Psyllid ID: psy15676

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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-------31
Protein Sequence
MDSNNNHAKCYIWSVVLYGSETWTMRKKEEKYLESFEMWLWRRMEKIKWSDKIRNEEVLRRGFSFLEDFEIVSGISKVCNKTHRYKLAVKCVQSNIIVFKRKNDIRITHAVILEDPYEDLPELVYPPSPEPTRELLANGLIGADEDIDETAGLSAQEIEELRAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEKEEIDEKKEEEEKEDRAMIGDRMEDGLREM
Secondary Structure (PSIPRED)
cccccccHHHHHHHEEEccccccccccccccccccccEEHHHHccccccccccccccccccccccccccccccccEEEEEEEccHHHHHHHHHHccccccccccEEEccEEEEEccccccccccccccccccHHHHHcccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccEEEEEcccccccHHHHHHHHcccccccEEEEEEEccccccccEEEEEEccHHHHHHHHHHHcccEEccEEEEEccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccEEEEEEEEEcccccccccccccccccccccccHccccccccccccccccccccccHHHHcHHHccccEEEEEEEEcHHHHHHHHHHHHHcccccccEEEEEEEEEcccccccccccccccccccHHHHcccccccHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccEEEEEEccccccHHHHHHHHHccccEEEEEEEEEcccccccEEEEEEEccHHHHHHHHHHcccEEEcccEEEEEccccHHHHHcccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mdsnnnhakcYIWSVVLYGSETWTMRKKEEKYLESFEMWLWRRMEKIKWSDKIRNEEVLRRGFSFLEDFEIVSGISKVCNKTHRYKLAVKCVQSNIIVfkrkndiriTHAViledpyedlpelvyppspeptRELLANgligadedidetaGLSAQEIEELRAEREAKARATILEIVgdlpeadaappenvlfvcklnpvtsdddlEIIFSRfgkvnccevirdkvtgdsLQYAFvefdnpksceDAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEKEEIDEKKEEEEKEDRAMIGDRMEDGLREM
Flexible Loop (DISEMBL)
mdsnnnhakcyiwsvvLYGSETWTMRKKEEKYLESFEMWLWRRMEkikwsdkirneEVLRRgfsfledfEIVSGISKVCNKTHRYKLAVKCVQSniivfkrkndirITHAViledpyedlpELVYPPSPEPTRELLANGLIGADEDIDETAGLSAQEIEELRAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDnvliddrrihargeewnmwkrreeeeekeeidekkeeeekedramigdrmedglrem
Low Complexity Region (SEG)
MDSNNNHAKCYIWSVVLYGSETWTMRKKEEKYLESFEMWLWRRMEKIKWSDKIRNEEVLRRGFSFLEDFEIVSGISKVCNKTHRYKLAVKCVQSNIIVFKRKNDIRITHAVILEDPYEDLPELVYPPSPEPTRELLANGLIGADEDIDETAGLSaqeieelraereakaraTILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWNMWkrreeeeekeeidekkeeeekedrAMIGDRMEDGLREM
Disordered region (IsUnstruct)
*******AKCYIWSVVLYGSETWTMRKKEEKYLESFEMWLWRRMEKIKWSDKIRNEEVLRRGFSFLEDFEIVSGISKVCNKTHRYKLAVKCVQSNIIVFKRKNDIRITHAVILEDPYEDLPELVY*************GLI*****************************ATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWN****************************************
Disordered Region (DISOPRED)
******H*KCYIWSVVLYGSETWTMRKKEEKYLESFEMW***************NEEVLRRGFSFLEDFEIVSGISKVCNKTHRYKLAVKCVQSNIIVFKRKNDIRITHAVILEDPYEDLPE**********************EDIDE*********************************ADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR*********************************************
Disordered Region (DISEMBL)
MDSNNNHAKCYIWSVVLYGSETWTMRKKEEKYLESFEMWLWRRMEKIKWSDKIRNEEVLRRGFSFLEDFEIVSGISKVCNKTHRYKLAVKCVQSNIIVFKRKNDIRITHAVILEDPYEDLPELVYPPSPEPTRELLANGLIGADEDIDETAGLSAQEIEELRAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWNMWK***********************AMIGDRMEDGLREM
Disordered Region (DISPRO)
****NNHAKCYIWSVVLYGSETWTMRKKEEKYLESFEMWLWRRMEKIKWSDKIRNEEVLRRGFSFLEDFEIVSGISKVCNKTHRYKLAVKCVQSNIIVFKRKNDIRITHAVILEDPYEDLPELVYPPSPEPTRE**ANGLIGADEDIDETAGLSAQEIEELRAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW*****************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDSNNNHAKCYIWSVVLYGSETWTMRKKEEKYLESFEMWLWRRMEKIKWSDKIRNEEVLRRGFSFLEDFEIVSGISKVCNKTHRYKLAVKCVQSNIIVFKRKNDIRITHAVILEDPYEDLPELVYPPSPEPTRELLANGLIGADEDIDETAGLSAQEIEELRAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWxxxxxxxxxxxxxxxxxxxxxxxxxxxxMIGDRMEDGLREM
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	309	2.2.26 [Sep-21-2011]
Q8WUA2	492	Peptidyl-prolyl cis-trans	yes	N/A	0.805	0.506	0.477	3e-52
Q9CXG3	492	Peptidyl-prolyl cis-trans	yes	N/A	0.805	0.506	0.477	6e-52
Q4WAQ9	459	Peptidyl-prolyl cis-trans	yes	N/A	0.508	0.342	0.625	1e-50
Q2U256	461	Peptidyl-prolyl cis-trans	yes	N/A	0.508	0.340	0.618	6e-50
Q5ARI5	461	Peptidyl-prolyl cis-trans	yes	N/A	0.508	0.340	0.637	2e-48
P0C1I6	446	Peptidyl-prolyl cis-trans	N/A	N/A	0.511	0.354	0.596	3e-47
Q9UUE4	432	Peptidyl-prolyl cis-trans	yes	N/A	0.508	0.363	0.596	3e-45
Q4IE79	485	Peptidyl-prolyl cis-trans	no	N/A	0.514	0.327	0.587	3e-43
P0C196	551	Peptidyl-prolyl cis-trans	N/A	N/A	0.504	0.283	0.553	3e-41
Q871A4	494	Peptidyl-prolyl cis-trans	N/A	N/A	0.517	0.323	0.576	4e-41

>sp|Q8WUA2|PPIL4_HUMAN Peptidyl-prolyl cis-trans isomerase-like 4 OS=Homo sapiens GN=PPIL4 PE=1 SV=1

 Score =  206 bits (523), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 126/264 (47%), Positives = 169/264 (64%), Gaps = 15/264 (5%)

Query: 15  VVLYGSETWTMRKKE----EKYLESFEMWLWRRMEKIKWSDK----IRNEEVLRRGFSFL 66
           ++  G  T T R  E    + Y +    +   ++ +IK   K    + N    + G  FL
Sbjct: 50  IIQTGDPTGTGRGGESIFGQLYGDQASFFEAEKVPRIKHKKKGTVSMVNNGSDQHGSQFL 109

Query: 67  ----EDFEIVSGISKVCNKTHRYKLAVKCVQSNIIV--FKRKNDIRITHAVILEDPYEDL 120
               E+ + + G+  V  +       +K +    +   F    DIRI H VIL+DP++D 
Sbjct: 110 ITTGENLDYLDGVHTVFGEVTEGMDIIKKINETFVDKDFVPYQDIRINHTVILDDPFDDP 169

Query: 121 PELVYPP-SPEPTRELLANGLIGADEDIDETAGLSAQEIEELRAEREAKARATILEIVGD 179
           P+L+ P  SPEPTRE L +G IGADE+ID+  G SA+E+EE++AE+EAK +A +LE+VGD
Sbjct: 170 PDLLIPDRSPEPTREQLDSGRIGADEEIDDFKGRSAEEVEEIKAEKEAKTQAILLEMVGD 229

Query: 180 LPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFD 239
           LP+AD  PPENVLFVCKLNPVT+D+DLEIIFSRFG +  CEVIRD  TG+SL YAF+EF+
Sbjct: 230 LPDADIKPPENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRDWKTGESLCYAFIEFE 289

Query: 240 NPKSCEDAYLKMDNVLIDDRRIHA 263
             + CE A+ KMDNVLIDDRRIH 
Sbjct: 290 KEEDCEKAFFKMDNVLIDDRRIHV 313

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.
Homo sapiens (taxid: 9606)
EC: 5EC: .EC: 2EC: .EC: 1EC: .EC: 8

>sp|Q9CXG3|PPIL4_MOUSE Peptidyl-prolyl cis-trans isomerase-like 4 OS=Mus musculus GN=Ppil4 PE=2 SV=2

 Score =  204 bits (519), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 126/264 (47%), Positives = 169/264 (64%), Gaps = 15/264 (5%)

Query: 15  VVLYGSETWTMRKKE----EKYLESFEMWLWRRMEKIKWSDK----IRNEEVLRRGFSFL 66
           ++  G  T T R  E    + Y +    +   ++ +IK   K    + N    + G  FL
Sbjct: 50  IIQTGDPTGTGRGGESIFGQLYGDQASFFEAEKVPRIKHKKKGTVSMVNNGSDQHGSQFL 109

Query: 67  ----EDFEIVSGISKVCNKTHRYKLAVKCVQSNIIV--FKRKNDIRITHAVILEDPYEDL 120
               E+ + + G+  V  +       VK +    +   F    DIRI H VIL+DP++D 
Sbjct: 110 ITTGENLDYLDGVHTVFGEVTEGMDIVKKINETFVDKDFVPYQDIRINHTVILDDPFDDP 169

Query: 121 PELVYPP-SPEPTRELLANGLIGADEDIDETAGLSAQEIEELRAEREAKARATILEIVGD 179
           P+L+ P  SPEPT+E L +G IGADE+ID+  G SA+E+EE++AE+EAK +A +LE+VGD
Sbjct: 170 PDLLIPDRSPEPTKEQLDSGRIGADEEIDDFKGRSAEEVEEIKAEKEAKTQAILLEMVGD 229

Query: 180 LPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFD 239
           LP+AD  PPENVLFVCKLNPVT+D+DLEIIFSRFG +  CEVIRD  TG+SL YAF+EF+
Sbjct: 230 LPDADIKPPENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRDWKTGESLCYAFIEFE 289

Query: 240 NPKSCEDAYLKMDNVLIDDRRIHA 263
             + CE A+ KMDNVLIDDRRIH 
Sbjct: 290 KEEDCEKAFFKMDNVLIDDRRIHV 313

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

Mus musculus (taxid: 10090)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|Q4WAQ9|PPIL4_ASPFU Peptidyl-prolyl cis-trans isomerase-like 4 OS=Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) GN=cyp6 PE=3 SV=1

 Score =  200 bits (509), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 100/160 (62%), Positives = 121/160 (75%), Gaps = 3/160 (1%)

Query: 104 DIRITHAVILEDPYEDLPELVYPP-SPEPTRELLANGLIGADEDIDETAGLSAQEIEELR 162
           DIRI H VIL+DPY+D P LV P  SP P++  LA   I  DE++D+   +  + +E+LR
Sbjct: 163 DIRIRHTVILDDPYDDPPGLVVPAESPLPSKAQLATVRIADDEELDDN--MDEEAMEKLR 220

Query: 163 AEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVI 222
            EREA+A+A  LE+VGDLP A+  PPENVLFVCKLNPVT D+DL++IFSRFG +  CEVI
Sbjct: 221 REREARAQALTLEMVGDLPFAEVKPPENVLFVCKLNPVTQDEDLQLIFSRFGPILSCEVI 280

Query: 223 RDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
           RDK TGDSLQYAF+EF+N K CE AY KM  VLIDD RIH
Sbjct: 281 RDKRTGDSLQYAFIEFENQKDCEQAYFKMQGVLIDDHRIH 320

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (taxid: 330879)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|Q2U256|PPIL4_ASPOR Peptidyl-prolyl cis-trans isomerase-like 4 OS=Aspergillus oryzae (strain ATCC 42149 / RIB 40) GN=cyp6 PE=3 SV=1

 Score =  197 bits (502), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 99/160 (61%), Positives = 120/160 (75%), Gaps = 3/160 (1%)

Query: 104 DIRITHAVILEDPYEDLPELVYPP-SPEPTRELLANGLIGADEDIDETAGLSAQEIEELR 162
           DIRI H VIL+DP++D P LV P  SP P++  LA   I  DE++D+   +  + +E+LR
Sbjct: 163 DIRIRHTVILDDPFDDPPGLVAPAESPLPSKAQLATVRIADDEELDDN--MDEESMEKLR 220

Query: 163 AEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVI 222
            EREA+A+A  LE+VGDLP A+  PPENVLFVCKLNPVT D+DL +IFSRFG +  CEVI
Sbjct: 221 REREARAQALTLEMVGDLPFAEVKPPENVLFVCKLNPVTQDEDLHLIFSRFGTILSCEVI 280

Query: 223 RDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
           RDK TGDSLQYAF+EF+N K CE AY KM  VLIDD RIH
Sbjct: 281 RDKRTGDSLQYAFIEFENQKDCEQAYFKMQGVLIDDHRIH 320

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

Aspergillus oryzae (strain ATCC 42149 / RIB 40) (taxid: 510516)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|Q5ARI5|PPIL4_EMENI Peptidyl-prolyl cis-trans isomerase-like 4 OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) GN=cyp6 PE=3 SV=1

 Score =  192 bits (489), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 102/160 (63%), Positives = 122/160 (76%), Gaps = 3/160 (1%)

Query: 104 DIRITHAVILEDPYEDLPELVYPP-SPEPTRELLANGLIGADEDIDETAGLSAQEIEELR 162
           DIRI H VIL+DP++D P LV PP SP PT+  LA   I  DED+ +    ++  +E+LR
Sbjct: 163 DIRIRHTVILDDPFDDPPGLVEPPESPLPTKAQLATVRIADDEDLGDDMDEAS--MEKLR 220

Query: 163 AEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVI 222
            EREA+A+A  LE+VGDLP A+  PPENVLFVCKLNPVT D+DLE+IFSRFGK+  CEVI
Sbjct: 221 REREARAQALTLEMVGDLPFAEVKPPENVLFVCKLNPVTQDEDLELIFSRFGKILSCEVI 280

Query: 223 RDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
           RDK TGDSLQYAF+EF++ K CE AY KM  VLIDD RIH
Sbjct: 281 RDKRTGDSLQYAFIEFESQKDCEQAYFKMQGVLIDDHRIH 320

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (taxid: 227321)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|P0C1I6|PPIL4_RHIO9 Peptidyl-prolyl cis-trans isomerase-like 4 OS=Rhizopus delemar (strain RA 99-880 / ATCC MYA-4621 / FGSC 9543 / NRRL 43880) GN=cyp13 PE=3 SV=1

 Score =  189 bits (480), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 96/161 (59%), Positives = 119/161 (73%), Gaps = 3/161 (1%)

Query: 104 DIRITHAVILEDPYEDLPELVYPP-SPEPTRELLANGLIGADEDIDETAGLSAQEIEELR 162
           DIRI H V+L+DP+ D   LV P  SP PT+E L +  IG DED++E      +E+E+  
Sbjct: 157 DIRIKHTVVLDDPFPDPDGLVIPDESPLPTKEQLESMRIGEDEDLEEMG--DPEELEKRV 214

Query: 163 AEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVI 222
             REAKA A  LE++GDLP A+  PPENVLFVCKLNPVT D+DLE+IFSRFG ++ CE+I
Sbjct: 215 RAREAKAHALTLEMIGDLPFAEVKPPENVLFVCKLNPVTRDEDLEMIFSRFGLIHSCEII 274

Query: 223 RDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA 263
           RD+ TGDSL YAFVEF+N +  E+AY KM +VLIDDRRIH 
Sbjct: 275 RDRQTGDSLSYAFVEFENKEDAEEAYFKMQSVLIDDRRIHV 315

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

Rhizopus delemar (strain RA 99-880 / ATCC MYA-4621 / FGSC 9543 / NRRL 43880) (taxid: 246409)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|Q9UUE4|PPIL4_SCHPO Peptidyl-prolyl cis-trans isomerase cyp6 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=cyp6 PE=1 SV=1

 Score =  182 bits (462), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 96/161 (59%), Positives = 114/161 (70%), Gaps = 4/161 (2%)

Query: 104 DIRITHAVILEDPYEDLPELVYP-PSPEPTRELLANGLIGADEDIDETAGLSAQEIEELR 162
           DIRI H +IL+DP+ED P+LV P  SP PT E LA   IG +E I+     S  +++  +
Sbjct: 160 DIRIKHTIILDDPFEDPPDLVEPLRSPSPTPEQLATVRIGENEQIESET--SEDKLQREK 217

Query: 163 AEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVI 222
                    T LE++GDLP A  APPENVLFVCKLNPVT D+DLE+IFSRFGK+  C+VI
Sbjct: 218 EMEAEAEAVT-LEMIGDLPFAHVAPPENVLFVCKLNPVTQDEDLELIFSRFGKIISCQVI 276

Query: 223 RDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA 263
           RDK TGDSLQYAF+EFDN +S E AY KM NVLIDD RIH 
Sbjct: 277 RDKETGDSLQYAFIEFDNKESVEKAYFKMQNVLIDDSRIHV 317

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

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

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|Q4IE79|PPIL4_GIBZE Peptidyl-prolyl cis-trans isomerase-like 4 OS=Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) GN=CYP6 PE=3 SV=2

 Score =  175 bits (444), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 94/160 (58%), Positives = 114/160 (71%), Gaps = 1/160 (0%)

Query: 104 DIRITHAVILEDPYEDLPELVYPP-SPEPTRELLANGLIGADEDIDETAGLSAQEIEELR 162
           DIRI H VIL+DPY D P L  P  SP PT + L    I  +  + E   +  +E+E  R
Sbjct: 164 DIRIKHTVILDDPYADPPGLREPSTSPPPTDQQLKTVRIADEAALHEDDNVDEEELERRR 223

Query: 163 AEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVI 222
             REA+A+A  LE++GDLP A+  PPENVLFVCKLNPVT D+DLE+IF RFGK+  CEVI
Sbjct: 224 RNREAQAQALTLEMMGDLPFAEVKPPENVLFVCKLNPVTGDEDLELIFGRFGKILSCEVI 283

Query: 223 RDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
           RD+ TGDSLQYAF+E+++  SCE AY KM  VLIDDRRIH
Sbjct: 284 RDQKTGDSLQYAFIEYEDKASCEAAYFKMQGVLIDDRRIH 323

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) (taxid: 229533)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|P0C196|PPIL4_USTMA Peptidyl-prolyl cis-trans isomerase-like 4 OS=Ustilago maydis (strain 521 / FGSC 9021) GN=CYP6 PE=3 SV=1

 Score =  169 bits (428), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 88/159 (55%), Positives = 106/159 (66%), Gaps = 3/159 (1%)

Query: 104 DIRITHAVILEDPYEDLPELVYPP-SPEPTRELLANGLIGADEDIDETAGLSAQEIEELR 162
           DIRI H V+LEDP+ D      P  SP PT   +    +  DED+      +++E  E+R
Sbjct: 177 DIRIRHVVVLEDPFADPDGFCAPSRSPSPTPCQVRALRLADDEDVHSDVDPASKE--EMR 234

Query: 163 AEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVI 222
              +  A A  LE+VGDLP A+  PPEN+LFVCKLNPVT  DDLE+IFSRFGK+  CEVI
Sbjct: 235 RNADTNAAALTLEMVGDLPFAEIRPPENILFVCKLNPVTRSDDLELIFSRFGKILSCEVI 294

Query: 223 RDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI 261
           +DK TGDSLQYAF+EFD     E AY KM NVL+DDRRI
Sbjct: 295 KDKKTGDSLQYAFIEFDKKDDAERAYFKMQNVLVDDRRI 333

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

Ustilago maydis (strain 521 / FGSC 9021) (taxid: 237631)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|Q871A4|PPIL4_NEUCR Peptidyl-prolyl cis-trans isomerase-like 4 OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=cyp-6 PE=3 SV=1

 Score =  168 bits (426), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 94/163 (57%), Positives = 116/163 (71%), Gaps = 3/163 (1%)

Query: 104 DIRITHAVILEDPYEDLPELVYP-PSPEPTRELLANGLIGADEDIDETAGLSAQEIEELR 162
           DIRI H VIL+DPY D   +  P  SP P++  LA   I   E++ +         E  R
Sbjct: 164 DIRIKHTVILDDPYPDPAGMREPSASPPPSKAQLATVRITEGEELLDVEASEEAAAEAER 223

Query: 163 AEREAKA--RATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCE 220
             RE +A  +A  LE++GDLP A+  PPENVLFVCKLNPVT+D+DLE+IFSRFGK+  CE
Sbjct: 224 RRREREAAAQALTLEMMGDLPFAEVKPPENVLFVCKLNPVTTDEDLELIFSRFGKILSCE 283

Query: 221 VIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA 263
           VIRD+ TGDSLQYAF+EF++ KSCE+AY KMD+VLIDDRRIH 
Sbjct: 284 VIRDQKTGDSLQYAFIEFEDKKSCEEAYSKMDSVLIDDRRIHV 326

PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (taxid: 367110)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

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	309
156545479	501	PREDICTED: peptidyl-prolyl cis-trans iso	0.517	0.319	0.739	2e-62
21355677	653	CG5808 [Drosophila melanogaster] gi|4972	0.530	0.251	0.715	2e-62
328791237	507	PREDICTED: peptidyl-prolyl cis-trans iso	0.517	0.315	0.726	3e-62
195158659	615	GL13859 [Drosophila persimilis] gi|19411	0.647	0.325	0.615	6e-62
380018663	613	PREDICTED: peptidyl-prolyl cis-trans iso	0.517	0.261	0.720	7e-62
91089021	467	PREDICTED: similar to CG5808 CG5808-PA [	0.517	0.342	0.732	7e-62
383847372	507	PREDICTED: peptidyl-prolyl cis-trans iso	0.517	0.315	0.720	1e-61
198449749	494	GA26948 [Drosophila pseudoobscura pseudo	0.818	0.512	0.513	1e-61
194745953	621	GF18772 [Drosophila ananassae] gi|190628	0.533	0.265	0.716	1e-61
328794028	330	PREDICTED: peptidyl-prolyl cis-trans iso	0.517	0.484	0.726	1e-61

>gi|156545479|ref|XP_001606947.1| PREDICTED: peptidyl-prolyl cis-trans isomerase-like 4-like [Nasonia vitripennis]

 Score =  245 bits (626), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 119/161 (73%), Positives = 137/161 (85%), Gaps = 1/161 (0%)

Query: 103 NDIRITHAVILEDPYEDLPELVYPP-SPEPTRELLANGLIGADEDIDETAGLSAQEIEEL 161
            DIRI+H VILEDPYED   L  P  SPEPT+E L +  IGADE ID+TAG++A+EI E+
Sbjct: 152 QDIRISHTVILEDPYEDPKGLEVPDRSPEPTKEALMSDRIGADEAIDDTAGMTAEEIAEM 211

Query: 162 RAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEV 221
           + E+EAKARATILEIVGD+P+A+ APPENVLFVCKLNPVTSDDDLE+IFSRFGK+  CEV
Sbjct: 212 QKEKEAKARATILEIVGDIPDAEMAPPENVLFVCKLNPVTSDDDLEVIFSRFGKIVGCEV 271

Query: 222 IRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
           IRD+ TGDSLQYAF+EF   KSCE+AY KMDNVLIDDRRIH
Sbjct: 272 IRDRQTGDSLQYAFIEFAERKSCEEAYFKMDNVLIDDRRIH 312

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|21355677|ref|NP_651291.1| CG5808 [Drosophila melanogaster] gi|4972682|gb|AAD34736.1| unknown [Drosophila melanogaster] gi|7301211|gb|AAF56342.1| CG5808 [Drosophila melanogaster] gi|220943598|gb|ACL84342.1| CG5808-PA [synthetic construct] gi|220953568|gb|ACL89327.1| CG5808-PA [synthetic construct]

 Score =  245 bits (625), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 118/165 (71%), Positives = 136/165 (82%), Gaps = 1/165 (0%)

Query: 99  FKRKNDIRITHAVILEDPYEDLPELVYPP-SPEPTRELLANGLIGADEDIDETAGLSAQE 157
           F+   DIRITH V+LEDP+ +   L  P  SP P+ E L NG I ADEDID+T G++A+E
Sbjct: 148 FRPYQDIRITHTVVLEDPFPNPRGLQAPSRSPSPSAERLKNGRIAADEDIDDTDGMTAEE 207

Query: 158 IEELRAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVN 217
           ++E+ AEREAKARATILEIVGDLP+AD APPENVLFVCKLNPVT+DDDLEIIFS FG + 
Sbjct: 208 MQEMLAEREAKARATILEIVGDLPDADMAPPENVLFVCKLNPVTTDDDLEIIFSSFGVLK 267

Query: 218 CCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
            CEVIRD+ TGDSLQYAFVEF++ KSCE AY KMDNVLIDDRRIH
Sbjct: 268 GCEVIRDRKTGDSLQYAFVEFEDQKSCEAAYFKMDNVLIDDRRIH 312

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328791237|ref|XP_001121334.2| PREDICTED: peptidyl-prolyl cis-trans isomerase-like 4-like [Apis mellifera]

 Score =  244 bits (624), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 117/161 (72%), Positives = 138/161 (85%), Gaps = 1/161 (0%)

Query: 104 DIRITHAVILEDPYEDLPELVYP-PSPEPTRELLANGLIGADEDIDETAGLSAQEIEELR 162
           DIRI+H VILEDP+ED    V P  SP PT+E+L +  IGADE ID+TAG++A+EI E++
Sbjct: 153 DIRISHTVILEDPFEDPKNFVVPDQSPPPTKEVLMSDRIGADEVIDDTAGMTAEEIIEMQ 212

Query: 163 AEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVI 222
            E+EAKARATILEIVGD+P+AD APPENVLFVCKLNPVT+DDDLEI+FSRFGK+  CEVI
Sbjct: 213 KEKEAKARATILEIVGDIPDADMAPPENVLFVCKLNPVTTDDDLEIVFSRFGKIIGCEVI 272

Query: 223 RDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA 263
           RD+ TGDSLQYAF+EF + KSCE+AY KMDNVLIDDRRIH 
Sbjct: 273 RDRQTGDSLQYAFIEFADRKSCEEAYFKMDNVLIDDRRIHV 313

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195158659|ref|XP_002020203.1| GL13859 [Drosophila persimilis] gi|194116972|gb|EDW39015.1| GL13859 [Drosophila persimilis]

 Score =  243 bits (621), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 125/203 (61%), Positives = 148/203 (72%), Gaps = 3/203 (1%)

Query: 63  FSFLEDFEIVSGISKVCNKTHRYKLAVKCVQSNII--VFKRKNDIRITHAVILEDPYEDL 120
           F+  ED   + G   V  +       ++ +   I+   F+   DIRITH V+LEDPY + 
Sbjct: 110 FTLGEDLTSLDGTHCVIGEVVEGHEVLRQLNDAIVDEKFRPYQDIRITHTVVLEDPYPNP 169

Query: 121 PELVYPP-SPEPTRELLANGLIGADEDIDETAGLSAQEIEELRAEREAKARATILEIVGD 179
             L  P  SP P+ E L NG I ADEDID+T G++ +E++E+ A+REAKARATILEIVGD
Sbjct: 170 RGLQAPSRSPSPSAERLKNGRIAADEDIDDTDGMTMEEMQEMLADREAKARATILEIVGD 229

Query: 180 LPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFD 239
           LP+AD APPENVLFVCKLNPVT+DDDLEIIFSRFG V  CEVIRD+ TGDSLQYAFVEF+
Sbjct: 230 LPDADMAPPENVLFVCKLNPVTTDDDLEIIFSRFGVVKGCEVIRDRKTGDSLQYAFVEFE 289

Query: 240 NPKSCEDAYLKMDNVLIDDRRIH 262
             KSCE AY KMDNVLIDDRRIH
Sbjct: 290 EQKSCEAAYFKMDNVLIDDRRIH 312

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380018663|ref|XP_003693245.1| PREDICTED: peptidyl-prolyl cis-trans isomerase-like 4-like [Apis florea]

 Score =  243 bits (621), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 116/161 (72%), Positives = 138/161 (85%), Gaps = 1/161 (0%)

Query: 104 DIRITHAVILEDPYEDLPELVYP-PSPEPTRELLANGLIGADEDIDETAGLSAQEIEELR 162
           DIRI+H VILEDP+ED    + P  SP PT+E+L +  IGADE ID+TAG++A+EI E++
Sbjct: 153 DIRISHTVILEDPFEDPKNFIVPDQSPPPTKEVLMSDRIGADEVIDDTAGMTAEEIIEMQ 212

Query: 163 AEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVI 222
            E+EAKARATILEIVGD+P+AD APPENVLFVCKLNPVT+DDDLEI+FSRFGK+  CEVI
Sbjct: 213 KEKEAKARATILEIVGDIPDADMAPPENVLFVCKLNPVTTDDDLEIVFSRFGKIIGCEVI 272

Query: 223 RDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA 263
           RD+ TGDSLQYAF+EF + KSCE+AY KMDNVLIDDRRIH 
Sbjct: 273 RDRQTGDSLQYAFIEFADRKSCEEAYFKMDNVLIDDRRIHV 313

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91089021|ref|XP_968771.1| PREDICTED: similar to CG5808 CG5808-PA [Tribolium castaneum] gi|270011537|gb|EFA07985.1| hypothetical protein TcasGA2_TC005570 [Tribolium castaneum]

 Score =  243 bits (620), Expect = 7e-62,   Method: Compositional matrix adjust.
 Identities = 118/161 (73%), Positives = 134/161 (83%), Gaps = 1/161 (0%)

Query: 103 NDIRITHAVILEDPYEDLPELVYPP-SPEPTRELLANGLIGADEDIDETAGLSAQEIEEL 161
            DIRITH V+L+DP+ D   L  P  SP P+ E L  G I  DE+IDETAG +A+EI E+
Sbjct: 152 QDIRITHTVVLDDPFPDGDRLRAPSRSPSPSAERLKGGRIAPDEEIDETAGKTAEEISEM 211

Query: 162 RAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEV 221
            AEREAKARATILE+VGD+P+A+ APPENVLFVCKLNPVTSDDDLEIIFSRFGK+  CEV
Sbjct: 212 LAEREAKARATILEMVGDIPDAEMAPPENVLFVCKLNPVTSDDDLEIIFSRFGKIKSCEV 271

Query: 222 IRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
           IRD+ TGDSLQYAFVEF++ KSCEDAY KMDNVLIDDRRIH
Sbjct: 272 IRDRKTGDSLQYAFVEFEDKKSCEDAYFKMDNVLIDDRRIH 312

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383847372|ref|XP_003699328.1| PREDICTED: peptidyl-prolyl cis-trans isomerase-like 4-like [Megachile rotundata]

 Score =  243 bits (619), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 116/161 (72%), Positives = 137/161 (85%), Gaps = 1/161 (0%)

Query: 104 DIRITHAVILEDPYEDLPELVYP-PSPEPTRELLANGLIGADEDIDETAGLSAQEIEELR 162
           DIRI+H VILEDP+ED  + + P  SP PT+E+L +  IGADE ID+TAG++ +EI E++
Sbjct: 153 DIRISHTVILEDPFEDPKDFIVPDQSPPPTKEVLMSDRIGADEVIDDTAGMTIEEITEMQ 212

Query: 163 AEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVI 222
            E+EAKARATILEIVGD+P+AD APPENVLFVCKLNPVT+DDDLEIIFSRFGK+  CEVI
Sbjct: 213 KEKEAKARATILEIVGDIPDADMAPPENVLFVCKLNPVTTDDDLEIIFSRFGKIIGCEVI 272

Query: 223 RDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA 263
           RDK TGDSLQYAF+EF   KSCE+A+ KMDNVLIDDRRIH 
Sbjct: 273 RDKQTGDSLQYAFIEFAERKSCEEAFFKMDNVLIDDRRIHV 313

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198449749|ref|XP_002136956.1| GA26948 [Drosophila pseudoobscura pseudoobscura] gi|198130740|gb|EDY67514.1| GA26948 [Drosophila pseudoobscura pseudoobscura]

 Score =  242 bits (618), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 135/263 (51%), Positives = 163/263 (61%), Gaps = 10/263 (3%)

Query: 3   SNNNHAKCYIWSVVLYGSETWTMRKKEEKYLESFEMWLWRRMEKIKWSDKIRNEEVLRRG 62
           S        IW VV    E    R  E +YL          +  +     +   +     
Sbjct: 57  SGAGDGGSSIWGVV----EGPQKRFFEAEYLPKIHHLNAGMLSLVSAGKNLVGSQFF--- 109

Query: 63  FSFLEDFEIVSGISKVCNKTHRYKLAVKCVQSNII--VFKRKNDIRITHAVILEDPYEDL 120
           F+  ED   + G   V  +       ++ +   I+   F+   DIRITH V+LEDPY + 
Sbjct: 110 FTLGEDLTSLDGTHCVIGEVVEGHEVLRQLNDAIVDEKFRPYQDIRITHTVVLEDPYPNP 169

Query: 121 PELVYPP-SPEPTRELLANGLIGADEDIDETAGLSAQEIEELRAEREAKARATILEIVGD 179
             L  P  SP P+ E L NG I ADEDID+T G++ +E++E+ A+REAKARATILEIVGD
Sbjct: 170 RGLQAPSRSPSPSAERLKNGRIAADEDIDDTDGMTMEEMQEMLADREAKARATILEIVGD 229

Query: 180 LPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFD 239
           LP+AD APPENVLFVCKLNPVT+DDDLEIIFSRFG V  CEVIRD+ TGDSLQYAFVEF+
Sbjct: 230 LPDADMAPPENVLFVCKLNPVTTDDDLEIIFSRFGVVKGCEVIRDRKTGDSLQYAFVEFE 289

Query: 240 NPKSCEDAYLKMDNVLIDDRRIH 262
             KSCE AY KMDNVLIDDRRIH
Sbjct: 290 EQKSCEAAYFKMDNVLIDDRRIH 312

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194745953|ref|XP_001955449.1| GF18772 [Drosophila ananassae] gi|190628486|gb|EDV44010.1| GF18772 [Drosophila ananassae]

 Score =  242 bits (618), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 119/166 (71%), Positives = 134/166 (80%), Gaps = 1/166 (0%)

Query: 98  VFKRKNDIRITHAVILEDPYEDLPELVYPP-SPEPTRELLANGLIGADEDIDETAGLSAQ 156
            F+   DIRITH V+LEDP+ +   L  P  SP P  E L NG I ADEDID+T G + +
Sbjct: 147 TFRPYQDIRITHTVVLEDPFPNPRGLQAPSRSPSPNPERLKNGRIAADEDIDDTGGKTLE 206

Query: 157 EIEELRAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKV 216
           E++E+ AEREAKARATILEIVGDLP+AD APPENVLFVCKLNPVT+DDDLEIIFSRFG V
Sbjct: 207 EMQEMLAEREAKARATILEIVGDLPDADMAPPENVLFVCKLNPVTTDDDLEIIFSRFGVV 266

Query: 217 NCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
             CEVIRD+ TGDSLQYAFVEF++ KSCE AY KMDNVLIDDRRIH
Sbjct: 267 KGCEVIRDRKTGDSLQYAFVEFEDQKSCEAAYFKMDNVLIDDRRIH 312

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328794028|ref|XP_003251965.1| PREDICTED: peptidyl-prolyl cis-trans isomerase-like 4-like, partial [Apis mellifera]

 Score =  242 bits (618), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 117/161 (72%), Positives = 138/161 (85%), Gaps = 1/161 (0%)

Query: 104 DIRITHAVILEDPYEDLPELVYP-PSPEPTRELLANGLIGADEDIDETAGLSAQEIEELR 162
           DIRI+H VILEDP+ED    V P  SP PT+E+L +  IGADE ID+TAG++A+EI E++
Sbjct: 89  DIRISHTVILEDPFEDPKNFVVPDQSPPPTKEVLMSDRIGADEVIDDTAGMTAEEIIEMQ 148

Query: 163 AEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVI 222
            E+EAKARATILEIVGD+P+AD APPENVLFVCKLNPVT+DDDLEI+FSRFGK+  CEVI
Sbjct: 149 KEKEAKARATILEIVGDIPDADMAPPENVLFVCKLNPVTTDDDLEIVFSRFGKIIGCEVI 208

Query: 223 RDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA 263
           RD+ TGDSLQYAF+EF + KSCE+AY KMDNVLIDDRRIH 
Sbjct: 209 RDRQTGDSLQYAFIEFADRKSCEEAYFKMDNVLIDDRRIHV 249

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	309
FB|FBgn0027617	653	CG5808 [Drosophila melanogaste	0.530	0.251	0.642	1.3e-50
UNIPROTKB|F1N6W2	492	PPIL4 "Uncharacterized protein	0.634	0.398	0.517	8.5e-49
UNIPROTKB|Q8WUA2	492	PPIL4 "Peptidyl-prolyl cis-tra	0.634	0.398	0.517	8.5e-49
MGI|MGI:1914668	492	Ppil4 "peptidylprolyl isomeras	0.634	0.398	0.517	1.4e-48
RGD|1311051	492	Ppil4 "peptidylprolyl isomeras	0.634	0.398	0.517	1.4e-48
UNIPROTKB|F1P661	526	PPIL4 "Uncharacterized protein	0.634	0.372	0.512	1.8e-48
UNIPROTKB|E1C3R0	478	PPIL4 "Uncharacterized protein	0.634	0.410	0.512	6e-48
UNIPROTKB|I3LGX0	471	PPIL4 "Uncharacterized protein	0.634	0.416	0.507	2e-47
WB|WBGene00000890	427	sig-7 [Caenorhabditis elegans	0.563	0.407	0.547	1.4e-46
ZFIN|ZDB-GENE-030131-6251	454	ppil4 "peptidylprolyl isomeras	0.543	0.370	0.563	4.8e-46

FB|FBgn0027617 CG5808 [Drosophila melanogaster (taxid:7227)]

 Score = 526 (190.2 bits), Expect = 1.3e-50, P = 1.3e-50
 Identities = 106/165 (64%), Positives = 120/165 (72%)

Query:    99 FKRKNDIRITHAVILEDPYEDLPELVYPP-SPEPTRELLANGLIGADEDIDETAGLSXXX 157
             F+   DIRITH V+LEDP+ +   L  P  SP P+ E L NG I ADEDID+T G++   
Sbjct:   148 FRPYQDIRITHTVVLEDPFPNPRGLQAPSRSPSPSAERLKNGRIAADEDIDDTDGMTAEE 207

Query:   158 XXXXXXXXXXXXXXTILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVN 217
                           TILEIVGDLP+AD APPENVLFVCKLNPVT+DDDLEIIFS FG + 
Sbjct:   208 MQEMLAEREAKARATILEIVGDLPDADMAPPENVLFVCKLNPVTTDDDLEIIFSSFGVLK 267

Query:   218 CCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
              CEVIRD+ TGDSLQYAFVEF++ KSCE AY KMDNVLIDDRRIH
Sbjct:   268 GCEVIRDRKTGDSLQYAFVEFEDQKSCEAAYFKMDNVLIDDRRIH 312

GO:0003729 "mRNA binding" evidence=ISS

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

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

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

GO:0071011 "precatalytic spliceosome" evidence=IDA

GO:0022008 "neurogenesis" evidence=IMP

UNIPROTKB|F1N6W2 PPIL4 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 509 (184.2 bits), Expect = 8.5e-49, P = 8.5e-49
 Identities = 103/199 (51%), Positives = 130/199 (65%)

Query:    67 EDFEIVSGISKVCNKTHRYKLAVKCVQSNIIV--FKRKNDIRITHAVILEDPYEDLPELV 124
             E+ + + G+  V  +       +K +    +   F    DIRI H VIL+DP++D P+L+
Sbjct:   114 ENLDYLDGVHTVFGEVTEGMDIIKKINETFVDKDFVPYQDIRINHTVILDDPFDDPPDLL 173

Query:   125 YPP-SPEPTRELLANGLIGADEDIDETAGLSXXXXXXXXXXXXXXXXXTILEIVGDLPEA 183
              P  SPEPTRE L +G IGADE+ID+  G S                  +LE+VGDLP+A
Sbjct:   174 IPDRSPEPTREQLDSGRIGADEEIDDFKGRSAEEVEEIKAEKEAKTQAILLEMVGDLPDA 233

Query:   184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
             D  PPENVLFVCKLNPVT+D+DLEIIFSRFG +  CEVIRD  TG+SL YAF+EF+  + 
Sbjct:   234 DIKPPENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRDWKTGESLCYAFIEFEKEED 293

Query:   244 CEDAYLKMDNVLIDDRRIH 262
             CE A+ KMDNVLIDDRRIH
Sbjct:   294 CEKAFFKMDNVLIDDRRIH 312

GO:0006457 "protein folding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q8WUA2 PPIL4 "Peptidyl-prolyl cis-trans isomerase-like 4" [Homo sapiens (taxid:9606)]

 Score = 509 (184.2 bits), Expect = 8.5e-49, P = 8.5e-49
 Identities = 103/199 (51%), Positives = 130/199 (65%)

Query:    67 EDFEIVSGISKVCNKTHRYKLAVKCVQSNIIV--FKRKNDIRITHAVILEDPYEDLPELV 124
             E+ + + G+  V  +       +K +    +   F    DIRI H VIL+DP++D P+L+
Sbjct:   114 ENLDYLDGVHTVFGEVTEGMDIIKKINETFVDKDFVPYQDIRINHTVILDDPFDDPPDLL 173

Query:   125 YPP-SPEPTRELLANGLIGADEDIDETAGLSXXXXXXXXXXXXXXXXXTILEIVGDLPEA 183
              P  SPEPTRE L +G IGADE+ID+  G S                  +LE+VGDLP+A
Sbjct:   174 IPDRSPEPTREQLDSGRIGADEEIDDFKGRSAEEVEEIKAEKEAKTQAILLEMVGDLPDA 233

Query:   184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
             D  PPENVLFVCKLNPVT+D+DLEIIFSRFG +  CEVIRD  TG+SL YAF+EF+  + 
Sbjct:   234 DIKPPENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRDWKTGESLCYAFIEFEKEED 293

Query:   244 CEDAYLKMDNVLIDDRRIH 262
             CE A+ KMDNVLIDDRRIH
Sbjct:   294 CEKAFFKMDNVLIDDRRIH 312

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

MGI|MGI:1914668 Ppil4 "peptidylprolyl isomerase (cyclophilin)-like 4" [Mus musculus (taxid:10090)]

 Score = 507 (183.5 bits), Expect = 1.4e-48, P = 1.4e-48
 Identities = 103/199 (51%), Positives = 130/199 (65%)

Query:    67 EDFEIVSGISKVCNKTHRYKLAVKCVQSNIIV--FKRKNDIRITHAVILEDPYEDLPELV 124
             E+ + + G+  V  +       VK +    +   F    DIRI H VIL+DP++D P+L+
Sbjct:   114 ENLDYLDGVHTVFGEVTEGMDIVKKINETFVDKDFVPYQDIRINHTVILDDPFDDPPDLL 173

Query:   125 YPP-SPEPTRELLANGLIGADEDIDETAGLSXXXXXXXXXXXXXXXXXTILEIVGDLPEA 183
              P  SPEPT+E L +G IGADE+ID+  G S                  +LE+VGDLP+A
Sbjct:   174 IPDRSPEPTKEQLDSGRIGADEEIDDFKGRSAEEVEEIKAEKEAKTQAILLEMVGDLPDA 233

Query:   184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
             D  PPENVLFVCKLNPVT+D+DLEIIFSRFG +  CEVIRD  TG+SL YAF+EF+  + 
Sbjct:   234 DIKPPENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRDWKTGESLCYAFIEFEKEED 293

Query:   244 CEDAYLKMDNVLIDDRRIH 262
             CE A+ KMDNVLIDDRRIH
Sbjct:   294 CEKAFFKMDNVLIDDRRIH 312

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0016853 "isomerase activity" evidence=IEA

RGD|1311051 Ppil4 "peptidylprolyl isomerase (cyclophilin)-like 4" [Rattus norvegicus (taxid:10116)]

 Score = 507 (183.5 bits), Expect = 1.4e-48, P = 1.4e-48
 Identities = 103/199 (51%), Positives = 130/199 (65%)

Query:    67 EDFEIVSGISKVCNKTHRYKLAVKCVQSNIIV--FKRKNDIRITHAVILEDPYEDLPELV 124
             E+ + + G+  V  +       VK +    +   F    DIRI H VIL+DP++D P+L+
Sbjct:   114 ENLDYLDGVHTVFGEVTEGMDIVKKINETFVDKDFVPYQDIRINHTVILDDPFDDPPDLL 173

Query:   125 YPP-SPEPTRELLANGLIGADEDIDETAGLSXXXXXXXXXXXXXXXXXTILEIVGDLPEA 183
              P  SPEPT+E L +G IGADE+ID+  G S                  +LE+VGDLP+A
Sbjct:   174 IPDRSPEPTKEQLDSGRIGADEEIDDFKGRSAEEVEEIKAEKEAKTQAILLEMVGDLPDA 233

Query:   184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
             D  PPENVLFVCKLNPVT+D+DLEIIFSRFG +  CEVIRD  TG+SL YAF+EF+  + 
Sbjct:   234 DIKPPENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRDWKTGESLCYAFIEFEKEED 293

Query:   244 CEDAYLKMDNVLIDDRRIH 262
             CE A+ KMDNVLIDDRRIH
Sbjct:   294 CEKAFFKMDNVLIDDRRIH 312

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

UNIPROTKB|F1P661 PPIL4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 506 (183.2 bits), Expect = 1.8e-48, P = 1.8e-48
 Identities = 102/199 (51%), Positives = 130/199 (65%)

Query:    67 EDFEIVSGISKVCNKTHRYKLAVKCVQSNIIV--FKRKNDIRITHAVILEDPYEDLPELV 124
             ++ + + G+  V  +       +K +    +   F    DIRI H VIL+DP++D P+L+
Sbjct:   148 DNLDYLDGVHTVFGEVTEGMDIIKKINETFVDKDFVPYQDIRINHTVILDDPFDDPPDLL 207

Query:   125 YPP-SPEPTRELLANGLIGADEDIDETAGLSXXXXXXXXXXXXXXXXXTILEIVGDLPEA 183
              P  SPEPTRE L +G IGADE+ID+  G S                  +LE+VGDLP+A
Sbjct:   208 IPDRSPEPTREQLDSGRIGADEEIDDFKGRSAEEVEEIKAEKEAKTQAILLEMVGDLPDA 267

Query:   184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
             D  PPENVLFVCKLNPVT+D+DLEIIFSRFG +  CEVIRD  TG+SL YAF+EF+  + 
Sbjct:   268 DIKPPENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRDWKTGESLCYAFIEFEKEED 327

Query:   244 CEDAYLKMDNVLIDDRRIH 262
             CE A+ KMDNVLIDDRRIH
Sbjct:   328 CEKAFFKMDNVLIDDRRIH 346

GO:0006457 "protein folding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E1C3R0 PPIL4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 501 (181.4 bits), Expect = 6.0e-48, P = 6.0e-48
 Identities = 102/199 (51%), Positives = 128/199 (64%)

Query:    67 EDFEIVSGISKVCNKTHRYKLAVKCVQSNIIV--FKRKNDIRITHAVILEDPYEDLPELV 124
             E+ + + G+  V  +       +K +    +   F    DIRI H VIL+DP++D P L 
Sbjct:   114 ENLDYLDGVHTVFGEVTEGMDVLKTINETFVDKDFIPYQDIRINHTVILDDPFDDPPGLP 173

Query:   125 YPP-SPEPTRELLANGLIGADEDIDETAGLSXXXXXXXXXXXXXXXXXTILEIVGDLPEA 183
              P  SPEPT+E L +G IGADE+ID+  G S                  +LE+VGDLP+A
Sbjct:   174 IPDRSPEPTKEQLDSGRIGADEEIDDMKGRSADEIEEVQAEKEAKTRAILLEMVGDLPDA 233

Query:   184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
             +  PPENVLFVCKLNPVT+D+DLEIIFSRFG +  CEVIRD  TG+SL YAF+EF+  + 
Sbjct:   234 EVKPPENVLFVCKLNPVTTDEDLEIIFSRFGPIKSCEVIRDWKTGESLCYAFIEFEKEED 293

Query:   244 CEDAYLKMDNVLIDDRRIH 262
             CE AY KMDNVLIDDRRIH
Sbjct:   294 CEKAYFKMDNVLIDDRRIH 312

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

UNIPROTKB|I3LGX0 PPIL4 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 496 (179.7 bits), Expect = 2.0e-47, P = 2.0e-47
 Identities = 101/199 (50%), Positives = 128/199 (64%)

Query:    67 EDFEIVSGISKVCNKTHRYKLAVKCVQSNIIV--FKRKNDIRITHAVILEDPYEDLPELV 124
             ++ + + G+  V  +       +K +    +   F    DIRI H VIL+DP++D P+L+
Sbjct:    91 DNLDYLDGVHTVFGEVTEGMDIIKKINETFVDKDFVPYQDIRINHTVILDDPFDDPPDLL 150

Query:   125 YPP-SPEPTRELLANGLIGADEDIDETAGLSXXXXXXXXXXXXXXXXXTILEIVGDLPEA 183
              P  SPEPTRE L +G IGADE+ID+  G S                  +LE+VGDLP+A
Sbjct:   151 IPDRSPEPTREQLDSGRIGADEEIDDFKGRSAEEVEEIKAEKEAKTQAILLEMVGDLPDA 210

Query:   184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
             D  PPENVLFVCKLN VT D+DLEIIFSRFG +  CEVIRD  TG+SL YAF+EF+  + 
Sbjct:   211 DIKPPENVLFVCKLNSVTPDEDLEIIFSRFGPIRSCEVIRDWKTGESLCYAFIEFEKEED 270

Query:   244 CEDAYLKMDNVLIDDRRIH 262
             CE A+ KMDNVLIDDRRIH
Sbjct:   271 CEKAFFKMDNVLIDDRRIH 289

GO:0006457 "protein folding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

WB|WBGene00000890 sig-7 [Caenorhabditis elegans (taxid:6239)]

 Score = 488 (176.8 bits), Expect = 1.4e-46, P = 1.4e-46
 Identities = 98/179 (54%), Positives = 122/179 (68%)

Query:    86 KLAVKCVQSNIIVFKRKNDIRITHAVILEDPYEDLPELVYPP-SPEPTRELLAN-GLIGA 143
             KL  +   +N   FK   DIRI+H ++L+DP+++   + +PP SP PT E+L     I  
Sbjct:   138 KLNEQLADTNNRPFK---DIRISHTIVLDDPFDEDARISFPPRSPSPTYEMLVKTDQIAL 194

Query:   144 DEDIDETAGLSXXXXXXXXXXXXXXXXXTILEIVGDLPEADAAPPENVLFVCKLNPVTSD 203
             DE  DE  G +                  ILE+VGDL +AD  PPENVLFVCKLNPVT+D
Sbjct:   195 DEKEDEDEGKTAEEIAEELQQREMAEQAQILEMVGDLKDADEVPPENVLFVCKLNPVTTD 254

Query:   204 DDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
             +DLEIIFSRFGK+N CE++RD+ +GDSLQYAF+EFDN KSCE A+ KMDNVLIDDRRIH
Sbjct:   255 EDLEIIFSRFGKINNCEIVRDRRSGDSLQYAFIEFDNAKSCEQAFFKMDNVLIDDRRIH 313

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

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

GO:0040007 "growth" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0040035 "hermaphrodite genitalia development" evidence=IMP

ZFIN|ZDB-GENE-030131-6251 ppil4 "peptidylprolyl isomerase (cyclophilin)-like 4" [Danio rerio (taxid:7955)]

 Score = 483 (175.1 bits), Expect = 4.8e-46, P = 4.8e-46
 Identities = 97/172 (56%), Positives = 119/172 (69%)

Query:    92 VQSNIIVFKRKNDIRITHAVILEDPYEDLPELVYPP-SPEPTRELLANGLIGADEDIDET 150
             V ++ I F+   DIRI H VIL+DP++D   L  P  SPEPT++ L +G IGADE I++ 
Sbjct:   144 VDNDFIPFQ---DIRINHTVILDDPFDDPAGLPVPDRSPEPTKQQLDSGRIGADEAINDD 200

Query:   151 AGLSXXXXXXXXXXXXXXXXXTILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIF 210
              G                    +LE+VGDLP+AD  PPENVLFVCKLNPVT+D+DLEIIF
Sbjct:   201 EGKDPEELDELIKDKEAKTQAILLEMVGDLPDADIKPPENVLFVCKLNPVTTDEDLEIIF 260

Query:   211 SRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
             SRFG + CCE+IRD  TG+SL YAF+EF+  + CE AY KMDNVLIDDRRIH
Sbjct:   261 SRFGLIKCCEIIRDWKTGESLCYAFIEFEKEEDCEKAYFKMDNVLIDDRRIH 312

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006457 "protein folding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003755 "peptidyl-prolyl cis-trans isomerase activity" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0016853 "isomerase activity" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q4WAQ9	PPIL4_ASPFU	5, ., 2, ., 1, ., 8	0.625	0.5080	0.3420	yes	N/A
Q9UUE4	PPIL4_SCHPO	5, ., 2, ., 1, ., 8	0.5962	0.5080	0.3634	yes	N/A
Q2U256	PPIL4_ASPOR	5, ., 2, ., 1, ., 8	0.6187	0.5080	0.3405	yes	N/A
P0CP88	PPIL4_CRYNJ	5, ., 2, ., 1, ., 8	0.5562	0.5016	0.3075	yes	N/A
Q5ARI5	PPIL4_EMENI	5, ., 2, ., 1, ., 8	0.6375	0.5080	0.3405	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	309
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	4e-51
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	2e-18
smart00360	73	smart00360, RRM, RNA recognition motif	6e-18
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	6e-15
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	3e-14
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	4e-13
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-12
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	9e-12
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-11
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	3e-11
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	4e-11
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	7e-11
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-10
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	5e-10
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	6e-10
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	7e-10
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	8e-10
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	1e-09
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-09
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	4e-09
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	6e-09
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	7e-09
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	7e-09
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	7e-09
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	8e-09
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-08
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	2e-08
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	2e-08
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-08
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	3e-08
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	3e-08
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	3e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	7e-08
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	8e-08
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	1e-07
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	2e-07
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-07
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	2e-07
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-07
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	2e-07
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	3e-07
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	3e-07
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	4e-07
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	5e-07
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	5e-07
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	7e-07
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	7e-07
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	8e-07
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	8e-07
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	9e-07
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	9e-07
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	1e-06
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	1e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-06
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	1e-06
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-06
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	2e-06
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-06
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	3e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	4e-06
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	4e-06
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	4e-06
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	4e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-06
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	5e-06
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	5e-06
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	5e-06
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	5e-06
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	6e-06
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	6e-06
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	7e-06
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	7e-06
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	8e-06
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	8e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-05
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	1e-05
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-05
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	2e-05
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	2e-05
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-05
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	2e-05
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	2e-05
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	2e-05
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	2e-05
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	3e-05
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	3e-05
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	3e-05
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	4e-05
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	4e-05
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	4e-05
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	5e-05
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	6e-05
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	6e-05
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	1e-04
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	1e-04
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-04
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	1e-04
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	1e-04
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	2e-04
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	2e-04
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	2e-04
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	2e-04
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	2e-04
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	3e-04
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	3e-04
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	4e-04
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	4e-04
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	4e-04
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	4e-04
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	5e-04
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	5e-04
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	5e-04
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	5e-04
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	6e-04
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	6e-04
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	7e-04
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	8e-04
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	8e-04
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	9e-04
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	9e-04
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	9e-04
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	9e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.001
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	0.001
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	0.001
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	0.001
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	0.001
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	0.001
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	0.001
cd12302	110	cd12302, RRM_scSet1p_like, RNA recognition motif i	0.001
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	0.001
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	0.001
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	0.001
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	0.002
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	0.002
cd01921	166	cd01921, cyclophilin_RRM, cyclophilin_RRM: cycloph	0.002
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	0.002
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	0.002
cd12467	78	cd12467, RRM_Srp1p_like, RNA recognition motif 1 i	0.002
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	0.003
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	0.003
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	0.003
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	0.003
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	0.003
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	0.004
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	0.004
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	0.004
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	0.004

>gnl|CDD|240681 cd12235, RRM_PPIL4, RNA recognition motif in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins

 Score =  163 bits (414), Expect = 4e-51
 Identities = 62/76 (81%), Positives = 69/76 (90%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
           PPENVLFVCKLNPVT+D+DLEIIFSRFGK+  CEVIRDK TGDSLQYAF+EF+  + CE+
Sbjct: 1   PPENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEE 60

Query: 247 AYLKMDNVLIDDRRIH 262
           AY KMDNVLIDDRRIH
Sbjct: 61  AYFKMDNVLIDDRRIH 76

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

 Score = 78.1 bits (193), Expect = 2e-18
 Identities = 27/74 (36%), Positives = 43/74 (58%)

Query: 188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           P   LFV +L+  T+++ L  +FSR+G +    ++RD VTG S  YAFVE+++ +    A
Sbjct: 2   PYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRA 61

Query: 248 YLKMDNVLIDDRRI 261
           Y     ++ID   I
Sbjct: 62  YRDAHKLVIDGSEI 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|214636 smart00360, RRM, RNA recognition motif

 Score = 76.5 bits (189), Expect = 6e-18
 Identities = 28/72 (38%), Positives = 44/72 (61%)

Query: 191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK 250
            LFV  L P T++++L  +FS+FGKV    ++RDK TG S  +AFVEF++ +  E A   
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 251 MDNVLIDDRRIH 262
           ++   +D R + 
Sbjct: 61  LNGKELDGRPLK 72

Length = 73

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

 Score = 68.1 bits (167), Expect = 6e-15
 Identities = 27/73 (36%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LFV  L P T+++DL  +FS+FG++    ++RDK  G S  +AFVEF++P+  E A   +
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 252 DNVLIDDRRIHAR 264
           +   +D R++   
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|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 = 66.5 bits (163), Expect = 3e-14
 Identities = 23/72 (31%), Positives = 43/72 (59%)

Query: 190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
           N LFV  L+  T++ +LE +FS+FG+V    +++D  TG+S  + FV F++ +  + A  
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 250 KMDNVLIDDRRI 261
            ++   ++ R I
Sbjct: 62  DLNGKELEGRVI 73

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

 Score = 63.8 bits (156), Expect = 4e-13
 Identities = 26/72 (36%), Positives = 39/72 (54%)

Query: 190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
             LFV +LN  T++  L   F  +G +    ++RDK TG    YAF+EF++ +  + AY 
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 250 KMDNVLIDDRRI 261
             D   ID RR+
Sbjct: 62  YADGKKIDGRRV 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|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins

 Score = 61.4 bits (150), Expect = 2e-12
 Identities = 24/73 (32%), Positives = 36/73 (49%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L V KL    + D L+ IFS +G V   ++  D+       YA+VEF++P+  E A   M
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 252 DNVLIDDRRIHAR 264
           D   ID + +   
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|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]

 Score = 64.2 bits (155), Expect = 9e-12
 Identities = 35/201 (17%), Positives = 76/201 (37%), Gaps = 1/201 (0%)

Query: 101 RKNDIRITHAVILEDPYEDLPELVYPPSPEPTRELLANGLIGADEDIDETAGLSAQEIEE 160
            +  ++  +  + E   ++L   V     E      +   + + E  +E      ++ + 
Sbjct: 27  TELLLKEEYGGLEEANSKELNLEVNSRKIESEISPPSKKRLLSSERKEENEREMEEQNDG 86

Query: 161 LRAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCE 220
            R   +                  +    N LFV  L    +++DL  +F +FG V    
Sbjct: 87  ERGYTKEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVR 146

Query: 221 VIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEK 280
           ++RD+ TG S  +AFVEF++ +S E A  +++   ++ R +  + +     + R E    
Sbjct: 147 LVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQ-KAQPASQPRSELSNN 205

Query: 281 EEIDEKKEEEEKEDRAMIGDR 301
            +    K+    +   +    
Sbjct: 206 LDASFAKKLSRGKALLLEKSD 226

Length = 306

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

 Score = 58.8 bits (143), Expect = 1e-11
 Identities = 25/71 (35%), Positives = 43/71 (60%), Gaps = 1/71 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LFV  L P T+++DL+ +FS+FG +    ++RD+ TG S  +AFVEF++ +  E A   +
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 252 DNVLIDDRRIH 262
           +   +  R + 
Sbjct: 60  NGKELGGRELR 70

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

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

 Score = 58.4 bits (142), Expect = 3e-11
 Identities = 23/64 (35%), Positives = 39/64 (60%)

Query: 190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
           N ++V  ++P  S+DD++ +F  FGK+  C +  D  TG    Y F+E++NP+S +DA  
Sbjct: 1   NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 250 KMDN 253
            M+ 
Sbjct: 61  SMNL 64

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

 Score = 57.5 bits (140), Expect = 4e-11
 Identities = 30/85 (35%), Positives = 41/85 (48%), Gaps = 10/85 (11%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L+P  ++  L  IFS  G V    V RD +T  SL YA+V F NP   E A   +
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 252 DNVLIDDR--RIHARGEEWNMWKRR 274
           +  +I  +  RI        MW +R
Sbjct: 62  NFDVIKGKPIRI--------MWSQR 78

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

 Score = 57.0 bits (138), Expect = 7e-11
 Identities = 24/70 (34%), Positives = 41/70 (58%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L V  L    + D++  +FS  G++  C++IRDKVTG SL Y FV + +P+  E A   +
Sbjct: 4   LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTL 63

Query: 252 DNVLIDDRRI 261
           + + + ++ I
Sbjct: 64  NGLRLQNKTI 73

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

 Score = 56.4 bits (137), Expect = 1e-10
 Identities = 24/70 (34%), Positives = 40/70 (57%), Gaps = 1/70 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LF+  L+  T+++ L   FS++G+V  C +++D +TG S  + FV F +P S  D  L  
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSV-DKVLAA 59

Query: 252 DNVLIDDRRI 261
              ++D R I
Sbjct: 60  KPHVLDGREI 69

This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs. . Length = 72

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

 Score = 54.5 bits (132), Expect = 5e-10
 Identities = 29/71 (40%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  L   T+DD L   FS+FG++    VI D+ TG S  Y FV F + +S E A  K 
Sbjct: 3   IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERA-CKD 61

Query: 252 DNVLIDDRRIH 262
            N +ID R+ +
Sbjct: 62  PNPIIDGRKAN 72

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|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 = 54.2 bits (131), Expect = 6e-10
 Identities = 25/70 (35%), Positives = 38/70 (54%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LF+  L    +D DL  +F+ FG V   +V  DK TG S  + FV +DNP+S + A   M
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 252 DNVLIDDRRI 261
           +   +  +R+
Sbjct: 61  NGFQVGGKRL 70

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

 Score = 54.3 bits (131), Expect = 7e-10
 Identities = 16/60 (26%), Positives = 35/60 (58%)

Query: 202 SDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI 261
           + ++L  +F   G +  C+++RD++TG SL Y FV++ +    + A   ++   I ++R+
Sbjct: 13  TQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRL 72

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|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 = 54.2 bits (131), Expect = 8e-10
 Identities = 23/71 (32%), Positives = 38/71 (53%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LFV  L   T++++L  +F  FG+++   +  DK T  S  +AFV F  P+    AY ++
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 252 DNVLIDDRRIH 262
           D  +   R +H
Sbjct: 62  DGSIFQGRLLH 72

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

 Score = 54.1 bits (131), Expect = 1e-09
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 5/80 (6%)

Query: 188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNC--CEVIRDKVTGDSLQYAFVEFDNPKSCE 245
           P N L +  L+ +T+++D+    S    V      +IRDK+TG S  +AFVEF + +   
Sbjct: 1   PTNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDAT 60

Query: 246 ---DAYLKMDNVLIDDRRIH 262
              DA   +D  +ID R + 
Sbjct: 61  QWMDALNNLDPFVIDGRVVR 80

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|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 = 53.7 bits (129), Expect = 1e-09
 Identities = 24/70 (34%), Positives = 44/70 (62%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LF+  L+  T++  LE +FS++G+++   V++D+ T  S  + FV F+NP   +DA + M
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 252 DNVLIDDRRI 261
           +   +D R+I
Sbjct: 63  NGKSVDGRQI 72

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

 Score = 52.2 bits (125), Expect = 4e-09
 Identities = 28/72 (38%), Positives = 40/72 (55%), Gaps = 3/72 (4%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK- 250
           +F+  LN  T+DD L   F +FG+V  C V+RD  TG S  + F+ F  PKS  +   K 
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 251 --MDNVLIDDRR 260
             +D  +ID +R
Sbjct: 61  HILDGKIIDPKR 72

This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. . Length = 76

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

 Score = 51.6 bits (124), Expect = 6e-09
 Identities = 22/70 (31%), Positives = 35/70 (50%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  L+P    + L   F+ FG+++   V++D  TG S  Y FV F   +  E+A   M
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 252 DNVLIDDRRI 261
           +   +  R I
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|240835 cd12389, RRM2_RAVER, RNA recognition motif 2 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 51.5 bits (124), Expect = 7e-09
 Identities = 21/73 (28%), Positives = 35/73 (47%)

Query: 191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK 250
           +L V  L    +D+    + S FG V  C ++  + TG+S  Y FVE+ +  S   A  +
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQ 60

Query: 251 MDNVLIDDRRIHA 263
           +D   I  R++  
Sbjct: 61  LDGKQIGGRKLQV 73

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

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

 Score = 51.5 bits (124), Expect = 7e-09
 Identities = 24/71 (33%), Positives = 43/71 (60%)

Query: 191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK 250
            L V  L+  T++ DL  +FSR+G +   +V+ D+ TG S  + FV F++ +  ++A  +
Sbjct: 1   CLGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKER 60

Query: 251 MDNVLIDDRRI 261
           ++ + ID RRI
Sbjct: 61  LNGMEIDGRRI 71

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

 Score = 51.6 bits (124), Expect = 7e-09
 Identities = 27/71 (38%), Positives = 41/71 (57%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LFV  L     +DDLE +FS+FG+++   V  DK +G S  +A+V F +P+    AY ++
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 252 DNVLIDDRRIH 262
           D  +   R IH
Sbjct: 65  DGKVFQGRLIH 75

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 51.0 bits (123), Expect = 8e-09
 Identities = 24/70 (34%), Positives = 41/70 (58%), Gaps = 2/70 (2%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L P  +++DL   FS +GKV    ++R+K       +AFVEF +P+  E A  K+
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKL 58

Query: 252 DNVLIDDRRI 261
           + +++D R +
Sbjct: 59  NGLVLDGRTL 68

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

>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 = 1e-08
 Identities = 23/75 (30%), Positives = 43/75 (57%), Gaps = 5/75 (6%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS----CEDA 247
           +F+  L    ++++L+ +FS+FG+V    +++DK+TG S   AFV+F   +S     E A
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 248 Y-LKMDNVLIDDRRI 261
              +   + +D RR+
Sbjct: 63  DNAEDSGLSLDGRRL 77

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

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 5/77 (6%)

Query: 191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQ-----YAFVEFDNPKSCE 245
            LFV  LN  T+++ L+  F + G V    + + K      +     Y FVEF + ++ +
Sbjct: 2   TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61

Query: 246 DAYLKMDNVLIDDRRIH 262
            A  ++   ++D   + 
Sbjct: 62  KALKRLQGTVLDGHALE 78

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|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins

 Score = 50.5 bits (120), Expect = 2e-08
 Identities = 24/70 (34%), Positives = 39/70 (55%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  L+P  + +D++  F+ FGK++   V++D  TG S  Y FV F N    E+A + M
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 252 DNVLIDDRRI 261
               +  R+I
Sbjct: 64  GGQWLGGRQI 73

This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

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

 Score = 50.0 bits (120), Expect = 2e-08
 Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK 250
            LFV  L       +L+  FS+FGKV  C V  DK TG S  Y FV F +    E+A  K
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 251 MDNVLIDDRRIH 262
               +++  ++ 
Sbjct: 61  -QKHILEGNKLQ 71

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

 Score = 49.9 bits (120), Expect = 3e-08
 Identities = 21/70 (30%), Positives = 36/70 (51%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L    +++DL+ +F +FG+V    VI D+ TG S  + FVE +  +    A  K+
Sbjct: 2   LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKL 61

Query: 252 DNVLIDDRRI 261
           +      R +
Sbjct: 62  NGTDFGGRTL 71

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 49.0 bits (118), Expect = 3e-08
 Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 5/56 (8%)

Query: 209 IFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR 264
           +FS FG V   ++++ K       +AFVEF   ++ E A   ++ VL   R +   
Sbjct: 4   LFSPFGNVEKIKLLKKKP-----GFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVD 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|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins

 Score = 49.5 bits (119), Expect = 3e-08
 Identities = 22/58 (37%), Positives = 33/58 (56%)

Query: 204 DDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI 261
            +L   FS+FG V    + R K TG S  YAFVEF++P+  +     M+N L+ +R +
Sbjct: 14  PELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLL 71

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

 Score = 53.3 bits (128), Expect = 7e-08
 Identities = 28/84 (33%), Positives = 39/84 (46%), Gaps = 6/84 (7%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L+P  ++  L  +F  FG V    V RD VT  SL Y +V F NP   E A   M
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 252 DNVLIDDRRIHARGEEWNMWKRRE 275
           +   +  + I        MW +R+
Sbjct: 63  NFKRLGGKPIRI------MWSQRD 80

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

 Score = 48.4 bits (116), Expect = 8e-08
 Identities = 19/61 (31%), Positives = 35/61 (57%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L+   ++DDL  IF  FG++   ++ RD  TG S  Y F++F + +  + A  ++
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 252 D 252
           +
Sbjct: 61  N 61

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|241213 cd12769, RRM1_HuR, RNA recognition motif 1 in vertebrate Hu-antigen R (HuR)

 Score = 47.8 bits (113), Expect = 1e-07
 Identities = 25/70 (35%), Positives = 37/70 (52%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L V  L    + D+L  +FS  G+V   ++IRDKV G SL Y FV + N K  E A   +
Sbjct: 4   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL 63

Query: 252 DNVLIDDRRI 261
           + + +  + I
Sbjct: 64  NGLRLQSKTI 73

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

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 2/79 (2%)

Query: 188 PEN--VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
           PEN   +FV  L    +D+ L   FS++      +V+RDK TG S  Y FV F +P    
Sbjct: 3   PENDFRIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYL 62

Query: 246 DAYLKMDNVLIDDRRIHAR 264
            A  +M+   + +R I  R
Sbjct: 63  KAMKEMNGKYVGNRPIKLR 81

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

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

 Score = 51.5 bits (123), Expect = 2e-07
 Identities = 20/56 (35%), Positives = 33/56 (58%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           L V  L    + +++  +F+  G++  C+++RDKVTG SL Y FV +  P+  E A
Sbjct: 6   LIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKA 61

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|241215 cd12771, RRM1_HuB, RNA recognition motif 1 in vertebrate Hu-antigen B (HuB)

 Score = 47.4 bits (112), Expect = 2e-07
 Identities = 22/70 (31%), Positives = 40/70 (57%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L V  L    + ++L+ +F   G++  C+++RDK+TG SL Y FV + +PK  E A   +
Sbjct: 7   LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 66

Query: 252 DNVLIDDRRI 261
           + + +  + I
Sbjct: 67  NGLRLQTKTI 76

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

 Score = 47.5 bits (113), Expect = 2e-07
 Identities = 21/70 (30%), Positives = 32/70 (45%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LFV  L    + +DL   FS    +    V+ D  TG+S  Y FV F   +  ++A  K+
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 252 DNVLIDDRRI 261
            N  +  R +
Sbjct: 62  KNKKLHGRIL 71

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

 Score = 47.4 bits (112), Expect = 2e-07
 Identities = 24/70 (34%), Positives = 39/70 (55%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  L+P  + DD++  F+ FG+++   V++D  TG S  Y FV F N    E+A  +M
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 252 DNVLIDDRRI 261
               +  R+I
Sbjct: 64  GGQWLGGRQI 73

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

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

 Score = 46.9 bits (112), Expect = 3e-07
 Identities = 21/59 (35%), Positives = 32/59 (54%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK 250
           LFV  L    +++DL   FS++G V   E++ DK TG    +AFV FD+    +   L+
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

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

 Score = 47.0 bits (112), Expect = 3e-07
 Identities = 27/80 (33%), Positives = 38/80 (47%), Gaps = 11/80 (13%)

Query: 188 PENVLFVCKLNPVTSDDDLEII----FSRFGKVNCCEVIRDKVTGDSLQ--YAFVEFDNP 241
           P   +FV  L    SDD+LE      FS++G      ++  KV  D  Q  YAFV+F N 
Sbjct: 1   PSACVFVASLPASKSDDELEAAVTEHFSKYG-----TLVFVKVLRDWRQRPYAFVQFTND 55

Query: 242 KSCEDAYLKMDNVLIDDRRI 261
              ++A  K    ++D R I
Sbjct: 56  DDAKNALAKGQGTILDGRHI 75

This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 86

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

 Score = 46.7 bits (111), Expect = 4e-07
 Identities = 23/74 (31%), Positives = 38/74 (51%)

