 009920          183 PKEF  186 (522)
Q Consensus       183 pk~~  186 (522)
                      +++.
T Consensus        85 ~k~~   88 (90)
T d2cqga1          85 SKQS   88 (90)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            8764

>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=99.77  E-value=6.3e-19  Score=149.32  Aligned_cols=84  Identities=38%  Similarity=0.760  Sum_probs=76.5

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeec
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a   80 (522)
                      |.+.++|||+|||+++||++|+++|++||+|++|+|++++.|+++||||||+|.++++|++|| ..++.|++++|.|+++
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l~V~~a   86 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLA   86 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEES
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEc
Confidence            345678999999999999999999999999999999999999999999999999999999999 4456899999999998


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      ..+..
T Consensus        87 ~~~~~   91 (103)
T d2cqda1          87 YLGAK   91 (103)
T ss_dssp             TTTCC
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=99.77  E-value=2.7e-19  Score=146.38  Aligned_cols=79  Identities=24%  Similarity=0.522  Sum_probs=75.8

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCCC
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVPR   83 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~k   83 (522)
                      ++|||+|||+++||++|+++|++||+|++|+|++|+.|+++|+||||+|.++++|++|+  ++++.|.+++|.|++|.+.
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            68999999999999999999999999999999999999999999999999999999999  8999999999999999765


Q ss_pred             c
Q 009920           84 D   84 (522)
Q Consensus        84 ~   84 (522)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=4.1e-19  Score=147.68  Aligned_cols=83  Identities=30%  Similarity=0.522  Sum_probs=78.4

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++|+++|+++|++||+|++|+|++++.++++||||||+|.+.++|++||  ++++.|++++|+|++|
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            34689999999999999999999999999999999999999999999999999999999999  8999999999999999


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      .++..
T Consensus        87 ~~~~~   91 (93)
T d1x5ua1          87 SAHNK   91 (93)
T ss_dssp             TTTSC
T ss_pred             CCCCC
Confidence            87653

>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=99.77  E-value=5.6e-19  Score=145.31  Aligned_cols=81  Identities=23%  Similarity=0.384  Sum_probs=76.7

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++|+++|+++|++||+|++|+|++++.++++||||||+|.+.++|++|+  +++..|++++|.|++|
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            45789999999999999999999999999999999999999999999999999999999999  8999999999999999


Q ss_pred             CCC
Q 009920           81 VPR   83 (522)
Q Consensus        81 ~~k   83 (522)
                      .++
T Consensus        85 ~~k   87 (88)
T d1rk8a_          85 FVK   87 (88)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            765

>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=99.77  E-value=8.7e-19  Score=141.76  Aligned_cols=78  Identities=27%  Similarity=0.548  Sum_probs=74.9

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCC
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~   82 (522)
                      .++|||+|||++++|++|+++|++||+|++|+|++++.+++++|||||+|.++++|++|+  ++++.|++++|.|++|+|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            467999999999999999999999999999999999999999999999999999999999  899999999999999876

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=1.1e-18  Score=147.46  Aligned_cols=85  Identities=21%  Similarity=0.380  Sum_probs=80.1

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      .+.++|||+|||+++|++||+++|++||.|+++.++.++.++++||||||+|.++++|++||+.++ ..|.+++|+|+++
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            345789999999999999999999999999999999999999999999999999999999998877 8999999999999


Q ss_pred             CCCCCC
Q 009920          182 VPKEFS  187 (522)
Q Consensus       182 ~pk~~~  187 (522)
                      +++.++
T Consensus        96 ~~k~~~  101 (102)
T d2cpza1          96 RSKNDS  101 (102)
T ss_dssp             CCSCCC
T ss_pred             CCCCCC
Confidence            998764

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=3.2e-19  Score=142.48  Aligned_cols=74  Identities=46%  Similarity=0.999  Sum_probs=71.3

Q ss_pred             EEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeec
Q 009920            7 KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         7 ~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a   80 (522)
                      +|||+|||+++||++|+++|++||+|.+|+|++++.++++||||||+|.++++|++|| ++.+.|+|++|+|++|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeEC
Confidence            6999999999999999999999999999999999999999999999999999999999 8889999999999765

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=7.9e-19  Score=144.96  Aligned_cols=83  Identities=24%  Similarity=0.464  Sum_probs=79.4

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ++.++|||+|||.++|+++|+++|++||+|++|.|++|+.++++||||||+|.+.++|++||+.++ ..|.+++|+|++|
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            467899999999999999999999999999999999999999999999999999999999999988 8999999999999


Q ss_pred             CCCC
Q 009920          182 VPKE  185 (522)
Q Consensus       182 ~pk~  185 (522)
                      +|+.
T Consensus        86 kp~~   89 (90)
T d2cq0a1          86 KPST   89 (90)
T ss_dssp             SCCC
T ss_pred             eCCC
Confidence            9875

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=5.3e-19  Score=146.03  Aligned_cols=82  Identities=27%  Similarity=0.459  Sum_probs=78.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||.++||++|+++|++||+|.+|+|++++.++++||||||+|.++++|++||  +++..|++++|.|++|
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            46789999999999999999999999999999999999999999999999999999999999  8999999999999999


Q ss_pred             CCCc
Q 009920           81 VPRD   84 (522)
Q Consensus        81 ~~k~   84 (522)
                      .|+.
T Consensus        86 kp~~   89 (90)
T d2cq0a1          86 KPST   89 (90)
T ss_dssp             SCCC
T ss_pred             eCCC
Confidence            8764

>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=7.8e-19  Score=146.00  Aligned_cols=84  Identities=27%  Similarity=0.434  Sum_probs=79.5

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      .+.++|||+|||.++|++||+++|++||+|++|+|++|+.++++||||||+|.++++|++||+.++ ..|+|++|+|++|
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            345799999999999999999999999999999999999999999999999999999999999888 8999999999999


Q ss_pred             CCCCC
Q 009920          182 VPKEF  186 (522)
Q Consensus       182 ~pk~~  186 (522)
                      +++.+
T Consensus        87 ~~~~~   91 (93)
T d1x5ua1          87 SAHNK   91 (93)
T ss_dssp             TTTSC
T ss_pred             CCCCC
Confidence            98764

>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=99.76  E-value=1.1e-18  Score=143.56  Aligned_cols=82  Identities=17%  Similarity=0.341  Sum_probs=77.5

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      .+..+|||+|||.++|+++|+++|++||+|++|+|++|+.++++||||||+|.++++|++|++.++ ..|+|++|+|++|
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            456799999999999999999999999999999999999999999999999999999999999877 8999999999999


Q ss_pred             CCC
Q 009920          182 VPK  184 (522)
Q Consensus       182 ~pk  184 (522)
                      .+|
T Consensus        85 ~~k   87 (88)
T d1rk8a_          85 FVK   87 (88)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            876

>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=99.76  E-value=7e-19  Score=142.44  Aligned_cols=79  Identities=23%  Similarity=0.379  Sum_probs=75.6

Q ss_pred             cceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCC
Q 009920          105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVP  183 (522)
Q Consensus       105 ~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~p  183 (522)
                      .++|||+|||+++|+++|+++|++||+|++++|++|+.+++++|||||+|.++++|++||+.++ ..|.+++|+|++|+|
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            3579999999999999999999999999999999999999999999999999999999999877 899999999999976

>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=99.76  E-value=4.1e-19  Score=150.63  Aligned_cols=84  Identities=43%  Similarity=0.792  Sum_probs=79.2

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcCC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVP  183 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~p  183 (522)
                      ..++|||+|||+++|+++|+++|++||+|+++.|++|+.++++||||||+|.+.++|++||+++++.|+|++|+|++|.|
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECcc
Confidence            34789999999999999999999999999999999999999999999999999999999998777899999999999999


Q ss_pred             CCCC
Q 009920          184 KEFS  187 (522)
Q Consensus       184 k~~~  187 (522)
                      ++++
T Consensus        99 ke~~  102 (103)
T d1x4ba1          99 REES  102 (103)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8763

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=2.5e-19  Score=143.26  Aligned_cols=74  Identities=35%  Similarity=0.635  Sum_probs=71.2

Q ss_pred             EEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeec
Q 009920            7 KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         7 ~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a   80 (522)
                      +|||+|||+++||++|+++|++||+|++|+|++++.++++||||||+|.++++|++|| ++.+.|+++.|+|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEEC
Confidence            6999999999999999999999999999999999999999999999999999999999 7788999999999875

>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=99.76  E-value=6e-19  Score=145.39  Aligned_cols=83  Identities=30%  Similarity=0.558  Sum_probs=78.6

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      ..++|||+|||+++|+++|+++|++||+|++|.|+.|+.++++||||||+|.++++|++|++.++ ..|+|++|+|++|+
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            45799999999999999999999999999999999999999999999999999999999999877 89999999999998


Q ss_pred             CCCC
Q 009920          183 PKEF  186 (522)
Q Consensus       183 pk~~  186 (522)
                      |++.
T Consensus        84 p~~~   87 (89)
T d2cqba1          84 PMRI   87 (89)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8754

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=2.4e-18  Score=142.97  Aligned_cols=84  Identities=18%  Similarity=0.345  Sum_probs=78.8

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ..+++|||+|||+++|+++|+++|++||+|++|.|++++.+++++|||||+|.++++|++||+.++ ..|+|++|+|+++
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            467899999999999999999999999999999999999999999999999999999999999888 8999999999998


Q ss_pred             CCCCC
Q 009920          182 VPKEF  186 (522)
Q Consensus       182 ~pk~~  186 (522)
                      .+...
T Consensus        85 ~~~~~   89 (93)
T d1h2vz_          85 AGFKE   89 (93)
T ss_dssp             SCCCT
T ss_pred             CCCCC
Confidence            75543

>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=99.76  E-value=7.5e-19  Score=149.02  Aligned_cols=81  Identities=47%  Similarity=0.902  Sum_probs=77.6

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecCCC
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAVPR   83 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~~k   83 (522)
                      .++|||+|||+++|+++|+++|++||+|+++.|++++.++++||||||+|.+.++|++|| ++.+.|+|++|.|++|.++
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            489999999999999999999999999999999999999999999999999999999999 9999999999999999887


Q ss_pred             cc
Q 009920           84 DD   85 (522)
Q Consensus        84 ~~   85 (522)
                      ++
T Consensus       100 e~  101 (103)
T d1x4ba1         100 EE  101 (103)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.76  E-value=1.2e-18  Score=139.98  Aligned_cols=77  Identities=39%  Similarity=0.824  Sum_probs=74.0

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      .++|||+|||+++||++|+++|++||+|..++++.++.+++++|||||+|.++|+|++|+ ++.+.|+||+|+|++|.
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V~~A~   79 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKAL   79 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEECC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            589999999999999999999999999999999999999999999999999999999999 99999999999999873

>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=99.76  E-value=2.1e-19  Score=152.26  Aligned_cols=85  Identities=29%  Similarity=0.630  Sum_probs=79.4

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      |++.++|||+|||+++||++|+++|++||+|.+|+|++++.++++||||||+|.++++|++||  ++++.|.+++|.|++
T Consensus         5 ~~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~   84 (104)
T d1p1ta_           5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN   84 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            456789999999999999999999999999999999999999999999999999999999999  799999999999999


Q ss_pred             cCCCccc
Q 009920           80 AVPRDDQ   86 (522)
Q Consensus        80 a~~k~~~   86 (522)
                      +.++...
T Consensus        85 a~~~~~~   91 (104)
T d1p1ta_          85 AASEKNK   91 (104)
T ss_dssp             TTCTTHH
T ss_pred             CCCCCCc
Confidence            8776543

>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=99.75  E-value=1.1e-18  Score=147.43  Aligned_cols=83  Identities=25%  Similarity=0.470  Sum_probs=78.7

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      +.++|||+|||+++||++|+++|++||+|++++++.++.++++||||||+|.++++|++||  ++++.|.+++|.|+++.
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            5678999999999999999999999999999999999999999999999999999999999  99999999999999998


Q ss_pred             CCccc
Q 009920           82 PRDDQ   86 (522)
Q Consensus        82 ~k~~~   86 (522)
                      ++.+.
T Consensus        97 ~k~~~  101 (102)
T d2cpza1          97 SKNDS  101 (102)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            87653

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=2e-18  Score=139.60  Aligned_cols=78  Identities=23%  Similarity=0.465  Sum_probs=75.0

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCC
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVP  183 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~p  183 (522)
                      ++|||+|||.+++|++|+++|++||+|++|+|++|+.+++++|||||+|.++++|++|++.++ +.|.|++|+|++|+|
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            479999999999999999999999999999999999999999999999999999999999877 899999999999986

>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=99.75  E-value=4.2e-19  Score=142.64  Aligned_cols=76  Identities=42%  Similarity=0.784  Sum_probs=73.1

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEc
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRA  181 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a  181 (522)
                      ++|||+|||+++||++|+++|++||+|++++|++|+.++++||||||+|.++++|++||+++.+.|+||+|+|++|
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            5899999999999999999999999999999999999999999999999999999999997669999999999987

>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=99.75  E-value=1.8e-18  Score=139.70  Aligned_cols=75  Identities=33%  Similarity=0.530  Sum_probs=72.9

Q ss_pred             EEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            7 KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         7 ~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      .|||+|||+++||++|+++|++||+|.+|+|++++.+++++|||||+|.++++|++|+  +++..|.+++|+|.+++
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  89999999999999885

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=4.2e-19  Score=141.96  Aligned_cols=75  Identities=37%  Similarity=0.741  Sum_probs=72.5

Q ss_pred             eeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEc
Q 009920          107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRA  181 (522)
Q Consensus       107 ~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a  181 (522)
                      +|||+|||+++|+++|+++|++||+|++|+|++|+.++++||||||+|.++++|++||+.++++|+|+.|+|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEEC
Confidence            699999999999999999999999999999999999999999999999999999999998889999999999875

>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=99.75  E-value=2e-18  Score=140.94  Aligned_cols=78  Identities=26%  Similarity=0.559  Sum_probs=73.5

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCC--eEEEEe
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDG--RTVEAK   78 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~G--r~I~V~   78 (522)
                      .+.++|||+|||++++|++|+++|++||+|++|+|++++.++++||||||+|.++++|++||  +++..+.+  ++|.|+
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            46788999999999999999999999999999999999999999999999999999999999  88888876  889998


Q ss_pred             ec
Q 009920           79 KA   80 (522)
Q Consensus        79 ~a   80 (522)
                      +|
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            76

>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=99.75  E-value=1.3e-18  Score=142.18  Aligned_cols=81  Identities=23%  Similarity=0.427  Sum_probs=77.2

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCC
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPK  184 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk  184 (522)
                      ++|||+|||+++||++|+++|++||+|++|+|++|+.|+++||||||+|.++++|++|++.++ +.|.|++|+|++|.+.
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            479999999999999999999999999999999999999999999999999999999999887 8999999999999876


