Citrus Sinensis ID: 046966

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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-------30
Protein Sequence
MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPPELADDSIPEGEPKDELEPPLNEQLSSEKEAHSRAVALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVSKIWKKSY
Secondary Structure (PSIPRED)
cEEEEEEccccEEEEEEccccHHHHHHHHHHHHccccccccEEEEEEccEEEcccccccccccccccccccccccccccccccccEEEEEEEccccccccEEEEEEcccccccccccEEEEEEEccHHHHHHHHccccccccccccccEEEEEEEEcccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccccccccccEEEccccccccccccHHHHHHccccEEEEEEEEcccccccEEEEEEEEccHHHHHHHHHccccEEEcccEEEEEccccHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cEEEEEEccEEEEEEEcccccHHHHHHHHHHHHccccccEEccEEEcccEEEEccccccccccccccccccccHccccccccccccEEEEcccccccEcccEEEEcccccHHccccEEEEEEEEcHHHHHHHHHHHHEcccccccccEEEEEEEEEcccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccccccccccEEEEEEccccccHHHHHHHHHccccEEEEEEEEEcccccccEEEEEEEccHHHHHHHHHHcccEEEcccEEEEEcHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MSVLIETSLGDIVIDLfvdkcprttnnflqhcknkyyngclfhnihkdfiaqtgdptgtgtggrsvyedrffVDEIRAdlkhdkvgtvgmasagrdlnASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAvvdeenrppqqiiikqtyvlyppeladdsipegepkdelepplneqlssekEAHSRAVALECigdipdadvkppdnvlfvcqlnpvtededlHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNaliddrricVDFSQSVSKIWKKSY
Flexible Loop (DISEMBL)
msvlietslgdividLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKHDKVGTvgmasagrdlnaSQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAvvdeenrppqqiiIKQTYVLYPPELADDSIPEGEPKDELEPPLNEQLSSEKEAHSRAVALECIGDipdadvkpPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFsqsvskiwkksy
Low Complexity Region (SEG)
MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQtgdptgtgtggRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPPELADDSIPEGEPKDELEPPLNEQLSSEKEAHSRAVALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVSKIWKKSY
Disordered region (IsUnstruct)
***LIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYP***********************************VALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVSKIW****
Disordered Region (DISOPRED)
MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGG**VYE**FF*DEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPPELA***********************************CIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVSKIW****
Disordered Region (DISEMBL)
MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPPELADDSI************************SRAVALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSV********
Disordered Region (DISPRO)
MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPPELAD*************PPLNEQLSSEKEAHSRAVALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVSKIWK*SY
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPPELADDSIPEGEPKDELEPPLNEQLSSEKEAHSRAVALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVSKIWKKSY
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	299	2.2.26 [Sep-21-2011]
Q8WUA2	492	Peptidyl-prolyl cis-trans	yes	no	0.959	0.583	0.510	2e-85
P0C1I6	446	Peptidyl-prolyl cis-trans	N/A	no	0.989	0.663	0.539	2e-85
Q9CXG3	492	Peptidyl-prolyl cis-trans	yes	no	0.959	0.583	0.510	5e-85
P0CP88	504	Peptidyl-prolyl cis-trans	yes	no	0.963	0.571	0.494	7e-81
P0CP89	504	Peptidyl-prolyl cis-trans	N/A	no	0.963	0.571	0.494	7e-81
Q4WAQ9	459	Peptidyl-prolyl cis-trans	yes	no	0.996	0.649	0.480	2e-78
Q2U256	461	Peptidyl-prolyl cis-trans	yes	no	0.996	0.646	0.480	3e-78
Q9UUE4	432	Peptidyl-prolyl cis-trans	yes	no	0.979	0.678	0.501	4e-76
Q5ARI5	461	Peptidyl-prolyl cis-trans	yes	no	0.963	0.624	0.463	2e-75
Q4IE79	485	Peptidyl-prolyl cis-trans	no	no	0.966	0.595	0.452	2e-70

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

 Score =  315 bits (807), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 166/325 (51%), Positives = 214/325 (65%), Gaps = 38/325 (11%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           M+VL+ET+LGD+VIDL+ ++ PR   NFL+ CK KYYN CL HN+ +DFI QTGDPTGTG
Sbjct: 1   MAVLLETTLGDVVIDLYTEERPRACLNFLKLCKIKYYNYCLIHNVQRDFIIQTGDPTGTG 60

Query: 61  TGGRSVY------EDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLD 114
            GG S++      +  FF  E    +KH K GTV M + G D + SQF IT  +NL YLD
Sbjct: 61  RGGESIFGQLYGDQASFFEAEKVPRIKHKKKGTVSMVNNGSDQHGSQFLITTGENLDYLD 120

Query: 115 EKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPPELADDS--IPEGEPK 172
             HT+FGEV EG++ + +IN+  VD++  P Q I I  T +L  P        IP+  P+
Sbjct: 121 GVHTVFGEVTEGMDIIKKINETFVDKDFVPYQDIRINHTVILDDPFDDPPDLLIPDRSPE 180