Query: 191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK 250
           V+++  L     + +L+  FS+FG V    V R K TG+S  Y F++F NP+    A   
Sbjct: 1   VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 251 MDNVLIDDRRIHAR 264
           M+N L+  + +   
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|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 46.6 bits (111), Expect = 5e-07
 Identities = 18/66 (27%), Positives = 38/66 (57%), Gaps = 3/66 (4%)

Query: 202 SDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI 261
           +D++   +F   G V  C+++RDK TG S  + FV++ + +  + A   ++ + + ++RI
Sbjct: 13  TDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRI 72

Query: 262 ---HAR 264
              +AR
Sbjct: 73  KVAYAR 78

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

 Score = 46.4 bits (111), Expect = 5e-07
 Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +F+  L+    +  L   FS FG +  C+V  D+  G S  Y FV F+  ++   A  K+
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDE-NGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 252 DNVLIDDRRIH 262
           + +L++D+++ 
Sbjct: 64  NGMLLNDKKVF 74

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|241214 cd12770, RRM1_HuD, RNA recognition motif 1 in vertebrate Hu-antigen D (HuD)

 Score = 46.3 bits (109), Expect = 7e-07
 Identities = 21/70 (30%), Positives = 38/70 (54%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L V  L    + ++   +F   G++  C+++RDK+TG SL Y FV + +PK  E A   +
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 252 DNVLIDDRRI 261
           + + +  + I
Sbjct: 65  NGLRLQTKTI 74

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|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 = 46.0 bits (109), Expect = 7e-07
 Identities = 24/70 (34%), Positives = 34/70 (48%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LF+  L     D +L  +F  FG V   +V  D+ T  S  + FV FDNP S + A   M
Sbjct: 7   LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66

Query: 252 DNVLIDDRRI 261
           +   I  +R+
Sbjct: 67  NGFQIGMKRL 76

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

 Score = 45.9 bits (109), Expect = 8e-07
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
           + LFV  L    + ++LE +F + G V    ++ ++ +G     A+VE++N  S   A L
Sbjct: 3   HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNR-SGKPKGLAYVEYENESSASQAVL 61

Query: 250 KMDNVLIDDRRI 261
           KMD   I ++ I
Sbjct: 62  KMDGTEIKEKTI 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|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 45.7 bits (109), Expect = 8e-07
 Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 10/77 (12%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQ------YAFVEFDNPKSCE 245
           ++V  L+    +DDL  IFS+FG+V   E IR     D  Q      +AFV F +  S E
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEV---ESIRIPKKQDEKQGRLNNGFAFVTFKDASSAE 59

Query: 246 DAYLKMDNVLIDDRRIH 262
           +A L+++   +  R+I 
Sbjct: 60  NA-LQLNGTELGGRKIS 75

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|241216 cd12772, RRM1_HuC, RNA recognition motif 1 in vertebrate Hu-antigen C (HuC)

 Score = 45.9 bits (108), Expect = 9e-07
 Identities = 19/70 (27%), Positives = 38/70 (54%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L V  L    + ++ + +F   G++  C+++RDK+TG SL Y FV + +P   + A   +
Sbjct: 6   LIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTL 65

Query: 252 DNVLIDDRRI 261
           + + +  + I
Sbjct: 66  NGLKLQTKTI 75

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

 Score = 45.7 bits (108), Expect = 9e-07
 Identities = 18/63 (28%), Positives = 34/63 (53%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L    +  +LE +FS++G++    ++RD++TG S    F+ FD     E+A   +
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 252 DNV 254
           +  
Sbjct: 63  NGQ 65

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|240915 cd12471, RRM1_MSSP2, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 45.5 bits (107), Expect = 1e-06
 Identities = 20/56 (35%), Positives = 32/56 (57%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           L++  L+P T+D DL  +   +GK+   + I DK T     Y FV+FD+P + + A
Sbjct: 4   LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 59

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

 Score = 45.6 bits (108), Expect = 1e-06
 Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 4/77 (5%)

Query: 189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAY 248
              LFV  LN  TSD  L   F+R+GK+  C V+ D  T  S  + F+ F +    ++A 
Sbjct: 2   LCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61

Query: 249 L----KMDNVLIDDRRI 261
                 +D   I+ +R 
Sbjct: 62  EAQPHSIDGNQIELKRA 78

This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 79

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

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 22/61 (36%), Positives = 35/61 (57%)

Query: 201 TSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRR 260
           T+ DDL  +F ++G+V    + RD+ T +S  +AFV F + +  EDA   MD   +D R 
Sbjct: 10  TTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKELDGRE 69

Query: 261 I 261
           +
Sbjct: 70  L 70

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|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 45.4 bits (107), Expect = 1e-06
 Identities = 27/75 (36%), Positives = 36/75 (48%), Gaps = 1/75 (1%)

Query: 188 PENV-LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
           PE   LF+  L    +D DL   F  FG V   +V  DK T  S  + FV +DNP S + 
Sbjct: 2   PEGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQA 61

Query: 247 AYLKMDNVLIDDRRI 261
           A   M+   I  +R+
Sbjct: 62  AIQAMNGFQIGTKRL 76

This subgroup corresponds to the RRM3 of Bruno protein, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 79

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

 Score = 44.7 bits (106), Expect = 2e-06
 Identities = 25/70 (35%), Positives = 38/70 (54%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LFV  L+    D+ L+  F +FG V    VI D+ TG S  + +V+F++P+  + A   M
Sbjct: 2   LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAM 61

Query: 252 DNVLIDDRRI 261
           D   +D R I
Sbjct: 62  DGKELDGRPI 71

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

 Score = 44.4 bits (105), Expect = 2e-06
 Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 189 ENVLFVCKLNPVTSDDDLEIIF-SRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           E  +FV  L+P  ++ DL  +F SRF      +++ D VTG S  Y FV F +    + A
Sbjct: 1   EYSIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRA 60

Query: 248 YLKMDNVLIDDR 259
            ++M  V    R
Sbjct: 61  LIEMQGVYCGGR 72

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|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK 250
            L V  L+   +++DLE +F R G+V   ++  D+ +G S   A V F+  +  E A  +
Sbjct: 2   RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQ 60

Query: 251 MDNVLIDDRRIH 262
            + VL+D + + 
Sbjct: 61  FNGVLLDGQPMQ 72

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

 Score = 44.1 bits (105), Expect = 3e-06
 Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 8/77 (10%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           ++V  L P  +  +LE  F ++G +    V R    G    +AFVEF++P+  EDA   +
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVAR-NPPG----FAFVEFEDPRDAEDAVRAL 56

Query: 252 DNVLIDDRRI---HARG 265
           D   I   R+    +RG
Sbjct: 57  DGRRICGNRVRVELSRG 73

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

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

 Score = 48.1 bits (114), Expect = 4e-06
 Identities = 17/63 (26%), Positives = 35/63 (55%)

Query: 190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
           N ++V  ++P  S+ D++ +F  FG++  C++ R         Y F+E++N +S  +A  
Sbjct: 205 NRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIA 264

Query: 250 KMD 252
            M+
Sbjct: 265 SMN 267

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

 Score = 43.4 bits (103), Expect = 4e-06
 Identities = 21/56 (37%), Positives = 33/56 (58%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           +++  L P T+D+DLE +   FGK+   + I DK T     Y FV+FD+P++   A
Sbjct: 3   VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKA 58

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

 Score = 47.3 bits (112), Expect = 4e-06
 Identities = 21/64 (32%), Positives = 38/64 (59%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L    +DD L+ IF ++G++    ++RDK+TG     AFV F+  +  ++A   +
Sbjct: 196 LYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISAL 255

Query: 252 DNVL 255
           +NV+
Sbjct: 256 NNVI 259

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

 Score = 43.6 bits (103), Expect = 4e-06
 Identities = 19/54 (35%), Positives = 31/54 (57%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
           +F+  L+  T+ + L   FS+FG++  C V+RD  T  S  + FV F +P S +
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVD 54

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

 Score = 47.5 bits (113), Expect = 5e-06
 Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  L+    +  L   FS+FG +  C+V  D   G S  Y FV F+  +S + A  K+
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKV 149

Query: 252 DNVLIDDRRI 261
           + +L++D+ +
Sbjct: 150 NGMLLNDKEV 159

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

 Score = 43.6 bits (103), Expect = 5e-06
 Identities = 26/81 (32%), Positives = 42/81 (51%), Gaps = 6/81 (7%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK- 250
           LFV  L+  T+ + L   FS++G+V  C +++DK T  S  + FV+F +P +C    L  
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDP-NCVGTVLAG 60

Query: 251 ----MDNVLIDDRRIHARGEE 267
               +D   ID +    RG +
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|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 43.7 bits (103), Expect = 5e-06
 Identities = 19/64 (29%), Positives = 33/64 (51%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L    ++D+L  IF  +G +  C ++RDK TG     AFV +D  +  + A   +
Sbjct: 3   LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 252 DNVL 255
           +  +
Sbjct: 63  NGTI 66

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

 Score = 43.4 bits (103), Expect = 5e-06
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 2/73 (2%)

Query: 189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAY 248
            N +FV  + P T++++L   FSRFG V   ++I D+  G S  Y FV F+  +  E   
Sbjct: 2   PNRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKI- 59

Query: 249 LKMDNVLIDDRRI 261
           L M N+    +++
Sbjct: 60  LAMGNLNFRGKKL 72

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

 Score = 43.5 bits (103), Expect = 5e-06
 Identities = 19/75 (25%), Positives = 31/75 (41%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
           P  + LFV  L    ++D+L+  F  FG V    +      G    + FV FD+P++ + 
Sbjct: 1   PDSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQK 60

Query: 247 AYLKMDNVLIDDRRI 261
                      D R+
Sbjct: 61  ILANKPIYFRGDHRL 75

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

 Score = 43.0 bits (102), Expect = 6e-06
 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 8/71 (11%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LFV  L   T+ ++L  +F ++G V  C+V+++        Y FV  +  +  EDA   +
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVVKN--------YGFVHMEEEEDAEDAIKAL 53

Query: 252 DNVLIDDRRIH 262
           +      +RI+
Sbjct: 54  NGYEFMGKRIN 64

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

 Score = 43.0 bits (102), Expect = 6e-06
 Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 9/66 (13%)

Query: 192 LFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK 250
           +FV  LN    S +DLE IFS++GK+    + +         Y FV+FDN +    A   
Sbjct: 3   VFVGNLNTDKVSKEDLEEIFSKYGKILGISLHKG--------YGFVQFDNEEDARAAVAG 54

Query: 251 MDNVLI 256
            +   I
Sbjct: 55  ENGREI 60

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

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

 Score = 44.6 bits (105), Expect = 7e-06
 Identities = 24/70 (34%), Positives = 36/70 (51%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LF+  L+  T D  L   F+ FG V   +VI D+ TG S  + FV F++  +   A  +M
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 252 DNVLIDDRRI 261
           D   ++ R I
Sbjct: 97  DGKELNGRHI 106

Length = 144

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

 Score = 43.1 bits (102), Expect = 7e-06
 Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 3/78 (3%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  +   T  DDL  +F ++G +    +  D  T     +A+V+F++ +  EDA   +
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 252 DNVLIDDRRIH---ARGE 266
           D      R I    A+G+
Sbjct: 63  DRTRFLGREIEIQFAQGD 80

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

>gnl|CDD|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 42.9 bits (102), Expect = 8e-06
 Identities = 19/48 (39%), Positives = 29/48 (60%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFD 239
           LFV  L+P  ++ DLE  FSRFG V+  E+I+ K  G    +A+++  
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLR 49

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

 Score = 42.7 bits (101), Expect = 8e-06
 Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 4/77 (5%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL-- 249
           LF+  L+  T+DD L+  FS++G++  C V++D  T  S  + FV F +    + A    
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNAR 61

Query: 250 --KMDNVLIDDRRIHAR 264
             K+D   ++ +R   R
Sbjct: 62  PHKVDGREVEPKRAVPR 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|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family

 Score = 46.3 bits (110), Expect = 1e-05
 Identities = 33/119 (27%), Positives = 62/119 (52%), Gaps = 7/119 (5%)

Query: 182 EADAAPPENV--LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFD 239
           E +AAP +    L+V  L+P  ++D L  +F++FG++    V++D  +G S  +AFV F+
Sbjct: 169 EREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFE 227

Query: 240 NPKSCEDAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEKEEIDEKKEEEEKEDRAMI 298
             +    A  +M+   I        G++  +  R ++  E+E    +K EE +++R M 
Sbjct: 228 KHEDAAKAVEEMNGKKIGLA---KEGKKLYV-GRAQKRAEREAELRRKFEELQQERKMK 282

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|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 = 42.6 bits (101), Expect = 1e-05
 Identities = 19/72 (26%), Positives = 39/72 (54%)

Query: 190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
           N +F+  L    S+D ++ +   FGK+    +++D  TG S  YAF E+ +P   + A  
Sbjct: 1   NKIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIA 60

Query: 250 KMDNVLIDDRRI 261
            ++ + + D+++
Sbjct: 61  GLNGMQLGDKKL 72

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

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 18/74 (24%), Positives = 42/74 (56%), Gaps = 2/74 (2%)

Query: 190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
           NV +V  L     D+ L+ +F ++GK+   +V++D   G S  + FV F+N ++ + A  
Sbjct: 3   NV-YVKNLGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVE 60

Query: 250 KMDNVLIDDRRIHA 263
           +++   ++ ++++ 
Sbjct: 61  ELNGKEVNGKKLYV 74

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

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

 Score = 42.0 bits (98), Expect = 2e-05
 Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 4/72 (5%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA---- 247
           +F+  L+  TS D L   FS+FG++  C V+RD  T  S  + FV F +P S +      
Sbjct: 2   MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQP 61

Query: 248 YLKMDNVLIDDR 259
           + ++D+  ID +
Sbjct: 62  HHELDSKTIDPK 73

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|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 42.5 bits (99), Expect = 2e-05
 Identities = 25/86 (29%), Positives = 42/86 (48%), Gaps = 10/86 (11%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L++  L P T+D DL  +   +GK+   + I DK T     Y FV+FD+P + + A    
Sbjct: 10  LYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAV--- 66

Query: 252 DNVLIDDRRIHARGEEWNMWKRREEE 277
                    + A G +  M K++E++
Sbjct: 67  -------SALKASGVQAQMAKQQEQD 85

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|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 193 FVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMD 252
           FV  ++  T+ ++L+  F   G +N   ++ DK TG    +A++EF +  S E+A L ++
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENA-LLLN 61

Query: 253 NVLIDDRRI 261
                 R+I
Sbjct: 62  ESEFRGRQI 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|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 41.9 bits (98), Expect = 2e-05
 Identities = 22/65 (33%), Positives = 37/65 (56%)

Query: 197 LNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLI 256
           L+  T++ DL  +FSR+G +    V+ D+ TG S  +AFV F+     ++A    + + +
Sbjct: 7   LSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMEL 66

Query: 257 DDRRI 261
           D RRI
Sbjct: 67  DGRRI 71

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

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 20/71 (28%), Positives = 39/71 (54%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LF+  L    +++DLE +FS++G ++   +  DK+T     +AFV +  P+    A+ ++
Sbjct: 5   LFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAEL 64

Query: 252 DNVLIDDRRIH 262
           D  +   R +H
Sbjct: 65  DGTVFQGRLLH 75

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

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGK-VNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK 250
           LF+  L+P   +  L   FS FG  +   +++RD  TG+S  +AF+ +D+ ++ + A   
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 251 MDNVLIDDRRIH 262
           M+   + +R I 
Sbjct: 64  MNGQYLCNRPIT 75

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|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 = 41.5 bits (98), Expect = 2e-05
 Identities = 15/61 (24%), Positives = 29/61 (47%)

Query: 201 TSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRR 260
            +++ L  IFS  G V    ++ D+ TG    Y F EF++ ++   A   ++    + R 
Sbjct: 10  ATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGYEFNGRA 69

Query: 261 I 261
           +
Sbjct: 70  L 70

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

 Score = 41.2 bits (97), Expect = 3e-05
 Identities = 19/55 (34%), Positives = 33/55 (60%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
           +FV  L P  ++++ +  FS+FGKV   ++++D  TG S  + FV FD+  + E 
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVER 56

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|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 41.6 bits (97), Expect = 3e-05
 Identities = 26/77 (33%), Positives = 35/77 (45%)

Query: 185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
             P    LF+  L     D DL  +F  FG V   +V  DK T  S  + FV +DNP S 
Sbjct: 3   EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSA 62

Query: 245 EDAYLKMDNVLIDDRRI 261
           + A   M+   I  +R+
Sbjct: 63  QAAIQAMNGFQIGMKRL 79

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

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 21/71 (29%), Positives = 33/71 (46%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LFV  L   T+D+ LE  FS  G +  C V++DK +     + +V F   +  + A  + 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 252 DNVLIDDRRIH 262
                  R+IH
Sbjct: 62  KKTKFGGRKIH 72

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

 Score = 41.0 bits (97), Expect = 4e-05
 Identities = 20/59 (33%), Positives = 31/59 (52%)

Query: 194 VCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMD 252
           V  L+    +DDL  +F  FG ++   + +DK TG S  +AFV F   +  E A  K++
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLN 62

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

>gnl|CDD|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 41.0 bits (95), Expect = 4e-05
 Identities = 20/56 (35%), Positives = 31/56 (55%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           L++  L P T+D DL  +   +GK+   + I DK T     Y FV+FD+P + + A
Sbjct: 7   LYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKA 62

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

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 3/69 (4%)

Query: 193 FVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMD 252
           +V  L+P T+ D L   FS+ G+V    +  D+      +YAFVEF    S  +A LK++
Sbjct: 8   YVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDE--TQPTRYAFVEFAEQTSVINA-LKLN 64

Query: 253 NVLIDDRRI 261
             +   R +
Sbjct: 65  GAMFGGRPL 73

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

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

 Score = 40.6 bits (95), Expect = 5e-05
 Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 4/73 (5%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAY--- 248
           +FV  L+  T+  DL+  FS+FG+V  C +  D VTG S  + FV F +  S E      
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 249 -LKMDNVLIDDRR 260
             K+D  +ID +R
Sbjct: 61  EHKLDGRVIDPKR 73

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|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 = 40.6 bits (96), Expect = 6e-05
 Identities = 19/62 (30%), Positives = 33/62 (53%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LFV +L    +++D+  +F  +G +    +IRDK TG S   AFV+F + +  + A   +
Sbjct: 2   LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 252 DN 253
             
Sbjct: 62  HG 63

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

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

 Score = 40.4 bits (95), Expect = 6e-05
 Identities = 18/54 (33%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
           L+V  L    +  +LE +FS +G++    ++ D VTG S    F+ FD  K  E
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFD--KRIE 54

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

 Score = 43.1 bits (101), Expect = 1e-04
 Identities = 18/60 (30%), Positives = 34/60 (56%)

Query: 202 SDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI 261
           +D +L  +F   G +N C ++RD  TG S  YAFV+F +    + A   ++ + + ++R+
Sbjct: 120 TDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRL 179

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

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 19/51 (37%), Positives = 29/51 (56%)

Query: 193 FVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
           FV +L+    + DL   FS+ GKV    +IRD+ +  S   A+VEF + +S
Sbjct: 3   FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEES 53

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 17/70 (24%), Positives = 40/70 (57%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +++  L    ++ D+  +FS++G++    ++RDK TG S  +AF+ +++ +S   A   +
Sbjct: 12  IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

Query: 252 DNVLIDDRRI 261
           + + +  R I
Sbjct: 72  NGIKLLGRTI 81

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

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 4/61 (6%)

Query: 201 TSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNV-LIDDR 259
           T++ DL+  FS FG++   +V +D  TG S  + FV F      ED    +    +ID R
Sbjct: 11  TTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRF---ADYEDQVKVLSQRHMIDGR 67

Query: 260 R 260
            
Sbjct: 68  W 68

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

 Score = 39.4 bits (92), Expect = 1e-04
 Identities = 22/70 (31%), Positives = 34/70 (48%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  L+P  +D  L   FS F   +   V+ D  +G S  Y FV F + +  E+A  +M
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 252 DNVLIDDRRI 261
           +   +  R I
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|241202 cd12758, RRM1_hnRPDL, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 27/73 (36%), Positives = 37/73 (50%), Gaps = 4/73 (5%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAY--- 248
           +F+  L+  TS  DL    SRFG+V  C +  D VTG S  + FV F +  S +      
Sbjct: 2   MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELK 61

Query: 249 -LKMDNVLIDDRR 260
             K+D  LID +R
Sbjct: 62  EHKLDGKLIDPKR 74

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|240813 cd12367, RRM2_RBM45, RNA recognition motif 2 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 13/40 (32%), Positives = 24/40 (60%)

Query: 202 SDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
           +++DL   F  FG +    +++DK TG+S  + +V+F  P
Sbjct: 13  TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKP 52

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|241217 cd12773, RRM2_HuR, RNA recognition motif 2 in vertebrate Hu-antigen R (HuR)

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 20/56 (35%), Positives = 31/56 (55%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           L++  L    +  D+E +FSRFG++    V+ D+ TG S   AF+ FD     E+A
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEA 58

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|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 38.7 bits (90), Expect = 2e-04
 Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 202 SDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI 261
           + ++LE  FS  G +N   ++ DK +G    YA++EF   +   +A + +D      R I
Sbjct: 12  TAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFAT-RDSVEAAVALDESSFRGRVI 70

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

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 4/73 (5%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL-- 249
           +FV  L+  TS  DL+  F++FG+V  C +  D  TG S  + F+ F +  S E      
Sbjct: 2   MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQK 61

Query: 250 --KMDNVLIDDRR 260
             ++D  LID ++
Sbjct: 62  EHRLDGRLIDPKK 74

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

 Score = 38.7 bits (90), Expect = 3e-04
 Identities = 24/56 (42%), Positives = 28/56 (50%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           LFV  L     + DL   FS+FG V   EVI DK TG    + FV F N  S + A
Sbjct: 2   LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKA 57

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

>gnl|CDD|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 38.9 bits (90), Expect = 3e-04
 Identities = 22/74 (29%), Positives = 41/74 (55%)

Query: 188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           P   L V  L+  T++ DL  +FS++G +    ++ D+ +  S  +AFV F+N    ++A
Sbjct: 8   PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 67

Query: 248 YLKMDNVLIDDRRI 261
             + + + +D RRI
Sbjct: 68  KERANGMELDGRRI 81

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|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 1/68 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L V  L+   SDDD++ +F+ FG +    V  D+ +G SL  A V F+       A  + 
Sbjct: 3   LLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDR-SGRSLGTADVVFERRADALKAMKQY 61

Query: 252 DNVLIDDR 259
           + V +D R
Sbjct: 62  NGVPLDGR 69

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

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

 Score = 38.2 bits (89), Expect = 4e-04
 Identities = 22/66 (33%), Positives = 38/66 (57%), Gaps = 4/66 (6%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN----PKSCEDA 247
           +FV  L+  T++DD++  FS+FGKV    ++ DK T     + FV F++     K CE  
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEIH 61

Query: 248 YLKMDN 253
           + +++N
Sbjct: 62  FHEINN 67

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

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 15/73 (20%), Positives = 35/73 (47%)

Query: 191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK 250
           ++FV  ++    ++D+   F+ FG++    +  D+ TG    YA +E++  K  + A   
Sbjct: 8   IIFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEG 67

Query: 251 MDNVLIDDRRIHA 263
           ++   +  + I  
Sbjct: 68  LNGKELLGQTISV 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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
           PP + LF+       ++DDL   F+ FG++    V++DK T +S   A+V+F    S   
Sbjct: 1   PPNSRLFIV-CGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAAR 59

Query: 247 AYLKMD 252
           A  +M+
Sbjct: 60  AMEEMN 65

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|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)

 Score = 37.6 bits (87), Expect = 5e-04
 Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 11/76 (14%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +F+ +LNP   + D+E  F  +G++   ++ R         + FVEFD+P+  +DA  ++
Sbjct: 2   VFIGRLNPAAREKDVERFFKGYGRIRDIDLKRG--------FGFVEFDDPRDADDAVYEL 53

Query: 252 DNVLIDDRRI---HAR 264
           D   + + R+   HAR
Sbjct: 54  DGKELCNERVTIEHAR 69

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

 Score = 37.5 bits (87), Expect = 5e-04
 Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L+P  ++D L+ IF   G V   ++I DK     + Y FVE+      E A   +
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDK-NNKGVNYGFVEYHQSHDAEIALQTL 59

Query: 252 DNVLIDDRRI 261
           +   I++  I
Sbjct: 60  NGRQIENNEI 69

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|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 37.5 bits (87), Expect = 5e-04
 Identities = 16/56 (28%), Positives = 31/56 (55%), Gaps = 8/56 (14%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           LFV  L P  ++ ++  +F ++GKV  C++I++        Y FV  D+  + ++A
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--------YGFVHMDDKTAADEA 50

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|241080 cd12636, RRM2_Bruno_like, RNA recognition motif 2 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 37.9 bits (88), Expect = 5e-04
 Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 1/59 (1%)

Query: 189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           E  LFV  L+   +++D+ I+F+ FG +  C V+RD+  G S   AFV F + +   +A
Sbjct: 1   ERKLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQ-NGQSRGCAFVTFASRQCALNA 58

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|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 37.7 bits (88), Expect = 6e-04
 Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 2/69 (2%)

Query: 193 FVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMD 252
           FV  L   T   DL+ IF     V    ++RDK T     + +VEF++ +S ++A L+ D
Sbjct: 5   FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEA-LEYD 62

Query: 253 NVLIDDRRI 261
             L DDR +
Sbjct: 63  GALFDDRSL 71

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

>gnl|CDD|241220 cd12776, RRM2_HuC, RNA recognition motif 2 in vertebrate Hu-antigen C (HuC)

 Score = 37.7 bits (87), Expect = 6e-04
 Identities = 18/56 (32%), Positives = 31/56 (55%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           L+V  L    S  ++E +FS++G++    ++ D+VTG S    F+ FD     E+A
Sbjct: 4   LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEA 59

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

 Score = 37.2 bits (87), Expect = 7e-04
 Identities = 16/63 (25%), Positives = 32/63 (50%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           ++V  L+   +++ L  +F + G V    + +D+VT     Y FVEF + +  + A   M
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 252 DNV 254
           + +
Sbjct: 61  NMI 63

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

 Score = 37.3 bits (87), Expect = 8e-04
 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIF-SRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK 250
           +FV  L P  +D  L+  F +R+  V   +V+ D VTG S  Y FV F +    + A  +
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 251 MDNVLIDDRRI 261
           M+ V    R +
Sbjct: 64  MNGVYCSSRPM 74

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|240736 cd12290, RRM1_LARP7, RNA recognition motif 1 in La-related protein 7 (LARP7) and similar proteins

 Score = 37.3 bits (87), Expect = 8e-04
 Identities = 19/62 (30%), Positives = 35/62 (56%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           ++V  L    + + L+ +FS++G V    + R K TGD   +AF+EF+ P+  + A   +
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 252 DN 253
           +N
Sbjct: 62  NN 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|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 36.9 bits (86), Expect = 9e-04
 Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
           LFV     VT  + L  +F     +  C++ RD  TG S  +A+V + NP S
Sbjct: 3   LFVVVSKSVT-QEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPAS 53

This subfamily corresponds to the RRM3 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 75

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

 Score = 37.4 bits (86), Expect = 9e-04
 Identities = 18/56 (32%), Positives = 31/56 (55%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           L+V  L    +  +LE +FS++G++    ++ D+VTG S    F+ FD     E+A
Sbjct: 5   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 60

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

 Score = 37.0 bits (86), Expect = 9e-04
 Identities = 18/59 (30%), Positives = 33/59 (55%)

Query: 203 DDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI 261
           +D +   FS FG +   ++  D VT     +AFVE++ P++ + A  +M+ V++  R I
Sbjct: 14  EDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGGRNI 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|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 36.9 bits (86), Expect = 9e-04
 Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEV--IRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
           L+V  L   T+D+DLE   +  G V+   +     K  G S  +A+VEF +  +      
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 250 KMDNVLIDDRR 260
           K++    + ++
Sbjct: 61  KLEGREFNGKK 71

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

 Score = 39.5 bits (92), Expect = 0.001
 Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 3/60 (5%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  L+P T +  L  +F  FG V   ++IRD  T     Y FV   N    ++A + +
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTN---YDEAAMAI 328

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 3/70 (4%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L+   ++D L  +FS+ G +  C++IR+    D   YAFVE+ + +S   A   M
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREH-GNDP--YAFVEYYDHRSAAAALQTM 57

Query: 252 DNVLIDDRRI 261
           +  LI  + I
Sbjct: 58  NGRLILGQEI 67

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

>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen B (HuB)

 Score = 37.5 bits (86), Expect = 0.001
 Identities = 18/56 (32%), Positives = 31/56 (55%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           L+V  L    +  +LE +FS++G++    ++ D+VTG S    F+ FD     E+A
Sbjct: 8   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 63

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 3/60 (5%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  L P   +  L  +FS FG V   +VIRD  T     Y FV      + E+AY  +
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFV---TMTNYEEAYSAI 60

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

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 15/56 (26%), Positives = 29/56 (51%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           +FV  L+P T+++ +   F +FG +   E+  DK T     + F+ FD+ +  +  
Sbjct: 2   IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKI 57

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|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 13/36 (36%), Positives = 20/36 (55%)

Query: 221 VIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLI 256
           +IR+K+TG    Y FVEF +  + E    K++   I
Sbjct: 32  IIRNKLTGGPAGYCFVEFADEATAERCLHKLNGKPI 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|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 3/70 (4%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LF+  L   T+  DL   F RFG++   ++   K  G+   YAF+++ +  S   A  KM
Sbjct: 5   LFIGNLEKTTTYSDLREAFERFGEI--IDIDIKKQGGNP-AYAFIQYADIASVVKAMRKM 61

Query: 252 DNVLIDDRRI 261
           D   + + R+
Sbjct: 62  DGEYLGNNRV 71

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|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast Saccharomyces cerevisiae SET domain-containing protein 1 (scSet1p) and similar proteins

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 20/104 (19%), Positives = 40/104 (38%), Gaps = 11/104 (10%)

Query: 197 LNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP--------KSCEDAY 248
             P TS+D ++  FS FG++       D  T   L    +++           K+   A 
Sbjct: 10  FQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYGSPGKPDRAAKAALKAV 69

Query: 249 LKMDNVLIDDRRIHARGEEWNMWKRREEEEEKEEIDEKKEEEEK 292
            K  +  I          E N  +R+ E+ + + I + +++ + 
Sbjct: 70  RKAQDCRIGGAEFKV---ELNPNERKLEKIKDKLIKQNRKKSQI 110

This subfamily corresponds to the RRM of scSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, which is encoded by SET1 from the yeast S. cerevisiae. It is a nuclear protein that may play a role in both silencing and activating transcription. scSet1p is closely related to the SET domain proteins of multicellular organisms, which are implicated in diverse aspects of cell morphology, growth control, and chromatin-mediated transcriptional silencing. scSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 110

>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 = 36.5 bits (85), Expect = 0.001
 Identities = 24/68 (35%), Positives = 42/68 (61%), Gaps = 2/68 (2%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  L+    +D+L  +FS+ G++    ++++   G S  YA+VEF+N +S ++A LK+
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEA-LKL 59

Query: 252 DNVLIDDR 259
           D  LI  R
Sbjct: 60  DRELIKGR 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|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 15/53 (28%), Positives = 27/53 (50%)

Query: 191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
            +FV  +    SDD +  +  + GKV   + ++D  TG    + F EF++P+ 
Sbjct: 2   TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEG 54

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

>gnl|CDD|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 18/70 (25%), Positives = 32/70 (45%), Gaps = 1/70 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           + V  L    ++D L   F   G+V   +V+R +  G S ++ FV F + +  + A    
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTR-DGKSRRFGFVGFKSEEDAQQAVKYF 61

Query: 252 DNVLIDDRRI 261
           +   ID  +I
Sbjct: 62  NKTFIDTSKI 71

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 1/69 (1%)

Query: 193 FVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMD 252
           FV  L     +++L   F   G V    ++RD+ TG    + +V F    S   A LK++
Sbjct: 3   FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALA-LKLN 61

Query: 253 NVLIDDRRI 261
            + +  R+I
Sbjct: 62  GIKLKGRKI 70

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

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 8/56 (14%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           L+V    P TS+  +  IFS +G V   ++I +        +AFVEF++ +S   A
Sbjct: 2   LYVRPFPPDTSESAIREIFSPYGAVKEVKMISN--------FAFVEFESLESAIRA 49

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|238902 cd01921, cyclophilin_RRM, cyclophilin_RRM: cyclophilin-type peptidylprolyl cis- trans isomerase domain occuring with a C-terminal RNA recognition motif domain (RRM)

 Score = 38.1 bits (89), Expect = 0.002
 Identities = 10/16 (62%), Positives = 12/16 (75%)

Query: 104 DIRITHAVILEDPYED 119
           DIRI H  IL+DP+ D
Sbjct: 150 DIRIKHTHILDDPFPD 165

This subfamily of the cyclophilin domain family contains a number of eukaryotic cyclophilins having the RRM domain including the nuclear proteins: human hCyP-57, Arabidopsis thaliana AtCYP59, Caenorhabditis elegans CeCyP-44 and Paramecium tetrurelia Kin241. The Kin241 protein has been shown to have a role in cell morphogenesis. Length = 166

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

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 19/71 (26%), Positives = 29/71 (40%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L     +  L   F  FG +   ++  D  T     +AFVEF+ P+    A   M
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 252 DNVLIDDRRIH 262
           +   +  R I 
Sbjct: 61  NESELFGRTIR 71

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

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 17/62 (27%), Positives = 32/62 (51%)

Query: 202 SDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI 261
           +++DL  IFS++GKV    +++DK T  S   AF+ F + +        ++N  +  R +
Sbjct: 14  TNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNNKELFGRTL 73

Query: 262 HA 263
             
Sbjct: 74  KC 75

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|240913 cd12467, RRM_Srp1p_like, RNA recognition motif 1 in fission yeast pre-mRNA-splicing factor Srp1p and similar proteins

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V      T   DL   F R+G++  C++   + T  S  +AFVE+++ +  EDAY +M
Sbjct: 2   LYVTGFGAETRARDLAYEFERYGRLVRCDIPPPR-TFQSRPFAFVEYESHRDAEDAYEEM 60

Query: 252 DNVLIDDRR 260
                 D  
Sbjct: 61  HGRRFPDTG 69

This subgroup corresponds to the RRM domain in Srp1p encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but not essential for growth. Srp1p is closely related to the SR protein family found in metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. Some family members also contain another RRM domain. Length = 78

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

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 3/62 (4%)

Query: 201 TSDDDLEIIFSRFGKVNCCEV-IRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDR 259
            ++ DL+ +FS FG V   EV I  K  G    +AFV+F +    E A   ++   I  R
Sbjct: 11  CTEADLKKLFSPFGFV--WEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGR 68

Query: 260 RI 261
            +
Sbjct: 69  PV 70

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|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 35.6 bits (83), Expect = 0.003
 Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 9/56 (16%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           L+V  L P TS  +LE  F RFG +   +    +       YA++E++   S E A
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRIDYDPGR------NYAYIEYE---SIEAA 47

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|240784 cd12338, RRM1_SRSF1_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 3/70 (4%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           ++V  L     + D+E +F ++G +   + I  K       +AFVEF++P+  EDA    
Sbjct: 2   IYVGNLPGDIRERDIEDLFYKYGPI---KAIDLKNRRRGPPFAFVEFEDPRDAEDAVRGR 58

Query: 252 DNVLIDDRRI 261
           D    D  R+
Sbjct: 59  DGYDFDGYRL 68

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

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 1/66 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L+    D+ L   FS FG +   +V+ D+  G S  + FV F +P+    A  +M
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDE-KGRSKGFGFVCFSSPEEATKAVTEM 62

Query: 252 DNVLID 257
           +  +I 
Sbjct: 63  NGRIIG 68

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|240783 cd12337, RRM1_SRSF4_like, RNA recognition motif 1 in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 19/77 (24%), Positives = 39/77 (50%), Gaps = 11/77 (14%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +++ +L     + D+E  F  +G+      IR+    +   + FVEF++P+  +DA  ++
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGR------IREINLKNG--FGFVEFEDPRDADDAVYEL 53

Query: 252 DNVLIDDRRI---HARG 265
           +   +   R+   HARG
Sbjct: 54  NGKELCGERVIVEHARG 70

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

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
           LFV  L+   ++DD+  +F  FG +  C ++R    G+S   AFV+F +
Sbjct: 4   LFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGP-DGNSKGCAFVKFSS 51

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

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

 Score = 35.0 bits (80), Expect = 0.004
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 4/73 (5%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL-- 249
           +F+  L+  T+  DL+  FS+FG+V  C +  D +TG S  + FV F   +S +      
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 250 --KMDNVLIDDRR 260
             K++  +ID +R
Sbjct: 61  EHKLNGKVIDPKR 73

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

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 18/56 (32%), Positives = 29/56 (51%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           LFV ++     + DL  +F +FGK+    V++DK TG     AF+ +   +S   A
Sbjct: 8   LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKA 63

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

 Score = 35.0 bits (81), Expect = 0.004
 Identities = 26/72 (36%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
            +LFV  L   T+ +DL   F   G      ++ DK TG S   AFVEFD  ++   A L
Sbjct: 1   FILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKA-L 59

Query: 250 KMDNVLIDDRRI 261
           K+ + L+  R+I
Sbjct: 60  KLHHTLLKGRKI 71

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	309
KOG0415|consensus	479		100.0
KOG0113|consensus	335		99.78
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.72
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.66
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.61
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.6
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.56
KOG0149|consensus	247		99.56
KOG0122|consensus	270		99.53
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.5
KOG0121|consensus	153		99.5
KOG0126|consensus	219		99.5
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.48
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.48
KOG4207|consensus	256		99.46
KOG0125|consensus	376		99.45
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.45
PLN03120	260	nucleic acid binding protein; Provisional	99.45
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.44
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.44
PLN03213	759	repressor of silencing 3; Provisional	99.43
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.43
smart00362	72	RRM_2 RNA recognition motif.	99.41
KOG0107|consensus	195		99.41
KOG0148|consensus	321		99.41
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.39
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.38
smart00360	71	RRM RNA recognition motif.	99.38
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.38
KOG0117|consensus	506		99.37
PLN03121	243	nucleic acid binding protein; Provisional	99.36
KOG0114|consensus	124		99.36
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.35
KOG0127|consensus	678		99.34
KOG0145|consensus	360		99.34
KOG0111|consensus	298		99.33
KOG0130|consensus	170		99.32
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.31
KOG0148|consensus	321		99.29
KOG0131|consensus	203		99.29
KOG0108|consensus	435		99.28
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.26
KOG0146|consensus	371		99.25
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.21
KOG0127|consensus	678		99.21
KOG0145|consensus	360		99.21
smart00361	70	RRM_1 RNA recognition motif.	99.2
KOG0144|consensus	510		99.2
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.18
KOG0147|consensus	549		99.18
KOG0124|consensus	544		99.17
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.16
KOG0131|consensus	203		99.16
KOG4208|consensus	214		99.12
KOG0117|consensus	506		99.11
KOG0144|consensus	510		99.11
KOG0226|consensus	290		99.09
KOG0105|consensus	241		99.09
KOG4206|consensus	221		99.08
KOG0109|consensus	346		99.0
KOG0123|consensus	369		98.98
KOG0109|consensus	346		98.93
KOG0123|consensus	369		98.88
KOG0124|consensus	544		98.86
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.86
KOG4212|consensus	608		98.85
KOG0110|consensus	725		98.84
KOG4205|consensus	311		98.77
KOG4661|consensus	940		98.77
KOG0146|consensus	371		98.75
KOG0132|consensus	894		98.74
KOG4205|consensus	311		98.72
KOG0153|consensus	377		98.7
KOG0533|consensus	243		98.67
KOG0110|consensus	725		98.66
KOG1548|consensus	382		98.65
KOG1457|consensus	284		98.59
KOG4209|consensus	231		98.57
KOG0151|consensus	877		98.54
KOG4212|consensus	608		98.54
KOG0116|consensus	419		98.51
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.29
KOG4454|consensus	267		98.25
KOG4660|consensus	549		98.21
KOG0106|consensus	216		98.16
KOG0120|consensus	500		98.15
KOG1190|consensus	492		97.98
KOG0147|consensus	549		97.86
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.85
KOG1995|consensus	351		97.78
KOG4211|consensus	510		97.69
KOG4210|consensus	285		97.68
KOG1457|consensus	284		97.66
KOG4206|consensus	221		97.62
KOG2314|consensus	698		97.58
KOG4211|consensus	510		97.51
KOG3152|consensus	278		97.5
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.47
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.44
KOG4849|consensus	498		97.43
KOG1190|consensus	492		97.24
KOG0129|consensus	520		97.18
KOG0106|consensus	216		97.17
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.15
KOG1548|consensus	382		96.97
KOG0120|consensus	500		96.88
KOG1456|consensus	494		96.79
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.65
KOG2193|consensus	584		96.62
KOG4307|consensus	944		96.59
KOG0128|consensus	881		96.55
KOG1855|consensus	484		96.45
KOG1456|consensus	494		96.24
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.23
KOG0112|consensus	975		96.16
KOG0105|consensus	241		96.15
KOG0129|consensus	520		96.1
KOG1365|consensus	508		96.05
KOG2416|consensus	718		95.89
KOG4307|consensus	944		95.85
KOG2202|consensus	260		95.77
KOG1996|consensus	378		95.32
KOG0115|consensus	275		95.24
KOG0128|consensus	881		95.12
KOG4676|consensus	479		94.92
KOG1365|consensus	508		94.61
KOG0112|consensus	975		94.47
KOG2068|consensus	327		94.13
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	93.62
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	93.49
KOG2253|consensus	668		92.53
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	92.46
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	91.33
cd01921	166	cyclophilin_RRM cyclophilin_RRM: cyclophilin-type	91.26
KOG2135|consensus	526		91.14
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	90.84
KOG4210|consensus	285		90.49
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	89.55
KOG2318|consensus	650		89.15
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	88.52
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	87.57
KOG4660|consensus	549		87.51
KOG2591|consensus	684		86.31
KOG4574|consensus	1007		85.44
KOG0804|consensus	493		85.01
KOG2891|consensus	445		84.3
KOG4285|consensus	350		83.8

>KOG0415|consensus

Probab=100.00  E-value=3.1e-39  Score=293.74  Aligned_cols=170  Identities=66%  Similarity=1.060  Sum_probs=166.7

Q ss_pred             ccccCCccccceEeecCCCCCCCCCCCC-CCCCCchhhhhcCCCCCCCCCccccCCCHHHHHHHHHHHHHHHHhhHHhHh
Q psy15676         99 FKRKNDIRITHAVILEDPYEDLPELVYP-PSPEPTRELLANGLIGADEDIDETAGLSAQEIEELRAEREAKARATILEIV  177 (309)
Q Consensus        99 ~rp~~~iri~h~~il~dPf~~p~~l~~p-~~p~p~~~~~~~~~~~~de~~~~~e~~~~~e~~e~~~~~e~~~~~~~~e~~  177 (309)
                      ++||+||||.||+||+|||++||.|..| ++|+|+++++..+++..|++.+++++.+.+++++..++++++++|.+++++
T Consensus       148 ~rPykdIRI~HTiiLdDPFddpp~l~~p~rspsPt~e~l~~g~i~~de~~d~~~g~saeel~e~~~e~ea~~~A~iLEmv  227 (479)
T KOG0415|consen  148 NRPYKDIRIKHTIILDDPFDDPPDLAEPMRSPSPTPEQLVKGRIRLDEDEDDDEGLSAEELEEVLAEKEAKAQAVILEMV  227 (479)
T ss_pred             CCcccceeeeeeEEecCCCCCchhhccCCCCCCCCHHHhhccccccCcccccccccCHHHHHHHHHHHHHHhhHhHHHHh
Confidence            7999999999999999999999999988 999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCCCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeC
Q psy15676        178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLID  257 (309)
Q Consensus       178 ~~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~  257 (309)
                      |++|.++..||.+.|||+.|+|.+|.++|..+|+.||.|.+|.+++|..||.+..||||+|.+.+++++|+..|++..|+
T Consensus       228 GDlpdAd~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLID  307 (479)
T KOG0415|consen  228 GDLPDADVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLID  307 (479)
T ss_pred             cCCcccccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeec
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CeeEEEEeecC
Q psy15676        258 DRRIHARGEEW  268 (309)
Q Consensus       258 gr~I~V~~a~~  268 (309)
                      +++|+|+|+++
T Consensus       308 DrRIHVDFSQS  318 (479)
T KOG0415|consen  308 DRRIHVDFSQS  318 (479)
T ss_pred             cceEEeehhhh
Confidence            99999999986

>KOG0113|consensus

Probab=99.78  E-value=2.5e-18  Score=154.47  Aligned_cols=92  Identities=36%  Similarity=0.582  Sum_probs=86.7

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .+|.+||||+.|+++++|..|+..|+.||.|..+.|+.|+.||+++|||||+|..+.++..|++..+|..|+|+.|.|++
T Consensus        98 gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDv  177 (335)
T KOG0113|consen   98 GDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDV  177 (335)
T ss_pred             CCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEe
Confidence            57889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecC---chhhccchH
Q psy15676        266 EEW---NMWKRREEE  277 (309)
Q Consensus       266 a~~---~~~~~r~~~  277 (309)
                      ...   ++|.+++..
T Consensus       178 ERgRTvkgW~PRRLG  192 (335)
T KOG0113|consen  178 ERGRTVKGWLPRRLG  192 (335)
T ss_pred             ccccccccccccccc
Confidence            874   678777653

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

Probab=99.72  E-value=5.1e-17  Score=135.88  Aligned_cols=85  Identities=28%  Similarity=0.359  Sum_probs=80.0

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ....++|||+|||+.+++++|+.+|++||.|.++.++.|..|+.++|||||+|.+.++|+.|+..||+..|+|+.|+|++
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      +....
T Consensus       111 a~~~~  115 (144)
T PLN03134        111 ANDRP  115 (144)
T ss_pred             CCcCC
Confidence            97543

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.66  E-value=5.6e-16  Score=146.90  Aligned_cols=82  Identities=26%  Similarity=0.387  Sum_probs=78.5

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      +.+|||+|||+.+++++|..+|++||.|.+++++.|..||.++|||||+|.+.++|.+|+..|||..++|+.|.|+|+.+
T Consensus       269 ~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~  348 (352)
T TIGR01661       269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTN  348 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccC
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999976


Q ss_pred             ch
Q psy15676        269 NM  270 (309)
Q Consensus       269 ~~  270 (309)
                      +.
T Consensus       349 ~~  350 (352)
T TIGR01661       349 KA  350 (352)
T ss_pred             CC
Confidence            54

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.61  E-value=4.4e-15  Score=107.41  Aligned_cols=70  Identities=36%  Similarity=0.680  Sum_probs=67.2

Q ss_pred             EEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEE
Q psy15676        192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH  262 (309)
Q Consensus       192 lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~  262 (309)
                      |||+|||+++|+++|..+|++||.|..+.+..+ .++.++|||||+|.+.++|.+|+..|+|..++|+.|+
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            799999999999999999999999999999988 6799999999999999999999999999999999885

(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 ....

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.60  E-value=3.8e-15  Score=141.22  Aligned_cols=81  Identities=26%  Similarity=0.546  Sum_probs=78.1

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      +.++|||+|||+.+++++|+.+|+.||+|.+|.+++|+.+|+++|||||+|.+.++|.+|+..|||..+.|+.|.|.+++
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            46899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             C
Q psy15676        268 W  268 (309)
Q Consensus       268 ~  268 (309)
                      +
T Consensus        82 ~   82 (352)
T TIGR01661        82 P   82 (352)
T ss_pred             c
Confidence            4

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.56  E-value=1.6e-14  Score=137.07  Aligned_cols=83  Identities=25%  Similarity=0.452  Sum_probs=79.3

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ....++|||+|||+++|+++|+.+|+.||.|.+|+|+.|..|++++|||||+|.+.++|..|+..|+|..+.+++|+|.+
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~  183 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSY  183 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeec
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecC
Q psy15676        266 EEW  268 (309)
Q Consensus       266 a~~  268 (309)
                      +.+
T Consensus       184 a~p  186 (346)
T TIGR01659       184 ARP  186 (346)
T ss_pred             ccc
Confidence            865

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).

>KOG0149|consensus

Probab=99.56  E-value=5.7e-15  Score=129.28  Aligned_cols=78  Identities=31%  Similarity=0.416  Sum_probs=73.6

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      -++||||||++.++.++|+.+|++||+|....++.|+.||+|+|||||+|.+.++|.+|++. .+-.||||+..|++|.
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA~   89 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLAS   89 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchhh
Confidence            36899999999999999999999999999999999999999999999999999999999975 6689999999998875

>KOG0122|consensus

Probab=99.53  E-value=4e-14  Score=124.46  Aligned_cols=83  Identities=27%  Similarity=0.349  Sum_probs=79.8

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ...++|-|.||+.++++++|.++|.+||.|.++.+.+|+.||.++|||||.|.+.++|.+|+..|||+-++.-.|.|.||
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            45689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCc
Q psy15676        267 EWN  269 (309)
Q Consensus       267 ~~~  269 (309)
                      ++.
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            864

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.50  E-value=1.4e-13  Score=100.23  Aligned_cols=70  Identities=34%  Similarity=0.639  Sum_probs=65.0

Q ss_pred             EEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEE
Q psy15676        192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH  262 (309)
Q Consensus       192 lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~  262 (309)
                      |||+|||+++++++|..+|+.||.|..+.+..++. |.++|+|||+|.+.++|..|+..++|..++|+.|.
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            79999999999999999999999999999999877 89999999999999999999999999999999874

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 ....

>KOG0121|consensus

Probab=99.50  E-value=4.6e-14  Score=112.87  Aligned_cols=80  Identities=21%  Similarity=0.341  Sum_probs=76.5

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      .++|||||||++.++|++|.++|+++|.|..|.|-.|+.+-.+.|||||+|.+.++|+.|++.++|..++.++|.+++.-
T Consensus        35 ~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   35 KSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             hcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            45899999999999999999999999999999999999999999999999999999999999999999999999999864

>KOG0126|consensus

Probab=99.50  E-value=3.2e-15  Score=126.08  Aligned_cols=80  Identities=24%  Similarity=0.382  Sum_probs=76.3

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      .+.-|||||||+..|+.||..+|++||.|.+|.+++|+.||+|+||||+.|++..+.-.|+..|||..|.||.|+|+...
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            45789999999999999999999999999999999999999999999999999999999999999999999999998653

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

Probab=99.48  E-value=1.8e-13  Score=137.28  Aligned_cols=80  Identities=21%  Similarity=0.380  Sum_probs=76.7

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      ..++|||+||++.+++++|+.+|++||.|.++.++.|+.||+++|||||+|.+.++|..|+..|||..++|+.|.|..+.
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999998654

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.

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

Probab=99.48  E-value=1.8e-13  Score=137.22  Aligned_cols=81  Identities=21%  Similarity=0.386  Sum_probs=77.9

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      ..++|||+||++++++++|+.+|+.||.|.++.+.+++.+|.++|||||+|.+.++|.+|+..|||+.++|+.|+|.++.
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            34799999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             C
Q psy15676        268 W  268 (309)
Q Consensus       268 ~  268 (309)
                      .
T Consensus       283 ~  283 (612)
T TIGR01645       283 T  283 (612)
T ss_pred             C
Confidence            5

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.

>KOG4207|consensus

Probab=99.46  E-value=7.9e-14  Score=119.91  Aligned_cols=79  Identities=33%  Similarity=0.513  Sum_probs=77.0

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      .+|-|-||.+-|+.++|..+|++||.|.+|.|++|+.|+.++|||||-|....+|+.|+..|+|..++|+.|.|++|+.
T Consensus        14 ~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ary   92 (256)
T KOG4207|consen   14 TSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMARY   92 (256)
T ss_pred             eeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhhc
Confidence            5899999999999999999999999999999999999999999999999999999999999999999999999999985

>KOG0125|consensus

Probab=99.45  E-value=2.2e-13  Score=124.18  Aligned_cols=81  Identities=25%  Similarity=0.422  Sum_probs=75.2

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      +.-.++|+|+|+|+..-+.||+.+|++||.|.+|+|+.+.  .-|||||||+|++.++|++|-.+|+|..|.||+|.|+.
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~  170 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNN  170 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEec
Confidence            3445899999999999999999999999999999999986  35899999999999999999999999999999999999


Q ss_pred             ecC
Q psy15676        266 EEW  268 (309)
Q Consensus       266 a~~  268 (309)
                      |..
T Consensus       171 ATa  173 (376)
T KOG0125|consen  171 ATA  173 (376)
T ss_pred             cch
Confidence            874

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.45  E-value=3.9e-13  Score=127.64  Aligned_cols=82  Identities=28%  Similarity=0.526  Sum_probs=76.5

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCC--eeEEEEe
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDD--RRIHARG  265 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~g--r~I~V~~  265 (309)
                      ..++|||+|||+.+|+++|+++|++||.|..+.++.++.||+++|||||+|.+.++|++|+..||+..+.|  ++|.|.+
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            35789999999999999999999999999999999999999999999999999999999999999998876  7899998


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      |...
T Consensus       272 a~~~  275 (346)
T TIGR01659       272 AEEH  275 (346)
T ss_pred             CCcc
Confidence            8753

This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.45  E-value=4.7e-13  Score=120.57  Aligned_cols=76  Identities=22%  Similarity=0.345  Sum_probs=70.6

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      .++|||+|||+.+++++|+.+|+.||.|.++.|+.+..   ++|||||+|.+.++|..|+. |+|..|+|+.|.|..+..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            47999999999999999999999999999999998763   56999999999999999995 999999999999999863

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

Probab=99.44  E-value=3.9e-13  Score=135.54  Aligned_cols=79  Identities=32%  Similarity=0.477  Sum_probs=76.1

Q ss_pred             EEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecCc
Q psy15676        191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWN  269 (309)
Q Consensus       191 ~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~~  269 (309)
                      +|||+|||+++|+++|..+|++||.|.+|++++|..|++++|||||+|.+.++|.+|+..+|+..+.|+.|+|.+++.+
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~~~   80 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRD   80 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccccc
Confidence            7999999999999999999999999999999999999999999999999999999999999999999999999998643

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

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

Probab=99.44  E-value=5.1e-13  Score=131.19  Aligned_cols=82  Identities=24%  Similarity=0.397  Sum_probs=78.2

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      +...+|||+|||+.+|+++|..+|++||.|..+.++.+..+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.++
T Consensus       184 p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a  263 (457)
T TIGR01622       184 PNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYA  263 (457)
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEc
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cC
Q psy15676        267 EW  268 (309)
Q Consensus       267 ~~  268 (309)
                      ..
T Consensus       264 ~~  265 (457)
T TIGR01622       264 QD  265 (457)
T ss_pred             cC
Confidence            63

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.

>PLN03213 repressor of silencing 3; Provisional

Probab=99.43  E-value=4.9e-13  Score=127.52  Aligned_cols=80  Identities=21%  Similarity=0.350  Sum_probs=73.3

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCH--HHHHHHHHHcCCceeCCeeEEEE
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP--KSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~--~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      ..+.+||||||++.+++++|...|+.||.|.++.|+  +.||  +|||||+|.+.  .++.+|+..|||..+.|+.|+|+
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            345799999999999999999999999999999999  4567  89999999987  68999999999999999999999


Q ss_pred             eecCch
Q psy15676        265 GEEWNM  270 (309)
Q Consensus       265 ~a~~~~  270 (309)
                      .|++..
T Consensus        84 KAKP~Y   89 (759)
T PLN03213         84 KAKEHY   89 (759)
T ss_pred             eccHHH
Confidence            998743

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

Probab=99.43  E-value=8.5e-13  Score=131.28  Aligned_cols=81  Identities=21%  Similarity=0.425  Sum_probs=77.4

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      +..+|||+|||+.+++++|..+|+.||.|..+.++.+..+|.++|||||+|.+.++|..|+..|||..|+|+.|.|.+|.
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            35799999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             C
Q psy15676        268 W  268 (309)
Q Consensus       268 ~  268 (309)
                      .
T Consensus       374 ~  374 (509)
T TIGR01642       374 V  374 (509)
T ss_pred             c
Confidence            4

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

>smart00362 RRM_2 RNA recognition motif

Probab=99.41  E-value=1.6e-12  Score=92.91  Aligned_cols=72  Identities=31%  Similarity=0.615  Sum_probs=67.3

Q ss_pred             EEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       191 ~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      +|||+|||..++.++|..+|.+||.+..+.+..+.  +.++|+|||+|.+.++|..|+..++|..++|+.|.|+
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            58999999999999999999999999999988776  7789999999999999999999999999999998873

>KOG0107|consensus

Probab=99.41  E-value=9.4e-13  Score=110.65  Aligned_cols=80  Identities=28%  Similarity=0.408  Sum_probs=72.9

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      -+-.++||||||+..+++.+|...|..||.+.++-|..+     +.|||||+|++..+|+.|+..|+|..|.|.+|.|.+
T Consensus         7 ~~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~   81 (195)
T KOG0107|consen    7 RNGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVEL   81 (195)
T ss_pred             cCCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEe
Confidence            345789999999999999999999999999999988764     459999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      +....
T Consensus        82 S~G~~   86 (195)
T KOG0107|consen   82 STGRP   86 (195)
T ss_pred             ecCCc
Confidence            97643

>KOG0148|consensus

Probab=99.41  E-value=3.8e-13  Score=119.86  Aligned_cols=82  Identities=32%  Similarity=0.479  Sum_probs=79.0

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      ...+||+-|.+.++.++|++.|.+||.|.++++++|..|++|+|||||.|.+.++|+.|+..|||.-|++|.|+-.||..
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            45899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             ch
Q psy15676        269 NM  270 (309)
Q Consensus       269 ~~  270 (309)
                      +.
T Consensus       142 Kp  143 (321)
T KOG0148|consen  142 KP  143 (321)
T ss_pred             Cc
Confidence            65

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

Probab=99.39  E-value=1.6e-12  Score=131.10  Aligned_cols=83  Identities=23%  Similarity=0.391  Sum_probs=77.9

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ....+|||+||++.+++++|+.+|++||.|.++.++.+ .+|.++|||||.|.+.++|.+|+..|||..++|++|.|.+|
T Consensus       283 ~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a  361 (562)
T TIGR01628       283 AQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALA  361 (562)
T ss_pred             cCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEec
Confidence            45678999999999999999999999999999999999 58999999999999999999999999999999999999999


Q ss_pred             cCch
Q psy15676        267 EWNM  270 (309)
Q Consensus       267 ~~~~  270 (309)
                      +.+.
T Consensus       362 ~~k~  365 (562)
T TIGR01628       362 QRKE  365 (562)
T ss_pred             cCcH
Confidence            7543

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

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

Probab=99.38  E-value=2.1e-12  Score=126.84  Aligned_cols=82  Identities=26%  Similarity=0.348  Sum_probs=76.9

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+..+|||+|||+.+++++|..+|++||.|..|.++.|+.||.++|||||+|.+.++|.+|+. |+|..+.|++|.|.+
T Consensus        86 ~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQS  164 (457)
T ss_pred             ccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEee
Confidence            3456899999999999999999999999999999999999999999999999999999999995 899999999999998


Q ss_pred             ecC
Q psy15676        266 EEW  268 (309)
Q Consensus       266 a~~  268 (309)
                      ++.
T Consensus       165 ~~~  167 (457)
T TIGR01622       165 SQA  167 (457)
T ss_pred             cch
Confidence            754

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.

>smart00360 RRM RNA recognition motif

Probab=99.38  E-value=2.8e-12  Score=91.18  Aligned_cols=71  Identities=34%  Similarity=0.640  Sum_probs=67.1

Q ss_pred             ecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        194 VCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       194 V~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      |+|||..+++++|..+|++||.|..+.+..++.++.++|||||+|.+.++|..|+..+++..++|+.|.|+
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            68999999999999999999999999999888789999999999999999999999999999999998873

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.38  E-value=2.3e-12  Score=114.90  Aligned_cols=80  Identities=31%  Similarity=0.545  Sum_probs=77.2

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      .++|||+|||+.+++++|..+|..||.|..+.+..++.+|.++|||||.|.+.++|..|+..++|..+.|++|.|.++..
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            59999999999999999999999999999999999998999999999999999999999999999999999999999763

>KOG0117|consensus

Probab=99.37  E-value=3.9e-12  Score=120.22  Aligned_cols=83  Identities=25%  Similarity=0.378  Sum_probs=78.0

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeC-CeeEEEEe
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLID-DRRIHARG  265 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~-gr~I~V~~  265 (309)
                      +.++-||||+||.++.|++|.-+|++.|.|-.+++++|+.+|.++|||||+|.+.+.|+.|++.||++.|- |+.|.|+.
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            44689999999999999999999999999999999999999999999999999999999999999999885 99999988


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      +..+
T Consensus       161 Svan  164 (506)
T KOG0117|consen  161 SVAN  164 (506)
T ss_pred             eeec
Confidence            8753

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.36  E-value=3.6e-12  Score=113.24  Aligned_cols=77  Identities=25%  Similarity=0.338  Sum_probs=69.8

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      +.+.+|||+||++.+|+++|+.+|+.||.|.+|.|++|.   ...|||||+|.+.++++.|+ .|+|..|.|++|.|..+
T Consensus         3 ~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~   78 (243)
T PLN03121          3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRW   78 (243)
T ss_pred             CCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeC
Confidence            346899999999999999999999999999999999884   44589999999999999999 59999999999998764


Q ss_pred             c
Q psy15676        267 E  267 (309)
Q Consensus       267 ~  267 (309)
                      .
T Consensus        79 ~   79 (243)
T PLN03121         79 G   79 (243)
T ss_pred             c
Confidence            4

>KOG0114|consensus

Probab=99.36  E-value=5.8e-12  Score=97.35  Aligned_cols=78  Identities=14%  Similarity=0.259  Sum_probs=71.8

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      ...|||+|||+.+|.++...+|++||.|..+++-..+   ..+|-|||.|++..+|.+|+..|+|..++++.+.|-+-++
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k---~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~   94 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK---ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQP   94 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecCcc---CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCH
Confidence            5789999999999999999999999999999986554   3579999999999999999999999999999999999876


Q ss_pred             c
Q psy15676        269 N  269 (309)
Q Consensus       269 ~  269 (309)
                      .
T Consensus        95 ~   95 (124)
T KOG0114|consen   95 E   95 (124)
T ss_pred             H
Confidence            3

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

Probab=99.35  E-value=2.8e-12  Score=128.39  Aligned_cols=79  Identities=23%  Similarity=0.305  Sum_probs=73.0

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeC-CeeEEEEee
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLID-DRRIHARGE  266 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~-gr~I~V~~a  266 (309)
                      ..++|||+|||+++++++|..+|++||.|.+++|++| .+|.++|||||+|.+.++|.+|+..||+..+. |+.|.|..+
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            3589999999999999999999999999999999999 78999999999999999999999999998885 788777765


Q ss_pred             c
Q psy15676        267 E  267 (309)
Q Consensus       267 ~  267 (309)
                      .
T Consensus       136 ~  136 (578)
T TIGR01648       136 V  136 (578)
T ss_pred             c
Confidence            4

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.

>KOG0127|consensus

Probab=99.34  E-value=3.4e-12  Score=123.07  Aligned_cols=80  Identities=30%  Similarity=0.441  Sum_probs=74.9

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHc-----CC-ceeCCeeEE
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM-----DN-VLIDDRRIH  262 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l-----~g-~~i~gr~I~  262 (309)
                      +.+|||.|||+++|+++|...|++||.|.++.++.++.||.++|.|||.|.+..+|..||...     .| ..++||.|.
T Consensus       292 ~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lk  371 (678)
T KOG0127|consen  292 GKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLK  371 (678)
T ss_pred             cceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEe
Confidence            479999999999999999999999999999999999999999999999999999999999865     23 789999999


Q ss_pred             EEeecC
Q psy15676        263 ARGEEW  268 (309)
Q Consensus       263 V~~a~~  268 (309)
                      |..|-.
T Consensus       372 v~~Av~  377 (678)
T KOG0127|consen  372 VTLAVT  377 (678)
T ss_pred             eeeccc
Confidence            999864

>KOG0145|consensus

Probab=99.34  E-value=4.2e-12  Score=112.73  Aligned_cols=83  Identities=28%  Similarity=0.537  Sum_probs=78.8

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ....+.|.|.=||...|+++++++|+..|+|++|++++|+.||.|.|||||.|.+..+|++|+..+||..+..+.|+|+|
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            34456788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecC
Q psy15676        266 EEW  268 (309)
Q Consensus       266 a~~  268 (309)
                      |++
T Consensus       118 ARP  120 (360)
T KOG0145|consen  118 ARP  120 (360)
T ss_pred             ccC
Confidence            986

>KOG0111|consensus

Probab=99.33  E-value=6.9e-13  Score=115.10  Aligned_cols=81  Identities=20%  Similarity=0.277  Sum_probs=78.5

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      ..++||||+|...+++.-|...|-+||.|..+.++.|..+++.+|||||+|...++|.+|+..||+..+.||.|+|++|+
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             C
Q psy15676        268 W  268 (309)
Q Consensus       268 ~  268 (309)
                      +
T Consensus        89 P   89 (298)
T KOG0111|consen   89 P   89 (298)
T ss_pred             C
Confidence            6

>KOG0130|consensus

Probab=99.32  E-value=3.4e-12  Score=103.08  Aligned_cols=83  Identities=17%  Similarity=0.241  Sum_probs=79.0

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      +..|||.++...+|++++...|..||.|.++.+-.|+.||..+|||+|+|.+...|++|+..+||..+.|..|.|+|+-.
T Consensus        72 GwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv  151 (170)
T KOG0130|consen   72 GWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFV  151 (170)
T ss_pred             eEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEe
Confidence            56999999999999999999999999999999999999999999999999999999999999999999999999999976


Q ss_pred             chh
Q psy15676        269 NMW  271 (309)
Q Consensus       269 ~~~  271 (309)
                      ++.
T Consensus       152 ~gp  154 (170)
T KOG0130|consen  152 KGP  154 (170)
T ss_pred             cCC
Confidence            443

>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=99.31  E-value=1.8e-11  Score=87.84  Aligned_cols=74  Identities=35%  Similarity=0.601  Sum_probs=68.6

Q ss_pred             EEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       191 ~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      +|+|+|||+.+++++|..+|..||.|..+.+..+..+ .++|+|||+|.+.++|..|+..+++..++|+.+.|.+
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            4899999999999999999999999999999887654 7789999999999999999999999999999999864

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).

>KOG0148|consensus

Probab=99.29  E-value=1.1e-11  Score=110.62  Aligned_cols=77  Identities=23%  Similarity=0.443  Sum_probs=72.0

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .+.+++|||||++..+|+++|+..|++||.|.+|++..++      |||||.|++.++|..|+..|||..|.|..+++.|
T Consensus       161 sp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q------GYaFVrF~tkEaAahAIv~mNntei~G~~VkCsW  234 (321)
T KOG0148|consen  161 SPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ------GYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSW  234 (321)
T ss_pred             CCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEeccc------ceEEEEecchhhHHHHHHHhcCceeCceEEEEec
Confidence            4667999999999999999999999999999999998764      8999999999999999999999999999999998


Q ss_pred             ecC
Q psy15676        266 EEW  268 (309)
Q Consensus       266 a~~  268 (309)
                      -+.
T Consensus       235 GKe  237 (321)
T KOG0148|consen  235 GKE  237 (321)
T ss_pred             ccc
Confidence            663

>KOG0131|consensus

Probab=99.29  E-value=4.1e-12  Score=107.47  Aligned_cols=81  Identities=23%  Similarity=0.334  Sum_probs=78.0

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ....|||||||+.-++++.|.++|-+.|+|.++.+++|+.|+..+||||++|.++++|+-|++.||...+.|++|+|..+
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            45689999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             c
Q psy15676        267 E  267 (309)
Q Consensus       267 ~  267 (309)
                      .
T Consensus        87 s   87 (203)
T KOG0131|consen   87 S   87 (203)
T ss_pred             c
Confidence            6

>KOG0108|consensus

Probab=99.28  E-value=7.8e-12  Score=120.97  Aligned_cols=80  Identities=23%  Similarity=0.378  Sum_probs=77.9

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecCc
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWN  269 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~~  269 (309)
                      +.+||||+|+++++++|..+|+..|.|.+++++.|+.||+++||||++|.+.+.+..|+..|||..+.|++|+|.|+...
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            89999999999999999999999999999999999999999999999999999999999999999999999999998753

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

Probab=99.26  E-value=2.6e-11  Score=120.29  Aligned_cols=78  Identities=21%  Similarity=0.336  Sum_probs=72.3

Q ss_pred             CCCCcEEEecCCCC-CCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        186 APPENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       186 ~~~~~~lfV~nL~~-~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      .+++++|||+||++ .+|+++|..+|+.||.|.+|.++.++     +|||||+|.+.++|..|+..|||..|+|+.|.|.
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~  346 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVC  346 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEE
Confidence            45778999999998 69999999999999999999998763     5999999999999999999999999999999999


Q ss_pred             eecC
Q psy15676        265 GEEW  268 (309)
Q Consensus       265 ~a~~  268 (309)
                      +++.
T Consensus       347 ~s~~  350 (481)
T TIGR01649       347 PSKQ  350 (481)
T ss_pred             Eccc
Confidence            9864

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).

>KOG0146|consensus

Probab=99.25  E-value=5.9e-12  Score=112.20  Aligned_cols=85  Identities=28%  Similarity=0.429  Sum_probs=81.1

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      +|.+|.|||-.||....+.+|..+|-.||.|.+.++..|+.|..|+|||||.|++..+++.|+..|||+.|+-++|+|++
T Consensus       282 GPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQL  361 (371)
T KOG0146|consen  282 GPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQL  361 (371)
T ss_pred             CCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhh
Confidence            57789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      -+++.
T Consensus       362 KRPkd  366 (371)
T KOG0146|consen  362 KRPKD  366 (371)
T ss_pred             cCccc
Confidence            87643

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

Probab=99.21  E-value=5.7e-11  Score=117.88  Aligned_cols=76  Identities=20%  Similarity=0.212  Sum_probs=69.1

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHH--cCCceeCCeeEEEEe
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK--MDNVLIDDRRIHARG  265 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~--l~g~~i~gr~I~V~~  265 (309)
                      |.++|||+|||+.+++++|..+|++||.|.++.++.      ++|||||+|.+.++|..|+..  +++..++|++|.|++
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~------~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~   74 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLP------GKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNY   74 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEEC------CCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEe
Confidence            468999999999999999999999999999999875      358999999999999999986  478999999999999


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      +...
T Consensus        75 s~~~   78 (481)
T TIGR01649        75 STSQ   78 (481)
T ss_pred             cCCc
Confidence            9753

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

Probab=99.21  E-value=4.1e-11  Score=115.71  Aligned_cols=81  Identities=30%  Similarity=0.345  Sum_probs=75.2

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      +...|.|.|||+.+...+|..+|+.||.|..+.|++.+. |+..|||||.|....+|..|++.|||..|+||+|-|+||.
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~d-gklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV  194 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKD-GKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAV  194 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCC-CCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeec
Confidence            457899999999999999999999999999999997765 6666999999999999999999999999999999999998


Q ss_pred             Cc
Q psy15676        268 WN  269 (309)
Q Consensus       268 ~~  269 (309)
                      ++
T Consensus       195 ~K  196 (678)
T KOG0127|consen  195 DK  196 (678)
T ss_pred             cc
Confidence            63

>KOG0145|consensus

Probab=99.21  E-value=8.4e-11  Score=104.55  Aligned_cols=81  Identities=25%  Similarity=0.343  Sum_probs=77.6

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      +..|||-||.+++.+.-|..+|++||.|.++++++|..|.+.+|||||.+.+.+.|..|+..|||..++++.|.|.|-.+
T Consensus       278 g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtn  357 (360)
T KOG0145|consen  278 GWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTN  357 (360)
T ss_pred             eeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecC
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999998765


Q ss_pred             c
Q psy15676        269 N  269 (309)
Q Consensus       269 ~  269 (309)
                      +
T Consensus       358 k  358 (360)
T KOG0145|consen  358 K  358 (360)
T ss_pred             C
Confidence            4

>smart00361 RRM_1 RNA recognition motif

Probab=99.20  E-value=8.3e-11  Score=86.11  Aligned_cols=62  Identities=24%  Similarity=0.455  Sum_probs=56.1

Q ss_pred             HHHHHHHHh----cCCceeEEE-EeeeCCC--CCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        203 DDDLEIIFS----RFGKVNCCE-VIRDKVT--GDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       203 e~~L~~~F~----~fG~I~~v~-i~~d~~t--g~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      +++|..+|+    .||.|.++. ++.++.+  |.++|||||+|.+.++|.+|+..|||..++|+.|++.
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            568888998    999999995 7777766  9999999999999999999999999999999999863

>KOG0144|consensus

Probab=99.20  E-value=1.5e-11  Score=115.82  Aligned_cols=81  Identities=26%  Similarity=0.432  Sum_probs=74.0

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCc-eeC--CeeEEEEe
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNV-LID--DRRIHARG  265 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~-~i~--gr~I~V~~  265 (309)
                      +.+||||-|+..+||.+++++|++||.|++|.|++|.. |.++|||||.|.+.+.|..|++.|||. .+.  ..+|.|.|
T Consensus       124 e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~-~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkF  202 (510)
T KOG0144|consen  124 ERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPD-GLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKF  202 (510)
T ss_pred             chhhhhhhccccccHHHHHHHHHhhCccchhhheeccc-ccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEe
Confidence            67899999999999999999999999999999999985 899999999999999999999999994 454  57899999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      |..+.
T Consensus       203 ADtqk  207 (510)
T KOG0144|consen  203 ADTQK  207 (510)
T ss_pred             cccCC
Confidence            97643

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

Probab=99.18  E-value=1.1e-10  Score=116.94  Aligned_cols=75  Identities=25%  Similarity=0.385  Sum_probs=69.1

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcC--CceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRF--GKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~f--G~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      ...++|||+||+.++++++|+.+|++|  |.|.+|.++        ++||||+|.+.++|.+|+..|||..|+|+.|+|+
T Consensus       231 ~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~  302 (578)
T TIGR01648       231 AKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVT  302 (578)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            345789999999999999999999999  999998765        3699999999999999999999999999999999


Q ss_pred             eecCc
Q psy15676        265 GEEWN  269 (309)
Q Consensus       265 ~a~~~  269 (309)
                      +|++.
T Consensus       303 ~Akp~  307 (578)
T TIGR01648       303 LAKPV  307 (578)
T ss_pred             EccCC
Confidence            99864

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.