Q ss_pred             CC
Q 009920          185 EF  186 (522)
Q Consensus       185 ~~  186 (522)
                      .+
T Consensus        82 ~~   83 (85)
T d2u2fa_          82 AK   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.75  E-value=1.9e-18  Score=143.94  Aligned_cols=84  Identities=24%  Similarity=0.460  Sum_probs=77.1

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCC-CCCcccEEEEEecCHHHHHHHH--H-cccccCCeEEEE
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRA-TGRARGFGFVVFADPAVAERVI--M-DKHMIDGRTVEA   77 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~-tg~srG~aFVeF~~~e~A~kAl--~-~~~~i~Gr~I~V   77 (522)
                      +.+.++|||+|||++++|++|+++|++||+|.+|+|++++. ++++||||||+|.++++|++||  + +...|+|++|.|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            35778999999999999999999999999999999998854 7899999999999999999999  5 788999999999


Q ss_pred             eecCCCcc
Q 009920           78 KKAVPRDD   85 (522)
Q Consensus        78 ~~a~~k~~   85 (522)
                      ++|.++..
T Consensus        85 ~~A~~~~~   92 (94)
T d2cpha1          85 EWADSEVT   92 (94)
T ss_dssp             EECCCCCC
T ss_pred             EEcCCCCC
Confidence            99987654

>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=99.75  E-value=9.9e-19  Score=139.56  Aligned_cols=75  Identities=44%  Similarity=0.849  Sum_probs=71.8

Q ss_pred             eeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEc
Q 009920          107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRA  181 (522)
Q Consensus       107 ~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a  181 (522)
                      +|||+|||+++||++|+++|++||+|+++.|++|+.++++||||||+|.++++|++||+++++.|+|++|+|++|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeEC
Confidence            599999999999999999999999999999999999999999999999999999999997679999999999765

>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=99.75  E-value=2.8e-19  Score=151.14  Aligned_cols=80  Identities=20%  Similarity=0.370  Sum_probs=76.3

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecCC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~~   82 (522)
                      +.++|||+|||+++||++|+++|++||+|.+|+|++++.++++||||||+|.++++|++|+ ++++.|+|++|.|+++.+
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            4689999999999999999999999999999999999999999999999999999999999 999999999999998765


Q ss_pred             C
Q 009920           83 R   83 (522)
Q Consensus        83 k   83 (522)
                      +
T Consensus        97 ~   97 (101)
T d2cq4a1          97 E   97 (101)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=99.75  E-value=2.5e-18  Score=140.43  Aligned_cols=78  Identities=28%  Similarity=0.548  Sum_probs=72.8

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCC--eEEEEe
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDG--RTVEAK   78 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~G--r~I~V~   78 (522)
                      .+.++|||+|||+++||++|+++|++||+|++|+|++++.++++|+||||+|.++++|++|+  +|+..++|  ++|.|+
T Consensus         4 ~k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           4 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK   83 (85)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEE
Confidence            45789999999999999999999999999999999999999999999999999999999999  89999987  558887


Q ss_pred             ec
Q 009920           79 KA   80 (522)
Q Consensus        79 ~a   80 (522)
                      +|
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.74  E-value=3.1e-18  Score=152.43  Aligned_cols=82  Identities=29%  Similarity=0.494  Sum_probs=77.5

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      ..++|||+|||+++||++|+++|++||+|++|+|++++.|+++||||||+|.+.++|++||  +++++|++++|+|+++.
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            4578999999999999999999999999999999999999999999999999999999999  79999999999999997


Q ss_pred             CCcc
Q 009920           82 PRDD   85 (522)
Q Consensus        82 ~k~~   85 (522)
                      ++..
T Consensus       121 ~~~~  124 (139)
T d1u6fa1         121 SGHQ  124 (139)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6654

>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=99.74  E-value=2.5e-18  Score=141.71  Aligned_cols=84  Identities=31%  Similarity=0.615  Sum_probs=79.1

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      +.++|||+|||+++|++||+++|++||+|+++.++.++.+++++|||||+|.++++|++||+.++ +.|.|++|+|++|.
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            56789999999999999999999999999999999999999999999999999999999998877 89999999999998


Q ss_pred             CCCCC
Q 009920          183 PKEFS  187 (522)
Q Consensus       183 pk~~~  187 (522)
                      ++...
T Consensus        84 ~~~~~   88 (90)
T d1x5sa1          84 KSSDN   88 (90)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.74  E-value=1.6e-18  Score=140.02  Aligned_cols=78  Identities=13%  Similarity=0.227  Sum_probs=68.3

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCC
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~   82 (522)
                      +++|||+|||+++|+++|+++|++||+|..+++++++.++++||||||+|.++++|++|+  ++++.|++++|.|+++.|
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            479999999999999999999999999999999988888999999999999999999999  899999999999999876

>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=139.10  Aligned_cols=74  Identities=32%  Similarity=0.506  Sum_probs=71.4

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEE
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEA   77 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V   77 (522)
                      ..++|||+|||+++||++|+++|++||+|++|+|++++.+++++|||||+|.++++|++||  ++++.|++++|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            4689999999999999999999999999999999999999999999999999999999999  8999999999987

>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=4.9e-18  Score=137.04  Aligned_cols=76  Identities=25%  Similarity=0.440  Sum_probs=73.7

Q ss_pred             eeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       107 ~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      .|||+|||+++||++|+++|++||+|++|+|++|+.+++++|||||+|.++++|++|++.++ ..|.||+|+|++++
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            69999999999999999999999999999999999999999999999999999999999888 89999999999985

>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=99.73  E-value=5.1e-18  Score=137.74  Aligned_cols=76  Identities=29%  Similarity=0.577  Sum_probs=72.6

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEV  178 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V  178 (522)
                      .+.++|||+|||+++||++|+++|++||+|++|+|++|+.+++++|||||+|.++++|++||++++ .+|+||+|+|
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            467899999999999999999999999999999999999999999999999999999999999877 8999999987

>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=99.73  E-value=7.1e-18  Score=135.41  Aligned_cols=78  Identities=37%  Similarity=0.823  Sum_probs=74.1

Q ss_pred             cceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcC
Q 009920          105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAV  182 (522)
Q Consensus       105 ~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~  182 (522)
                      .++|||+|||+++|+++|+++|++||+|+.+.++.++.+++++|||||+|.+++++++|++++.+.|+||+|+|++|.
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V~~A~   79 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKAL   79 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEECC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            479999999999999999999999999999999999999999999999999999999999876699999999999873

>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=99.73  E-value=6.8e-18  Score=140.50  Aligned_cols=85  Identities=20%  Similarity=0.388  Sum_probs=77.7

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecC-CCCCcceEEEEEecCHHHHHHHHHhc-C-CccCCeEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDH-NTQRPRGFGFITYDSEEAVDRVLHKT-F-HELNGKMVEV  178 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~-~tg~~rG~aFVeF~s~e~A~~Al~~~-~-~~l~Gr~I~V  178 (522)
                      ...+++|||+|||++++|++|+++|++||.|++|+|+++. .++++||||||+|.++++|++||+.+ + ..|+|++|.|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            3467889999999999999999999999999999999885 47899999999999999999999986 5 7899999999


Q ss_pred             EEcCCCCC
Q 009920          179 KRAVPKEF  186 (522)
Q Consensus       179 ~~a~pk~~  186 (522)
                      ++|+++..
T Consensus        85 ~~A~~~~~   92 (94)
T d2cpha1          85 EWADSEVT   92 (94)
T ss_dssp             EECCCCCC
T ss_pred             EEcCCCCC
Confidence            99987754

>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=99.73  E-value=8e-18  Score=138.79  Aligned_cols=81  Identities=21%  Similarity=0.357  Sum_probs=74.4

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||.++||++|+++|++||+|++|+|++++.+  .++||||+|.+.++|++|+  ++++.|.++.|+|.++
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            46799999999999999999999999999999999998764  4899999999999999999  8999999999999999


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      .++..
T Consensus        84 ~~~~~   88 (90)
T d2cqia1          84 TTPSS   88 (90)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            76543

>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=99.73  E-value=2.8e-18  Score=139.21  Aligned_cols=78  Identities=31%  Similarity=0.600  Sum_probs=73.0

Q ss_pred             EEECCCCCCCCHHHHHHHHhccCCeEEE-EEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCCCc
Q 009920            8 LFIGGISWDTDEERLKEYFSRYGEVVEA-VIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVPRD   84 (522)
Q Consensus         8 LfVgnLP~~~teedL~e~F~~~G~V~~v-~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~k~   84 (522)
                      |||+|||+++||++|+++|++||+|.++ +|++++.+++++|||||+|.++++|++||  ++++.|++++|.|+++.+++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            8999999999999999999999999765 78999999999999999999999999999  89999999999999998765


Q ss_pred             c
Q 009920           85 D   85 (522)
Q Consensus        85 ~   85 (522)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            3

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=9.7e-18  Score=139.21  Aligned_cols=81  Identities=26%  Similarity=0.568  Sum_probs=75.3

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++|+++|+++|++||+|++|+|++++.  .+|+||||+|.++++|++||  +++.+|++++|.|++|
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            5678999999999999999999999999999999999864  47999999999999999999  8999999999999999


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      .++..
T Consensus        87 ~~r~~   91 (93)
T d2cq3a1          87 TARVM   91 (93)
T ss_dssp             CSSCC
T ss_pred             CcCCC
Confidence            88654

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.72  E-value=6.8e-18  Score=137.69  Aligned_cols=79  Identities=24%  Similarity=0.482  Sum_probs=73.6

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCC--eEEEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNG--KMVEVK  179 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~G--r~I~V~  179 (522)
                      .+.++|||+|||++++|++|+++|++||+|++++|++|+.++++||||||+|.++++|++||+.++ ..+.+  ++|+|+
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            345679999999999999999999999999999999999999999999999999999999999887 77776  889999


Q ss_pred             Ec
Q 009920          180 RA  181 (522)
Q Consensus       180 ~a  181 (522)
                      +|
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=5.6e-18  Score=136.07  Aligned_cols=75  Identities=25%  Similarity=0.496  Sum_probs=71.4

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      .+|||+|||+++||++|+++|++||+|++|+|++++ +++++|||||+|.++++|++|+  +|++.+++++|+|+++.
T Consensus         1 grl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           1 GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            379999999999999999999999999999999987 6999999999999999999999  89999999999999875

>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=99.72  E-value=5.4e-18  Score=138.11  Aligned_cols=76  Identities=30%  Similarity=0.610  Sum_probs=70.8

Q ss_pred             EEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCC---CcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCC
Q 009920            8 LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATG---RARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         8 LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg---~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~   82 (522)
                      |||+|||+++|+++|+++|++||+|++|+|++++.+.   ++||||||+|.++++|++|+  ++++.|++++|.|+++.+
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            8999999999999999999999999999999987665   57999999999999999999  799999999999999864


Q ss_pred             C
Q 009920           83 R   83 (522)
Q Consensus        83 k   83 (522)
                      +
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
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=99.72  E-value=5.3e-18  Score=137.58  Aligned_cols=79  Identities=28%  Similarity=0.468  Sum_probs=74.2

Q ss_pred             eEecCCCCCCCHHHHHHHHhhcCCeeEE-EEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCCC
Q 009920          108 IFVGGLASTVTESDFKKYFDQFGTITDV-VVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPKE  185 (522)
Q Consensus       108 LfVgnLp~~vteedL~~~F~~fG~I~~v-~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk~  185 (522)
                      |||+|||+++||+||+++|++||.|.++ .|++++.+++++|||||+|.++++|++||+.++ ..|+|++|+|++|.+++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            7999999999999999999999999765 789999999999999999999999999999888 89999999999999875


Q ss_pred             C
Q 009920          186 F  186 (522)
Q Consensus       186 ~  186 (522)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=9.2e-18  Score=137.03  Aligned_cols=78  Identities=28%  Similarity=0.543  Sum_probs=72.7

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCC--eEEEEEE
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNG--KMVEVKR  180 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~G--r~I~V~~  180 (522)
                      +.++|||+|||+++|+++|+++|++||+|++++|++|+.++++||||||+|.++++|++|++.++ ..+.|  ++|+|++
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            45689999999999999999999999999999999999999999999999999999999999887 88887  5699988


Q ss_pred             c
Q 009920          181 A  181 (522)
Q Consensus       181 a  181 (522)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.72  E-value=9.8e-18  Score=136.57  Aligned_cols=78  Identities=26%  Similarity=0.496  Sum_probs=72.3

Q ss_pred             eEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCC---CcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCC
Q 009920          108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQ---RPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVP  183 (522)
Q Consensus       108 LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg---~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~p  183 (522)
                      |||+|||+++|+++|+++|++||+|++|+|++++.+.   ++||||||+|+++++|++|++.++ +.|+|++|+|+++++
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            7999999999999999999999999999999988765   468999999999999999999888 899999999999875


Q ss_pred             CC
Q 009920          184 KE  185 (522)
Q Consensus       184 k~  185 (522)
                      +.
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            44

>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=99.72  E-value=2e-17  Score=136.41  Aligned_cols=82  Identities=22%  Similarity=0.395  Sum_probs=75.2

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      .+.++|||+|||.++||++|+++|++||+|++|+|+.|+.+.  ++||||+|.+.++|++|++.++ ..|.|++|+|.+|
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            456799999999999999999999999999999999987754  7899999999999999999877 7999999999999


Q ss_pred             CCCCC
Q 009920          182 VPKEF  186 (522)
Q Consensus       182 ~pk~~  186 (522)
                      +++..
T Consensus        84 ~~~~~   88 (90)
T d2cqia1          84 TTPSS   88 (90)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            87654

>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=99.72  E-value=6.4e-18  Score=136.45  Aligned_cols=78  Identities=13%  Similarity=0.257  Sum_probs=68.5

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCC
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVP  183 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~p  183 (522)
                      ++|||+|||+++|+++|+++|++||+|+.+.++.++.+++++|||||+|.++++|++|++.++ ..|+|++|+|++++|
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            689999999999999999999999999999999988889999999999999999999999887 899999999999987

>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=99.72  E-value=2.4e-17  Score=136.84  Aligned_cols=82  Identities=27%  Similarity=0.613  Sum_probs=75.6

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ...++|||+|||+++++++|+++|++||+|++|+|+.++.+  ++|||||+|.++++|++||+.++ .+|+|++|+|++|
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~--~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT--TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC--CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            45678999999999999999999999999999999988754  68999999999999999999877 8999999999999


Q ss_pred             CCCCC
Q 009920          182 VPKEF  186 (522)
Q Consensus       182 ~pk~~  186 (522)
                      ++|..
T Consensus        87 ~~r~~   91 (93)
T d2cq3a1          87 TARVM   91 (93)
T ss_dssp             CSSCC
T ss_pred             CcCCC
Confidence            98754