Query: 173 DELEPPLNEQLSS-------------------------EKEAHSRAVALECIGDIPDADV 207
                P  EQL S                         EKEA ++A+ LE +GD+PDAD+
Sbjct: 181 -----PTREQLDSGRIGADEEIDDFKGRSAEEVEEIKAEKEAKTQAILLEMVGDLPDADI 235

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
           KPP+NVLFVC+LNPVT DEDL +IFS+FG + S E++RD++TGESLCYAF+EFEK E CE
Sbjct: 236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRDWKTGESLCYAFIEFEKEEDCE 295

Query: 268 QAYFKMNNALIDDRRICVDFSQSVS 292
           +A+FKM+N LIDDRRI VDFSQSV+
Sbjct: 296 KAFFKMDNVLIDDRRIHVDFSQSVA 320

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|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 =  315 bits (807), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 176/326 (53%), Positives = 219/326 (67%), Gaps = 30/326 (9%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           MSVLIETSLGDIVIDL+ ++CP+TT NFL+ CK KYYN   F N+ KDF+AQTGDPTG G
Sbjct: 1   MSVLIETSLGDIVIDLYTEECPKTTLNFLKLCKIKYYNFAPFFNVQKDFMAQTGDPTGKG 60

Query: 61  TGGRSVYE----DRFFVDEIRADLKHDKVGTVGMASAG------RDLNASQFYITLRDNL 110
             G+SVY      R+F  EI   LKH + G V MA A         ++ SQF+ITL +NL
Sbjct: 61  DQGQSVYGILGGSRYFPAEIHPTLKHVRRGMVSMAVAADASIETGGVSGSQFFITLGENL 120

Query: 111 HYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPPELADDS--IPE 168
            YLD K+T+FGE+AEG + L +IN+A  DE+ RP + I IK T VL  P    D   IP+
Sbjct: 121 DYLDGKYTLFGEIAEGFDVLDKINEAYCDEQGRPFRDIRIKHTVVLDDPFPDPDGLVIPD 180

Query: 169 GEP---KDELE---------------PPLNEQLSSEKEAHSRAVALECIGDIPDADVKPP 210
             P   K++LE               P   E+    +EA + A+ LE IGD+P A+VKPP
Sbjct: 181 ESPLPTKEQLESMRIGEDEDLEEMGDPEELEKRVRAREAKAHALTLEMIGDLPFAEVKPP 240

Query: 211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
           +NVLFVC+LNPVT DEDL +IFS+FG + S EI+RD +TG+SL YAFVEFE +E  E+AY
Sbjct: 241 ENVLFVCKLNPVTRDEDLEMIFSRFGLIHSCEIIRDRQTGDSLSYAFVEFENKEDAEEAY 300

Query: 271 FKMNNALIDDRRICVDFSQSVSKIWK 296
           FKM + LIDDRRI VDFSQSVSK+ K
Sbjct: 301 FKMQSVLIDDRRIHVDFSQSVSKLHK 326

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

 Score =  314 bits (805), Expect = 5e-85,   Method: Compositional matrix adjust.
 Identities = 166/325 (51%), Positives = 214/325 (65%), Gaps = 38/325 (11%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           M+VL+ET+LGD+VIDL+ ++ PR   NFL+ CK KYYN CL HN+ +DFI QTGDPTGTG
Sbjct: 1   MAVLLETTLGDVVIDLYTEERPRACLNFLKLCKIKYYNYCLIHNVQRDFIIQTGDPTGTG 60

Query: 61  TGGRSVY------EDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLD 114
            GG S++      +  FF  E    +KH K GTV M + G D + SQF IT  +NL YLD
Sbjct: 61  RGGESIFGQLYGDQASFFEAEKVPRIKHKKKGTVSMVNNGSDQHGSQFLITTGENLDYLD 120

Query: 115 EKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPPELADDS--IPEGEPK 172
             HT+FGEV EG++ + +IN+  VD++  P Q I I  T +L  P        IP+  P+
Sbjct: 121 GVHTVFGEVTEGMDIVKKINETFVDKDFVPYQDIRINHTVILDDPFDDPPDLLIPDRSPE 180

Query: 173 DELEPPLNEQLSS-------------------------EKEAHSRAVALECIGDIPDADV 207
                P  EQL S                         EKEA ++A+ LE +GD+PDAD+
Sbjct: 181 -----PTKEQLDSGRIGADEEIDDFKGRSAEEVEEIKAEKEAKTQAILLEMVGDLPDADI 235

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
           KPP+NVLFVC+LNPVT DEDL +IFS+FG + S E++RD++TGESLCYAF+EFEK E CE
Sbjct: 236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRDWKTGESLCYAFIEFEKEEDCE 295

Query: 268 QAYFKMNNALIDDRRICVDFSQSVS 292
           +A+FKM+N LIDDRRI VDFSQSV+
Sbjct: 296 KAFFKMDNVLIDDRRIHVDFSQSVA 320

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|P0CP88|PPIL4_CRYNJ Peptidyl-prolyl cis-trans isomerase-like 4 OS=Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) GN=CYP6 PE=3 SV=1