>KOG0147|consensus

Probab=99.18  E-value=4.5e-11  Score=115.72  Aligned_cols=80  Identities=26%  Similarity=0.415  Sum_probs=75.1

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      |...||||||.++++++.|+.+|..||.|..+.+..|..||.++||||++|.+.++|.+|+..|||+.|-|+.|+|..-.
T Consensus       277 p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~  356 (549)
T KOG0147|consen  277 PMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVT  356 (549)
T ss_pred             chhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEee
Confidence            33449999999999999999999999999999999999999999999999999999999999999999999999987654

>KOG0124|consensus

Probab=99.17  E-value=1.9e-11  Score=113.10  Aligned_cols=78  Identities=22%  Similarity=0.409  Sum_probs=75.3

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      +++|||.+.+...++.|+..|..||+|.++.+.+|+.||+.+|||||+|+-.+.|..|++.|||..++||.|+|....
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCC
Confidence            789999999999999999999999999999999999999999999999999999999999999999999999998543

>PF13893 RRM_5: RNA recognition motif

Probab=99.16  E-value=1.9e-10  Score=80.27  Aligned_cols=56  Identities=25%  Similarity=0.464  Sum_probs=50.3

Q ss_pred             HHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        206 LEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       206 L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      |..+|++||.|.++.+..+.     +|+|||+|.+.++|..|+..|||..++|++|+|+||
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            67899999999999886543     589999999999999999999999999999999987

(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 ....

>KOG0131|consensus

Probab=99.16  E-value=5.1e-11  Score=100.90  Aligned_cols=85  Identities=22%  Similarity=0.284  Sum_probs=78.5

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeE-EEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNC-CEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~-v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      +.+..+||+||.+.+++..|...|+.||.+.. -.++++..||.++|||||.|.+.+.+.+|+..|||..+.+++|+|.+
T Consensus        94 ~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~y  173 (203)
T KOG0131|consen   94 DVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSY  173 (203)
T ss_pred             cccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEE
Confidence            45689999999999999999999999999866 48899999999999999999999999999999999999999999999


Q ss_pred             ecCchh
Q psy15676        266 EEWNMW  271 (309)
Q Consensus       266 a~~~~~  271 (309)
                      +..+..
T Consensus       174 a~k~~~  179 (203)
T KOG0131|consen  174 AFKKDT  179 (203)
T ss_pred             EEecCC
Confidence            976543

>KOG4208|consensus

Probab=99.12  E-value=1.6e-10  Score=99.79  Aligned_cols=82  Identities=27%  Similarity=0.350  Sum_probs=75.2

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcC-CceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRF-GKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~f-G~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .....+||..+|..+.+..+..+|.+| |.+...++.+++.||.|+|||||+|++.+.|+-|.+.||++.+.|+.|.|.+
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~v  126 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHV  126 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEE
Confidence            345689999999999999999999888 7888888889999999999999999999999999999999999999999887


Q ss_pred             ecC
Q psy15676        266 EEW  268 (309)
Q Consensus       266 a~~  268 (309)
                      -.+
T Consensus       127 mpp  129 (214)
T KOG4208|consen  127 MPP  129 (214)
T ss_pred             eCc
Confidence            544

>KOG0117|consensus

Probab=99.11  E-value=1.8e-10  Score=109.08  Aligned_cols=74  Identities=28%  Similarity=0.394  Sum_probs=69.2

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      -+.|||.||+.++|++.|+..|++||.|..|..++|        ||||.|.+.++|.+|++.|||..|+|..|.|.+|++
T Consensus       259 VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP  330 (506)
T KOG0117|consen  259 VKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKP  330 (506)
T ss_pred             eeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCC
Confidence            468999999999999999999999999999987754        999999999999999999999999999999999987


Q ss_pred             ch
Q psy15676        269 NM  270 (309)
Q Consensus       269 ~~  270 (309)
                      ..
T Consensus       331 ~~  332 (506)
T KOG0117|consen  331 VD  332 (506)
T ss_pred             hh
Confidence            43

>KOG0144|consensus

Probab=99.11  E-value=2e-10  Score=108.36  Aligned_cols=81  Identities=25%  Similarity=0.420  Sum_probs=73.4

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCc-eeCC--eeEEEEe
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNV-LIDD--RRIHARG  265 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~-~i~g--r~I~V~~  265 (309)
                      .-++|||.+|...+|.||+.+|++||.|.+|.+++|+.||.++|||||.|.+.++|.+|+..|++. .+-|  .+|.|.+
T Consensus        34 ~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~  113 (510)
T KOG0144|consen   34 AVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKY  113 (510)
T ss_pred             hhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecc
Confidence            357999999999999999999999999999999999999999999999999999999999999884 4544  6788888


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      |...
T Consensus       114 Ad~E  117 (510)
T KOG0144|consen  114 ADGE  117 (510)
T ss_pred             cchh
Confidence            8753

>KOG0226|consensus

Probab=99.09  E-value=2.5e-10  Score=101.20  Aligned_cols=83  Identities=33%  Similarity=0.513  Sum_probs=77.8

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .....+||+|.|.-.++.+.|...|.+|-.....++++|+.||+++||+||.|.+..++..|+..|+|..++.++|.+.-
T Consensus       187 ~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRk  266 (290)
T KOG0226|consen  187 DEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRK  266 (290)
T ss_pred             ccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhh
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             ecC
Q psy15676        266 EEW  268 (309)
Q Consensus       266 a~~  268 (309)
                      +.|
T Consensus       267 S~w  269 (290)
T KOG0226|consen  267 SEW  269 (290)
T ss_pred             hhH
Confidence            744

>KOG0105|consensus

Probab=99.09  E-value=2.2e-10  Score=97.31  Aligned_cols=79  Identities=23%  Similarity=0.382  Sum_probs=70.7

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ...++|||+|||.++.+.++..+|.+||.|..|.+-..   -...+||||+|++..+|+.|+..-+|..++|.+|.|.++
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            35689999999999999999999999999999887432   234689999999999999999999999999999999999


Q ss_pred             cC
Q psy15676        267 EW  268 (309)
Q Consensus       267 ~~  268 (309)
                      ..
T Consensus        81 rg   82 (241)
T KOG0105|consen   81 RG   82 (241)
T ss_pred             cC
Confidence            74

>KOG4206|consensus

Probab=99.08  E-value=2.9e-10  Score=99.46  Aligned_cols=79  Identities=22%  Similarity=0.360  Sum_probs=72.4

Q ss_pred             CCcEEEecCCCCCCCHHHHHH----HHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEE
Q psy15676        188 PENVLFVCKLNPVTSDDDLEI----IFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA  263 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~----~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V  263 (309)
                      |..||||.||+.-+..++|+.    +|++||.|..|....   |.+.+|-|||.|.+.+.|-.|+..|+|+.+.|+.++|
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            444999999999999998877    999999999887754   7889999999999999999999999999999999999


Q ss_pred             EeecCc
Q psy15676        264 RGEEWN  269 (309)
Q Consensus       264 ~~a~~~  269 (309)
                      +||.++
T Consensus        85 qyA~s~   90 (221)
T KOG4206|consen   85 QYAKSD   90 (221)
T ss_pred             ecccCc
Confidence            999874

>KOG0109|consensus

Probab=99.00  E-value=5.4e-10  Score=100.85  Aligned_cols=72  Identities=22%  Similarity=0.519  Sum_probs=68.1

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecCc
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWN  269 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~~  269 (309)
                      ..|||||||..+++.+|+.+|++||.|..|.|+++        ||||..++...++.|+..|+|..|+|..|+|.-|+++
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            46999999999999999999999999999999864        8999999999999999999999999999999998875

>KOG0123|consensus

Probab=98.98  E-value=1.5e-09  Score=104.02  Aligned_cols=83  Identities=27%  Similarity=0.468  Sum_probs=75.7

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecCc
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWN  269 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~~  269 (309)
                      ..+||.||+++++..+|..+|+.||.|.+|++..+.. | ++|| ||+|.++++|.+|+..+||..+.|+.|-|.....+
T Consensus        77 ~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~  153 (369)
T KOG0123|consen   77 SLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERK  153 (369)
T ss_pred             ceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccch
Confidence            3499999999999999999999999999999999874 5 9999 99999999999999999999999999999998876


Q ss_pred             hhhccc
Q psy15676        270 MWKRRE  275 (309)
Q Consensus       270 ~~~~r~  275 (309)
                      .++...
T Consensus       154 ~er~~~  159 (369)
T KOG0123|consen  154 EEREAP  159 (369)
T ss_pred             hhhccc
Confidence            655443

>KOG0109|consensus

Probab=98.93  E-value=1.2e-09  Score=98.70  Aligned_cols=75  Identities=25%  Similarity=0.545  Sum_probs=70.2

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      .+..+|+|||+.+.++..+|+..|.+||+|.+|.|++        +|+||.|.-.++|..|+..|+|..++|++++|+++
T Consensus        76 k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk--------dy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~s  147 (346)
T KOG0109|consen   76 KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK--------DYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLS  147 (346)
T ss_pred             CCccccccCCCCccccCHHHhhhhcccCCceeeeeec--------ceeEEEEeeccchHHHHhcccccccccceeeeeee
Confidence            3567999999999999999999999999999999975        59999999999999999999999999999999999


Q ss_pred             cCc
Q psy15676        267 EWN  269 (309)
Q Consensus       267 ~~~  269 (309)
                      .+.
T Consensus       148 tsr  150 (346)
T KOG0109|consen  148 TSR  150 (346)
T ss_pred             ccc
Confidence            863

>KOG0123|consensus

Probab=98.88  E-value=4.7e-09  Score=100.54  Aligned_cols=75  Identities=31%  Similarity=0.373  Sum_probs=70.9

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecCc
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWN  269 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~~  269 (309)
                      ..||||   +++|+..|..+|+.+|++.++++++|. |  |.|||||.|.+..+|++|+..||...+.|++|++.+++.+
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            468999   999999999999999999999999998 6  9999999999999999999999999999999999999864


Q ss_pred             h
Q psy15676        270 M  270 (309)
Q Consensus       270 ~  270 (309)
                      .
T Consensus        76 ~   76 (369)
T KOG0123|consen   76 P   76 (369)
T ss_pred             C
Confidence            3

>KOG0124|consensus

Probab=98.86  E-value=4.5e-09  Score=97.50  Aligned_cols=79  Identities=22%  Similarity=0.413  Sum_probs=75.3

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      -++|||..+.++.+++||+++|+.||.|.+|.+.+++.++..+||||++|.+..+...|+..||=+.++|.-|+|..+-
T Consensus       210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~v  288 (544)
T KOG0124|consen  210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  288 (544)
T ss_pred             hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEeccccc
Confidence            3799999999999999999999999999999999999888999999999999999999999999999999999998765

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

Probab=98.86  E-value=9.5e-09  Score=102.31  Aligned_cols=87  Identities=21%  Similarity=0.267  Sum_probs=72.0

Q ss_pred             CCCcEEEecCCCCC----------CCHHHHHHHHhcCCceeEEEEeeeC---CCCCcccEEEEEecCHHHHHHHHHHcCC
Q psy15676        187 PPENVLFVCKLNPV----------TSDDDLEIIFSRFGKVNCCEVIRDK---VTGDSLQYAFVEFDNPKSCEDAYLKMDN  253 (309)
Q Consensus       187 ~~~~~lfV~nL~~~----------~te~~L~~~F~~fG~I~~v~i~~d~---~tg~skG~aFV~F~~~~~a~~Al~~l~g  253 (309)
                      .+..+|+|.||...          ...++|+..|++||.|..|.|+++.   .++.+.|+|||+|.+.++|.+|+..|||
T Consensus       407 ~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnG  486 (509)
T TIGR01642       407 KPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNG  486 (509)
T ss_pred             CCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCC
Confidence            35678999999642          1125789999999999999998753   3466789999999999999999999999


Q ss_pred             ceeCCeeEEEEeecCchhhc
Q psy15676        254 VLIDDRRIHARGEEWNMWKR  273 (309)
Q Consensus       254 ~~i~gr~I~V~~a~~~~~~~  273 (309)
                      ..|+|+.|.|.|.....|..
T Consensus       487 r~~~gr~v~~~~~~~~~~~~  506 (509)
T TIGR01642       487 RKFNDRVVVAAFYGEDCYKA  506 (509)
T ss_pred             CEECCeEEEEEEeCHHHhhc
Confidence            99999999999987655543

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

>KOG4212|consensus

Probab=98.85  E-value=9e-09  Score=97.45  Aligned_cols=80  Identities=21%  Similarity=0.409  Sum_probs=73.5

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHH-hcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIF-SRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F-~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      ....+.+||.|+|+++...+|+.+| .+.|.|..|.+..|. +|+++|+|.|+|.+++.+++|++.||.+.+.||+|.|.
T Consensus        41 ~~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vK  119 (608)
T KOG4212|consen   41 AARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVK  119 (608)
T ss_pred             ccccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEe
Confidence            3445679999999999999999999 688999999999997 69999999999999999999999999999999999986


Q ss_pred             ee
Q psy15676        265 GE  266 (309)
Q Consensus       265 ~a  266 (309)
                      -.
T Consensus       120 Ed  121 (608)
T KOG4212|consen  120 ED  121 (608)
T ss_pred             cc
Confidence            43

>KOG0110|consensus

Probab=98.84  E-value=1.1e-08  Score=101.94  Aligned_cols=78  Identities=32%  Similarity=0.458  Sum_probs=70.2

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCC---CCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVT---GDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~t---g~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ++|||.||++++|.++|...|...|.|.++.|..-+..   -.|.|||||+|.+.++|+.|++.|+|+.++|+.|.|.++
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            34999999999999999999999999999988765432   135699999999999999999999999999999999999


Q ss_pred             c
Q psy15676        267 E  267 (309)
Q Consensus       267 ~  267 (309)
                      .
T Consensus       596 ~  596 (725)
T KOG0110|consen  596 E  596 (725)
T ss_pred             c
Confidence            7

>KOG4205|consensus

Probab=98.77  E-value=5e-09  Score=97.61  Aligned_cols=81  Identities=25%  Similarity=0.402  Sum_probs=75.7

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      ...+|||++||+++++.+++..|.+||.|..+.++.|..+.+++||+||.|.+.+++.+++. ...+.|+|+.+.|..|.
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~-~~f~~~~gk~vevkrA~  174 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTL-QKFHDFNGKKVEVKRAI  174 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecc-cceeeecCceeeEeecc
Confidence            34699999999999999999999999999999999999999999999999999999999985 57899999999999998


Q ss_pred             Cc
Q psy15676        268 WN  269 (309)
Q Consensus       268 ~~  269 (309)
                      ++
T Consensus       175 pk  176 (311)
T KOG4205|consen  175 PK  176 (311)
T ss_pred             ch
Confidence            64

>KOG4661|consensus

Probab=98.77  E-value=9.2e-09  Score=100.05  Aligned_cols=80  Identities=21%  Similarity=0.345  Sum_probs=75.9

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      +..|||++|+..+...+|+.+|++||.|.-.+++.+..+.-.+||+||++.+.+.|.+||..|+-+.+.|+.|.|..++.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            46899999999999999999999999999999999988888899999999999999999999999999999999999874

>KOG0146|consensus

Probab=98.75  E-value=1.7e-08  Score=90.32  Aligned_cols=80  Identities=26%  Similarity=0.436  Sum_probs=71.9

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCc-eeC--CeeEEEE
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNV-LID--DRRIHAR  264 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~-~i~--gr~I~V~  264 (309)
                      .+++||||-|+..-+|+|++.+|..||.|.+|.+.+..+ |.++|+|||.|.+..+|..|+..|+|. .+-  ...|.|.
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            568999999999999999999999999999999999875 999999999999999999999999994 333  4668999


Q ss_pred             eecC
Q psy15676        265 GEEW  268 (309)
Q Consensus       265 ~a~~  268 (309)
                      |+..
T Consensus        97 ~ADT  100 (371)
T KOG0146|consen   97 FADT  100 (371)
T ss_pred             eccc
Confidence            9864

>KOG0132|consensus

Probab=98.74  E-value=2.2e-08  Score=100.52  Aligned_cols=78  Identities=23%  Similarity=0.322  Sum_probs=71.9

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      .+|||||+|+..+++.+|..+|+.||.|.+|.++.      ++|+|||.+....+|.+|+.+|++..+.++.|+|.|+.+
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 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP------PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeecc------CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            36999999999999999999999999999998864      468999999999999999999999999999999999987


Q ss_pred             chhh
Q psy15676        269 NMWK  272 (309)
Q Consensus       269 ~~~~  272 (309)
                      ++.+
T Consensus       495 ~G~k  498 (894)
T KOG0132|consen  495 KGPK  498 (894)
T ss_pred             CCcc
Confidence            6543

>KOG4205|consensus

Probab=98.72  E-value=1e-08  Score=95.49  Aligned_cols=81  Identities=28%  Similarity=0.476  Sum_probs=73.7

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      ..+++||++|++.++++.|+..|++||.|..|.+++|+.|++++||+||+|.+.+.+..++. ..-+.|+|+.|.+..|.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~-~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLN-ARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeec-ccccccCCccccceecc
Confidence            46899999999999999999999999999999999999999999999999999888888875 35688999999888876


Q ss_pred             Cc
Q psy15676        268 WN  269 (309)
Q Consensus       268 ~~  269 (309)
                      +.
T Consensus        84 ~r   85 (311)
T KOG4205|consen   84 SR   85 (311)
T ss_pred             Cc
Confidence            53

>KOG0153|consensus

Probab=98.70  E-value=4.3e-08  Score=90.62  Aligned_cols=74  Identities=20%  Similarity=0.352  Sum_probs=65.9

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHH-cCCceeCCeeEEEEeec
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK-MDNVLIDDRRIHARGEE  267 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~-l~g~~i~gr~I~V~~a~  267 (309)
                      -.+|||+||...+++.+|+.+|.+||.|.++.+...      +|+|||+|.+.++|+.|... ++...|+|++|.|.|..
T Consensus       228 I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~  301 (377)
T KOG0153|consen  228 IKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGR  301 (377)
T ss_pred             eeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCC
Confidence            369999999999999999999999999999988653      36999999999999988765 55588999999999987


Q ss_pred             C
Q psy15676        268 W  268 (309)
Q Consensus       268 ~  268 (309)
                      +
T Consensus       302 ~  302 (377)
T KOG0153|consen  302 P  302 (377)
T ss_pred             C
Confidence            7

>KOG0533|consensus

Probab=98.67  E-value=7.1e-08  Score=86.77  Aligned_cols=82  Identities=27%  Similarity=0.304  Sum_probs=75.4

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      -..+|+|+||++.++++||.++|..||.+..+.+.+++ +|.+.|.|-|.|...++|..|++.++|..++|+++++....
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIIS  160 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEec
Confidence            34789999999999999999999999999999998887 69999999999999999999999999999999999998876


Q ss_pred             Cch
Q psy15676        268 WNM  270 (309)
Q Consensus       268 ~~~  270 (309)
                      +..
T Consensus       161 ~~~  163 (243)
T KOG0533|consen  161 SPS  163 (243)
T ss_pred             Ccc
Confidence            543

>KOG0110|consensus

Probab=98.66  E-value=2.1e-08  Score=99.92  Aligned_cols=83  Identities=14%  Similarity=0.309  Sum_probs=76.7

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      .+.|.|.|+|+..+-.+++.+|+.||.+.+|+++.-...+.++|||||.|-+...|..|+..|.++.+.||+|+++||.+
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~  692 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKS  692 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhcc
Confidence            46899999999999999999999999999999987655677899999999999999999999999999999999999987


Q ss_pred             chh
Q psy15676        269 NMW  271 (309)
Q Consensus       269 ~~~  271 (309)
                      ...
T Consensus       693 d~~  695 (725)
T KOG0110|consen  693 DNT  695 (725)
T ss_pred             chH
Confidence            654

>KOG1548|consensus

Probab=98.65  E-value=1.1e-07  Score=87.82  Aligned_cols=79  Identities=16%  Similarity=0.235  Sum_probs=72.0

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCcee--------EEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCee
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVN--------CCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRR  260 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~--------~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~  260 (309)
                      +..|||+|||.++|.+++..+|++||.|.        .|++.++.. |..+|=|.+.|...+++..|+..|++..+.|+.
T Consensus       134 Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~  212 (382)
T KOG1548|consen  134 NTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDELRGKK  212 (382)
T ss_pred             CceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCcccccCcE
Confidence            35699999999999999999999999884        367777764 999999999999999999999999999999999


Q ss_pred             EEEEeecC
Q psy15676        261 IHARGEEW  268 (309)
Q Consensus       261 I~V~~a~~  268 (309)
                      |+|+.|+-
T Consensus       213 ~rVerAkf  220 (382)
T KOG1548|consen  213 LRVERAKF  220 (382)
T ss_pred             EEEehhhh
Confidence            99999974

>KOG1457|consensus

Probab=98.59  E-value=2.1e-07  Score=81.55  Aligned_cols=87  Identities=20%  Similarity=0.193  Sum_probs=70.1

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeee-CCCCCcccEEEEEecCHHHHHHHHHHcCCceeC---CeeEEEE
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRD-KVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLID---DRRIHAR  264 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d-~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~---gr~I~V~  264 (309)
                      -+||||++||.++...+|..+|..|-..+.+.+-.. +.....+-+||++|.+..+|..|...|||..+|   +..|+++
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            479999999999999999999999876666655332 211223479999999999999999999999998   7899999


Q ss_pred             eecCchhhccc
Q psy15676        265 GEEWNMWKRRE  275 (309)
Q Consensus       265 ~a~~~~~~~r~  275 (309)
                      +|+++....++
T Consensus       114 lAKSNtK~kr~  124 (284)
T KOG1457|consen  114 LAKSNTKRKRR  124 (284)
T ss_pred             ehhcCcccccC
Confidence            99986544443

>KOG4209|consensus

Probab=98.57  E-value=8.8e-08  Score=86.06  Aligned_cols=81  Identities=23%  Similarity=0.349  Sum_probs=75.8

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      .....+||+|+.+.+|.+++...|+.||.|..+.+..|+.+|.++|||||+|.+.+.++.||. |+|..|.|+.+.|.+.
T Consensus        99 ~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~~  177 (231)
T KOG4209|consen   99 VDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTLK  177 (231)
T ss_pred             cCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeeee
Confidence            345789999999999999999999999999999999999999999999999999999999998 9999999999999887


Q ss_pred             cC
Q psy15676        267 EW  268 (309)
Q Consensus       267 ~~  268 (309)
                      +.
T Consensus       178 r~  179 (231)
T KOG4209|consen  178 RT  179 (231)
T ss_pred             ee
Confidence            64

>KOG0151|consensus

Probab=98.54  E-value=2.6e-07  Score=92.10  Aligned_cols=81  Identities=21%  Similarity=0.385  Sum_probs=72.2

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCC---CCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEE
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKV---TGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA  263 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~---tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V  263 (309)
                      |..+.+||+||++.++++.|...|++||+|.+++|++.+.   ..+.+-+|||.|.+..+++.|++.|+|..+.+..+++
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            3456899999999999999999999999999999987652   2345678999999999999999999999999999999


Q ss_pred             Eeec
Q psy15676        264 RGEE  267 (309)
Q Consensus       264 ~~a~  267 (309)
                      .|++
T Consensus       252 gWgk  255 (877)
T KOG0151|consen  252 GWGK  255 (877)
T ss_pred             cccc
Confidence            9885

>KOG4212|consensus

Probab=98.54  E-value=1.5e-07  Score=89.35  Aligned_cols=75  Identities=21%  Similarity=0.227  Sum_probs=68.6

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      +..++|||.|||+++|...|+.-|..||.|.++.|+.   .|+++|  .|.|.+.++|+.|+..|+|..++|+.|.|.|.
T Consensus       534 rKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  534 RKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             ccccEEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            4468999999999999999999999999999998843   578887  89999999999999999999999999999874

>KOG0116|consensus

Probab=98.51  E-value=2.6e-07  Score=89.27  Aligned_cols=78  Identities=23%  Similarity=0.388  Sum_probs=67.0

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      .+|||.|||++++..+|.++|.+||.|....|..-...+++.+||||+|.+.++++.|+.+ +-..++|+++.|.--++
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEeccc
Confidence            5799999999999999999999999999887765433355559999999999999999986 67899999999986543

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.29  E-value=6.1e-06  Score=64.19  Aligned_cols=79  Identities=16%  Similarity=0.185  Sum_probs=69.0

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhc--CCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeC----CeeEEE
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSR--FGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLID----DRRIHA  263 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~--fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~----gr~I~V  263 (309)
                      +||-|.|+|...|.+.|.+++..  .|....+.++.|..++-+.|||||.|.+.+.|..-...++|..+.    .+.+.|
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            58999999999999999988843  367778889999999999999999999999999999999997775    566788


Q ss_pred             EeecC
Q psy15676        264 RGEEW  268 (309)
Q Consensus       264 ~~a~~  268 (309)
                      .+|+-
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).

>KOG4454|consensus

Probab=98.25  E-value=4.8e-07  Score=79.05  Aligned_cols=81  Identities=17%  Similarity=0.132  Sum_probs=72.8

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      +...||||+|+...++++-|.++|-+-|+|..+.|..++. +..+ ||||.|.++.++.-|+..|||..+.+..+.+.+-
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            3458999999999999999999999999999999988775 5566 9999999999999999999999999999999876


Q ss_pred             cCc
Q psy15676        267 EWN  269 (309)
Q Consensus       267 ~~~  269 (309)
                      ...
T Consensus        85 ~G~   87 (267)
T KOG4454|consen   85 CGN   87 (267)
T ss_pred             cCC
Confidence            543

>KOG4660|consensus

Probab=98.21  E-value=9e-07  Score=86.40  Aligned_cols=70  Identities=27%  Similarity=0.385  Sum_probs=64.2

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEE
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH  262 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~  262 (309)
                      +..+|+|-|||.++++++|..+|+.||+|..++.     |-..+|..||+|.+..+|+.|++.|++..|.|++|.
T Consensus        74 ~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   74 NQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             ccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            5679999999999999999999999999988665     445679999999999999999999999999999988

>KOG0106|consensus

Probab=98.16  E-value=1.8e-06  Score=76.30  Aligned_cols=71  Identities=21%  Similarity=0.426  Sum_probs=65.2

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      ..+|||+||+.+.+.+|..+|..||.+..+.+.        .||+||.|.+..+|..|+..+||..+.|-.+.|.++..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            368999999999999999999999999988773        37999999999999999999999999998899999884

>KOG0120|consensus

Probab=98.15  E-value=2e-06  Score=84.38  Aligned_cols=80  Identities=21%  Similarity=0.471  Sum_probs=76.2

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      ....+||++||...++.++.++...||.+....++.|..+|.++||||.+|.+......|+..+||..++++.++|+.|-
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            35799999999999999999999999999999999999999999999999999999999999999999999999999875

>KOG1190|consensus

Probab=97.98  E-value=2.5e-05  Score=73.95  Aligned_cols=74  Identities=18%  Similarity=0.317  Sum_probs=68.6

Q ss_pred             CcEEEecCCCCC-CCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        189 ENVLFVCKLNPV-TSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       189 ~~~lfV~nL~~~-~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      +..|.|.||+.. +|.+.|..+|+-||.|.+++|..+++     --|.|+|.+...|+.|+..|+|..+.|++|+|.+++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            578999999865 99999999999999999999998764     479999999999999999999999999999999997

>KOG0147|consensus

Probab=97.86  E-value=6.8e-06  Score=80.24  Aligned_cols=79  Identities=25%  Similarity=0.276  Sum_probs=73.3

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      ..|+|+..|+-.++..+|..+|+.+|.|..|.++.|+.++.++|.|||+|.+.+++..|+ .|.|..+.|-+|.|+.+..
T Consensus       179 ~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq~sEa  257 (549)
T KOG0147|consen  179 QRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQLSEA  257 (549)
T ss_pred             HHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEecccHH
Confidence            368888888888999999999999999999999999999999999999999999999999 6899999999999997753

>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=97.85  E-value=7.4e-05  Score=56.10  Aligned_cols=68  Identities=22%  Similarity=0.228  Sum_probs=47.5

Q ss_pred             cEEEecCCCCCCCHHH----HHHHHhcCC-ceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        190 NVLFVCKLNPVTSDDD----LEIIFSRFG-KVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~----L~~~F~~fG-~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      ..|||.|||-+.....    |+.++..+| .|.++          +.|.|++.|.+.+.|..|.+.|+|-.+.|++|.|+
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v----------~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV----------SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE----------eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            5799999999888665    566776776 44443          23689999999999999999999999999999999


Q ss_pred             eec
Q psy15676        265 GEE  267 (309)
Q Consensus       265 ~a~  267 (309)
                      |+.
T Consensus        73 ~~~   75 (90)
T PF11608_consen   73 FSP   75 (90)
T ss_dssp             SS-
T ss_pred             EcC
Confidence            984

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG1995|consensus

Probab=97.78  E-value=2.7e-05  Score=72.70  Aligned_cols=81  Identities=19%  Similarity=0.208  Sum_probs=74.2

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCcee--------EEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCe
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVN--------CCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDR  259 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~--------~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr  259 (309)
                      ...++||.+||..++++++..+|.++|.|.        .+.+-+++.|+.++|-|.|+|.+...|+.|+.-+++..+.|.
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn  144 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGN  144 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCC
Confidence            457899999999999999999999999884        356778889999999999999999999999999999999999


Q ss_pred             eEEEEeecC
Q psy15676        260 RIHARGEEW  268 (309)
Q Consensus       260 ~I~V~~a~~  268 (309)
                      .|+|.+|..
T Consensus       145 ~ikvs~a~~  153 (351)
T KOG1995|consen  145 TIKVSLAER  153 (351)
T ss_pred             Cchhhhhhh
Confidence            999998864

>KOG4211|consensus

Probab=97.69  E-value=0.00013  Score=70.72  Aligned_cols=76  Identities=21%  Similarity=0.253  Sum_probs=62.8

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      +....|-+.+||+++|+++|..+|+.++ |.++.+  .+.+|+..|-|||+|.+.+++++|++. +-..+..+-|.|--+
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~--~r~~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNCG-IENLEI--PRRNGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVFTA   83 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcCc-eeEEEE--eccCCCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEEcc
Confidence            3456778899999999999999999875 566544  445799999999999999999999975 777777888887555

>KOG4210|consensus

Probab=97.68  E-value=2.2e-05  Score=72.78  Aligned_cols=80  Identities=25%  Similarity=0.359  Sum_probs=72.8

Q ss_pred             CcEEE-ecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        189 ENVLF-VCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       189 ~~~lf-V~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      ..++| |+||++.++.++|...|..+|.|..+++..+..+|..+||||+.|.+...+..++.. +...++++++.+.+..
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~  262 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDE  262 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCC
Confidence            34555 999999999999999999999999999999999999999999999999999999876 7899999999999886


Q ss_pred             Cc
Q psy15676        268 WN  269 (309)
Q Consensus       268 ~~  269 (309)
                      ..
T Consensus       263 ~~  264 (285)
T KOG4210|consen  263 PR  264 (285)
T ss_pred             CC
Confidence            53

>KOG1457|consensus

Probab=97.66  E-value=4.9e-05  Score=66.87  Aligned_cols=66  Identities=21%  Similarity=0.469  Sum_probs=54.1

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeC
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLID  257 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~  257 (309)
                      ...||||.||.+++++++|+.+|+.|......+|- .+   ..-+.||+.|++.+.|..|+..|+|..|.
T Consensus       209 acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~-~~---~g~~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  209 ACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIR-AR---GGMPVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             hhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEe-cC---CCcceEeecHHHHHHHHHHHHHhhcceec
Confidence            34699999999999999999999999776655552 22   23468999999999999999999997653

>KOG4206|consensus

Probab=97.62  E-value=0.00023  Score=62.79  Aligned_cols=78  Identities=22%  Similarity=0.359  Sum_probs=68.9

Q ss_pred             CCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeC-CeeEEE
Q psy15676        185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLID-DRRIHA  263 (309)
Q Consensus       185 ~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~-gr~I~V  263 (309)
                      ..+|..++|+.|||..++.+.|..+|.+|+....++++...     .+.|||+|.+...+..|...++|..|- ...+.|
T Consensus       142 ~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i  216 (221)
T KOG4206|consen  142 MAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQI  216 (221)
T ss_pred             CCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEe
Confidence            36788999999999999999999999999999999987654     479999999999999999999998887 788888


Q ss_pred             Eeec
Q psy15676        264 RGEE  267 (309)
Q Consensus       264 ~~a~  267 (309)
                      .+|.
T Consensus       217 ~~a~  220 (221)
T KOG4206|consen  217 TFAK  220 (221)
T ss_pred             cccC
Confidence            8764

>KOG2314|consensus

Probab=97.58  E-value=0.0004  Score=68.37  Aligned_cols=77  Identities=22%  Similarity=0.276  Sum_probs=64.1

Q ss_pred             CCcEEEecCCCCCCCH------HHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeC-Cee
Q psy15676        188 PENVLFVCKLNPVTSD------DDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLID-DRR  260 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te------~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~-gr~  260 (309)
                      -...|+|.|.|-.-..      .-|..+|+++|.+.+..++.+..+| .+||.|++|.+..+|+.|++.+||+.++ ++.
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            3478999999865432      2367889999999999999888755 9999999999999999999999999887 566


Q ss_pred             EEEEe
Q psy15676        261 IHARG  265 (309)
Q Consensus       261 I~V~~  265 (309)
                      ..|..
T Consensus       136 f~v~~  140 (698)
T KOG2314|consen  136 FFVRL  140 (698)
T ss_pred             EEeeh
Confidence            66653

>KOG4211|consensus

Probab=97.51  E-value=0.00024  Score=68.92  Aligned_cols=78  Identities=22%  Similarity=0.221  Sum_probs=65.3

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeE-EEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNC-CEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~-v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      +..+|-+.+||+.||++||.++|+..-.+.. +.++.++ .+++.|-|||.|.+.+.|++|+.. +...|+-+-|.|-.|
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRS  179 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehh
Confidence            4568889999999999999999988765554 5566666 478999999999999999999976 777888888888766


Q ss_pred             c
Q psy15676        267 E  267 (309)
Q Consensus       267 ~  267 (309)
                      .
T Consensus       180 s  180 (510)
T KOG4211|consen  180 S  180 (510)
T ss_pred             H
Confidence            4

>KOG3152|consensus

Probab=97.50  E-value=0.00011  Score=65.82  Aligned_cols=73  Identities=18%  Similarity=0.339  Sum_probs=61.9

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCC--------CCcccE----EEEEecCHHHHHHHHHHcCCce
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVT--------GDSLQY----AFVEFDNPKSCEDAYLKMDNVL  255 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~t--------g~skG~----aFV~F~~~~~a~~Al~~l~g~~  255 (309)
                      ....||++++|+.....-|+.+|++||.|-.|.+.....+        |.+.++    |.|+|.+...|..+...|||..
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            3468999999999999999999999999999988665544        333332    5799999999999999999999


Q ss_pred             eCCee
Q psy15676        256 IDDRR  260 (309)
Q Consensus       256 i~gr~  260 (309)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99876

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.47  E-value=0.00059  Score=63.42  Aligned_cols=77  Identities=21%  Similarity=0.441  Sum_probs=61.0

Q ss_pred             CcEEEecCCCCCCCHHH----H--HHHHhcCCceeEEEEeeeCCCC---Cccc-E-EEEEecCHHHHHHHHHHcCCceeC
Q psy15676        189 ENVLFVCKLNPVTSDDD----L--EIIFSRFGKVNCCEVIRDKVTG---DSLQ-Y-AFVEFDNPKSCEDAYLKMDNVLID  257 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~----L--~~~F~~fG~I~~v~i~~d~~tg---~skG-~-aFV~F~~~~~a~~Al~~l~g~~i~  257 (309)
                      .+-+||-+||+.+..++    |  .++|++||.|..+.+  ++.|.   ...+ + .||+|.+.++|..|+...+|..++
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvv--Nkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~D  191 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVV--NKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLD  191 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEe--cccccccccccccceEEEEecchHHHHHHHHHhcccccc
Confidence            46789999999877666    2  578999999988766  33331   1112 3 299999999999999999999999


Q ss_pred             CeeEEEEeec
Q psy15676        258 DRRIHARGEE  267 (309)
Q Consensus       258 gr~I~V~~a~  267 (309)
                      |+-|+..|-.
T Consensus       192 Gr~lkatYGT  201 (480)
T COG5175         192 GRVLKATYGT  201 (480)
T ss_pred             CceEeeecCc
Confidence            9999998854

>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=97.44  E-value=0.00023  Score=56.31  Aligned_cols=71  Identities=24%  Similarity=0.391  Sum_probs=43.4

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCC-----ceeCCeeEEEE
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDN-----VLIDDRRIHAR  264 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g-----~~i~gr~I~V~  264 (309)
                      +.|++.+++..++-++|+..|++||.|..|.+...      -..|||-|.+.++|+.|+..+..     ..|.+..+.+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            57889999999999999999999999998877542      23789999999999998876543     45666666555


Q ss_pred             ee
Q psy15676        265 GE  266 (309)
Q Consensus       265 ~a  266 (309)
                      .-
T Consensus        76 vL   77 (105)
T PF08777_consen   76 VL   77 (105)
T ss_dssp             --
T ss_pred             EC
Confidence            43

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG4849|consensus

Probab=97.43  E-value=0.00018  Score=67.03  Aligned_cols=78  Identities=15%  Similarity=0.186  Sum_probs=67.4

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCC--ceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFG--KVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG--~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ...+|||||-+.+|++||.+.....|  .+..+++..++.+|.|+|||+|...+..++++.++.|.-..|.|..-.|--.
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~  159 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSY  159 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeecc
Confidence            35899999999999999999887766  5567778888889999999999999999999999999999999977666543

>KOG1190|consensus

Probab=97.24  E-value=0.00069  Score=64.44  Aligned_cols=79  Identities=15%  Similarity=0.273  Sum_probs=66.3

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCe-eEEEEe
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDR-RIHARG  265 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr-~I~V~~  265 (309)
                      ||..++..+|+|+++++++|...|..-|...+.....    ++.+.+|++.+.+.+.|-.|+..++++.+++. -++|+|
T Consensus       412 PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff----~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSF  487 (492)
T KOG1190|consen  412 PPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFF----QKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSF  487 (492)
T ss_pred             CchhheeeccCCcccchhHHHHhhhcCCceEEeeeec----CCCcceeecccCChhHhhhhccccccccCCCCceEEEEe
Confidence            6778999999999999999999998877665544322    44556999999999999999999999998865 889999


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      +++.
T Consensus       488 Sks~  491 (492)
T KOG1190|consen  488 SKST  491 (492)
T ss_pred             eccc
Confidence            9863

>KOG0129|consensus

Probab=97.18  E-value=0.00092  Score=65.29  Aligned_cols=65  Identities=22%  Similarity=0.235  Sum_probs=60.1

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHh-cCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHH
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFS-RFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK  250 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~-~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~  250 (309)
                      -+|.+|||||+||.-++.++|..+|. -||.|..+.|-.|++-+.++|-|=|+|.+..+-.+|+.+
T Consensus       367 lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  367 IDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            36778999999999999999999997 899999999999988899999999999999999999974

>KOG0106|consensus

Probab=97.17  E-value=0.00026  Score=62.63  Aligned_cols=72  Identities=28%  Similarity=0.368  Sum_probs=62.4

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      ..+.++|.|++-.+...+|..+|.++|.+....+        ..+++||.|.+..++..|+..++|..+.|+.|.+.++.
T Consensus        98 s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~~  169 (216)
T KOG0106|consen   98 THFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKNS  169 (216)
T ss_pred             ccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeeecccC
Confidence            3578889999999999999999999999844333        45799999999999999999999999999999995443

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.15  E-value=0.0015  Score=54.25  Aligned_cols=76  Identities=24%  Similarity=0.421  Sum_probs=53.4

Q ss_pred             CCCCCcEEEecCCCC------CCCH---HHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCce
Q psy15676        185 AAPPENVLFVCKLNP------VTSD---DDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVL  255 (309)
Q Consensus       185 ~~~~~~~lfV~nL~~------~~te---~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~  255 (309)
                      .+||..||.|.=+.+      ...+   .+|...|..||.+.-++++.+        .-+|+|.+-.+|.+|+. ++|..
T Consensus        23 ~GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~   93 (146)
T PF08952_consen   23 QGPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQ   93 (146)
T ss_dssp             ---TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSE
T ss_pred             cCCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcE
Confidence            368889998876662      2222   267788999999988887643        46999999999999996 79999


Q ss_pred             eCCeeEEEEeecCc
Q psy15676        256 IDDRRIHARGEEWN  269 (309)
Q Consensus       256 i~gr~I~V~~a~~~  269 (309)
                      ++|+.|+|..-.++
T Consensus        94 v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   94 VNGRTLKIRLKTPD  107 (146)
T ss_dssp             ETTEEEEEEE----
T ss_pred             ECCEEEEEEeCCcc
Confidence            99999999976654

; PDB: 1UFW_A 2DNR_A.

>KOG1548|consensus

Probab=96.97  E-value=0.0091  Score=55.88  Aligned_cols=79  Identities=20%  Similarity=0.247  Sum_probs=62.8

Q ss_pred             CCCCcEEEecCCCC----CCC-------HHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCc
Q psy15676        186 APPENVLFVCKLNP----VTS-------DDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNV  254 (309)
Q Consensus       186 ~~~~~~lfV~nL~~----~~t-------e~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~  254 (309)
                      ....++|.+.|+=-    ..+       .++|.+-.++||.|.++.+. +   ..+.|.+-|.|.+.+.|..|++.|+|.
T Consensus       262 ~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~-d---~hPdGvvtV~f~n~eeA~~ciq~m~GR  337 (382)
T KOG1548|consen  262 ARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVY-D---RHPDGVVTVSFRNNEEADQCIQTMDGR  337 (382)
T ss_pred             ccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEe-c---cCCCceeEEEeCChHHHHHHHHHhcCe
Confidence            34467888998721    233       34566778899999998764 3   246799999999999999999999999


Q ss_pred             eeCCeeEEEEeecC
Q psy15676        255 LIDDRRIHARGEEW  268 (309)
Q Consensus       255 ~i~gr~I~V~~a~~  268 (309)
                      .++||.|+.+....
T Consensus       338 ~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  338 WFDGRQLTASIWDG  351 (382)
T ss_pred             eecceEEEEEEeCC
Confidence            99999999987754

>KOG0120|consensus

Probab=96.88  E-value=0.0028  Score=62.64  Aligned_cols=70  Identities=20%  Similarity=0.277  Sum_probs=57.1

Q ss_pred             HHHHHHhcCCceeEEEEeeeCC---CCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecCchhhcc
Q psy15676        205 DLEIIFSRFGKVNCCEVIRDKV---TGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWNMWKRR  274 (309)
Q Consensus       205 ~L~~~F~~fG~I~~v~i~~d~~---tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~~~~~~r  274 (309)
                      +++.-+++||.|.+|.+.++..   ..-+.|-.||+|.+.++++.|.+.|+|..++|+.+...|.....|..+
T Consensus       425 dvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeDkY~~r  497 (500)
T KOG0120|consen  425 DVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDEDKYHAR  497 (500)
T ss_pred             HHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHHHhhcc
Confidence            3455677899999999988722   233457789999999999999999999999999999999876666544

>KOG1456|consensus

Probab=96.79  E-value=0.0079  Score=56.81  Aligned_cols=79  Identities=20%  Similarity=0.302  Sum_probs=69.9

Q ss_pred             CCCCCCcEEEecCCCCC-CCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEE
Q psy15676        184 DAAPPENVLFVCKLNPV-TSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH  262 (309)
Q Consensus       184 ~~~~~~~~lfV~nL~~~-~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~  262 (309)
                      ....+++.+.|.+|.-. .+-+-|..+|..||.|..+++++.+     .|-|.|++.+..+++.|+..||+..+-|.+|.
T Consensus       282 ~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~  356 (494)
T KOG1456|consen  282 GGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLN  356 (494)
T ss_pred             CCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEE
Confidence            34567899999999876 5667799999999999999998765     37899999999999999999999999999999


Q ss_pred             EEeec
Q psy15676        263 ARGEE  267 (309)
Q Consensus       263 V~~a~  267 (309)
                      |.+++
T Consensus       357 v~~Sk  361 (494)
T KOG1456|consen  357 VCVSK  361 (494)
T ss_pred             Eeecc
Confidence            99886

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.65  E-value=0.0049  Score=42.45  Aligned_cols=52  Identities=19%  Similarity=0.353  Sum_probs=41.0

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHH
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAY  248 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al  248 (309)
                      +.|-|.+.+++..+. +..+|..||.|..+.+.      ...-+.||.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~------~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVP------ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcC------CCCcEEEEEECCHHHHHhhC
Confidence            467788888876655 55588899999998774      23358999999999999985

>KOG2193|consensus

Probab=96.62  E-value=0.002  Score=61.58  Aligned_cols=79  Identities=20%  Similarity=0.297  Sum_probs=60.8

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCC-ceeCCeeEEEEeecC
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDN-VLIDDRRIHARGEEW  268 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g-~~i~gr~I~V~~a~~  268 (309)
                      +.+|++||++.++..+|..+|+..-.-.+-.++.      ..|||||.+.+...|.+|++.++| ..+.|+++.|..+-+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            4689999999999999999996541111111111      238999999999999999999999 588899999998876


Q ss_pred             chhhcc
Q psy15676        269 NMWKRR  274 (309)
Q Consensus       269 ~~~~~r  274 (309)
                      +..+.+
T Consensus        76 kkqrsr   81 (584)
T KOG2193|consen   76 KKQRSR   81 (584)
T ss_pred             HHHHhh
Confidence            554443

>KOG4307|consensus

Probab=96.59  E-value=0.0065  Score=61.42  Aligned_cols=75  Identities=19%  Similarity=0.202  Sum_probs=64.2

Q ss_pred             EEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       191 ~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .|-+.|+|++++-+|+..+|.-|-.+-.-.+++-.+.|...|-|.|.|++.+.|..|...+++..|.++.+.+.+
T Consensus       869 V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  869 VLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             EEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            778899999999999999999997664333333345699999999999999999999999999999999988764

>KOG0128|consensus

Probab=96.55  E-value=0.00044  Score=70.96  Aligned_cols=78  Identities=10%  Similarity=0.094  Sum_probs=70.4

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      ..+||+|.|+..|.+.|+.+|+.+|.+.+..++..+ .|+++|-|||.|.+..++..+...+++..+.-+.+.|+.+.+
T Consensus       737 ~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  737 ISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhheeCCCCCCchHHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            589999999999999999999999999999887776 599999999999999999999988888888888888887765

>KOG1855|consensus

Probab=96.45  E-value=0.0031  Score=60.40  Aligned_cols=67  Identities=18%  Similarity=0.284  Sum_probs=56.2

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeee---CCC--CCc--------ccEEEEEecCHHHHHHHHHHcCC
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRD---KVT--GDS--------LQYAFVEFDNPKSCEDAYLKMDN  253 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d---~~t--g~s--------kG~aFV~F~~~~~a~~Al~~l~g  253 (309)
                      -+.++|.+.|||.+-.-+.|..+|+.+|.|..|+|+..   +..  |.+        +-+|||+|...+.|.+|-+.|+.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            36789999999999888999999999999999999876   322  222        35799999999999999987754

>KOG1456|consensus

Probab=96.24  E-value=0.024  Score=53.69  Aligned_cols=81  Identities=25%  Similarity=0.247  Sum_probs=65.4

Q ss_pred             CCCCCCCcEEEecCCC--CCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCC--
Q psy15676        183 ADAAPPENVLFVCKLN--PVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDD--  258 (309)
Q Consensus       183 ~~~~~~~~~lfV~nL~--~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~g--  258 (309)
                      .++..++..|.+.=|+  +.+|.+-|..+....|.|.++.|.+-  +|.   .|.|+|++.+.|++|...|||..|..  
T Consensus       114 ~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ngV---QAmVEFdsv~~AqrAk~alNGADIYsGC  188 (494)
T KOG1456|consen  114 DESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NGV---QAMVEFDSVEVAQRAKAALNGADIYSGC  188 (494)
T ss_pred             CCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cce---eeEEeechhHHHHHHHhhcccccccccc
Confidence            3445566777766555  46899999999999999999988653  443   79999999999999999999987753  


Q ss_pred             eeEEEEeecC
Q psy15676        259 RRIHARGEEW  268 (309)
Q Consensus       259 r~I~V~~a~~  268 (309)
                      ..|+|+||++
T Consensus       189 CTLKIeyAkP  198 (494)
T KOG1456|consen  189 CTLKIEYAKP  198 (494)
T ss_pred             eeEEEEecCc
Confidence            6789999986

>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=96.23  E-value=0.023  Score=44.43  Aligned_cols=77  Identities=19%  Similarity=0.304  Sum_probs=50.1

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEE-EeeeC------CCCCcccEEEEEecCHHHHHHHHHHcCCceeCCe-e
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCE-VIRDK------VTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDR-R  260 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~-i~~d~------~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr-~  260 (309)
                      ...|.|-+.|+. ....+...|++||.|.+.. +..+.      .......+-.|.|.+..+|.+||.. ||..++|. .
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~~g~~m   83 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIFSGSLM   83 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEETTCEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEEcCcEE
Confidence            456777799888 5566788899999997664 11110      0012335889999999999999975 99999885 4


Q ss_pred             EEEEeec
Q psy15676        261 IHARGEE  267 (309)
Q Consensus       261 I~V~~a~  267 (309)
                      +-|.++.
T Consensus        84 vGV~~~~   90 (100)
T PF05172_consen   84 VGVKPCD   90 (100)
T ss_dssp             EEEEE-H
T ss_pred             EEEEEcH
Confidence            5577764

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.

>KOG0112|consensus

Probab=96.16  E-value=0.0062  Score=63.12  Aligned_cols=76  Identities=21%  Similarity=0.365  Sum_probs=66.6

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCC--eeEEEE
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDD--RRIHAR  264 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~g--r~I~V~  264 (309)
                      .+.+.+|+++|.+++....|...|..||.|..|.+-      +..-||+|.|++...++.|+..|-|..++|  +++.|+
T Consensus       453 t~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~------hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvd  526 (975)
T KOG0112|consen  453 TPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR------HGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVD  526 (975)
T ss_pred             ccceeeccCCCCCCChHHHHHHHhhccCcceeeecc------cCCcceeeecccCccchhhHHHHhcCcCCCCCcccccc
Confidence            456789999999999999999999999999887652      234699999999999999999999999985  779999


Q ss_pred             eecC
Q psy15676        265 GEEW  268 (309)
Q Consensus       265 ~a~~  268 (309)
                      |+..
T Consensus       527 la~~  530 (975)
T KOG0112|consen  527 LASP  530 (975)
T ss_pred             cccC
Confidence            9874

>KOG0105|consensus

Probab=96.15  E-value=0.017  Score=49.70  Aligned_cols=63  Identities=27%  Similarity=0.274  Sum_probs=56.1

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeC
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLID  257 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~  257 (309)
                      +...+.|++||++.+.++|+.++..-|.|....+.+|       |++.|+|...++++-|+..|+...+.
T Consensus       114 Se~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  114 SEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             cceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhcccccc
Confidence            4568999999999999999999999999999888765       58999999999999999998876554

>KOG0129|consensus

Probab=96.10  E-value=0.011  Score=57.88  Aligned_cols=61  Identities=18%  Similarity=0.308  Sum_probs=45.5

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCC---CCCccc---EEEEEecCHHHHHHHHHH
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKV---TGDSLQ---YAFVEFDNPKSCEDAYLK  250 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~---tg~skG---~aFV~F~~~~~a~~Al~~  250 (309)
                      .+.||||+||++++|+.|...|..||.+. +.......   ---++|   |+|+.|+++.++..-+.+
T Consensus       259 S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~a  325 (520)
T KOG0129|consen  259 SRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSA  325 (520)
T ss_pred             ccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHH
Confidence            57999999999999999999999999873 33332110   012355   999999998887765544

>KOG1365|consensus

Probab=96.05  E-value=0.0078  Score=57.02  Aligned_cols=78  Identities=15%  Similarity=0.209  Sum_probs=64.9

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCc-eeE--EEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGK-VNC--CEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~-I~~--v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ...|-+.+||+..+.++|..+|+.|.. |..  +.++.+. .|+..|-|||+|.+.++|..|....+.....++-|.|--
T Consensus       280 kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp  358 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFP  358 (508)
T ss_pred             CCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEee
Confidence            457889999999999999999988863 333  6777765 599999999999999999999988888777788888765


Q ss_pred             ec
Q psy15676        266 EE  267 (309)
Q Consensus       266 a~  267 (309)
                      +.
T Consensus       359 ~S  360 (508)
T KOG1365|consen  359 CS  360 (508)
T ss_pred             cc
Confidence            53

>KOG2416|consensus

Probab=95.89  E-value=0.0086  Score=59.60  Aligned_cols=77  Identities=19%  Similarity=0.201  Sum_probs=62.4

Q ss_pred             CCCCCcEEEecCCCCCCCHHHHHHHHhc-CCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCcee---CCee
Q psy15676        185 AAPPENVLFVCKLNPVTSDDDLEIIFSR-FGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLI---DDRR  260 (309)
Q Consensus       185 ~~~~~~~lfV~nL~~~~te~~L~~~F~~-fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i---~gr~  260 (309)
                      -..+.+.|||.||-.-+|..+|+.++++ .|.|...  ..|+    -+..|||.|.+.+.|.....+|+|..+   +++.
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~--WmDk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~  513 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF--WMDK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKH  513 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHH--HHHH----hhcceeEecccHHHHHHHHHHHhccccCCCCCce
Confidence            4566789999999999999999999984 5555554  2233    456899999999999999999999765   5688


Q ss_pred             EEEEeec
Q psy15676        261 IHARGEE  267 (309)
Q Consensus       261 I~V~~a~  267 (309)
                      |.+.|..
T Consensus       514 L~adf~~  520 (718)
T KOG2416|consen  514 LIADFVR  520 (718)
T ss_pred             eEeeecc
Confidence            8888875

>KOG4307|consensus

Probab=95.85  E-value=0.013  Score=59.39  Aligned_cols=81  Identities=21%  Similarity=0.081  Sum_probs=65.3

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeE-EEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNC-CEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~-v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      .+.+..|||-.||..+++.++..+|...-.|++ |.+.+.+ +++-++-|||.|...+++..|+..-..+.++.+.|.|+
T Consensus       431 ~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~  509 (944)
T KOG4307|consen  431 GGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVD  509 (944)
T ss_pred             CCccceEEeccCCccccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEee
Confidence            344679999999999999999999987766665 6666655 68889999999999887777776556677888889998


Q ss_pred             eec
Q psy15676        265 GEE  267 (309)
Q Consensus       265 ~a~  267 (309)
                      -..
T Consensus       510 si~  512 (944)
T KOG4307|consen  510 SIA  512 (944)
T ss_pred             chh
Confidence            543

>KOG2202|consensus

Probab=95.77  E-value=0.0049  Score=55.49  Aligned_cols=63  Identities=19%  Similarity=0.325  Sum_probs=51.4

Q ss_pred             HHHHHHHh-cCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        204 DDLEIIFS-RFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       204 ~~L~~~F~-~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      +++...|+ +||.|.++.+..+. .-...|-+||.|...++|++|+..|||-.+.|++|+..++.
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 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            34445555 89999988766543 24567889999999999999999999999999999998875

>KOG1996|consensus

Probab=95.32  E-value=0.052  Score=49.91  Aligned_cols=68  Identities=18%  Similarity=0.224  Sum_probs=53.5

Q ss_pred             HHHHHHHhcCCceeEEEEeeeCCCCCcc-cEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecCchh
Q psy15676        204 DDLEIIFSRFGKVNCCEVIRDKVTGDSL-QYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWNMW  271 (309)
Q Consensus       204 ~~L~~~F~~fG~I~~v~i~~d~~tg~sk-G~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~~~~  271 (309)
                      ++.....++||.|.+|.|...+..-... ---||+|...++|.+|+-.|||..|+|+.+...|..-..+
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~ekf  369 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNLEKF  369 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccHHhh
Confidence            4567778999999999877665322222 2469999999999999999999999999999888754444

>KOG0115|consensus

Probab=95.24  E-value=0.021  Score=51.49  Aligned_cols=75  Identities=24%  Similarity=0.301  Sum_probs=60.5

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcC--C--ceeCCeeEEEEe
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMD--N--VLIDDRRIHARG  265 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~--g--~~i~gr~I~V~~  265 (309)
                      ..|||.||+..++.+.|...|+.||+|....++.|- -+++.+-++|.|...-.+.+|+..+.  |  ....+++.-|..
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            789999999999999999999999999887666664 47888899999999999999887763  2  334455555543

>KOG0128|consensus

Probab=95.12  E-value=0.0015  Score=67.14  Aligned_cols=64  Identities=28%  Similarity=0.375  Sum_probs=55.8

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCC
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDN  253 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g  253 (309)
                      .++||+||++.+.+.+|...|+.+|.+..+.+.....+++.+|+||+.|...+++.+|+....+
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~  731 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDS  731 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhh
Confidence            5899999999999999999999999998887765556789999999999999999998864433

>KOG4676|consensus

Probab=94.92  E-value=0.052  Score=51.72  Aligned_cols=75  Identities=20%  Similarity=0.326  Sum_probs=58.9

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCC---CCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKV---TGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~---tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      ...|-|.||.+++|.+++..+|+..|.|..+.+..+..   .....-.|||.|.+...+..|-. |.++.+-|+-|.|-
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQh-Ltntvfvdraliv~   84 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQH-LTNTVFVDRALIVR   84 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhh-hccceeeeeeEEEE
Confidence            34899999999999999999999999999988765432   12345689999999998888764 67766666666554

>KOG1365|consensus

Probab=94.61  E-value=0.1  Score=49.70  Aligned_cols=59  Identities=19%  Similarity=0.128  Sum_probs=47.9

Q ss_pred             EEEecCCCCCCCHHHHHHHHhcC----CceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHH
Q psy15676        191 VLFVCKLNPVTSDDDLEIIFSRF----GKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK  250 (309)
Q Consensus       191 ~lfV~nL~~~~te~~L~~~F~~f----G~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~  250 (309)
                      .|-..+||+++++.++..+|.+-    |....+.++..+ .|+..|-|||.|..+++|+.||..
T Consensus       163 ivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~k  225 (508)
T KOG1365|consen  163 IVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRK  225 (508)
T ss_pred             EEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHH
Confidence            55677999999999999999743    234556666554 588999999999999999999975

>KOG0112|consensus

Probab=94.47  E-value=0.01  Score=61.54  Aligned_cols=86  Identities=19%  Similarity=0.241  Sum_probs=68.6

Q ss_pred             CCCCCCCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCe
Q psy15676        180 LPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDR  259 (309)
Q Consensus       180 ~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr  259 (309)
                      +...+....+.|||+|||+..+++.+|+..|..+|.+..+.|-..+ -+...-||||.|.+...+-.|+..+.+..|...
T Consensus       363 v~~~DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g  441 (975)
T KOG0112|consen  363 VLKLDDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNG  441 (975)
T ss_pred             cccccchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccC
Confidence            3344445567899999999999999999999999999999875543 234456999999999999999999999887755


Q ss_pred             eEEEEee
Q psy15676        260 RIHARGE  266 (309)
Q Consensus       260 ~I~V~~a  266 (309)
                      .+.+.+.
T Consensus       442 ~~r~glG  448 (975)
T KOG0112|consen  442 THRIGLG  448 (975)
T ss_pred             ccccccc
Confidence            5555554

>KOG2068|consensus

Probab=94.13  E-value=0.042  Score=51.39  Aligned_cols=79  Identities=16%  Similarity=0.297  Sum_probs=61.0

Q ss_pred             cEEEecCCCCCCCHHHH---HHHHhcCCceeEEEEeeeCC--CCC-cccEEEEEecCHHHHHHHHHHcCCceeCCeeEEE
Q psy15676        190 NVLFVCKLNPVTSDDDL---EIIFSRFGKVNCCEVIRDKV--TGD-SLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA  263 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L---~~~F~~fG~I~~v~i~~d~~--tg~-skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V  263 (309)
                      +-+||-+|++....+.+   .+.|++||.|..+.+-.+.-  .+. .-.-++|+|...++|..||...+|...+|+.++.
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            57889999988765554   35799999999988876552  111 1234799999999999999999999999999777


Q ss_pred             EeecC
Q psy15676        264 RGEEW  268 (309)
Q Consensus       264 ~~a~~  268 (309)
                      .+...
T Consensus       158 ~~gtt  162 (327)
T KOG2068|consen  158 SLGTT  162 (327)
T ss_pred             hhCCC
Confidence            76654

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=93.62  E-value=0.32  Score=40.41  Aligned_cols=74  Identities=22%  Similarity=0.270  Sum_probs=54.3

Q ss_pred             CCCCcEEEecCCCCCCC-HHHHH---HHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeE
Q psy15676        186 APPENVLFVCKLNPVTS-DDDLE---IIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI  261 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~t-e~~L~---~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I  261 (309)
                      .||=.||.|.=|..+.. .+||+   ..++.||+|.++...     |  +..|.|.|.+..+|-.|+.+++. ...|..+
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----G--rqsavVvF~d~~SAC~Av~Af~s-~~pgtm~  154 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----G--RQSAVVVFKDITSACKAVSAFQS-RAPGTMF  154 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----C--CceEEEEehhhHHHHHHHHhhcC-CCCCceE
Confidence            46667888886665543 34444   446899999998763     3  35799999999999999988765 5667777


Q ss_pred             EEEeec
Q psy15676        262 HARGEE  267 (309)
Q Consensus       262 ~V~~a~  267 (309)
                      .+.+-+
T Consensus       155 qCsWqq  160 (166)
T PF15023_consen  155 QCSWQQ  160 (166)
T ss_pred             Eeeccc
Confidence            777654

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=93.49  E-value=0.26  Score=37.17  Aligned_cols=55  Identities=22%  Similarity=0.362  Sum_probs=40.7

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMD  252 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~  252 (309)
                      ....||+ .|......||..+|+.||.|. |..+.|       ..|||...+.+.|..++..+.
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d-------TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND-------TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT-------TEEEEEECCCHHHHHHHHHHT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC-------CcEEEEeecHHHHHHHHHHhc
Confidence            3455665 999999999999999999983 555544       379999999999998888765

; 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.

>KOG2253|consensus

Probab=92.53  E-value=0.083  Score=53.43  Aligned_cols=75  Identities=20%  Similarity=0.276  Sum_probs=64.1

Q ss_pred             CCCCCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeE
Q psy15676        182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI  261 (309)
Q Consensus       182 ~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I  261 (309)
                      .....++..++||+|+...+..+-+..+...+|.|.++....         |||..|........|+..++...++|..+
T Consensus        33 ~~~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl  103 (668)
T KOG2253|consen   33 VFQPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKL  103 (668)
T ss_pred             cccCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchh
Confidence            334467788999999999999999999999999987765432         99999999999999999999999999888


Q ss_pred             EEEe
Q psy15676        262 HARG  265 (309)
Q Consensus       262 ~V~~  265 (309)
                      .+..
T Consensus       104 ~~~~  107 (668)
T KOG2253|consen  104 IENV  107 (668)
T ss_pred             hccc
Confidence            7765

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=92.46  E-value=0.72  Score=32.81  Aligned_cols=54  Identities=20%  Similarity=0.293  Sum_probs=43.2

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcC---CceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHc
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRF---GKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM  251 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~f---G~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l  251 (309)
                      ..|+|.|+. +.+.+++..+|..|   .....+.++-|.       .|-|.|.+...|.+||..|
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            578999985 46778899999888   234578888774       4789999999999999754

>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=91.33  E-value=0.26  Score=42.51  Aligned_cols=81  Identities=12%  Similarity=0.134  Sum_probs=49.5

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhc-CCce---eEEEEeeeCCCCC--cccEEEEEecCHHHHHHHHHHcCCceeCC---
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSR-FGKV---NCCEVIRDKVTGD--SLQYAFVEFDNPKSCEDAYLKMDNVLIDD---  258 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~-fG~I---~~v~i~~d~~tg~--skG~aFV~F~~~~~a~~Al~~l~g~~i~g---  258 (309)
                      ....|.|++||++.|++++...++. ++.-   ..+.-.....+..  ...-|||.|.+.+++..-...++|+.+.+   
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            4568999999999999998886665 5544   2332122221111  23458999999999999999999976642   


Q ss_pred             --eeEEEEeecC
Q psy15676        259 --RRIHARGEEW  268 (309)
Q Consensus       259 --r~I~V~~a~~  268 (309)
                        .+..|.+|-.
T Consensus        86 ~~~~~~VE~Apy   97 (176)
T PF03467_consen   86 NEYPAVVEFAPY   97 (176)
T ss_dssp             -EEEEEEEE-SS
T ss_pred             CCcceeEEEcch
Confidence              3446677754

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.

>cd01921 cyclophilin_RRM cyclophilin_RRM: cyclophilin-type peptidylprolyl cis- trans isomerase domain occuring with a C-terminal RNA recognition motif domain (RRM)

Probab=91.26  E-value=0.12  Score=44.04  Aligned_cols=23  Identities=43%  Similarity=0.645  Sum_probs=21.4

Q ss_pred             cccccCCccccceEeecCCCCCC
Q psy15676         98 VFKRKNDIRITHAVILEDPYEDL  120 (309)
Q Consensus        98 ~~rp~~~iri~h~~il~dPf~~p  120 (309)
                      .++|+.+|+|.++.|++|||+||
T Consensus       144 ~~~P~~~i~I~~~~i~~~pf~~~  166 (166)
T cd01921         144 DGRPLKDIRIKHTHILDDPFPDP  166 (166)
T ss_pred             CCCCCCCeEEEEEEEECCCCCCC
Confidence            37999999999999999999986

This subfamily of the cyclophilin domain family contains a number of eukaryotic cyclophilins having the RRM domain including the nuclear proteins: human hCyP-57, Arabidopsis thaliana AtCYP59, Caenorhabditis elegans CeCyP-44 and Paramecium tetrurelia Kin241. The Kin241 protein has been shown to have a role in cell morphogenesis.

>KOG2135|consensus

Probab=91.14  E-value=0.16  Score=49.55  Aligned_cols=72  Identities=21%  Similarity=0.194  Sum_probs=56.8

Q ss_pred             cEEEecCCCCC-CCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        190 NVLFVCKLNPV-TSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       190 ~~lfV~nL~~~-~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      +.|-+...++. -+-++|...|.+||.|..|.+-..      --.|.|+|.+...|-.|+. ..+..|+|+.|+|-|-..
T Consensus       373 s~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  373 SPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             chhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhc-cccceecCceeEEEEecC
Confidence            34444444554 346789999999999999987443      3468999999999988885 699999999999998775

>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=90.84  E-value=2.3  Score=33.88  Aligned_cols=75  Identities=15%  Similarity=0.202  Sum_probs=51.3

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcC-CceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCC---eeEEEEe
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRF-GKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDD---RRIHARG  265 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~f-G~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~g---r~I~V~~  265 (309)
                      ..+.+...|..++.++|..+.+.+ ..|..++|++|.  ..++-.+.+.|.+..+|..-+..+||..++.   -.++|-|
T Consensus        14 ~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~FnslEpE~Chvvf   91 (110)
T PF07576_consen   14 TLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNSLEPETCHVVF   91 (110)
T ss_pred             eEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCCCCCceeEEEE
Confidence            344454555556666676555555 456778888864  2355678999999999999999999987764   3345444


Q ss_pred             e
Q psy15676        266 E  266 (309)
Q Consensus       266 a  266 (309)
                      -
T Consensus        92 V   92 (110)
T PF07576_consen   92 V   92 (110)
T ss_pred             E
Confidence            3

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG4210|consensus

Probab=90.49  E-value=0.11  Score=48.30  Aligned_cols=80  Identities=13%  Similarity=0.009  Sum_probs=66.2

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      ..+++|++++...+.+.+...+|..+|....+.+........++|++++.|...+.+..|+........+++.+...+..
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            46799999999999999889999999988888777777788999999999999999999997544356667666665554

>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=89.55  E-value=1.2  Score=38.82  Aligned_cols=61  Identities=16%  Similarity=0.231  Sum_probs=44.5

Q ss_pred             CHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcC--CceeCCeeEEEEeecC
Q psy15676        202 SDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMD--NVLIDDRRIHARGEEW  268 (309)
Q Consensus       202 te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~--g~~i~gr~I~V~~a~~  268 (309)
                      ....|+.+|..|+.+.....+..      -+-..|.|.+.++|..|...++  +..+.|..+++.|++.
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            34679999999998877766542      3457899999999999999999  9999999999999863

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.

>KOG2318|consensus

Probab=89.15  E-value=3.3  Score=41.70  Aligned_cols=80  Identities=21%  Similarity=0.362  Sum_probs=59.9

Q ss_pred             CCCCcEEEecCCCCC-CCHHHHHHHHhcC----CceeEEEEeeeC----------CCCC---------------------
Q psy15676        186 APPENVLFVCKLNPV-TSDDDLEIIFSRF----GKVNCCEVIRDK----------VTGD---------------------  229 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~-~te~~L~~~F~~f----G~I~~v~i~~d~----------~tg~---------------------  229 (309)
                      +.+.++|-|+||.++ +...+|..+|..|    |.|.+|.|....          .+|.                     
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~  250 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEE  250 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhh
Confidence            456789999999997 8889999999766    688888874432          1121                     


Q ss_pred             ---------------c-ccEEEEEecCHHHHHHHHHHcCCceeCC--eeEEEEe
Q psy15676        230 ---------------S-LQYAFVEFDNPKSCEDAYLKMDNVLIDD--RRIHARG  265 (309)
Q Consensus       230 ---------------s-kG~aFV~F~~~~~a~~Al~~l~g~~i~g--r~I~V~~  265 (309)
                                     - .=||.|+|.+...|.+.+..++|..+..  ..+-+.|
T Consensus       251 ~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRF  304 (650)
T KOG2318|consen  251 EDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRF  304 (650)
T ss_pred             hhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeee
Confidence                           0 1278999999999999999999988864  4444443

>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=88.52  E-value=2.6  Score=30.75  Aligned_cols=67  Identities=12%  Similarity=0.224  Sum_probs=38.0

Q ss_pred             EEEec-CCCCCCCHHHHHHHHhcCCce-----eEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        191 VLFVC-KLNPVTSDDDLEIIFSRFGKV-----NCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       191 ~lfV~-nL~~~~te~~L~~~F~~fG~I-----~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      ++||. +=-..++..+|..++...+.+     -.+.+..        .|+||+-.. +.+..++..|++..+.|+++.|.
T Consensus         2 rl~in~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~--------~~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve   72 (74)
T PF03880_consen    2 RLFINVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFD--------NFSFVEVPE-EVAEKVLEALNGKKIKGKKVRVE   72 (74)
T ss_dssp             EEEES-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-S--------S-EEEEE-T-T-HHHHHHHHTT--SSS----EE
T ss_pred             EEEEEcccccCCCHHHHHHHHHhccCCCHHhEEEEEEee--------eEEEEEECH-HHHHHHHHHhcCCCCCCeeEEEE
Confidence            45553 223457788888888766544     4555532        388998875 57888999999999999999998


Q ss_pred             ee
Q psy15676        265 GE  266 (309)
Q Consensus       265 ~a  266 (309)
                      .|
T Consensus        73 ~A   74 (74)
T PF03880_consen   73 RA   74 (74)
T ss_dssp             E-
T ss_pred             EC
Confidence            65

; PDB: 2G0C_A 3MOJ_B.