>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=99.72  E-value=3.7e-18  Score=135.57  Aligned_cols=74  Identities=45%  Similarity=0.815  Sum_probs=71.6

Q ss_pred             EEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeec
Q 009920            7 KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         7 ~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a   80 (522)
                      +|||+|||+++||++|+++|++||+|+.+.+++++.++++++||||+|.++++|++|+ ++++.|++++|+|++|
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            6999999999999999999999999999999999999999999999999999999999 9999999999999875

>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=99.71  E-value=4e-18  Score=143.94  Aligned_cols=82  Identities=21%  Similarity=0.432  Sum_probs=76.4

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcCC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVP  183 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~p  183 (522)
                      +.++|||+|||+++|+++|+++|++||+|++|+|++|+.++++||||||+|.++++|++||+++...|.|++|+|+++.+
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            35689999999999999999999999999999999999999999999999999999999997655899999999999876


Q ss_pred             CC
Q 009920          184 KE  185 (522)
Q Consensus       184 k~  185 (522)
                      ++
T Consensus        97 ~~   98 (101)
T d2cq4a1          97 EK   98 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            53

>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=99.71  E-value=5e-18  Score=138.95  Aligned_cols=81  Identities=21%  Similarity=0.352  Sum_probs=71.5

Q ss_pred             CCCcEEEECCCCCCCC-HHHHHHHHhccCCeEEEEEeec-CCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEee
Q 009920            3 SDLGKLFIGGISWDTD-EERLKEYFSRYGEVVEAVIMRD-RATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKK   79 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~t-eedL~e~F~~~G~V~~v~i~~d-~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~   79 (522)
                      .+.++|||+|||++++ |++|+++|++||+|++|+|+++ +.++++||||||+|.+.++|++|| ++++.|++++|+|++
T Consensus         2 ~e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           2 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSL   81 (86)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEE
Confidence            3689999999999975 6679999999999999998764 568899999999999999999999 999999999999999


Q ss_pred             cCCC
Q 009920           80 AVPR   83 (522)
Q Consensus        80 a~~k   83 (522)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9865

>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=99.71  E-value=1.3e-17  Score=139.13  Aligned_cols=83  Identities=25%  Similarity=0.496  Sum_probs=76.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hc------ccccCCeE
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MD------KHMIDGRT   74 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~------~~~i~Gr~   74 (522)
                      .+.++|||+|||+++||++|+++|++||+|.++.++.++.+++++|||||+|.++++|++||  ++      +..|++|+
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            46789999999999999999999999999999999999999999999999999999999999  43      56789999


Q ss_pred             EEEeecCCCcc
Q 009920           75 VEAKKAVPRDD   85 (522)
Q Consensus        75 I~V~~a~~k~~   85 (522)
                      |.|+++.++.+
T Consensus        86 l~v~~a~~k~~   96 (98)
T d1x4ha1          86 LKVDLAVTRDE   96 (98)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEECCCCCc
Confidence            99999987643

>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=99.71  E-value=8.2e-18  Score=137.43  Aligned_cols=78  Identities=18%  Similarity=0.233  Sum_probs=73.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      .+.++|||+|||+++|+++|+++|++||+|++|+|++++ ++++||||||+|.++++|++|| ++++.+.+++|.|+++.
T Consensus         4 ~~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           4 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HHTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEGG
T ss_pred             CCcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            357899999999999999999999999999999998876 6899999999999999999999 99999999999998764

>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=99.71  E-value=1e-17  Score=137.81  Aligned_cols=80  Identities=28%  Similarity=0.571  Sum_probs=74.0

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      ...+|||+|||+++|+++|+++|++||+|++|+|++++.  .++|||||+|.++++|++||  ++++.|++++|.|+++.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~   84 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   84 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT--BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            457899999999999999999999999999999999864  57899999999999999999  89999999999999998


Q ss_pred             CCcc
Q 009920           82 PRDD   85 (522)
Q Consensus        82 ~k~~   85 (522)
                      ++.+
T Consensus        85 ~~~~   88 (89)
T d1cvja2          85 SRKE   88 (89)
T ss_dssp             CTTT
T ss_pred             CCCC
Confidence            7653

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=9.5e-18  Score=141.90  Aligned_cols=83  Identities=25%  Similarity=0.579  Sum_probs=77.9

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      ..++|||+|||+++|+++|+++|++||+|++|+|++++.++++||||||+|.++++|++||++++ ..|.|++|+|+++.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~   86 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            34689999999999999999999999999999999999999999999999999999999999887 89999999999998


Q ss_pred             CCCC
Q 009920          183 PKEF  186 (522)
Q Consensus       183 pk~~  186 (522)
                      ++..
T Consensus        87 ~~~~   90 (104)
T d1p1ta_          87 SEKN   90 (104)
T ss_dssp             CTTH
T ss_pred             CCCC
Confidence            7643

>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=99.71  E-value=1.9e-17  Score=138.05  Aligned_cols=84  Identities=24%  Similarity=0.433  Sum_probs=77.8

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-------CccCCeE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-------HELNGKM  175 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-------~~l~Gr~  175 (522)
                      .+.++|||+|||+++||++|+++|++||+|.++.++.++.+++++|||||+|.++++|++||+.++       ..|+||+
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            456799999999999999999999999999999999999999999999999999999999999875       3688999


Q ss_pred             EEEEEcCCCCC
Q 009920          176 VEVKRAVPKEF  186 (522)
Q Consensus       176 I~V~~a~pk~~  186 (522)
                      |+|+++++|++
T Consensus        86 l~v~~a~~k~~   96 (98)
T d1x4ha1          86 LKVDLAVTRDE   96 (98)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEECCCCCc
Confidence            99999998764

>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=1.9e-17  Score=132.89  Aligned_cols=75  Identities=21%  Similarity=0.454  Sum_probs=71.5

Q ss_pred             eeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       107 ~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      +|||+|||+++++++|+++|++||+|++++|+.++ +++++|||||+|.++++|++|++.++ ..|+|++|+|+++.
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            69999999999999999999999999999999987 68899999999999999999999877 89999999999985

>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=99.70  E-value=1.8e-17  Score=136.38  Aligned_cols=80  Identities=28%  Similarity=0.511  Sum_probs=74.2

Q ss_pred             cceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCC
Q 009920          105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVP  183 (522)
Q Consensus       105 ~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~p  183 (522)
                      ..+|||+|||+++|+++|+++|++||.|++++|+.++.  .++|||||+|+++++|++||+.++ ..|+|++|.|+++++
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            45799999999999999999999999999999999875  468999999999999999999888 899999999999998


Q ss_pred             CCC
Q 009920          184 KEF  186 (522)
Q Consensus       184 k~~  186 (522)
                      +++
T Consensus        86 ~~~   88 (89)
T d1cvja2          86 RKE   88 (89)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            764

>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=99.70  E-value=2.1e-17  Score=139.84  Aligned_cols=85  Identities=24%  Similarity=0.378  Sum_probs=77.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      .+...|||+|||+++||+||+++|+.++.|..+.++.+..+++++|||||+|.++++|++|+ ++++.|.+|.|+|.++.
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            35568999999999999999999999999998888888778999999999999999999999 99999999999999998


Q ss_pred             CCcccc
Q 009920           82 PRDDQN   87 (522)
Q Consensus        82 ~k~~~~   87 (522)
                      +++.+.
T Consensus        93 ~~~~~~   98 (104)
T d1wg5a_          93 RAEVRT   98 (104)
T ss_dssp             TTTSCC
T ss_pred             HHHhcc
Confidence            775443

>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=132.40  Aligned_cols=75  Identities=53%  Similarity=0.977  Sum_probs=71.4

Q ss_pred             eeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEc
Q 009920          107 KIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRA  181 (522)
Q Consensus       107 ~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a  181 (522)
                      +|||+|||+++||+||+++|++||.|+.+.++.++.++++++||||+|.++++|++||+++++.|+||+|+|++|
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            599999999999999999999999999999999999999999999999999999999985559999999999986

>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=99.69  E-value=4.7e-17  Score=137.72  Aligned_cols=88  Identities=14%  Similarity=0.289  Sum_probs=78.9

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR  180 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~  180 (522)
                      ......+|||+|||+++||+||+++|..++.|+.+.++.+..+++++|+|||+|.++++|++||+++.+.|.+|.|+|.+
T Consensus        11 ~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFK   90 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEE
Confidence            34566789999999999999999999999999988888888889999999999999999999998666899999999999


Q ss_pred             cCCCCCCC
Q 009920          181 AVPKEFSP  188 (522)
Q Consensus       181 a~pk~~~~  188 (522)
                      +.+++...
T Consensus        91 ~~~~~~~~   98 (104)
T d1wg5a_          91 SSRAEVRT   98 (104)
T ss_dssp             ECTTTSCC
T ss_pred             CCHHHhcc
Confidence            99876543

>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=1.7e-17  Score=135.64  Aligned_cols=82  Identities=17%  Similarity=0.353  Sum_probs=70.6

Q ss_pred             CcceeEecCCCCCCC-HHHHHHHHhhcCCeeEEEEEec-CCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEc
Q 009920          104 RTKKIFVGGLASTVT-ESDFKKYFDQFGTITDVVVMYD-HNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRA  181 (522)
Q Consensus       104 ~~~~LfVgnLp~~vt-eedL~~~F~~fG~I~~v~i~~d-~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a  181 (522)
                      +.++|||+|||+++| |++|+++|++||+|++|+|+.+ +.+++++|||||+|.++++|++||+++++.|+|++|+|+++
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            467999999999986 5669999999999999998764 57889999999999999999999975558999999999999


Q ss_pred             CCCC
Q 009920          182 VPKE  185 (522)
Q Consensus       182 ~pk~  185 (522)
                      ++++
T Consensus        83 ~~kP   86 (86)
T d2ghpa3          83 DKKP   86 (86)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            9763

>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=99.69  E-value=2.7e-17  Score=141.18  Aligned_cols=102  Identities=16%  Similarity=0.266  Sum_probs=84.7

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      +.+++|||+|||.++|+++|+++|++||+|++|+|.++   +++||||||+|.+.++|++||  ++++.|++++|.|.++
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45689999999999999999999999999999999865   567999999999999999999  8999999999999988


Q ss_pred             CCCccccccccccCCCCCCCCCCCcceeEecCCCCCCCHHHHHHHHhhcCC
Q 009920           81 VPRDDQNMLNRNTSSIHSSPGPGRTKKIFVGGLASTVTESDFKKYFDQFGT  131 (522)
Q Consensus        81 ~~k~~~~~~~~~~~~~~~~~~~~~~~~LfVgnLp~~vteedL~~~F~~fG~  131 (522)
                      .+.....                        .+.....+++++++.+++|.
T Consensus        82 ~~~~~~~------------------------~~~~~~~~~~~~~~~~~~g~  108 (114)
T d2f9da1          82 NANRAFQ------------------------KMDTKKKEEQLKLLKEKYGI  108 (114)
T ss_dssp             CHHHHTT------------------------TSCHHHHHHHHHHHHHHHCC
T ss_pred             CCCchhh------------------------hhHHHHHHHHHHHHHHHhCC
Confidence            6432211                        11122456788888888875

>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=99.68  E-value=1.2e-17  Score=137.33  Aligned_cols=79  Identities=33%  Similarity=0.627  Sum_probs=71.5

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHHHcccccCCeEEEEeecCC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVIMDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl~~~~~i~Gr~I~V~~a~~   82 (522)
                      ..+++|||+|||+++||++|+++|++||+|.+|+++.     ++++||||+|.++++|++||++.+.|++++|.|+++.+
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~~~~~i~g~~l~v~~a~~   77 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEP   77 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTTCEEEETTEEEEEECCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHhCCCEECCEEeEEEeCCC
Confidence            5689999999999999999999999999999988754     46789999999999999999888999999999999987


Q ss_pred             Cccc
Q 009920           83 RDDQ   86 (522)
Q Consensus        83 k~~~   86 (522)
                      +...
T Consensus        78 k~~~   81 (88)
T d1wf0a_          78 KHNS   81 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>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=99.68  E-value=3.6e-17  Score=137.16  Aligned_cols=84  Identities=23%  Similarity=0.425  Sum_probs=76.3

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeE--------EEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccC
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVV--------EAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMID   71 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~--------~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~   71 (522)
                      +.+.++|||+|||+++||++|+++|++||+|.        .+.+.+++.++++++||||+|.++++|++||  +++..|+
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   84 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   84 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEEC
Confidence            35678999999999999999999999999874        5677888888999999999999999999999  8999999


Q ss_pred             CeEEEEeecCCCcc
Q 009920           72 GRTVEAKKAVPRDD   85 (522)
Q Consensus        72 Gr~I~V~~a~~k~~   85 (522)
                      +|+|.|++++++..
T Consensus        85 gr~i~V~~a~~~~p   98 (101)
T d2cpea1          85 GSKLKVSLARKKPP   98 (101)
T ss_dssp             TEECEEECSSCCCC
T ss_pred             CEEEEEEEcCCCCC
Confidence            99999999987543

>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=99.68  E-value=6.1e-17  Score=136.76  Aligned_cols=85  Identities=24%  Similarity=0.385  Sum_probs=74.5

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecC-CCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDH-NTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~-~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a  181 (522)
                      .+.++|||+|||+++||+||+++|++|| |++++++.++ .++++||||||+|.++++|++|+++++++|++|+|+|++|
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4568999999999999999999999998 6677777665 5788999999999999999988876669999999999999


Q ss_pred             CCCCCCC
Q 009920          182 VPKEFSP  188 (522)
Q Consensus       182 ~pk~~~~  188 (522)
                      .++....
T Consensus        92 ~~~~~~~   98 (104)
T d1wi8a_          92 DQAQDKD   98 (104)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9876544

>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=99.68  E-value=5.5e-17  Score=136.04  Aligned_cols=84  Identities=23%  Similarity=0.408  Sum_probs=76.8

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCee--------EEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCC
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTIT--------DVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNG  173 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~--------~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~G  173 (522)
                      .+.++|||+|||+.+||++|+++|++||+|.        .+.+.+++.++++++||||+|.++++|++||++++ ..|+|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            4577999999999999999999999999884        56778888999999999999999999999999887 89999


Q ss_pred             eEEEEEEcCCCCC
Q 009920          174 KMVEVKRAVPKEF  186 (522)
Q Consensus       174 r~I~V~~a~pk~~  186 (522)
                      |+|+|++|+++..
T Consensus        86 r~i~V~~a~~~~p   98 (101)
T d2cpea1          86 SKLKVSLARKKPP   98 (101)
T ss_dssp             EECEEECSSCCCC
T ss_pred             EEEEEEEcCCCCC
Confidence            9999999987653

>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=99.68  E-value=4.2e-17  Score=137.78  Aligned_cols=83  Identities=22%  Similarity=0.453  Sum_probs=73.6