>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=87.57  E-value=2.5  Score=30.45  Aligned_cols=55  Identities=18%  Similarity=0.388  Sum_probs=42.7

Q ss_pred             CCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEE
Q psy15676        200 VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA  263 (309)
Q Consensus       200 ~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V  263 (309)
                      .++-++++..+..|+-.   .|..|+ ||    | ||.|.+..+|++|+...+|..+.+.+|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~~---~I~~d~-tG----f-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRWD---RIRDDR-TG----F-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCcc---eEEecC-CE----E-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            46778999999999642   333343 33    3 89999999999999999999888877654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG4660|consensus

Probab=87.51  E-value=0.84  Score=45.51  Aligned_cols=80  Identities=11%  Similarity=0.097  Sum_probs=56.9

Q ss_pred             CcEEEecCCCCCCCHHHHHHHH-hcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCcee---C-CeeEEE
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIF-SRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLI---D-DRRIHA  263 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F-~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i---~-gr~I~V  263 (309)
                      .+++-|.|++...|..-|...- ...|.-..+.++.|-.+.-+.|||||.|.+.+++..+++++||...   + .+.+.+
T Consensus       388 rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~i  467 (549)
T KOG4660|consen  388 RTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASI  467 (549)
T ss_pred             hhhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeee
Confidence            3556666666555544433332 3456667778888887778899999999999999999999999544   3 345577


Q ss_pred             EeecC
Q psy15676        264 RGEEW  268 (309)
Q Consensus       264 ~~a~~  268 (309)
                      .||+.
T Consensus       468 tYArI  472 (549)
T KOG4660|consen  468 TYARI  472 (549)
T ss_pred             ehhhh
Confidence            77754

>KOG2591|consensus

Probab=86.31  E-value=1.1  Score=44.92  Aligned_cols=69  Identities=17%  Similarity=0.358  Sum_probs=54.4

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHh--cCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCC--ceeCCeeEEEE
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFS--RFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDN--VLIDDRRIHAR  264 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~--~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g--~~i~gr~I~V~  264 (309)
                      -+.+.+.-+|.++-.++++.+|.  .+-.+.+|.+-.+.       -=||+|++..+|+.|++.|..  ..|.|++|...
T Consensus       175 RcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  175 RCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             eeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            36788999999999999999995  46778888876542       138999999999999987765  56667766443

>KOG4574|consensus

Probab=85.44  E-value=0.67  Score=48.38  Aligned_cols=77  Identities=16%  Similarity=0.102  Sum_probs=64.0

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCcee--CCeeEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLI--DDRRIHA  263 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i--~gr~I~V  263 (309)
                      -|-..+.++.|.+-..+...|..+|+.||.+.++...++-      -.|.|.|.+.++|-.|+.+++|..+  -|-+.+|
T Consensus       295 ~plqp~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V  368 (1007)
T KOG4574|consen  295 FPLQPKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRV  368 (1007)
T ss_pred             ccCcchhhhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeE
Confidence            3444566677777788889999999999999998887764      3799999999999999999999644  5888999


Q ss_pred             EeecC
Q psy15676        264 RGEEW  268 (309)
Q Consensus       264 ~~a~~  268 (309)
                      .+|+.
T Consensus       369 ~~ak~  373 (1007)
T KOG4574|consen  369 SFAKT  373 (1007)
T ss_pred             Eeccc
Confidence            99974

>KOG0804|consensus

Probab=85.01  E-value=3.5  Score=40.31  Aligned_cols=69  Identities=12%  Similarity=0.292  Sum_probs=57.0

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcC-CceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCC
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRF-GKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDD  258 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~f-G~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~g  258 (309)
                      ++..|+|=.+|-..|..||..|...| -.|..+++++|..  .++=.+.+.|.+.++|..-+..+||..++.
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~--pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGM--PNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCC--CceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            37899999999999999999998765 4778999999642  223346899999999999999999987764

>KOG2891|consensus

Probab=84.30  E-value=1.6  Score=40.07  Aligned_cols=82  Identities=17%  Similarity=0.279  Sum_probs=48.6

Q ss_pred             CCcEEEecCCCC------------CCCHHHHHHHHhcCCceeEEEEeee-----CCCCCcc-----cEEE---------E
Q psy15676        188 PENVLFVCKLNP------------VTSDDDLEIIFSRFGKVNCCEVIRD-----KVTGDSL-----QYAF---------V  236 (309)
Q Consensus       188 ~~~~lfV~nL~~------------~~te~~L~~~F~~fG~I~~v~i~~d-----~~tg~sk-----G~aF---------V  236 (309)
                      .+.|||+.+||-            -.+++-|+..|..||.|..+.|+..     ..||+..     ||+|         |
T Consensus       148 rpdti~la~ip~kwf~lkedg~~dlpse~rlr~a~eafg~ir~vdipicdplr~~mn~kisgiq~~gfg~g~dlffeayv  227 (445)
T KOG2891|consen  148 RPDTIHLAGIPCKWFALKEDGSEDLPSEDRLRKAFEAFGEIRNVDIPICDPLREEMNGKISGIQFHGFGFGGDLFFEAYV  227 (445)
T ss_pred             CCCceeecCCcceeeeecccccccCChHHHHHHHHHHhccceecCCcccchhHHHhcCccccceeeccccCcchhHHHHH
Confidence            345778877764            2457789999999999998877533     2345543     3333         3


Q ss_pred             EecCHHHHHHHHHHcCCc----eeCCe----eEEEEeecCc
Q psy15676        237 EFDNPKSCEDAYLKMDNV----LIDDR----RIHARGEEWN  269 (309)
Q Consensus       237 ~F~~~~~a~~Al~~l~g~----~i~gr----~I~V~~a~~~  269 (309)
                      .|........|+..+.|.    .++|.    .++|+|.++.
T Consensus       228 qfmeykgfa~amdalr~~k~akk~d~~ffqanvkvdfdrsr  268 (445)
T KOG2891|consen  228 QFMEYKGFAQAMDALRGMKLAKKGDDGFFQANVKVDFDRSR  268 (445)
T ss_pred             HHHHHHhHHHHHHHHhcchHHhhcCCcccccccccccchhh
Confidence            333333334455555553    33333    4677777664

>KOG4285|consensus

Probab=83.80  E-value=2.4  Score=39.40  Aligned_cols=66  Identities=18%  Similarity=0.223  Sum_probs=47.7

Q ss_pred             ecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCee-EEEEeec
Q psy15676        194 VCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRR-IHARGEE  267 (309)
Q Consensus       194 V~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~-I~V~~a~  267 (309)
                      |-+.++.-. .-+...|++||.|.+....      ..-.+-+|.|.+..+|.+||.. ||..|+|.. |-|.-+.
T Consensus       202 VfGFppg~~-s~vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkpCt  268 (350)
T KOG4285|consen  202 VFGFPPGQV-SIVLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKPCT  268 (350)
T ss_pred             EeccCccch-hHHHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhhh-cCeeeccceEEeeeecC
Confidence            347776644 4467789999999775432      2224889999999999999975 999998754 3454443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	309
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		7e-08
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		2e-07
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		3e-07
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		3e-07
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		6e-07
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		9e-07
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		1e-06
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		4e-06
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		4e-06
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		1e-05
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		3e-05
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		3e-05
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		3e-05
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		3e-05
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		3e-05
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		3e-05
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		4e-05
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		7e-05
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		7e-05
1sxl_A	97	Resonance Assignments And Solution Structure Of The		8e-05
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		1e-04
2khc_A	118	Bruno Rrm3+ Length = 118		1e-04
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		1e-04
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		2e-04
1x4e_A	85	Solution Structure Of Rrm Domain In Rna Binding Mot		3e-04
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		3e-04
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		4e-04
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		4e-04
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		5e-04
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		6e-04
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		6e-04
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		6e-04
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		7e-04
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		7e-04
2cpf_A	98	Solution Structure Of The Penultimate Rna Recogniti		8e-04

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 54.7 bits (130), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 40/70 (57%)
Query: 183 ADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
           A+ A   N ++V  ++   SDDD++ +F  FGK+  C + RD  TG    Y F+E++  +
Sbjct: 104 AEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQ 163
Query: 243 SCEDAYLKMD 252
           S +DA   M+
Sbjct: 164 SSQDAVSSMN 173

>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 = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/58 (36%), Positives = 35/58 (60%)
Query: 190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           N ++V  ++   SDDD++ +F  FGK+  C + RD  TG    Y F+E++  +S +DA
Sbjct: 110 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDA 167

>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 = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 36/63 (57%)
Query: 190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
           N ++V  ++   SDDD++ +F  FGK+    + RD  TG    Y F+E++  +S +DA  
Sbjct: 126 NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS 185
Query: 250 KMD 252
            M+
Sbjct: 186 SMN 188

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 39/70 (55%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  L+P  + +D++  F+ FGK++   V++D  TG S  Y FV F N    E+A + M
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 252 DNVLIDDRRI 261
               +  R+I
Sbjct: 78  GGQWLGGRQI 87

>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 = 51.6 bits (122), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 23/70 (32%), Positives = 39/70 (55%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  L+P  + +D++  F+ FG+++   V++D  TG S  Y FV F N    E+A  +M
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 252 DNVLIDDRRI 261
               +  R+I
Sbjct: 78  GGQWLGGRQI 87

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 50.8 bits (120), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 42/80 (52%), Gaps = 5/80 (6%)
Query: 187 PPENV-----LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
           PP +V     L V  L   TS D L  +F ++G+V    + RD+ T +S  +AFV F + 
Sbjct: 40  PPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDK 99
Query: 242 KSCEDAYLKMDNVLIDDRRI 261
           +  EDA   MD  ++D R +
Sbjct: 100 RDAEDAMDAMDGAVLDGREL 119

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 26/76 (34%), Positives = 45/76 (59%)
Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
           A  E  LFV  L+  T++  LE +FS++G+++   V++D+ T  S  + FV F+N    +
Sbjct: 9   ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAK 68
Query: 246 DAYLKMDNVLIDDRRI 261
           DA + M+   +D R+I
Sbjct: 69  DAMMAMNGKSVDGRQI 84

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 38/71 (53%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L V  L    + ++   +F   G++  C+++RDK+TG SL Y FV + +PK  E A   +
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 252 DNVLIDDRRIH 262
           + + +  + I 
Sbjct: 65  NGLRLQTKTIK 75

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/70 (35%), Positives = 38/70 (54%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L V  L   TS D L  +F ++G+V    + RD+ T +S  +AFV F + +  EDA   M
Sbjct: 73  LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 252 DNVLIDDRRI 261
           D  ++D R +
Sbjct: 133 DGAVLDGREL 142

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/71 (28%), Positives = 37/71 (52%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L V  L    + D+ + +F   G +  C+++RDK+TG SL Y FV + +P   + A   +
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 252 DNVLIDDRRIH 262
           + + +  + I 
Sbjct: 67  NGLKLQTKTIK 77

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 17/60 (28%), Positives = 34/60 (56%)
Query: 202 SDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI 261
           + D+ + +F   G +  C+++RDK+TG SL Y FV + +P   + A   ++ + +  + I
Sbjct: 17  TQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTI 76

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 36/70 (51%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L V  L    + D+L  +FS  G+V   ++IRDKV G SL Y FV +   K  E A   +
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 252 DNVLIDDRRI 261
           + + +  + I
Sbjct: 65  NGLRLQSKTI 74

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/70 (34%), Positives = 36/70 (51%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L V  L    + D+L  +FS  G+V   ++IRDKV G SL Y FV +   K  E A   +
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 252 DNVLIDDRRI 261
           + + +  + I
Sbjct: 65  NGLRLQSKTI 74

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/64 (31%), Positives = 37/64 (57%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L    +DD L+ IF ++G +    ++RDK+TG     AFV ++  +  ++A   +
Sbjct: 92  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 252 DNVL 255
           +NV+
Sbjct: 152 NNVI 155

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/64 (31%), Positives = 37/64 (57%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L    +DD L+ IF ++G +    ++RDK+TG     AFV ++  +  ++A   +
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 162
Query: 252 DNVL 255
           +NV+
Sbjct: 163 NNVI 166

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 36/71 (50%)
Query: 191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK 250
            LFV ++N  T++  L   F  +G +    ++  K +G    YAF+E+++ +    AY  
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 251 MDNVLIDDRRI 261
            D   ID RR+
Sbjct: 164 ADGKKIDGRRV 174

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 36/71 (50%)
Query: 191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK 250
            LFV ++N  T++  L   F  +G +    ++  K +G    YAF+E+++ +    AY  
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 251 MDNVLIDDRRI 261
            D   ID RR+
Sbjct: 164 ADGKKIDGRRV 174

>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 = 44.7 bits (104), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 25/76 (32%), Positives = 37/76 (48%)
Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
            P    L V  L    + D+L  +FS  G+V   ++IRDKV G SL Y FV +   K  E
Sbjct: 1   GPGRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAE 60
Query: 246 DAYLKMDNVLIDDRRI 261
            A   ++ + +  + I
Sbjct: 61  RAINTLNGLRLQSKTI 76

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 44.7 bits (104), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 3/79 (3%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK- 250
           +F+  LN  T++D+L   F ++G V   ++++D  TG S  + F+ F+ P S ++     
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65
Query: 251 --MDNVLIDDRRIHARGEE 267
             +D  +ID +R   R E+
Sbjct: 66  HILDGKVIDPKRAIPRDEQ 84

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 20/64 (31%), Positives = 37/64 (57%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L    +DD L+ IF ++G +    ++RDK+TG     AFV ++  +  ++A   +
Sbjct: 16  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 252 DNVL 255
           +NV+
Sbjct: 76  NNVI 79

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/90 (30%), Positives = 39/90 (43%)
Query: 175 EIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYA 234
           + +G        P    LF+  L     D DL  +F  FG V   +V  DK T  S  + 
Sbjct: 11  QSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFG 70
Query: 235 FVEFDNPKSCEDAYLKMDNVLIDDRRIHAR 264
           FV +DNP S + A   M+   I  +R+  +
Sbjct: 71  FVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ 100

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 35/73 (47%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LF+  L    +D DL   F  FG V   +V  DK T  S  + FV FDNP S + A   M
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 252 DNVLIDDRRIHAR 264
           +   +  +R+  +
Sbjct: 103 NGFQVGTKRLKVQ 115

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/70 (34%), Positives = 36/70 (51%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L V  L    + D+L  +FS  G+V   ++IRDKV G SL Y FV +   K  E A   +
Sbjct: 22  LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 252 DNVLIDDRRI 261
           + + +  + I
Sbjct: 82  NGLRLQSKTI 91

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/78 (29%), Positives = 42/78 (53%)
Query: 188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           P   L V  L+  T++ DL  +FS++G +    ++ D+ +  S  +AFV F+N    ++A
Sbjct: 14  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73
Query: 248 YLKMDNVLIDDRRIHARG 265
             + + + +D RRI   G
Sbjct: 74  KERANGMELDGRRIRVSG 91

>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif, Single-Stranded Interacting Protein 2 Length = 85

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 20/56 (35%), Positives = 31/56 (55%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           L++  L P T+D DL  +   +GK+   + I DK T     Y FV+FD+P + + A
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LFV  L+  T+ + L   FS++G+V  C +++DK T  S  + FV+F +P +C    L  
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP-NCVGTVLAS 77
Query: 252 DNVLIDDRRIHAR 264
               +D R I  +
Sbjct: 78  RPHTLDGRNIDPK 90

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 18/60 (30%), Positives = 34/60 (56%)
Query: 202 SDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI 261
           +D +L  +F   G +N C ++RD  TG S  YAFV+F +    + A   ++ + + ++R+
Sbjct: 16  TDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRL 75

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +F+  L+    +  L   FS FG +  C+V+ D+    S  Y FV F+  ++ E A  KM
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 65
Query: 252 DNVLIDDRRI 261
           + +L++DR++
Sbjct: 66  NGMLLNDRKV 75

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 41/74 (55%)
Query: 188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           P   L V  L+  T++ DL  +FS++G +    ++ D+ +  S  +AFV F+N    ++A
Sbjct: 45  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104
Query: 248 YLKMDNVLIDDRRI 261
             + + + +D RRI
Sbjct: 105 KERANGMELDGRRI 118

>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 = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +F+  L+    +  L   FS FG +  C+V+ D+    S  Y FV F+  ++ E A  KM
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 158
Query: 252 DNVLIDDRRI 261
           + +L++DR++
Sbjct: 159 NGMLLNDRKV 168

>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 = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +F+  L+    +  L   FS FG +  C+V+ D+    S  Y FV F+  ++ E A  KM
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 163
Query: 252 DNVLIDDRRI 261
           + +L++DR++
Sbjct: 164 NGMLLNDRKV 173

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 23/71 (32%), Positives = 38/71 (53%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LFV  L+  +S++DLE +FS +G ++      D +T     +AFV F  P+    AY ++
Sbjct: 11  LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 252 DNVLIDDRRIH 262
           D  +   R +H
Sbjct: 71  DGQVFQGRMLH 81

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 2/70 (2%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +F+  L+    +  L   FS FG +  C+V+ D+    S  Y FV F+  ++ E A  KM
Sbjct: 14  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKM 71
Query: 252 DNVLIDDRRI 261
           + +L++DR++
Sbjct: 72  NGMLLNDRKV 81

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LF+  LN  T++  L+ +F + G ++   +I+D+ T  S  +AF+ F+NP   ++A   M
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 252 DNVLIDDRRI 261
           +   +  + I
Sbjct: 69  NGKSLHGKAI 78

>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 98

Iteration: 1
 Score = 41.2 bits (95), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 3/79 (3%)
Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGD---SLQYAFVEFDNPKSCEDAY 248
           LF+  LN  T+++ L+ +FS+ G +  C + + K       S+ + FVE+  P+  + A 
Sbjct: 8   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 249 LKMDNVLIDDRRIHARGEE 267
            ++    +D  ++  R  E
Sbjct: 68  KQLQGHTVDGHKLEVRISE 86

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	309
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	7e-27
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-26
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-20
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	5e-18
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-13
1x4e_A	85	RNA binding motif, single-stranded interacting pro	3e-17
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-17
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-13
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	4e-17
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-16
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-16
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-16
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-16
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-16
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-16
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	8e-16
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	9e-16
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-15
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-15
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-12
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-15
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-15
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-15
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-10
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-07
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	9e-15
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	9e-15
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-14
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-14
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-14
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-14
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-14
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-13
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-14
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	3e-14
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	4e-14
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-14
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	4e-14
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-14
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-10
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	5e-14
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	7e-14
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	8e-14
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	8e-14
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	9e-14
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-13
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-13
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-10
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-13
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-13
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-13
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	1e-13
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-13
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-13
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-09
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-13
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-13
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-13
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-13
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	3e-13
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	3e-13
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	4e-13
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	4e-13
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	4e-13
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-13
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	5e-13
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	5e-13
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-13
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-12
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	7e-13
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	8e-13
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	9e-13
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	9e-13
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-12
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-12
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	1e-12
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-12
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	1e-12
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-12
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-12
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-12
2div_A	99	TRNA selenocysteine associated protein; structural	3e-12
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-12
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-12
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	3e-12
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-12
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-12
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	4e-12
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	4e-12
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	4e-12
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-12
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-08
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	5e-12
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	5e-12
1x5p_A	97	Negative elongation factor E; structure genomics,	5e-12
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-12
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-08
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	7e-12
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	9e-12
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-11
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-11
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	9e-11
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-11
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-11
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-11
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-11
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-11
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-11
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-11
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-11
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-11
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	4e-11
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-11
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	5e-11
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	6e-11
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	6e-11
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	6e-11
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-10
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	6e-11
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	8e-11
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	8e-11
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	8e-11
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	9e-11
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-10
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-09
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	9e-11
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-10
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-10
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-10
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-10
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-10
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-10
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-10
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-10
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-10
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-10
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-10
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-10
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	4e-10
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	6e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-05
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	8e-10
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	9e-10
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	8e-08
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-09
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-09
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-09
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	4e-09
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	4e-09
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	5e-09
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-08
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-08
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	3e-08
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	4e-08
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	4e-08
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	4e-08
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	5e-08
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	7e-08
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	9e-08
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-07
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	3e-07
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	4e-07
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	4e-07
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	5e-07
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	6e-07
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	7e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	8e-07
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	9e-07
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-06
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	2e-06
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-06
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	5e-06
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	5e-06
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	5e-06
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	8e-06
3bkp_A	232	Cyclophilin; malaria, isomerase, structural GENO s	1e-05
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	1e-05
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	1e-05
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	4e-05
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	5e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	3e-04
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-04
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	6e-04

>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 =  108 bits (270), Expect = 7e-27
 Identities = 39/205 (19%), Positives = 66/205 (32%), Gaps = 11/205 (5%)

Query: 115 DPYEDLPELVYPPSPE----------PTRELLANGLIGADEDIDETAGLSAQEIEELRAE 164
           DP   LP L   P  +          P      +          ET     +     + E
Sbjct: 17  DPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRAETREERMERKRREKIE 76

Query: 165 REAKARATILEIVGDLPEADAAP-PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIR 223
           R  +   T L++     + +A       LFV ++N  T++  L   F  +G +    ++ 
Sbjct: 77  RRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVY 136

Query: 224 DKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEKEEI 283
            K +G    YAF+E+++ +    AY   D   ID RR+    E     K          +
Sbjct: 137 SKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGL 196

Query: 284 DEKKEEEEKEDRAMIGDRMEDGLRE 308
              +      +    G        E
Sbjct: 197 GGTRRGGADVNIRHSGRDDTSRYDE 221

>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 =  100 bits (250), Expect = 1e-26
 Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 8/79 (10%)

Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
           A P   L+V  L P TS   L   F RFG +   + ++         +A++++++  + +
Sbjct: 14  ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD------SFAYIQYESLDAAQ 67

Query: 246 DAYLKMDNVLID--DRRIH 262
            A  KM    +   DRR+ 
Sbjct: 68  AACAKMRGFPLGGPDRRLR 86

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 83.6 bits (207), Expect = 2e-20
 Identities = 15/78 (19%), Positives = 32/78 (41%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
            P   +   +LN    +  L+ +  ++G+V   E++    T   L  A V F + +  ++
Sbjct: 4   IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKE 63

Query: 247 AYLKMDNVLIDDRRIHAR 264
               +    +    IHA+
Sbjct: 64  TVKNLHLTSVMGNIIHAQ 81

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 78.8 bits (195), Expect = 5e-18
 Identities = 23/106 (21%), Positives = 46/106 (43%), Gaps = 16/106 (15%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L V  L    + ++   +F   G++  C+++RDK+TG SL Y FV + +PK  E A   +
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 252 DNVLIDDRRIHARGEEWNMWKRREEEEEKE----------EIDEKK 287
           + + +  + I         + R      ++           + +K+
Sbjct: 65  NGLRLQTKTIKV------SYARPSSASIRDANLYVSGLPKTMTQKE 104

>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 = 66.1 bits (162), Expect = 2e-13
 Identities = 18/66 (27%), Positives = 33/66 (50%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L    +  +LE +FS++G++    ++ D+VTG S    F+ FD     E+A   +
Sbjct: 91  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150

Query: 252 DNVLID 257
           +     
Sbjct: 151 NGQKPS 156

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 74.5 bits (184), Expect = 3e-17
 Identities = 20/70 (28%), Positives = 34/70 (48%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L++  L P T+D DL  +   +GK+   + I DK T     Y FV+FD+P + + A   +
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67

Query: 252 DNVLIDDRRI 261
               +  +  
Sbjct: 68  KASGVQAQMA 77

>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 = 76.8 bits (190), Expect = 3e-17
 Identities = 25/106 (23%), Positives = 45/106 (42%), Gaps = 16/106 (15%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L V  L    +D +L  +F   G +N C ++RD  TG S  YAFV+F +    + A   +
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65

Query: 252 DNVLIDDRRIHARGEEWNMWKRREEEEEKE----------EIDEKK 287
           + + + ++R+         + R   E  K+           I + +
Sbjct: 66  NGITVRNKRLKV------SYARPGGESIKDTNLYVTNLPRTITDDQ 105

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 66.8 bits (164), Expect = 1e-13
 Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
           P  ++    N L+V  L    +DD L+ IF ++G +    ++RDK+TG     AFV ++ 
Sbjct: 82  PGGESIKDTN-LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNK 140

Query: 241 PKSCEDAYLKMDNVLID 257
            +  ++A   ++NV+ +
Sbjct: 141 REEAQEAISALNNVIPE 157

>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 = 75.5 bits (186), Expect = 4e-17
 Identities = 22/81 (27%), Positives = 41/81 (50%)

Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
                  P   L V  L+  T++ DL  +FS++G +    ++ D+ +  S  +AFV F+N
Sbjct: 38  GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 97

Query: 241 PKSCEDAYLKMDNVLIDDRRI 261
               ++A  + + + +D RRI
Sbjct: 98  VDDAKEAKERANGMELDGRRI 118

>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 = 72.6 bits (179), Expect = 1e-16
 Identities = 22/78 (28%), Positives = 41/78 (52%)

Query: 184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
               P   L V  L+  T++ DL  +FS++G +    ++ D+ +  S  +AFV F+N   
Sbjct: 10  ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 69

Query: 244 CEDAYLKMDNVLIDDRRI 261
            ++A  + + + +D RRI
Sbjct: 70  AKEAKERANGMELDGRRI 87

>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 = 1e-16
 Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 1/79 (1%)

Query: 183 ADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
                  + +FV  L+P  +   +   F+ FG+++   V++D  TG S  Y FV F N  
Sbjct: 1   GPLGSHFH-VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKW 59

Query: 243 SCEDAYLKMDNVLIDDRRI 261
             E+A  +M    +  R+I
Sbjct: 60  DAENAIQQMGGQWLGGRQI 78

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 73.2 bits (180), Expect = 2e-16
 Identities = 25/70 (35%), Positives = 34/70 (48%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LF+  L    +D DL   F  FG V   +V  DK T  S  + FV FDNP S + A   M
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102

Query: 252 DNVLIDDRRI 261
           +   +  +R+
Sbjct: 103 NGFQVGTKRL 112

>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 = 72.7 bits (179), Expect = 2e-16
 Identities = 27/84 (32%), Positives = 37/84 (44%), Gaps = 3/84 (3%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
           P    LF+  L     D DL  +F  FG V   +V  DK T  S  + FV +DNP S + 
Sbjct: 23  PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQA 82

Query: 247 AYLKMDNVLIDDRRI---HARGEE 267
           A   M+   I  +R+     R + 
Sbjct: 83  AIQSMNGFQIGMKRLKVQLKRSKN 106

>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 = 2e-16
 Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 1/81 (1%)

Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
            + D +   + +FV  L+P  + +D++  F+ FG+++   V++D  TG S  Y FV F N
Sbjct: 8   QKKDTSNHFH-VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 66

Query: 241 PKSCEDAYLKMDNVLIDDRRI 261
               E+A  +M    +  R+I
Sbjct: 67  KWDAENAIQQMGGQWLGGRQI 87

>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 = 73.2 bits (180), Expect = 3e-16
 Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 3/86 (3%)

Query: 185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
                  L V  +     +  L  +F R+G +   +++ D+ T  S  Y FV+F +  S 
Sbjct: 38  EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSA 97

Query: 245 EDAYLKMDNVLIDDRRI---HARGEE 267
           + A   ++   I ++R+    A    
Sbjct: 98  QQAIAGLNGFNILNKRLKVALAASGH 123

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 70.9 bits (174), Expect = 8e-16
 Identities = 16/86 (18%), Positives = 30/86 (34%), Gaps = 8/86 (9%)

Query: 179 DLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEF 238
           +  +    P   V+ +  L     + DL      FG ++   V+  K      + A VEF
Sbjct: 11  NYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK------RQALVEF 64

Query: 239 DNPKSCEDA--YLKMDNVLIDDRRIH 262
           ++     +A  Y   + + I      
Sbjct: 65  EDVLGACNAVNYAADNQIYIAGHPAF 90

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 70.4 bits (173), Expect = 9e-16
 Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 6/82 (7%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEV--IRDKVTGDSLQYAFVEFDNPKSC 244
              + + +  + P T  D +    S +  +    +  I+DK T  +  +AFV+  +    
Sbjct: 7   HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDA 66

Query: 245 EDAYLKMDNV----LIDDRRIH 262
                 + ++     ID + I 
Sbjct: 67  SQLLQILQSLHPPLKIDGKTIG 88

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 70.0 bits (172), Expect = 2e-15
 Identities = 27/84 (32%), Positives = 47/84 (55%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
           G    +  A  E  LFV  L+  T++  LE +FS++G+++   V++D+ T  S  + FV 
Sbjct: 1   GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVT 60

Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
           F+N    +DA + M+   +D R+I
Sbjct: 61  FENIDDAKDAMMAMNGKSVDGRQI 84

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 72.3 bits (178), Expect = 2e-15
 Identities = 19/82 (23%), Positives = 40/82 (48%)

Query: 180 LPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFD 239
                A    + ++V  +     +D +   F+ FG +   ++  D VT     +AFVE++
Sbjct: 19  AQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYE 78

Query: 240 NPKSCEDAYLKMDNVLIDDRRI 261
            P++ + A  +M++V++  R I
Sbjct: 79  VPEAAQLALEQMNSVMLGGRNI 100

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 65.0 bits (159), Expect = 1e-12
 Identities = 22/87 (25%), Positives = 43/87 (49%), Gaps = 1/87 (1%)

Query: 175 EIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYA 234
           + + D    +A     + +V  ++   SDDD++ +F  FGK+    + RD  TG    Y 
Sbjct: 112 QPIIDQLAEEARAFNRI-YVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYG 170

Query: 235 FVEFDNPKSCEDAYLKMDNVLIDDRRI 261
           F+E++  +S +DA   M+   +  + +
Sbjct: 171 FIEYEKAQSSQDAVSSMNLFDLGGQYL 197

>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 = 69.2 bits (170), Expect = 3e-15
 Identities = 18/81 (22%), Positives = 40/81 (49%), Gaps = 3/81 (3%)

Query: 185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGD---SLQYAFVEFDNP 241
            +   + LF+  LN  T+++ L+ +FS+ G +  C + + K       S+ + FVE+  P
Sbjct: 1   GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60

Query: 242 KSCEDAYLKMDNVLIDDRRIH 262
           +  + A  ++    +D  ++ 
Sbjct: 61  EQAQKALKQLQGHTVDGHKLE 81

>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 = 69.2 bits (170), Expect = 3e-15
 Identities = 23/78 (29%), Positives = 39/78 (50%)

Query: 185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
            +     LFV  L+  +S++DLE +FS +G ++      D +T     +AFV F  P+  
Sbjct: 4   GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 245 EDAYLKMDNVLIDDRRIH 262
             AY ++D  +   R +H
Sbjct: 64  VKAYAEVDGQVFQGRMLH 81

>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 = 73.1 bits (180), Expect = 5e-15
 Identities = 19/96 (19%), Positives = 33/96 (34%), Gaps = 3/96 (3%)

Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
            P + +L V  L P  +    E +   FG +  C ++  + TG S  Y F E+    S  
Sbjct: 92  QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAA 151

Query: 246 DAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEKE 281
            A   +    +  R ++     W    +        
Sbjct: 152 RAKSDLLGKPLGPRTLYVH---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 = 60.4 bits (147), Expect = 1e-10
 Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 2/82 (2%)

Query: 181 PEADAAPPENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFD 239
               A      L V +L P     D L    S       C++   +  G    +A +E++
Sbjct: 176 QLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYE 234

Query: 240 NPKSCEDAYLKMDNVLIDDRRI 261
             +  E+A  + D + +    +
Sbjct: 235 TAEMAEEAQQQADGLSLGGSHL 256

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 50.0 bits (120), Expect = 3e-07
 Identities = 13/73 (17%), Positives = 28/73 (38%), Gaps = 7/73 (9%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           + +  L    ++ ++  + S +  +  C V + K  G     AFV   N +  E A    
Sbjct: 25  ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYK--G----TAFVTLLNGEQAEAAINAF 77

Query: 252 DNVLIDDRRIHAR 264
               + +R +  +
Sbjct: 78  HQSRLRERELSVQ 90

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 69.4 bits (170), Expect = 9e-15
 Identities = 25/125 (20%), Positives = 49/125 (39%), Gaps = 18/125 (14%)

Query: 184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
                   L+V  L+  T+++ +  +FS+ G +    +  DK+   +  + FVE+ +   
Sbjct: 34  KLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRAD 93

Query: 244 CEDAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEKEEIDEKKEEEEKEDRAMIGDRME 303
            E+A   ++   +DDR I         W            D   +E  +  R   G ++ 
Sbjct: 94  AENAMRYINGTRLDDRIIRT------DW------------DAGFKEGRQYGRGRSGGQVR 135

Query: 304 DGLRE 308
           D  R+
Sbjct: 136 DEYRQ 140

>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 = 68.0 bits (167), Expect = 9e-15
 Identities = 22/74 (29%), Positives = 34/74 (45%)

Query: 188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
               L V  L   TS D L  +F ++G+V    + R+  T     +AFV F + +  +DA
Sbjct: 12  GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDA 71

Query: 248 YLKMDNVLIDDRRI 261
              MD   +D R +
Sbjct: 72  EAAMDGAELDGREL 85

>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 = 68.0 bits (167), Expect = 1e-14
 Identities = 19/77 (24%), Positives = 34/77 (44%)

Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
           A     + V  L+  T + DL+ +F  FG ++   + +DK TG S  +AF+ F   +   
Sbjct: 12  ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 71

Query: 246 DAYLKMDNVLIDDRRIH 262
            A   +     D   ++
Sbjct: 72  RAIAGVSGFGYDHLILN 88

>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 = 67.6 bits (166), Expect = 1e-14
 Identities = 23/79 (29%), Positives = 42/79 (53%)

Query: 183 ADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
              AP ++ ++V  L    +++DL  IFS++GKV    +++DK T  S   AF+ F +  
Sbjct: 10  GGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKD 69

Query: 243 SCEDAYLKMDNVLIDDRRI 261
           S ++    ++N  +  R I
Sbjct: 70  SAQNCTRAINNKQLFGRVI 88

>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 = 67.6 bits (166), Expect = 1e-14
 Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 1/79 (1%)

Query: 185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKV-NCCEVIRDKVTGDSLQYAFVEFDNPKS 243
            +   + +F+  L+P   +  L   FS FG +    +++RD  TG+S  YAF+ F +  +
Sbjct: 1   GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60

Query: 244 CEDAYLKMDNVLIDDRRIH 262
            + A   M+   + +R I 
Sbjct: 61  SDAAIEAMNGQYLCNRPIT 79

>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 = 68.1 bits (167), Expect = 1e-14
 Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
           A     LF+  LN  T++  L+ +F + G ++   +I+D+ T  S  +AF+ F+NP   +
Sbjct: 4   ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAK 62

Query: 246 DAYLKMDNVLIDDRRI 261
           +A   M+   +  + I
Sbjct: 63  NAAKDMNGKSLHGKAI 78

>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 = 70.4 bits (173), Expect = 2e-14
 Identities = 29/105 (27%), Positives = 46/105 (43%), Gaps = 6/105 (5%)

Query: 177 VGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFV 236
           +G +  +  + P   L+V  L+P  ++  L   FS  G +    V RD +T  SL YA+V
Sbjct: 3   LGSMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYV 62

Query: 237 EFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEKE 281
            F  P   E A   M+  +I  + +        MW +R+    K 
Sbjct: 63  NFQQPADAERALDTMNFDVIKGKPVRI------MWSQRDPSLRKS 101

>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 = 66.9 bits (164), Expect = 2e-13
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 2/71 (2%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +F+  L+    +  L   FS FG +  C+V+ D     S  Y FV F+  ++ E A  KM
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 163

Query: 252 DNVLIDDRRIH 262
           + +L++DR++ 
Sbjct: 164 NGMLLNDRKVF 174

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 68.3 bits (167), Expect = 2e-14
 Identities = 27/121 (22%), Positives = 40/121 (33%), Gaps = 8/121 (6%)

Query: 149 ETAGLSAQEIEEL--------RAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPV 200
           +   LS +  E L                R       G      +A  + VL+V  L   
Sbjct: 15  KCENLSDEMYEILSNLPESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEE 74

Query: 201 TSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRR 260
             D  L   F  FG +   ++  D  T     +AFVEF+  +    A   M+   +  R 
Sbjct: 75  VDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRT 134

Query: 261 I 261
           I
Sbjct: 135 I 135

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 67.5 bits (165), Expect = 3e-14
 Identities = 25/76 (32%), Positives = 38/76 (50%)

Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
                 L V  L   TS D L  +F ++G+V    + RD+ T +S  +AFV F + +  E
Sbjct: 44  VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 103

Query: 246 DAYLKMDNVLIDDRRI 261
           DA   MD  ++D R +
Sbjct: 104 DAMDAMDGAVLDGREL 119

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 66.4 bits (162), Expect = 4e-14
 Identities = 16/84 (19%), Positives = 29/84 (34%), Gaps = 8/84 (9%)

Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
                     V+ V  L     + DL     +FG +    ++  K      + A VEF+N
Sbjct: 7   GSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK------RQALVEFEN 60

Query: 241 PKSCEDA--YLKMDNVLIDDRRIH 262
             S ++   +     V I  ++  
Sbjct: 61  IDSAKECVTFAADVPVYIAGQQAF 84

>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 = 65.6 bits (161), Expect = 4e-14
 Identities = 21/70 (30%), Positives = 29/70 (41%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LFV  LN    D+ L   F  F       V+ D  TG S  Y FV F +    ++A   M
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63

Query: 252 DNVLIDDRRI 261
               ++ R +
Sbjct: 64  QGQDLNGRPL 73

>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 = 66.5 bits (163), Expect = 4e-14
 Identities = 27/96 (28%), Positives = 47/96 (48%), Gaps = 7/96 (7%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +F+  L+    +  L   FS FG +  C+V+ D     S  Y FV F+  ++ E A  KM
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65

Query: 252 DNVLIDDRRIHARGEEWNMWKRREEEEEKEEIDEKK 287
           + +L++DR++         +K R+E E +     K+
Sbjct: 66  NGMLLNDRKVFV-----GRFKSRKEREAELGARAKE 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 = 68.0 bits (167), Expect = 4e-14
 Identities = 21/98 (21%), Positives = 43/98 (43%), Gaps = 8/98 (8%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGD--SLQYAFVEFDNPKSCEDAYL 249
           +FV ++    S+ DL  +F ++G V    V+RD+      S    FV F   K+  +A  
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65

Query: 250 KMDNVLIDDRRIHARGEEWNMWKRREEEEEKEEIDEKK 287
            + N+ +     H       +  +  + E+   ++++K
Sbjct: 66  ALHNMKVLPGMHHP------IQMKPADSEKNNAVEDRK 97

>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 = 58.4 bits (142), Expect = 1e-10
 Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LF+  ++   +++D+ ++FS FG++  C ++R    G S   AFV F      + A   M
Sbjct: 98  LFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAM 156

Query: 252 DNVLI 256
                
Sbjct: 157 HQAQT 161

>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 = 66.1 bits (162), Expect = 5e-14
 Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 2/84 (2%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
           G     +       L+V  L+   ++  +  +FS+ G    C++I +  + D   Y FVE
Sbjct: 4   GSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVE 61

Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
           F   +    A   M+   I  + +
Sbjct: 62  FYEHRDAAAALAAMNGRKILGKEV 85

>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 = 65.3 bits (160), Expect = 7e-14
 Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 1/70 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  +     + +L   F +FG V    +I D        + F+ F++ +S + A + M
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQA-VNM 71

Query: 252 DNVLIDDRRI 261
               I  +++
Sbjct: 72  HFHDIMGKKV 81

>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 = 65.8 bits (161), Expect = 8e-14
 Identities = 25/70 (35%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  L   T+D  L   F  FG +    VI D+ TG S  Y FV   +  + E A  K 
Sbjct: 20  IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA-CKD 78

Query: 252 DNVLIDDRRI 261
            N +ID R+ 
Sbjct: 79  PNPIIDGRKA 88

>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 = 65.4 bits (160), Expect = 8e-14
 Identities = 16/62 (25%), Positives = 30/62 (48%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LF+ ++     + DL+ +F  FGK+    V++D+ TG     AF+ +   +S   A   +
Sbjct: 16  LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSAL 75

Query: 252 DN 253
             
Sbjct: 76  HE 77

>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 = 65.5 bits (160), Expect = 9e-14
 Identities = 20/80 (25%), Positives = 37/80 (46%), Gaps = 9/80 (11%)

Query: 184 DAAPPENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
           D     + +F+  LN  +    D+E IFS++G+V  C V +         YAFV++ N +
Sbjct: 22  DPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKG--------YAFVQYSNER 73

Query: 243 SCEDAYLKMDNVLIDDRRIH 262
               A L  +  ++  + + 
Sbjct: 74  HARAAVLGENGRVLAGQTLD 93

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 65.4 bits (160), Expect = 1e-13
 Identities = 21/84 (25%), Positives = 37/84 (44%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
           G          +  ++V  L+   S+  L  +F + G V    + +D+VTG    Y FVE
Sbjct: 4   GSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVE 63

Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
           F + +  + A   MD + +  + I
Sbjct: 64  FLSEEDADYAIKIMDMIKLYGKPI 87

>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 = 66.9 bits (164), Expect = 1e-13
 Identities = 17/70 (24%), Positives = 37/70 (52%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LF+  L    +DD ++ + + FG +    +++D  TG S  YAF E+ +    + A   +
Sbjct: 97  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156

Query: 252 DNVLIDDRRI 261
           + + + D+++
Sbjct: 157 NGMQLGDKKL 166

>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 = 58.0 bits (141), Expect = 2e-10
 Identities = 9/75 (12%), Positives = 27/75 (36%), Gaps = 6/75 (8%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCC-----EVIRDKVTGDSLQYAFVEFDNPKSCED 246
           L+V  +    +++ +   F+   ++          +          +AF+EF +      
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 247 AYLKMDNVLIDDRRI 261
           A +  D ++   + +
Sbjct: 67  A-MAFDGIIFQGQSL 80

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 65.0 bits (159), Expect = 1e-13
 Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 1/79 (1%)

Query: 184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
             +  ++ LF+  L    + ++LE I    G V    ++ ++  G     A+VE++N   
Sbjct: 12  STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQ 70

Query: 244 CEDAYLKMDNVLIDDRRIH 262
              A +KMD + I +  I 
Sbjct: 71  ASQAVMKMDGMTIKENIIK 89

>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 = 64.6 bits (158), Expect = 1e-13
 Identities = 16/85 (18%), Positives = 38/85 (44%), Gaps = 6/85 (7%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
           G           + LFV  L P  +++++  +F ++GK     + +DK       + F+ 
Sbjct: 4   GSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIR 57

Query: 238 FDNPKSCEDAYLKMDNVLIDDRRIH 262
            +     E A +++DN+ +  +++ 
Sbjct: 58  LETRTLAEIAKVELDNMPLRGKQLR 82

>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 = 65.0 bits (159), Expect = 1e-13
 Identities = 17/78 (21%), Positives = 35/78 (44%)

Query: 184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
           +   P  VL++  L+P  ++ DL  +F+RF +     +    +TG     AF+ F N + 
Sbjct: 20  NPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEI 79

Query: 244 CEDAYLKMDNVLIDDRRI 261
              A   ++   +  + +
Sbjct: 80  AWQALHLVNGYKLYGKIL 97

>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 = 64.6 bits (158), Expect = 1e-13
 Identities = 17/74 (22%), Positives = 36/74 (48%)

Query: 188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           P  V+++  +    +++ +  + S  G V   +++ D  TG S  YAF+EF + +S   A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

Query: 248 YLKMDNVLIDDRRI 261
              ++   +  R +
Sbjct: 61  VRNLNGYQLGSRFL 74

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 63.6 bits (156), Expect = 1e-13
 Identities = 18/70 (25%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  L+  T+ +D++  F +FGKV+   ++ DK T     + FV F++    E    ++
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV-CEI 60

Query: 252 DNVLIDDRRI 261
               I+++ +
Sbjct: 61  HFHEINNKMV 70

>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 = 67.0 bits (164), Expect = 2e-13
 Identities = 18/100 (18%), Positives = 42/100 (42%), Gaps = 1/100 (1%)

Query: 162 RAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEV 221
                  +    + + G +           LF+  L    +DD ++ + + FG +    +
Sbjct: 88  YQPLPGMSENPSVYVPGVVSTVVPDSAHK-LFIGGLPNYLNDDQVKELLTSFGPLKAFNL 146

Query: 222 IRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI 261
           ++D  TG S  YAF E+ +    + A   ++ + + D+++
Sbjct: 147 VKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKL 186

>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 = 55.0 bits (133), Expect = 3e-09
 Identities = 10/78 (12%), Positives = 28/78 (35%), Gaps = 6/78 (7%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCC-----EVIRDKVTGDSLQYAFVEFDNPKSCED 246
           L+V  +    +++ +   F+   ++          +          +AF+EF +      
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 247 AYLKMDNVLIDDRRIHAR 264
           A +  D ++   + +  R
Sbjct: 67  A-MAFDGIIFQGQSLKIR 83

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 66.4 bits (162), Expect = 2e-13
 Identities = 26/106 (24%), Positives = 44/106 (41%), Gaps = 6/106 (5%)

Query: 162 RAEREAKARATILEIVGDLPEADAAPPENV-----LFVCKLNPVTSDDDLEIIFSRFGKV 216
           R    ++ +    +   DL ++     E V     L V  L+   SD D++ +F+ FG +
Sbjct: 56  RPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTL 115

Query: 217 NCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
               V  D+ +G SL  A V F+       A  +   V +D R + 
Sbjct: 116 KKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMD 160

>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 = 64.1 bits (157), Expect = 2e-13
 Identities = 19/77 (24%), Positives = 38/77 (49%)

Query: 185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
            +   + L+V  L+   ++D L  IF  FGK++   +++D  TG S  Y F+ F + +  
Sbjct: 1   GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60

Query: 245 EDAYLKMDNVLIDDRRI 261
             A  +++   +  R +
Sbjct: 61  RRALEQLNGFELAGRPM 77

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 64.6 bits (158), Expect = 2e-13
 Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 1/71 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L++  L     + +LE +   FG+V    ++RD  +G S    F   ++ + CE      
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHF 86

Query: 252 DNVLIDDRRIH 262
           +   I      
Sbjct: 87  NGKFIKTPPGV 97

>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 = 63.7 bits (156), Expect = 2e-13
 Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKV-TGDSLQYAFVEFDNPKSC 244
           +     + + +L    + D +  IFS +GK+   ++  +++    S  YA+VEF+NP   
Sbjct: 1   SMKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEA 60

Query: 245 EDAYLKMDNVLIDDRRI 261
           E A   MD   ID + I
Sbjct: 61  EKALKHMDGGQIDGQEI 77

>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 = 64.7 bits (158), Expect = 3e-13
 Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 1/81 (1%)

Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
             +       L V  L+   SD D++ +F+ FG +    V  D+ +G SL  A V F+  
Sbjct: 28  GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERR 86

Query: 242 KSCEDAYLKMDNVLIDDRRIH 262
                A  +   V +D R + 
Sbjct: 87  ADALKAMKQYKGVPLDGRPMD 107

>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 = 62.9 bits (154), Expect = 3e-13
 Identities = 14/70 (20%), Positives = 29/70 (41%), Gaps = 1/70 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  L+P T ++ +   F  FG+V   E+  D  T     + F+ F   +  +   ++ 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI-MEK 60

Query: 252 DNVLIDDRRI 261
               +   + 
Sbjct: 61  KYHNVGLSKC 70

>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 = 63.4 bits (155), Expect = 4e-13
 Identities = 17/79 (21%), Positives = 36/79 (45%), Gaps = 11/79 (13%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  ++   +  +L  +F R G+V  C+V++D        YAFV  +     + A  ++
Sbjct: 12  IFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQL 63

Query: 252 DNVLIDDRRI---HARGEE 267
           +   +  +RI    +   +
Sbjct: 64  NGKEVKGKRINVELSTKGQ 82

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 63.4 bits (155), Expect = 4e-13
 Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 9/82 (10%)

Query: 182 EADAAPPENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
           E    PP++ LF+  L     S +DL  IFS +G +    +           + F++FDN
Sbjct: 3   EMHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA--------FGFIQFDN 54

Query: 241 PKSCEDAYLKMDNVLIDDRRIH 262
           P+S  DA       +   +++ 
Sbjct: 55  PQSVRDAIECESQEMNFGKKLI 76

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 64.9 bits (158), Expect = 4e-13
 Identities = 16/127 (12%), Positives = 42/127 (33%), Gaps = 7/127 (5%)

Query: 137 ANGLIGADEDIDETAGLSAQEIEELRAEREAKARATILEIVGDLPEADAAPPENVLFVCK 196
           ++G+    E++   +      + +  + +       IL        +        ++V  
Sbjct: 8   SSGVDLGTENLYFQSMEPPPPVRQEPSPKPNNKTPAILY-----TYSGLRNRRAAVYVGS 62

Query: 197 LNPVTSDDDLEIIFSRFGKVNCCE--VIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNV 254
            +  T+D  L  +    G  +  E     ++  G S  YA V   +  S       +   
Sbjct: 63  FSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGK 122

Query: 255 LIDDRRI 261
           +++  ++
Sbjct: 123 VLNGEKV 129

>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 = 65.2 bits (159), Expect = 4e-13
 Identities = 25/74 (33%), Positives = 38/74 (51%)

Query: 188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
               L V  L   TS D L  +F ++G+V    + RD+ T +S  +AFV F + +  EDA
Sbjct: 69  GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 128

Query: 248 YLKMDNVLIDDRRI 261
              MD  ++D R +
Sbjct: 129 MDAMDGAVLDGREL 142

>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 = 63.5 bits (155), Expect = 5e-13
 Identities = 20/76 (26%), Positives = 32/76 (42%), Gaps = 1/76 (1%)

Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
                   +  LFV  LN   S++D+  +F  FG ++ C V+R    G S   AFV+F +
Sbjct: 7   GSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSS 65

Query: 241 PKSCEDAYLKMDNVLI 256
               + A   +     
Sbjct: 66  HTEAQAAIHALHGSQT 81

>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 = 63.0 bits (154), Expect = 5e-13
 Identities = 21/79 (26%), Positives = 32/79 (40%)

Query: 183 ADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
           +  A  + VL+V  L     D  L   F  FG +   ++  D  T     +AFVEF+  +
Sbjct: 6   SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 65

Query: 243 SCEDAYLKMDNVLIDDRRI 261
               A   M+   +  R I
Sbjct: 66  DAAAAIDNMNESELFGRTI 84

>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 = 64.5 bits (158), Expect = 6e-13
 Identities = 22/82 (26%), Positives = 33/82 (40%), Gaps = 1/82 (1%)

Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
            ++ +    N LFV  LN    D+ L   F  F       V+ D  TG S  Y FV F +
Sbjct: 80  QQSSSDDTFN-LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTS 138

Query: 241 PKSCEDAYLKMDNVLIDDRRIH 262
               ++A   M    ++ R + 
Sbjct: 139 QDDAQNAMDSMQGQDLNGRPLR 160

>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 = 61.8 bits (151), Expect = 6e-12
 Identities = 17/90 (18%), Positives = 38/90 (42%), Gaps = 7/90 (7%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L+   ++D L+  F   G +   +++ DK    ++ YAFVE+        A   +
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61

Query: 252 DNVLIDDRRIHARGEEWNMWKRREEEEEKE 281
           +   I++  +         W  + ++   +
Sbjct: 62  NGKQIENNIVKI------NWAFQSQQSSSD 85

>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 = 63.1 bits (154), Expect = 7e-13
 Identities = 21/84 (25%), Positives = 34/84 (40%), Gaps = 1/84 (1%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
                         L V  L+   SD D++ +F+ FG +    V  D+ +G SL  A V 
Sbjct: 18  SGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVH 76

Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
           F+       A  + + V +D R +
Sbjct: 77  FERKADALKAMKQYNGVPLDGRPM 100

>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 = 62.6 bits (153), Expect = 8e-13
 Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 2/70 (2%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L V  L   T++ DL+  FS FG+V   +V +D  TG S  + FV F   ++     +  
Sbjct: 18  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKV-MSQ 76

Query: 252 DNVLIDDRRI 261
            ++ ID R  
Sbjct: 77  RHM-IDGRWC 85

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 62.7 bits (153), Expect = 9e-13
 Identities = 22/86 (25%), Positives = 37/86 (43%), Gaps = 8/86 (9%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           ++V  L       +LE  FS +G +    + R+        +AFVEF++P+  EDA   +
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57

Query: 252 DNVLIDDRRI---HARGEEWNMWKRR 274
           D  +I   R+    + G        R
Sbjct: 58  DGKVICGSRVRVELSTGMPRRSRFDR 83

>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 = 62.3 bits (152), Expect = 9e-13
 Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 9/80 (11%)

Query: 184 DAAPPENVLFVCKLNPVT-SDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
             +  ++ LF+  L     S +DL  IFS +G +    +           + F++FDNP+
Sbjct: 17  RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNA--------FGFIQFDNPQ 68

Query: 243 SCEDAYLKMDNVLIDDRRIH 262
           S  DA       +   +++ 
Sbjct: 69  SVRDAIEXESQEMNFGKKLI 88

>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 = 65.5 bits (159), Expect = 1e-12
 Identities = 12/82 (14%), Positives = 26/82 (31%), Gaps = 2/82 (2%)

Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFG--KVNCCEVIRDKVTGDSLQYAFVEFD 239
                     L++  L   T+D+DL       G   +   +   ++  G S  +A V   
Sbjct: 61  VYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVG 120

Query: 240 NPKSCEDAYLKMDNVLIDDRRI 261
           +  S +     +    +  +  
Sbjct: 121 SEASSKKLMDLLPKRELHGQNP 142

>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 = 63.2 bits (154), Expect = 1e-12
 Identities = 18/85 (21%), Positives = 39/85 (45%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
           GD P    +    +LFV  ++   +++D+   F+ +G++    +  D+ TG    Y  VE
Sbjct: 11  GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 70

Query: 238 FDNPKSCEDAYLKMDNVLIDDRRIH 262
           ++  K  + A   ++   +  + I 
Sbjct: 71  YETYKEAQAAMEGLNGQDLMGQPIS 95

>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 = 61.9 bits (151), Expect = 1e-12
 Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 8/71 (11%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L V  ++P  ++ +L   F  +G V  C++++D        YAFV  +  +   +A   +
Sbjct: 13  LHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGL 64

Query: 252 DNVLIDDRRIH 262
           DN     +R+H
Sbjct: 65  DNTEFQGKRMH 75

>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 = 62.7 bits (153), Expect = 1e-12
 Identities = 21/87 (24%), Positives = 34/87 (39%), Gaps = 1/87 (1%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
           G      A    + +FV  L+       L+ +FS  G V   +++ DK  G S     V 
Sbjct: 4   GSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVT 62

Query: 238 FDNPKSCEDAYLKMDNVLIDDRRIHAR 264
           F+       A    +  L+ DR +H +
Sbjct: 63  FEQSIEAVQAISMFNGQLLFDRPMHVK 89

>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 = 63.4 bits (154), Expect = 1e-12
 Identities = 22/108 (20%), Positives = 41/108 (37%), Gaps = 8/108 (7%)

Query: 161 LRAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCE 220
                +                 D+ P +  ++V  L    +  +LE  F  +G +    
Sbjct: 45  YDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVW 104

Query: 221 VIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI---HARG 265
           V R+   G    +AFVEF++P+   DA  ++D   +   R+    + G
Sbjct: 105 VARNP-PG----FAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNG 147

>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 = 61.4 bits (150), Expect = 1e-12
 Identities = 21/76 (27%), Positives = 31/76 (40%)

Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
           A  + VL+V  L     D  L   F  FG +   ++  D  T     +AFVEF+  +   
Sbjct: 4   ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 63

Query: 246 DAYLKMDNVLIDDRRI 261
            A   M+   +  R I
Sbjct: 64  AAIDNMNESELFGRTI 79

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 62.4 bits (152), Expect = 1e-12
 Identities = 18/111 (16%), Positives = 48/111 (43%), Gaps = 11/111 (9%)

Query: 187 PPE--NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
           PPE   +L++  L    + +++  IF ++G +     IR   T ++   A+V +++    
Sbjct: 4   PPEVNRILYIRNLPYKITAEEMYDIFGKYGPI---RQIRVGNTPETRGTAYVVYEDIFDA 60

Query: 245 EDAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEKEEIDEKKEEEEKEDR 295
           ++A   +    + +R +        ++       +K +  +K+E+ +    
Sbjct: 61  KNAVDHLSGFNVSNRYLVV------LYYNANRAFQKMDTKKKEEQLKLLKE 105

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 60.6 bits (148), Expect = 2e-12
 Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +F+  L+  T+ + L   F +FG+V  C V+RD +T  S  + FV F +    +   L  
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV-LAQ 61

Query: 252 DNVLIDDRRI 261
               +D + I
Sbjct: 62  SRHELDSKTI 71

>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 = 61.2 bits (149), Expect = 3e-12
 Identities = 17/80 (21%), Positives = 36/80 (45%), Gaps = 1/80 (1%)

Query: 183 ADAAPPENVLFVCKLNPVTSDDDLEIIFSRFG-KVNCCEVIRDKVTGDSLQYAFVEFDNP 241
           + ++     L++  L P   ++ +   F+  G  V   ++IR+++TG    Y FVEF + 
Sbjct: 3   SGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADL 62

Query: 242 KSCEDAYLKMDNVLIDDRRI 261
            + E    K++   +     
Sbjct: 63  ATAEKCLHKINGKPLPGATP 82

>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 = 61.1 bits (149), Expect = 3e-12
 Identities = 21/85 (24%), Positives = 41/85 (48%), Gaps = 7/85 (8%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L+    D+ L   FS FG +   +V+ +   G S  + FV F +P+    A  +M
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75

Query: 252 DNVLIDDRRIHARGEEWNMWKRREE 276
           +  ++  + ++       + +R+EE
Sbjct: 76  NGRIVATKPLYV-----ALAQRKEE 95

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 61.2 bits (149), Expect = 3e-12
 Identities = 13/78 (16%), Positives = 30/78 (38%), Gaps = 7/78 (8%)

Query: 185 AAPPENV-LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
           +APP     ++  +    ++ DL  +F  FG +   +   +K         F+++D  + 
Sbjct: 22  SAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK------GCCFIKYDTHEQ 75

Query: 244 CEDAYLKMDNVLIDDRRI 261
                + + N     R +
Sbjct: 76  AAVCIVALANFPFQGRNL 93

>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 = 61.1 bits (149), Expect = 3e-12
 Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +F+  L+  T+ + L   F +FG+V  C V+RD +T  S  + FV F +    +   L  
Sbjct: 28  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV-LAQ 86

Query: 252 DNVLIDDRRI 261
               +D + I
Sbjct: 87  SRHELDSKTI 96

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 61.2 bits (149), Expect = 3e-12
 Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 6/78 (7%)

Query: 184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
            ++P    ++   +    +D  +   FS FG++    V  +K       Y+FV F   +S
Sbjct: 20  QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHES 73

Query: 244 CEDAYLKMDNVLIDDRRI 261
              A + ++   I+   +
Sbjct: 74  AAHAIVSVNGTTIEGHVV 91

>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 = 60.7 bits (148), Expect = 3e-12
 Identities = 20/87 (22%), Positives = 40/87 (45%), Gaps = 2/87 (2%)

Query: 175 EIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYA 234
            ++ D  E   +     LF+  LNP  S  +L++  S     N    + D  TG + ++ 
Sbjct: 3   HMLEDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFG 61

Query: 235 FVEFDNPKSCEDAYLKMDNVLIDDRRI 261
           +V+F++ +  E A L++  + +    I
Sbjct: 62  YVDFESAEDLEKA-LELTGLKVFGNEI 87

>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 = 61.2 bits (149), Expect = 4e-12
 Identities = 21/86 (24%), Positives = 37/86 (43%), Gaps = 6/86 (6%)

Query: 185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
           A   +  ++V  L P     D+E +F ++G +   ++   +       +AFVEF++P+  
Sbjct: 18  AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFVEFEDPRDA 74

Query: 245 EDAYLKMDNVLIDDRRI---HARGEE 267
           EDA    D    D  R+     R   
Sbjct: 75  EDAVYGRDGYDYDGYRLRVEFPRSGR 100

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 61.1 bits (149), Expect = 4e-12
 Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LFV  L+  T+ + L   FS++G+V  C +++DK T  S  + FV+F +P       L  
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV-LAS 77

Query: 252 DNVLIDDRRI 261
               +D R I
Sbjct: 78  RPHTLDGRNI 87

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 60.7 bits (148), Expect = 4e-12
 Identities = 18/85 (21%), Positives = 39/85 (45%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
           GD P    +    +LFV  ++   +++D+   F+ +G++    +  D+ TG    Y  VE
Sbjct: 12  GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 71

Query: 238 FDNPKSCEDAYLKMDNVLIDDRRIH 262
           ++  K  + A   ++   +  + I 
Sbjct: 72  YETYKEAQAAMEGLNGQDLMGQPIS 96

>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 = 62.2 bits (152), Expect = 5e-12
 Identities = 19/101 (18%), Positives = 42/101 (41%), Gaps = 8/101 (7%)

Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
           E   +     LF+  LNP  S  +L++  S     N   V+  + TG + ++ +V+F++ 
Sbjct: 6   EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESA 64

Query: 242 KSCEDAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEKEE 282
           +  E A L++  + +    I           +  + ++   
Sbjct: 65  EDLEKA-LELTGLKVFGNEIKL------EKPKGRDSKKVRA 98

>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 = 51.8 bits (125), Expect = 2e-08
 Identities = 14/81 (17%), Positives = 27/81 (33%), Gaps = 6/81 (7%)

Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
                      L    L+   ++D+L+ +F    ++           G S   A++EF +
Sbjct: 92  DSKKVRAART-LLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKS 145

Query: 241 PKSCEDAYLKMDNVLIDDRRI 261
               E    +     ID R +
Sbjct: 146 EADAEKNLEEKQGAEIDGRSV 166

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 60.4 bits (147), Expect = 5e-12
 Identities = 15/80 (18%), Positives = 34/80 (42%), Gaps = 4/80 (5%)

Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
            +  +     L +  L+   +++ L+ +F +   +     +     G S  YAF+EF + 
Sbjct: 8   NSTWSGESKTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEFASF 63

Query: 242 KSCEDAYLKMDNVLIDDRRI 261
           +  ++A    +   I+ R I
Sbjct: 64  EDAKEALNSCNKREIEGRAI 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 = 59.9 bits (146), Expect = 5e-12
 Identities = 16/79 (20%), Positives = 37/79 (46%), Gaps = 11/79 (13%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LF+  L    ++ ++  +F ++GKV  C++I++        Y FV  ++  + EDA   +
Sbjct: 11  LFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHIEDKTAAEDAIRNL 62

Query: 252 DNVLIDDRRI---HARGEE 267
            +  +    I    ++ + 
Sbjct: 63  HHYKLHGVNINVEASKNKS 81

>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 = 60.4 bits (147), Expect = 5e-12
 Identities = 17/102 (16%), Positives = 37/102 (36%), Gaps = 14/102 (13%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
           G   E  A    N L+V   +   +   L   FS FG +    +   +        AFV 
Sbjct: 4   GSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVT 55

Query: 238 FDNPKSCEDAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEE 279
           ++  +S + A  +++   ++  ++           R++   +
Sbjct: 56  YEKMESADQAVAELNGTQVESVQLKV------NIARKQPMLD 91

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 63.1 bits (153), Expect = 6e-12
 Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 6/83 (7%)

Query: 181 PEADAAPPENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFD 239
               A    +VL V  LNP   +   L I+F  +G V   +++ +K        A V+  
Sbjct: 26  IPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMA 80

Query: 240 NPKSCEDAYLKMDNVLIDDRRIH 262
           +    + A   ++   +  + I 
Sbjct: 81  DGNQAQLAMSHLNGHKLHGKPIR 103

>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 = 52.3 bits (125), Expect = 3e-08
 Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 4/78 (5%)

Query: 183 ADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
            +  PP   L +  + P  S++DL+++FS  G V        K        A ++  + +
Sbjct: 145 QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK----MALIQMGSVE 200

Query: 243 SCEDAYLKMDNVLIDDRR 260
               A + + N  + +  
Sbjct: 201 EAVQALIDLHNHDLGENH 218

>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 = 60.0 bits (146), Expect = 7e-12
 Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 8/80 (10%)

Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
            +       VLFV  L    +++ LE  FS+FGK+   + ++D        YAF+ FD  
Sbjct: 4   GSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDER 55

Query: 242 KSCEDAYLKMDNVLIDDRRI 261
                A  +M+   ++   I
Sbjct: 56  DGAVKAMEEMNGKDLEGENI 75

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 59.8 bits (145), Expect = 9e-12
 Identities = 11/85 (12%), Positives = 27/85 (31%), Gaps = 3/85 (3%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
           G             L +  + P    + L+ +  ++G V  CE +             V 
Sbjct: 4   GSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVT 60

Query: 238 FDNPKSCEDAYLKMDNVLIDDRRIH 262
           + +      A  K++   +++  + 
Sbjct: 61  YSSKDQARQALDKLNGFQLENFTLK 85

>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 = 59.6 bits (145), Expect = 1e-11
 Identities = 20/84 (23%), Positives = 40/84 (47%), Gaps = 3/84 (3%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
           G       + P   LFV  L+  T+++ L+  F    +     ++ D+ TG S  + FV+
Sbjct: 4   GSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRAR---IVTDRETGSSKGFGFVD 60

Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
           F++ +  + A   M++  ID  ++
Sbjct: 61  FNSEEDAKAAKEAMEDGEIDGNKV 84

>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 = 61.9 bits (151), Expect = 1e-11
 Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LF+  L+  T+D+ L   F ++G +  C V+RD  T  S  + FV +   +  + A +  
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA-MNA 74

Query: 252 DNVLIDDRRI 261
               +D R +
Sbjct: 75  RPHKVDGRVV 84

>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 = 59.2 bits (144), Expect = 9e-11
 Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  +   T +  L   F ++GK+   E++ D+ +G    +AFV FD+  S +   +  
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI-VIQ 165

Query: 252 DNVLIDDRRIHAR 264
               ++      R
Sbjct: 166 KYHTVNGHNCEVR 178

>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 = 58.7 bits (143), Expect = 1e-11
 Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  L+  TS  DL+  F++FG+V  C +  D  TG S  + F+ F +  S E   L  
Sbjct: 14  MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKV-LDQ 72

Query: 252 DNVLIDDRRI 261
               +D R I
Sbjct: 73  KEHRLDGRVI 82

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 58.8 bits (143), Expect = 2e-11
 Identities = 19/85 (22%), Positives = 34/85 (40%), Gaps = 6/85 (7%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
           G   + D      +L+V  L   TS++ +E  F+         V + +       YAFV 
Sbjct: 4   GSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR------DYAFVH 57

Query: 238 FDNPKSCEDAYLKMDNVLIDDRRIH 262
           F N +   +A   ++  ++D   I 
Sbjct: 58  FSNREDAVEAMKALNGKVLDGSPIE 82

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 58.7 bits (142), Expect = 2e-11
 Identities = 14/80 (17%), Positives = 33/80 (41%), Gaps = 8/80 (10%)

Query: 185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
           +  P  V+ + KL    ++ ++  +   FGKV    +++ K        AF+E +  ++ 
Sbjct: 12  SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAA 65

Query: 245 EDA--YLKMDNVLIDDRRIH 262
                Y      ++  + I+
Sbjct: 66  NTMVNYYTSVTPVLRGQPIY 85

>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 = 58.4 bits (142), Expect = 2e-11
 Identities = 16/75 (21%), Positives = 33/75 (44%), Gaps = 1/75 (1%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
             +  +FV  L     ++ L  +F + G +    + +D+  G    + FV F +P+S   
Sbjct: 14  EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSY 72

Query: 247 AYLKMDNVLIDDRRI 261
           A   ++ + +  R I
Sbjct: 73  AIALLNGIRLYGRPI 87

>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 = 59.2 bits (143), Expect = 2e-11
 Identities = 15/80 (18%), Positives = 33/80 (41%), Gaps = 8/80 (10%)

Query: 185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
           A  P  V+ + KL    ++ ++  +   FGKV    +++ K        AF+E +  ++ 
Sbjct: 27  AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAA 80

Query: 245 EDA--YLKMDNVLIDDRRIH 262
                Y      ++  + I+
Sbjct: 81  NTMVNYYTSVTPVLRGQPIY 100

>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 = 58.5 bits (142), Expect = 2e-11
 Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 2/84 (2%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
           G    +++      L V  +     D DL  +F +FGK+   E+I ++    S  + FV 
Sbjct: 4   GSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVT 61

Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
           F+N    + A  K+   +++ R+I
Sbjct: 62  FENSADADRAREKLHGTVVEGRKI 85

>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 = 58.4 bits (142), Expect = 3e-11
 Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 5/82 (6%)

Query: 180 LPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFD 239
           LPE    P  N +FV  ++    + ++   F+R+G V   ++I D+ TG S  Y FV F 
Sbjct: 2   LPEGKIMP--NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFY 58

Query: 240 NPKSCEDAYLKMDNVLIDDRRI 261
           N    +       N     +++
Sbjct: 59  NDVDVQKIVESQIN--FHGKKL 78

>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 = 58.1 bits (141), Expect = 4e-11
 Identities = 20/84 (23%), Positives = 41/84 (48%), Gaps = 1/84 (1%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
            +  +  +A P   L+V  L+   ++D L  IF  FG++   +++ D  TG S  Y F+ 
Sbjct: 16  ANNLQKGSAGPMR-LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFIT 74

Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
           F + +  + A  +++   +  R +
Sbjct: 75  FSDSECAKKALEQLNGFELAGRPM 98

>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 = 58.5 bits (142), Expect = 4e-11
 Identities = 20/81 (24%), Positives = 31/81 (38%), Gaps = 1/81 (1%)

Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
             +        +F  +L       DLE  FS  GKV    +I D+ +  S   A+VEF  
Sbjct: 17  NLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCE 76

Query: 241 PKSCEDAYLKMDNVLIDDRRI 261
            +S   A + +    +    I
Sbjct: 77  IQSVPLA-IGLTGQRLLGVPI 96

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 57.6 bits (140), Expect = 4e-11
 Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 2/73 (2%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  L    +   L+  F+  G V   ++  +   G S     V+F++P+  E A   M
Sbjct: 11  IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMM 68

Query: 252 DNVLIDDRRIHAR 264
           + + +  R I  R
Sbjct: 69  NGMKLSGREIDVR 81

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 58.1 bits (141), Expect = 5e-11
 Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LF+  L+  T+++ L   + ++GK+  C V+RD  +  S  + FV F +    + A +  
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA-MAA 88

Query: 252 DNVLIDDRRI 261
               ID R +
Sbjct: 89  RPHSIDGRVV 98

>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 = 57.1 bits (139), Expect = 6e-11
 Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           ++V  ++   + ++LE  F   G VN   ++ DK +G    +A++EF + +S   + L +
Sbjct: 9   IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS-LAL 67

Query: 252 DNVLIDDRRI 261
           D  L   R+I
Sbjct: 68  DESLFRGRQI 77

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 57.7 bits (140), Expect = 6e-11
 Identities = 15/81 (18%), Positives = 30/81 (37%), Gaps = 8/81 (9%)

Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
             +       LFV        + +L  IF  FG +   +++          +AFVEF+  
Sbjct: 24  RQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG--------FAFVEFEEA 75

Query: 242 KSCEDAYLKMDNVLIDDRRIH 262
           +S   A  ++      ++ + 
Sbjct: 76  ESAAKAIEEVHGKSFANQPLE 96

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 59.1 bits (144), Expect = 6e-11
 Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 1/81 (1%)

Query: 184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
           D       +FV  + P     + E  FS++G +   +++ DK TG S  + FV +D+  +
Sbjct: 82  DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA 141

Query: 244 CEDAYLKMDNVLIDDRRIHAR 264
            +    +   +   DR+I  +
Sbjct: 142 VDRV-CQNKFIDFKDRKIEIK 161

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 57.5 bits (140), Expect = 2e-10
 Identities = 20/70 (28%), Positives = 41/70 (58%), Gaps = 2/70 (2%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +F+  LN  T++D+L   F ++G V   ++++D  TG S  + F+ F+ P S ++  +K 
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV-VKT 64

Query: 252 DNVLIDDRRI 261
            ++ +D + I
Sbjct: 65  QHI-LDGKVI 73

>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 = 59.1 bits (143), Expect = 6e-11
 Identities = 19/82 (23%), Positives = 37/82 (45%)

Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
           P    +    +LFV  ++    +D+++  F  +G++    +  D+ TG S  YA VE++ 
Sbjct: 64  PGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYET 123

Query: 241 PKSCEDAYLKMDNVLIDDRRIH 262
            K    A   ++   I  + I 
Sbjct: 124 HKQALAAKEALNGAEIMGQTIQ 145

>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 = 56.9 bits (138), Expect = 8e-11
 Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 5/87 (5%)

Query: 175 EIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYA 234
            ++ D   +        L    L+   ++D+L+ +F         E+      G S   A
Sbjct: 2   HMLEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIA 56

Query: 235 FVEFDNPKSCEDAYLKMDNVLIDDRRI 261
           ++EF +    E    +     ID R +
Sbjct: 57  YIEFKSEADAEKNLEEKQGAEIDGRSV 83

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 57.6 bits (139), Expect = 8e-11
 Identities = 18/80 (22%), Positives = 36/80 (45%), Gaps = 6/80 (7%)

Query: 190 NVLFVCKLNPVTSDDDL---EIIFSRFGKVNCCEVIRDKVTGDSLQ---YAFVEFDNPKS 243
           N++FV  L+   +D ++      F +FGK++   +        S      A+V +   + 
Sbjct: 16  NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75