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecC-CCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDR-ATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~-~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||+++||++|+++|++|| |+++++++++ .++++||||||+|.++|+|++|+ +++++|++++|+|+++
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3468999999999999999999999998 6678777765 47889999999999999999888 9999999999999998


Q ss_pred             CCCccc
Q 009920           81 VPRDDQ   86 (522)
Q Consensus        81 ~~k~~~   86 (522)
                      .++..+
T Consensus        92 ~~~~~~   97 (104)
T d1wi8a_          92 DQAQDK   97 (104)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.67  E-value=2.8e-17  Score=138.27  Aligned_cols=85  Identities=26%  Similarity=0.364  Sum_probs=79.8

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      .++++|||+|||.++++++|+++|++||.|+.+.++.+..++++++||||+|.++++|++||+.++ ..|.|++|+|++|
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            457899999999999999999999999999999999998889999999999999999999999988 8999999999999


Q ss_pred             CCCCCC
Q 009920          182 VPKEFS  187 (522)
Q Consensus       182 ~pk~~~  187 (522)
                      ++++++
T Consensus        96 k~k~~r  101 (102)
T d2cpxa1          96 KNKKQR  101 (102)
T ss_dssp             CCCSCC
T ss_pred             CCcccC
Confidence            987753

>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=99.66  E-value=9.4e-17  Score=133.78  Aligned_cols=82  Identities=24%  Similarity=0.369  Sum_probs=72.6

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCC-eEEEEEeecC-CCCCcccEEEEEecCHHHHHHHH--Hc--ccccCCeEEEEe
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGE-VVEAVIMRDR-ATGRARGFGFVVFADPAVAERVI--MD--KHMIDGRTVEAK   78 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~-V~~v~i~~d~-~tg~srG~aFVeF~~~e~A~kAl--~~--~~~i~Gr~I~V~   78 (522)
                      .|+|||+|||.++|+++|+++|++||+ |++++|++++ .++++||||||+|.++++|++|+  ++  ...+.+++|.|+
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            479999999999999999999999996 9999999885 46899999999999999999999  44  446679999999


Q ss_pred             ecCCCccc
Q 009920           79 KAVPRDDQ   86 (522)
Q Consensus        79 ~a~~k~~~   86 (522)
                      +|.++.+.
T Consensus        81 ~A~p~~~~   88 (96)
T d2disa1          81 WAEPEIDV   88 (96)
T ss_dssp             ESCSSCST
T ss_pred             EcCCCCCC
Confidence            99876544

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.66  E-value=1.6e-17  Score=137.43  Aligned_cols=82  Identities=18%  Similarity=0.361  Sum_probs=73.8

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEc
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRA  181 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a  181 (522)
                      +....+|||+|||+++|+++|+++|++||.|+.++|+.+ .++++||||||+|+++++|++||++++++|.|++|+|++|
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            345679999999999999999999999999999988654 5789999999999999999999985558999999999999


Q ss_pred             CCC
Q 009920          182 VPK  184 (522)
Q Consensus       182 ~pk  184 (522)
                      ++|
T Consensus        89 k~k   91 (91)
T d1fjeb1          89 KGR   91 (91)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            864

>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=99.66  E-value=5.3e-17  Score=136.70  Aligned_cols=80  Identities=28%  Similarity=0.528  Sum_probs=73.9

Q ss_pred             CCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            2 ESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         2 e~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      +.+.++|||+|||+++|+++|+++|++||+|..++++.+. +++++|||||+|.++++|++||  +|+..|.+|++.|.+
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            4567899999999999999999999999999999999885 6899999999999999999999  999999999998877


Q ss_pred             cCC
Q 009920           80 AVP   82 (522)
Q Consensus        80 a~~   82 (522)
                      +.|
T Consensus        94 ~~P   96 (101)
T d1x5oa1          94 TEP   96 (101)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            654

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.66  E-value=1.1e-17  Score=138.48  Aligned_cols=80  Identities=23%  Similarity=0.311  Sum_probs=73.7

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      ...++|||+|||+++||++|+++|++||+|.+++|+.+ .++++||||||+|.++++|++|| ++++.|++++|+|++++
T Consensus        11 ~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~ak   89 (91)
T d1fjeb1          11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPK   89 (91)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCC
T ss_pred             CCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEecC
Confidence            45678999999999999999999999999999988765 47999999999999999999999 99999999999999987


Q ss_pred             CC
Q 009920           82 PR   83 (522)
Q Consensus        82 ~k   83 (522)
                      .+
T Consensus        90 ~k   91 (91)
T d1fjeb1          90 GR   91 (91)
T ss_dssp             CS
T ss_pred             CC
Confidence            64

>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=99.66  E-value=2.5e-17  Score=139.00  Aligned_cols=86  Identities=15%  Similarity=0.173  Sum_probs=76.1

Q ss_pred             CCCCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEee
Q 009920            1 MESDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKK   79 (522)
Q Consensus         1 me~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~   79 (522)
                      |+....+|||+|||+++|++||+++|+.||.|..+.++....+++++|+|||+|.++++|++|| ++++.|.+|+|.|.+
T Consensus         4 v~~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~   83 (103)
T d2cpya1           4 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHV   83 (103)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEE
T ss_pred             CCCCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEE
Confidence            3456678999999999999999999999999988767666678999999999999999999999 999999999999998


Q ss_pred             cCCCccc
Q 009920           80 AVPRDDQ   86 (522)
Q Consensus        80 a~~k~~~   86 (522)
                      +.+++..
T Consensus        84 ~~~~~~~   90 (103)
T d2cpya1          84 VTLEDMR   90 (103)
T ss_dssp             ECHHHHH
T ss_pred             CCHHHhh
Confidence            8655443

>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=99.66  E-value=1.1e-16  Score=127.52  Aligned_cols=73  Identities=11%  Similarity=0.217  Sum_probs=68.0

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeec
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a   80 (522)
                      ++|||+|||+++++++|+++|++||+|++|+|++++..  .++||||+|.++++|++|| ++++.|++++|.|+.+
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            58999999999999999999999999999999998753  4579999999999999999 9999999999999875

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.4e-16  Score=132.49  Aligned_cols=78  Identities=21%  Similarity=0.385  Sum_probs=71.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||+++|++||+++|++||+|+.++++++   ..+++||||+|.++++|++||  +++++|++++|+|+++
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            56789999999999999999999999999999887654   457899999999999999999  8999999999999998


Q ss_pred             CCC
Q 009920           81 VPR   83 (522)
Q Consensus        81 ~~k   83 (522)
                      ++.
T Consensus        89 ~~~   91 (95)
T d1x4aa1          89 RSG   91 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            753

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=1.6e-16  Score=132.21  Aligned_cols=80  Identities=16%  Similarity=0.346  Sum_probs=71.9

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ....++|||+|||+++|++||+++|++||.|+.+.+..+   ...++||||+|+++++|++||++++ ++|++++|+|++
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~   87 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            345678999999999999999999999999999887654   4568999999999999999999887 899999999999


Q ss_pred             cCCC
Q 009920          181 AVPK  184 (522)
Q Consensus       181 a~pk  184 (522)
                      |++.
T Consensus        88 a~~~   91 (95)
T d1x4aa1          88 PRSG   91 (95)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            8764

>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=99.66  E-value=6.1e-17  Score=136.58  Aligned_cols=81  Identities=21%  Similarity=0.226  Sum_probs=72.9

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      .+.++|||+|||+++||+||+++|++|++ ++|.++++. +++.+|||||+|.++++|++|| ++++.|++|.|+|.++.
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~s~   90 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec-CCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            45679999999999999999999999975 478888876 4899999999999999999999 99999999999999988


Q ss_pred             CCcc
Q 009920           82 PRDD   85 (522)
Q Consensus        82 ~k~~   85 (522)
                      ++..
T Consensus        91 ~~~~   94 (102)
T d1weza_          91 TAGT   94 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.65  E-value=1.2e-16  Score=134.73  Aligned_cols=84  Identities=17%  Similarity=0.207  Sum_probs=74.2

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEc
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRA  181 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a  181 (522)
                      ....++|||+|||+++||+||+++|+.|+ |++|.++++.. ++++|||||+|+++++|++||+++.+.|++|.|+|.++
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 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESSS-SCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEecC-CcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            35667999999999999999999999997 45788888765 78899999999999999999986559999999999999


Q ss_pred             CCCCCC
Q 009920          182 VPKEFS  187 (522)
Q Consensus       182 ~pk~~~  187 (522)
                      .++...
T Consensus        90 ~~~~~~   95 (102)
T d1weza_          90 STAGTS   95 (102)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            887644

>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=99.65  E-value=1.9e-16  Score=129.17  Aligned_cols=78  Identities=13%  Similarity=0.293  Sum_probs=72.2

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAV  182 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~  182 (522)
                      ..++|||+|||.++|+++|+++|++||+|++|+|+.++ ++++||||||+|.++++|++||++.+..+.|++|.|+++.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            35689999999999999999999999999999998875 6899999999999999999999876699999999999865

>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=99.65  E-value=2.3e-17  Score=138.80  Aligned_cols=83  Identities=20%  Similarity=0.308  Sum_probs=77.9

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ..+++|||+|||.++++++|+++|++||+|+.++++.++.++++++||||+|.++++|++||  +++..|.+++|.|+++
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            35789999999999999999999999999999999998888999999999999999999999  8999999999999999


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      +++++
T Consensus        96 k~k~~  100 (102)
T d2cpxa1          96 KNKKQ  100 (102)
T ss_dssp             CCCSC
T ss_pred             CCccc
Confidence            87654

>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=99.65  E-value=6.7e-17  Score=132.65  Aligned_cols=80  Identities=25%  Similarity=0.482  Sum_probs=70.6

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcC
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAV  182 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~  182 (522)
                      ..+++|||+|||+++||+||+++|++||+|++|+++.     ++++||||+|+++++|++||+ ..++|+|++|+|++++
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 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG-EDLIIKGISVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT-CEEEETTEEEEEECCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh-CCCEECCEEeEEEeCC
Confidence            3577999999999999999999999999999998753     457899999999999999985 3489999999999999


Q ss_pred             CCCCCC
Q 009920          183 PKEFSP  188 (522)
Q Consensus       183 pk~~~~  188 (522)
                      |+....
T Consensus        77 ~k~~~~   82 (88)
T d1wf0a_          77 PKHNSN   82 (88)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            877544

>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=99.64  E-value=2.8e-16  Score=131.65  Aligned_cols=76  Identities=22%  Similarity=0.493  Sum_probs=68.3

Q ss_pred             CCcceeEecCCC-CCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEE
Q 009920          103 GRTKKIFVGGLA-STVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKR  180 (522)
Q Consensus       103 ~~~~~LfVgnLp-~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~  180 (522)
                      ...++|||+||| ..++++||+++|++||+|++|+|.        ||||||+|+++++|++||+.++ ++|.|++|+|++
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            455689999996 678899999999999999999983        6899999999999999999988 899999999999


Q ss_pred             cCCCCC
Q 009920          181 AVPKEF  186 (522)
Q Consensus       181 a~pk~~  186 (522)
                      ++++..
T Consensus        85 a~~~~~   90 (98)
T d1wf2a_          85 AAEPKV   90 (98)
T ss_dssp             TTSCCC
T ss_pred             CCCCCC
Confidence            986543

>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=99.64  E-value=1.1e-16  Score=130.46  Aligned_cols=78  Identities=14%  Similarity=0.278  Sum_probs=70.0

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ...++|||+|||++++|+||+++|+.|+.|.++.++.+..+++++|+|||+|.++++|++||  ++++.|.+|+|+|+.+
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34567999999999999999999999999987655555567999999999999999999999  7999999999999864

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.64  E-value=3.9e-16  Score=130.03  Aligned_cols=81  Identities=20%  Similarity=0.340  Sum_probs=72.4

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      .+.++|||+|||+++|++||+++|++||.|..+..     ++++++||||+|.+.++|++|++.++ ..|+|++|+|+++
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a   88 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45789999999999999999999999998866542     47789999999999999999999888 8999999999999


Q ss_pred             CCCCCCC
Q 009920          182 VPKEFSP  188 (522)
Q Consensus       182 ~pk~~~~  188 (522)
                      .++...+
T Consensus        89 ~~k~~~r   95 (96)
T d1fjca_          89 GEKGGTR   95 (96)
T ss_dssp             SSSCCCC
T ss_pred             CCCCCCC
Confidence            9887543

>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=3.8e-16  Score=130.30  Aligned_cols=76  Identities=21%  Similarity=0.465  Sum_probs=70.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .+.++|||+|||.+++|++|+++|++||+|++|+|+++      |+||||+|.++++|++|+  +++..|.+++|+|.++
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~a   89 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   89 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            35679999999999999999999999999999999876      579999999999999999  8999999999999998


Q ss_pred             CCCc
Q 009920           81 VPRD   84 (522)
Q Consensus        81 ~~k~   84 (522)
                      +++.
T Consensus        90 k~~p   93 (96)
T d1x4ga1          90 KESP   93 (96)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

>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=99.63  E-value=3.5e-16  Score=130.28  Aligned_cols=82  Identities=23%  Similarity=0.420  Sum_probs=74.1

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCC-eeEEEEEecC-CCCCcceEEEEEecCHHHHHHHHHhcC---CccCCeEEEEEE
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGT-ITDVVVMYDH-NTQRPRGFGFITYDSEEAVDRVLHKTF---HELNGKMVEVKR  180 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~-I~~v~i~~d~-~tg~~rG~aFVeF~s~e~A~~Al~~~~---~~l~Gr~I~V~~  180 (522)
                      ++|||+|||.++|+++|+++|++||+ |+++.|++|. .++++||||||+|.++++|++|+++++   ..+.+++|+|+|
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            58999999999999999999999996 8999999885 468899999999999999999999875   366899999999


Q ss_pred             cCCCCCC
Q 009920          181 AVPKEFS  187 (522)
Q Consensus       181 a~pk~~~  187 (522)
                      |+|+...
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9987654

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=2.5e-16  Score=128.31  Aligned_cols=79  Identities=14%  Similarity=0.235  Sum_probs=71.1

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ....+|||+|||++++++||+++|+.|+.|.+..++.+..+++++|+|||+|.++++|++||++++ +.|.+|+|+|+++
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            345689999999999999999999999999876555556779999999999999999999999887 8999999999875

>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=4.1e-16  Score=130.11  Aligned_cols=76  Identities=20%  Similarity=0.501  Sum_probs=70.2

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      ..++|||+|||..+++++|+++|++||+|++|+|+++      ||||||+|+++++|++||+.++ ..|.+++|+|.|++
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            4568999999999999999999999999999999966      6799999999999999999877 89999999999998


Q ss_pred             CCC
Q 009920          183 PKE  185 (522)
Q Consensus       183 pk~  185 (522)
                      +++
T Consensus        91 ~~p   93 (96)
T d1x4ga1          91 ESP   93 (96)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            754