Query: 244 CEDAYLKMDNVLIDDRRIHA 263
              A   ++NV++D R + A
Sbjct: 76  ALRAIQCVNNVVVDGRTLKA 95

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 58.0 bits (140), Expect = 8e-11
 Identities = 15/129 (11%), Positives = 37/129 (28%), Gaps = 10/129 (7%)

Query: 161 LRAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDL----EIIFSRFGKV 216
           ++    AK     ++            P  V+ +  +NP    + L      + S  G +
Sbjct: 1   MKETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDI 60

Query: 217 NCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH---ARGEEWNMWKR 273
                I   ++ D+   A++ F   +S +               +    +   +  + + 
Sbjct: 61  LD---IVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAED 117

Query: 274 REEEEEKEE 282
              E     
Sbjct: 118 GSLEHHHHH 126

>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 = 60.4 bits (147), Expect = 9e-11
 Identities = 8/93 (8%), Positives = 32/93 (34%), Gaps = 6/93 (6%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L++    P  +  ++  +      V     +       S ++A+++  + +       K+
Sbjct: 120 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 179

Query: 252 DNVLIDDRRIHARGEEWNMWKRREEEEEKEEID 284
           + + I+   +  +           E+ ++ +  
Sbjct: 180 NGLKIEGYTLVTK------VSNPLEKSKRTDSA 206

>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 = 60.0 bits (146), Expect = 1e-10
 Identities = 19/84 (22%), Positives = 34/84 (40%), Gaps = 3/84 (3%)

Query: 181 PEADAAPPENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRD-KVTGDSLQYAFVEF 238
               A      + +  L+  +  ++ L   F  FG +    +    K    +   AF+ F
Sbjct: 202 RTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVF 261

Query: 239 DNPKSCEDAYLKMDNVLIDDRRIH 262
           +N  S E A L+M+  L+ +R I 
Sbjct: 262 ENKDSAERA-LQMNRSLLGNREIS 284

>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 = 56.5 bits (137), Expect = 2e-09
 Identities = 10/70 (14%), Positives = 24/70 (34%), Gaps = 3/70 (4%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           + V  L    + + +   F   G +   +V        + ++A +EF        A +  
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAA-ITK 100

Query: 252 DNVLIDDRRI 261
            + ++    I
Sbjct: 101 THKVVGQNEI 110

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 57.4 bits (139), Expect = 9e-11
 Identities = 27/108 (25%), Positives = 45/108 (41%), Gaps = 2/108 (1%)

Query: 155 AQEIEELRAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFG 214
           A  ++   ++  A A            E       +V +V  ++  ++  DLE  FS  G
Sbjct: 3   APCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSV-YVGNVDYGSTAQDLEAHFSSCG 61

Query: 215 KVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
            +N   ++ DK +G    YA++EF    S  DA + MD  +   R I 
Sbjct: 62  SINRITILCDKFSGHPKGYAYIEFAERNS-VDAAVAMDETVFRGRTIK 108

>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 = 60.1 bits (146), Expect = 1e-10
 Identities = 25/101 (24%), Positives = 42/101 (41%), Gaps = 5/101 (4%)

Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
           A     L V  L+PV S++ LE  FS+FG V    V+ D   G +    FVEF       
Sbjct: 93  ATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPAR 151

Query: 246 DAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEKEEIDEK 286
            A  +  +       +        + +  E+ ++++ + EK
Sbjct: 152 KALERCGDGAF----LLTTTPRPVIVEPMEQFDDEDGLPEK 188

>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 = 59.3 bits (144), Expect = 2e-10
 Identities = 17/81 (20%), Positives = 36/81 (44%), Gaps = 6/81 (7%)

Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
           P          LFV  L    +++D + +F R+G+ +   + RD+  G    + F+  ++
Sbjct: 14  PGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR--G----FGFIRLES 67

Query: 241 PKSCEDAYLKMDNVLIDDRRI 261
               E A  ++D  ++  R +
Sbjct: 68  RTLAEIAKAELDGTILKSRPL 88

>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 = 56.8 bits (137), Expect = 1e-10
 Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 8/79 (10%)

Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
             P  VL + KL    ++ ++  +   FGKV    +++ K        AF+E    ++  
Sbjct: 12  GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQAFLELATEEAAI 65

Query: 246 DA--YLKMDNVLIDDRRIH 262
               Y       + ++ I+
Sbjct: 66  TMVNYYSAVTPHLRNQPIY 84

>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 = 56.9 bits (138), Expect = 1e-10
 Identities = 19/82 (23%), Positives = 37/82 (45%)

Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
           P    +    +LFV  ++    +D+++  F  +G++    +  D+ TG S  YA VE++ 
Sbjct: 18  PGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYET 77

Query: 241 PKSCEDAYLKMDNVLIDDRRIH 262
            K    A   ++   I  + I 
Sbjct: 78  HKQALAAKEALNGAEIMGQTIQ 99

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 56.7 bits (137), Expect = 1e-10
 Identities = 20/105 (19%), Positives = 37/105 (35%), Gaps = 9/105 (8%)

Query: 190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
            V+    L   T   +++  FSRFG +    +    +T      A VEF  P     A+ 
Sbjct: 11  TVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGIT------AIVEFLEPLEARKAFR 64

Query: 250 KMDNVLIDDRRIHARGEEWNMWKRREEEEEKEEIDEKKEEEEKED 294
            +         ++    EW          +K++   ++  E+ E 
Sbjct: 65  HLAYSKFHHVPLYL---EWAPIGVFGAAPQKKDSQHEQPAEKAES 106

>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 = 56.6 bits (137), Expect = 1e-10
 Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 6/77 (7%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +F+  L+  + ++ L  +  +FG +    V+    T  S   AF +F   ++ +      
Sbjct: 18  VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 77

Query: 252 DNVL------IDDRRIH 262
                     +D R++ 
Sbjct: 78  SLEAEGGGLKLDGRQLK 94

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 56.3 bits (136), Expect = 2e-10
 Identities = 15/101 (14%), Positives = 36/101 (35%), Gaps = 8/101 (7%)

Query: 189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAY 248
              +++       + DD++      G+V   ++ R           FV FD+ +S +   
Sbjct: 11  NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKF- 68

Query: 249 LKMDNVLIDDRRIHARGEEWNMWKRREEEEEKEEIDEKKEE 289
           ++       +  +        ++K     ++ EE  + K E
Sbjct: 69  VETPGQKYKETDLLI------LFKDDYFAKKNEERKQNKVE 103

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 55.8 bits (135), Expect = 2e-10
 Identities = 18/73 (24%), Positives = 25/73 (34%), Gaps = 6/73 (8%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV           L   F  FG V    V+ DK  G    +A VE  +  + E   L  
Sbjct: 11  VFVSGFPRGVDSAQLSEYFLAFGPVA--SVVMDKDKG---VFAIVEMGDVGAREAV-LSQ 64

Query: 252 DNVLIDDRRIHAR 264
               +   R+  R
Sbjct: 65  SQHSLGGHRLRVR 77

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 56.2 bits (136), Expect = 2e-10
 Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 2/84 (2%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
           G     +       L V  +     D DL  +F +FGK+   E+I ++    S  + FV 
Sbjct: 18  GSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVT 75

Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
           F+N    + A  K+   +++ R+I
Sbjct: 76  FENSADADRAREKLHGTVVEGRKI 99

>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 = 58.2 bits (140), Expect = 3e-10
 Identities = 9/75 (12%), Positives = 23/75 (30%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
            P NVL         ++++   I    G      V       +      +E+D+     +
Sbjct: 121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALE 180

Query: 247 AYLKMDNVLIDDRRI 261
               +++  + +   
Sbjct: 181 TLGFLNHYQMKNPNG 195

>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 = 57.4 bits (138), Expect = 4e-10
 Identities = 16/125 (12%), Positives = 41/125 (32%), Gaps = 12/125 (9%)

Query: 186 APPENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
                VL V  L+    + D +  +F  +G V   + ++ K        A VE  +  + 
Sbjct: 1   GADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPG-----AAMVEMADGYAV 55

Query: 245 EDAYLKMDNVLIDDRRI------HARGEEWNMWKRREEEEEKEEIDEKKEEEEKEDRAMI 298
           + A   ++N  +  +++               +   +     ++  E +           
Sbjct: 56  DRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAA 115

Query: 299 GDRME 303
            +R++
Sbjct: 116 KNRIQ 120

>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 = 55.3 bits (134), Expect = 3e-10
 Identities = 20/101 (19%), Positives = 41/101 (40%), Gaps = 8/101 (7%)

Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
           +         +FV  +    +++ L+ IFS  G V    ++ D+ TG    Y F E+ + 
Sbjct: 1   DPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQ 60

Query: 242 KSCEDAYLKMDNVLIDDRRI---HARGEEWNMWKRREEEEE 279
           ++   A   ++      R +   +A  E+      +EE + 
Sbjct: 61  ETALSAMRNLNGREFSGRALRVDNAASEK-----NKEELKS 96

>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 = 56.0 bits (135), Expect = 4e-10
 Identities = 28/153 (18%), Positives = 57/153 (37%), Gaps = 16/153 (10%)

Query: 139 GLIGADEDIDETAGLSAQEIEELRAEREAKARATILEIVGDLPEADAAPPENVLFVCKLN 198
           G +G+D D   +  +S +E+E+ R  RE     ++          +   P   ++V  L 
Sbjct: 1   GPLGSDSDEMPSECISRRELEKGRISREEMETLSVFRSY------EPGEPNCRIYVKNLA 54

Query: 199 PVTSDDDLEIIFSRFGKVNCCEV-----IRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDN 253
               + DL+ IF R+   +         IR    G     AF+   N K+   A  + + 
Sbjct: 55  KHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANG 114

Query: 254 VLIDDRRIHARGEEWNMWKRREEEEEKEEIDEK 286
            ++  + +          +    +++ +E   K
Sbjct: 115 YVLFGKPMVV-----QFARSARPKQDPKEGKRK 142

>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 = 54.1 bits (131), Expect = 6e-10
 Identities = 12/72 (16%), Positives = 26/72 (36%), Gaps = 2/72 (2%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFG--KVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
           L++  L   T+D+DL       G   +   +   ++  G S  +A V   +  S +    
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 250 KMDNVLIDDRRI 261
            +    +  +  
Sbjct: 64  LLPKRELHGQNP 75

>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 = 58.0 bits (139), Expect = 7e-10
 Identities = 27/119 (22%), Positives = 50/119 (42%), Gaps = 10/119 (8%)

Query: 186 APPENVLFVCKLNPVTSDDDLE----IIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
             P + +++  LN     D+L+     IFS+FG++    V R   +      AFV F   
Sbjct: 6   TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEV 62

Query: 242 KSCEDAYLKMDNVLIDDRRIH---ARGEEWNMWKRREEEEEKEEIDEKKEEEEKEDRAM 297
            S  +A   M      D+ +    A+ +   + K +    E++   EK++ + +E  A 
Sbjct: 63  SSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPAT 121

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 44.5 bits (104), Expect = 2e-05
 Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 5/74 (6%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
           PP ++LF+  L   T++  L ++F++F       ++  +        AFVEFDN      
Sbjct: 205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD-----IAFVEFDNEVQAGA 259

Query: 247 AYLKMDNVLIDDRR 260
           A   +    I    
Sbjct: 260 ARDALQGFKITQNN 273

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 54.6 bits (132), Expect = 8e-10
 Identities = 13/82 (15%), Positives = 34/82 (41%), Gaps = 2/82 (2%)

Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDK-VTGDSLQYAFVEFDN 240
           +       + + V  +    +  ++  +FS FG++    + +    TG    + FV+F  
Sbjct: 8   QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 67

Query: 241 PKSCEDAYLKMDN-VLIDDRRI 261
            +  + A+  + +   +  RR+
Sbjct: 68  KQDAKKAFNALCHSTHLYGRRL 89

>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 = 56.4 bits (136), Expect = 9e-10
 Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 6/73 (8%)

Query: 191 VLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
           VL V  LNP   +   L I+F  +G V   +++ +K        A V+  +    + A  
Sbjct: 5   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQLAMS 59

Query: 250 KMDNVLIDDRRIH 262
            ++   +  + I 
Sbjct: 60  HLNGHKLHGKPIR 72

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 50.7 bits (121), Expect = 8e-08
 Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 4/78 (5%)

Query: 183 ADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
            +  PP   L +  + P  S++DL+++FS  G V        K        A ++  + +
Sbjct: 114 QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK----MALIQMGSVE 169

Query: 243 SCEDAYLKMDNVLIDDRR 260
               A + + N  + +  
Sbjct: 170 EAVQALIDLHNHDLGENH 187

>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 = 53.5 bits (129), Expect = 1e-09
 Identities = 19/94 (20%), Positives = 31/94 (32%), Gaps = 8/94 (8%)

Query: 177 VGDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNC--------CEVIRDKVTG 228
           +G      +    N +FV  L    + + +   F + G +            +  D+ TG
Sbjct: 1   MGHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETG 60

Query: 229 DSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
                A V FD+P S + A    D        I 
Sbjct: 61  KLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIK 94

>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 = 53.6 bits (129), Expect = 2e-09
 Identities = 11/74 (14%), Positives = 31/74 (41%), Gaps = 4/74 (5%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGK-VNCCEVIRD-KVTGDSLQYAFVEFDNPKSCEDAYL 249
           LF+  +  +   +++    ++  + V    V         +  +AFVE+++ ++   A  
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

Query: 250 KM--DNVLIDDRRI 261
           K+    + +   +I
Sbjct: 71  KLMPGRIQLWGHQI 84

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 53.2 bits (128), Expect = 2e-09
 Identities = 14/72 (19%), Positives = 24/72 (33%)

Query: 190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
               +           L  +FS+ GKV   E   D+ TG +  + FVE  +    +    
Sbjct: 13  GAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72

Query: 250 KMDNVLIDDRRI 261
                 +D +  
Sbjct: 73  SFHGKRLDLKHR 84

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 51.9 bits (125), Expect = 4e-09
 Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 7/71 (9%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L    ++ DL   F +FG++    V++ +      Q AF++F   ++ E A  K 
Sbjct: 15  LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAFIQFATRQAAEVAAEKS 68

Query: 252 DN-VLIDDRRI 261
            N ++++ RR+
Sbjct: 69  FNKLIVNGRRL 79

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 52.8 bits (127), Expect = 4e-09
 Identities = 18/84 (21%), Positives = 28/84 (33%), Gaps = 8/84 (9%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNC--------CEVIRDKVTGDSLQYAFVEF 238
              N +FV  L    + + +   F + G +            +  D+ TG     A V F
Sbjct: 5   SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 64

Query: 239 DNPKSCEDAYLKMDNVLIDDRRIH 262
           D+P S + A    D        I 
Sbjct: 65  DDPPSAKAAIDWFDGKEFSGNPIK 88

>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 = 51.9 bits (125), Expect = 5e-09
 Identities = 12/82 (14%), Positives = 30/82 (36%)

Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
             +   P   ++ V  +    S D++   F  +  +     ++    G     A V F++
Sbjct: 7   GASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 66

Query: 241 PKSCEDAYLKMDNVLIDDRRIH 262
                 A + +++  I  R++ 
Sbjct: 67  RDEATAAVIDLNDRPIGSRKVK 88

>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 = 49.9 bits (120), Expect = 2e-08
 Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           ++V  L    + + ++ +FS+FGKV   ++I D+ T     + FVE    +S  +A  K+
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAIAKL 62

Query: 252 DNVLIDDRRI 261
           DN     R I
Sbjct: 63  DNTDFMGRTI 72

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 50.0 bits (120), Expect = 2e-08
 Identities = 13/82 (15%), Positives = 30/82 (36%)

Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
             +   P   V+ V  +    S D++   F  +  +     ++    G     A V F++
Sbjct: 7   GSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 66

Query: 241 PKSCEDAYLKMDNVLIDDRRIH 262
                 A + +++  I  R++ 
Sbjct: 67  RDEATAAVIDLNDRPIGSRKVK 88

>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 = 49.6 bits (119), Expect = 3e-08
 Identities = 15/82 (18%), Positives = 33/82 (40%), Gaps = 10/82 (12%)

Query: 190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
           N L++  L+P  + DDL  +F         +V+          YAFV++ +      A  
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS------GYAFVDYPDQNWAIRAIE 62

Query: 250 KMD-NVLIDDRRI---HARGEE 267
            +   V +  + +   ++  ++
Sbjct: 63  TLSGKVELHGKIMEVDYSVSKK 84

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 49.5 bits (119), Expect = 4e-08
 Identities = 20/80 (25%), Positives = 32/80 (40%), Gaps = 7/80 (8%)

Query: 187 PPENVLFVCKLNPVTSDDDLE----IIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
            P + +++  LN     D+L+     IFSRFG++     I    +      AFV F    
Sbjct: 6   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQI---LDILVSRSLKMRGQAFVIFKEVS 62

Query: 243 SCEDAYLKMDNVLIDDRRIH 262
           S  +A   M      D+ + 
Sbjct: 63  SATNALRSMQGFPFYDKPMR 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 = 49.1 bits (118), Expect = 4e-08
 Identities = 15/73 (20%), Positives = 30/73 (41%), Gaps = 7/73 (9%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV +     ++D+L   FS++G V    + +         +AFV F + +  +      
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSL-CGE 61

Query: 252 DNVLIDDRRIHAR 264
           D + I    +H  
Sbjct: 62  DLI-IKGISVHIS 73

>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 = 49.7 bits (119), Expect = 4e-08
 Identities = 20/93 (21%), Positives = 34/93 (36%), Gaps = 8/93 (8%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVN--------CCEVIRDKVTGD 229
           G   + D     + ++V  LN   + DDL   F + G V            +  DK TG 
Sbjct: 4   GSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGK 63

Query: 230 SLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
               A V +++P + + A    D       ++ 
Sbjct: 64  PKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLK 96

>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 = 49.5 bits (118), Expect = 5e-08
 Identities = 13/77 (16%), Positives = 28/77 (36%), Gaps = 8/77 (10%)

Query: 186 APPENVLFVC--KLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
           +     L V    L    S + L  +  + G V+   +  +K       Y+F  +   + 
Sbjct: 22  SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEE 75

Query: 244 CEDAYLKMDNVLIDDRR 260
            + AY+ ++   + D  
Sbjct: 76  SKRAYVTLNGKEVVDDL 92

>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 = 49.0 bits (117), Expect = 7e-08
 Identities = 20/95 (21%), Positives = 32/95 (33%), Gaps = 4/95 (4%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
           G    +     +  + +  L    S +++   FS    V     +     G S   AFV+
Sbjct: 4   GSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQ 63

Query: 238 FDNPKSCEDAYLKMDNVLIDDRRIH---ARGEEWN 269
           F + +  E A LK     I  R I    +   E  
Sbjct: 64  FASQEIAEKA-LKKHKERIGHRYIEIFKSSRAEVR 97

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 48.4 bits (116), Expect = 9e-08
 Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 2/75 (2%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
            P    +V  L   T   D++ IF     +    ++RDK T     + +VEFD   S ++
Sbjct: 13  EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKE 71

Query: 247 AYLKMDNVLIDDRRI 261
           A L  D  L+ DR +
Sbjct: 72  A-LTYDGALLGDRSL 85

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 3/76 (3%)

Query: 188 PENVLFVCKLNPVTSDDDLEIIFS-RFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
           PE  LFV  L P   D  L   F   +      +V+ D+ TG S  Y FV+F +    + 
Sbjct: 8   PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKR 66

Query: 247 AYLKMDN-VLIDDRRI 261
           A  +    V +  + +
Sbjct: 67  ALTECQGAVGLGSKPV 82

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 47.4 bits (113), Expect = 3e-07
 Identities = 10/80 (12%), Positives = 22/80 (27%), Gaps = 1/80 (1%)

Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
           E D    +    +  +    +  D+               +     G  L  A V+F N 
Sbjct: 8   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 67

Query: 242 KSCEDAYLKMDNVLIDDRRI 261
                +  ++    ++ R  
Sbjct: 68  DDARKS-ERLHRKKLNGREA 86

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 46.7 bits (111), Expect = 4e-07
 Identities = 13/82 (15%), Positives = 29/82 (35%), Gaps = 7/82 (8%)

Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQ-YAFVEFD 239
           P  + AP    ++V  L       DL+      G V        ++T    +  AF+ + 
Sbjct: 11  PPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPL------RLTWQGPRRRAFLHYP 64

Query: 240 NPKSCEDAYLKMDNVLIDDRRI 261
           +  + + A   +  + +    +
Sbjct: 65  DSAAAQQAVSCLQGLRLGTDTL 86

>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 = 47.1 bits (112), Expect = 4e-07
 Identities = 14/82 (17%), Positives = 24/82 (29%), Gaps = 1/82 (1%)

Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
                      +++  L     +  +   F +   V     I     G +    FVEF N
Sbjct: 17  RSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRN 76

Query: 241 PKSCEDAYLKMDNVLIDDRRIH 262
               + A L      + +R I 
Sbjct: 77  EADYKAA-LCRHKQYMGNRFIQ 97

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 46.3 bits (110), Expect = 5e-07
 Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 8/79 (10%)

Query: 189 ENVLFVCKLNPVTSD------DDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
           ++V+ V  +  V  D      + +  IFS+FGK+        +  G +  Y F+E+ +P 
Sbjct: 15  DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKIT--NDFYPEEDGKTKGYIFLEYASPA 72

Query: 243 SCEDAYLKMDNVLIDDRRI 261
              DA    D   +D +  
Sbjct: 73  HAVDAVKNADGYKLDKQHT 91

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 45.5 bits (108), Expect = 6e-07
 Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 10/80 (12%)

Query: 189 ENVLFVCKLNPVTSDDDLEI-------IFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
           ++V+ V  + P    D LE        IFS+FGK+        +  G +  Y F+E+ +P
Sbjct: 1   DSVIVVDNV-PQVGPDRLEKLKNVIHKIFSKFGKIT--NDFYPEEDGKTKGYIFLEYASP 57

Query: 242 KSCEDAYLKMDNVLIDDRRI 261
               DA    D   +D +  
Sbjct: 58  AHAVDAVKNADGYKLDKQHT 77

>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 = 46.4 bits (110), Expect = 7e-07
 Identities = 16/84 (19%), Positives = 29/84 (34%), Gaps = 1/84 (1%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
           G    +  +  +  + +  L    + +++   FS    V     +     G     AFV+
Sbjct: 31  GRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQ 90

Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
           F + +  E A L      I  R I
Sbjct: 91  FASQELAEKA-LGKHKERIGHRYI 113

>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 = 45.3 bits (108), Expect = 8e-07
 Identities = 14/73 (19%), Positives = 30/73 (41%), Gaps = 7/73 (9%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV +     + ++L+  F ++G+V    + +         +AFV F + K  +      
Sbjct: 14  VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK-----PFRAFAFVTFADDKVAQSL-CGE 67

Query: 252 DNVLIDDRRIHAR 264
           D + I    +H  
Sbjct: 68  DLI-IKGISVHIS 79

>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 = 45.7 bits (109), Expect = 9e-07
 Identities = 13/75 (17%), Positives = 32/75 (42%), Gaps = 3/75 (4%)

Query: 188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQ-YAFVEFDNPKSCED 246
           P    F+  L    +++ ++  F          + R+    + L+ + + EF++  S   
Sbjct: 14  PPYTAFLGNLPYDVTEESIKEFFRGLNISAVR-LPREPSNPERLKGFGYAEFEDLDSLLS 72

Query: 247 AYLKMDNVLIDDRRI 261
           A L ++   + ++RI
Sbjct: 73  A-LSLNEESLGNKRI 86

>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 = 45.1 bits (107), Expect = 1e-06
 Identities = 17/85 (20%), Positives = 38/85 (44%), Gaps = 6/85 (7%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
           P +  + V  +     ++D+   F    +V+   +++D   G +     V+F +P+   +
Sbjct: 14  PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFE 71

Query: 247 AYLKMDNVLIDDRRIH---ARGEEW 268
           A LK + +L+  R +    A   +W
Sbjct: 72  A-LKRNRMLMIQRYVEVSPATERQW 95

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 45.0 bits (106), Expect = 2e-06
 Identities = 19/86 (22%), Positives = 32/86 (37%), Gaps = 13/86 (15%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDK--VTGDSLQYAFVEFDNPKSCEDA-- 247
           +FV  L P   +D++   F RFG +      + +         YAF+ F    S +    
Sbjct: 11  VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70

Query: 248 ---------YLKMDNVLIDDRRIHAR 264
                    YL + +  I D+ +  R
Sbjct: 71  ACLEEDGKLYLCVSSPTIKDKPVQIR 96

>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 = 45.9 bits (108), Expect = 3e-06
 Identities = 20/86 (23%), Positives = 29/86 (33%), Gaps = 6/86 (6%)

Query: 181 PEADAAPPENVLFVCKLNPVTS--DDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEF 238
                A    VL +   N       D L  IFS+FG V                 A +++
Sbjct: 36  AGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQF----QALLQY 91

Query: 239 DNPKSCEDAYLKMDNVLIDDRRIHAR 264
            +P S + A L +D   I +     R
Sbjct: 92  ADPVSAQHAKLSLDGQNIYNACCTLR 117

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 44.4 bits (105), Expect = 3e-06
 Identities = 20/73 (27%), Positives = 25/73 (34%), Gaps = 7/73 (9%)

Query: 189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAY 248
           EN + V  L P  S  DL+      G V   +V RD           VEF   +    A 
Sbjct: 15  ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-------TGVVEFVRKEDMTYAV 67

Query: 249 LKMDNVLIDDRRI 261
            K+DN        
Sbjct: 68  RKLDNTKFRSHEG 80

>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 = 44.0 bits (104), Expect = 5e-06
 Identities = 23/85 (27%), Positives = 28/85 (32%), Gaps = 11/85 (12%)

Query: 181 PEADAAPP----ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFV 236
           P     PP    EN + V  L P  S  DL+      G V   +V RD           V
Sbjct: 4   PRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-------TGVV 56

Query: 237 EFDNPKSCEDAYLKMDNVLIDDRRI 261
           EF   +    A  K+DN        
Sbjct: 57  EFVRKEDMTYAVRKLDNTKFRSHEG 81

>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 = 43.2 bits (102), Expect = 5e-06
 Identities = 9/75 (12%), Positives = 27/75 (36%), Gaps = 6/75 (8%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEV-----IRDKVTGDSLQYAFVEFDNPKSCED 246
           L+V  +    +++ +   F+   ++          +          +AF+EF +      
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 247 AYLKMDNVLIDDRRI 261
           A +  D ++   + +
Sbjct: 69  A-MAFDGIIFQGQSL 82

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 44.2 bits (104), Expect = 5e-06
 Identities = 22/81 (27%), Positives = 31/81 (38%), Gaps = 8/81 (9%)

Query: 181 PEADAAPPENVLFVCKLN---PVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
                A    VL +   N   PVT  D L  IFS+FG V                 A ++
Sbjct: 18  AGMAMAGQSPVLRIIVENLFYPVT-LDVLHQIFSKFGTVLKIITFTKNNQF----QALLQ 72

Query: 238 FDNPKSCEDAYLKMDNVLIDD 258
           + +P S + A L +D   I +
Sbjct: 73  YADPVSAQHAKLSLDGQNIYN 93

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 42.4 bits (100), Expect = 8e-06
 Identities = 7/70 (10%), Positives = 23/70 (32%), Gaps = 7/70 (10%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           + V  L   ++  ++  +   +        ++      + + AFV   N +  ++A    
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMF 60

Query: 252 DNVLIDDRRI 261
                  + +
Sbjct: 61  HQYSFRGKDL 70

>3bkp_A Cyclophilin; malaria, isomerase, structural GENO structural genomics consortium, SGC; 1.80A {Toxoplasma gondii} Length = 232

 Score = 44.7 bits (106), Expect = 1e-05
 Identities = 10/46 (21%), Positives = 13/46 (28%), Gaps = 1/46 (2%)

Query: 102 KNDIRITHAVILEDPYEDLPELVYPP-SPEPTRELLANGLIGADED 146
                I    +L +P+EDL     P   P    E       G    
Sbjct: 181 MTPPFIKSVDVLWNPFEDLVPRRLPDAPPAQKDERKRARAAGGRTT 226

>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 = 42.2 bits (100), Expect = 1e-05
 Identities = 14/75 (18%), Positives = 32/75 (42%), Gaps = 3/75 (4%)

Query: 188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQ-YAFVEFDNPKSCED 246
           P    F+  L    +++ ++  F          + R+    + L+ + + EF++  S   
Sbjct: 18  PPYTAFLGNLPYDVTEESIKEFFRGLNISAVR-LPREPSNPERLKGFGYAEFEDLDSLLS 76

Query: 247 AYLKMDNVLIDDRRI 261
           A L ++   + +RRI
Sbjct: 77  A-LSLNEESLGNRRI 90

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 11/79 (13%), Positives = 24/79 (30%), Gaps = 5/79 (6%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFG-KVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
                + +  L    S  DL+ +      +     V      G       +EF + +   
Sbjct: 26  AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDG----TGALEFPSEEILV 81

Query: 246 DAYLKMDNVLIDDRRIHAR 264
           +A  +++N+      I   
Sbjct: 82  EALERLNNIEFRGSVITVE 100

>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 = 41.6 bits (98), Expect = 3e-05
 Identities = 13/84 (15%), Positives = 27/84 (32%), Gaps = 3/84 (3%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
           G    +  +   + + +  L    +++D+   FS         +      G     A VE
Sbjct: 4   GSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGP-DGRVTGEADVE 61

Query: 238 FDNPKSCEDAYLKMDNVLIDDRRI 261
           F   +    A +  D   +  R +
Sbjct: 62  FATHEDAVAA-MAKDKANMQHRYV 84

>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 = 42.5 bits (99), Expect = 4e-05
 Identities = 21/143 (14%), Positives = 47/143 (32%), Gaps = 9/143 (6%)

Query: 140 LIGADEDIDETAGLSAQEIEELRAEREAKARATILEIVGDLPEADAAPPENVLFVCKLNP 199
           L      I E    S  E+ E+  ++    R+    +     E         +++     
Sbjct: 60  LTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPT 119

Query: 200 VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDR 259
             + DD++      G+V   ++ R           FV FD+ +S +   ++       + 
Sbjct: 120 DATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKF-VETPGQKYKET 177

Query: 260 RIHARGEEWNMWKRREEEEEKEE 282
            +        ++K  +   +K E
Sbjct: 178 DLLI------LFK-DDYFAKKNE 193

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 41.2 bits (96), Expect = 5e-05
 Identities = 17/92 (18%), Positives = 31/92 (33%), Gaps = 7/92 (7%)

Query: 175 EIVGDLPEADAAPPENVLFVCKLNPV--TSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQ 232
            I       D +    VL +   NP+   + D L  + +  GKV    + +         
Sbjct: 9   RITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGI----- 63

Query: 233 YAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR 264
            A VEF++    + A   ++   I       +
Sbjct: 64  QAMVEFESVLCAQKAKAALNGADIYAGCCTLK 95

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 43.3 bits (101), Expect = 7e-05
 Identities = 55/393 (13%), Positives = 102/393 (25%), Gaps = 146/393 (37%)

Query: 23  WTMRKKEEKYLESF--EM------WLWRRMEK------------IKWSDKI--------- 53
           WT+  K+E+ ++ F  E+      +L   ++             I+  D++         
Sbjct: 69  WTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAK 128

Query: 54  ----RNEEV--LRRGFSFLEDFEIVS-----GISKVCNKTHRYKLAVKCVQSNIIVFKRK 102
               R +    LR+    L   + V      G  K         +A+    S  +  K  
Sbjct: 129 YNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTW-------VALDVCLSYKVQCKMD 181

Query: 103 NDI--------RITHAVI---------LEDPYEDLPELVYPPSPEPT-------RELLA- 137
             I             V+         ++  +    +                 R LL  
Sbjct: 182 FKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNI-KLRIHSIQAELRRLLKS 240

Query: 138 ----NGLIGADE---------------------DIDETAGLSAQEIEELR--------AE 164
               N L+                             T  LSA     +           
Sbjct: 241 KPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTP 300

Query: 165 REAKAR-ATILEI-VGDLPEADAAPPENVLFVCKLNPV------TSDDDLEIIFSRFGKV 216
            E K+     L+    DLP            V   NP        S  D    +  +  V
Sbjct: 301 DEVKSLLLKYLDCRPQDLPRE----------VLTTNPRRLSIIAESIRDGLATWDNWKHV 350

Query: 217 NCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM----DNVLIDDRRIHARGEEWNMWK 272
           NC     DK+T  ++  + +    P      + ++     +  I    +        +W 
Sbjct: 351 NC-----DKLT--TIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSL------IWF 397

Query: 273 RREEEEEKEEIDE--KK---EEEEKEDRAMIGD 300
              + +    +++  K    E++ KE    I  
Sbjct: 398 DVIKSDVMVVVNKLHKYSLVEKQPKESTISIPS 430

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 39.4 bits (92), Expect = 3e-04
 Identities = 15/82 (18%), Positives = 26/82 (31%), Gaps = 3/82 (3%)

Query: 181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN 240
                +   + + +  L    +++D+   FS    V     I     G     A VEF  
Sbjct: 38  EFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVH--IEIGPDGRVTGEADVEFAT 95

Query: 241 PKSCEDAYLKMDNVLIDDRRIH 262
            +    A +  D   +  R I 
Sbjct: 96  HEEAVAA-MSKDRANMQHRYIE 116

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 38.8 bits (90), Expect = 4e-04
 Identities = 17/86 (19%), Positives = 28/86 (32%), Gaps = 3/86 (3%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIR--DKVTGDSLQYAF 235
           G +          V+ +  L    S +D++   S     +    +       G     AF
Sbjct: 33  GSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAF 92

Query: 236 VEFDNPKSCEDAYLKMDNVLIDDRRI 261
           VE  +    + A LK D   +  R I
Sbjct: 93  VELGSEDDVKMA-LKKDRESMGHRYI 117

>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 = 37.3 bits (87), Expect = 6e-04
 Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 3/77 (3%)

Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
               + + +       ++ ++    +   K     ++R+   G+   Y FV+F N +  +
Sbjct: 7   GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNA-HGNKTGYIFVDFSNEEEVK 64

Query: 246 DAYLKMDNVLIDDRRIH 262
            A LK +   +  R I 
Sbjct: 65  QA-LKCNREYMGGRYIE 80

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	309
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.84
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.82
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.8
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.8
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.79
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.79
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.79
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.79
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.78
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.78
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.78
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.78
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.78
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.78
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.77
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.77
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.77
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.77
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.77
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.77
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.77
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.77
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.77
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.77
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.77
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.77
2div_A	99	TRNA selenocysteine associated protein; structural	99.76
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.76
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.76
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.76
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.76
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.76
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.76
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.76
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.76
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.76
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.76
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.76
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.76
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.76
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.76
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.75
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.75
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.75
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.75
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.75
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.75
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.75
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.75
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.75
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.74
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.74
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.74
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.74
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.74
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.74
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.74
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.74
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.74
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.74
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.74
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.74
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.74
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.73
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.73
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.73
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.73
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.73
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.73
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.73
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.73
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.73
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.73
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.72
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.72
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.72
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.72
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.72
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.72
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.72
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.72
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.71
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.71
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.71
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.71
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.71
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.71
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.71
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.71
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.7
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.7
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.7
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.7
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.7
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.69
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.69
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.69
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.69
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.69
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.69
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.69
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.69
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.69
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.69
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.69
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.68
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.68
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.68
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.68
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.68
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.68
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.68
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.68
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.68
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.68
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.68
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.67
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.67
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.67
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.49
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.67
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.67
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.67
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.67
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.67
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.67
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.66
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.66
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.66
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.66
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.66
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.66
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.66
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.66
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.65
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.65
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.65
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.65
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.64
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.64
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.64
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.64
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.64
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.63
1x5p_A	97	Negative elongation factor E; structure genomics,	99.63
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.63
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.63
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.62
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.62
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.62
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.62
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.62
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.62
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.61
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.61
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.61
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.61
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.6
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.6
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.6
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.6
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.59
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.59
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.58
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.57
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.57
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.57
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.57
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.57
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.56
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.56
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.55
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.55
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.55
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.55
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.54
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.54
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.54
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.53
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.52
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.52
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.51
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.51
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.5
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.5
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.48
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.47
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.47
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.46
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.46
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.45
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.44
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.43
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.43
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.43
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.42
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.41
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.4
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.4
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.37
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.37
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.28
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.26
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.23
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.17
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.0
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.93
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.84
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.15
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.34
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.69
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.68
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.57
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.01
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	95.86
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	94.6
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	94.35
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	94.25
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	93.67
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	93.09
3bkp_A	232	Cyclophilin; malaria, isomerase, structural GENO s	82.54

>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=99.84  E-value=9.9e-21  Score=147.12  Aligned_cols=83  Identities=29%  Similarity=0.427  Sum_probs=79.4

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ...+++|||+|||+++|+++|+.+|++||.|.++.+++|+.||.++|||||+|.+.++|.+|+..|||..++|++|.|++
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~   95 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY   95 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecC
Q psy15676        266 EEW  268 (309)
Q Consensus       266 a~~  268 (309)
                      |++
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            975

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.82  E-value=6.6e-20  Score=145.26  Aligned_cols=84  Identities=18%  Similarity=0.210  Sum_probs=80.1

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .+|.++|||+|||+.+++++|+.+|++||.|.++.|+.|+.||+++|||||+|.+.++|.+|+..|||..++|+.|.|.+
T Consensus         3 ~~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~   82 (110)
T 3s8s_A            3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQL   82 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            35778999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      |...
T Consensus        83 a~~~   86 (110)
T 3s8s_A           83 DIKG   86 (110)
T ss_dssp             CSTT
T ss_pred             CCCC
Confidence            9643

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.80  E-value=6.3e-20  Score=141.72  Aligned_cols=80  Identities=20%  Similarity=0.311  Sum_probs=75.5

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCc--eeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCc----eeCCeeEE
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGK--VNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNV----LIDDRRIH  262 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~--I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~----~i~gr~I~  262 (309)
                      =+||||+|||+++|+++|+.+|++||.  +.+|++++|+.||.++|||||+|.+.++|.+|++.|||.    .|+|++|.
T Consensus         9 m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~   88 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIG   88 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEE
T ss_pred             cCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEE
Confidence            379999999999999999999999995  678999999999999999999999999999999999995    69999999


Q ss_pred             EEeecC
Q psy15676        263 ARGEEW  268 (309)
Q Consensus       263 V~~a~~  268 (309)
                      |++|++
T Consensus        89 V~~Aks   94 (95)
T 2lkz_A           89 VDFAKS   94 (95)
T ss_dssp             EEECCC
T ss_pred             EEEccC
Confidence            999975

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.80  E-value=3.9e-19  Score=133.69  Aligned_cols=83  Identities=27%  Similarity=0.424  Sum_probs=77.3

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ++.++|||+|||+++++++|+.+|++||.|.++.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+|
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            46789999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             cCc
Q psy15676        267 EWN  269 (309)
Q Consensus       267 ~~~  269 (309)
                      +++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            764

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.79  E-value=6.1e-20  Score=140.33  Aligned_cols=81  Identities=19%  Similarity=0.311  Sum_probs=75.8

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCC-ceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcC-CceeCCeeEEEEee
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFG-KVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMD-NVLIDDRRIHARGE  266 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG-~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~-g~~i~gr~I~V~~a  266 (309)
                      +++|||+|||+++|+++|+.+|++|| .|.++++++|+.||.++|||||+|.+.++|.+|++.++ +..++|++|.|++|
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            36899999999999999999999999 89999999999999999999999999999999998875 57899999999999


Q ss_pred             cCc
Q psy15676        267 EWN  269 (309)
Q Consensus       267 ~~~  269 (309)
                      .++
T Consensus        81 ~~~   83 (91)
T 2lxi_A           81 DPK   83 (91)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            764

>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=99.79  E-value=5.1e-19  Score=132.46  Aligned_cols=82  Identities=26%  Similarity=0.319  Sum_probs=78.6

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++.++|||+|||+++++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|+|++
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            45779999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ec
Q psy15676        266 EE  267 (309)
Q Consensus       266 a~  267 (309)
                      |+
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            84

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.79  E-value=7.9e-19  Score=134.85  Aligned_cols=83  Identities=20%  Similarity=0.300  Sum_probs=79.5

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      |.++|||+|||+.+++++|..+|++||.|.++.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+|.
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   80 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSS   80 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcC
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             Cch
Q psy15676        268 WNM  270 (309)
Q Consensus       268 ~~~  270 (309)
                      ++.
T Consensus        81 ~~~   83 (96)
T 2x1f_A           81 NSD   83 (96)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            754

>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=99.79  E-value=9.7e-19  Score=130.33  Aligned_cols=80  Identities=26%  Similarity=0.307  Sum_probs=77.3

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecCc
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWN  269 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~~  269 (309)
                      .+|||+|||+++++++|+.+|++||.|.++.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|++|+++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999764

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.78  E-value=9.2e-19  Score=135.25  Aligned_cols=85  Identities=21%  Similarity=0.254  Sum_probs=80.1

Q ss_pred             CCCCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeE--------EEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCc
Q psy15676        183 ADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNC--------CEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNV  254 (309)
Q Consensus       183 ~~~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~--------v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~  254 (309)
                      ....++.++|||+|||+++++++|+.+|++||.|..        +.++.++.||.++|||||+|.+.++|.+|+..|||.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~   86 (99)
T 2la6_A            7 HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   86 (99)
T ss_dssp             CCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            344567899999999999999999999999999999        999999999999999999999999999999999999


Q ss_pred             eeCCeeEEEEeec
Q psy15676        255 LIDDRRIHARGEE  267 (309)
Q Consensus       255 ~i~gr~I~V~~a~  267 (309)
                      .++|+.|+|++|+
T Consensus        87 ~~~g~~l~V~~A~   99 (99)
T 2la6_A           87 EFSGNPIKVSFAT   99 (99)
T ss_dssp             BSSSSBCEEEECC
T ss_pred             EeCCcEEEEEecC
Confidence            9999999999984

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=1.1e-18  Score=133.23  Aligned_cols=84  Identities=27%  Similarity=0.447  Sum_probs=79.9

Q ss_pred             CCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       185 ~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      ..++.++|||+|||+.+++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.
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            35567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecC
Q psy15676        265 GEEW  268 (309)
Q Consensus       265 ~a~~  268 (309)
                      +|++
T Consensus        91 ~a~~   94 (95)
T 2cqc_A           91 GPSS   94 (95)
T ss_dssp             CCSC
T ss_pred             ecCC
Confidence            9875

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=7e-19  Score=134.81  Aligned_cols=85  Identities=25%  Similarity=0.324  Sum_probs=80.6

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEE-EEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCC-EVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v-~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ++.++|||+|||+.+++++|..+|++||.|..+ .++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
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            467899999999999999999999999999999 9999988999999999999999999999999999999999999999


Q ss_pred             ecCchh
Q psy15676        266 EEWNMW  271 (309)
Q Consensus       266 a~~~~~  271 (309)
                      |.++..
T Consensus        83 a~~~~~   88 (96)
T 1x5t_A           83 AFKKDS   88 (96)
T ss_dssp             SCCCCC
T ss_pred             ecccCC
Confidence            987543

>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=99.78  E-value=1.5e-18  Score=133.84  Aligned_cols=86  Identities=27%  Similarity=0.391  Sum_probs=81.2

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+++++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
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            35678999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             ecCchh
Q psy15676        266 EEWNMW  271 (309)
Q Consensus       266 a~~~~~  271 (309)
                      ++++..
T Consensus        85 a~~~~~   90 (99)
T 1whw_A           85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             cCCCcc
Confidence            987543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=1.5e-18  Score=133.95  Aligned_cols=85  Identities=20%  Similarity=0.288  Sum_probs=80.1

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+.+++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+. |+|..++|+.|.|.+
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~   85 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKR   85 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEE
Confidence            4567899999999999999999999999999999999999999999999999999999999998 999999999999999


Q ss_pred             ecCchh
Q psy15676        266 EEWNMW  271 (309)
Q Consensus       266 a~~~~~  271 (309)
                      +.++..
T Consensus        86 a~~~~~   91 (99)
T 2dgs_A           86 AEPRDS   91 (99)
T ss_dssp             CCCCCC
T ss_pred             CCCCcc
Confidence            987543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=1.5e-18  Score=134.91  Aligned_cols=86  Identities=22%  Similarity=0.302  Sum_probs=81.3

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++.++|||+|||+.+++++|..+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCchh
Q psy15676        266 EEWNMW  271 (309)
Q Consensus       266 a~~~~~  271 (309)
                      ++++..
T Consensus        92 a~~~~~   97 (103)
T 2cq0_A           92 AKPSTN   97 (103)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            987543

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=1.7e-18  Score=132.18  Aligned_cols=82  Identities=29%  Similarity=0.391  Sum_probs=78.6

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++.++|||+|||+.+++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|+|++
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            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ec
Q psy15676        266 EE  267 (309)
Q Consensus       266 a~  267 (309)
                      |+
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            84

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.1e-18  Score=136.33  Aligned_cols=85  Identities=18%  Similarity=0.237  Sum_probs=80.4

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+.+++++|..+|++||.|.++.++.++.||.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   99 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   99 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEe
Confidence            45668999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      |.++.
T Consensus       100 a~~~~  104 (106)
T 1p27_B          100 CFVRG  104 (106)
T ss_dssp             SEESS
T ss_pred             ecCCC
Confidence            97643

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=1.4e-18  Score=132.88  Aligned_cols=84  Identities=23%  Similarity=0.375  Sum_probs=80.2

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ++.++|||+|||+.+++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|+|.++
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            56789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCch
Q psy15676        267 EWNM  270 (309)
Q Consensus       267 ~~~~  270 (309)
                      ..+.
T Consensus        83 ~~~~   86 (95)
T 2dnz_A           83 TERL   86 (95)
T ss_dssp             SCCC
T ss_pred             cccc
Confidence            8643

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1e-18  Score=135.52  Aligned_cols=87  Identities=24%  Similarity=0.258  Sum_probs=81.9

Q ss_pred             CCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       185 ~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      ..++.++|||+|||+.+++++|..+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.
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            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCchh
Q psy15676        265 GEEWNMW  271 (309)
Q Consensus       265 ~a~~~~~  271 (309)
                      ++++...
T Consensus        88 ~a~~~~~   94 (102)
T 2cqb_A           88 LAKPMRI   94 (102)
T ss_dssp             ECCCCCC
T ss_pred             eCCCCCC
Confidence            9987543

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D*

Probab=99.77  E-value=1.3e-18  Score=136.79  Aligned_cols=85  Identities=21%  Similarity=0.272  Sum_probs=80.5

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+.+++++|..+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
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            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      |.++.
T Consensus       103 a~~~~  107 (110)
T 1oo0_B          103 CFVKG  107 (110)
T ss_dssp             SEESS
T ss_pred             cccCC
Confidence            98654

>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=99.77  E-value=2e-18  Score=135.75  Aligned_cols=87  Identities=15%  Similarity=0.232  Sum_probs=81.7

Q ss_pred             CCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcC------CceeCC
Q psy15676        185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMD------NVLIDD  258 (309)
Q Consensus       185 ~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~------g~~i~g  258 (309)
                      ...+.++|||+|||+++++++|+.+|++||.|..|.++.++.+|.++|||||+|.+.++|.+|+..||      |..++|
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            34567899999999999999999999999999999999999999999999999999999999999999      999999


Q ss_pred             eeEEEEeecCchh
Q psy15676        259 RRIHARGEEWNMW  271 (309)
Q Consensus       259 r~I~V~~a~~~~~  271 (309)
                      +.|.|.++.++..
T Consensus        91 ~~l~v~~a~~~~~  103 (111)
T 1x4h_A           91 RQLKVDLAVTRDE  103 (111)
T ss_dssp             CEEEEECCCCCCC
T ss_pred             EEEEEEECCCCcc
Confidence            9999999987543

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.77  E-value=2.9e-19  Score=135.92  Aligned_cols=81  Identities=15%  Similarity=0.165  Sum_probs=73.0

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCC--ceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFG--KVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG--~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      .+|||+|||+++|+++|+.+|++||  .|.++.++.++.||.++|||||+|.+.++|.+|+..|||..++|+.|.|.++.
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  99999999999999999999999999999999999999999999999999998


Q ss_pred             Cch
Q psy15676        268 WNM  270 (309)
Q Consensus       268 ~~~  270 (309)
                      +..
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            654

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.77  E-value=3.2e-18  Score=135.62  Aligned_cols=86  Identities=27%  Similarity=0.421  Sum_probs=81.3

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+.+++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45678999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             ecCchh
Q psy15676        266 EEWNMW  271 (309)
Q Consensus       266 a~~~~~  271 (309)
                      +.++..
T Consensus        92 a~~~~~   97 (115)
T 2dgo_A           92 ATRKPP   97 (115)
T ss_dssp             SSCCCC
T ss_pred             ccCCCC
Confidence            987543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=3.1e-18  Score=132.36  Aligned_cols=84  Identities=23%  Similarity=0.362  Sum_probs=79.6

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+.+++++|+.+|++||.|..+.++.++ +|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
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            4567899999999999999999999999999999999998 899999999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      |+++.
T Consensus        93 a~~~~   97 (100)
T 2do4_A           93 SNSGP   97 (100)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            98654

>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=99.77  E-value=2.3e-18  Score=134.24  Aligned_cols=85  Identities=24%  Similarity=0.298  Sum_probs=80.8

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++.++|||+|||+.+++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   91 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   91 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            45678999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      |.++.
T Consensus        92 a~~~~   96 (105)
T 1x5u_A           92 ASAHN   96 (105)
T ss_dssp             TTTTS
T ss_pred             CCCCC
Confidence            98643

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.9e-18  Score=133.94  Aligned_cols=86  Identities=30%  Similarity=0.478  Sum_probs=81.3

Q ss_pred             CCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       185 ~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      ..++.++|||+|||+++++++|+.+|++||.|..+.++.++.++.++|||||+|.+.++|.+|+..|||..++|+.|+|.
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            35677999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCch
Q psy15676        265 GEEWNM  270 (309)
Q Consensus       265 ~a~~~~  270 (309)
                      +|+++.
T Consensus        88 ~a~~~~   93 (102)
T 1x5s_A           88 QAGKSS   93 (102)
T ss_dssp             EEECCC
T ss_pred             ECCCCC
Confidence            998654

>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=99.77  E-value=2.3e-18  Score=135.66  Aligned_cols=84  Identities=21%  Similarity=0.365  Sum_probs=80.0

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++.++|||+|||+.+++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  102 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGH  102 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      |+++
T Consensus       103 a~~k  106 (108)
T 2jrs_A          103 VTER  106 (108)
T ss_dssp             SCSS
T ss_pred             cccC
Confidence            9754

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=2.2e-18  Score=132.84  Aligned_cols=85  Identities=19%  Similarity=0.356  Sum_probs=80.4

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCcee-EEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCee----
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVN-CCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRR----  260 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~-~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~----  260 (309)
                      ..+.++|||+|||+++++++|+.+|++||.|. ++.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.    
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            45679999999999999999999999999999 9999999999999999999999999999999999999999999    


Q ss_pred             EEEEeecCch
Q psy15676        261 IHARGEEWNM  270 (309)
Q Consensus       261 I~V~~a~~~~  270 (309)
                      |+|++|++..
T Consensus        86 l~v~~a~~~~   95 (99)
T 2div_A           86 FKLNYATYSG   95 (99)
T ss_dssp             CCEEETTCCS
T ss_pred             EEEeecCCCC
Confidence            9999997643

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=1.9e-18  Score=134.36  Aligned_cols=85  Identities=26%  Similarity=0.369  Sum_probs=80.4

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+++++++|..+|++||.|..+.++.++.||.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV   89 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      |+...
T Consensus        90 a~~~~   94 (103)
T 2dnm_A           90 ARYGR   94 (103)
T ss_dssp             CSSCC
T ss_pred             CCcCC
Confidence            98643

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.76  E-value=4.8e-18  Score=127.87  Aligned_cols=80  Identities=29%  Similarity=0.409  Sum_probs=75.6

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+++++++|+.+|++||.|.++.++.++.||.++|||||+|.+.++|.+|+. ++|..++|+.|.|.+
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD-QKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHH-SSCEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHH-hCCCEECCEEEEEEe
Confidence            4567899999999999999999999999999999999999999999999999999999999996 588999999999987


Q ss_pred             e
Q psy15676        266 E  266 (309)
Q Consensus       266 a  266 (309)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            6

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.76  E-value=2.5e-18  Score=144.42  Aligned_cols=83  Identities=16%  Similarity=0.221  Sum_probs=78.2

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCC--ceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFG--KVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG--~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..++|||+|||+++|+++|+.+|++||  .|.++.++.|+.||.++|||||+|.+.++|.+|+..|||..|+|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            458999999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      |.++.
T Consensus       134 a~~~~  138 (156)
T 3n9u_C          134 ATRQN  138 (156)
T ss_dssp             CCHHH
T ss_pred             cCCCc
Confidence            97643

>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=99.76  E-value=2.8e-18  Score=136.06  Aligned_cols=85  Identities=31%  Similarity=0.426  Sum_probs=80.6

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++.++|||+|||+++++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.+
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            35668999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      ++++.
T Consensus       102 a~~~~  106 (115)
T 2cpz_A          102 KRSKN  106 (115)
T ss_dssp             CCCSC
T ss_pred             cCCCC
Confidence            98654

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.76  E-value=5e-19  Score=137.46  Aligned_cols=81  Identities=20%  Similarity=0.208  Sum_probs=77.9

Q ss_pred             CCcEEEecCCCC------CCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCC-ee
Q psy15676        188 PENVLFVCKLNP------VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDD-RR  260 (309)
Q Consensus       188 ~~~~lfV~nL~~------~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~g-r~  260 (309)
                      .+++|||+|||+      ++++++|+.+|++||.|.++.++.++.||.++|||||+|.+.++|.+|+..|||..++| +.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~   84 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHR   84 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCB
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeE
Confidence            458999999999      99999999999999999999999999999999999999999999999999999999999 99


Q ss_pred             EEEEeecC
Q psy15676        261 IHARGEEW  268 (309)
Q Consensus       261 I~V~~a~~  268 (309)
                      |.|.+|.+
T Consensus        85 l~V~~a~~   92 (100)
T 3ns6_A           85 LFLYTMKD   92 (100)
T ss_dssp             CEEEESHH
T ss_pred             EEEEECch
Confidence            99999964

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=2.4e-18  Score=132.40  Aligned_cols=84  Identities=24%  Similarity=0.461  Sum_probs=79.0

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCC---CCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEE
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKV---TGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA  263 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~---tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V  263 (309)
                      ++.++|||+|||+++++++|+.+|++||.|..+.++.++.   |+.++|||||+|.+.++|.+|+..|||..++|+.|.|
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            4678999999999999999999999999999999999876   6799999999999999999999999999999999999


Q ss_pred             EeecCch
Q psy15676        264 RGEEWNM  270 (309)
Q Consensus       264 ~~a~~~~  270 (309)
                      .++.++.
T Consensus        83 ~~a~~~~   89 (98)
T 2cpf_A           83 RISERAT   89 (98)
T ss_dssp             ECSSCSS
T ss_pred             EEccCCC
Confidence            9998644

>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=99.76  E-value=2.9e-18  Score=136.45  Aligned_cols=80  Identities=28%  Similarity=0.500  Sum_probs=74.8

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      ..+|||+|||+++++++|+.+|++||.|.+|.|+.+.  +.++|||||+|.+.++|.+|+..|+|..|+|+.|.|.++.+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999999999999986  45899999999999999999999999999999999999876


Q ss_pred             ch
Q psy15676        269 NM  270 (309)
Q Consensus       269 ~~  270 (309)
                      +.
T Consensus        83 ~~   84 (115)
T 4f25_A           83 RK   84 (115)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>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=99.76  E-value=3.2e-18  Score=144.64  Aligned_cols=86  Identities=21%  Similarity=0.249  Sum_probs=80.0

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+.+++++|..+|++||.|..|.++.++.||.++|||||+|.+.++|.+|+..|||..|+|+.|.|.+
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  148 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW  148 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45567999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCchh
Q psy15676        266 EEWNMW  271 (309)
Q Consensus       266 a~~~~~  271 (309)
                      |.++..
T Consensus       149 a~~~~~  154 (165)
T 1rk8_A          149 CFVKGP  154 (165)
T ss_dssp             SEECC-
T ss_pred             ecCCCC
Confidence            987543

>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=99.76  E-value=5.2e-18  Score=132.63  Aligned_cols=82  Identities=26%  Similarity=0.342  Sum_probs=78.2

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++.++|||+|||+.+++++|..+|++||.|.++.++.++ +|.++|||||+|.+.++|.+|+..|||..++|+.|.|++
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            4567899999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             ecC
Q psy15676        266 EEW  268 (309)
Q Consensus       266 a~~  268 (309)
                      |.+
T Consensus       105 a~s  107 (107)
T 3ulh_A          105 VTS  107 (107)
T ss_dssp             ECC
T ss_pred             eCC
Confidence            863

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.76  E-value=3.3e-18  Score=128.72  Aligned_cols=82  Identities=28%  Similarity=0.432  Sum_probs=77.5

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCC-cccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGD-SLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~-skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ..++|||+|||+++++++|..+|++||.|.++.++.+..++. ++|||||+|.+.++|.+|+..|||..++|+.|.|.++
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            458999999999999999999999999999999999988766 9999999999999999999999999999999999999


Q ss_pred             cCc
Q psy15676        267 EWN  269 (309)
Q Consensus       267 ~~~  269 (309)
                      .+.
T Consensus        83 ~~~   85 (88)
T 4a8x_A           83 LAP   85 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.76  E-value=5.7e-18  Score=131.68  Aligned_cols=83  Identities=27%  Similarity=0.420  Sum_probs=78.4

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+++++++|+.+|++|| |..+.++.++.||.++|||||+|.+.++|.+|+ .|||..|+|+.|.|.+
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            45678999999999999999999999997 999999999999999999999999999999999 8999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      +.+..
T Consensus        90 a~~~~   94 (103)
T 2dng_A           90 AEGRK   94 (103)
T ss_dssp             CCCCC
T ss_pred             ecCCC
Confidence            98644

>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=99.76  E-value=5e-18  Score=132.25  Aligned_cols=85  Identities=24%  Similarity=0.350  Sum_probs=79.6

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCC---eeEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDD---RRIH  262 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~g---r~I~  262 (309)
                      .++.++|||+|||+.+++++|..+|++||.|..+.++.++ +|.++|||||+|.+.++|.+|+..|||..+.|   +.|.
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            4567999999999999999999999999999999999998 79999999999999999999999999999998   9999


Q ss_pred             EEeecCchh
Q psy15676        263 ARGEEWNMW  271 (309)
Q Consensus       263 V~~a~~~~~  271 (309)
                      |.+|+++..
T Consensus        91 V~~a~~~~~   99 (105)
T 2dnh_A           91 VKFADTDKE   99 (105)
T ss_dssp             EEESCSSCC
T ss_pred             EEECccCcc
Confidence            999987543

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=4.1e-18  Score=132.77  Aligned_cols=85  Identities=14%  Similarity=0.271  Sum_probs=79.5

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCC-CCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVT-GDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~t-g~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      .++.++|||+|||+++++++|+.+|++|| |..+.++.++.| |.++|||||+|.+.++|.+|+ .|||..++|+.|.|.
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 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEE
Confidence            45678999999999999999999999999 999999999988 999999999999999999999 999999999999999


Q ss_pred             eecCchhh
Q psy15676        265 GEEWNMWK  272 (309)
Q Consensus       265 ~a~~~~~~  272 (309)
                      +|.++...
T Consensus        90 ~a~~~~~~   97 (104)
T 1wi8_A           90 VADQAQDK   97 (104)
T ss_dssp             ECCCCCCC
T ss_pred             EccCCCCC
Confidence            99875443

>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=99.76  E-value=2.6e-18  Score=138.40  Aligned_cols=91  Identities=18%  Similarity=0.230  Sum_probs=83.3

Q ss_pred             CCCCCCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCee
Q psy15676        181 PEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRR  260 (309)
Q Consensus       181 ~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~  260 (309)
                      +......+.++|||+|||+.+|+++|..+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..|+|+.
T Consensus        14 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   93 (126)
T 3ex7_B           14 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQP   93 (126)
T ss_dssp             CCBCCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSB
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeE
Confidence            34444566789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeecCchh
Q psy15676        261 IHARGEEWNMW  271 (309)
Q Consensus       261 I~V~~a~~~~~  271 (309)
                      |.|.+|.+...
T Consensus        94 l~v~~a~~~~~  104 (126)
T 3ex7_B           94 ISVDWCFVRGP  104 (126)
T ss_dssp             CEEEESEESSS
T ss_pred             EEEEEecCCCC
Confidence            99999986443

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=4.3e-18  Score=132.97  Aligned_cols=85  Identities=15%  Similarity=0.318  Sum_probs=80.4

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeee-CCCCCcccEEEEEecCHHHHHHHHHHc-CCceeCCeeEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRD-KVTGDSLQYAFVEFDNPKSCEDAYLKM-DNVLIDDRRIHA  263 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d-~~tg~skG~aFV~F~~~~~a~~Al~~l-~g~~i~gr~I~V  263 (309)
                      .++.++|||+|||+.+++++|+.+|++||.|..+.++.+ +.+|.++|||||+|.+.++|.+|+..| ||..++|+.|.|
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            456789999999999999999999999999999999999 789999999999999999999999999 999999999999


Q ss_pred             EeecCch
Q psy15676        264 RGEEWNM  270 (309)
Q Consensus       264 ~~a~~~~  270 (309)
                      .+|.++.
T Consensus        92 ~~a~~~~   98 (107)
T 2cph_A           92 EWADSEV   98 (107)
T ss_dssp             EECCCCC
T ss_pred             EeCCCCC
Confidence            9998754

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.75  E-value=1e-17  Score=162.64  Aligned_cols=83  Identities=27%  Similarity=0.442  Sum_probs=79.3

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+.+|+++|..+|++||.|..|.|+.++.||.++|||||+|.+.++|.+|+..|||..|+|+.|.|.+
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~  178 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  178 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecC
Q psy15676        266 EEW  268 (309)
Q Consensus       266 a~~  268 (309)
                      |.+
T Consensus       179 a~~  181 (437)
T 3pgw_S          179 ERG  181 (437)
T ss_pred             eCC
Confidence            975

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.75  E-value=4.6e-18  Score=135.37  Aligned_cols=81  Identities=32%  Similarity=0.466  Sum_probs=77.4

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ++.++|||+|||+++++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|+|+++
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            46689999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             c
Q psy15676        267 E  267 (309)
Q Consensus       267 ~  267 (309)
                      +
T Consensus       118 k  118 (118)
T 2khc_A          118 K  118 (118)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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=99.75  E-value=5.6e-18  Score=127.82  Aligned_cols=80  Identities=24%  Similarity=0.446  Sum_probs=76.7

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      .++|||+|||+++++++|+.+|++||.|.++.++.++.+|.++|||||+|.+.++|.+|+ .|||..++|+.|.|.++++
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEccC
Confidence            479999999999999999999999999999999999989999999999999999999999 8999999999999999976


Q ss_pred             c
Q psy15676        269 N  269 (309)
Q Consensus       269 ~  269 (309)
                      +
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.75  E-value=3.6e-18  Score=133.29  Aligned_cols=85  Identities=21%  Similarity=0.313  Sum_probs=80.1

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCcee---CCeeEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLI---DDRRIH  262 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i---~gr~I~  262 (309)
                      .++.++|||+|||+++++++|+.+|++||.|..+.++.++.||.++|||||+|.+.++|.+|+..|||..+   +|+.|.
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            45678999999999999999999999999999999999999999999999999999999999999999887   899999


Q ss_pred             EEeecCch
Q psy15676        263 ARGEEWNM  270 (309)
Q Consensus       263 V~~a~~~~  270 (309)
                      |.++.+..
T Consensus        90 v~~a~~~~   97 (106)
T 2dgp_A           90 VKPADSES   97 (106)
T ss_dssp             EEECCCCS
T ss_pred             EEECCccc
Confidence            99998654

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.75  E-value=4.9e-18  Score=133.94  Aligned_cols=85  Identities=22%  Similarity=0.344  Sum_probs=76.2

Q ss_pred             CCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       185 ~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      ...+.++|||+|||+++++++|+.+|++||.|.++.++.++.||.++|||||+|.+.++|.+|+..+ |..++|+.|.|.
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~   99 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPK   99 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEE
Confidence            3456789999999999999999999999999999999999999999999999999999999999875 699999999999


Q ss_pred             eecCch
Q psy15676        265 GEEWNM  270 (309)
Q Consensus       265 ~a~~~~  270 (309)
                      ++.+..
T Consensus       100 ~a~~~~  105 (109)
T 2rs2_A          100 VAFPRR  105 (109)
T ss_dssp             ECCCCC
T ss_pred             EccCCC
Confidence            998654

>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=99.75  E-value=5.5e-18  Score=135.17  Aligned_cols=83  Identities=24%  Similarity=0.424  Sum_probs=78.8

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      .+.++|||+|||+++++++|..+|++||.|.++.++.+. +|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            456899999999999999999999999999999999998 8999999999999999999999999999999999999999


Q ss_pred             cCch
Q psy15676        267 EWNM  270 (309)
Q Consensus       267 ~~~~  270 (309)
                      ++..
T Consensus        84 ~~~~   87 (116)
T 2fy1_A           84 KKPS   87 (116)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            8643

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=7.2e-18  Score=131.03  Aligned_cols=83  Identities=22%  Similarity=0.359  Sum_probs=78.5

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+.+++++|+.+|++||.|..+.++.+  +|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            456789999999999999999999999999999999988  899999999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      |.++.
T Consensus        90 a~~~~   94 (103)
T 2d9p_A           90 AQRKE   94 (103)
T ss_dssp             CSSCC
T ss_pred             ecccc
Confidence            98754

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=7.2e-18  Score=133.19  Aligned_cols=85  Identities=21%  Similarity=0.266  Sum_probs=80.2

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCcee--------EEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeC
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVN--------CCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLID  257 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~--------~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~  257 (309)
                      ..+.++|||+|||+.+++++|+.+|++||.|.        .+.++.++.+|.++|||||+|.+.++|.+|+..|||..|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   91 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   91 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccC
Confidence            45678999999999999999999999999998        6999999899999999999999999999999999999999


Q ss_pred             CeeEEEEeecCch
Q psy15676        258 DRRIHARGEEWNM  270 (309)
Q Consensus       258 gr~I~V~~a~~~~  270 (309)
                      |+.|+|.+++++.
T Consensus        92 g~~l~V~~a~~~~  104 (113)
T 2cpe_A           92 GSKLKVSLARKKP  104 (113)
T ss_dssp             TEECEEECSSCCC
T ss_pred             CCEEEEEECCCCC
Confidence            9999999998754

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.8e-18  Score=134.52  Aligned_cols=83  Identities=19%  Similarity=0.344  Sum_probs=79.0

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      +.++|||+|||+.+++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+|.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             Cch
Q psy15676        268 WNM  270 (309)
Q Consensus       268 ~~~  270 (309)
                      +..
T Consensus        87 ~~~   89 (104)
T 1p1t_A           87 SEK   89 (104)
T ss_dssp             CTT
T ss_pred             Ccc
Confidence            644

>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=99.74  E-value=7.7e-18  Score=128.71  Aligned_cols=82  Identities=21%  Similarity=0.375  Sum_probs=77.4

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++.++|||+|||+.+++++|+.+|++||.|.++.++.++. |.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
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            34668999999999999999999999999999999999985 99999999999999999999999999999999999999


Q ss_pred             ecC
Q psy15676        266 EEW  268 (309)
Q Consensus       266 a~~  268 (309)
                      |++
T Consensus        92 a~~   94 (95)
T 2ywk_A           92 PSS   94 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            864

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=4.4e-18  Score=132.33  Aligned_cols=85  Identities=24%  Similarity=0.319  Sum_probs=79.8

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhc-CCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCce-eCCeeEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSR-FGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVL-IDDRRIHA  263 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~-fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~-i~gr~I~V  263 (309)
                      .++.++|||+|||+++++++|+.+|++ ||.|.++.++.++ +|.++|||||+|.+.++|.+|+..|+|.. ++|+.|.|
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 9999999999998 99999999999999999999999999999 99999999


Q ss_pred             EeecCchh
Q psy15676        264 RGEEWNMW  271 (309)
Q Consensus       264 ~~a~~~~~  271 (309)
                      .++.++..
T Consensus        85 ~~a~~~~~   92 (104)
T 2dhg_A           85 SVAIPKAS   92 (104)
T ss_dssp             CBCCCCCS
T ss_pred             EEccCCCc
Confidence            99976543

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.74  E-value=3e-18  Score=131.01  Aligned_cols=83  Identities=17%  Similarity=0.241  Sum_probs=76.6

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++.++|||+|||+.+++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            45568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecC
Q psy15676        266 EEW  268 (309)
Q Consensus       266 a~~  268 (309)
                      +.+
T Consensus        92 a~s   94 (95)
T 2ek1_A           92 PSS   94 (95)
T ss_dssp             CC-
T ss_pred             ccC
Confidence            864

>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=99.74  E-value=6.1e-18  Score=130.12  Aligned_cols=84  Identities=14%  Similarity=0.179  Sum_probs=78.9

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++.++|||+|||+.+++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
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            45568999999999999999999999999999888899999999999999999999999999999999999999999999


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      +...
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8753

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.1e-18  Score=130.85  Aligned_cols=82  Identities=26%  Similarity=0.430  Sum_probs=77.8

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ++.++|||+|||+++++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|+++++
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            56789999999999999999999999999999999999999999999999999999999999999999999999998876


Q ss_pred             cC
Q psy15676        267 EW  268 (309)
Q Consensus       267 ~~  268 (309)
                      .+
T Consensus        83 ~s   84 (85)
T 1x4e_A           83 SS   84 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.74  E-value=1.6e-18  Score=142.80  Aligned_cols=89  Identities=18%  Similarity=0.255  Sum_probs=76.2

Q ss_pred             CCCCCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEE--E---eeeCCCCCcccEEEEEecCHHHHHHHHHHcCCcee
Q psy15676        182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCE--V---IRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLI  256 (309)
Q Consensus       182 ~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~--i---~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i  256 (309)
                      ......+.++|||+|||+.+|+++|..+|++||.|..+.  +   +....+|.++|||||+|.+.++|.+|+..|||..+
T Consensus        38 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~  117 (143)
T 3egn_A           38 SYEPGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVL  117 (143)
T ss_dssp             TCCCCSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEE
T ss_pred             ccCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEe
Confidence            334466789999999999999999999999999987641  1   11124789999999999999999999999999999


Q ss_pred             CCeeEEEEeecCch
Q psy15676        257 DDRRIHARGEEWNM  270 (309)
Q Consensus       257 ~gr~I~V~~a~~~~  270 (309)
                      +|+.|.|.+|++..
T Consensus       118 ~g~~l~V~~a~~~~  131 (143)
T 3egn_A          118 FGKPMVVQFARSAR  131 (143)
T ss_dssp             TTEECEEEECCCSC
T ss_pred             CCcEEEEEECCCCC
Confidence            99999999998654

>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=99.74  E-value=5.4e-18  Score=137.88  Aligned_cols=86  Identities=26%  Similarity=0.384  Sum_probs=81.1

Q ss_pred             CCCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEE
Q psy15676        184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA  263 (309)
Q Consensus       184 ~~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V  263 (309)
                      ...++.++|||+|||+.+++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V  120 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV  120 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            33567789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCc
Q psy15676        264 RGEEWN  269 (309)
Q Consensus       264 ~~a~~~  269 (309)
                      .++.++
T Consensus       121 ~~a~~~  126 (129)
T 2kxn_B          121 DFSITK  126 (129)
T ss_dssp             SCCSSS
T ss_pred             EEecCC
Confidence            999764

>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=99.74  E-value=2.7e-17  Score=127.71  Aligned_cols=86  Identities=23%  Similarity=0.402  Sum_probs=78.5

Q ss_pred             CCCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEE
Q psy15676        184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA  263 (309)
Q Consensus       184 ~~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V  263 (309)
                      ....+.++|||+|||+.+++++|+.+|++||.|..+.++.+..  .++|||||+|.+.++|.+|+..|||..|+|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   87 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            3356679999999999999999999999999999999998864  38999999999999999999999999999999999


Q ss_pred             EeecCchh
Q psy15676        264 RGEEWNMW  271 (309)
Q Consensus       264 ~~a~~~~~  271 (309)
                      .++.++..
T Consensus        88 ~~a~~~~~   95 (103)
T 2cq3_A           88 NNATARVM   95 (103)
T ss_dssp             EECCSSCC
T ss_pred             EEcccCCC
Confidence            99987543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.74  E-value=1.2e-17  Score=136.63  Aligned_cols=85  Identities=20%  Similarity=0.320  Sum_probs=80.5

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      .+.++|||+|||+++++++|+.+|+.||.|.++.++.++.||.++|||||+|.+.++|.+|+..|||..++|+.|.|.+|
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            45689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCchh
Q psy15676        267 EWNMW  271 (309)
Q Consensus       267 ~~~~~  271 (309)
                      .+...
T Consensus       120 ~~~~~  124 (139)
T 1u6f_A          120 ASGHQ  124 (139)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87543

>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=99.74  E-value=2.3e-17  Score=128.14  Aligned_cols=83  Identities=19%  Similarity=0.308  Sum_probs=77.0

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+.+++++|+.+|++||.|..|.++.++.  .++|||||+|.+.++|.+|+..|||..++|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            45678999999999999999999999999999999999864  3689999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      +++..
T Consensus        90 a~~~~   94 (103)
T 2cqi_A           90 ATTPS   94 (103)
T ss_dssp             CCCTT
T ss_pred             CCCCc
Confidence            98754

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=9.9e-18  Score=130.68  Aligned_cols=84  Identities=27%  Similarity=0.416  Sum_probs=79.7

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++.++|||+|||+.+++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+.. +|..|+|+.|.|.+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKP   91 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEE
Confidence            45678999999999999999999999999999999999999999999999999999999999998 99999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      +.++.
T Consensus        92 a~~~~   96 (105)
T 2dh8_A           92 CTPRG   96 (105)
T ss_dssp             SCCSS
T ss_pred             ccCCC
Confidence            98654

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=5.4e-18  Score=132.66  Aligned_cols=79  Identities=13%  Similarity=0.074  Sum_probs=74.9

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      .+.++|||+|||+++|+++|..+|++||.|.+|.++.++. |.++|||||+|.+.++|.+|+. ++|..++|+.|.|.++
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            4568999999999999999999999999999999999987 9999999999999999999998 8999999999999977


Q ss_pred             c
Q psy15676        267 E  267 (309)
Q Consensus       267 ~  267 (309)
                      .
T Consensus        87 ~   87 (103)
T 1s79_A           87 D   87 (103)
T ss_dssp             H
T ss_pred             h
Confidence            5

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=2.6e-17  Score=130.02  Aligned_cols=84  Identities=25%  Similarity=0.328  Sum_probs=78.8

Q ss_pred             CCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       185 ~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      ..++.++|||+|||+.+++++|+.+|++||.|..+.++.++ +|.++|||||+|.+.++|.+|+..|||..++|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   89 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK   89 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEE
Confidence            35667899999999999999999999999999999999997 69999999999999999999999999999999999999


Q ss_pred             eecCc
Q psy15676        265 GEEWN  269 (309)
Q Consensus       265 ~a~~~  269 (309)
                      ++...
T Consensus        90 ~a~~~   94 (114)
T 2do0_A           90 MDERA   94 (114)
T ss_dssp             ECSCC
T ss_pred             EcccC
Confidence            99753

>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=99.73  E-value=1.5e-17  Score=127.91  Aligned_cols=82  Identities=18%  Similarity=0.155  Sum_probs=76.1

Q ss_pred             CCCCcEEEecCCCCCCCHHHHH----HHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLE----IIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI  261 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~----~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I  261 (309)
                      ..+.++|||+|||+.+++++|+    .+|++||.|.++.++.++.+   +|||||+|.+.++|.+|+..|||..++|+.|
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l   82 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKI   82 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            3456899999999999999999    99999999999999998765   8999999999999999999999999999999


Q ss_pred             EEEeecCch
Q psy15676        262 HARGEEWNM  270 (309)
Q Consensus       262 ~V~~a~~~~  270 (309)
                      +|++|++..
T Consensus        83 ~V~~a~~~~   91 (96)
T 2dgx_A           83 LVSLATGAS   91 (96)
T ss_dssp             EEEECCCSS
T ss_pred             EEEEcCCCC
Confidence            999997643

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.8e-17  Score=131.58  Aligned_cols=83  Identities=28%  Similarity=0.372  Sum_probs=78.6

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+.+++++|+.+|++||.|..+.++.++.|+.++|||||+|.+.++|.+|+..+++ .++|+.|.|.+
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            45678999999999999999999999999999999999999999999999999999999999999998 89999999999


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      |...
T Consensus        93 a~~~   96 (116)
T 2cqd_A           93 AYLG   96 (116)
T ss_dssp             STTT
T ss_pred             cccC
Confidence            9753

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.73  E-value=3.7e-18  Score=124.94  Aligned_cols=75  Identities=24%  Similarity=0.393  Sum_probs=72.1

Q ss_pred             EEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       191 ~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      +|||+|||+++++++|+.+|++||.|.++.++.++.+|.++|||||+|.+.++|++|+. ++|..++|++|.|.+|
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            48999999999999999999999999999999999899999999999999999999997 9999999999999875

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.73  E-value=1.2e-17  Score=139.45  Aligned_cols=85  Identities=29%  Similarity=0.444  Sum_probs=80.6

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+..+|||+|||+++++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  146 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  146 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            35578999999999999999999999999999999999998999999999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      |++..
T Consensus       147 a~~~~  151 (158)
T 2kn4_A          147 ARYGR  151 (158)
T ss_dssp             ECCSS
T ss_pred             CCCCC
Confidence            98753

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=3.3e-17  Score=124.36  Aligned_cols=81  Identities=15%  Similarity=0.239  Sum_probs=76.5

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ....++|||+|||+++++++|+.+|++| .|..+.++.+ .+|.++|||||+|.+.++|.+|+. |||..++|+.|.|.+
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            3457899999999999999999999999 9999999999 789999999999999999999999 999999999999999


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      |++.
T Consensus        84 a~~~   87 (91)
T 2dgw_A           84 EKSG   87 (91)
T ss_dssp             ESSC
T ss_pred             CCcC
Confidence            9765

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.73  E-value=1.7e-17  Score=126.01  Aligned_cols=83  Identities=22%  Similarity=0.262  Sum_probs=77.5

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++.++|||+|||+++++++|+.+|++||.|..+.++.+  +|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
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            456789999999999999999999999999999999874  789999999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      +++..
T Consensus        83 a~~~~   87 (92)
T 2dgv_A           83 DRNAS   87 (92)
T ss_dssp             CSCCS
T ss_pred             cCCCC
Confidence            98643

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1e-17  Score=132.60  Aligned_cols=79  Identities=25%  Similarity=0.274  Sum_probs=76.3

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecCc
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWN  269 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~~  269 (309)
                      ++|||+|||+.+++++|+.+|++||.|..+.++.++.||.++|||||+|.+.++|.+|+ .|||..|+|+.|.|.++...
T Consensus        26 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~  104 (114)
T 2cq4_A           26 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQAE  104 (114)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCCC
Confidence            79999999999999999999999999999999999999999999999999999999999 99999999999999999753

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.73  E-value=3.1e-17  Score=137.00  Aligned_cols=84  Identities=21%  Similarity=0.292  Sum_probs=80.2

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ++.++|||+|||+.+|+++|..+|++||.|..|.|+.++.|+.++|||||+|.+.++|.+|+..|||..|+|+.|.|.+|
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            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCch
Q psy15676        267 EWNM  270 (309)
Q Consensus       267 ~~~~  270 (309)
                      .+..
T Consensus       117 ~~~~  120 (156)
T 1h2v_Z          117 AGFK  120 (156)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8643

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.73  E-value=2.5e-17  Score=132.36  Aligned_cols=84  Identities=25%  Similarity=0.327  Sum_probs=79.4

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+.+++++|+.+|++||.|.++.++.++ +|.++|||||+|.+.++|.+|+..|||..++|+.|.|++
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            4567899999999999999999999999999999999998 899999999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      |....
T Consensus       111 a~~~~  115 (124)
T 2kt5_A          111 VASQI  115 (124)
T ss_dssp             ECCTT
T ss_pred             eCCCC
Confidence            98643

>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=99.72  E-value=3.9e-18  Score=132.22  Aligned_cols=82  Identities=15%  Similarity=0.295  Sum_probs=75.0

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeC-CCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDK-VTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~-~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      .++.++|||+|||+++++++|+.+|++|| |.++.++.++ .+|.++|||||+|.+.++|.+|+ .|+|..++|+.|.|+
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVD   93 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEE
Confidence            45678999999999999999999999999 9999999998 68999999999999999999999 899999999999999


Q ss_pred             eecCc
Q psy15676        265 GEEWN  269 (309)
Q Consensus       265 ~a~~~  269 (309)
                      +|++.
T Consensus        94 ~a~~~   98 (100)
T 2j76_E           94 VADQA   98 (100)
T ss_dssp             ECCCS
T ss_pred             eccCC
Confidence            99764

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.72  E-value=2e-17  Score=128.66  Aligned_cols=81  Identities=17%  Similarity=0.192  Sum_probs=72.4

Q ss_pred             CCCCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCc--eeCCee
Q psy15676        183 ADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNV--LIDDRR  260 (309)
Q Consensus       183 ~~~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~--~i~gr~  260 (309)
                      ....+|+++|||+|||+.+|+++|..+|++||.|.++.+++      ++|||||+|.+.++|.+|+..|+|.  .++|++
T Consensus        15 ~~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~   88 (100)
T 3r27_A           15 PHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHP   88 (100)
T ss_dssp             --CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEE
T ss_pred             cccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcE
Confidence            34467889999999999999999999999999999999874      4689999999999999999999986  489999


Q ss_pred             EEEEeecCc
Q psy15676        261 IHARGEEWN  269 (309)
Q Consensus       261 I~V~~a~~~  269 (309)
                      |.|+||+++
T Consensus        89 i~V~~S~~k   97 (100)
T 3r27_A           89 AFVNYSTSQ   97 (100)
T ss_dssp             EEEEECSCS
T ss_pred             EEEEecccc
Confidence            999999764

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.72  E-value=2.6e-17  Score=134.41  Aligned_cols=81  Identities=26%  Similarity=0.318  Sum_probs=76.9

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++.++|||+|||+.+++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|+|++
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  139 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL  139 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             e
Q psy15676        266 E  266 (309)
Q Consensus       266 a  266 (309)
                      |
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            6

>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=99.72  E-value=4.5e-17  Score=128.99  Aligned_cols=83  Identities=13%  Similarity=0.197  Sum_probs=75.8

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++.++|||+|||+.+++++|..+|++||.|.++.++.+   +.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   81 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLY   81 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            346789999999999999999999999999999999865   55699999999999999999999999999999999999


Q ss_pred             ecCchh
Q psy15676        266 EEWNMW  271 (309)
Q Consensus       266 a~~~~~  271 (309)
                      +.+...
T Consensus        82 a~~~~~   87 (115)
T 3lqv_A           82 YNANRA   87 (115)
T ss_dssp             CCHHHH
T ss_pred             ecCChh
Confidence            986443

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=6.3e-17  Score=125.65  Aligned_cols=83  Identities=27%  Similarity=0.318  Sum_probs=77.5

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+.+++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+.  ++..++|+.|.|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEEC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEe
Confidence            3567899999999999999999999999999999999999999999999999999999999998  58899999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      +.++.
T Consensus        90 a~~~~   94 (103)
T 2cqg_A           90 PNSKQ   94 (103)
T ss_dssp             CCTTC
T ss_pred             cCCCC
Confidence            98643

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.6e-17  Score=130.40  Aligned_cols=81  Identities=15%  Similarity=0.206  Sum_probs=73.1

Q ss_pred             CCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCC--ceeCCeeEE
Q psy15676        185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDN--VLIDDRRIH  262 (309)
Q Consensus       185 ~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g--~~i~gr~I~  262 (309)
                      +.++.++|||+|||+++|+++|+.+|++||.|.++.++.+      +|||||+|.+.++|.+|+..|++  ..++|++|.
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~   85 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY   85 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            3567899999999999999999999999999999999864      69999999999999999998864  799999999


Q ss_pred             EEeecCchh
Q psy15676        263 ARGEEWNMW  271 (309)
Q Consensus       263 V~~a~~~~~  271 (309)
                      |++|+++.-
T Consensus        86 V~~A~~~~~   94 (105)
T 1sjq_A           86 IQFSNHKEL   94 (105)
T ss_dssp             BCCCSSSSC
T ss_pred             EEEcCCCCC
Confidence            999987543

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=6.9e-18  Score=123.88  Aligned_cols=76  Identities=25%  Similarity=0.427  Sum_probs=73.3

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ++|||+|||+++++++|+.+|++||.|.++.++.++.+|.++|||||+|.+.++|.+|+..++ ..++|+.|.|++|
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            479999999999999999999999999999999999999999999999999999999999988 9999999999987

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.72  E-value=2.9e-18  Score=129.94  Aligned_cols=81  Identities=25%  Similarity=0.355  Sum_probs=74.2

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecCc
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWN  269 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~~  269 (309)
                      ++|||+|||+++++++|+.+|++||.|.++.++.++.+|.++|||||+|.+.+ |.+|+..|||..++|+.|.|.+|...
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 99999999999999999999999865


Q ss_pred             hh
Q psy15676        270 MW  271 (309)
Q Consensus       270 ~~  271 (309)
                      ..
T Consensus        81 ~~   82 (90)
T 2ki2_A           81 KS   82 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.71  E-value=4.8e-18  Score=138.18  Aligned_cols=82  Identities=17%  Similarity=0.291  Sum_probs=77.8

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeE--EEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCc----eeCCee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNC--CEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNV----LIDDRR  260 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~--v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~----~i~gr~  260 (309)
                      .+.++|||+|||+++|+++|+.+|++||.|..  |.|++|+.||.++|||||+|.+. +|.+|+..|||.    .++|+.
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            45689999999999999999999999999976  99999999999999999999999 999999999999    999999


Q ss_pred             EEEEeecCc
Q psy15676        261 IHARGEEWN  269 (309)
Q Consensus       261 I~V~~a~~~  269 (309)
                      |.|.+|.+.
T Consensus       100 l~V~~a~~~  108 (131)
T 2m2b_A          100 INVEFAKGS  108 (131)
T ss_dssp             CCCEECCCS
T ss_pred             EEEEECCCC
Confidence            999999764

>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=99.71  E-value=1.9e-17  Score=131.39  Aligned_cols=82  Identities=13%  Similarity=0.159  Sum_probs=77.0

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCce-eEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKV-NCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I-~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      ..+.++|||+|||+++|+++|+.+|+.||.| ..+.|+.++ +|.++|||||+|.+.++|.+|+.. ||..|+|+.|.|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~   89 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVH   89 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEE
Confidence            4567899999999999999999999999999 899999998 999999999999999999999986 9999999999999


Q ss_pred             eecCc
Q psy15676        265 GEEWN  269 (309)
Q Consensus       265 ~a~~~  269 (309)
                      +|..+
T Consensus        90 ~a~~~   94 (114)
T 2cpy_A           90 VVTLE   94 (114)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            99653

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.8e-17  Score=129.94  Aligned_cols=84  Identities=14%  Similarity=0.150  Sum_probs=78.2

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCc-eeEEEEe-eeCCCCCcccEEEEEecCHHHHHHHHHHcC--CceeCCeeEE
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGK-VNCCEVI-RDKVTGDSLQYAFVEFDNPKSCEDAYLKMD--NVLIDDRRIH  262 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~-I~~v~i~-~d~~tg~skG~aFV~F~~~~~a~~Al~~l~--g~~i~gr~I~  262 (309)
                      .+.++|||+|||+.+++++|+.+|++||. |..+.++ .+..+|.++|||||+|.+.++|.+|+..|+  +..++|+.|.
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            46789999999999999999999999998 9999998 888899999999999999999999999996  5999999999


Q ss_pred             EEeecCch
Q psy15676        263 ARGEEWNM  270 (309)
Q Consensus       263 V~~a~~~~  270 (309)
                      |.+|.++.
T Consensus        86 V~~a~~~~   93 (109)
T 2dis_A           86 VDWAEPEI   93 (109)
T ss_dssp             EEESCSSC
T ss_pred             EEEcCCCC
Confidence            99998643

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.71  E-value=2.4e-17  Score=128.96  Aligned_cols=80  Identities=23%  Similarity=0.299  Sum_probs=74.3

Q ss_pred             CCCcEEEecCCCCCC------CHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCe-
Q psy15676        187 PPENVLFVCKLNPVT------SDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDR-  259 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~------te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr-  259 (309)
                      ...++|||+|||+.+      |+++|+.+|++||.|.++.++  +.+|.++|||||+|.+.++|.+|+..|||..++|+ 
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  46899999999999999999999999999999998 


Q ss_pred             eEEEEeecC
Q psy15676        260 RIHARGEEW  268 (309)
Q Consensus       260 ~I~V~~a~~  268 (309)
                      .|.|.+|..
T Consensus        91 ~l~V~~a~~   99 (105)
T 2nlw_A           91 TFRVNLFTD   99 (105)
T ss_dssp             EEEEECSCC
T ss_pred             eEEEEEcch
Confidence            999999864

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.71  E-value=2.7e-17  Score=133.60  Aligned_cols=82  Identities=16%  Similarity=0.201  Sum_probs=74.3

Q ss_pred             CCCCcEEEecCCCCCCCHHHHH----HHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLE----IIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI  261 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~----~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I  261 (309)
                      .+|.++|||+|||+.+++++|+    .+|++||.|.+|.+..   +|.++|||||+|.+.++|..|+..|||..++|++|
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l  102 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL  102 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEE
Confidence            4567899999999999999876    6999999999987743   68899999999999999999999999999999999


Q ss_pred             EEEeecCch
Q psy15676        262 HARGEEWNM  270 (309)
Q Consensus       262 ~V~~a~~~~  270 (309)
                      .|++|+.+.
T Consensus       103 ~V~~a~~~~  111 (127)
T 2a3j_A          103 VITFSETPQ  111 (127)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEccCcc
Confidence            999998643

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.71  E-value=3.3e-17  Score=131.48  Aligned_cols=79  Identities=28%  Similarity=0.463  Sum_probs=76.3

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecCc
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWN  269 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~~  269 (309)
                      ++|||+|||+++++++|+.+|++||.|.++.++.++.+|.++|||||+|.+.++|.+|+ .|||..++|+.|.|.++++.
T Consensus        37 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~~  115 (124)
T 2jwn_A           37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRTN  115 (124)
T ss_dssp             TEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCCC
Confidence            79999999999999999999999999999999999999999999999999999999999 79999999999999999864

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=3.9e-17  Score=128.64  Aligned_cols=82  Identities=24%  Similarity=0.406  Sum_probs=76.3

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+++++++|+.+|++||.|..+.++.+.  +.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
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            4567899999999999999999999999999999999885  45899999999999999999999999999999999999


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      |+++
T Consensus       104 a~~~  107 (109)
T 2err_A          104 ATAR  107 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            9764

>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=3.5e-17  Score=129.89  Aligned_cols=81  Identities=23%  Similarity=0.362  Sum_probs=77.3

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      .++|||+|||+.+++++|+.+|++||.|..+.++.++.||.++|||||+|.+.++|.+|+.. +|..|+|+.|.|.++.+
T Consensus        27 ~~~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           27 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAVA  105 (116)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECCC
Confidence            37999999999999999999999999999999999999999999999999999999999987 99999999999999987


Q ss_pred             ch
Q psy15676        269 NM  270 (309)
Q Consensus       269 ~~  270 (309)
                      +.
T Consensus       106 ~~  107 (116)
T 1x4b_A          106 RE  107 (116)
T ss_dssp             CC
T ss_pred             Cc
Confidence            54

>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=99.70  E-value=9.9e-17  Score=125.88  Aligned_cols=82  Identities=23%  Similarity=0.391  Sum_probs=75.3

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+++++++|+.+|++||.|..+.+..   ++.++|||||+|.+.++|.+|+..|||..|+|+.|.|++
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE---CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            45678999999999999999999999999999999865   456899999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      +++..
T Consensus        96 a~~~~  100 (109)
T 1x4a_A           96 PRSGR  100 (109)
T ss_dssp             CCCCC
T ss_pred             cccCC
Confidence            98754

>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=99.70  E-value=2e-17  Score=130.69  Aligned_cols=84  Identities=20%  Similarity=0.296  Sum_probs=77.3

Q ss_pred             CCCcEEEecCCCCCCCHHHHH---HHHhcCCceeEEEEeeeCCCC---CcccEEEEEecCHHHHHHHHHHcCCceeCCee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLE---IIFSRFGKVNCCEVIRDKVTG---DSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRR  260 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~---~~F~~fG~I~~v~i~~d~~tg---~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~  260 (309)
                      .+.++|||+|||+++++++|.   .+|++||.|..+.++.+..++   .++|||||+|.+.++|.+|+..|||..++|+.
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~   92 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   92 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEE
Confidence            346899999999999999999   999999999999999888754   45699999999999999999999999999999


Q ss_pred             EEEEeecCch
Q psy15676        261 IHARGEEWNM  270 (309)
Q Consensus       261 I~V~~a~~~~  270 (309)
                      |.|.+|.++.
T Consensus        93 l~V~~a~~k~  102 (111)
T 2cpi_A           93 LKASLGTTKY  102 (111)
T ss_dssp             EEEESCCCCS
T ss_pred             EEEEeccccc
Confidence            9999998765

>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=5.2e-17  Score=126.81  Aligned_cols=83  Identities=22%  Similarity=0.187  Sum_probs=76.5

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeE-EEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNC-CEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~-v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      ..+.++|||+|||+++|+++|+.+|++||.|.. +.|+.+ .+|+++|||||+|.+.++|.+|+.. ++..++|+.|.|.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~   89 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIF   89 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEE
Confidence            456789999999999999999999999999987 888888 6899999999999999999999987 9999999999999


Q ss_pred             eecCch
Q psy15676        265 GEEWNM  270 (309)
Q Consensus       265 ~a~~~~  270 (309)
                      .+....
T Consensus        90 ~~~~~~   95 (104)
T 1wg5_A           90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            987543

>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=99.70  E-value=1.8e-17  Score=133.40  Aligned_cols=82  Identities=16%  Similarity=0.148  Sum_probs=76.0

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      .+.++|||+|||+++|+++|..+|+.||.|..+.++.+..+|.++|||||+|.+.++|.+|+. |||..|+|+.|.|.+|
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            456899999999999999999999999999887777777899999999999999999999999 9999999999999999


Q ss_pred             cCc
Q psy15676        267 EWN  269 (309)
Q Consensus       267 ~~~  269 (309)
                      ..+
T Consensus       102 ~~~  104 (124)
T 1wel_A          102 TKK  104 (124)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            653

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=9.4e-17  Score=124.22  Aligned_cols=81  Identities=20%  Similarity=0.298  Sum_probs=74.2

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+.+++++|+.+|++||.|   .++.+ .+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
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            4567999999999999999999999999987   56666 5899999999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      ++++.
T Consensus        88 a~~~~   92 (101)
T 2fc9_A           88 QGPRG   92 (101)
T ss_dssp             CSSCC
T ss_pred             cCCCC
Confidence            98753

>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=99.69  E-value=1.5e-17  Score=131.64  Aligned_cols=87  Identities=20%  Similarity=0.250  Sum_probs=75.1

Q ss_pred             CCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       185 ~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      ..++.++|||+|||+.+|+++|..+|++||.|..+.+..+..+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~  100 (115)
T 2cpx_A           21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE  100 (115)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34577999999999999999999999999999443332233378999999999999999999999999999999999999


Q ss_pred             eecCchh
Q psy15676        265 GEEWNMW  271 (309)
Q Consensus       265 ~a~~~~~  271 (309)
                      +|.++..
T Consensus       101 ~a~~~~~  107 (115)
T 2cpx_A          101 FGKNKKQ  107 (115)
T ss_dssp             ECCCCSC
T ss_pred             EccCCCC
Confidence            9987543

>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=99.69  E-value=8.8e-17  Score=127.08  Aligned_cols=82  Identities=18%  Similarity=0.359  Sum_probs=76.8

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCcee--------CC
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLI--------DD  258 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i--------~g  258 (309)
                      .+.++|||+|||+++++++|+.+|++||.|..+.++.++ +|.++|||||+|.+.++|.+|+..|||..+        .|
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            456899999999999999999999999999999999998 899999999999999999999999999999        57


Q ss_pred             eeEEEEeecCc
Q psy15676        259 RRIHARGEEWN  269 (309)
Q Consensus       259 r~I~V~~a~~~  269 (309)
                      ++|.|.||.+.
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            88999999753

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.69  E-value=1.8e-17  Score=123.29  Aligned_cols=74  Identities=24%  Similarity=0.402  Sum_probs=68.4

Q ss_pred             CcEEEecCCCCCC------CHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCe-eE
Q psy15676        189 ENVLFVCKLNPVT------SDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDR-RI  261 (309)
Q Consensus       189 ~~~lfV~nL~~~~------te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr-~I  261 (309)
                      +++|||+|||+.+      ++++|+.+|++||.|.++.++  +.+|.++|||||+|.+.++|.+|+..|||..++|+ +|
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            3689999999999      779999999999999999987  46899999999999999999999999999999999 88


Q ss_pred             EEE
Q psy15676        262 HAR  264 (309)
Q Consensus       262 ~V~  264 (309)
                      +|+
T Consensus        79 ~V~   81 (81)
T 2krb_A           79 RVN   81 (81)
T ss_dssp             CCC
T ss_pred             EeC
Confidence            763

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.69  E-value=9.2e-17  Score=121.47  Aligned_cols=75  Identities=12%  Similarity=0.192  Sum_probs=70.3

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ....-|||+||++.+|+++|+.+|.+||+|.++.+..      ++|||||+|.+.++|.+|++.|||..++|+.|.|++|
T Consensus         5 ~~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            5 WGSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            3467899999999999999999999999999999854      6899999999999999999999999999999999999


Q ss_pred             c
Q psy15676        267 E  267 (309)
Q Consensus       267 ~  267 (309)
                      .
T Consensus        79 ~   79 (89)
T 2wbr_A           79 S   79 (89)
T ss_dssp             C
T ss_pred             C
Confidence            4

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.69  E-value=1e-16  Score=140.51  Aligned_cols=85  Identities=28%  Similarity=0.389  Sum_probs=78.2

Q ss_pred             CCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       185 ~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      +..|.++|||+|||+++|+++|+.+|++||.|.+|.|++|+.||.++|||||+|.+.++|.+|+..++|..+.|+.|.+.
T Consensus        11 p~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~   90 (213)
T 4f02_A           11 PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIM   90 (213)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccc
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCc
Q psy15676        265 GEEWN  269 (309)
Q Consensus       265 ~a~~~  269 (309)
                      ++...
T Consensus        91 ~~~~~   95 (213)
T 4f02_A           91 WSQRD   95 (213)
T ss_dssp             ECCCC
T ss_pred             ccccc
Confidence            98753

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.69  E-value=7.8e-18  Score=130.36  Aligned_cols=83  Identities=20%  Similarity=0.279  Sum_probs=76.3

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+++++++|+.+|++||.|.. .++.+..+|.++|||||+|.+.++|.+|+. |||..++|+.|.|.+
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~   91 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   91 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEE
Confidence            346789999999999999999999999999987 677777789999999999999999999998 999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      |+++.
T Consensus        92 a~~~~   96 (101)
T 1fj7_A           92 PKGRD   96 (101)
T ss_dssp             CSCCC
T ss_pred             cCCCC
Confidence            98643

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.69  E-value=1.4e-17  Score=121.63  Aligned_cols=75  Identities=19%  Similarity=0.318  Sum_probs=71.7

Q ss_pred             EEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       191 ~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      +|||+|||+++++++|+.+|++||.|.++.++.++.+|.++|||||+|.+.++|.+|+. ++|..++|+.|.|.+|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~-~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHT-TSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHH-hCCCeECCEEEEEEEC
Confidence            58999999999999999999999999999999999999999999999999999999997 4999999999999875

>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=99.69  E-value=1.6e-16  Score=123.96  Aligned_cols=79  Identities=16%  Similarity=0.192  Sum_probs=71.8

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHc--CCceeCCeeEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM--DNVLIDDRRIHA  263 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l--~g~~i~gr~I~V  263 (309)
                      .+|.++|||+|||+.+++++|+.+|++||.|.++.++.+      +|||||+|.+.++|.+|+..|  ++..++|++|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   85 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   85 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEE
Confidence            567899999999999999999999999999999988753      699999999999999999976  568899999999


Q ss_pred             EeecCch
Q psy15676        264 RGEEWNM  270 (309)
Q Consensus       264 ~~a~~~~  270 (309)
                      ++|+++.
T Consensus        86 ~~a~~~~   92 (101)
T 2cq1_A           86 QYSNHKE   92 (101)
T ss_dssp             EECSCSS
T ss_pred             EEcCccc
Confidence            9998654

>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=99.69  E-value=4e-17  Score=125.18  Aligned_cols=82  Identities=26%  Similarity=0.362  Sum_probs=75.3

Q ss_pred             CCCCcEEEecCCCCCCCHHHHH----HHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLE----IIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI  261 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~----~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I  261 (309)
                      .++.++|||+|||+++++++|+    .+|++||.|..+.+..   +|.++|||||+|.+.++|.+|+..|||..++|+.|
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            4578999999999999999999    9999999999998863   57889999999999999999999999999999999


Q ss_pred             EEEeecCch
Q psy15676        262 HARGEEWNM  270 (309)
Q Consensus       262 ~V~~a~~~~  270 (309)
                      .|.+++++.
T Consensus        82 ~v~~a~~~~   90 (97)
T 1nu4_A           82 RIQYAKTDS   90 (97)
T ss_dssp             EEEECSSCC
T ss_pred             EEEEccCCC
Confidence            999998643

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.69  E-value=7.9e-17  Score=128.82  Aligned_cols=80  Identities=20%  Similarity=0.128  Sum_probs=75.4

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCc---eeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEE
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGK---VNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA  263 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~---I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V  263 (309)
                      ...++|||+|||+++|+++|+.+|+.||.   |..+.++.++. |+++|||||+|.+.++|.+|+. +||..|+|+.|.|
T Consensus        15 ~~~~~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           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV   92 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEE
Confidence            45689999999999999999999999999   89999999986 9999999999999999999998 9999999999999


Q ss_pred             EeecC
Q psy15676        264 RGEEW  268 (309)
Q Consensus       264 ~~a~~  268 (309)
                      .+|..
T Consensus        93 ~~a~~   97 (118)
T 2db1_A           93 FKSHR   97 (118)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            99864

>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=99.69  E-value=8.3e-17  Score=129.13  Aligned_cols=81  Identities=16%  Similarity=0.215  Sum_probs=73.4

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCC--ceeCCeeEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDN--VLIDDRRIHA  263 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g--~~i~gr~I~V  263 (309)
                      .+|.++|||+|||+++++++|+.+|++||.|.++.++.+      +|||||+|.+.++|.+|+..|++  ..++|++|.|
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            567899999999999999999999999999999999864      69999999999999999998874  6899999999


Q ss_pred             EeecCchhh
Q psy15676        264 RGEEWNMWK  272 (309)
Q Consensus       264 ~~a~~~~~~  272 (309)
                      ++|+++..+
T Consensus       102 ~~a~~k~~~  110 (119)
T 2ad9_A          102 QFSNHKELK  110 (119)
T ss_dssp             EECSSSSCC
T ss_pred             EEccCCCCC
Confidence            999875443

>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=99.68  E-value=1.8e-16  Score=118.47  Aligned_cols=76  Identities=24%  Similarity=0.429  Sum_probs=70.8

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHc-CCceeCCeeEEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM-DNVLIDDRRIHAR  264 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l-~g~~i~gr~I~V~  264 (309)
                      .++.++|||+|||+.+++++|+.+|++||.|..+.++.      ++|||||+|.+.++|.+|+..| +|..++|++|.|+
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~------~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~   82 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ------RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK   82 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC------CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEE
Confidence            45678999999999999999999999999999999975      4699999999999999999988 9999999999999


Q ss_pred             eec
Q psy15676        265 GEE  267 (309)
Q Consensus       265 ~a~  267 (309)
                      +|+
T Consensus        83 ~ak   85 (85)
T 2ytc_A           83 WGR   85 (85)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            984

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.68  E-value=7.6e-17  Score=127.89  Aligned_cols=81  Identities=14%  Similarity=0.061  Sum_probs=72.4

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCC-ceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFG-KVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG-~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      .+...+|||+|||+++++++|+.+|++|| .|..+.+..    +.++|||||+|.+.++|++|+..|||..++|+.|.|.
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~  100 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVE  100 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34568999999999999999999999999 899988853    3588999999999999999999999999999999999


Q ss_pred             eecCch
Q psy15676        265 GEEWNM  270 (309)
Q Consensus       265 ~a~~~~  270 (309)
                      ++....
T Consensus       101 ~a~~~p  106 (111)
T 2jvr_A          101 RDDNPP  106 (111)
T ss_dssp             ESCC--
T ss_pred             ECCCCC
Confidence            997654

>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=99.68  E-value=8.2e-17  Score=125.52  Aligned_cols=81  Identities=15%  Similarity=0.123  Sum_probs=74.6

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+..+|||+|||+++|+++|+.+|++||.+ .+.|+.++ +|+++|||||+|.+.++|++|+. +|+..++|+.|.|..
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~   88 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            4566899999999999999999999999954 99999998 89999999999999999999994 799999999999999


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      +...
T Consensus        89 ~~~~   92 (102)
T 1wez_A           89 NSTA   92 (102)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            8754

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=1.6e-16  Score=122.98  Aligned_cols=83  Identities=23%  Similarity=0.326  Sum_probs=76.1

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++.++|||+|||+++++++|+.+|+.|+   .+.++.++.++.++|||||+|.+.++|.+|+..|||..|+|+.|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDW   88 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            45678999999999999999999999874   677888888999999999999999999999999999999999999999


Q ss_pred             ecCchh
Q psy15676        266 EEWNMW  271 (309)
Q Consensus       266 a~~~~~  271 (309)
                      |+++..
T Consensus        89 a~~~~~   94 (102)
T 2fc8_A           89 AKPKGE   94 (102)
T ss_dssp             CCCCCS
T ss_pred             ecCCCC
Confidence            987543

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.68  E-value=2.1e-17  Score=135.34  Aligned_cols=84  Identities=30%  Similarity=0.449  Sum_probs=79.4

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ++.++|||+|||+++|+++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.++
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            34579999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             cCch
Q psy15676        267 EWNM  270 (309)
Q Consensus       267 ~~~~  270 (309)
                      ++..
T Consensus       125 ~~~~  128 (135)
T 2lea_A          125 RYGR  128 (135)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8643

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.68  E-value=2.5e-16  Score=127.05  Aligned_cols=81  Identities=11%  Similarity=0.173  Sum_probs=73.0

Q ss_pred             cEEEecCC----CCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecC----HHH----HHHHHH--HcCCce
Q psy15676        190 NVLFVCKL----NPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN----PKS----CEDAYL--KMDNVL  255 (309)
Q Consensus       190 ~~lfV~nL----~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~----~~~----a~~Al~--~l~g~~  255 (309)
                      ..|||+||    |+.+++.+|+.+|++||.|.++.++.|+.||.++|||||+|.+    ..+    |.+|+.  .++|..
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  789999


Q ss_pred             eCCeeEEEEeecCch
Q psy15676        256 IDDRRIHARGEEWNM  270 (309)
Q Consensus       256 i~gr~I~V~~a~~~~  270 (309)
                      |+|+.|+|.+.....
T Consensus        83 I~Gr~irV~ln~~g~   97 (136)
T 2j8a_A           83 IMGFKFEVILNKHSI   97 (136)
T ss_dssp             ETTEEEEEEECCTTH
T ss_pred             ecCcEEEEEECcccH
Confidence            999999999886533

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.68  E-value=5.4e-17  Score=144.52  Aligned_cols=82  Identities=15%  Similarity=0.177  Sum_probs=77.4

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCC--ceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFG--KVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG--~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..++|||+||++++|+++|+.+|++||  .|.+|.|+.|+.||+++|||||+|.+.++|.+|+..|||..|+|+.|.|.+
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            457899999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      |++.
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            9754

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.68  E-value=1.7e-16  Score=124.89  Aligned_cols=77  Identities=19%  Similarity=0.325  Sum_probs=72.1

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+++++++|+.+|++||.|..+.++        +|||||+|.+.++|.+|+..|||..++|+.|.|.+
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            4567899999999999999999999999999999987        68999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      +++..
T Consensus       100 a~~~~  104 (108)
T 2jvo_A          100 SKLPA  104 (108)
T ss_dssp             CSCCC
T ss_pred             ecCCC
Confidence            98754

>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=99.68  E-value=2.6e-16  Score=121.35  Aligned_cols=76  Identities=25%  Similarity=0.356  Sum_probs=71.2

Q ss_pred             CCCCcEEEecCCCC-CCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        186 APPENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       186 ~~~~~~lfV~nL~~-~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      .++.++|||+|||+ ++++++|+.+|++||.|..+.+.        +|||||+|.+.++|.+|+..|||..++|+.|.|+
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            56789999999998 99999999999999999999882        6999999999999999999999999999999999


Q ss_pred             eecCc
Q psy15676        265 GEEWN  269 (309)
Q Consensus       265 ~a~~~  269 (309)
                      +++++
T Consensus        91 ~a~~~   95 (97)
T 2xnq_A           91 VSSSN   95 (97)
T ss_dssp             ECCCC
T ss_pred             ecCCC
Confidence            99764

>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=99.68  E-value=1.9e-16  Score=121.72  Aligned_cols=79  Identities=25%  Similarity=0.419  Sum_probs=73.0

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeC--CeeEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLID--DRRIHA  263 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~--gr~I~V  263 (309)
                      .++.++|||+|||+++++++|+.+|++||.|.++.+..+      +|||||+|.+.++|.+|+..|||..++  |+.|.|
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            466789999999999999999999999999999988643      689999999999999999999999999  999999


Q ss_pred             EeecCch
Q psy15676        264 RGEEWNM  270 (309)
Q Consensus       264 ~~a~~~~  270 (309)
                      ++|+++.
T Consensus        88 ~~a~~~~   94 (97)
T 1why_A           88 DFAKSGP   94 (97)
T ss_dssp             EECCCCC
T ss_pred             EECCCCC
Confidence            9998753

>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=99.68  E-value=1.4e-16  Score=124.85  Aligned_cols=80  Identities=19%  Similarity=0.196  Sum_probs=71.8

Q ss_pred             CCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCC--ceeCCeeEE
Q psy15676        185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDN--VLIDDRRIH  262 (309)
Q Consensus       185 ~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g--~~i~gr~I~  262 (309)
                      ..+|.++|||+|||+.+++++|+.+|++||.|.++.++.+      +|||||+|.+.++|.+|+..|++  ..++|++|.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~   84 (104)
T 1wex_A           11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            3567899999999999999999999999999999988753      69999999999999999998865  469999999


Q ss_pred             EEeecCch
Q psy15676        263 ARGEEWNM  270 (309)
Q Consensus       263 V~~a~~~~  270 (309)
                      |++|+.+.
T Consensus        85 V~~a~~~~   92 (104)
T 1wex_A           85 FNYSTSKR   92 (104)
T ss_dssp             EEECSSSS
T ss_pred             EEEccCcc
Confidence            99998644

>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=8.8e-17  Score=132.02  Aligned_cols=80  Identities=19%  Similarity=0.104  Sum_probs=75.5

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCc---eeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEE
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGK---VNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA  263 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~---I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V  263 (309)
                      ...++|||+|||+++|+++|+.+|++||.   |..+.++.++. |+++|||||+|.+.++|.+|+. +||..++|+.|.|
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  119 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEV  119 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEE
Confidence            45689999999999999999999999999   89999999987 9999999999999999999998 9999999999999


Q ss_pred             EeecC
Q psy15676        264 RGEEW  268 (309)
Q Consensus       264 ~~a~~  268 (309)
                      .+|..
T Consensus       120 ~~a~~  124 (136)
T 2hgl_A          120 FKSHR  124 (136)
T ss_dssp             EECCH
T ss_pred             EECCh
Confidence            99853

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=2.4e-16  Score=119.44  Aligned_cols=77  Identities=21%  Similarity=0.441  Sum_probs=72.0

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++.++|||+|||+++++++|+.+|++||.|..+.++        +|||||+|.+.++|.+|+..|||..++|+.|.|.+
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            4567899999999999999999999999999999986        58999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      ++++.
T Consensus        77 a~~~~   81 (90)
T 2dnq_A           77 SKNKS   81 (90)
T ss_dssp             SSCCC
T ss_pred             CCCCC
Confidence            98654

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=9.8e-17  Score=126.81  Aligned_cols=80  Identities=19%  Similarity=0.347  Sum_probs=74.2

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      ..+|||+|||+++|+++|+.+|+.| .|..+.|+.++. |+++|||||+|.+.++|.+|+ .+||..++|+.|.|..+..
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            4699999999999999999999999 899999999975 999999999999999999999 6899999999999998875


Q ss_pred             chh
Q psy15676        269 NMW  271 (309)
Q Consensus       269 ~~~  271 (309)
                      ..|
T Consensus        93 ~~~   95 (109)
T 2dnn_A           93 RQW   95 (109)
T ss_dssp             HHH
T ss_pred             cch
Confidence            544

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.49  E-value=3.9e-18  Score=135.57  Aligned_cols=85  Identities=21%  Similarity=0.226  Sum_probs=80.0

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeE--------EEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCC
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNC--------CEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDD  258 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~--------v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~g  258 (309)
                      ++.++|||+|||+.+++++|+.+|++||.|..        +.++.++.+|.++|||||+|.+.++|.+|+..|||..++|
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        8999998899999999999999999999999999999999


Q ss_pred             eeEEEEeecCchh
Q psy15676        259 RRIHARGEEWNMW  271 (309)
Q Consensus       259 r~I~V~~a~~~~~  271 (309)
                      +.|.|.+|+++..
T Consensus        85 ~~l~V~~a~~~~~   97 (116)
T 2lcw_A           85 NPIKVSFATRRAD   97 (116)
Confidence            9999999987543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=2.2e-16  Score=121.45  Aligned_cols=79  Identities=14%  Similarity=0.206  Sum_probs=71.8

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .+..++|||+|||+.+++++|+.+|++||.|. +.++.    +.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
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-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVAL   90 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            44578999999999999999999999999996 66664    46789999999999999999999999999999999999


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      |+++
T Consensus        91 a~~~   94 (97)
T 2e5j_A           91 ARQQ   94 (97)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9764

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.67  E-value=1.8e-16  Score=122.67  Aligned_cols=76  Identities=13%  Similarity=0.258  Sum_probs=71.0

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      +..++|||+|||+++++++|+.+|++||.|.++.+.      .++|||||+|.+.++|.+|+..|||..++|+.|+|.+|
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            356899999999999999999999999999999986      46799999999999999999999999999999999998


Q ss_pred             cC
Q psy15676        267 EW  268 (309)
Q Consensus       267 ~~  268 (309)
                      ++
T Consensus        99 ~~  100 (101)
T 2la4_A           99 KE  100 (101)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.67  E-value=3.6e-16  Score=122.71  Aligned_cols=77  Identities=27%  Similarity=0.258  Sum_probs=72.0

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCC-----eeE
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDD-----RRI  261 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~g-----r~I  261 (309)
                      .+.++|||+|||+++++++|+.+|++||.|..+.++.+       |||||+|.+.++|.+|+..|||..++|     +.|
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            45689999999999999999999999999999999865       899999999999999999999999999     999


Q ss_pred             EEEeecCch
Q psy15676        262 HARGEEWNM  270 (309)
Q Consensus       262 ~V~~a~~~~  270 (309)
                      .|.+|++..
T Consensus        86 ~V~~a~~~~   94 (108)
T 1x4c_A           86 RVKVDGPRS   94 (108)
T ss_dssp             EEEESSCCS
T ss_pred             EEEeCCCCC
Confidence            999998743

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.67  E-value=9.2e-17  Score=124.49  Aligned_cols=80  Identities=21%  Similarity=0.375  Sum_probs=75.4

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      .+.++|||+|||+++++++|+.+|++||.|..+.++.++ +|.++|||||+|.+.++|.+|+.  +|..++|+.|.|.++
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a   83 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPA   83 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEEC
Confidence            346899999999999999999999999999999999998 99999999999999999999997  999999999999998


Q ss_pred             cCc
Q psy15676        267 EWN  269 (309)
Q Consensus       267 ~~~  269 (309)
                      .++
T Consensus        84 ~~~   86 (102)
T 2xs2_A           84 IRK   86 (102)
T ss_dssp             EEC
T ss_pred             CcC
Confidence            753

>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=99.67  E-value=1.3e-16  Score=124.67  Aligned_cols=78  Identities=12%  Similarity=0.182  Sum_probs=71.1

Q ss_pred             CCCCcEEEecCCCC-CCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCC--ceeCCeeEE
Q psy15676        186 APPENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDN--VLIDDRRIH  262 (309)
Q Consensus       186 ~~~~~~lfV~nL~~-~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g--~~i~gr~I~  262 (309)
                      .+|.++|||+|||+ .+|+++|+.+|++||.|.++.++.+      +|||||+|.+.++|..|+..|++  ..++|++|.
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   85 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   85 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEE
Confidence            45788999999999 9999999999999999999999764      48999999999999999998886  569999999


Q ss_pred             EEeecCc
Q psy15676        263 ARGEEWN  269 (309)
Q Consensus       263 V~~a~~~  269 (309)
                      |++|+..
T Consensus        86 V~~a~~~   92 (102)
T 1x4d_A           86 VHLSQKY   92 (102)
T ss_dssp             EEEECCC
T ss_pred             EEECCCC
Confidence            9999853

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.67  E-value=2.7e-16  Score=134.63  Aligned_cols=84  Identities=25%  Similarity=0.327  Sum_probs=79.6

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++.++|||+|||+.+++++|..+|++||.|..|.++.+. +|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~  163 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4567899999999999999999999999999999999998 899999999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      |....
T Consensus       164 a~~~~  168 (177)
T 2f3j_A          164 VASQI  168 (177)
T ss_dssp             ESSGG
T ss_pred             ecCCC
Confidence            98644

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.66  E-value=5.4e-16  Score=128.75  Aligned_cols=82  Identities=26%  Similarity=0.324  Sum_probs=78.7

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++..+|||+|||+.+++++|..+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|++
T Consensus        84 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  163 (166)
T 3md3_A           84 SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW  163 (166)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ec
Q psy15676        266 EE  267 (309)
Q Consensus       266 a~  267 (309)
                      |+
T Consensus       164 a~  165 (166)
T 3md3_A          164 AA  165 (166)
T ss_dssp             SC
T ss_pred             cC
Confidence            85

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.66  E-value=1.2e-16  Score=122.28  Aligned_cols=80  Identities=18%  Similarity=0.211  Sum_probs=72.7

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+.+++++|+.+|++||.|..+     ..+|.++|||||+|.+.++|.+|+..|+|..++|+.|.|.+
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            4467899999999999999999999999988766     34789999999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      |.++.
T Consensus        88 a~~~~   92 (96)
T 1fjc_A           88 TGEKG   92 (96)
T ss_dssp             CSSSC
T ss_pred             cCCCC
Confidence            97643

>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=99.66  E-value=5.5e-17  Score=127.30  Aligned_cols=81  Identities=12%  Similarity=0.092  Sum_probs=76.0

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCc---eeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGK---VNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH  262 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~---I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~  262 (309)
                      ....++|||+|||+++|+++|+.+|+.||.   |..+.++.++. |+++|||||+|.+.++|.+|+. ++|..++|+.|.
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            456789999999999999999999999998   89999999987 9999999999999999999998 999999999999


Q ss_pred             EEeecC
Q psy15676        263 ARGEEW  268 (309)
Q Consensus       263 V~~a~~  268 (309)
                      |.+|..
T Consensus        86 V~~a~~   91 (107)
T 2lmi_A           86 VYEINN   91 (107)
T ss_dssp             CEECCH
T ss_pred             EEECCH
Confidence            999864

>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=99.66  E-value=2.7e-16  Score=121.28  Aligned_cols=79  Identities=18%  Similarity=0.382  Sum_probs=73.0

Q ss_pred             CCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       185 ~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      ..++.++|||+|||+.+++++|+.+|++||.|..+.+..      ++|||||+|.+.++|.+|+..|+|..++|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~------~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~   84 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK------DKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVR   84 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEET------TTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEE
Confidence            356678999999999999999999999999999999874      36899999999999999999999999999999999


Q ss_pred             eecCc
Q psy15676        265 GEEWN  269 (309)
Q Consensus       265 ~a~~~  269 (309)
                      +++++
T Consensus        85 ~a~~~   89 (99)
T 2cpj_A           85 FACHS   89 (99)
T ss_dssp             ESSCC
T ss_pred             EcCCC
Confidence            99864

>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=99.66  E-value=1.3e-16  Score=126.09  Aligned_cols=81  Identities=17%  Similarity=0.207  Sum_probs=73.9

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      +.++|||+|||+.+++++|+.+|++||.|..+.++.      ++|||||+|.+.++|.+|+..|||..++|+.|.|++|.
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            457999999999999999999999999999998863      56899999999999999999999999999999999998


Q ss_pred             Cchhhcc
Q psy15676        268 WNMWKRR  274 (309)
Q Consensus       268 ~~~~~~r  274 (309)
                      ...+...
T Consensus        83 ~~~~~~~   89 (111)
T 1whx_A           83 IGVFGAA   89 (111)
T ss_dssp             TTTTCCC
T ss_pred             CCccCCC
Confidence            7665543

>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=99.66  E-value=3.1e-16  Score=123.14  Aligned_cols=78  Identities=18%  Similarity=0.307  Sum_probs=72.9

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ++.++|||+|||+.+++++|+.+|++||.|..+.++.+      +|||||+|.+.++|.+|+..|+|..++|+.|.|.++
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            45689999999999999999999999999999999865      689999999999999999999999999999999999


Q ss_pred             cCch
Q psy15676        267 EWNM  270 (309)
Q Consensus       267 ~~~~  270 (309)
                      +++.
T Consensus        97 ~~~~  100 (109)
T 1x4g_A           97 KESP  100 (109)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8754

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.66  E-value=5.8e-16  Score=128.69  Aligned_cols=82  Identities=26%  Similarity=0.530  Sum_probs=78.4

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      +.++|||+|||+++++++|..+|+.||.|.++.++.++.+|.++|||||+|.+.++|.+|+..|+|..++|+.|.|.++.
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            35899999999999999999999999999999999999899999999999999999999999999999999999999997


Q ss_pred             Cc
Q psy15676        268 WN  269 (309)
Q Consensus       268 ~~  269 (309)
                      +.
T Consensus        81 ~~   82 (167)
T 1fxl_A           81 PS   82 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=9.2e-16  Score=118.25  Aligned_cols=80  Identities=25%  Similarity=0.345  Sum_probs=72.4

Q ss_pred             CCCCCCCcEEEecCCCCCCCHHHHHHHHhcC--CceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCee
Q psy15676        183 ADAAPPENVLFVCKLNPVTSDDDLEIIFSRF--GKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRR  260 (309)
Q Consensus       183 ~~~~~~~~~lfV~nL~~~~te~~L~~~F~~f--G~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~  260 (309)
                      .+..++.++|||+|||+.+++++|+.+|++|  |.|..+.+.        +|||||+|.+.++|.+|+..|||..++|+.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (99)
T 2cpd_A            9 EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSP   80 (99)
T ss_dssp             CSCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEE
T ss_pred             ccccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            3445677899999999999999999999999  899888763        579999999999999999999999999999


Q ss_pred             EEEEeecCch
Q psy15676        261 IHARGEEWNM  270 (309)
Q Consensus       261 I~V~~a~~~~  270 (309)
                      |.|.+|+++.
T Consensus        81 l~v~~a~~~~   90 (99)
T 2cpd_A           81 IEVTLAKPVD   90 (99)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEECCCCC
Confidence            9999998754

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.65  E-value=4.8e-16  Score=129.66  Aligned_cols=82  Identities=26%  Similarity=0.446  Sum_probs=78.7

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      +.++|||+|||+++++++|..+|++||.|.++.++.++.+|.++|||||+|.+.++|.+|+..|+|..++|+.|.|.++.
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            56899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             Cc
Q psy15676        268 WN  269 (309)
Q Consensus       268 ~~  269 (309)
                      +.
T Consensus        82 ~~   83 (168)
T 1b7f_A           82 PG   83 (168)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.65  E-value=2.5e-16  Score=120.94  Aligned_cols=77  Identities=27%  Similarity=0.412  Sum_probs=70.6

Q ss_pred             CCCCcEEEecCCCC-CCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        186 APPENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       186 ~~~~~~lfV~nL~~-~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      .++.++|||+|||+ .+++++|+.+|++||.|..+.+.        +|||||+|.+.++|.+|+..|||..++|+.|.|.
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            46789999999999 99999999999999999999883        6899999999999999999999999999999999


Q ss_pred             eecCch
Q psy15676        265 GEEWNM  270 (309)
Q Consensus       265 ~a~~~~  270 (309)
                      +++++.
T Consensus        79 ~a~~~~   84 (96)
T 2kvi_A           79 VSSSNA   84 (96)
T ss_dssp             EEECCC
T ss_pred             EcCcCC
Confidence            998643

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=9.9e-16  Score=116.48  Aligned_cols=77  Identities=22%  Similarity=0.482  Sum_probs=71.3

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+.+++++|+.+|++||.|..+.++        ++||||+|.+.++|.+|+..|||..++|+.|.|++
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   78 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC--------SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            4567899999999999999999999999999999986        34999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      ++++.
T Consensus        79 a~~~~   83 (92)
T 2dgt_A           79 STSRL   83 (92)
T ss_dssp             SSCCC
T ss_pred             ccCCC
Confidence            98653

>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=8.3e-16  Score=119.44  Aligned_cols=77  Identities=26%  Similarity=0.361  Sum_probs=71.2

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+++|+++|+.+|++||.|..+.++        +|||||+|.+.++|.+|+..|||..++|+.|.|.+
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            3567899999999999999999999999999999885        46999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      +.+..
T Consensus        80 a~~~~   84 (103)
T 2dgu_A           80 AKPPD   84 (103)
T ss_dssp             CCCCC
T ss_pred             cCCCc
Confidence            98644

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.64  E-value=1.8e-16  Score=122.67  Aligned_cols=76  Identities=26%  Similarity=0.409  Sum_probs=71.6

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecCc
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWN  269 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~~  269 (309)
                      ++|||+|||+++|+++|+.+|++||.|.++.++.+     ++|||||+|.+.++|.+|+..|+|..++|+.|.|.++++.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            48999999999999999999999999999999876     7899999999999999999999999999999999999864


Q ss_pred             h
Q psy15676        270 M  270 (309)
Q Consensus       270 ~  270 (309)
                      .
T Consensus        76 ~   76 (101)
T 2hvz_A           76 P   76 (101)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.64  E-value=3.3e-16  Score=119.26  Aligned_cols=79  Identities=18%  Similarity=0.259  Sum_probs=70.3

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCc-eeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCC-ceeCCeeEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGK-VNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDN-VLIDDRRIHA  263 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~-I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g-~~i~gr~I~V  263 (309)
                      .++.++|||+|||+++++++|+.+|++||. |..+.+.       ++|||||+|.+.++|.+|+..||| ..++|+.|.|
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v   77 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEV   77 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEE
Confidence            456789999999999999999999999999 6555552       579999999999999999999999 9999999999


Q ss_pred             EeecCchh
Q psy15676        264 RGEEWNMW  271 (309)
Q Consensus       264 ~~a~~~~~  271 (309)
                      .+|+++..
T Consensus        78 ~~a~~~~~   85 (93)
T 2cqh_A           78 DYSVSKKL   85 (93)
T ss_dssp             EECCCCCC
T ss_pred             EEccCccc
Confidence            99987543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=7.3e-16  Score=116.73  Aligned_cols=77  Identities=21%  Similarity=0.401  Sum_probs=71.4

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++.++|||+|||+.+++++|+.+|++||.|..+.++        ++||||+|.+.++|.+|+..|||..++|+.|.|.+
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 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            4567899999999999999999999999999999986        34999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      +++..
T Consensus        78 a~~~~   82 (90)
T 2dnp_A           78 STKGQ   82 (90)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            98753

>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=99.64  E-value=7.9e-16  Score=121.00  Aligned_cols=75  Identities=25%  Similarity=0.475  Sum_probs=70.3

Q ss_pred             CCCCcEEEecCCCCC-CCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        186 APPENVLFVCKLNPV-TSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~-~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      .++.++|||+|||+. +++++|+.+|++||.|..+.+        ++|||||+|.+.++|.+|+..|+|..++|+.|.|.
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   95 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDIN   95 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            445689999999999 999999999999999999988        57999999999999999999999999999999999


Q ss_pred             eecC
Q psy15676        265 GEEW  268 (309)
Q Consensus       265 ~a~~  268 (309)
                      +++.
T Consensus        96 ~a~~   99 (110)
T 1wf1_A           96 MAGE   99 (110)
T ss_dssp             ESCC
T ss_pred             ECCC
Confidence            9975

>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=99.64  E-value=1.2e-15  Score=127.96  Aligned_cols=81  Identities=22%  Similarity=0.461  Sum_probs=77.4

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ++..+|||+|||+.+++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|++|.|++|
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            34689999999999999999999999999999999999889999999999999999999999999999999999999987


Q ss_pred             c
Q psy15676        267 E  267 (309)
Q Consensus       267 ~  267 (309)
                      .
T Consensus       172 s  172 (172)
T 2g4b_A          172 S  172 (172)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.63  E-value=4.6e-16  Score=129.03  Aligned_cols=79  Identities=24%  Similarity=0.416  Sum_probs=73.8

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+++++++|+.+|++||.|.++.++.+     ++|||||+|.+.++|.+|+..|||..++|++|+|.+
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  144 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVEL  144 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            456789999999999999999999999999999999875     579999999999999999999999999999999999


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      |+++
T Consensus       145 a~~~  148 (150)
T 2i2y_A          145 SNGE  148 (150)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9764

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=2.2e-15  Score=115.73  Aligned_cols=80  Identities=18%  Similarity=0.207  Sum_probs=71.9

Q ss_pred             CCCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEE
Q psy15676        184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA  263 (309)
Q Consensus       184 ~~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V  263 (309)
                      ....+.++|||+||  ++++++|+.+|++||.|..+.+.      .++|||||+|.+.++|.+|+..|||..++|+.|.|
T Consensus        10 ~~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v   81 (97)
T 1x5p_A           10 RAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKV   81 (97)
T ss_dssp             CCCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            33456789999996  89999999999999999999883      56799999999999999999999999999999999


Q ss_pred             EeecCchh
Q psy15676        264 RGEEWNMW  271 (309)
Q Consensus       264 ~~a~~~~~  271 (309)
                      .+|+++..
T Consensus        82 ~~a~~~~~   89 (97)
T 1x5p_A           82 NIARKQPM   89 (97)
T ss_dssp             ECCSSCCC
T ss_pred             EECCCCCC
Confidence            99987543

>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=99.63  E-value=4.3e-16  Score=123.65  Aligned_cols=78  Identities=15%  Similarity=0.169  Sum_probs=70.4

Q ss_pred             CCCCcEEEecCCCCC-CCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcC--CceeCCeeEE
Q psy15676        186 APPENVLFVCKLNPV-TSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMD--NVLIDDRRIH  262 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~-~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~--g~~i~gr~I~  262 (309)
                      .+|.++|||+|||++ +++++|+.+|++||.|.++.+++      ++|||||+|.+.++|..|+..|+  +..++|++|.
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            456789999999998 99999999999999999999863      47999999999999999999886  4679999999


Q ss_pred             EEeecCc
Q psy15676        263 ARGEEWN  269 (309)
Q Consensus       263 V~~a~~~  269 (309)
                      |++|+..
T Consensus        96 V~~a~~~  102 (112)
T 1x4f_A           96 VDLSEKY  102 (112)
T ss_dssp             EEEECSC
T ss_pred             EEECccc
Confidence            9999764

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=3e-16  Score=126.69  Aligned_cols=80  Identities=15%  Similarity=0.151  Sum_probs=73.2

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCce----eEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEE
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKV----NCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH  262 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I----~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~  262 (309)
                      .+..+|||+|||+++|+++|+.+|++||.|    ..|.|+.+. +|+++|||||+|.+.++|.+|+.. |+..++|+.|.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            356899999999999999999999999875    689999985 899999999999999999999986 99999999999


Q ss_pred             EEeecC
Q psy15676        263 ARGEEW  268 (309)
Q Consensus       263 V~~a~~  268 (309)
                      |..+..
T Consensus        99 V~~a~~  104 (123)
T 2dha_A           99 LFRSTA  104 (123)
T ss_dssp             CEEECH
T ss_pred             EEECCH
Confidence            998854

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=9.1e-16  Score=117.41  Aligned_cols=79  Identities=15%  Similarity=0.220  Sum_probs=72.1

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEE-EEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCC-EVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v-~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ...++|||+|||+.+++++|+.+|++||.|..+ .++.++.+|    .|||+|.+.++|.+|+..|||..++|+.|.|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   88 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVAY   88 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            456899999999999999999999999999999 588776554    399999999999999999999999999999999


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      |.++
T Consensus        89 a~~~   92 (96)
T 2e44_A           89 IPDE   92 (96)
T ss_dssp             CCCC
T ss_pred             cCcc
Confidence            9865

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.62  E-value=2.3e-15  Score=129.00  Aligned_cols=85  Identities=20%  Similarity=0.405  Sum_probs=80.4

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+.+++++|..+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
T Consensus       111 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  190 (198)
T 2yh0_A          111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR  190 (198)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            35678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      |.++.
T Consensus       191 a~~~~  195 (198)
T 2yh0_A          191 ASVGA  195 (198)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            98653

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.62  E-value=1.6e-15  Score=131.67  Aligned_cols=83  Identities=25%  Similarity=0.441  Sum_probs=79.6

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      +.++|||+|||+++++++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..|+|+.|.|.+|.
T Consensus       124 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~  203 (216)
T 2qfj_A          124 AFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV  203 (216)
T ss_dssp             TSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECS
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEec
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             Cch
Q psy15676        268 WNM  270 (309)
Q Consensus       268 ~~~  270 (309)
                      +..
T Consensus       204 ~~~  206 (216)
T 2qfj_A          204 TPP  206 (216)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            754

>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=99.62  E-value=1.3e-15  Score=115.71  Aligned_cols=76  Identities=18%  Similarity=0.302  Sum_probs=62.8

Q ss_pred             CCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCc--eeCCeeEE
Q psy15676        185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNV--LIDDRRIH  262 (309)
Q Consensus       185 ~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~--~i~gr~I~  262 (309)
                      ..++.++|||+|||+++|+++|+.+|++||.|.++.++.+     ++|||||+|.+.++|.+    ++|.  .+.|+.|.
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~   77 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVH   77 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEE
Confidence            3567899999999999999999999999999999999864     78999999999999883    4554  45699999


Q ss_pred             EEeecCc
Q psy15676        263 ARGEEWN  269 (309)
Q Consensus       263 V~~a~~~  269 (309)
                      |.+|.++
T Consensus        78 v~~a~~k   84 (89)
T 3d2w_A           78 ISNAEPK   84 (89)
T ss_dssp             EEECC--
T ss_pred             EEEcCCC
Confidence            9999764

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=1.7e-15  Score=115.73  Aligned_cols=77  Identities=22%  Similarity=0.278  Sum_probs=70.0

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      ..++|||+|||+++++++|+.+|++||.|.+|  +.++.+|.   ||||+|.+.++|.+|+. |||..++|+.|.|.++.
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~   80 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPRE   80 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECC
Confidence            45799999999999999999999999999987  66766665   99999999999999999 99999999999999887


Q ss_pred             Cch
Q psy15676        268 WNM  270 (309)
Q Consensus       268 ~~~  270 (309)
                      ...
T Consensus        81 ~~~   83 (94)
T 2e5g_A           81 QKE   83 (94)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            543

>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=99.62  E-value=7.3e-16  Score=122.61  Aligned_cols=82  Identities=16%  Similarity=0.238  Sum_probs=73.0

Q ss_pred             CCCCcEEEe--cCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCcee-----CC
Q psy15676        186 APPENVLFV--CKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLI-----DD  258 (309)
Q Consensus       186 ~~~~~~lfV--~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i-----~g  258 (309)
                      .+|..+|||  |||++++++++|+.+|++||.|.++.++.      ++|||||+|.+.++|++|+..|||..+     .|
T Consensus        22 ~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g   95 (114)
T 2cq2_A           22 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   95 (114)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCC
Confidence            456789999  77999999999999999999999988753      369999999999999999999999988     78


Q ss_pred             eeEEEEeecCchhhc
Q psy15676        259 RRIHARGEEWNMWKR  273 (309)
Q Consensus       259 r~I~V~~a~~~~~~~  273 (309)
                      ++|.|.|++.-.|..
T Consensus        96 ~~l~v~~a~~~p~~~  110 (114)
T 2cq2_A           96 ITLYLNFVEKVQWSG  110 (114)
T ss_dssp             EECEEEEESCCCCSS
T ss_pred             cEEEEEecccCcccC
Confidence            999999998766543

>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=99.61  E-value=8.4e-16  Score=124.53  Aligned_cols=80  Identities=18%  Similarity=0.157  Sum_probs=72.7

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCcee--EEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVN--CCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA  263 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~--~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V  263 (309)
                      ..+..+|||+|||+++|+++|+.+|++| .|.  .|.|+.|+. |+++|||||+|.+.++|.+|+. +++..|+|+.|.|
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~-~~~~~l~gR~I~V  115 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALG-KHKERIGHRYIEV  115 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHT-TTTCCBTTBCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHH-HCCCEECCEEEEE
Confidence            3456899999999999999999999999 566  899999986 9999999999999999999997 4889999999999


Q ss_pred             EeecC
Q psy15676        264 RGEEW  268 (309)
Q Consensus       264 ~~a~~  268 (309)
                      ..+..
T Consensus       116 ~~a~~  120 (126)
T 2hgm_A          116 FKSSQ  120 (126)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            98854

>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=99.61  E-value=2.3e-15  Score=128.72  Aligned_cols=83  Identities=20%  Similarity=0.372  Sum_probs=75.9

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      +.++|||+|||+++|+++|+.+|++||.|..+.++.+..+|.++|||||+|.+.++|.+|+.. +|..++|+.|.|.+|.
T Consensus       103 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~  181 (196)
T 1l3k_A          103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKAL  181 (196)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecC
Confidence            558999999999999999999999999999999999998999999999999999999999975 8999999999999998


Q ss_pred             Cchh
Q psy15676        268 WNMW  271 (309)
Q Consensus       268 ~~~~  271 (309)
                      ++..
T Consensus       182 ~k~~  185 (196)
T 1l3k_A          182 SKQE  185 (196)
T ss_dssp             ----
T ss_pred             ChhH
Confidence            7543

>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=99.61  E-value=2.3e-15  Score=128.74  Aligned_cols=83  Identities=23%  Similarity=0.347  Sum_probs=77.4

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+++|+++|..+|+.||.|.++.++.++.+|.++|||||+|.+.++|.+|+.. +|..++|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~   88 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKR   88 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeec
Confidence            34568999999999999999999999999999999999999999999999999999999999975 99999999999999


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      +.+.
T Consensus        89 ~~~~   92 (196)
T 1l3k_A           89 AVSR   92 (196)
T ss_dssp             CCC-
T ss_pred             ccCc
Confidence            8754

>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=99.61  E-value=6.3e-16  Score=128.99  Aligned_cols=80  Identities=24%  Similarity=0.419  Sum_probs=76.5

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      ..+|||+|||+++++++|..+|++||.|.++.++.++.+|.++|||||+|.+.++|.+|+. ++|..++|++|.|.+|.+
T Consensus        87 ~~~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           87 TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEP  165 (167)
T ss_dssp             CEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCC
T ss_pred             CCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCC
Confidence            5799999999999999999999999999999999998899999999999999999999997 899999999999999976


Q ss_pred             c
Q psy15676        269 N  269 (309)
Q Consensus       269 ~  269 (309)
                      +
T Consensus       166 k  166 (167)
T 2cjk_A          166 R  166 (167)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.60  E-value=2.2e-15  Score=113.79  Aligned_cols=75  Identities=12%  Similarity=0.181  Sum_probs=69.9

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      +.++|||+|||+.+++++|+.+|++| .|.++.+.      .++|||||+|.+.++|.+|+..|||..++|++|.|++|.
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            56899999999999999999999999 99999883      578999999999999999999999999999999999997


Q ss_pred             Cc
Q psy15676        268 WN  269 (309)
Q Consensus       268 ~~  269 (309)
                      .+
T Consensus        77 ~~   78 (88)
T 1wg1_A           77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.60  E-value=4e-15  Score=116.74  Aligned_cols=89  Identities=16%  Similarity=0.232  Sum_probs=78.0

Q ss_pred             CCCCcEEEecCCCC-----CCCHHHHHHHHhcCCceeEEEEeeeCCC-CCcccEEEEEecCHHHHHHHHHHcCCceeCCe
Q psy15676        186 APPENVLFVCKLNP-----VTSDDDLEIIFSRFGKVNCCEVIRDKVT-GDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDR  259 (309)
Q Consensus       186 ~~~~~~lfV~nL~~-----~~te~~L~~~F~~fG~I~~v~i~~d~~t-g~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr  259 (309)
                      ..|.++|+|.||..     +-++++|+..|++||.|.++.|+.++.+ +.++|||||+|.+.++|.+|+..|||..++|+
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            35778999999963     2378999999999999999999998754 68999999999999999999999999999999


Q ss_pred             eEEEEeecCchhhcc
Q psy15676        260 RIHARGEEWNMWKRR  274 (309)
Q Consensus       260 ~I~V~~a~~~~~~~r  274 (309)
                      .|.|.++....|..+
T Consensus        85 ~i~v~~a~~~~f~~~   99 (105)
T 2pe8_A           85 VVKACFYNLDKFRVL   99 (105)
T ss_dssp             ECEEEECCHHHHHTT
T ss_pred             EEEEEEcCHHHhhhh
Confidence            999999987666554

>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=99.60  E-value=3.4e-16  Score=128.99  Aligned_cols=80  Identities=16%  Similarity=0.097  Sum_probs=74.0

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ...++|||+|||+++|+++|+.+|++|| |.+|.|+.++. |+++|||||+|.+.++|.+|+ .+|+..++|+.|.|..+
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLN  120 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEEC
Confidence            4568999999999999999999999999 67999999985 999999999999999999999 78999999999999998


Q ss_pred             cCc
Q psy15676        267 EWN  269 (309)
Q Consensus       267 ~~~  269 (309)
                      ...
T Consensus       121 ~~~  123 (139)
T 2hgn_A          121 STT  123 (139)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            764

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.60  E-value=2.6e-15  Score=114.68  Aligned_cols=73  Identities=27%  Similarity=0.247  Sum_probs=65.2

Q ss_pred             CCCcE-EEecCCCCCCCHHH----HHHHHhcC-CceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCee
Q psy15676        187 PPENV-LFVCKLNPVTSDDD----LEIIFSRF-GKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRR  260 (309)
Q Consensus       187 ~~~~~-lfV~nL~~~~te~~----L~~~F~~f-G~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~  260 (309)
                      +|..| |||+|||+.+++++    |..+|++| |.|.++       ||   |+|||.|.+.++|..|++.|+|..+.||+
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~   75 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNR   75 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSC
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCce
Confidence            44555 99999999999988    56899999 599887       44   99999999999999999999999999999


Q ss_pred             EEEEeecCc
Q psy15676        261 IHARGEEWN  269 (309)
Q Consensus       261 I~V~~a~~~  269 (309)
                      |+|+||+.+
T Consensus        76 i~v~~A~~~   84 (96)
T 2diu_A           76 IIVSFTPKN   84 (96)
T ss_dssp             CEEESSCCS
T ss_pred             EEEEecCCC
Confidence            999999853

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.59  E-value=4.2e-15  Score=130.15  Aligned_cols=79  Identities=28%  Similarity=0.503  Sum_probs=74.3

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      ..+|||+|||+.+|+++|+.+|++||.|..+.++.+.  +.++|||||+|.+.++|.+|+..|||..|+|++|.|.+|++
T Consensus       103 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          103 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            4689999999999999999999999999999999985  45899999999999999999999999999999999999975


Q ss_pred             c
Q psy15676        269 N  269 (309)
Q Consensus       269 ~  269 (309)
                      +
T Consensus       181 ~  181 (213)
T 4f02_A          181 R  181 (213)
T ss_dssp             H
T ss_pred             C
Confidence            3

>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=99.59  E-value=5.5e-15  Score=123.17  Aligned_cols=80  Identities=26%  Similarity=0.511  Sum_probs=76.3

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCC--eeEEEE
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDD--RRIHAR  264 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~g--r~I~V~  264 (309)
                      .+.++|||+|||+.+++++|+.+|++||.|..+.++.+..+|.++|||||+|.+.++|.+|+..|||..++|  ++|.|.
T Consensus        87 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~  166 (168)
T 1b7f_A           87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR  166 (168)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEE
Confidence            456899999999999999999999999999999999999899999999999999999999999999999988  999999


Q ss_pred             ee
Q psy15676        265 GE  266 (309)
Q Consensus       265 ~a  266 (309)
                      +|
T Consensus       167 ~A  168 (168)
T 1b7f_A          167 LA  168 (168)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=2.8e-15  Score=118.80  Aligned_cols=78  Identities=19%  Similarity=0.218  Sum_probs=68.0

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCC---CCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEE
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVT---GDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA  263 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~t---g~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V  263 (309)
                      .+.++|||+|||+++++++|+.+|++||.|. +.++.+..+   |.++|||||+|.+.++|.+|+..|+  .++|+.+.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            4568999999999999999999999999999 888888777   7999999999999999999999884  366776666