>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=99.63  E-value=4.2e-16  Score=133.62  Aligned_cols=80  Identities=13%  Similarity=0.262  Sum_probs=72.5

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ...++|||+|||.++|+++|+++|++||.|++|++..+   +++||||||+|.+.++|++||+.++ +.|.|++|.|+++
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            35679999999999999999999999999999999865   4568999999999999999999887 8999999999998


Q ss_pred             CCCC
Q 009920          182 VPKE  185 (522)
Q Consensus       182 ~pk~  185 (522)
                      .++.
T Consensus        82 ~~~~   85 (114)
T d2f9da1          82 NANR   85 (114)
T ss_dssp             CHHH
T ss_pred             CCCc
Confidence            7643

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=1.3e-16  Score=135.83  Aligned_cols=76  Identities=14%  Similarity=0.145  Sum_probs=68.9

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      +..++|||+|||+++++++|+++|++||+|++|.|.+      +|+||||+|.++++|++||  ++++.|++++|.|+++
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a   81 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEEC
Confidence            4568999999999999999999999999999998843      5689999999999999999  8999999999999988


Q ss_pred             CCCc
Q 009920           81 VPRD   84 (522)
Q Consensus        81 ~~k~   84 (522)
                      ....
T Consensus        82 ~~~~   85 (111)
T d1whxa_          82 PIGV   85 (111)
T ss_dssp             ETTT
T ss_pred             CCCc
Confidence            6543

>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=1.1e-16  Score=126.04  Aligned_cols=69  Identities=25%  Similarity=0.583  Sum_probs=66.2

Q ss_pred             EEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEE
Q 009920            8 LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVE   76 (522)
Q Consensus         8 LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~   76 (522)
                      |||+|||+++||++|+++|++||+|..+++++++.+++++++|||+|.++++|++|+  +|+..|+++.|+
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            899999999999999999999999999999999999999999999999999999999  899999998763

>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=99.62  E-value=9.5e-16  Score=124.91  Aligned_cols=78  Identities=21%  Similarity=0.284  Sum_probs=70.5

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ...++|||+|||+++|+++|+++|++||.|+.+.+.+      +|+||||+|.++++|++||+.++ ..|.|++|.|+++
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~a   79 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA   79 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            3567999999999999999999999999998877743      47799999999999999999887 8999999999999


Q ss_pred             CCCCC
Q 009920          182 VPKEF  186 (522)
Q Consensus       182 ~pk~~  186 (522)
                      +|+++
T Consensus        80 kP~~~   84 (86)
T d2cpda1          80 KPVDK   84 (86)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98765

>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=99.62  E-value=6.7e-16  Score=122.92  Aligned_cols=74  Identities=19%  Similarity=0.261  Sum_probs=68.1

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEc
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRA  181 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a  181 (522)
                      .+|||+|||+++++++|+++|++||+|++|+|+.++..  .++||||+|+++++|++||+++.+.|+|++|+|+.+
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  357999999999999999987669999999999976

>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=99.62  E-value=6.6e-16  Score=131.13  Aligned_cols=75  Identities=17%  Similarity=0.319  Sum_probs=68.6

Q ss_pred             CcEEEECCCCC-CCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            5 LGKLFIGGISW-DTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         5 ~r~LfVgnLP~-~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      +++|||+|||+ .+||++|+++|++||+|++|+|++++     ||||||+|.++++|++||  +++..|++++|.|+++.
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 59999999999999999999999874     689999999999999999  89999999999999986


Q ss_pred             CCc
Q 009920           82 PRD   84 (522)
Q Consensus        82 ~k~   84 (522)
                      .+.
T Consensus        77 ~~~   79 (109)
T d2adca1          77 HQN   79 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            554

>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=99.62  E-value=3e-16  Score=126.47  Aligned_cols=76  Identities=26%  Similarity=0.503  Sum_probs=68.8

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-C-ccCCeEEEEEEcCC
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-H-ELNGKMVEVKRAVP  183 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~-~l~Gr~I~V~~a~p  183 (522)
                      ++|||+|||.++|+++|+++|++||.|.+++++++      ||||||+|.++++|++|++.++ . +|+|++|+|+++.|
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 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            57999999999999999999999999988877754      6799999999999999999887 4 69999999999998


Q ss_pred             CCCC
Q 009920          184 KEFS  187 (522)
Q Consensus       184 k~~~  187 (522)
                      +..+
T Consensus        76 k~~r   79 (80)
T d2cqha1          76 KKLR   79 (80)
T ss_dssp             CCCC
T ss_pred             cCcC
Confidence            7653

>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=99.61  E-value=3.6e-16  Score=130.24  Aligned_cols=78  Identities=24%  Similarity=0.368  Sum_probs=70.5

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ++.++|||+|||+++||+||+++|++||+|..++.     ++++++||||+|.+.++|++|+  ++++.|++++|.|+++
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a   88 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            56799999999999999999999999998765432     5789999999999999999999  8999999999999999


Q ss_pred             CCCcc
Q 009920           81 VPRDD   85 (522)
Q Consensus        81 ~~k~~   85 (522)
                      .++..
T Consensus        89 ~~k~~   93 (96)
T d1fjca_          89 GEKGG   93 (96)
T ss_dssp             SSSCC
T ss_pred             CCCCC
Confidence            88754

>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=99.61  E-value=3.7e-16  Score=131.44  Aligned_cols=80  Identities=16%  Similarity=0.344  Sum_probs=73.2

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      .+.++|||+|||.++|+++|+++|++||+|+.+.++.+. +++++|||||+|.++++|++||++++ ..|.||++.|.++
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            345789999999999999999999999999999998885 68899999999999999999999877 8999999998877


Q ss_pred             CC
Q 009920          182 VP  183 (522)
Q Consensus       182 ~p  183 (522)
                      +|
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>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=99.61  E-value=5.9e-16  Score=126.48  Aligned_cols=75  Identities=28%  Similarity=0.581  Sum_probs=69.4

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      ..++|||+|||+++++++|+++|++||+|.+|+++++      |+||||+|.++++|++|+  +++..|++++|+|++|.
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            4578999999999999999999999999999999865      469999999999999999  89999999999999997


Q ss_pred             CCc
Q 009920           82 PRD   84 (522)
Q Consensus        82 ~k~   84 (522)
                      +..
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            654

>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=99.60  E-value=1.5e-15  Score=124.26  Aligned_cols=77  Identities=18%  Similarity=0.283  Sum_probs=68.5

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hccccc-CCeEEEEee
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMI-DGRTVEAKK   79 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i-~Gr~I~V~~   79 (522)
                      ..+++|||+|||+++||++|+++|++||+|++++++..    +.++||||+|.++++|++|+  +++..| ++++|+|.+
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            45789999999999999999999999999988877654    45789999999999999999  888887 689999999


Q ss_pred             cCCC
Q 009920           80 AVPR   83 (522)
Q Consensus        80 a~~k   83 (522)
                      ++++
T Consensus        84 sk~~   87 (88)
T d2adca2          84 SKST   87 (88)
T ss_dssp             CSSC
T ss_pred             CCCC
Confidence            8753

>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=99.60  E-value=6.8e-16  Score=129.27  Aligned_cols=73  Identities=26%  Similarity=0.526  Sum_probs=66.1

Q ss_pred             CCCcEEEECCCC-CCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEee
Q 009920            3 SDLGKLFIGGIS-WDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKK   79 (522)
Q Consensus         3 ~d~r~LfVgnLP-~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~   79 (522)
                      ...++|||+||| ..+++++|+++|++||+|++|+|        +|+||||+|.++++|++||  +++++|++++|.|++
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            456789999997 56889999999999999999998        3689999999999999999  899999999999999


Q ss_pred             cCCC
Q 009920           80 AVPR   83 (522)
Q Consensus        80 a~~k   83 (522)
                      +.++
T Consensus        85 a~~~   88 (98)
T d1wf2a_          85 AAEP   88 (98)
T ss_dssp             TTSC
T ss_pred             CCCC
Confidence            8754

>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=4.3e-16  Score=128.13  Aligned_cols=75  Identities=24%  Similarity=0.475  Sum_probs=68.2

Q ss_pred             CCcEEEECCCCCCCCHHHH---HHHHhccCCeEEEEEeecCCCCCc---ccEEEEEecCHHHHHHHH--HcccccCCeEE
Q 009920            4 DLGKLFIGGISWDTDEERL---KEYFSRYGEVVEAVIMRDRATGRA---RGFGFVVFADPAVAERVI--MDKHMIDGRTV   75 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL---~e~F~~~G~V~~v~i~~d~~tg~s---rG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I   75 (522)
                      +.++|||+|||++++++||   +++|++||+|++|+|++++.++.+   ++||||+|.++++|++|+  +|+..|+++.|
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            3567999999999999999   778999999999999999877655   499999999999999999  99999999999


Q ss_pred             EEe
Q 009920           76 EAK   78 (522)
Q Consensus        76 ~V~   78 (522)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            873

>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=99.59  E-value=1.6e-15  Score=128.77  Aligned_cols=77  Identities=14%  Similarity=0.335  Sum_probs=69.6

Q ss_pred             cceeEecCCC-CCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          105 TKKIFVGGLA-STVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       105 ~~~LfVgnLp-~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      .++|||+||| ..+|+++|+++|++||+|++|+|++++     ||||||+|+++++|++||+.++ ..|.|++|+|++++
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            4689999995 569999999999999999999999764     6899999999999999999888 89999999999997


Q ss_pred             CCCC
Q 009920          183 PKEF  186 (522)
Q Consensus       183 pk~~  186 (522)
                      .+..
T Consensus        77 ~~~~   80 (109)
T d2adca1          77 HQNV   80 (109)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>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=99.59  E-value=2e-16  Score=135.72  Aligned_cols=83  Identities=16%  Similarity=0.360  Sum_probs=75.6

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      ...++|||+|||+++|++||+++|+.||.|.++.++.+..+++++|+|||+|.++++|++|| ++++.|.+|.|+|.++.
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEEC
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEcC
Confidence            35678999999999999999999999999988777777778999999999999999999999 99999999999999887


Q ss_pred             CCcc
Q 009920           82 PRDD   85 (522)
Q Consensus        82 ~k~~   85 (522)
                      ++..
T Consensus        96 ~~~~   99 (112)
T d1wela1          96 KKGM   99 (112)
T ss_dssp             HHHH
T ss_pred             hHHH
Confidence            6654

>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=99.59  E-value=8e-16  Score=126.49  Aligned_cols=77  Identities=21%  Similarity=0.407  Sum_probs=69.6

Q ss_pred             CCcceeEecCCCCCCCHHHH---HHHHhhcCCeeEEEEEecCCCCCc---ceEEEEEecCHHHHHHHHHhcC-CccCCeE
Q 009920          103 GRTKKIFVGGLASTVTESDF---KKYFDQFGTITDVVVMYDHNTQRP---RGFGFITYDSEEAVDRVLHKTF-HELNGKM  175 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL---~~~F~~fG~I~~v~i~~d~~tg~~---rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~  175 (522)
                      .+.++|||+|||++++++||   +++|++||+|++|.|++|+.+...   +|||||+|+++++|++|++.++ ..|+||+
T Consensus         6 iq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~   85 (89)
T d2cpia1           6 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   85 (89)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             EecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEE
Confidence            34568999999999999999   778999999999999999877654   4999999999999999999888 8999999


Q ss_pred             EEEE
Q 009920          176 VEVK  179 (522)
Q Consensus       176 I~V~  179 (522)
                      |+|+
T Consensus        86 lkvS   89 (89)
T d2cpia1          86 LKAS   89 (89)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9985

>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=99.59  E-value=3.4e-16  Score=123.27  Aligned_cols=70  Identities=23%  Similarity=0.542  Sum_probs=67.0

Q ss_pred             eEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEE
Q 009920          108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVE  177 (522)
Q Consensus       108 LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~  177 (522)
                      |||+|||.++|+++|+++|++||+|..+++++++.+++++|+|||+|.++++|++|++.++ ..|+|++|+
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            7999999999999999999999999999999999999999999999999999999999888 899998764

>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=99.59  E-value=8.8e-16  Score=126.59  Aligned_cols=80  Identities=21%  Similarity=0.441  Sum_probs=71.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHHH----HHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEE
Q 009920            3 SDLGKLFIGGISWDTDEERLKE----YFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVE   76 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e----~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~   76 (522)
                      +.+++|||+|||++++++||++    +|++||+|.+|++.+   ++++++||||+|.++++|++|+  ++++.+++++|.
T Consensus         1 ~P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~   77 (91)
T d1nu4a_           1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   77 (91)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3578999999999999999875    579999999988865   3678999999999999999999  899999999999


Q ss_pred             EeecCCCcc
Q 009920           77 AKKAVPRDD   85 (522)
Q Consensus        77 V~~a~~k~~   85 (522)
                      |.+++++.+
T Consensus        78 v~~ak~~~~   86 (91)
T d1nu4a_          78 IQYAKTDSD   86 (91)
T ss_dssp             EEECSSCCT
T ss_pred             EEEeCCCch
Confidence            999987643

>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=99.59  E-value=1.9e-15  Score=122.36  Aligned_cols=74  Identities=18%  Similarity=0.254  Sum_probs=67.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hccccc-CCeEEEEee
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMI-DGRTVEAKK   79 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i-~Gr~I~V~~   79 (522)
                      ..+++|||+|||.++|+++|+++|++||+|++|++++++     ++||||+|.+.++|++|+  +++..| ++++|.|.+
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~   80 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITF   80 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEE
Confidence            467899999999999999999999999999999998653     689999999999999999  888888 468999998


Q ss_pred             cC
Q 009920           80 AV   81 (522)
Q Consensus        80 a~   81 (522)
                      |+
T Consensus        81 ak   82 (83)
T d2b0ga1          81 AK   82 (83)
T ss_dssp             CC
T ss_pred             ec
Confidence            85

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=2.2e-16  Score=133.13  Aligned_cols=82  Identities=12%  Similarity=0.199  Sum_probs=73.0

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcCC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVP  183 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~p  183 (522)
                      ...+|||+|||+++|++||+++|+.||.|..+.++.+..+++++|+|||+|.++++|++||+++.+.|+||+|.|.++.+
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            45679999999999999999999999999886666676789999999999999999999998555899999999999875


Q ss_pred             CC
Q 009920          184 KE  185 (522)
Q Consensus       184 k~  185 (522)
                      ++
T Consensus        87 ~~   88 (103)
T d2cpya1          87 ED   88 (103)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=99.58  E-value=1.7e-15  Score=123.63  Aligned_cols=76  Identities=28%  Similarity=0.557  Sum_probs=70.0

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      ..++|||+|||.+++++||+++|++||+|++|+++++      |+||||+|+++++|++|++.++ ..|+|++|+|++|.
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            3457999999999999999999999999999999865      5699999999999999999888 89999999999998


Q ss_pred             CCC
Q 009920          183 PKE  185 (522)
Q Consensus       183 pk~  185 (522)
                      ++.
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            764

>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=99.58  E-value=4.5e-16  Score=127.37  Aligned_cols=71  Identities=20%  Similarity=0.286  Sum_probs=65.3

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCCC
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVPR   83 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~k   83 (522)
                      ++|||+|||+++|+++|+++|++||+|++|+|+++       |||||+|.++++|++||  +++.+|+++.|.|.++.++
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 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            47999999999999999999999999999998764       79999999999999999  9999999999998876544

>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=99.58  E-value=2.8e-16  Score=128.59  Aligned_cols=74  Identities=19%  Similarity=0.222  Sum_probs=67.0

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCC
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPK  184 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk  184 (522)
                      ++|||+|||+++|++||+++|++||+|++++|+.|       |||||+|.++++|++||++++ .+|.++.|+|.+++++
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 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            47999999999999999999999999999998643       799999999999999999887 8999999998887765


Q ss_pred             CC
Q 009920          185 EF  186 (522)
Q Consensus       185 ~~  186 (522)
                      ..
T Consensus        74 ~~   75 (87)
T d3begb1          74 VD   75 (87)
T ss_dssp             EC
T ss_pred             cC
Confidence            54

>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=99.58  E-value=2.2e-15  Score=122.05  Aligned_cols=75  Identities=13%  Similarity=0.248  Sum_probs=67.7

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-Ccc-CCeEEEEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HEL-NGKMVEVKR  180 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l-~Gr~I~V~~  180 (522)
                      .++++|||+|||.++|+++|+++|++||+|++|+++++     .++||||+|.+.++|++|++.++ ..| ++++|+|++
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~   80 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITF   80 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEE
Confidence            35789999999999999999999999999999999754     36799999999999999999887 677 579999999


Q ss_pred             cC
Q 009920          181 AV  182 (522)
Q Consensus       181 a~  182 (522)
                      |+
T Consensus        81 ak   82 (83)
T d2b0ga1          81 AK   82 (83)
T ss_dssp             CC
T ss_pred             ec
Confidence            86

>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=99.58  E-value=1.5e-15  Score=127.21  Aligned_cols=78  Identities=18%  Similarity=0.207  Sum_probs=70.6

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ....+|||+|||++++++||+++|++||+|++++|..       +|||||+|.++++|++||++++ .+|+++.|+|.++
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 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEE
Confidence            4567899999999999999999999999999999863       4799999999999999999887 8999999999999


Q ss_pred             CCCCCC
Q 009920          182 VPKEFS  187 (522)
Q Consensus       182 ~pk~~~  187 (522)
                      ++++.+
T Consensus        86 ~~~~~~   91 (98)
T d1wg4a_          86 RVYPER   91 (98)
T ss_dssp             EEECCC
T ss_pred             ecCCCC
Confidence            876643

>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=3.5e-15  Score=121.47  Aligned_cols=76  Identities=21%  Similarity=0.398  Sum_probs=68.8

Q ss_pred             CCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920            4 DLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         4 d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      ..++|||+|||+++||++|+++|++||.|..+.+.+      +|+||||+|.++++|++|+  +++..|.+++|.|++++
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 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            358899999999999999999999999998777744      5689999999999999999  89999999999999998


Q ss_pred             CCcc
Q 009920           82 PRDD   85 (522)
Q Consensus        82 ~k~~   85 (522)
                      |++.
T Consensus        81 P~~~   84 (86)
T d2cpda1          81 PVDK   84 (86)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.58  E-value=2.3e-15  Score=123.08  Aligned_cols=77  Identities=18%  Similarity=0.334  Sum_probs=68.5

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-Ccc-CCeEEEEEEc
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HEL-NGKMVEVKRA  181 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l-~Gr~I~V~~a  181 (522)
                      ++++|||+|||.++|+++|+++|++||.|+++.++.+    +.+++|||+|+++++|++|+..++ ..| +|++|+|+++
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            5789999999999999999999999999988877654    347799999999999999999887 677 6899999999


Q ss_pred             CCC
Q 009920          182 VPK  184 (522)
Q Consensus       182 ~pk  184 (522)
                      +++
T Consensus        85 k~~   87 (88)
T d2adca2          85 KST   87 (88)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            764

>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=99.58  E-value=9.3e-16  Score=123.52  Aligned_cols=74  Identities=23%  Similarity=0.426  Sum_probs=66.9

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hccc-ccCCeEEEEeecCC
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKH-MIDGRTVEAKKAVP   82 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~-~i~Gr~I~V~~a~~   82 (522)
                      ++|||+|||+++||++|+++|++||+|.++++++.      |+||||+|.++++|++|+  +++. .|+|++|.|+++.+
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 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            57999999999999999999999999988877764      579999999999999999  7864 69999999999988


Q ss_pred             Ccc
Q 009920           83 RDD   85 (522)
Q Consensus        83 k~~   85 (522)
                      +..
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            654

>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=99.58  E-value=2e-15  Score=128.41  Aligned_cols=77  Identities=10%  Similarity=0.172  Sum_probs=69.3

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      ..++|||+|||+++++++|+++|++||+|++|.|.      +.|+||||+|.++++|++||++++ ..|.+++|.|+++.
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            35689999999999999999999999999999884      347899999999999999999888 89999999999987


Q ss_pred             CCCC
Q 009920          183 PKEF  186 (522)
Q Consensus       183 pk~~  186 (522)
                      ....
T Consensus        83 ~~~~   86 (111)
T d1whxa_          83 IGVF   86 (111)
T ss_dssp             TTTT
T ss_pred             CCcc
Confidence            6543

>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=99.58  E-value=2.6e-15  Score=138.07  Aligned_cols=83  Identities=36%  Similarity=0.783  Sum_probs=78.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      ...++|||+|||+++|+++|+++|+.||+|+.+.|++++.+++++|||||+|.++++|++|| ++.+.|+|++|+|++|.
T Consensus        95 ~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~~~~~~~~G~~i~V~~A~  174 (183)
T d1u1qa_          95 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKAL  174 (183)
T ss_dssp             CCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHTSSCEEETTEEEEEEECC
T ss_pred             cccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHHhCCCeECCEEEEEEecC
Confidence            45689999999999999999999999999999999999999999999999999999999999 88889999999999998


Q ss_pred             CCcc
Q 009920           82 PRDD   85 (522)
Q Consensus        82 ~k~~   85 (522)
                      ++++
T Consensus       175 ~k~e  178 (183)
T d1u1qa_         175 SKQE  178 (183)
T ss_dssp             CHHH
T ss_pred             Cccc
Confidence            7654

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=3e-15  Score=127.23  Aligned_cols=79  Identities=16%  Similarity=0.280  Sum_probs=70.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hccccc--CCeEEEEe
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMI--DGRTVEAK   78 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i--~Gr~I~V~   78 (522)
                      +...+|||+|||+++||++|+++|++||+|++|+|++++    .+++|||+|.++++|++||  +++..|  .+++|.|.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            456789999999999999999999999999999999874    5899999999999999999  888888  57889998


Q ss_pred             ecCCCcc
Q 009920           79 KAVPRDD   85 (522)
Q Consensus        79 ~a~~k~~   85 (522)
                      +++++..
T Consensus        81 ~s~~~~~   87 (108)
T d2adba1          81 FSKLTSL   87 (108)
T ss_dssp             ECSSCSC
T ss_pred             ecCCccc
Confidence            8876543

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=2.8e-15  Score=127.43  Aligned_cols=82  Identities=12%  Similarity=0.188  Sum_probs=72.9

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-Ccc--CCeEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HEL--NGKMVEV  178 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l--~Gr~I~V  178 (522)
                      +.+..+|||+|||+++||++|+++|++||.|++|.|++++    .+|+|||+|+++++|++||+.++ ..|  .+++|+|
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v   79 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI   79 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEE
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEE
Confidence            4567899999999999999999999999999999999874    48999999999999999999887 666  6789999


Q ss_pred             EEcCCCCCC
Q 009920          179 KRAVPKEFS  187 (522)
Q Consensus       179 ~~a~pk~~~  187 (522)
                      .+++++...
T Consensus        80 ~~s~~~~~~   88 (108)
T d2adba1          80 DFSKLTSLN   88 (108)
T ss_dssp             EECSSCSCC
T ss_pred             EecCCcccc
Confidence            999876543

>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=99.57  E-value=2.9e-15  Score=122.79  Aligned_cols=76  Identities=14%  Similarity=0.231  Sum_probs=65.8

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      .+++|||+|||++++++||+++|++|| ++.+.+      .+.|+||||+|+++++|++||+.++ .+|+|++|+|++++
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            457899999999999999999999999 333444      3457899999999999999999888 89999999999997


Q ss_pred             CCCC
Q 009920          183 PKEF  186 (522)
Q Consensus       183 pk~~  186 (522)
                      ++..
T Consensus        77 ~~~~   80 (88)
T d1wg1a_          77 TDAL   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6654

>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=99.57  E-value=1.6e-15  Score=124.41  Aligned_cols=75  Identities=12%  Similarity=0.242  Sum_probs=65.0

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      +.+++|||+|||++++++||+++|++||. ..+.+      .+.|+||||+|.++++|++|+  +++++|++++|.|+++
T Consensus         3 s~s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a   75 (88)
T d1wg1a_           3 SGSSGILVKNLPQDSNCQEVHDLLKDYDL-KYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSCC-CCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCccChHHHHHHHHhcCc-eeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45789999999999999999999999993 23333      346789999999999999999  9999999999999998


Q ss_pred             CCCc
Q 009920           81 VPRD   84 (522)
Q Consensus        81 ~~k~   84 (522)
                      .++.
T Consensus        76 ~~~~   79 (88)
T d1wg1a_          76 PTDA   79 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>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=2.9e-15  Score=120.24  Aligned_cols=75  Identities=21%  Similarity=0.367  Sum_probs=68.2

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ...++|||+||+  +||++|+++|++||+|++|++.++      ++||||+|+++++|++|++.++ ..|+|++|+|+++
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            456799999996  899999999999999999999754      5699999999999999999888 8999999999999


Q ss_pred             CCCC
Q 009920          182 VPKE  185 (522)
Q Consensus       182 ~pk~  185 (522)
                      ++++
T Consensus        75 ~~~P   78 (79)
T d2bz2a1          75 RKQP   78 (79)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            8764

>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=99.56  E-value=9.4e-16  Score=131.38  Aligned_cols=83  Identities=13%  Similarity=0.300  Sum_probs=74.9

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcC
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAV  182 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~  182 (522)
                      ....+|||+|||+++|++||+++|+.||.|+.+.++.+..+++++|+|||+|.++++|++||+++.+.|++|+|+|..+.
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEEC
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEcC
Confidence            45679999999999999999999999999988777777778999999999999999999999865589999999999987


Q ss_pred             CCC
Q 009920          183 PKE  185 (522)
Q Consensus       183 pk~  185 (522)
                      ++.
T Consensus        96 ~~~   98 (112)
T d1wela1          96 KKG   98 (112)
T ss_dssp             HHH
T ss_pred             hHH
Confidence            653

>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=99.56  E-value=1.8e-15  Score=124.73  Aligned_cols=80  Identities=20%  Similarity=0.403  Sum_probs=70.7

Q ss_pred             CcceeEecCCCCCCCHHHHHH----HHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEE
Q 009920          104 RTKKIFVGGLASTVTESDFKK----YFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEV  178 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~----~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V  178 (522)
                      ++++|||+|||+.++++||++    +|++||+|++|++.+   +++++|||||+|+++++|++|++.++ ..|++++|.|
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            467999999999999999865    579999999988764   35678999999999999999999887 8999999999


Q ss_pred             EEcCCCCC
Q 009920          179 KRAVPKEF  186 (522)
Q Consensus       179 ~~a~pk~~  186 (522)
                      .+|+++.+
T Consensus        79 ~~ak~~~~   86 (91)
T d1nu4a_          79 QYAKTDSD   86 (91)
T ss_dssp             EECSSCCT
T ss_pred             EEeCCCch
Confidence            99988753

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.56  E-value=2e-15  Score=126.43  Aligned_cols=75  Identities=16%  Similarity=0.206  Sum_probs=68.5

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      ++.++|||+|||++++++||+++|++||+|++|+|.+       +|||||+|.++++|++||  +|+.+|+++.|+|.++
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 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEE
Confidence            5678899999999999999999999999999999864       379999999999999999  8999999999999887


Q ss_pred             CCCc
Q 009920           81 VPRD   84 (522)
Q Consensus        81 ~~k~   84 (522)
                      .++.
T Consensus        86 ~~~~   89 (98)
T d1wg4a_          86 RVYP   89 (98)
T ss_dssp             EEEC
T ss_pred             ecCC
Confidence            6544

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=1.7e-14  Score=121.65  Aligned_cols=82  Identities=17%  Similarity=0.286  Sum_probs=71.8

Q ss_pred             CCCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC---CccCCeEEE
Q 009920          101 GPGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF---HELNGKMVE  177 (522)
Q Consensus       101 ~~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~---~~l~Gr~I~  177 (522)
                      ...++++|||.|||..+||+||+++|++||.|++|.+.++      |++|||+|+++++|++|++.++   ..+.+++|+
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            3356889999999999999999999999999999999754      5699999999999999998763   578999999


Q ss_pred             EEEcCCCCCCC
Q 009920          178 VKRAVPKEFSP  188 (522)
Q Consensus       178 V~~a~pk~~~~  188 (522)
                      |.+++.++...
T Consensus        85 v~~s~~~~~~~   95 (104)
T d1wexa_          85 FNYSTSKRITR   95 (104)
T ss_dssp             EEECSSSSCCC
T ss_pred             EEEcCCCccCC
Confidence            99998765443

>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=99.55  E-value=5.7e-15  Score=123.12  Aligned_cols=75  Identities=19%  Similarity=0.371  Sum_probs=67.6

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCC--eEEEEe
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDG--RTVEAK   78 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~G--r~I~V~   78 (522)
                      ..+++|||+|||++++|++|+++|++||+|++|+++++      ++||||+|.++++|++|+  +++.+|.+  ++|+|+
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            35789999999999999999999999999999999765      469999999999999999  89999976  589999


Q ss_pred             ecCCC
Q 009920           79 KAVPR   83 (522)
Q Consensus        79 ~a~~k   83 (522)
                      ++++.
T Consensus        89 ~ak~~   93 (97)
T d1whya_          89 FAKSG   93 (97)
T ss_dssp             ECCCC
T ss_pred             eCCCC
Confidence            98754

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=1.3e-14  Score=122.36  Aligned_cols=78  Identities=15%  Similarity=0.178  Sum_probs=68.8

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--H--cccccCCeEEEEe
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--M--DKHMIDGRTVEAK   78 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~--~~~~i~Gr~I~V~   78 (522)
                      ..+++|||+|||.++||+||+++|++||+|++|+|.++      |++|||+|.+.++|++||  +  +...+.+++|+|.
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~   86 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEE
Confidence            46889999999999999999999999999999999764      579999999999999999  3  4567889999999