Q ss_pred             Eeec
Q psy15676        264 RGEE  267 (309)
Q Consensus       264 ~~a~  267 (309)
                      ..+.
T Consensus        83 ~~~~   86 (114)
T 2dnl_A           83 VSSP   86 (114)
T ss_dssp             ECCS
T ss_pred             ccCC
Confidence            5443

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.57  E-value=6.6e-15  Score=122.12  Aligned_cols=79  Identities=22%  Similarity=0.354  Sum_probs=73.8

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecCc
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWN  269 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~~  269 (309)
                      ++|||+|||+++|+++|..+|++||.|.++.++.++ +|.++|||||+|.+.++|.+|+..|+|..++|+.|.|.++...
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            489999999999999999999999999999999987 4789999999999999999999999999999999999998653

>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=99.57  E-value=8.7e-15  Score=121.51  Aligned_cols=79  Identities=24%  Similarity=0.407  Sum_probs=74.6

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCee--EEEEe
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRR--IHARG  265 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~--I~V~~  265 (309)
                      +..+|||+|||+.+++++|..+|++||.|..+.++.+..+|.++|||||+|.+.++|.+|+..|||..++|+.  |.|+|
T Consensus        87 ~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~  166 (167)
T 1fxl_A           87 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF  166 (167)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEe
Confidence            4679999999999999999999999999999999999989999999999999999999999999999999965  88887


Q ss_pred             e
Q psy15676        266 E  266 (309)
Q Consensus       266 a  266 (309)
                      |
T Consensus       167 A  167 (167)
T 1fxl_A          167 A  167 (167)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.57  E-value=7.9e-15  Score=128.27  Aligned_cols=78  Identities=17%  Similarity=0.246  Sum_probs=72.5

Q ss_pred             CCCcEEEecCCC-CCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        187 PPENVLFVCKLN-PVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       187 ~~~~~lfV~nL~-~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      +++++|||+||| +.+++++|..+|++||.|.++.++.+     ++|||||+|.+.++|..|+..|||..+.|+.|.|.+
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   76 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCV   76 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            567899999999 79999999999999999999999764     479999999999999999999999999999999999


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      |+.+
T Consensus        77 s~~~   80 (205)
T 3tyt_A           77 SKQP   80 (205)
T ss_dssp             CSCS
T ss_pred             ccCC
Confidence            9743

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.57  E-value=7.7e-15  Score=127.37  Aligned_cols=82  Identities=22%  Similarity=0.357  Sum_probs=75.0

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      .++|||+|||+++|+++|+.+|+.||.|.++.++.++.+|.++|||||+|.+.++|.+|+..|+|..++|+.|.|.++..
T Consensus        28 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~  107 (216)
T 2qfj_A           28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN  107 (216)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCC
Confidence            47999999999999999999999999999999999998999999999999999999999999999999999999998875


Q ss_pred             ch
Q psy15676        269 NM  270 (309)
Q Consensus       269 ~~  270 (309)
                      ..
T Consensus       108 ~~  109 (216)
T 2qfj_A          108 IG  109 (216)
T ss_dssp             CG
T ss_pred             cc
Confidence            43

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.56  E-value=1.6e-14  Score=117.45  Aligned_cols=75  Identities=24%  Similarity=0.272  Sum_probs=68.6

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccE-EEEEecCHHHHHHHHHHcCCceeCC--eeEEEEee
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQY-AFVEFDNPKSCEDAYLKMDNVLIDD--RRIHARGE  266 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~-aFV~F~~~~~a~~Al~~l~g~~i~g--r~I~V~~a  266 (309)
                      -.|||+||++.+|+++|..+|++||.|.++.+...     ++|| |||+|.+.++|..|+..|||..|.|  +.|+|+||
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            47789999999999999999999999999988753     3577 9999999999999999999999988  99999999


Q ss_pred             cCc
Q psy15676        267 EWN  269 (309)
Q Consensus       267 ~~~  269 (309)
                      +..
T Consensus       104 k~~  106 (130)
T 3zzy_A          104 KLT  106 (130)
T ss_dssp             SCS
T ss_pred             CCC
Confidence            864

>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=99.56  E-value=3.9e-15  Score=118.28  Aligned_cols=74  Identities=28%  Similarity=0.293  Sum_probs=66.4

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCee-----EE
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRR-----IH  262 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~-----I~  262 (309)
                      ..++|||+|||+++++++|..+|++||.|..+.++.+       |||||+|.+.++|++|+..|||..|+|+.     |.
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~   87 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   87 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEE
Confidence            4589999999999999999999999999999999764       89999999999999999999999999998     67


Q ss_pred             EEeecC
Q psy15676        263 ARGEEW  268 (309)
Q Consensus       263 V~~a~~  268 (309)
                      |..+.+
T Consensus        88 v~~~~~   93 (115)
T 3beg_B           88 VKVDGP   93 (115)
T ss_dssp             EEECC-
T ss_pred             eccCCC
Confidence            766654

>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=99.55  E-value=8e-15  Score=122.23  Aligned_cols=79  Identities=24%  Similarity=0.460  Sum_probs=74.3

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      +.++|||+|||+++|+++|+.+|++||.|.++.++.++.+|.++|||||+|.+.++|.+|+.  ++..++|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK--TQHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH--SCCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh--cccccCCeEccccccc
Confidence            45899999999999999999999999999999999999999999999999999999999998  4689999999999886


Q ss_pred             C
Q psy15676        268 W  268 (309)
Q Consensus       268 ~  268 (309)
                      +
T Consensus        80 ~   80 (167)
T 2cjk_A           80 P   80 (167)
T ss_dssp             C
T ss_pred             c
Confidence            5

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.55  E-value=1.5e-14  Score=121.16  Aligned_cols=81  Identities=23%  Similarity=0.338  Sum_probs=74.2

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCC--CcccEEEEEecCHHHHHHHHHHcCCceeC---CeeEE
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTG--DSLQYAFVEFDNPKSCEDAYLKMDNVLID---DRRIH  262 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg--~skG~aFV~F~~~~~a~~Al~~l~g~~i~---gr~I~  262 (309)
                      +.++|||+|||+++|+++|+.+|++||.|.++.++.++.+|  .++|||||+|.+.++|.+|+..|+|..+.   ++.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            46899999999999999999999999999999999999887  89999999999999999999999998776   67788


Q ss_pred             EEeecC
Q psy15676        263 ARGEEW  268 (309)
Q Consensus       263 V~~a~~  268 (309)
                      +.++.+
T Consensus        82 ~~~~~~   87 (175)
T 3nmr_A           82 MKPADS   87 (175)
T ss_dssp             EEECGG
T ss_pred             Eccccc
Confidence            887764

>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=99.55  E-value=1.1e-14  Score=109.14  Aligned_cols=72  Identities=18%  Similarity=0.355  Sum_probs=66.1

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcC----C-------ceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCce
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRF----G-------KVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVL  255 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~f----G-------~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~  255 (309)
                      .+.++|||+|||+++++++|+.+|++|    |       .|.++.+..+      +|||||+|.+.++|.+|+ .|||..
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       8999988643      699999999999999999 999999


Q ss_pred             eCCeeEEEEe
Q psy15676        256 IDDRRIHARG  265 (309)
Q Consensus       256 i~gr~I~V~~  265 (309)
                      ++|+.|.|+.
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            9999999874

>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=99.55  E-value=1.6e-14  Score=121.73  Aligned_cols=76  Identities=22%  Similarity=0.232  Sum_probs=69.2

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCC--eeEEEEeec
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDD--RRIHARGEE  267 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~g--r~I~V~~a~  267 (309)
                      .+|||+||++.+|+++|+.+|++||.|.++.+...    .++|||||+|.+.++|..|+..|||..|.|  +.|+|++|+
T Consensus        47 l~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak  122 (164)
T 1sjr_A           47 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  122 (164)
T ss_dssp             EEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECS
T ss_pred             EEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEec
Confidence            47899999999999999999999999999998643    357899999999999999999999999965  999999998


Q ss_pred             Cc
Q psy15676        268 WN  269 (309)
Q Consensus       268 ~~  269 (309)
                      +.
T Consensus       123 ~~  124 (164)
T 1sjr_A          123 LT  124 (164)
T ss_dssp             SS
T ss_pred             CC
Confidence            64

>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=99.54  E-value=1.6e-14  Score=121.00  Aligned_cols=78  Identities=22%  Similarity=0.416  Sum_probs=73.1

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeC---CeeEEEE
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLID---DRRIHAR  264 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~---gr~I~V~  264 (309)
                      +.++|||+|||+.+|+++|+.+|++||.|.++.++.+. +|.++|||||+|.+.++|.+|+..|||..+.   |++|.|.
T Consensus        94 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~  172 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK  172 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEE
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEE
Confidence            56899999999999999999999999999999999986 5999999999999999999999999998776   4999999


Q ss_pred             ee
Q psy15676        265 GE  266 (309)
Q Consensus       265 ~a  266 (309)
                      ||
T Consensus       173 ~a  174 (175)
T 3nmr_A          173 FA  174 (175)
T ss_dssp             EC
T ss_pred             ec
Confidence            97

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.54  E-value=3.7e-14  Score=114.49  Aligned_cols=78  Identities=17%  Similarity=0.113  Sum_probs=68.5

Q ss_pred             CCCCcE--EEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccE-EEEEecCHHHHHHHHHHcCCceeCC--ee
Q psy15676        186 APPENV--LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQY-AFVEFDNPKSCEDAYLKMDNVLIDD--RR  260 (309)
Q Consensus       186 ~~~~~~--lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~-aFV~F~~~~~a~~Al~~l~g~~i~g--r~  260 (309)
                      .+|..+  |||+||++.+++++|..+|++||.|.++.+.. +     .|| |||+|.+.++|..|+..|||..|.|  +.
T Consensus        20 ~~ps~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~   93 (124)
T 2e5i_A           20 SGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCT   93 (124)
T ss_dssp             CCCCSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSE
T ss_pred             CCCCcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeE
Confidence            345554  67999999999999999999999999999864 2     286 9999999999999999999999987  68


Q ss_pred             EEEEeecCc
Q psy15676        261 IHARGEEWN  269 (309)
Q Consensus       261 I~V~~a~~~  269 (309)
                      |+|++|++.
T Consensus        94 l~V~~Ak~~  102 (124)
T 2e5i_A           94 LKIEYARPT  102 (124)
T ss_dssp             EEEECCSCS
T ss_pred             EEEEEecCC
Confidence            999999864

>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=99.54  E-value=6.3e-15  Score=111.06  Aligned_cols=77  Identities=19%  Similarity=0.315  Sum_probs=66.0

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      .+.++|||+|||+++++++|+.+|++||.|.++.++.+     ++|||||+|.+.++|++|..  .+..++|+.|.|.++
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~--~~~~~~g~~l~v~~a   75 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhc--CCceeCCEEEEEEec
Confidence            35689999999999999999999999999999998754     78999999999999976432  235669999999999


Q ss_pred             cCch
Q psy15676        267 EWNM  270 (309)
Q Consensus       267 ~~~~  270 (309)
                      .++.
T Consensus        76 ~~~~   79 (88)
T 1wf0_A           76 EPKH   79 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8654

>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=99.53  E-value=2.3e-14  Score=120.64  Aligned_cols=78  Identities=18%  Similarity=0.231  Sum_probs=71.9

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      .+.++|||+|||+.+++++|+.+|++||.|..+     ..+|.++|||||+|.+.++|.+|+..|||..++|+.|.|++|
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            356899999999999999999999999988765     457999999999999999999999999999999999999999


Q ss_pred             cCc
Q psy15676        267 EWN  269 (309)
Q Consensus       267 ~~~  269 (309)
                      .++
T Consensus       172 ~~k  174 (175)
T 1fje_B          172 GEK  174 (175)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            764

>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=3.8e-14  Score=122.81  Aligned_cols=77  Identities=13%  Similarity=0.063  Sum_probs=71.1

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      ++|||+|||+++|+++|..+|++||.|.++.++++. +|.++|||||+|.+.++|.+|+..+ +..++|+.|.|.+++.
T Consensus       110 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             CEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            799999999999999999999999999999999987 5999999999999999999999754 5699999999997653

>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=99.52  E-value=5.2e-14  Score=127.70  Aligned_cols=81  Identities=25%  Similarity=0.359  Sum_probs=75.0

Q ss_pred             CCCCcEEEecCCCCCCCHHHHH----HHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLE----IIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI  261 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~----~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I  261 (309)
                      .++.++|||+|||+++++++|+    .+|++||.|.+|.++.   +|.++|||||+|.+.++|.+|+..|||..++|+.|
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   82 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   82 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEE
Confidence            4578999999999999999966    8999999999998875   78899999999999999999999999999999999


Q ss_pred             EEEeecCc
Q psy15676        262 HARGEEWN  269 (309)
Q Consensus       262 ~V~~a~~~  269 (309)
                      .|.++...
T Consensus        83 ~v~~a~~~   90 (282)
T 3pgw_A           83 RIQYAKTD   90 (282)
T ss_pred             EEEEeccC
Confidence            99999754

>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=99.51  E-value=2.9e-14  Score=130.06  Aligned_cols=83  Identities=19%  Similarity=0.273  Sum_probs=76.4

Q ss_pred             CCCCcEEEecCCCCC-CCHHHHHHHHhcCCceeEEEEeeeCC-CCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEE
Q psy15676        186 APPENVLFVCKLNPV-TSDDDLEIIFSRFGKVNCCEVIRDKV-TGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA  263 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~-~te~~L~~~F~~fG~I~~v~i~~d~~-tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V  263 (309)
                      ..+..+|||+|||+. +++++|..+|++||.|..+.++.+.. ||.++|||||+|.+.++|.+|+ .|||..|+|+.|.|
T Consensus       207 ~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V  285 (292)
T 2ghp_A          207 TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISV  285 (292)
T ss_dssp             CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEE
T ss_pred             CCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEE
Confidence            345689999999999 99999999999999999999999876 6999999999999999999999 99999999999999


Q ss_pred             EeecCc
Q psy15676        264 RGEEWN  269 (309)
Q Consensus       264 ~~a~~~  269 (309)
                      .+|+++
T Consensus       286 ~~a~~k  291 (292)
T 2ghp_A          286 SLADKK  291 (292)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            999864

>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=99.51  E-value=6.8e-14  Score=127.05  Aligned_cols=84  Identities=21%  Similarity=0.367  Sum_probs=79.9

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++.++|||+|||+++++++|..+|++||.|..+.++.+..+|.++|||||+|.+.++|.+|+..|+|..++|+.|.|.+
T Consensus        92 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~  171 (284)
T 3smz_A           92 QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW  171 (284)
T ss_dssp             CCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      +.+.
T Consensus       172 a~~~  175 (284)
T 3smz_A          172 TDAG  175 (284)
T ss_dssp             CCGG
T ss_pred             CCCC
Confidence            9764

>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=99.50  E-value=1.4e-13  Score=124.21  Aligned_cols=82  Identities=29%  Similarity=0.353  Sum_probs=74.5

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcC-CceeC---CeeE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMD-NVLID---DRRI  261 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~-g~~i~---gr~I  261 (309)
                      ..+..+|||+|||+.+|+++|..+|+.||.|.++.++.+ .+|.++|||||+|.+.++|.+|+..|| |..+.   |++|
T Consensus        93 a~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i  171 (261)
T 3sde_A           93 ATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPV  171 (261)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBC
T ss_pred             cccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceE
Confidence            346789999999999999999999999999999999999 589999999999999999999999994 55555   9999


Q ss_pred             EEEeecC
Q psy15676        262 HARGEEW  268 (309)
Q Consensus       262 ~V~~a~~  268 (309)
                      .|.++.+
T Consensus       172 ~v~~~~~  178 (261)
T 3sde_A          172 IVEPMEQ  178 (261)
T ss_dssp             EEEECCC
T ss_pred             EEeeccc
Confidence            9998864

>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=99.50  E-value=8.3e-14  Score=126.48  Aligned_cols=84  Identities=17%  Similarity=0.176  Sum_probs=78.5

Q ss_pred             CCCcEEEecCCCCCC-CHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        187 PPENVLFVCKLNPVT-SDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~-te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .+.++|||+|||+++ ++++|..+|+.||.|.++.++.+. +|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
T Consensus       182 ~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~  260 (284)
T 3smz_A          182 LHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSF  260 (284)
T ss_dssp             TSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEE
Confidence            467899999999995 999999999999999999999987 799999999999999999999999999999999999999


Q ss_pred             ecCchh
Q psy15676        266 EEWNMW  271 (309)
Q Consensus       266 a~~~~~  271 (309)
                      +.++..
T Consensus       261 a~~~~~  266 (284)
T 3smz_A          261 CAPGPP  266 (284)
T ss_dssp             CCSSSC
T ss_pred             ecCCCc
Confidence            987554

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.48  E-value=9.7e-14  Score=108.74  Aligned_cols=88  Identities=19%  Similarity=0.236  Sum_probs=75.2

Q ss_pred             CCCCcEEEecCCC--CCCC--------HHHHHHHHhcCCceeEEEEeeeCCC--CCcccEEEEEecCHHHHHHHHHHcCC
Q psy15676        186 APPENVLFVCKLN--PVTS--------DDDLEIIFSRFGKVNCCEVIRDKVT--GDSLQYAFVEFDNPKSCEDAYLKMDN  253 (309)
Q Consensus       186 ~~~~~~lfV~nL~--~~~t--------e~~L~~~F~~fG~I~~v~i~~d~~t--g~skG~aFV~F~~~~~a~~Al~~l~g  253 (309)
                      +.|.+.|.+.|+-  ....        +++|+..|++||.|.++.|+++..+  +.++|||||+|.+.++|.+|+..|||
T Consensus         2 g~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG   81 (105)
T 3v4m_A            2 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG   81 (105)
T ss_dssp             CSCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCC
Confidence            3577899999982  2332        3689999999999999999988764  46899999999999999999999999


Q ss_pred             ceeCCeeEEEEeecCchhhc
Q psy15676        254 VLIDDRRIHARGEEWNMWKR  273 (309)
Q Consensus       254 ~~i~gr~I~V~~a~~~~~~~  273 (309)
                      ..++||.|+|.++....|..
T Consensus        82 ~~f~GR~i~v~~~~~~~f~~  101 (105)
T 3v4m_A           82 RKFANRVVVTKYCDPDSYHR  101 (105)
T ss_dssp             CEETTEECEEEEECHHHHHT
T ss_pred             CEeCCCEEEEEEeCHHHHhh
Confidence            99999999999997665544

>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=99.47  E-value=6.8e-14  Score=123.76  Aligned_cols=79  Identities=20%  Similarity=0.349  Sum_probs=73.6

Q ss_pred             CCCCcEEEecCCCC-CCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        186 APPENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       186 ~~~~~~lfV~nL~~-~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      .++.++|||+|||+ ++++++|+.+|++||.|.++.++.++     +|||||+|.+.++|.+|+..|+|..++|+.|.|.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~  105 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRIT  105 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            46678999999999 99999999999999999999998764     6899999999999999999999999999999999


Q ss_pred             eecCc
Q psy15676        265 GEEWN  269 (309)
Q Consensus       265 ~a~~~  269 (309)
                      ++...
T Consensus       106 ~a~~~  110 (229)
T 2adc_A          106 LSKHQ  110 (229)
T ss_dssp             CCSCC
T ss_pred             EecCc
Confidence            99753

>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=99.47  E-value=2.1e-14  Score=120.87  Aligned_cols=82  Identities=21%  Similarity=0.311  Sum_probs=73.0

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+++++++|+.+|+.||.+.. .++.+..+|.++|||||+|.+.++|.+|+ .|||..++|+.|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~   87 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK   87 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEec
Confidence            456789999999999999999999999998766 34455567899999999999999999999 5999999999999999


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      +.+.
T Consensus        88 ~~~~   91 (175)
T 1fje_B           88 PKGR   91 (175)
T ss_dssp             CCCS
T ss_pred             CCCc
Confidence            8753

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.46  E-value=8.3e-14  Score=124.52  Aligned_cols=77  Identities=18%  Similarity=0.315  Sum_probs=70.3

Q ss_pred             CCCcEEEecCCCCCC---------CHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCcee-
Q psy15676        187 PPENVLFVCKLNPVT---------SDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLI-  256 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~---------te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i-  256 (309)
                      .+.++|||+||++.+         ++++|+.+|++||.|.+|.++.      ++|||||+|.+.++|+.|+..|+|..+ 
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~~l~  205 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQTLL  205 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHTTCCCC
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhCCCEEe
Confidence            467899999999998         7999999999999999999974      479999999999999999999999999 


Q ss_pred             -----------CCeeEEEEeecCc
Q psy15676        257 -----------DDRRIHARGEEWN  269 (309)
Q Consensus       257 -----------~gr~I~V~~a~~~  269 (309)
                                 +|+.|.|.+|..+
T Consensus       206 ~~~~~e~~~~~~gr~L~V~wA~~~  229 (240)
T 3u1l_A          206 LPSDKEWDDRREGTGLLVKWANED  229 (240)
T ss_dssp             CTTSTTGGGGGGSCCCEEEECC--
T ss_pred             ccccccccccCCCCEEEEEEccCC
Confidence                       8999999999864

>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=99.46  E-value=2.6e-13  Score=123.02  Aligned_cols=77  Identities=23%  Similarity=0.396  Sum_probs=71.8

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeC-CeeEEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLID-DRRIHAR  264 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~-gr~I~V~  264 (309)
                      .++.++|||+|||+.+++++|+.+|++||.|.++.++.++     +|||||+|.+.++|.+|+..|||..++ |+.|+|+
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  278 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKIS  278 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEE
Confidence            4567899999999999999999999999999999998543     589999999999999999999999999 9999999


Q ss_pred             eec
Q psy15676        265 GEE  267 (309)
Q Consensus       265 ~a~  267 (309)
                      ||+
T Consensus       279 ~ak  281 (282)
T 3pgw_A          279 FAK  281 (282)
T ss_pred             Eec
Confidence            985

>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=99.45  E-value=5.5e-13  Score=105.20  Aligned_cols=80  Identities=20%  Similarity=0.288  Sum_probs=69.4

Q ss_pred             CCCCcEEEecCCCCCCC-----------HHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCc
Q psy15676        186 APPENVLFVCKLNPVTS-----------DDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNV  254 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~t-----------e~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~  254 (309)
                      ..+.++|+|.||.....           +++|+.+|++||.|..+.| .++   .++|||||+|.+.++|.+|+..|||.
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~   87 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGR   87 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCC
Confidence            45678999999954432           5799999999999999965 444   37999999999999999999999999


Q ss_pred             eeCCeeEEEEeecCc
Q psy15676        255 LIDDRRIHARGEEWN  269 (309)
Q Consensus       255 ~i~gr~I~V~~a~~~  269 (309)
                      .++|+.|.|.++.+.
T Consensus        88 ~~~gr~l~v~~a~~~  102 (112)
T 2dit_A           88 WFGGRQITAQAWDGT  102 (112)
T ss_dssp             EETTEECEEEECCSC
T ss_pred             EECCcEEEEEEeCCC
Confidence            999999999999763

>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=99.44  E-value=1.7e-13  Score=119.71  Aligned_cols=79  Identities=13%  Similarity=0.188  Sum_probs=70.9

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCce--eEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCe----
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKV--NCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDR----  259 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I--~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr----  259 (309)
                      .+|..+|||+|||+++|+++|+.+|++||.|  .++.++.+.  |.++|||||+|.+.++|.+|+..|||..|+|.    
T Consensus       120 ~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~  197 (205)
T 3tyt_A          120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPY  197 (205)
T ss_dssp             CCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSS
T ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCc
Confidence            4577899999999999999999999999999  899988775  55679999999999999999999999999986    


Q ss_pred             eEEEEee
Q psy15676        260 RIHARGE  266 (309)
Q Consensus       260 ~I~V~~a  266 (309)
                      ++.|.+|
T Consensus       198 p~~vk~~  204 (205)
T 3tyt_A          198 PYTLKLC  204 (205)
T ss_dssp             CEECEEE
T ss_pred             ceEEEec
Confidence            5777765

>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=99.43  E-value=3.1e-13  Score=121.88  Aligned_cols=77  Identities=19%  Similarity=0.350  Sum_probs=71.0

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+++|+++|..+|++||.|..+.+..      ++|||||+|.+.++|.+|+..++|..++|+.|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~   92 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR------DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            34567999999999999999999999999999998853      469999999999999999999999999999999999


Q ss_pred             ecC
Q psy15676        266 EEW  268 (309)
Q Consensus       266 a~~  268 (309)
                      +.+
T Consensus        93 a~~   95 (261)
T 3sde_A           93 ATH   95 (261)
T ss_dssp             CCC
T ss_pred             ccc
Confidence            874

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.43  E-value=1.5e-13  Score=118.06  Aligned_cols=76  Identities=21%  Similarity=0.366  Sum_probs=71.2

Q ss_pred             CcEEEecCCCC-CCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        189 ENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       189 ~~~lfV~nL~~-~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      +++|||+|||+ .+++++|..+|++||.|.++.++.++     +|||||+|.+.++|.+|+..|+|..++|+.|.|.++.
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 99999999999999999999998764     6899999999999999999999999999999999987


Q ss_pred             Cc
Q psy15676        268 WN  269 (309)
Q Consensus       268 ~~  269 (309)
                      ..
T Consensus        78 ~~   79 (198)
T 1qm9_A           78 HQ   79 (198)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.43  E-value=3.9e-13  Score=115.49  Aligned_cols=79  Identities=18%  Similarity=0.373  Sum_probs=72.9

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCC-ceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeC-CeeEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFG-KVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLID-DRRIHA  263 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG-~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~-gr~I~V  263 (309)
                      .+|.++|||+|||+.+++++|+.+|++|| .|..+.++.+     ++|||||+|.+.++|.+|+..|||..++ |+.|.|
T Consensus       117 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v  191 (198)
T 1qm9_A          117 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRV  191 (198)
T ss_dssp             CCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEE
Confidence            46789999999999999999999999999 9999998653     3699999999999999999999999999 999999


Q ss_pred             EeecCc
Q psy15676        264 RGEEWN  269 (309)
Q Consensus       264 ~~a~~~  269 (309)
                      .|+++.
T Consensus       192 ~~a~~~  197 (198)
T 1qm9_A          192 SFSKST  197 (198)
T ss_dssp             EEECCC
T ss_pred             Eeeccc
Confidence            999764

>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=99.42  E-value=3.9e-13  Score=107.56  Aligned_cols=87  Identities=15%  Similarity=0.240  Sum_probs=75.1

Q ss_pred             CCCcEEEecCCCCC-----CCHHHHHHHHhcCCceeEEEEeeeCC----CCCcccEEEEEecCHHHHHHHHHHcCCceeC
Q psy15676        187 PPENVLFVCKLNPV-----TSDDDLEIIFSRFGKVNCCEVIRDKV----TGDSLQYAFVEFDNPKSCEDAYLKMDNVLID  257 (309)
Q Consensus       187 ~~~~~lfV~nL~~~-----~te~~L~~~F~~fG~I~~v~i~~d~~----tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~  257 (309)
                      +|+++|++.|+-..     --+++|+..|++||.|.++.|+.+..    ++.++|||||+|.+.++|.+|+..|||..++
T Consensus        18 ~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~   97 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA   97 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            36789999998421     23689999999999999999999864    4678899999999999999999999999999


Q ss_pred             CeeEEEEeecCchhhc
Q psy15676        258 DRRIHARGEEWNMWKR  273 (309)
Q Consensus       258 gr~I~V~~a~~~~~~~  273 (309)
                      ||.|.|.++....|..
T Consensus        98 GR~i~v~~~~~~~f~~  113 (118)
T 3ue2_A           98 GRKVVAEVYDQERFDN  113 (118)
T ss_dssp             TEECEEEEECHHHHHT
T ss_pred             CcEEEEEEcChHhccc
Confidence            9999999997655543

>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=99.41  E-value=7.9e-13  Score=116.85  Aligned_cols=79  Identities=18%  Similarity=0.373  Sum_probs=72.7

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCC-ceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeC-CeeEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFG-KVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLID-DRRIHA  263 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG-~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~-gr~I~V  263 (309)
                      .++.++|||+|||+.+++++|+.+|++|| .|..+.++.+     ++|||||+|.+.++|.+|+..|||..++ |+.|.|
T Consensus       148 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v  222 (229)
T 2adc_A          148 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRV  222 (229)
T ss_dssp             CCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEE
Confidence            45789999999999999999999999999 9999998642     4689999999999999999999999999 999999


Q ss_pred             EeecCc
Q psy15676        264 RGEEWN  269 (309)
Q Consensus       264 ~~a~~~  269 (309)
                      .||++.
T Consensus       223 ~~a~~~  228 (229)
T 2adc_A          223 SFSKST  228 (229)
T ss_dssp             EECSSC
T ss_pred             EEecCC
Confidence            999764

>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=99.40  E-value=1.2e-13  Score=107.98  Aligned_cols=72  Identities=19%  Similarity=0.343  Sum_probs=64.2

Q ss_pred             ecCCCCCCCHHHHHHHH------------hcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeE
Q psy15676        194 VCKLNPVTSDDDLEIIF------------SRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI  261 (309)
Q Consensus       194 V~nL~~~~te~~L~~~F------------~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I  261 (309)
                      +.||++.+++++|...|            ++||.|.++.++.+. +|.++|||||+|.+.++|.+|+..|||..++|+.|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56777777887777666            999999999999876 48899999999999999999999999999999999


Q ss_pred             EEEee
Q psy15676        262 HARGE  266 (309)
Q Consensus       262 ~V~~a  266 (309)
                      .|+++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>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=99.40  E-value=5.8e-13  Score=121.37  Aligned_cols=82  Identities=9%  Similarity=0.171  Sum_probs=71.0

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCC-ceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFG-KVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG-~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      +.++|||+|||+.+++++|..+|++|| .|..+.++.+.. |.++|||||+|.+.++|.+|+..|+|..++|+.|.|.++
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            568999999999999999999999999 999999998875 889999999999999999999999999999999999998


Q ss_pred             cCch
Q psy15676        267 EWNM  270 (309)
Q Consensus       267 ~~~~  270 (309)
                      .+..
T Consensus       195 ~~~~  198 (292)
T 2ghp_A          195 NPLE  198 (292)
T ss_dssp             CCC-
T ss_pred             CCCc
Confidence            7643

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.37  E-value=1.2e-12  Score=111.89  Aligned_cols=75  Identities=15%  Similarity=0.254  Sum_probs=65.7

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCC-----------ceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCcee
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFG-----------KVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLI  256 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG-----------~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i  256 (309)
                      ..++|||+|||+++|+++|..+|++||           .|.++.+      +.++|||||+|.+.++|.+|+ .|||..+
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEE
Confidence            468999999999999999999999994           4554444      567899999999999999999 8999999


Q ss_pred             CCeeEEEEeecCc
Q psy15676        257 DDRRIHARGEEWN  269 (309)
Q Consensus       257 ~gr~I~V~~a~~~  269 (309)
                      +|+.|.|.++...
T Consensus        76 ~g~~i~v~~~~~~   88 (198)
T 2yh0_A           76 QGQSLKIRRPHDY   88 (198)
T ss_dssp             TTEEEEEECCCCC
T ss_pred             cCceEEEeCCCCC
Confidence            9999999998753

>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=99.37  E-value=1.2e-12  Score=109.43  Aligned_cols=74  Identities=16%  Similarity=0.321  Sum_probs=66.2

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcC----C-------ceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCcee
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRF----G-------KVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLI  256 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~f----G-------~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i  256 (309)
                      +.++|||+|||+++|+++|..+|++|    |       .|.++.+      +.++|||||+|.+.++|.+|+ .++|..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEE------ETTTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEe------cCCCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            45899999999999999999999999    6       6666655      456899999999999999999 8999999


Q ss_pred             CCeeEEEEeecC
Q psy15676        257 DDRRIHARGEEW  268 (309)
Q Consensus       257 ~gr~I~V~~a~~  268 (309)
                      +|+.|.|.++..
T Consensus        76 ~g~~i~v~~~~~   87 (172)
T 2g4b_A           76 QGQSLKIRRPHD   87 (172)
T ss_dssp             TTEECEEECCSS
T ss_pred             cCceeeecCCcc
Confidence            999999998865

>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=99.28  E-value=8.7e-12  Score=116.99  Aligned_cols=76  Identities=16%  Similarity=0.246  Sum_probs=65.8

Q ss_pred             CCCCcEEEecC--CCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeC---Ce-
Q psy15676        186 APPENVLFVCK--LNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLID---DR-  259 (309)
Q Consensus       186 ~~~~~~lfV~n--L~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~---gr-  259 (309)
                      ..|..+|||||  |++.+|+++|+++|++||.|.++.+..      ++|||||+|.+.++|++|++.|||..+.   |+ 
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            56789999999  578999999999999999999887642      5799999999999999999999998773   44 


Q ss_pred             -eEEEEeec
Q psy15676        260 -RIHARGEE  267 (309)
Q Consensus       260 -~I~V~~a~  267 (309)
                       .|.|.|+.
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             57778875

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.26  E-value=3.3e-11  Score=93.46  Aligned_cols=65  Identities=22%  Similarity=0.109  Sum_probs=57.8

Q ss_pred             CCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecCch
Q psy15676        199 PVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWNM  270 (309)
Q Consensus       199 ~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~~~  270 (309)
                      ..+++++|+.+|++||.|..+.|+     +.++|||||+|.+.++|..|+..+++  +.|++|+|++++...
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQP   91 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCC
Confidence            568999999999999999999987     46899999999999999999987554  679999999998654

>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=99.23  E-value=3.5e-11  Score=95.57  Aligned_cols=85  Identities=11%  Similarity=0.039  Sum_probs=70.2

Q ss_pred             CCCcEEEecCCCCCCC----------HHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCcee
Q psy15676        187 PPENVLFVCKLNPVTS----------DDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLI  256 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~t----------e~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i  256 (309)
                      .|.+.|.+.|+=..-.          +++|+..|++||.|.++.+.++.    ++|||||+|.+.++|.+|+..|||..+
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            3567888988743221          35789999999999999886542    589999999999999999999999999


Q ss_pred             CCeeEEEEeecCchhhccc
Q psy15676        257 DDRRIHARGEEWNMWKRRE  275 (309)
Q Consensus       257 ~gr~I~V~~a~~~~~~~r~  275 (309)
                      +|+.|.|.++....|..+-
T Consensus        81 ~GR~i~v~~~~~~~y~~~f   99 (114)
T 3s6e_A           81 AGKMITAAYVPLPTYHNLF   99 (114)
T ss_dssp             TTEECEEEEECHHHHHHHC
T ss_pred             CCEEEEEEEEcHHHHHHhC
Confidence            9999999999876665543

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.17  E-value=8.3e-11  Score=88.93  Aligned_cols=78  Identities=19%  Similarity=0.210  Sum_probs=66.9

Q ss_pred             CCCCCCcEEEecCCCC----CCCH----HHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCce
Q psy15676        184 DAAPPENVLFVCKLNP----VTSD----DDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVL  255 (309)
Q Consensus       184 ~~~~~~~~lfV~nL~~----~~te----~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~  255 (309)
                      ..+||..||+|.-++.    +...    .+|...|++||.|..++++.++        +||+|.+.++|.+|+. |||..
T Consensus         2 ~~GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~   72 (91)
T 2dnr_A            2 SSGSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKE   72 (91)
T ss_dssp             CCCCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCE
T ss_pred             CCCCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeE
Confidence            3578999999988762    3333    5789999999999999998764        8999999999999998 99999


Q ss_pred             eCCeeEEEEeecCch
Q psy15676        256 IDDRRIHARGEEWNM  270 (309)
Q Consensus       256 i~gr~I~V~~a~~~~  270 (309)
                      ++|+.|+|++++++.
T Consensus        73 v~Gr~LkV~lkt~dW   87 (91)
T 2dnr_A           73 LLNRTITIALKSPSG   87 (91)
T ss_dssp             ETTEEEEEEECCCSS
T ss_pred             eCCeEEEEEeCCCCc
Confidence            999999999998653

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.00  E-value=8.3e-10  Score=88.30  Aligned_cols=77  Identities=17%  Similarity=0.196  Sum_probs=68.8

Q ss_pred             CCCCcEEEecCCCCC-CCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecC-HHHHHHHHHHcC--CceeCCeeE
Q psy15676        186 APPENVLFVCKLNPV-TSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDN-PKSCEDAYLKMD--NVLIDDRRI  261 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~-~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~-~~~a~~Al~~l~--g~~i~gr~I  261 (309)
                      -++++.|||+||++. ++.++|+.+|++||.|.+|.++.+..      .|||.|.+ ..+|..|+..+|  |..|.|..+
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~   88 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEV   88 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEE
Confidence            467899999999999 99999999999999999999987654      59999999 899999999995  689999999


Q ss_pred             EEEeecC
Q psy15676        262 HARGEEW  268 (309)
Q Consensus       262 ~V~~a~~  268 (309)
                      ++.....
T Consensus        89 ~~evL~G   95 (121)
T 1owx_A           89 TWEVLEG   95 (121)
T ss_dssp             EEEECCH
T ss_pred             EEEECCC
Confidence            9887653

>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=98.93  E-value=1.7e-09  Score=82.17  Aligned_cols=75  Identities=15%  Similarity=0.295  Sum_probs=64.4

Q ss_pred             CCCCCCcEEEecCCCCC------CCH---HHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCc
Q psy15676        184 DAAPPENVLFVCKLNPV------TSD---DDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNV  254 (309)
Q Consensus       184 ~~~~~~~~lfV~nL~~~------~te---~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~  254 (309)
                      ..+||..||+|.-++.+      ..+   .+|...|++||.|..++++.++        +||+|.+.++|.+|+. |||.
T Consensus        10 ~~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~   80 (95)
T 1ufw_A           10 FQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGM   80 (95)
T ss_dssp             CCCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGS
T ss_pred             ecCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCe
Confidence            45789999999988743      221   4688999999999999998764        9999999999999998 9999


Q ss_pred             eeCCeeEEEEeec
Q psy15676        255 LIDDRRIHARGEE  267 (309)
Q Consensus       255 ~i~gr~I~V~~a~  267 (309)
                      .++|+.|+|++-.
T Consensus        81 ~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           81 KVKGRAVKISGPS   93 (95)
T ss_dssp             EETTEEEEEECCC
T ss_pred             eeCCeEEEEeccC
Confidence            9999999998753

>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=98.84  E-value=5.3e-09  Score=91.67  Aligned_cols=74  Identities=16%  Similarity=0.259  Sum_probs=64.8

Q ss_pred             CCHHHHHHHHhcCCceeEEEEeeeCC----CCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecCchhhcc
Q psy15676        201 TSDDDLEIIFSRFGKVNCCEVIRDKV----TGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWNMWKRR  274 (309)
Q Consensus       201 ~te~~L~~~F~~fG~I~~v~i~~d~~----tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~~~~~~r  274 (309)
                      -.+++|...|++||.|.++.++.+..    +|.++|++||+|.+.++|.+|+..|||..++||.|.+.|+....|..+
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~~~f~~~  218 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQERFDNS  218 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCHHHHHTT
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCHHHhhhc
Confidence            34678999999999999999986644    458999999999999999999999999999999999999876555544

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.15  E-value=1.3e-05  Score=62.14  Aligned_cols=74  Identities=11%  Similarity=0.108  Sum_probs=66.4

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcC-----CceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeE
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRF-----GKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI  261 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~f-----G~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I  261 (309)
                      ...++|-+-|||..++...++.+...+     |.+..+.+..|.      |-|+|+|.+...|-+|.-.++|..|+|+.|
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 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVI   92 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEE
Confidence            346888899999999999999999999     999999888775      469999999999999988999999999999


Q ss_pred             EEEee
Q psy15676        262 HARGE  266 (309)
Q Consensus       262 ~V~~a  266 (309)
                      ++.-.
T Consensus        93 r~gTv   97 (117)
T 2l9w_A           93 RSGTI   97 (117)
T ss_dssp             EEECH
T ss_pred             EecCH
Confidence            98743

>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=97.34  E-value=0.00049  Score=52.94  Aligned_cols=74  Identities=19%  Similarity=0.284  Sum_probs=61.9

Q ss_pred             CcEEEecCCCCCC-CH----HHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEE
Q psy15676        189 ENVLFVCKLNPVT-SD----DDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA  263 (309)
Q Consensus       189 ~~~lfV~nL~~~~-te----~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V  263 (309)
                      .++|+|+||+..+ +.    +.++.+|..|+++........-      .-..|.|.+.++|.+|-..|++..++|+.|+|
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            4789999998854 32    4678999999998876665432      34689999999999999999999999999999


Q ss_pred             EeecC
Q psy15676        264 RGEEW  268 (309)
Q Consensus       264 ~~a~~  268 (309)
                      -++++
T Consensus        79 YFgq~   83 (104)
T 1wey_A           79 YFAQT   83 (104)
T ss_dssp             ECCCC
T ss_pred             EecCC
Confidence            99984

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.69  E-value=0.012  Score=45.15  Aligned_cols=71  Identities=17%  Similarity=0.213  Sum_probs=57.9

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhc-----CCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeE
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSR-----FGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI  261 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~-----fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I  261 (309)
                      ....+|.|.|||+.+.++.|.-+|+.     -|.|..+....        +-|+|+|.+...|+..++. ..+.++|.+|
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~L   76 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQL   76 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEE
Confidence            34689999999999999999999976     25777776532        5789999999999999863 4788999999


Q ss_pred             EEEee
Q psy15676        262 HARGE  266 (309)
Q Consensus       262 ~V~~a  266 (309)
                      .|.-.
T Consensus        77 sV~P~   81 (104)
T 2dhx_A           77 SLRPA   81 (104)
T ss_dssp             EEEEC
T ss_pred             EEEcC
Confidence            88643

>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=96.68  E-value=0.0054  Score=46.48  Aligned_cols=61  Identities=30%  Similarity=0.393  Sum_probs=47.8

Q ss_pred             CCCCCCCC-cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHc
Q psy15676        182 EADAAPPE-NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM  251 (309)
Q Consensus       182 ~~~~~~~~-~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l  251 (309)
                      ..+..+.. ..+++ +.|+.....||..+|+.||.| .|..+-|.       .|||.|.+.+.|..|+..+
T Consensus         8 g~d~~p~r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A            8 GPDLQPKRDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CSCCCCCCCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHH
T ss_pred             CCCCCCCCCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhc
Confidence            33444443 45555 999999999999999999954 56666653       7999999999999999865

>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=96.57  E-value=0.009  Score=44.84  Aligned_cols=68  Identities=12%  Similarity=0.176  Sum_probs=55.3

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCC--cccEEEEEecCHHHHHHHHHHcCCceeC
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGD--SLQYAFVEFDNPKSCEDAYLKMDNVLID  257 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~--skG~aFV~F~~~~~a~~Al~~l~g~~i~  257 (309)
                      .+|.|.+||++.|++++.+.++..+.+.....+..+.+.+  .-+-|||.|.+.+++..-...++|+.+-
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            4688999999999999999999988877766665544332  2356899999999999999999997664

>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=96.01  E-value=0.012  Score=44.69  Aligned_cols=54  Identities=30%  Similarity=0.381  Sum_probs=45.2

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcC
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMD  252 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~  252 (309)
                      ..++| +.|+.....||..+|+.||.| .|..+-|.       .|||.|.+.+.|..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            45566 999999999999999999943 57776653       79999999999999998764

>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=95.86  E-value=0.026  Score=44.35  Aligned_cols=72  Identities=10%  Similarity=0.176  Sum_probs=56.2

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCC-eeEEEEee
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDD-RRIHARGE  266 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~g-r~I~V~~a  266 (309)
                      ...-|-|-+.|+.. ...+...|++||.|.+....      ....+-.|.|.+..+|++||.. ||..++| -.|-|...
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~------~~~NWihI~Y~s~~~A~rAL~k-NG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALSK-DGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHTT-TTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC------CCCCeEEEEeCCHHHHHHHHHh-CCeEecCCEEEEEEEC
Confidence            35677888999885 56677889999999887651      1235889999999999999975 9999985 66676655


Q ss_pred             c
Q psy15676        267 E  267 (309)
Q Consensus       267 ~  267 (309)
                      .
T Consensus        95 ~   95 (119)
T 1wwh_A           95 I   95 (119)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=94.60  E-value=0.063  Score=40.63  Aligned_cols=78  Identities=14%  Similarity=0.160  Sum_probs=52.7

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCC--cccEEEEEecCHHHHHHHHHHcCCceeCC-----eeE
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGD--SLQYAFVEFDNPKSCEDAYLKMDNVLIDD-----RRI  261 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~--skG~aFV~F~~~~~a~~Al~~l~g~~i~g-----r~I  261 (309)
                      .-+|.|+.||++.|++++.+.++..-.+.....+....+.+  .-.-|||.|.+.+++..-...++|..+-+     .+.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~~~a   88 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLEYPA   88 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCEeee
Confidence            35788999999999999887776654443322222221111  12468999999999999999999976643     234


Q ss_pred             EEEee
Q psy15676        262 HARGE  266 (309)
Q Consensus       262 ~V~~a  266 (309)
                      .|.+|
T Consensus        89 ~VE~A   93 (97)
T 2l08_A           89 VVEFA   93 (97)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            55555

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=94.35  E-value=0.023  Score=54.91  Aligned_cols=55  Identities=22%  Similarity=0.253  Sum_probs=40.8

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHH
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLK  250 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~  250 (309)
                      ++|||. .+..+++.+|..+|++||+|.++.+-.+.  |   -||.|+|.+.+++..++..
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~--g---~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF--G---LYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS--S---EEEEEECC---CCHHHHSS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC--C---eEEEEEeCCHHHHHHHHhc
Confidence            689997 78999999999999999999998775432  3   6999999999998877643

>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=94.25  E-value=0.039  Score=44.67  Aligned_cols=34  Identities=12%  Similarity=0.070  Sum_probs=28.4

Q ss_pred             EEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCC
Q psy15676        218 CCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDN  253 (309)
Q Consensus       218 ~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g  253 (309)
                      .+.++.+.  +.++|||||+|.+.++|++|+..+++
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~   35 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYAN   35 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHH
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhcc
Confidence            45667775  36899999999999999999988775

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=93.67  E-value=0.09  Score=41.95  Aligned_cols=77  Identities=19%  Similarity=0.296  Sum_probs=52.9

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeE-EEEeee--------CCC----C-CcccEEEEEecCHHHHHHHHHHcCCc
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNC-CEVIRD--------KVT----G-DSLQYAFVEFDNPKSCEDAYLKMDNV  254 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~-v~i~~d--------~~t----g-~skG~aFV~F~~~~~a~~Al~~l~g~  254 (309)
                      ..-|.|-+.|++.+ ..+...|++||.|.. .....+        +.+    + ....+..|+|.+..+|.+||.. ||.
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~-NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE-NGA   84 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT-TTC
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh-CCe
Confidence            35566778877655 456678999999865 211110        000    0 1245779999999999999975 999


Q ss_pred             eeCCeeEEEEeec
Q psy15676        255 LIDDRRIHARGEE  267 (309)
Q Consensus       255 ~i~gr~I~V~~a~  267 (309)
                      .|+|..|-|....
T Consensus        85 ii~G~mIGV~Py~   97 (132)
T 3p3d_A           85 VFNGVLLGVIPYT   97 (132)
T ss_dssp             EETTEECEEEECC
T ss_pred             EeCcEEEEEEECC
Confidence            9999988877653

>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=93.09  E-value=0.028  Score=45.29  Aligned_cols=41  Identities=7%  Similarity=-0.019  Sum_probs=37.1

Q ss_pred             CCCcccEEEEEecCHHHHHHHHHHc-CCceeCCeeEEEEeecC
Q psy15676        227 TGDSLQYAFVEFDNPKSCEDAYLKM-DNVLIDDRRIHARGEEW  268 (309)
Q Consensus       227 tg~skG~aFV~F~~~~~a~~Al~~l-~g~~i~gr~I~V~~a~~  268 (309)
                      ....+|+++|+|.+.++|++|+..| ||..++| .+.++++..
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            3567899999999999999999999 9999999 999998764

>3bkp_A Cyclophilin; malaria, isomerase, structural GENO structural genomics consortium, SGC; 1.80A {Toxoplasma gondii}

Probab=82.54  E-value=0.78  Score=40.12  Aligned_cols=29  Identities=24%  Similarity=0.234  Sum_probs=24.3

Q ss_pred             cccccCCccccceEeecCCCCCCCCCCCC
Q psy15676         98 VFKRKNDIRITHAVILEDPYEDLPELVYP  126 (309)
Q Consensus        98 ~~rp~~~iri~h~~il~dPf~~p~~l~~p  126 (309)
                      .++|+.+|+|.+..++.|||+|+.....|
T Consensus       177 ~~~P~~~i~I~~~~vl~dPf~d~~~~~~~  205 (232)
T 3bkp_A          177 EDRPMTPPFIKSVDVLWNPFEDLVPRRLP  205 (232)
T ss_dssp             GGCBSSCCBEEEEEEEECCCTTCCCSSCC
T ss_pred             CCCcCCCeEEEEEEEEcCChhhhhhcccc
Confidence            37999999999999999999987744433

---

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	309
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-13
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-12
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-12
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-12
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-12
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-12
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	5e-12
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	7e-12
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-11
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-11
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-11
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	7e-11
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	1e-10
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-10
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-10
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-10
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-10
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-10
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-10
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-10
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-09
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-09
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	3e-09
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	4e-09
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	4e-09
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-09
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	5e-09
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	6e-09
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	7e-09
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	8e-09
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	8e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	9e-09
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	9e-09
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-08
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-08
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-08
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	4e-08
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	4e-08
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	5e-08
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	5e-08
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	7e-08
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 7e-08
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-07
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-07
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-07
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	3e-07
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	4e-07
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	4e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	5e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-05
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	7e-07
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	8e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-06
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-06
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-06
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	3e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	4e-06
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	5e-06
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	5e-06
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	5e-06
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	6e-06
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	7e-06
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-05
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-05
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	4e-05
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	8e-05
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	1e-04
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-04
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-04
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	8e-04
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	0.001
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	0.002
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	0.003
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	0.003
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	0.004
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	0.004

>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 = 62.6 bits (152), Expect = 2e-13
 Identities = 23/71 (32%), Positives = 34/71 (47%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L+P  ++  L   FS  G +    V RD +T  SL YA+V F  P   E A   M
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 252 DNVLIDDRRIH 262
           +  +I  + + 
Sbjct: 63  NFDVIKGKPVR 73

>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 = 61.0 bits (148), Expect = 1e-12
 Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 9/86 (10%)

Query: 178 GDLPEADAAPPENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFV 236
           G   + D     + +F+  LN  V    D+E IFS++GK+  C V +         +AFV
Sbjct: 4   GSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKG--------FAFV 55

Query: 237 EFDNPKSCEDAYLKMDNVLIDDRRIH 262
           ++ N ++   A    D  +I  + + 
Sbjct: 56  QYVNERNARAAVAGEDGRMIAGQVLD 81

>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 = 60.5 bits (146), Expect = 1e-12
 Identities = 22/76 (28%), Positives = 41/76 (53%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
            P   L V  L+  T++ DL  +FS++G +    ++ D+ +  S  +AFV F+N    ++
Sbjct: 7   DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 66

Query: 247 AYLKMDNVLIDDRRIH 262
           A  + + + +D RRI 
Sbjct: 67  AKERANGMELDGRRIR 82

>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 = 60.4 bits (146), Expect = 1e-12
 Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L    +DD L+ IF ++G +    ++RDK+TG     AFV ++  +  ++A   +
Sbjct: 9   LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 68

Query: 252 DNVLID--DRRIHAR 264
           +NV+ +   + +  R
Sbjct: 69  NNVIPEGGSQPLSVR 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 = 59.2 bits (143), Expect = 2e-12
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +F+  L+  T+ + L   F +FG+V  C V+RD +T  S  + FV F +    +   L  
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV-LAQ 61

Query: 252 DNVLIDDRRIHAR 264
               +D + I  +
Sbjct: 62  SRHELDSKTIDPK 74

>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 = 60.4 bits (146), Expect = 3e-12
 Identities = 17/106 (16%), Positives = 50/106 (47%), Gaps = 6/106 (5%)

Query: 187 PPE--NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
           PPE   +L++  L    + +++  IF ++G +      R   T ++   A+V +++    
Sbjct: 3   PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIFDA 59

Query: 245 EDAYLKMDNVLIDDRRIH-ARGEEWNMWKRREEEEEKEEIDEKKEE 289
           ++A   +    + +R +          +++ + ++++E++   KE+
Sbjct: 60  KNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEK 105

>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 = 59.2 bits (143), Expect = 5e-12
 Identities = 13/78 (16%), Positives = 33/78 (42%), Gaps = 2/78 (2%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRD-KVTGDSLQYAFVEFDNPKSCE 245
              + + V  +    +  ++  +FS FG++    + +    TG    + FV+F   +  +
Sbjct: 6   QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 65

Query: 246 DAYLKMDN-VLIDDRRIH 262
            A+  + +   +  RR+ 
Sbjct: 66  KAFNALCHSTHLYGRRLV 83

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 58.5 bits (141), Expect = 7e-12
 Identities = 12/80 (15%), Positives = 30/80 (37%)

Query: 183 ADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
           +   P   ++ V  +    S D++   F  +  +     ++    G     A V F++  
Sbjct: 3   SSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRD 62

Query: 243 SCEDAYLKMDNVLIDDRRIH 262
               A + +++  I  R++ 
Sbjct: 63  EATAAVIDLNDRPIGSRKVK 82

>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 = 56.5 bits (136), Expect = 3e-11
 Identities = 21/71 (29%), Positives = 37/71 (52%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L V  L    +D +L  +F   G +N C ++RD  TG S  YAFV+F +    + A   +
Sbjct: 5   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 64

Query: 252 DNVLIDDRRIH 262
           + + + ++R+ 
Sbjct: 65  NGITVRNKRLK 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 = 56.1 bits (135), Expect = 3e-11
 Identities = 14/73 (19%), Positives = 30/73 (41%), Gaps = 1/73 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  L+P T ++ +   F  FG+V   E+  D  T     + F+ F   +  +   ++ 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI-MEK 60

Query: 252 DNVLIDDRRIHAR 264
               +   +   +
Sbjct: 61  KYHNVGLSKCEIK 73

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.9 bits (137), Expect = 3e-11
 Identities = 18/71 (25%), Positives = 37/71 (52%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L+  T+++ +  +FS+ G +    +  DK+   +  + FVE+ +    E+A   +
Sbjct: 10  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 69

Query: 252 DNVLIDDRRIH 262
           +   +DDR I 
Sbjct: 70  NGTRLDDRIIR 80

>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 = 55.3 bits (133), Expect = 7e-11
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L V  L+   SD D++ +F+ FG +    V  D+ +G SL  A V F+       A  + 
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQY 61

Query: 252 DNVLIDDRRIH 262
           + V +D R ++
Sbjct: 62  NGVPLDGRPMN 72

>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 = 55.4 bits (133), Expect = 1e-10
 Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 3/87 (3%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
             +  ++V  L+   S+  L  +F + G V    + +D+VTG    Y FVEF + +  + 
Sbjct: 7   NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 66

Query: 247 AYLKMDNVLIDDRRI---HARGEEWNM 270
           A   MD + +  + I    A     N+
Sbjct: 67  AIKIMDMIKLYGKPIRVNKASAHNKNL 93

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.6 bits (131), Expect = 1e-10
 Identities = 17/71 (23%), Positives = 37/71 (52%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LF+  L    +DD ++ + + FG +    +++D  TG S  YAF E+ +    + A   +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 252 DNVLIDDRRIH 262
           + + + D+++ 
Sbjct: 64  NGMQLGDKKLL 74

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.2 bits (132), Expect = 2e-10
 Identities = 13/82 (15%), Positives = 25/82 (30%), Gaps = 11/82 (13%)

Query: 187 PPENVLFVCKLNP-----VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
              + L  C  N        +    E +F  + K    +  +        +   + F NP
Sbjct: 3   SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNP 56

Query: 242 KSCEDAYLKMDNVLIDDRRIHA 263
            S  DA L++       + +  
Sbjct: 57  LSAADARLRLHKTEFLGKEMKL 78

>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 = 54.2 bits (130), Expect = 2e-10
 Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +F+  L+  T+  DL+  FS+FG+V  C +  D +TG S  + FV F   +S +   +  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKV-MDQ 60

Query: 252 DNVLIDDRRIHAR 264
               ++ + I  +
Sbjct: 61  KEHKLNGKVIDPK 73

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.7 bits (131), Expect = 2e-10
 Identities = 21/77 (27%), Positives = 31/77 (40%)

Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
           A  + VL+V  L     D  L   F  FG +   ++  D  T     +AFVEF+  +   
Sbjct: 2   ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 61

Query: 246 DAYLKMDNVLIDDRRIH 262
            A   M+   +  R I 
Sbjct: 62  AAIDNMNESELFGRTIR 78

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.9 bits (129), Expect = 2e-10
 Identities = 18/74 (24%), Positives = 38/74 (51%), Gaps = 3/74 (4%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDK---VTGDSLQYAFVEFDNPKSCEDAY 248
           LF+  LN  T+++ L+ +FS+ G +  C + + K       S+ + FVE+  P+  + A 
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 249 LKMDNVLIDDRRIH 262
            ++    +D  ++ 
Sbjct: 61  KQLQGHTVDGHKLE 74

>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 = 53.6 bits (128), Expect = 3e-10
 Identities = 21/71 (29%), Positives = 38/71 (53%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L V  L    + ++   +F   G++  C+++RDK+TG SL Y FV + +PK  E A   +
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 252 DNVLIDDRRIH 262
           + + +  + I 
Sbjct: 65  NGLRLQTKTIK 75

>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 = 53.6 bits (128), Expect = 5e-10
 Identities = 23/77 (29%), Positives = 39/77 (50%)

Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
           +     LFV  L+  +S++DLE +FS +G ++      D +T     +AFV F  P+   
Sbjct: 5   SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAV 64

Query: 246 DAYLKMDNVLIDDRRIH 262
            AY ++D  +   R +H
Sbjct: 65  KAYAEVDGQVFQGRMLH 81

>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 = 52.3 bits (125), Expect = 1e-09
 Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 3/76 (3%)

Query: 188 PENV--LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
           PE +  LF+  L+  T+D+ L   F ++G +  C V+RD  T  S  + FV +   +  +
Sbjct: 3   PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 62

Query: 246 DAYLKMDNVLIDDRRI 261
            A +      +D R +
Sbjct: 63  AA-MNARPHKVDGRVV 77

>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 = 52.4 bits (125), Expect = 1e-09
 Identities = 19/77 (24%), Positives = 34/77 (44%)

Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
           A     + V  L+  T + DL+ +F  FG ++   + +DK TG S  +AF+ F   +   
Sbjct: 5   ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 64

Query: 246 DAYLKMDNVLIDDRRIH 262
            A   +     D   ++
Sbjct: 65  RAIAGVSGFGYDHLILN 81

>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 = 51.6 bits (123), Expect = 3e-09
 Identities = 28/91 (30%), Positives = 40/91 (43%), Gaps = 6/91 (6%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
           P    LF+  L     D DL  +F  FG V   +V  DK T  S  + FV +DNP S + 
Sbjct: 16  PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQA 75

Query: 247 AYLKMDNVLIDDRRIHARGEEWNMWKRREEE 277
           A   M+   I  +R+  +       KR + +
Sbjct: 76  AIQSMNGFQIGMKRLKVQ------LKRSKND 100

>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 = 50.8 bits (121), Expect = 4e-09
 Identities = 18/68 (26%), Positives = 33/68 (48%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L+V  L    +  +LE +FS++G++    ++ D+VTG S    F+ FD     E+A   +
Sbjct: 9   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 68

Query: 252 DNVLIDDR 259
           +       
Sbjct: 69  NGQKPSGA 76

>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 = 51.2 bits (122), Expect = 4e-09
 Identities = 21/85 (24%), Positives = 38/85 (44%), Gaps = 3/85 (3%)

Query: 178 GDLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
           G +    A   +  ++V  L P     D+E +F ++G +   ++   +       +AFVE
Sbjct: 3   GGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGP---PFAFVE 59

Query: 238 FDNPKSCEDAYLKMDNVLIDDRRIH 262
           F++P+  EDA    D    D  R+ 
Sbjct: 60  FEDPRDAEDAVYGRDGYDYDGYRLR 84

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 50.5 bits (120), Expect = 4e-09
 Identities = 18/73 (24%), Positives = 35/73 (47%)

Query: 190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
            +LFV  ++    +D+++  F  +G++    +  D+ TG S  YA VE++  K    A  
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 250 KMDNVLIDDRRIH 262
            ++   I  + I 
Sbjct: 68  ALNGAEIMGQTIQ 80

>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 = 50.7 bits (121), Expect = 5e-09
 Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 6/79 (7%)

Query: 184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
            ++P    ++   +    +D  +   FS FG++    V  +K       Y+FV F   +S
Sbjct: 13  QSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHES 66

Query: 244 CEDAYLKMDNVLIDDRRIH 262
              A + ++   I+   + 
Sbjct: 67  AAHAIVSVNGTTIEGHVVK 85

>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 = 49.7 bits (118), Expect = 6e-09
 Identities = 18/73 (24%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  L+  T+ +D++  F +FGKV+   ++ DK T     + FV F++    E    ++
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV-CEI 60

Query: 252 DNVLIDDRRIHAR 264
               I+++ +  +
Sbjct: 61  HFHEINNKMVECK 73

>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 = 49.7 bits (118), Expect = 7e-09
 Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 1/73 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  +   T +  L   F ++GK+   E++ D+ +G    +AFV FD+  S +   +  
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI-VIQ 63

Query: 252 DNVLIDDRRIHAR 264
               ++      R
Sbjct: 64  KYHTVNGHNCEVR 76

>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 = 50.0 bits (119), Expect = 8e-09
 Identities = 23/80 (28%), Positives = 36/80 (45%), Gaps = 2/80 (2%)

Query: 185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
           A    + L V  L   T++ DL+  FS FG+V   +V +D  TG S  + FV F   ++ 
Sbjct: 4   AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQ 63

Query: 245 EDAYLKMDNVLIDDRRIHAR 264
                +    +ID R    +
Sbjct: 64  VKVMSQRH--MIDGRWCDCK 81

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.0 bits (119), Expect = 8e-09
 Identities = 15/76 (19%), Positives = 28/76 (36%), Gaps = 1/76 (1%)

Query: 188 PENVLFVCKLNPVTSDDDL-EIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
           P + +++  LN     D+L + + + F +      I    +      AFV F    S  +
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 247 AYLKMDNVLIDDRRIH 262
           A   M      D+ + 
Sbjct: 62  ALRSMQGFPFYDKPMR 77

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.7 bits (118), Expect = 9e-09
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVI-RDKVTGDSLQYAFVEFDNPKSCEDAYLK 250
           +F+  L+P   +  L   FS FG +     I RD  TG+S  YAF+ F +  + + A   
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 251 MDNVLIDDRRIH 262
           M+   + +R I 
Sbjct: 61  MNGQYLCNRPIT 72

>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 = 50.1 bits (119), Expect = 9e-09
 Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           LF+  L+  T+++ L   + ++GK+  C V+RD  +  S  + FV F +    + A +  
Sbjct: 23  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA-MAA 81

Query: 252 DNVLIDDRRIHAR 264
               ID R +  +
Sbjct: 82  RPHSIDGRVVEPK 94

>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 = 48.8 bits (116), Expect = 2e-08
 Identities = 16/76 (21%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAY 248
            + LFV  L P  +++++  +F ++GK     + +DK       + F+  +     E A 
Sbjct: 8   RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAK 61

Query: 249 LKMDNVLIDDRRIHAR 264
           +++DN+ +  +++  R
Sbjct: 62  VELDNMPLRGKQLRVR 77

>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 = 49.3 bits (117), Expect = 2e-08
 Identities = 22/85 (25%), Positives = 34/85 (40%), Gaps = 4/85 (4%)

Query: 181 PEADAAPPE---NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVE 237
           P  + +P E     +F  +L       DLE  FS  GKV    +I D+ +  S   A+VE
Sbjct: 7   PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 66

Query: 238 FDNPKSCEDAYLKMDNVLIDDRRIH 262
           F   +S     + +    +    I 
Sbjct: 67  FCEIQSVP-LAIGLTGQRLLGVPII 90

>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 = 48.9 bits (116), Expect = 2e-08
 Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 2/80 (2%)

Query: 183 ADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
           +++      L V  +     D DL  +F +FGK+   E+I ++    S  + FV F+N  
Sbjct: 5   SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSA 62

Query: 243 SCEDAYLKMDNVLIDDRRIH 262
             + A  K+   +++ R+I 
Sbjct: 63  DADRAREKLHGTVVEGRKIE 82

>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 = 48.2 bits (114), Expect = 4e-08
 Identities = 11/75 (14%), Positives = 26/75 (34%), Gaps = 1/75 (1%)

Query: 188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDA 247
           P    F+  L    +++ ++  F                      + + EF++  S   A
Sbjct: 14  PPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 73

Query: 248 YLKMDNVLIDDRRIH 262
            L ++   + ++RI 
Sbjct: 74  -LSLNEESLGNKRIR 87

>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 = 47.9 bits (113), Expect = 4e-08
 Identities = 17/80 (21%), Positives = 35/80 (43%), Gaps = 6/80 (7%)

Query: 190 NVLFVCKLNPVTSDDDLEIIF---SRFGKVNCCEVIRDKVTGDSLQ---YAFVEFDNPKS 243
           N++FV  L+   +D ++        +FGK++   +        S      A+V +   + 
Sbjct: 9   NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 244 CEDAYLKMDNVLIDDRRIHA 263
              A   ++NV++D R + A
Sbjct: 69  ALRAIQCVNNVVVDGRTLKA 88

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.7 bits (113), Expect = 5e-08
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 6/81 (7%)

Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
           + D      +L+V  L   TS++ +E  F+         V + +       YAFV F N 
Sbjct: 1   DEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIR------DYAFVHFSNR 54

Query: 242 KSCEDAYLKMDNVLIDDRRIH 262
           +   +A   ++  ++D   I 
Sbjct: 55  EDAVEAMKALNGKVLDGSPIE 75

>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 = 47.9 bits (113), Expect = 5e-08
 Identities = 19/89 (21%), Positives = 33/89 (37%), Gaps = 8/89 (8%)

Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVI--------RDKVTGDSLQY 233
           + D     + ++V  LN   + DDL   F + G V   +           DK TG     
Sbjct: 1   DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD 60

Query: 234 AFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
           A V +++P + + A    D       ++ 
Sbjct: 61  ATVSYEDPPTAKAAVEWFDGKDFQGSKLK 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 = 47.3 bits (112), Expect = 7e-08
 Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 2/71 (2%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +F+  L+    +  L   FS FG +  C+V+ D+    S  Y FV F+  ++ E A  KM
Sbjct: 11  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKM 68

Query: 252 DNVLIDDRRIH 262
           + +L++DR++ 
Sbjct: 69  NGMLLNDRKVF 79

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.7 bits (113), Expect = 7e-08
 Identities = 11/61 (18%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 203 DDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
           ++    +  ++G+V    V  +      +   +V+F   +  E A + ++N   + + IH
Sbjct: 41  EEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99

Query: 263 A 263
           A
Sbjct: 100 A 100

>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 = 46.3 bits (109), Expect = 1e-07
 Identities = 10/78 (12%), Positives = 28/78 (35%), Gaps = 6/78 (7%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEV-----IRDKVTGDSLQYAFVEFDNPKSCED 246
           L+V  +    +++ +   F+   ++          +          +AF+EF +      
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 247 AYLKMDNVLIDDRRIHAR 264
           A +  D ++   + +  R
Sbjct: 64  A-MAFDGIIFQGQSLKIR 80

>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 = 46.6 bits (110), Expect = 1e-07
 Identities = 16/84 (19%), Positives = 30/84 (35%), Gaps = 5/84 (5%)

Query: 179 DLPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEF 238
           D   +        L    L+   ++D+L+ +F      +  E+      G S   A++EF
Sbjct: 6   DPCTSKKVRAARTLLAKNLSFNITEDELKEVFE-----DALEIRLVSQDGKSKGIAYIEF 60

Query: 239 DNPKSCEDAYLKMDNVLIDDRRIH 262
            +    E    +     ID R + 
Sbjct: 61  KSEADAEKNLEEKQGAEIDGRSVS 84

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 2e-07
 Identities = 16/76 (21%), Positives = 31/76 (40%), Gaps = 2/76 (2%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
                L+V  L+   ++  +  +FS+ G    C++I +     +  Y FVEF   +    
Sbjct: 6   GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAA 63

Query: 247 AYLKMDNVLIDDRRIH 262
           A   M+   I  + + 
Sbjct: 64  ALAAMNGRKILGKEVK 79

>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 = 45.9 bits (108), Expect = 3e-07
 Identities = 17/79 (21%), Positives = 35/79 (44%)

Query: 184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKS 243
           +   P  VL++  L+P  ++ DL  +F+RF +     +    +TG     AF+ F N + 
Sbjct: 13  NPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEI 72

Query: 244 CEDAYLKMDNVLIDDRRIH 262
              A   ++   +  + + 
Sbjct: 73  AWQALHLVNGYKLYGKILV 91

>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 = 46.4 bits (109), Expect = 4e-07
 Identities = 21/101 (20%), Positives = 44/101 (43%), Gaps = 3/101 (2%)

Query: 165 REAKARATILEIVGDLPEADAAPPENV---LFVCKLNPVTSDDDLEIIFSRFGKVNCCEV 221
           + A+ +    +    +P     P  +V   L V  +     +  L  +F R+G +   ++
Sbjct: 15  QTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKI 74

Query: 222 IRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH 262
           + D+ T  S  Y FV+F +  S + A   ++   I ++R+ 
Sbjct: 75  VCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLK 115

>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 = 45.5 bits (107), Expect = 4e-07
 Identities = 25/71 (35%), Positives = 34/71 (47%), Gaps = 1/71 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  L   T+D  L   F  FG +    VI D+ TG S  Y FV   +  + E A  K 
Sbjct: 13  IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA-CKD 71

Query: 252 DNVLIDDRRIH 262
            N +ID R+ +
Sbjct: 72  PNPIIDGRKAN 82

>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 = 46.9 bits (110), Expect = 5e-07
 Identities = 17/78 (21%), Positives = 33/78 (42%), Gaps = 1/78 (1%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
                +FV  +   T +  L   F ++GK+   E++ D+ +G    +AFV FD+  S + 
Sbjct: 95  LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 154

Query: 247 AYLKMDNVLIDDRRIHAR 264
             +      ++      R
Sbjct: 155 I-VIQKYHTVNGHNCEVR 171

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.1 bits (100), Expect = 1e-05
 Identities = 22/98 (22%), Positives = 40/98 (40%), Gaps = 2/98 (2%)

Query: 188 PENV--LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
           PE +  LF+  L+  T+D+ L   F ++G +  C V+RD  T  S  + FV +   +  +
Sbjct: 3   PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVD 62

Query: 246 DAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEKEEI 283
            A     + +        R       +R       ++I
Sbjct: 63  AAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKI 100

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 44.4 bits (104), Expect = 7e-07
 Identities = 8/76 (10%), Positives = 28/76 (36%)

Query: 189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAY 248
           E  L++    P  +  ++  +      V     +       S ++A+++  + +      
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 60

Query: 249 LKMDNVLIDDRRIHAR 264
            K++ + I+   +  +
Sbjct: 61  EKLNGLKIEGYTLVTK 76

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.8 bits (105), Expect = 8e-07
 Identities = 17/93 (18%), Positives = 41/93 (44%), Gaps = 9/93 (9%)

Query: 190 NVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAY 248
           +VL V  LNP   +   L I+F  +G V   +++ +K      + A V+  +    + A 
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK-----ENALVQMADGNQAQLAM 57

Query: 249 LKMDNVLIDDRRIH---ARGEEWNMWKRREEEE 278
             ++   +  + I    ++ +   + +  +E++
Sbjct: 58  SHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQ 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 = 44.0 bits (103), Expect = 1e-06
 Identities = 25/74 (33%), Positives = 44/74 (59%)

Query: 189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAY 248
           E  LFV  L+  T++  LE +FS++G+++   V++D+ T  S  + FV F+N    +DA 
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 64

Query: 249 LKMDNVLIDDRRIH 262
           + M+   +D R+I 
Sbjct: 65  MAMNGKSVDGRQIR 78

>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 = 2e-06
 Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 4/61 (6%)

Query: 204 DDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA 263
           +DL +  S+FG++    +      G     A V F +P+  +     +D      R+I A
Sbjct: 34  EDLRVECSKFGQIRKLLLFDRHPDG----VASVSFRDPEEADYCIQTLDGRWFGGRQITA 89

Query: 264 R 264
           +
Sbjct: 90  Q 90

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.5 bits (102), Expect = 2e-06
 Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 8/79 (10%)

Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
           A P   L+V  L P TS   L   F RFG +   + ++         +A++++++  + +
Sbjct: 14  ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD------SFAYIQYESLDAAQ 67

Query: 246 DAYLKMDNVLID--DRRIH 262
            A  KM    +   DRR+ 
Sbjct: 68  AACAKMRGFPLGGPDRRLR 86

>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 = 42.8 bits (100), Expect = 3e-06
 Identities = 13/78 (16%), Positives = 28/78 (35%), Gaps = 8/78 (10%)

Query: 185 AAPPENVLFVCK--LNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPK 242
            +     L V    L    S + L  +  + G V+   +  +K       Y+F  +   +
Sbjct: 14  VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTE 67