Q ss_pred             ecCCCccc
Q 009920           79 KAVPRDDQ   86 (522)
Q Consensus        79 ~a~~k~~~   86 (522)
                      +++.++..
T Consensus        87 ~s~~~~~~   94 (104)
T d1wexa_          87 YSTSKRIT   94 (104)
T ss_dssp             ECSSSSCC
T ss_pred             EcCCCccC
Confidence            99765443

>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=99.55  E-value=5.2e-15  Score=118.69  Aligned_cols=73  Identities=15%  Similarity=0.330  Sum_probs=67.2

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      +..++|||+|||  +||++|+++|++||+|.+|++.++      ++||||+|.++++|++|+  +++..|++++|+|+++
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            567899999996  899999999999999999999764      469999999999999999  8999999999999999


Q ss_pred             CCC
Q 009920           81 VPR   83 (522)
Q Consensus        81 ~~k   83 (522)
                      .++
T Consensus        75 ~~~   77 (79)
T d2bz2a1          75 RKQ   77 (79)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            765

>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=99.55  E-value=9.1e-15  Score=119.55  Aligned_cols=76  Identities=11%  Similarity=0.186  Sum_probs=68.7

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH----HcccccCCeEEEEe
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI----MDKHMIDGRTVEAK   78 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl----~~~~~i~Gr~I~V~   78 (522)
                      +.+++|||+|||+++++++|+++|++||.|.+++++++      +++|||+|.++++|++|+    .+...+++++|.|.
T Consensus         6 ~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~   79 (88)
T d2cq1a1           6 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   79 (88)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEE
Confidence            56899999999999999999999999999999998865      369999999999999998    35678999999999


Q ss_pred             ecCCCc
Q 009920           79 KAVPRD   84 (522)
Q Consensus        79 ~a~~k~   84 (522)
                      +++.++
T Consensus        80 ~sk~~~   85 (88)
T d2cq1a1          80 YSNHKE   85 (88)
T ss_dssp             ECSCSS
T ss_pred             ECCCCC
Confidence            987654

>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=99.55  E-value=7.3e-15  Score=122.47  Aligned_cols=77  Identities=26%  Similarity=0.465  Sum_probs=69.1

Q ss_pred             CCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCC--eEEEEE
Q 009920          103 GRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNG--KMVEVK  179 (522)
Q Consensus       103 ~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~G--r~I~V~  179 (522)
                      .++++|||+|||+++++++|+++|++||+|++|+++++      ++||||+|.++++|++|++.++ .+|.+  ++|+|+
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            45789999999999999999999999999999999755      5699999999999999999988 77876  589999


Q ss_pred             EcCCCC
Q 009920          180 RAVPKE  185 (522)
Q Consensus       180 ~a~pk~  185 (522)
                      ++++.+
T Consensus        89 ~ak~~~   94 (97)
T d1whya_          89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             eCCCCC
Confidence            998754

>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=114.87  Aligned_cols=69  Identities=17%  Similarity=0.357  Sum_probs=61.8

Q ss_pred             EEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecCCC
Q 009920            8 LFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAVPR   83 (522)
Q Consensus         8 LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~~k   83 (522)
                      |||+|||++++++||+++|++|| +..+++      .++|+||||+|.++++|++|+  +|+..+++++|.|+++...
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            79999999999999999999998 544554      346789999999999999999  9999999999999998654

>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=2.3e-14  Score=117.12  Aligned_cols=79  Identities=18%  Similarity=0.300  Sum_probs=70.5

Q ss_pred             CCCcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhc--C-CccCCeEEEE
Q 009920          102 PGRTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT--F-HELNGKMVEV  178 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~--~-~~l~Gr~I~V  178 (522)
                      ..++++|||+|||.++++++|+++|++||.|++++++++      +++|||+|+++++|++|++.+  + ..|.|++|+|
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            357889999999999999999999999999999998855      469999999999999999864  3 6899999999


Q ss_pred             EEcCCCCC
Q 009920          179 KRAVPKEF  186 (522)
Q Consensus       179 ~~a~pk~~  186 (522)
                      .+++.++.
T Consensus        79 ~~sk~~~l   86 (88)
T d2cq1a1          79 QYSNHKEL   86 (88)
T ss_dssp             EECSCSSC
T ss_pred             EECCCCCC
Confidence            99987653

>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=99.52  E-value=2.4e-16  Score=129.64  Aligned_cols=77  Identities=14%  Similarity=0.363  Sum_probs=68.1

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEe-----ecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEe
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIM-----RDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAK   78 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~-----~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~   78 (522)
                      .|+|||+|||+++||++|+++|++||.|..+.++     .+..++++++||||+|.++|+|++|+ ++++.+++++|+|+
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            3799999999999999999999999987766653     44567789999999999999999999 99999999999997


Q ss_pred             ecC
Q 009920           79 KAV   81 (522)
Q Consensus        79 ~a~   81 (522)
                      +++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>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=2.5e-14  Score=113.64  Aligned_cols=71  Identities=17%  Similarity=0.347  Sum_probs=62.6

Q ss_pred             eEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcCCCC
Q 009920          108 IFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAVPKE  185 (522)
Q Consensus       108 LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~pk~  185 (522)
                      |||+|||++++++||+++|++|| ++.+.+      .+.++||||+|+++++|++|+++++ .+|+|++|+|+++.++.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            79999999999999999999999 444444      3457899999999999999999888 89999999999997543

>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=99.49  E-value=1.5e-14  Score=121.03  Aligned_cols=76  Identities=12%  Similarity=0.200  Sum_probs=68.0

Q ss_pred             CCCcEEEECCCCCC-CCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH----HcccccCCeEEEE
Q 009920            3 SDLGKLFIGGISWD-TDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI----MDKHMIDGRTVEA   77 (522)
Q Consensus         3 ~d~r~LfVgnLP~~-~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl----~~~~~i~Gr~I~V   77 (522)
                      +.+++|||+|||.+ +||++|+++|++||+|.+|+|+++      |++|||+|.++++|++|+    ++...|++++|.|
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V   89 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   89 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEE
Confidence            45789999999986 899999999999999999999875      469999999999999998    5677899999999


Q ss_pred             eecCCCc
Q 009920           78 KKAVPRD   84 (522)
Q Consensus        78 ~~a~~k~   84 (522)
                      .+++.+.
T Consensus        90 ~~s~~~~   96 (99)
T d1x4fa1          90 DLSEKYK   96 (99)
T ss_dssp             EEECSCS
T ss_pred             EEcCCcc
Confidence            9987654

>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=99.49  E-value=8.2e-16  Score=126.36  Aligned_cols=77  Identities=13%  Similarity=0.351  Sum_probs=66.8

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEE-----ecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEE
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVM-----YDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKR  180 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~-----~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~  180 (522)
                      ++|||+|||+++||++|+++|++||.|..+.+.     .+..+.+++|||||+|.++++|++|++++..+|.|++|+|++
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V~r   81 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR   81 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCCBC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEECC
Confidence            589999999999999999999999988766553     455678889999999999999999997545999999999975


Q ss_pred             cC
Q 009920          181 AV  182 (522)
Q Consensus       181 a~  182 (522)
                      ++
T Consensus        82 ~k   83 (90)
T d1u2fa_          82 PH   83 (90)
T ss_dssp             TT
T ss_pred             CC
Confidence            43

>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=4.1e-14  Score=118.42  Aligned_cols=78  Identities=17%  Similarity=0.270  Sum_probs=68.2

Q ss_pred             CCCcceeEecCCCCC-CCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHh--cC-CccCCeEEE
Q 009920          102 PGRTKKIFVGGLAST-VTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHK--TF-HELNGKMVE  177 (522)
Q Consensus       102 ~~~~~~LfVgnLp~~-vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~--~~-~~l~Gr~I~  177 (522)
                      ....++|||+|||.+ +|+++|+++|++||.|++|.++++      |++|||+|+++++|++|++.  ++ ..|.|++|+
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            346689999999975 899999999999999999999865      56999999999999999973  33 689999999


Q ss_pred             EEEcCCCC
Q 009920          178 VKRAVPKE  185 (522)
Q Consensus       178 V~~a~pk~  185 (522)
                      |.+++.+.
T Consensus        89 V~~s~~~~   96 (99)
T d1x4fa1          89 VDLSEKYK   96 (99)
T ss_dssp             EEEECSCS
T ss_pred             EEEcCCcc
Confidence            99997654

>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=99.47  E-value=4.3e-14  Score=116.01  Aligned_cols=75  Identities=12%  Similarity=0.164  Sum_probs=67.3

Q ss_pred             CCCcEEEECCCCCC-CCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH----HcccccCCeEEEE
Q 009920            3 SDLGKLFIGGISWD-TDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI----MDKHMIDGRTVEA   77 (522)
Q Consensus         3 ~d~r~LfVgnLP~~-~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl----~~~~~i~Gr~I~V   77 (522)
                      +.+++|||+|||.. +|++||+++|++||+|.+|+|++++      ++|||+|.+.++|++|+    ++...+.+++|.|
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V   79 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   79 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCCceEEE
Confidence            57899999999986 8899999999999999999998765      48999999999999999    3566899999999


Q ss_pred             eecCCC
Q 009920           78 KKAVPR   83 (522)
Q Consensus        78 ~~a~~k   83 (522)
                      .+++..
T Consensus        80 ~~s~~~   85 (89)
T d1x4da1          80 HLSQKY   85 (89)
T ss_dssp             EEECCC
T ss_pred             EECCCc
Confidence            998754

>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=99.44  E-value=1.2e-13  Score=113.30  Aligned_cols=77  Identities=13%  Similarity=0.182  Sum_probs=68.1

Q ss_pred             CCcceeEecCCCCC-CCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhc--C-CccCCeEEEE
Q 009920          103 GRTKKIFVGGLAST-VTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKT--F-HELNGKMVEV  178 (522)
Q Consensus       103 ~~~~~LfVgnLp~~-vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~--~-~~l~Gr~I~V  178 (522)
                      ..+++|||+|||.. +|++||.++|++||.|++|.++.++      ++|||+|++.++|++|++.+  + ..++|++|+|
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V   79 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   79 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCCceEEE
Confidence            56789999999986 8899999999999999999998664      48999999999999999865  3 5899999999


Q ss_pred             EEcCCCC
Q 009920          179 KRAVPKE  185 (522)
Q Consensus       179 ~~a~pk~  185 (522)
                      +++++..
T Consensus        80 ~~s~~~~   86 (89)
T d1x4da1          80 HLSQKYK   86 (89)
T ss_dssp             EEECCCT
T ss_pred             EECCCcc
Confidence            9997543

>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=99.44  E-value=7.6e-14  Score=117.91  Aligned_cols=79  Identities=14%  Similarity=0.098  Sum_probs=69.4

Q ss_pred             CCCcEEEECCCCCCC-C----HHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEE
Q 009920            3 SDLGKLFIGGISWDT-D----EERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTV   75 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~-t----eedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I   75 (522)
                      +..++|||+||+.++ +    +++|+++|++||+|+++++++      ++++|||+|.++++|++|+  +++..|++++|
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            567899999999885 3    357999999999999999985      4579999999999999999  99999999999


Q ss_pred             EEeecCCCcccc
Q 009920           76 EAKKAVPRDDQN   87 (522)
Q Consensus        76 ~V~~a~~k~~~~   87 (522)
                      +|.+++++....
T Consensus        77 ~v~~a~~~~~~~   88 (104)
T d1weya_          77 KLYFAQTLHIGS   88 (104)
T ss_dssp             EEECCCCSSCCS
T ss_pred             EEeecccCCCCC
Confidence            999998765544

>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=99.38  E-value=2.9e-13  Score=114.21  Aligned_cols=78  Identities=13%  Similarity=0.110  Sum_probs=68.9

Q ss_pred             CcceeEecCCCCCC-CH----HHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEE
Q 009920          104 RTKKIFVGGLASTV-TE----SDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVE  177 (522)
Q Consensus       104 ~~~~LfVgnLp~~v-te----edL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~  177 (522)
                      .+.+|||.||+.++ ++    ++|+++|++||+|+++++++      .+++|||+|+++++|++|+++++ ..|+|++|+
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            46789999999987 33    56999999999999999984      36699999999999999999999 899999999


Q ss_pred             EEEcCCCCCC
Q 009920          178 VKRAVPKEFS  187 (522)
Q Consensus       178 V~~a~pk~~~  187 (522)
                      |.+++++...
T Consensus        78 v~~a~~~~~~   87 (104)
T d1weya_          78 LYFAQTLHIG   87 (104)
T ss_dssp             EECCCCSSCC
T ss_pred             EeecccCCCC
Confidence            9999877653

>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=99.34  E-value=5.1e-14  Score=119.01  Aligned_cols=73  Identities=21%  Similarity=0.269  Sum_probs=67.1

Q ss_pred             EEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeec
Q 009920            7 KLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKA   80 (522)
Q Consensus         7 ~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a   80 (522)
                      .|+|.+++.+++|++|+++|++||+|++|+|+++. ++++||+|||+|.+.++|++|+  ++++.+++|+|+|+++
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            46777888889999999999999999999998775 6899999999999999999999  9999999999999864

>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=99.34  E-value=1.1e-13  Score=116.87  Aligned_cols=75  Identities=12%  Similarity=0.213  Sum_probs=69.9

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEc
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRA  181 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a  181 (522)
                      ..++|.+++..++|++|+++|++||+|++|+|+++ .++++||+|||+|+++++|++|++.++ +.|+||+|+|++.
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            46889999999999999999999999999999876 468999999999999999999999988 8999999999874

>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=99.25  E-value=4.6e-12  Score=106.16  Aligned_cols=63  Identities=10%  Similarity=0.236  Sum_probs=55.8

Q ss_pred             CCCCcEEEECC--CCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hccccc
Q 009920            2 ESDLGKLFIGG--ISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMI   70 (522)
Q Consensus         2 e~d~r~LfVgn--LP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i   70 (522)
                      ++..++|+|.|  ||.++||++|+++|++||+|++|+++++      ++||||+|.+.++|++|+  +++.+|
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            35678899955  9999999999999999999999998765      469999999999999999  787766

>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=99.24  E-value=4.9e-12  Score=108.03  Aligned_cols=73  Identities=18%  Similarity=0.176  Sum_probs=61.6

Q ss_pred             cceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCH-HHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          105 TKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSE-EAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       105 ~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~-e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      ...+||+|||+.+|+++|+++|++||+|.+|.|+++      ++||||+|.++ ++|.+|+..++ ..|.++.+.|.++.
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            456699999999999999999999999999999854      67999999885 78888888887 67777666666655