Query: 243 SCEDAYLKMDNVLIDDRR 260
             + AY+ ++   + D  
Sbjct: 68  ESKRAYVTLNGKEVVDDL 85

>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 = 42.3 bits (99), Expect = 4e-06
 Identities = 14/71 (19%), Positives = 31/71 (43%), Gaps = 7/71 (9%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV +     ++D+L   FS++G V         +      +AFV F + +  +      
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDV-----FIPKPFRAFAFVTFADDQIAQSL--CG 60

Query: 252 DNVLIDDRRIH 262
           ++++I    +H
Sbjct: 61  EDLIIKGISVH 71

>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 = 42.5 bits (99), Expect = 5e-06
 Identities = 10/81 (12%), Positives = 22/81 (27%), Gaps = 1/81 (1%)

Query: 182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP 241
           E D    +    +  +    +  D+               +     G  L  A V+F N 
Sbjct: 1   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 60

Query: 242 KSCEDAYLKMDNVLIDDRRIH 262
                +  ++    ++ R   
Sbjct: 61  DDARKS-ERLHRKKLNGREAF 80

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.7 bits (100), Expect = 5e-06
 Identities = 20/97 (20%), Positives = 32/97 (32%), Gaps = 7/97 (7%)

Query: 185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
              P   + V  L    + D L  IFS+FG V                 A +++ +P S 
Sbjct: 3   GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQF----QALLQYADPVSA 58

Query: 245 EDAYLKMDNVLIDDRRIHARGEEWNMWKRREEEEEKE 281
           + A L +D   I +     R    +  K      +  
Sbjct: 59  QHAKLSLDGQNIYNACCTLR---IDFSKLTSLNVKYN 92

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.6 bits (97), Expect = 5e-06
 Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 7/74 (9%)

Query: 190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
           N L++  L+P  + DDL  +F         +V+          YAFV++ +      A  
Sbjct: 2   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS------GYAFVDYPDQNWAIRAIE 55

Query: 250 KMD-NVLIDDRRIH 262
            +   V +  + + 
Sbjct: 56  TLSGKVELHGKIME 69

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.5 bits (97), Expect = 6e-06
 Identities = 15/78 (19%), Positives = 33/78 (42%), Gaps = 9/78 (11%)

Query: 186 APPE-NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSC 244
           AP + N L+V   +   +   L   FS FG +    +   +        AFV ++  +S 
Sbjct: 1   APRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESA 52

Query: 245 EDAYLKMDNVLIDDRRIH 262
           + A  +++   ++  ++ 
Sbjct: 53  DQAVAELNGTQVESVQLK 70

>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 = 41.6 bits (97), Expect = 7e-06
 Identities = 12/96 (12%), Positives = 38/96 (39%), Gaps = 7/96 (7%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKV--NCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL 249
           LF+  +  +   +++    ++  +   +            +  +AFVE+++ ++   A  
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 250 KMDN--VLIDDRRIHARGEEWNMWKRREEEEEKEEI 283
           K+    + +   +I     +W   +   +E+  E +
Sbjct: 64  KLMPGRIQLWGHQIAV---DWAEPEIDVDEDVMETV 96

>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 = 40.5 bits (94), Expect = 1e-05
 Identities = 20/70 (28%), Positives = 34/70 (48%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L++  L P T+D DL  +   +GK+   + I DK T     Y FV+FD+P + + A   +
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 252 DNVLIDDRRI 261
               +  +  
Sbjct: 61  KASGVQAQMA 70

>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 = 3e-05
 Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 4/74 (5%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
           PP   L +  + P  S++DL+++FS  G V    V   K      + A ++  + +    
Sbjct: 8   PPSATLHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVEEAVQ 63

Query: 247 AYLKMDNVLIDDRR 260
           A + + N  + +  
Sbjct: 64  ALIDLHNHDLGENH 77

>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 = 3e-05
 Identities = 18/86 (20%), Positives = 28/86 (32%), Gaps = 11/86 (12%)

Query: 183 ADAAPP----ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEF 238
           +   PP    +  + V  L P  S  DL+      G V   +V +D           VE+
Sbjct: 5   SSGGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD-------GMGMVEY 57

Query: 239 DNPKSCEDAYLKMDNVLIDDRRIHAR 264
              +  E A  K+D+           
Sbjct: 58  LRKEDMEYALRKLDDTKFRSHEGETS 83

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.2 bits (93), Expect = 4e-05
 Identities = 16/78 (20%), Positives = 29/78 (37%), Gaps = 8/78 (10%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
               V+ V  L     + DL     +FG +    ++  K      + A VEF+N  S ++
Sbjct: 13  SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK------RQALVEFENIDSAKE 66

Query: 247 A--YLKMDNVLIDDRRIH 262
              +     V I  ++  
Sbjct: 67  CVTFAADVPVYIAGQQAF 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 = 39.7 bits (92), Expect = 4e-05
 Identities = 8/71 (11%), Positives = 22/71 (30%), Gaps = 7/71 (9%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           + V  L   ++  ++  +   +    C           + + AFV   N +  ++A    
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYDLKYCYVD-------RNKRTAFVTLLNGEQAQNAIQMF 60

Query: 252 DNVLIDDRRIH 262
                  + + 
Sbjct: 61  HQYSFRGKDLI 71

>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 = 39.0 bits (90), Expect = 8e-05
 Identities = 16/71 (22%), Positives = 32/71 (45%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           +FV  +    +++ L+ IFS  G V    ++ D+ TG    Y F E+ + ++   A   +
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70

Query: 252 DNVLIDDRRIH 262
           +      R + 
Sbjct: 71  NGREFSGRALR 81

>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 = 38.0 bits (87), Expect = 1e-04
 Identities = 19/83 (22%), Positives = 39/83 (46%), Gaps = 2/83 (2%)

Query: 180 LPEADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFD 239
           + E   +     LF+  LNP  S  +L++  S     N   V+  + TG + ++ +V+F+
Sbjct: 4   MVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFE 62

Query: 240 NPKSCEDAYLKMDNVLIDDRRIH 262
           + +  E A L++  + +    I 
Sbjct: 63  SAEDLEKA-LELTGLKVFGNEIK 84

>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 = 37.8 bits (87), Expect = 2e-04
 Identities = 10/78 (12%), Positives = 23/78 (29%), Gaps = 9/78 (11%)

Query: 188 PENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
              V+ +            L  +   FG ++   ++           AF+E    +  + 
Sbjct: 7   TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQA 60

Query: 247 A--YLKMDNVLIDDRRIH 262
           A  Y      L+  + + 
Sbjct: 61  AVDYYTTTPALVFGKPVR 78

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.5 bits (86), Expect = 2e-04
 Identities = 13/83 (15%), Positives = 32/83 (38%), Gaps = 6/83 (7%)

Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
                 +F+  L+  + ++ L  +  +FG +    V+    T  S   AF +F   ++ +
Sbjct: 5   VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQ 64

Query: 246 DA------YLKMDNVLIDDRRIH 262
                     +   + +D R++ 
Sbjct: 65  KCLAAASLEAEGGGLKLDGRQLK 87

>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 = 36.1 bits (83), Expect = 8e-04
 Identities = 13/62 (20%), Positives = 24/62 (38%), Gaps = 2/62 (3%)

Query: 204 DDLEIIFSRFGKVNCCEVIRDKVTGDSLQ--YAFVEFDNPKSCEDAYLKMDNVLIDDRRI 261
           +D+    S++G V   E+ R     +       FVEF +   C+ A   +      +R +
Sbjct: 29  EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 88

Query: 262 HA 263
             
Sbjct: 89  VT 90

>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 = 35.2 bits (80), Expect = 0.001
 Identities = 16/74 (21%), Positives = 29/74 (39%), Gaps = 5/74 (6%)

Query: 187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCED 246
           PP  +LF+  L   T++  L ++F++F       ++ ++        AFVEF        
Sbjct: 6   PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFTTELQSNA 60

Query: 247 AYLKMDNVLIDDRR 260
           A   +    I    
Sbjct: 61  AKEALQGFKITPTH 74

>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 = 34.3 bits (78), Expect = 0.002
 Identities = 8/74 (10%), Positives = 23/74 (31%), Gaps = 2/74 (2%)

Query: 189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAY 248
              +++       + DD++              +R  +        FV FD+ +S +   
Sbjct: 6   NRSVYIKGFPTDATLDDIKEWLEDK-GQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKF- 63

Query: 249 LKMDNVLIDDRRIH 262
           ++       +  + 
Sbjct: 64  VETPGQKYKETDLL 77

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.1 bits (78), Expect = 0.003
 Identities = 7/69 (10%), Positives = 21/69 (30%), Gaps = 8/69 (11%)

Query: 193 FVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMD 252
            V      ++   L   F+++G +    +           +  + + +      A L  D
Sbjct: 8   TVFGFPQASASYILLQ-FAQYGNILKHVMSNTG------NWMHIRYQSKLQARKA-LSKD 59

Query: 253 NVLIDDRRI 261
             +  +  +
Sbjct: 60  GRIFGESIM 68

>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 = 33.7 bits (76), Expect = 0.003
 Identities = 10/71 (14%), Positives = 22/71 (30%), Gaps = 7/71 (9%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           + +  L    ++ ++  + S +    C               AFV   N +  E A    
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKYCF-------VDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 252 DNVLIDDRRIH 262
               + +R + 
Sbjct: 54  HQSRLRERELS 64

>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 = 34.1 bits (77), Expect = 0.004
 Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 8/79 (10%)

Query: 186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCE 245
             P  VL + KL    ++ ++  +   FGKV    +++ K        AF+E    ++  
Sbjct: 5   GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQAFLELATEEAAI 58

Query: 246 DA--YLKMDNVLIDDRRIH 262
               Y       + ++ I+
Sbjct: 59  TMVNYYSAVTPHLRNQPIY 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 = 34.0 bits (77), Expect = 0.004
 Identities = 12/73 (16%), Positives = 23/73 (31%), Gaps = 1/73 (1%)

Query: 192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM 251
           L++  L     + +LE +   F        I    +G S    F   ++ + CE      
Sbjct: 21  LYISNLPLSMDEQELENMLKPF-GQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 79

Query: 252 DNVLIDDRRIHAR 264
           +   I      + 
Sbjct: 80  NGKFIKTPPGVSA 92

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	309
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.84
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.83
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.83
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.83
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.83
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.83
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.83
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.82
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.82
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.82
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.8
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.8
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.8
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.8
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.8
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.8
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.79
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.79
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.79
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.79
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.79
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.79
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.79
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.79
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.79
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.78
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.78
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.78
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.77
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.77
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.77
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.77
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.77
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.76
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.76
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.76
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.75
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.73
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.73
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.72
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.72
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.72
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.72
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.71
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.71
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.71
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.71
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.71
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.7
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.7
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.7
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.7
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.69
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.68
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.68
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.68
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.68
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.68
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.67
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.67
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.67
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.66
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.65
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.65
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.65
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.65
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.64
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.63
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.63
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.62
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.59
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.59
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.59
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.57
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.56
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.54
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.53
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	99.47
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.46
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.4
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.4
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.33
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.32
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.31
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.4
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.92
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.68
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	93.08

>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=99.84  E-value=5.2e-21  Score=141.64  Aligned_cols=80  Identities=26%  Similarity=0.454  Sum_probs=77.6

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      +++|||+|||+++|+++|..+|++||.|.++.+++++.+|.++|||||+|.+.++|++|+..|||..++|+.|+|++|++
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            57899999999999999999999999999999999999999999999999999999999999999999999999999975

>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=99.83  E-value=1.5e-20  Score=141.33  Aligned_cols=82  Identities=22%  Similarity=0.299  Sum_probs=78.5

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      .+.+|||+|||+.+|+++|..+|++||.|.++.++.|+.||.++|||||+|.+.++|++|+..|||..++|+.|.|+||.
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~   85 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF   85 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEec
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             Cc
Q psy15676        268 WN  269 (309)
Q Consensus       268 ~~  269 (309)
                      ++
T Consensus        86 ~k   87 (88)
T d1rk8a_          86 VK   87 (88)
T ss_dssp             EC
T ss_pred             CC
Confidence            65

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.1e-20  Score=139.39  Aligned_cols=79  Identities=29%  Similarity=0.392  Sum_probs=76.2

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      .+|||+|||+.+|+++|..+|++||.|.++.++.|+.||.++|||||+|.+.++|..|++.|||..++|++|+|++|+.
T Consensus         1 aslfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           1 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            3699999999999999999999999999999999999999999999999999999999999999999999999999964

>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=99.83  E-value=2.3e-20  Score=141.73  Aligned_cols=82  Identities=22%  Similarity=0.317  Sum_probs=79.0

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      .++++|||+|||+++|+++|+.+|++||.|.++.++.++.+|.++|||||+|.+.++|..|++.|||..++|+.|+|+||
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            46689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cC
Q psy15676        267 EW  268 (309)
Q Consensus       267 ~~  268 (309)
                      .+
T Consensus        85 ~~   86 (93)
T d1h2vz_          85 AG   86 (93)
T ss_dssp             SC
T ss_pred             CC
Confidence            75

>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=99.83  E-value=2.3e-20  Score=137.99  Aligned_cols=80  Identities=26%  Similarity=0.537  Sum_probs=77.2

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      .++|||+|||+++++++|+.+|++||.|.++.++.+..+|.++|||||+|.+.++|+.|+..|||..++|+.|+|++|++
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            36799999999999999999999999999999999999999999999999999999999999999999999999999975

>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=99.83  E-value=1.5e-20  Score=145.22  Aligned_cols=86  Identities=30%  Similarity=0.421  Sum_probs=81.6

Q ss_pred             CCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       185 ~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      ..|++++|||+|||+++++++|..+|++||.|.++.++.++.+|.++|||||+|.+.++|..|+..|||..|+|+.|.|+
T Consensus        14 ~~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~   93 (102)
T d2cpza1          14 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ   93 (102)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            35778899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecCch
Q psy15676        265 GEEWNM  270 (309)
Q Consensus       265 ~a~~~~  270 (309)
                      +|+++.
T Consensus        94 ~a~~k~   99 (102)
T d2cpza1          94 LKRSKN   99 (102)
T ss_dssp             CCCCSC
T ss_pred             EeCCCC
Confidence            998753

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=7.6e-21  Score=143.13  Aligned_cols=83  Identities=24%  Similarity=0.277  Sum_probs=79.2

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ...++|||+|||+++|+++|+.+|++||.|.++.++.|+.||.++|||||+|.+.++|.+|+..|||..++|+.|.|++|
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a   82 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   82 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCc
Q psy15676        267 EWN  269 (309)
Q Consensus       267 ~~~  269 (309)
                      +++
T Consensus        83 ~p~   85 (89)
T d2cqba1          83 KPM   85 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>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=99.82  E-value=1.8e-20  Score=142.26  Aligned_cols=85  Identities=24%  Similarity=0.298  Sum_probs=80.2

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .++.++|||+|||+.+|+++|+.+|++||.|.++.++.++.||.++|||||+|.+.++|.+|+..|||..++|+.|+|++
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      |.++.
T Consensus        86 A~~~~   90 (93)
T d1x5ua1          86 ASAHN   90 (93)
T ss_dssp             TTTTS
T ss_pred             cCCCC
Confidence            97643

>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=99.82  E-value=2.3e-20  Score=140.77  Aligned_cols=83  Identities=22%  Similarity=0.320  Sum_probs=79.3

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      .+.++|||+|||+++++++|..+|++||.|.++.++.++.||.++|||||+|.+.++|.+|+..|||..++|+.|.|++|
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            45689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCc
Q psy15676        267 EWN  269 (309)
Q Consensus       267 ~~~  269 (309)
                      ++.
T Consensus        86 kp~   88 (90)
T d2cq0a1          86 KPS   88 (90)
T ss_dssp             SCC
T ss_pred             eCC
Confidence            763

>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=99.82  E-value=3.6e-20  Score=137.44  Aligned_cols=78  Identities=28%  Similarity=0.471  Sum_probs=74.8

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA  263 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V  263 (309)
                      .+|.++|||+|||+.+|+++|+.+|++||.|.++.++.++.||.++|||||+|.+.++|.+|+..|||..++|++|+|
T Consensus         6 p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            346789999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.81  E-value=6.2e-20  Score=140.73  Aligned_cols=84  Identities=27%  Similarity=0.413  Sum_probs=79.6

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      .+.++|||+|||+++++++|+.+|++||.|.++.++.++.||.++|||||+|.+.++|.+|+..|||..++|+.|+|.+|
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            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCch
Q psy15676        267 EWNM  270 (309)
Q Consensus       267 ~~~~  270 (309)
                      +.+.
T Consensus        86 ~~~~   89 (99)
T d1whwa_          86 TIKK   89 (99)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            8643

>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=99.80  E-value=5e-20  Score=135.98  Aligned_cols=80  Identities=10%  Similarity=0.191  Sum_probs=70.1

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      ++||||+|||+++|+++|.++|++||.|..+.++.+..+|.++|||||+|.+.++|.+|+..|||..++|++|.|++|++
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            37999999999999999999999999999988888888999999999999999999999999999999999999999975

>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=99.80  E-value=4.9e-20  Score=137.55  Aligned_cols=79  Identities=22%  Similarity=0.437  Sum_probs=76.6

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      .+|||+|||+++|+++|..+|++||.|.++.+++|+.||.++|||||+|.+.++|..|+..|||..++|++|.|.+|.+
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~   80 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASV   80 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            4799999999999999999999999999999999999999999999999999999999999999999999999999975

>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=99.80  E-value=1.8e-19  Score=136.00  Aligned_cols=82  Identities=27%  Similarity=0.321  Sum_probs=75.9

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ...++|||+|||+++|+++|+.+|++||.|.++.++.|+.||.++|||||+|.+.++|.+|++  ++..++|+.|.|.+|
T Consensus         6 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~--~~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           6 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh--cCCccCCEEeEEEeC
Confidence            356789999999999999999999999999999999999999999999999999999999997  456899999999999


Q ss_pred             cCch
Q psy15676        267 EWNM  270 (309)
Q Consensus       267 ~~~~  270 (309)
                      .++.
T Consensus        84 ~~k~   87 (90)
T d2cqga1          84 NSKQ   87 (90)
T ss_dssp             CTTC
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=99.80  E-value=1.4e-19  Score=134.80  Aligned_cols=79  Identities=24%  Similarity=0.364  Sum_probs=75.1

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      .++|||+|||+++|+++|..+|++||.|..+.++.|+.||.++|||||+|.+.++|.+|+. ++|..|+|+.|.|..|.+
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~s   84 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeeeC
Confidence            4689999999999999999999999999999999999999999999999999999999996 699999999999998854

>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=99.80  E-value=9e-20  Score=138.62  Aligned_cols=84  Identities=15%  Similarity=0.330  Sum_probs=78.0

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCC-CCCcccEEEEEecCHHHHHHHHHHc-CCceeCCeeEEEE
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKV-TGDSLQYAFVEFDNPKSCEDAYLKM-DNVLIDDRRIHAR  264 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~-tg~skG~aFV~F~~~~~a~~Al~~l-~g~~i~gr~I~V~  264 (309)
                      .+.++|||+|||+++++++|+.+|++||.|.++.++.+.. +|.++|||||+|.+.++|.+|+..| ||..++|++|.|+
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            4568899999999999999999999999999999998854 8999999999999999999999998 8999999999999


Q ss_pred             eecCch
Q psy15676        265 GEEWNM  270 (309)
Q Consensus       265 ~a~~~~  270 (309)
                      +|.++.
T Consensus        86 ~A~~~~   91 (94)
T d2cpha1          86 WADSEV   91 (94)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            998753

>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=99.80  E-value=1.2e-19  Score=135.40  Aligned_cols=78  Identities=24%  Similarity=0.417  Sum_probs=74.2

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCC--eeEEEEee
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDD--RRIHARGE  266 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~g--r~I~V~~a  266 (309)
                      +++|||+|||+++|+++|+.+|++||.|.++.++.|+.+|.++|||||+|.+.++|..|++.|||..++|  ++|.|+||
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            4789999999999999999999999999999999999999999999999999999999999999999997  55899886

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=2.9e-20  Score=136.28  Aligned_cols=76  Identities=25%  Similarity=0.427  Sum_probs=73.3

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ++|||+|||+++|+++|+.+|++||.|.++.++.|+.||.++|||||+|.+.++|.+|+. ++++.++|+.|.|+.|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            579999999999999999999999999999999999999999999999999999999996 7999999999999986

>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=99.79  E-value=1.5e-19  Score=132.68  Aligned_cols=77  Identities=27%  Similarity=0.367  Sum_probs=74.1

Q ss_pred             EEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       191 ~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      +|||+|||+++++++|..+|++||.|.++.++.++ +|.++|||||+|.+.++|..|+..|||..++|++|+|++|.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            69999999999999999999999999999999886 799999999999999999999999999999999999999864

>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=99.79  E-value=1.7e-19  Score=134.37  Aligned_cols=79  Identities=27%  Similarity=0.529  Sum_probs=75.3

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCC--eeEEEEe
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDD--RRIHARG  265 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~g--r~I~V~~  265 (309)
                      .+++|||+|||+++++++|+.+|++||.|.++.+++++.+|.++|||||+|.+.++|.+|++.|||..+.|  ++|.|++
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            45789999999999999999999999999999999999999999999999999999999999999999976  8899998


Q ss_pred             e
Q psy15676        266 E  266 (309)
Q Consensus       266 a  266 (309)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.79  E-value=1.9e-19  Score=146.25  Aligned_cols=83  Identities=20%  Similarity=0.341  Sum_probs=78.9

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      ..++|||+|||+++|+++|+.+|++||.|.++.++.++.||.++|||||+|.+.++|..|+..|||..|+|+.|+|.+|+
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            34689999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             Cch
Q psy15676        268 WNM  270 (309)
Q Consensus       268 ~~~  270 (309)
                      +..
T Consensus       121 ~~~  123 (139)
T d1u6fa1         121 SGH  123 (139)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.1e-19  Score=134.84  Aligned_cols=79  Identities=27%  Similarity=0.366  Sum_probs=74.4

Q ss_pred             EEecCCCCCCCHHHHHHHHhcCCceeE-EEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecCch
Q psy15676        192 LFVCKLNPVTSDDDLEIIFSRFGKVNC-CEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWNM  270 (309)
Q Consensus       192 lfV~nL~~~~te~~L~~~F~~fG~I~~-v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~~~  270 (309)
                      |||+|||+++|+++|..+|++||.|.. +.++.++.||.++|||||+|.+.++|..|+..|+|..++|++|+|++|.++.
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            799999999999999999999999965 4789999999999999999999999999999999999999999999998643

>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=99.79  E-value=3.8e-19  Score=133.96  Aligned_cols=82  Identities=20%  Similarity=0.315  Sum_probs=75.7

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ++.++|||+|||+++|+++|+.+|++||.|.++.++.+..++  +|||||+|.+.++|..|+..|+|..++|+.|+|++|
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            456799999999999999999999999999999999987554  799999999999999999999999999999999999


Q ss_pred             cCch
Q psy15676        267 EWNM  270 (309)
Q Consensus       267 ~~~~  270 (309)
                      +++.
T Consensus        84 ~~~~   87 (90)
T d2cqia1          84 TTPS   87 (90)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            7643

>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=99.79  E-value=1.5e-19  Score=136.01  Aligned_cols=83  Identities=30%  Similarity=0.487  Sum_probs=78.7

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      ...+|||+|||+++++++|..+|++||.|..+.++.+..+|.++|||||+|.+.++|+.|+..|||..++|+.|+|++|.
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            45789999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             Cch
Q psy15676        268 WNM  270 (309)
Q Consensus       268 ~~~  270 (309)
                      ++.
T Consensus        84 ~~~   86 (90)
T d1x5sa1          84 KSS   86 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.79  E-value=1.2e-19  Score=140.24  Aligned_cols=81  Identities=20%  Similarity=0.357  Sum_probs=77.5

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      .++|||+|||+++++++|..+|++||.|.++.++.++.||.++|||||+|.+.++|.+|+..|||..++|+.|.|++|.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            36899999999999999999999999999999999999999999999999999999999999999999999999999865


Q ss_pred             c
Q psy15676        269 N  269 (309)
Q Consensus       269 ~  269 (309)
                      +
T Consensus        88 ~   88 (104)
T d1p1ta_          88 E   88 (104)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.79  E-value=5.6e-19  Score=138.56  Aligned_cols=80  Identities=15%  Similarity=0.223  Sum_probs=73.9

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      +.+++|||+|||+.+++++|..+|++||.|.+|.+..   ++.++|||||+|.+.++|..|+..|||..|+|+.|.|.++
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 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC---STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc---cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            3567999999999999999999999999999999875   4677999999999999999999999999999999999998


Q ss_pred             cCc
Q psy15676        267 EWN  269 (309)
Q Consensus       267 ~~~  269 (309)
                      ...
T Consensus        82 ~~~   84 (114)
T d2f9da1          82 NAN   84 (114)
T ss_dssp             CHH
T ss_pred             CCC
Confidence            754

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.7e-19  Score=138.99  Aligned_cols=78  Identities=26%  Similarity=0.259  Sum_probs=74.9

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      ++|||+|||+++++++|+.+|+.||.|.++.++.+..||.++|||||+|.+.++|.+|+. |||..++|+.|.|++|++
T Consensus        19 ~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          19 RTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             TEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            689999999999999999999999999999999999999999999999999999999995 999999999999999853

>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=99.78  E-value=1.4e-19  Score=131.76  Aligned_cols=75  Identities=27%  Similarity=0.433  Sum_probs=71.6

Q ss_pred             EEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       191 ~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      +|||+|||+++|+++|..+|++||.|.++.++.++.||+++|||||+|.+.++|++|+. +++..|+|+.|.|..|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            48999999999999999999999999999999999999999999999999999999996 7999999999999754

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=4.9e-19  Score=136.75  Aligned_cols=81  Identities=28%  Similarity=0.382  Sum_probs=75.8

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      ..++|||+|||+.+++++|+++|++||.|.++.++.++.||.++|||||+|.+.++|.+|++.+|+ .++|+.|.|++|.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            446899999999999999999999999999999999999999999999999999999999998776 7999999999987


Q ss_pred             Cc
Q psy15676        268 WN  269 (309)
Q Consensus       268 ~~  269 (309)
                      ..
T Consensus        88 ~~   89 (103)
T d2cqda1          88 LG   89 (103)
T ss_dssp             TT
T ss_pred             CC
Confidence            53

>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=99.78  E-value=3.6e-19  Score=132.53  Aligned_cols=77  Identities=26%  Similarity=0.543  Sum_probs=72.8

Q ss_pred             EEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCC---CcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTG---DSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       192 lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg---~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      |||+|||+++|+++|+.+|++||.|.++.++.++.++   .++|||||+|.+.++|.+|+..|||..++|+.|.|++|++
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            7999999999999999999999999999999987665   4789999999999999999999999999999999999864

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=7.7e-19  Score=128.82  Aligned_cols=76  Identities=22%  Similarity=0.449  Sum_probs=73.1

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ++|||+|||+++|+++|+++|++||.|..+.++.++.++.++|||||+|.+.+++.+|+. ++|..|+|+.|+|+.|
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            689999999999999999999999999999999999999999999999999999999995 8999999999999876

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=4.7e-19  Score=136.96  Aligned_cols=79  Identities=24%  Similarity=0.395  Sum_probs=75.6

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecCc
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWN  269 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~~  269 (309)
                      ++|||+|||+++++++|+.+|++||.|..+.|+.|+.|+.++|||||+|.+.++|.+|++ ++|..|+|+.|.|.+|.++
T Consensus        21 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          21 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSSC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECccc
Confidence            689999999999999999999999999999999999999999999999999999999995 7999999999999998764

>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=99.77  E-value=2e-18  Score=130.81  Aligned_cols=82  Identities=24%  Similarity=0.404  Sum_probs=76.1

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ....++|||+|||+++++++|..+|++||.|.++.++.+..  .++|||||+|.+.++|.+|+..|||..++|+.|.|++
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   85 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   85 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            45567999999999999999999999999999999998864  4789999999999999999999999999999999999


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      |+++
T Consensus        86 A~~r   89 (93)
T d2cq3a1          86 ATAR   89 (93)
T ss_dssp             CCSS
T ss_pred             cCcC
Confidence            9864

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=1.2e-19  Score=139.59  Aligned_cols=88  Identities=19%  Similarity=0.264  Sum_probs=82.0

Q ss_pred             CCCCCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeE
Q psy15676        182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI  261 (309)
Q Consensus       182 ~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I  261 (309)
                      ......|.++|||+|||+++++++|..+|++||.|..+.++.+..+|.++|||||+|.+.++|..|+..|||..|+|++|
T Consensus        11 ~~~~~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l   90 (102)
T d2cpxa1          11 SYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKIL   90 (102)
T ss_dssp             CCCCCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEE
Confidence            44456678999999999999999999999999999999998888899999999999999999999999999999999999


Q ss_pred             EEEeecCc
Q psy15676        262 HARGEEWN  269 (309)
Q Consensus       262 ~V~~a~~~  269 (309)
                      .|++|+++
T Consensus        91 ~V~~ak~k   98 (102)
T d2cpxa1          91 VIEFGKNK   98 (102)
T ss_dssp             EEEECCCC
T ss_pred             EEEeCCCc
Confidence            99999864

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=8e-19  Score=134.57  Aligned_cols=85  Identities=21%  Similarity=0.266  Sum_probs=77.8

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCcee--------EEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeC
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVN--------CCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLID  257 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~--------~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~  257 (309)
                      .+..++|||+|||+.+|+++|..+|++||.|.        .+.+..++.+|.++|||||+|.+.++|.+|++.|||..++
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            35678999999999999999999999999873        5677888889999999999999999999999999999999


Q ss_pred             CeeEEEEeecCch
Q psy15676        258 DRRIHARGEEWNM  270 (309)
Q Consensus       258 gr~I~V~~a~~~~  270 (309)
                      |+.|+|++|+++.
T Consensus        85 gr~i~V~~a~~~~   97 (101)
T d2cpea1          85 GSKLKVSLARKKP   97 (101)
T ss_dssp             TEECEEECSSCCC
T ss_pred             CEEEEEEEcCCCC
Confidence            9999999998643

>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=99.77  E-value=2.4e-19  Score=130.64  Aligned_cols=75  Identities=19%  Similarity=0.318  Sum_probs=71.4

Q ss_pred             EEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       191 ~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      +|||||||+++|+++|+.+|++||.|.++.++.++.||.++|||||+|.+.++|.+|++ ++++.++|+.|.|..|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~-~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTT-CSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHh-hCCCEECCEEeEEEEC
Confidence            58999999999999999999999999999999999999999999999999999999996 5888999999999875

>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=99.76  E-value=7e-19  Score=132.19  Aligned_cols=79  Identities=28%  Similarity=0.503  Sum_probs=73.9

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      ..+|||+|||+++++++|..+|++||.|.++.++.+.  +.++|||||+|.+.++|.+|+..|||..++|+.|.|.+|++
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 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999999999999886  44789999999999999999999999999999999999976


Q ss_pred             c
Q psy15676        269 N  269 (309)
Q Consensus       269 ~  269 (309)
                      +
T Consensus        86 ~   86 (89)
T d1cvja2          86 R   86 (89)
T ss_dssp             T
T ss_pred             C
Confidence            4

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=1.5e-18  Score=132.28  Aligned_cols=83  Identities=16%  Similarity=0.274  Sum_probs=77.6

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcC------CceeCCee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMD------NVLIDDRR  260 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~------g~~i~gr~  260 (309)
                      ..+++|||+|||+++|+++|+.+|++||.|.++.++.+..++.++|||||+|.+.++|.+|++.+|      |..++|+.
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            456899999999999999999999999999999999999999999999999999999999999886      67899999


Q ss_pred             EEEEeecCc
Q psy15676        261 IHARGEEWN  269 (309)
Q Consensus       261 I~V~~a~~~  269 (309)
                      |+|++|.++
T Consensus        86 l~v~~a~~k   94 (98)
T d1x4ha1          86 LKVDLAVTR   94 (98)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEECCCC
Confidence            999999764

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=5.3e-19  Score=128.26  Aligned_cols=75  Identities=24%  Similarity=0.393  Sum_probs=72.2

Q ss_pred             EEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        191 VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       191 ~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      +|||+|||+++|+++|+.+|++||.|..+.++.++.+|.++|||||+|.+.++|.+|++ +||..++|+.|+|+.|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            48999999999999999999999999999999999999999999999999999999996 9999999999999876

>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=99.75  E-value=7.8e-19  Score=131.12  Aligned_cols=81  Identities=21%  Similarity=0.270  Sum_probs=70.6

Q ss_pred             CCcEEEecCCCCCCC-HHHHHHHHhcCCceeEEEEeee-CCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        188 PENVLFVCKLNPVTS-DDDLEIIFSRFGKVNCCEVIRD-KVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       188 ~~~~lfV~nL~~~~t-e~~L~~~F~~fG~I~~v~i~~d-~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..++|||+|||++++ +++|+++|++||.|.++.++.+ ..+|.++|||||+|.+.++|.+|++ |||..++|+.|+|++
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            357999999999876 5669999999999999998764 5689999999999999999999995 999999999999999


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      |.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9764

>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=99.73  E-value=9.8e-18  Score=127.32  Aligned_cols=80  Identities=24%  Similarity=0.406  Sum_probs=73.6

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..++++|||+|||+++|+++|+.+|++||.|..+.+..   ++.++|||||+|.+.++|..|+..|||..++|++|+|++
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 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN---RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC---SSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecc---cccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            45678999999999999999999999999999988754   356789999999999999999999999999999999999


Q ss_pred             ecC
Q psy15676        266 EEW  268 (309)
Q Consensus       266 a~~  268 (309)
                      |++
T Consensus        88 a~~   90 (95)
T d1x4aa1          88 PRS   90 (95)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            975

>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=99.73  E-value=6.9e-19  Score=132.92  Aligned_cols=81  Identities=21%  Similarity=0.299  Sum_probs=74.1

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .....+|||+|||+++|+++|+.+|++||.|.++.++.+ .+|+++|||||+|.+.++|.+|++ |||..++|+.|.|.+
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~   87 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEK   87 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEEC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEe
Confidence            345579999999999999999999999999998888654 589999999999999999999995 999999999999999


Q ss_pred             ecC
Q psy15676        266 EEW  268 (309)
Q Consensus       266 a~~  268 (309)
                      |++
T Consensus        88 ak~   90 (91)
T d1fjeb1          88 PKG   90 (91)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            975

>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=99.72  E-value=7.7e-18  Score=128.31  Aligned_cols=77  Identities=18%  Similarity=0.321  Sum_probs=71.8

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ++.++|||+|||+.+++++|+.+|++||.|.++.++.+      +|||||+|.+.++|..|+..|||..|+|+.|+|.|+
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            45679999999999999999999999999999999864      689999999999999999999999999999999999


Q ss_pred             cCc
Q psy15676        267 EWN  269 (309)
Q Consensus       267 ~~~  269 (309)
                      +++
T Consensus        90 k~~   92 (96)
T d1x4ga1          90 KES   92 (96)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>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=99.72  E-value=1.2e-17  Score=124.85  Aligned_cols=80  Identities=18%  Similarity=0.308  Sum_probs=72.0

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCcee-CCeeEEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLI-DDRRIHAR  264 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i-~gr~I~V~  264 (309)
                      -||.++|||+|||+++++++|..+|++||.|..+.+..    ++++|||||+|.+.++|.+|+..|+|..+ +|+.|+|+
T Consensus         7 ~pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~   82 (88)
T d2adca2           7 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS   82 (88)
T ss_dssp             CCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEE
Confidence            46789999999999999999999999999998876653    45679999999999999999999999988 58999999


Q ss_pred             eecCc
Q psy15676        265 GEEWN  269 (309)
Q Consensus       265 ~a~~~  269 (309)
                      ||++.
T Consensus        83 ~sk~~   87 (88)
T d2adca2          83 FSKST   87 (88)
T ss_dssp             ECSSC
T ss_pred             eCCCC
Confidence            99763

>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=99.72  E-value=1.2e-17  Score=123.68  Aligned_cols=77  Identities=21%  Similarity=0.357  Sum_probs=70.8

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCcee-CCeeEEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLI-DDRRIHAR  264 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i-~gr~I~V~  264 (309)
                      .||+++|||+|||+++++++|..+|++||.|..+.++.+     .+|||||+|.+.++|..|+..|+|..+ +|++|+|+
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~   79 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKIT   79 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEE
Confidence            578899999999999999999999999999999999754     368999999999999999999999888 57899999


Q ss_pred             eec
Q psy15676        265 GEE  267 (309)
Q Consensus       265 ~a~  267 (309)
                      ||+
T Consensus        80 ~ak   82 (83)
T d2b0ga1          80 FAK   82 (83)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            985

>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=99.72  E-value=7.8e-18  Score=128.14  Aligned_cols=81  Identities=17%  Similarity=0.192  Sum_probs=73.0

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ..+.++|||+|||+++|+++|+.+|++||.|..+.     .+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~   87 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34568999999999999999999999999886654     2688999999999999999999999999999999999999


Q ss_pred             ecCchh
Q psy15676        266 EEWNMW  271 (309)
Q Consensus       266 a~~~~~  271 (309)
                      |.++..
T Consensus        88 a~~k~~   93 (96)
T d1fjca_          88 TGEKGG   93 (96)
T ss_dssp             CSSSCC
T ss_pred             eCCCCC
Confidence            987543

>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=2.2e-17  Score=122.90  Aligned_cols=77  Identities=13%  Similarity=0.093  Sum_probs=71.9

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      .++|||+|||+++|+++|..+|+.||.|..+.+..+. +|.++|||||+|.+.++|.+|++ ++|..+.|+.|.|.++.
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            4799999999999999999999999999999998775 89999999999999999999995 79999999999998753

>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=99.71  E-value=1.8e-17  Score=123.37  Aligned_cols=78  Identities=22%  Similarity=0.264  Sum_probs=70.6

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      ....++|||+|||+++++++|..+|++||.|..+.+      +.++|||||+|.+.++|..|+..|||..|+|+.|.|++
T Consensus         5 ~~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~------~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~   78 (86)
T d2cpda1           5 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTL   78 (86)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEE------EECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             ccCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEE------ccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            345579999999999999999999999999987766      34679999999999999999999999999999999999


Q ss_pred             ecCc
Q psy15676        266 EEWN  269 (309)
Q Consensus       266 a~~~  269 (309)
                      |++.
T Consensus        79 akP~   82 (86)
T d2cpda1          79 AKPV   82 (86)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            9764

>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=99.71  E-value=1e-17  Score=124.73  Aligned_cols=81  Identities=15%  Similarity=0.205  Sum_probs=72.6

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .|+..+|||+|||+++++++|..+|+.||.+....++.+..+|.++|||||+|.+.++|.+|+..|||..++|++|+|.+
T Consensus         6 ~p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           6 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            45567899999999999999999999999997654444556899999999999999999999999999999999999987


Q ss_pred             e
Q psy15676        266 E  266 (309)
Q Consensus       266 a  266 (309)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            5

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=7.9e-18  Score=126.85  Aligned_cols=79  Identities=27%  Similarity=0.383  Sum_probs=71.6

Q ss_pred             CCcEEEecCCCCCCCHHHHH----HHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEE
Q psy15676        188 PENVLFVCKLNPVTSDDDLE----IIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA  263 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~----~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V  263 (309)
                      |+++|||+|||+.+++++|+    .+|++||.|.++.+..   ++.++|||||+|.+.++|.+|+..|||..++|+.|+|
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            57899999999999999886    4689999999988753   5778999999999999999999999999999999999


Q ss_pred             EeecCc
Q psy15676        264 RGEEWN  269 (309)
Q Consensus       264 ~~a~~~  269 (309)
                      .+|+++
T Consensus        79 ~~ak~~   84 (91)
T d1nu4a_          79 QYAKTD   84 (91)
T ss_dssp             EECSSC
T ss_pred             EEeCCC
Confidence            999764

>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=99.71  E-value=7.2e-18  Score=126.65  Aligned_cols=76  Identities=24%  Similarity=0.391  Sum_probs=70.0

Q ss_pred             CcEEEecCCCCCCCHHHH---HHHHhcCCceeEEEEeeeCCCCCcc---cEEEEEecCHHHHHHHHHHcCCceeCCeeEE
Q psy15676        189 ENVLFVCKLNPVTSDDDL---EIIFSRFGKVNCCEVIRDKVTGDSL---QYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH  262 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L---~~~F~~fG~I~~v~i~~d~~tg~sk---G~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~  262 (309)
                      .++|||+|||+++++++|   .++|++||.|.++.++.++.++.++   |||||+|.+.++|.+|++.|||..++|+.|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            468999999999999999   6789999999999999998776554   8999999999999999999999999999999


Q ss_pred             EE
Q psy15676        263 AR  264 (309)
Q Consensus       263 V~  264 (309)
                      |+
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            85

>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=99.70  E-value=8.6e-18  Score=129.11  Aligned_cols=81  Identities=20%  Similarity=0.350  Sum_probs=74.7

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ...++|||+|||+++++++|..+|++||.|..+.+..+. ++.++|||||+|.+.++|.+|+..|||..|.|+++.|..+
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            345799999999999999999999999999999988875 7899999999999999999999999999999999988776


Q ss_pred             cC
Q psy15676        267 EW  268 (309)
Q Consensus       267 ~~  268 (309)
                      ++
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            54

>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=99.70  E-value=6.6e-18  Score=131.48  Aligned_cols=77  Identities=18%  Similarity=0.222  Sum_probs=70.8

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      ..++|||+|||+.+++++|+.+|++||.|..|.|.      .++|||||+|.+.++|.+|++.|||..|.|++|.|++|.
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            45799999999999999999999999999998873      457999999999999999999999999999999999997


Q ss_pred             Cch
Q psy15676        268 WNM  270 (309)
Q Consensus       268 ~~~  270 (309)
                      ...
T Consensus        83 ~~~   85 (111)
T d1whxa_          83 IGV   85 (111)
T ss_dssp             TTT
T ss_pred             CCc
Confidence            643

>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=99.70  E-value=2.7e-17  Score=126.71  Aligned_cols=82  Identities=13%  Similarity=0.284  Sum_probs=72.7

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeC-CCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDK-VTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~-~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .|.++|||+|||+++|+++|+.+|+.|| +..+.++.+. .+|.++|||||+|.+.++|++|+ .|||..|+|+.|+|++
T Consensus        13 ~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEEEEE
Confidence            4568999999999999999999999999 6677777665 47899999999999999998777 5999999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      |.++.
T Consensus        91 a~~~~   95 (104)
T d1wi8a_          91 ADQAQ   95 (104)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            97643

>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=99.70  E-value=4.9e-18  Score=122.27  Aligned_cols=71  Identities=28%  Similarity=0.500  Sum_probs=68.5

Q ss_pred             EEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEE
Q psy15676        192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH  262 (309)
Q Consensus       192 lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~  262 (309)
                      |||+|||+++|+++|..+|++||.|..+.++.++.++.++|||||+|.+.++|.+|+..|||..++|+.|+
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            79999999999999999999999999999999999999999999999999999999999999999998763

>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=99.69  E-value=2.2e-17  Score=125.52  Aligned_cols=81  Identities=15%  Similarity=0.147  Sum_probs=73.1

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCc-eeEEEEeeeC-CCCCcccEEEEEecCHHHHHHHHHHcCC--ceeCCeeEEEE
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGK-VNCCEVIRDK-VTGDSLQYAFVEFDNPKSCEDAYLKMDN--VLIDDRRIHAR  264 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~-I~~v~i~~d~-~tg~skG~aFV~F~~~~~a~~Al~~l~g--~~i~gr~I~V~  264 (309)
                      +++|||+|||.++++++|+.+|++||. |..+.++.+. .+|.++|||||+|.+.++|..|++.|++  ..++|+.|.|+
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            368999999999999999999999995 8999998875 4689999999999999999999999864  56689999999


Q ss_pred             eecCc
Q psy15676        265 GEEWN  269 (309)
Q Consensus       265 ~a~~~  269 (309)
                      +|.++
T Consensus        81 ~A~p~   85 (96)
T d2disa1          81 WAEPE   85 (96)
T ss_dssp             ESCSS
T ss_pred             EcCCC
Confidence            99764

>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=99.68  E-value=3.8e-17  Score=121.84  Aligned_cols=76  Identities=20%  Similarity=0.423  Sum_probs=70.6

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      ..++|||+|||+++++++|..+|++||.|.++.+..+      +|||||+|.+.++|.+|+..|||..|+|+.|+|++|.
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            4578999999999999999999999999999998754      5899999999999999999999999999999999997


Q ss_pred             Cc
Q psy15676        268 WN  269 (309)
Q Consensus       268 ~~  269 (309)
                      .+
T Consensus        81 ~~   82 (86)
T d2cpja1          81 HS   82 (86)
T ss_dssp             CC
T ss_pred             Cc
Confidence            54

>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=99.68  E-value=4.1e-17  Score=119.65  Aligned_cols=75  Identities=17%  Similarity=0.247  Sum_probs=68.5

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ..+++|||+|++  +|+++|+.+|++||.|.++.+..      .+|||||+|.+.++|..|+..|||..++|++|+|++|
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP------PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET------TTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeecc------CCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            456899999986  89999999999999999998854      4589999999999999999999999999999999999


Q ss_pred             cCc
Q psy15676        267 EWN  269 (309)
Q Consensus       267 ~~~  269 (309)
                      +++
T Consensus        75 ~~~   77 (79)
T d2bz2a1          75 RKQ   77 (79)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            754

>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=99.68  E-value=4.5e-17  Score=124.47  Aligned_cols=78  Identities=27%  Similarity=0.438  Sum_probs=69.9

Q ss_pred             CCCCCCcEEEecCCC-CCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEE
Q psy15676        184 DAAPPENVLFVCKLN-PVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIH  262 (309)
Q Consensus       184 ~~~~~~~~lfV~nL~-~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~  262 (309)
                      +.....++|||+||+ ..+++++|+.+|++||.|.++.+        ++|||||+|.+.++|.+|+..|||..++|+.|+
T Consensus        10 ~~~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~   81 (98)
T d1wf2a_          10 DPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLD   81 (98)
T ss_dssp             CCSSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECE
T ss_pred             CCCCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            344556789999997 56888999999999999999988        468999999999999999999999999999999


Q ss_pred             EEeecCc
Q psy15676        263 ARGEEWN  269 (309)
Q Consensus       263 V~~a~~~  269 (309)
                      |++|..+
T Consensus        82 V~~a~~~   88 (98)
T d1wf2a_          82 INLAAEP   88 (98)
T ss_dssp             EEETTSC
T ss_pred             EEECCCC
Confidence            9999753

>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=99.68  E-value=7.3e-17  Score=117.20  Aligned_cols=74  Identities=14%  Similarity=0.188  Sum_probs=68.0

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ++|||+|||+++++++|+.+|+.||.|..+.++.++.+  ++|||||+|.+.++|.+|+ .+||..|+|++|.|..+
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--NFRFARIEFARYDGALAAI-TKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHH-HhcCcEECCEEEEEEEC
Confidence            48999999999999999999999999999999988753  4579999999999999999 48999999999999865

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=3.3e-17  Score=126.05  Aligned_cols=84  Identities=11%  Similarity=0.101  Sum_probs=73.7

Q ss_pred             CCCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEE
Q psy15676        184 DAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHA  263 (309)
Q Consensus       184 ~~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V  263 (309)
                      +......+|||+|||+++|+++|..+|+.||.+..+.++....+|.++|||||+|.+.++|++|+. +||..|+|+.|.|
T Consensus         3 dv~~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V   81 (103)
T d2cpya1           3 DVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFV   81 (103)
T ss_dssp             SCCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEE
T ss_pred             CCCCCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEE
Confidence            334456789999999999999999999999999775555555689999999999999999999995 8999999999999


Q ss_pred             EeecC
Q psy15676        264 RGEEW  268 (309)
Q Consensus       264 ~~a~~  268 (309)
                      ..+..
T Consensus        82 ~~~~~   86 (103)
T d2cpya1          82 HVVTL   86 (103)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            98753

>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=99.67  E-value=5.6e-17  Score=125.80  Aligned_cols=75  Identities=21%  Similarity=0.368  Sum_probs=69.5

Q ss_pred             CcEEEecCCCC-CCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        189 ENVLFVCKLNP-VTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       189 ~~~lfV~nL~~-~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      +.+|||+|||+ .+|+++|+.+|+.||.|..+.|+.++     +|||||+|.+.++|.+|+..|||..++|+.|.|.+++
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            47999999976 59999999999999999999998763     6899999999999999999999999999999999986


Q ss_pred             C
Q psy15676        268 W  268 (309)
Q Consensus       268 ~  268 (309)
                      .
T Consensus        77 ~   77 (109)
T d2adca1          77 H   77 (109)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.67  E-value=3.8e-17  Score=120.16  Aligned_cols=75  Identities=19%  Similarity=0.261  Sum_probs=67.4

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCc-eeCCeeEEEEeecC
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNV-LIDDRRIHARGEEW  268 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~-~i~gr~I~V~~a~~  268 (309)
                      ++|||+|||+++|+++|+.+|++||.|.++.+..      ++|||||+|.+.++|.+|++.|||. .++|++|.|++|.+
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            4799999999999999999999999987666543      5689999999999999999999995 69999999999987


Q ss_pred             ch
Q psy15676        269 NM  270 (309)
Q Consensus       269 ~~  270 (309)
                      +.
T Consensus        76 k~   77 (80)
T d2cqha1          76 KK   77 (80)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>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=99.67  E-value=1.6e-16  Score=122.40  Aligned_cols=84  Identities=19%  Similarity=0.145  Sum_probs=75.8

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .....+|||+|||+++|+++|+.+|..||.+....++.+..++.++|||||+|.+.++|.+|++ +++..|+||.|.|..
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~   90 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFK   90 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEE
Confidence            3455689999999999999999999999999887777777789999999999999999999995 899999999999999


Q ss_pred             ecCch
Q psy15676        266 EEWNM  270 (309)
Q Consensus       266 a~~~~  270 (309)
                      +....
T Consensus        91 ~~~~~   95 (104)
T d1wg5a_          91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            97643

>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=99.66  E-value=1.9e-16  Score=114.94  Aligned_cols=71  Identities=15%  Similarity=0.251  Sum_probs=64.1

Q ss_pred             EEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecCc
Q psy15676        192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWN  269 (309)
Q Consensus       192 lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~~  269 (309)
                      |||+|||+++++++|+.+|++|| +..+.+      ++++|||||+|.+.++|.+|+..|||..++|++|.|++++.+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 433333      567899999999999999999999999999999999999764

>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=99.65  E-value=2.2e-17  Score=123.31  Aligned_cols=73  Identities=26%  Similarity=0.218  Sum_probs=67.3

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecCc
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEWN  269 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~~  269 (309)
                      ++|||+|||+++++++|..+|++||.|.++.+..+       |||||+|.+.++|++|+..|||..++|+.|.|.+++.+
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            46999999999999999999999999999988543       89999999999999999999999999999999887643

>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=99.65  E-value=1.3e-16  Score=119.47  Aligned_cols=75  Identities=12%  Similarity=0.179  Sum_probs=66.4

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      ..++|||+|||+++++++|+.+|++||. ..+.+      +.++|||||+|.+.++|.+|+..|||..++|++|.|++++
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 GSSGILVKNLPQDSNCQEVHDLLKDYDL-KYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSCC-CCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcCc-eeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            4578999999999999999999999992 22332      4578999999999999999999999999999999999997


Q ss_pred             Cc
Q psy15676        268 WN  269 (309)
Q Consensus       268 ~~  269 (309)
                      .+
T Consensus        77 ~~   78 (88)
T d1wg1a_          77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=6.8e-17  Score=120.90  Aligned_cols=77  Identities=19%  Similarity=0.298  Sum_probs=69.0

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      .+.++|||+|||+.+|+++|+.+|++||.|.++.+.     +.++|||||+|.+.++|++|+.  +++.|+|+.|.|.+|
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNA   75 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeC
Confidence            356899999999999999999999999999998764     4578999999999999999984  889999999999999


Q ss_pred             cCch
Q psy15676        267 EWNM  270 (309)
Q Consensus       267 ~~~~  270 (309)
                      +++.
T Consensus        76 ~~k~   79 (88)
T d1wf0a_          76 EPKH   79 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

>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=1.5e-16  Score=122.33  Aligned_cols=83  Identities=14%  Similarity=0.077  Sum_probs=73.6

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEe
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARG  265 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~  265 (309)
                      .+.+.+|||+|||+++|+++|+.+|+.||. ..+.++.+. +|.++|||||+|.+.++|++|+. +|+..|+||.|.|.+
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~~   88 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEE
Confidence            455679999999999999999999999984 577777775 68999999999999999999985 899999999999999


Q ss_pred             ecCchh
Q psy15676        266 EEWNMW  271 (309)
Q Consensus       266 a~~~~~  271 (309)
                      +.....
T Consensus        89 s~~~~~   94 (102)
T d1weza_          89 NSTAGT   94 (102)
T ss_dssp             ECCCCC
T ss_pred             cCCCCC
Confidence            886543

>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=99.64  E-value=4.7e-16  Score=116.14  Aligned_cols=78  Identities=17%  Similarity=0.203  Sum_probs=70.7

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHc--CCceeCCeeEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM--DNVLIDDRRIHA  263 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l--~g~~i~gr~I~V  263 (309)
                      .+|+++|||+|||+.+++++|..+|++||.|.++.+..+      +|||||+|.+.++|..|+..+  ++..++|++|.|
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            568899999999999999999999999999999988643      589999999999999999865  578999999999


Q ss_pred             EeecCc
Q psy15676        264 RGEEWN  269 (309)
Q Consensus       264 ~~a~~~  269 (309)
                      +||+.+
T Consensus        79 ~~sk~~   84 (88)
T d2cq1a1          79 QYSNHK   84 (88)
T ss_dssp             EECSCS
T ss_pred             EECCCC
Confidence            999754

>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=99.63  E-value=4.2e-16  Score=118.60  Aligned_cols=79  Identities=24%  Similarity=0.399  Sum_probs=71.4

Q ss_pred             CCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCC--eeEEE
Q psy15676        186 APPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDD--RRIHA  263 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~g--r~I~V  263 (309)
                      .+|.++|||+|||+++++++|+++|++||.|..+.+.++      ++||||+|.+.++|..|+..|||..|+|  ++|+|
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v   87 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEE
Confidence            357799999999999999999999999999999988653      5899999999999999999999999986  58999


Q ss_pred             EeecCch
Q psy15676        264 RGEEWNM  270 (309)
Q Consensus       264 ~~a~~~~  270 (309)
                      +||++..
T Consensus        88 ~~ak~~~   94 (97)
T d1whya_          88 DFAKSGP   94 (97)
T ss_dssp             EECCCCC
T ss_pred             EeCCCCC
Confidence            9998643

>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=99.63  E-value=1.5e-16  Score=124.31  Aligned_cols=81  Identities=16%  Similarity=0.147  Sum_probs=73.6

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      .++.+|||+|||+++|+++|..+|+.||.+..+.++.+..+|.++|||||+|.+.++|.+|+. +||..|+|+.|.|..+
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEc
Confidence            456799999999999999999999999999876666777789999999999999999999995 8999999999999987


Q ss_pred             cC
Q psy15676        267 EW  268 (309)
Q Consensus       267 ~~  268 (309)
                      ..
T Consensus        95 ~~   96 (112)
T d1wela1          95 TK   96 (112)
T ss_dssp             CH
T ss_pred             Ch
Confidence            53

>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=99.62  E-value=3.6e-16  Score=121.26  Aligned_cols=79  Identities=23%  Similarity=0.230  Sum_probs=71.2

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCcee--CCeeEEEE
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLI--DDRRIHAR  264 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i--~gr~I~V~  264 (309)
                      .+..+|||+|||+.+|+++|..+|++||.|.++.+..++    ++|||||+|.+.++|..|+..|||..|  .|+.|.|.
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            455789999999999999999999999999999998764    579999999999999999999999988  47889999


Q ss_pred             eecCc
Q psy15676        265 GEEWN  269 (309)
Q Consensus       265 ~a~~~  269 (309)
                      +++..
T Consensus        81 ~s~~~   85 (108)
T d2adba1          81 FSKLT   85 (108)
T ss_dssp             ECSSC
T ss_pred             ecCCc
Confidence            88753

>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=99.59  E-value=1.9e-15  Score=115.29  Aligned_cols=74  Identities=20%  Similarity=0.167  Sum_probs=68.9

Q ss_pred             CCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeec
Q psy15676        188 PENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEE  267 (309)
Q Consensus       188 ~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~  267 (309)
                      +..+|||+|||+.+++++|..+|++||.|.++.+..       +|||||+|.+.++|.+|++.|||..++|+.|.|.+++
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~   86 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIR   86 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEe
Confidence            456899999999999999999999999999998853       4899999999999999999999999999999999987


Q ss_pred             C
Q psy15676        268 W  268 (309)
Q Consensus       268 ~  268 (309)
                      .
T Consensus        87 ~   87 (98)
T d1wg4a_          87 V   87 (98)
T ss_dssp             E
T ss_pred             c
Confidence            5

>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=99.59  E-value=3.4e-15  Score=114.90  Aligned_cols=79  Identities=19%  Similarity=0.189  Sum_probs=70.9

Q ss_pred             CCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHc--CCceeCCeeEE
Q psy15676        185 AAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM--DNVLIDDRRIH  262 (309)
Q Consensus       185 ~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l--~g~~i~gr~I~  262 (309)
                      ..+|..+|||+|||+.+|+++|..+|++||.|.++.+.+      .+|||||+|.+.++|..|+..|  ++..++|++|.
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~------~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP------FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEe------cceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            356788999999999999999999999999999998864      4689999999999999999977  56789999999


Q ss_pred             EEeecCc
Q psy15676        263 ARGEEWN  269 (309)
Q Consensus       263 V~~a~~~  269 (309)
                      |+||+.+
T Consensus        85 v~~s~~~   91 (104)
T d1wexa_          85 FNYSTSK   91 (104)
T ss_dssp             EEECSSS
T ss_pred             EEEcCCC
Confidence            9999753

>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=99.59  E-value=3.7e-15  Score=124.97  Aligned_cols=81  Identities=21%  Similarity=0.379  Sum_probs=76.7

Q ss_pred             CCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        187 PPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      .+.++|||+|||+.+|+++|+.+|+.||.|..+.++.+..+|.++|||||+|.+.++|.+|+. +++..++|++|.|.+|
T Consensus        95 ~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A  173 (183)
T d1u1qa_          95 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA  173 (183)
T ss_dssp             CCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEEC
T ss_pred             cccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEec
Confidence            456899999999999999999999999999999999999999999999999999999999996 7999999999999998


Q ss_pred             cC
Q psy15676        267 EW  268 (309)
Q Consensus       267 ~~  268 (309)
                      .+
T Consensus       174 ~~  175 (183)
T d1u1qa_         174 LS  175 (183)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=99.57  E-value=3.5e-15  Score=111.75  Aligned_cols=78  Identities=12%  Similarity=0.170  Sum_probs=69.5

Q ss_pred             CCCCcEEEecCCCCC-CCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHc--CCceeCCeeEE
Q psy15676        186 APPENVLFVCKLNPV-TSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM--DNVLIDDRRIH  262 (309)
Q Consensus       186 ~~~~~~lfV~nL~~~-~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l--~g~~i~gr~I~  262 (309)
                      ..++++|||+|||.. +|+++|..+|++||.|.++.++.+      +++|||.|.+.++|..|+..+  ++..++|++|.
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            456789999999986 789999999999999999999754      469999999999999999865  67899999999


Q ss_pred             EEeecCc
Q psy15676        263 ARGEEWN  269 (309)
Q Consensus       263 V~~a~~~  269 (309)
                      |+||++.
T Consensus        79 V~~s~~~   85 (89)
T d1x4da1          79 VHLSQKY   85 (89)
T ss_dssp             EEEECCC
T ss_pred             EEECCCc
Confidence            9999753

>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=99.56  E-value=2.9e-15  Score=114.37  Aligned_cols=76  Identities=16%  Similarity=0.179  Sum_probs=68.4

Q ss_pred             CCCcEEEecCCCCC-CCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHH--HcCCceeCCeeEEE
Q psy15676        187 PPENVLFVCKLNPV-TSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYL--KMDNVLIDDRRIHA  263 (309)
Q Consensus       187 ~~~~~lfV~nL~~~-~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~--~l~g~~i~gr~I~V  263 (309)
                      .++++|||+|||.. +|+++|..+|++||.|.++.++.+      +|||||+|.+.++|..|+.  .+++..++|++|.|
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            45689999999985 899999999999999999998643      5899999999999999997  57889999999999


Q ss_pred             EeecC
Q psy15676        264 RGEEW  268 (309)
Q Consensus       264 ~~a~~  268 (309)
                      ++|+.
T Consensus        90 ~~s~~   94 (99)
T d1x4fa1          90 DLSEK   94 (99)
T ss_dssp             EEECS
T ss_pred             EEcCC
Confidence            99965

>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=99.54  E-value=9e-17  Score=120.58  Aligned_cols=77  Identities=13%  Similarity=0.246  Sum_probs=67.7

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEE-----eeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEE
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEV-----IRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i-----~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      ++|||+|||+.+|+++|.++|++||.+..+.+     +.+..++.++|||||+|.+.++|++|+. |||..++|+.|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            58999999999999999999999998866554     3455678899999999999999999985 99999999999997


Q ss_pred             eec
Q psy15676        265 GEE  267 (309)
Q Consensus       265 ~a~  267 (309)
                      .++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>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=99.53  E-value=4e-15  Score=114.67  Aligned_cols=77  Identities=19%  Similarity=0.286  Sum_probs=68.5

Q ss_pred             CCCcEEEecCCCCCC-CH----HHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeE
Q psy15676        187 PPENVLFVCKLNPVT-SD----DDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRI  261 (309)
Q Consensus       187 ~~~~~lfV~nL~~~~-te----~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I  261 (309)
                      +..++|||+||+..+ ++    ++|+.+|++||.|.++.+.+      ++|||||+|.+.++|.+|+..|||..|+|++|
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            456899999999986 33    56999999999999998863      56899999999999999999999999999999


Q ss_pred             EEEeecCc
Q psy15676        262 HARGEEWN  269 (309)
Q Consensus       262 ~V~~a~~~  269 (309)
                      +|.||+..
T Consensus        77 ~v~~a~~~   84 (104)
T d1weya_          77 KLYFAQTL   84 (104)
T ss_dssp             EEECCCCS
T ss_pred             EEeecccC
Confidence            99999753

>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=99.47  E-value=3.7e-15  Score=114.88  Aligned_cols=74  Identities=15%  Similarity=0.242  Sum_probs=68.0

Q ss_pred             EEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEee
Q psy15676        192 LFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGE  266 (309)
Q Consensus       192 lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a  266 (309)
                      ++|.+++..+++++|.++|++||.|.++.|+.+ .+|.++|||||+|.+.++|.+|+..|||..++|++|.|+|+
T Consensus        30 ~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          30 VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             HHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            556677777889999999999999999999877 48999999999999999999999999999999999999986

>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=99.46  E-value=7.7e-14  Score=108.86  Aligned_cols=77  Identities=19%  Similarity=0.250  Sum_probs=66.5

Q ss_pred             CCCc-EEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCH-HHHHHHHHHcCCceeCCeeEEEE
Q psy15676        187 PPEN-VLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNP-KSCEDAYLKMDNVLIDDRRIHAR  264 (309)
Q Consensus       187 ~~~~-~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~-~~a~~Al~~l~g~~i~gr~I~V~  264 (309)
                      +.++ .+||||||+.+|+++|+.+|++||+|.+|.++.      .+|||||.|.+. ++|..|+..+++..+.++.+.|.
T Consensus         8 ~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~------~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~   81 (113)
T d1owxa_           8 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVR------GAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   81 (113)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCT------TCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             CCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEec------CCceEEEEecCcHHHHHHHHHHhcCCceecCceEEE
Confidence            3445 559999999999999999999999999999974      368999999985 67889999999999988888888


Q ss_pred             eecCc
Q psy15676        265 GEEWN  269 (309)
Q Consensus       265 ~a~~~  269 (309)
                      ++...
T Consensus        82 ~~~~~   86 (113)
T d1owxa_          82 WEVLE   86 (113)
T ss_dssp             EEECC
T ss_pred             Eeecc
Confidence            87643

>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=99.40  E-value=6.6e-13  Score=110.95  Aligned_cols=78  Identities=24%  Similarity=0.380  Sum_probs=72.4

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      ++|||+|||+++|+++|..+|++||.|.++.++.+..+|.++|||||+|.+.++|.+|+. +++..++++.+.+....+
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~-~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHH-hcCCcccccchhhhhhhh
Confidence            699999999999999999999999999999999999999999999999999999999997 577888999888877654

>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=99.40  E-value=2.1e-13  Score=104.22  Aligned_cols=69  Identities=19%  Similarity=0.332  Sum_probs=59.6

Q ss_pred             CCCCcEEEecC--CCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCcee-CCee
Q psy15676        186 APPENVLFVCK--LNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLI-DDRR  260 (309)
Q Consensus       186 ~~~~~~lfV~n--L~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i-~gr~  260 (309)
                      ..|..++||+|  ||+++|+++|..+|++||.|..+.+..+      +|||||+|.+.++|..|+..|||..+ ++..
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i~~~~~   86 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLG   86 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTS
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCCCCCCC
Confidence            35678888854  9999999999999999999999987643      57999999999999999999999876 4433

>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=99.33  E-value=5.3e-13  Score=102.42  Aligned_cols=88  Identities=19%  Similarity=0.241  Sum_probs=73.6

Q ss_pred             CCCCcEEEecCC--CCCCC--------HHHHHHHHhcCCceeEEEEeeeCCCC--CcccEEEEEecCHHHHHHHHHHcCC
Q psy15676        186 APPENVLFVCKL--NPVTS--------DDDLEIIFSRFGKVNCCEVIRDKVTG--DSLQYAFVEFDNPKSCEDAYLKMDN  253 (309)
Q Consensus       186 ~~~~~~lfV~nL--~~~~t--------e~~L~~~F~~fG~I~~v~i~~d~~tg--~skG~aFV~F~~~~~a~~Al~~l~g  253 (309)
                      ++|+++|.+.||  +..+.        .++|+..|++||.|.++.|+++..+.  .+.|++||.|.+.++|.+|+..|||
T Consensus         1 g~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~G   80 (104)
T d1o0pa_           1 GHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG   80 (104)
T ss_dssp             CCCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSS
T ss_pred             CCCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCC
Confidence            467899999999  44332        35789999999999999998876543  3568999999999999999999999


Q ss_pred             ceeCCeeEEEEeecCchhhc
Q psy15676        254 VLIDDRRIHARGEEWNMWKR  273 (309)
Q Consensus       254 ~~i~gr~I~V~~a~~~~~~~  273 (309)
                      ..++||.|.|.|+....+..
T Consensus        81 r~f~gR~v~v~f~~~~~y~~  100 (104)
T d1o0pa_          81 RKFANRVVVTKYCDPDSYHR  100 (104)
T ss_dssp             CCSSSSCCEEEEECHHHHHH
T ss_pred             CEECCeEEEEEEcCHHHhhh
Confidence            99999999999987655543

>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=99.32  E-value=1.4e-12  Score=95.56  Aligned_cols=72  Identities=10%  Similarity=0.158  Sum_probs=61.3

Q ss_pred             CcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCee-EEEEeec
Q psy15676        189 ENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRR-IHARGEE  267 (309)
Q Consensus       189 ~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~-I~V~~a~  267 (309)
                      ++.|||+|+|++++++.| ..|++||.|.++.+      +.++|||||.|.+.++|++|++ +||..++|+. |.|..+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~------~~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVM------SNTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEE------CSSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEe------cCCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            467999999999987655 57999999999876      3457999999999999999995 8999999974 5687775


Q ss_pred             C
Q psy15676        268 W  268 (309)
Q Consensus       268 ~  268 (309)
                      .
T Consensus        76 ~   76 (81)
T d1wwha1          76 D   76 (81)
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=99.31  E-value=3.8e-12  Score=96.75  Aligned_cols=78  Identities=19%  Similarity=0.271  Sum_probs=66.9

Q ss_pred             CCCcEEEecCC--CCCCC---------HHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCce
Q psy15676        187 PPENVLFVCKL--NPVTS---------DDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVL  255 (309)
Q Consensus       187 ~~~~~lfV~nL--~~~~t---------e~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~  255 (309)
                      ....+|+|.||  |.++.         .++|+..|++||.|..+.+..+    .++|||||.|.+.++|.+|+..|||..
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            45689999999  44321         3678999999999999988643    467999999999999999999999999


Q ss_pred             eCCeeEEEEeecC
Q psy15676        256 IDDRRIHARGEEW  268 (309)
Q Consensus       256 i~gr~I~V~~a~~  268 (309)
                      ++|++|+|.++.+
T Consensus        82 ~~gr~i~v~~~~g   94 (99)
T d2dita1          82 FGGRQITAQAWDG   94 (99)
T ss_dssp             ETTEECEEEECCS
T ss_pred             ECCEEEEEEEeCC
Confidence            9999999999865

>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=97.40  E-value=0.00013  Score=52.68  Aligned_cols=73  Identities=15%  Similarity=0.312  Sum_probs=60.0

Q ss_pred             CCCCCcEEEecCCCCCCCH---------HHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCce
Q psy15676        185 AAPPENVLFVCKLNPVTSD---------DDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVL  255 (309)
Q Consensus       185 ~~~~~~~lfV~nL~~~~te---------~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~  255 (309)
                      .+||..||.|.=..++..+         .+|.+.|..||.|.-++++.+        -..|+|.+-.+|.+|+. ++|..
T Consensus        11 qGPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~   81 (95)
T d1ufwa_          11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMK   81 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSE
T ss_pred             cCCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeE
Confidence            4788899999655544333         357888999999999999765        47999999999999996 79999


Q ss_pred             eCCeeEEEEee
Q psy15676        256 IDDRRIHARGE  266 (309)
Q Consensus       256 i~gr~I~V~~a  266 (309)
                      +.|+.|+|...
T Consensus        82 v~G~~l~It~~   92 (95)
T d1ufwa_          82 VKGRAVKISGP   92 (95)
T ss_dssp             ETTEEEEEECC
T ss_pred             EcceEEEEecC
Confidence            99999999754

>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=96.92  E-value=0.0023  Score=43.79  Aligned_cols=62  Identities=21%  Similarity=0.187  Sum_probs=52.4

Q ss_pred             HHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHcCCceeCCeeEEEEeecC
Q psy15676        204 DDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKMDNVLIDDRRIHARGEEW  268 (309)
Q Consensus       204 ~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l~g~~i~gr~I~V~~a~~  268 (309)
                      +.|...|.++|.|.++.+....+   ..-.|-|...+..+|..|+..|+-..|++++|.|.++..
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~d---g~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTD---YQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCS---TTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEeccC---CcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            34677899999999998865432   234799999999999999999999999999999999864

>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=96.68  E-value=0.0033  Score=45.42  Aligned_cols=77  Identities=12%  Similarity=0.139  Sum_probs=60.8

Q ss_pred             cEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCc--ccEEEEEecCHHHHHHHHHHcCCceeCC-----eeEE
Q psy15676        190 NVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDS--LQYAFVEFDNPKSCEDAYLKMDNVLIDD-----RRIH  262 (309)
Q Consensus       190 ~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~s--kG~aFV~F~~~~~a~~Al~~l~g~~i~g-----r~I~  262 (309)
                      ++|.|.+||++.|++++.+.++..|.+........+.+.+.  -.-|||.|.+.+++......++|+.+.+     .+-.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~~a~   81 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEYPAI   81 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEEECE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEeeeE
Confidence            47889999999999999999999999888777766544332  2468999999999999999999977642     2335


Q ss_pred             EEee
Q psy15676        263 ARGE  266 (309)
Q Consensus       263 V~~a  266 (309)
                      |.+|
T Consensus        82 VE~A   85 (91)
T d1uw4a_          82 VEFA   85 (91)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            5665

>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=93.08  E-value=0.17  Score=36.41  Aligned_cols=62  Identities=26%  Similarity=0.363  Sum_probs=48.9

Q ss_pred             CCCCCCCCcEEEecCCCCCCCHHHHHHHHhcCCceeEEEEeeeCCCCCcccEEEEEecCHHHHHHHHHHc
Q psy15676        182 EADAAPPENVLFVCKLNPVTSDDDLEIIFSRFGKVNCCEVIRDKVTGDSLQYAFVEFDNPKSCEDAYLKM  251 (309)
Q Consensus       182 ~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~fG~I~~v~i~~d~~tg~skG~aFV~F~~~~~a~~Al~~l  251 (309)
                      ..+..|.-..+|.-..|......+|..+|+.||.|. +..+-|  |     -|||...+.++|..++..+
T Consensus         8 G~d~~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIdd--T-----Sa~V~L~~~e~~~~v~~~~   69 (100)
T d1whva_           8 GPDLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDD--T-----SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CSCCCCCCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEET--T-----EEEEECSCHHHHHHHHHHH
T ss_pred             CCCCCCCcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecC--c-----eEEEEecCHHHHHHHHHHh
Confidence            344556667889889999999999999999999884 444433  2     6999999999988887653