Q ss_pred             C
Q 009920          183 P  183 (522)
Q Consensus       183 p  183 (522)
                      .
T Consensus        85 ~   85 (113)
T d1owxa_          85 L   85 (113)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.22  E-value=1.6e-11  Score=102.29  Aligned_cols=80  Identities=11%  Similarity=0.261  Sum_probs=69.1

Q ss_pred             CCcceeEecCC--CCCCC---------HHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-Cc
Q 009920          103 GRTKKIFVGGL--ASTVT---------ESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HE  170 (522)
Q Consensus       103 ~~~~~LfVgnL--p~~vt---------eedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~  170 (522)
                      ..+++|+|.||  |.++.         ++||++.|++||.|..|.+..+    +++|+|||+|+++++|++|++.++ ..
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            46789999999  65432         3689999999999999988765    457999999999999999999999 89


Q ss_pred             cCCeEEEEEEcCCCCC
Q 009920          171 LNGKMVEVKRAVPKEF  186 (522)
Q Consensus       171 l~Gr~I~V~~a~pk~~  186 (522)
                      |+||+|+|+++.++.+
T Consensus        82 ~~gr~i~v~~~~g~~~   97 (99)
T d2dita1          82 FGGRQITAQAWDGTTD   97 (99)
T ss_dssp             ETTEECEEEECCSCCC
T ss_pred             ECCEEEEEEEeCCcCC
Confidence            9999999999988764

>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=99.21  E-value=1e-11  Score=99.93  Aligned_cols=74  Identities=14%  Similarity=0.246  Sum_probs=63.1

Q ss_pred             CCCcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeE-EEEeec
Q 009920            3 SDLGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRT-VEAKKA   80 (522)
Q Consensus         3 ~d~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~-I~V~~a   80 (522)
                      .|.+.|+|.+||++++++.| ++|++||+|+++++.+      .++||||+|.++++|++|| +|+..|.++. |.|++.
T Consensus         2 ~~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~   74 (81)
T d1wwha1           2 LDDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPC   74 (81)
T ss_dssp             GGGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEEC
T ss_pred             CcccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeC
Confidence            36788999999999986555 5799999999998754      4679999999999999999 9999999974 678887


Q ss_pred             CCC
Q 009920           81 VPR   83 (522)
Q Consensus        81 ~~k   83 (522)
                      .++
T Consensus        75 ~~k   77 (81)
T d1wwha1          75 IDK   77 (81)
T ss_dssp             CCH
T ss_pred             CCh
Confidence            654

>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=99.20  E-value=3.8e-12  Score=108.74  Aligned_cols=72  Identities=22%  Similarity=0.179  Sum_probs=59.5

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCH-HHHHHHH--HcccccCCeEEEEeecCC
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADP-AVAERVI--MDKHMIDGRTVEAKKAVP   82 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~-e~A~kAl--~~~~~i~Gr~I~V~~a~~   82 (522)
                      ..+||+|||+++||++|+++|++||+|.+|+|+++      ++||||+|.++ ++|.+|+  ++...|..+.+.|.++..
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            34599999999999999999999999999999865      57999999996 6788777  777777766666665544


Q ss_pred             C
Q 009920           83 R   83 (522)
Q Consensus        83 k   83 (522)
                      +
T Consensus        86 ~   86 (113)
T d1owxa_          86 E   86 (113)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.20  E-value=1.4e-11  Score=102.81  Aligned_cols=79  Identities=23%  Similarity=0.384  Sum_probs=68.3

Q ss_pred             CCCcEEEECCC--CCCCC---------HHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--Hcccc
Q 009920            3 SDLGKLFIGGI--SWDTD---------EERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHM   69 (522)
Q Consensus         3 ~d~r~LfVgnL--P~~~t---------eedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~   69 (522)
                      +.+++|+|+||  |.++.         ++||++.|++||+|++|++.++    ..+|+|||+|.++++|++|+  +++..
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            57899999999  66532         3689999999999999988765    35799999999999999999  99999


Q ss_pred             cCCeEEEEeecCCCcc
Q 009920           70 IDGRTVEAKKAVPRDD   85 (522)
Q Consensus        70 i~Gr~I~V~~a~~k~~   85 (522)
                      +++|+|.|+.+.++.+
T Consensus        82 ~~gr~i~v~~~~g~~~   97 (99)
T d2dita1          82 FGGRQITAQAWDGTTD   97 (99)
T ss_dssp             ETTEECEEEECCSCCC
T ss_pred             ECCEEEEEEEeCCcCC
Confidence            9999999999876643

>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=99.19  E-value=1.4e-11  Score=103.10  Aligned_cols=63  Identities=16%  Similarity=0.323  Sum_probs=55.5

Q ss_pred             CCcceeEecC--CCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-Ccc
Q 009920          103 GRTKKIFVGG--LASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HEL  171 (522)
Q Consensus       103 ~~~~~LfVgn--Lp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l  171 (522)
                      .++++|+|.|  ||.++||++|+++|++||.|++|.++++      ++||||+|.+.++|++|++.|+ ++|
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            4567888855  9999999999999999999999988755      4699999999999999999988 555

>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=99.11  E-value=4.6e-11  Score=95.96  Aligned_cols=74  Identities=22%  Similarity=0.259  Sum_probs=62.2

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCe-EEEEEEcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGK-MVEVKRAV  182 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr-~I~V~~a~  182 (522)
                      +.+.|+|.++|++++++.| ++|++||+|.++++.+      .++||||+|+++++|++||+++...|+|+ .|.|+.+.
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCC
Confidence            3567999999999997666 5799999999998753      46799999999999999997655899997 56798887


Q ss_pred             CC
Q 009920          183 PK  184 (522)
Q Consensus       183 pk  184 (522)
                      +|
T Consensus        76 ~k   77 (81)
T d1wwha1          76 DK   77 (81)
T ss_dssp             CH
T ss_pred             Ch
Confidence            65

>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=99.08  E-value=3.9e-11  Score=100.78  Aligned_cols=81  Identities=11%  Similarity=0.194  Sum_probs=69.0

Q ss_pred             CcceeEecCC--CCCCC--------HHHHHHHHhhcCCeeEEEEEecCCCC--CcceEEEEEecCHHHHHHHHHhcC-Cc
Q 009920          104 RTKKIFVGGL--ASTVT--------ESDFKKYFDQFGTITDVVVMYDHNTQ--RPRGFGFITYDSEEAVDRVLHKTF-HE  170 (522)
Q Consensus       104 ~~~~LfVgnL--p~~vt--------eedL~~~F~~fG~I~~v~i~~d~~tg--~~rG~aFVeF~s~e~A~~Al~~~~-~~  170 (522)
                      ++++|.|.|+  |..+.        .+||++.|++||.|++|.|++++.+.  ..+|++||+|.++++|++|++.|+ ..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            5788999999  55543        36799999999999999999876553  346899999999999999999988 89


Q ss_pred             cCCeEEEEEEcCCC
Q 009920          171 LNGKMVEVKRAVPK  184 (522)
Q Consensus       171 l~Gr~I~V~~a~pk  184 (522)
                      ++||+|.|.+..+.
T Consensus        83 f~gR~v~v~f~~~~   96 (104)
T d1o0pa_          83 FANRVVVTKYCDPD   96 (104)
T ss_dssp             SSSSCCEEEEECHH
T ss_pred             ECCeEEEEEEcCHH
Confidence            99999999998653

>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=99.06  E-value=6.1e-11  Score=99.55  Aligned_cols=80  Identities=20%  Similarity=0.179  Sum_probs=68.3

Q ss_pred             CCcEEEECCC--CCCC--------CHHHHHHHHhccCCeEEEEEeecCCCC--CcccEEEEEecCHHHHHHHH--Hcccc
Q 009920            4 DLGKLFIGGI--SWDT--------DEERLKEYFSRYGEVVEAVIMRDRATG--RARGFGFVVFADPAVAERVI--MDKHM   69 (522)
Q Consensus         4 d~r~LfVgnL--P~~~--------teedL~e~F~~~G~V~~v~i~~d~~tg--~srG~aFVeF~~~e~A~kAl--~~~~~   69 (522)
                      .++.|.|+||  |.++        ..+||++.|++||+|++|+|++++++.  ..+|++||+|.++++|++|+  +++..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            5788999999  5553        346789999999999999998876543  45789999999999999999  99999


Q ss_pred             cCCeEEEEeecCCC
Q 009920           70 IDGRTVEAKKAVPR   83 (522)
Q Consensus        70 i~Gr~I~V~~a~~k   83 (522)
                      +++|+|.|....+.
T Consensus        83 f~gR~v~v~f~~~~   96 (104)
T d1o0pa_          83 FANRVVVTKYCDPD   96 (104)
T ss_dssp             SSSSCCEEEEECHH
T ss_pred             ECCeEEEEEEcCHH
Confidence            99999999987643

>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=97.14  E-value=0.00054  Score=54.39  Aligned_cols=56  Identities=16%  Similarity=0.266  Sum_probs=50.2

Q ss_pred             HHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcCCccCCeEEEEEEcCC
Q 009920          120 SDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTFHELNGKMVEVKRAVP  183 (522)
Q Consensus       120 edL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~~~l~Gr~I~V~~a~p  183 (522)
                      .+|.+.|.+||+|.-|+++.|        -..|+|.+-++|.+|+++...++.|+.|+|+...|
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~l~g~~v~G~~l~It~~~~   94 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLDVDGMKVKGRAVKISGPSS   94 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHHGGGSEETTEEEEEECCCC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhccCCeEEcceEEEEecCCC
Confidence            468888899999999999977        57999999999999999999999999999987543

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.08  E-value=0.00046  Score=55.26  Aligned_cols=65  Identities=12%  Similarity=0.078  Sum_probs=53.4

Q ss_pred             cEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCc--ccEEEEEecCHHHHHHHH--Hccccc
Q 009920            6 GKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRA--RGFGFVVFADPAVAERVI--MDKHMI   70 (522)
Q Consensus         6 r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~s--rG~aFVeF~~~e~A~kAl--~~~~~i   70 (522)
                      ++|.|+.||+.+||+++.+.+...+++........+.+-+.  -.-|||.|.+.+++....  .+++.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F   70 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVF   70 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEE
Confidence            68999999999999999999999999988887776554332  245999999999998887  565554

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.68  E-value=0.0032  Score=47.46  Aligned_cols=60  Identities=10%  Similarity=0.134  Sum_probs=51.2

Q ss_pred             HHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC-CccCCeEEEEEEcC
Q 009920          120 SDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF-HELNGKMVEVKRAV  182 (522)
Q Consensus       120 edL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~-~~l~Gr~I~V~~a~  182 (522)
                      +.|.+.|.+++.|..+.|....+ ...  .|-|...+.++|+.|+..++ .+|..|+|.|.++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~d-g~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTD-YQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCS-TTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccC-CcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            44566788999999999987654 333  69999999999999999999 89999999999875

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.66  E-value=0.0017  Score=51.46  Aligned_cols=54  Identities=28%  Similarity=0.385  Sum_probs=47.6

Q ss_pred             HHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH-HcccccCCeEEEEeecC
Q 009920           20 ERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI-MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus        20 edL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl-~~~~~i~Gr~I~V~~a~   81 (522)
                      .+|.+.|+.||+|.-|+++.+        -..|+|.+-+.|.+|+ ++..++.++.|+|....
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~l~g~~v~G~~l~It~~~   93 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLDVDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHHGGGSEETTEEEEEECCC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhccCCeEEcceEEEEecCC
Confidence            367788899999999999887        4799999999999999 99999999999987543

>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=96.48  E-value=0.0039  Score=49.68  Aligned_cols=63  Identities=11%  Similarity=0.197  Sum_probs=52.7

Q ss_pred             ceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCc--ceEEEEEecCHHHHHHHHHhcC
Q 009920          106 KKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRP--RGFGFITYDSEEAVDRVLHKTF  168 (522)
Q Consensus       106 ~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~--rG~aFVeF~s~e~A~~Al~~~~  168 (522)
                      ++|.|+.||+.+||+++.+.+...+++.....+..+.+.++  -.-|+|.|.+.+++..-.+..+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~   66 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFD   66 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHT
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcC
Confidence            58999999999999999999999988888777766554432  2478999999999998888776

>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=95.29  E-value=0.029  Score=42.10  Aligned_cols=58  Identities=17%  Similarity=0.165  Sum_probs=48.1

Q ss_pred             HHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH--HcccccCCeEEEEeecC
Q 009920           21 RLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI--MDKHMIDGRTVEAKKAV   81 (522)
Q Consensus        21 dL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl--~~~~~i~Gr~I~V~~a~   81 (522)
                      -|.+.|.++++|.++.|..-.+   -.-.|-|...+.++|..|+  ++...|..++|.|..+.
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~d---g~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHTD---YQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCCS---TTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEeccC---CcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            3456789999999999866432   2346999999999999999  99999999999998764

>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=93.77  E-value=0.1  Score=41.61  Aligned_cols=57  Identities=18%  Similarity=0.326  Sum_probs=46.1

Q ss_pred             CcceeEecCCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcceEEEEEecCHHHHHHHHHhcC
Q 009920          104 RTKKIFVGGLASTVTESDFKKYFDQFGTITDVVVMYDHNTQRPRGFGFITYDSEEAVDRVLHKTF  168 (522)
Q Consensus       104 ~~~~LfVgnLp~~vteedL~~~F~~fG~I~~v~i~~d~~tg~~rG~aFVeF~s~e~A~~Al~~~~  168 (522)
                      ....||.-..|..+...||.++|++||.|. |..+.|.       .|||...++|+|+.+++...
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-------eEEEEecCHHHHHHHHHHhc
Confidence            445678889999999999999999999874 4444332       79999999999998886544

>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=91.64  E-value=0.15  Score=40.55  Aligned_cols=52  Identities=15%  Similarity=0.279  Sum_probs=43.4

Q ss_pred             CcEEEECCCCCCCCHHHHHHHHhccCCeEEEEEeecCCCCCcccEEEEEecCHHHHHHHH
Q 009920            5 LGKLFIGGISWDTDEERLKEYFSRYGEVVEAVIMRDRATGRARGFGFVVFADPAVAERVI   64 (522)
Q Consensus         5 ~r~LfVgnLP~~~teedL~e~F~~~G~V~~v~i~~d~~tg~srG~aFVeF~~~e~A~kAl   64 (522)
                      ...||.-..|.++...||.++|+.||.|. |..+-+ .      -|||...+.|+|+.++
T Consensus        15 RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIdd-T------Sa~V~L~~~e~~~~v~   66 (100)
T d1whva_          15 RDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDD-T------SAFVSLSQPEQVQIAV   66 (100)
T ss_dssp             CCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEET-T------EEEEECSCHHHHHHHH
T ss_pred             cceeEEEeCCcccchhHHHHHhcCCCceE-EEEecC-c------eEEEEecCHHHHHHHH
Confidence            34578888999999999999999999985 444433 2      7999999999999988