 Score =  300 bits (769), Expect = 7e-81,   Method: Compositional matrix adjust.
 Identities = 165/334 (49%), Positives = 216/334 (64%), Gaps = 46/334 (13%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           MSV++ETSLGD++IDL VDKCPRT  NF++ CK KYY    F N+ K+FIAQ+GDPT TG
Sbjct: 1   MSVMLETSLGDLIIDLEVDKCPRTCENFIKLCKLKYYALNAFFNVSKNFIAQSGDPTATG 60

Query: 61  TGGRS----VYED--------RFFVDEIRADLKHDKVGTVGMASAGRDLNA--SQFYITL 106
           TGG S    VY          R+F  EI   LKH   GT+ MA A  +     SQF+ITL
Sbjct: 61  TGGESLASYVYSQSPSGPRPPRYFTPEILNSLKHTHKGTLSMAVAPINPPGCGSQFFITL 120

Query: 107 RDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPPELADDSI 166
            DN+ YLD KH +FG V EGL+TL +IN A  D+E RP Q I I+   +L      +D  
Sbjct: 121 ADNIDYLDGKHAVFGHVIEGLDTLDKINDAFTDKEGRPLQNIRIRHVEIL------EDPF 174

Query: 167 PEGE-----PKDELEPP--LNEQLSSEKE-------------------AHSRAVALECIG 200
           P+ +     P+  + PP  L++   ++ E                   A S A+ LE IG
Sbjct: 175 PDPDNFMPIPQSPIRPPDDLSKVRIADTEDPNAVIPEEEAEELRRRTEAASSALTLEMIG 234

Query: 201 DIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEF 260
           D+P A V+PP+N+LFVC+LNPVT+DEDL +IFS+FG ++S E++RD ++G+SL YAF+EF
Sbjct: 235 DLPFAAVRPPENILFVCKLNPVTQDEDLELIFSRFGKILSCEVVRDKKSGDSLQYAFIEF 294

Query: 261 EKREACEQAYFKMNNALIDDRRICVDFSQSVSKI 294
           ++REA EQAYFKM N L+DDRRI VDFSQSV+K+
Sbjct: 295 DEREAAEQAYFKMQNVLVDDRRIWVDFSQSVAKM 328

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

Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565) (taxid: 214684)

EC: 5

EC: .

EC: 2

EC: .

EC: 1

EC: .

EC: 8

>sp|P0CP89|PPIL4_CRYNB Peptidyl-prolyl cis-trans isomerase-like 4 OS=Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) GN=CYP6 PE=3 SV=1

 Score =  300 bits (769), Expect = 7e-81,   Method: Compositional matrix adjust.
 Identities = 165/334 (49%), Positives = 216/334 (64%), Gaps = 46/334 (13%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           MSV++ETSLGD++IDL VDKCPRT  NF++ CK KYY    F N+ K+FIAQ+GDPT TG
Sbjct: 1   MSVMLETSLGDLIIDLEVDKCPRTCENFIKLCKLKYYALNAFFNVSKNFIAQSGDPTATG 60

Query: 61  TGGRS----VYED--------RFFVDEIRADLKHDKVGTVGMASAGRDLNA--SQFYITL 106
           TGG S    VY          R+F  EI   LKH   GT+ MA A  +     SQF+ITL
Sbjct: 61  TGGESLASYVYSQSPSGPRPPRYFTPEILNSLKHTHKGTLSMAVAPINPPGCGSQFFITL 120

Query: 107 RDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPPELADDSI 166
            DN+ YLD KH +FG V EGL+TL +IN A  D+E RP Q I I+   +L      +D  
Sbjct: 121 ADNIDYLDGKHAVFGHVIEGLDTLDKINDAFTDKEGRPLQNIRIRHVEIL------EDPF 174

Query: 167 PEGE-----PKDELEPP--LNEQLSSEKE-------------------AHSRAVALECIG 200
           P+ +     P+  + PP  L++   ++ E                   A S A+ LE IG
Sbjct: 175 PDPDNFMPIPQSPIRPPDDLSKVRIADTEDPNAVIPEEEAEELRRRTEAASSALTLEMIG 234

Query: 201 DIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEF 260
           D+P A V+PP+N+LFVC+LNPVT+DEDL +IFS+FG ++S E++RD ++G+SL YAF+EF
Sbjct: 235 DLPFAAVRPPENILFVCKLNPVTQDEDLELIFSRFGKILSCEVVRDKKSGDSLQYAFIEF 294

Query: 261 EKREACEQAYFKMNNALIDDRRICVDFSQSVSKI 294
           ++REA EQAYFKM N L+DDRRI VDFSQSV+K+
Sbjct: 295 DEREAAEQAYFKMQNVLVDDRRIWVDFSQSVAKM 328

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

Cryptococcus neoformans var. neoformans serotype D (strain B-3501A) (taxid: 283643)

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 =  292 bits (748), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 162/337 (48%), Positives = 215/337 (63%), Gaps = 39/337 (11%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           MSVL+ETSLGDIVIDL VD+ P+   NFL+ CK KYYN    H++ K+F  QTGDP G  
Sbjct: 1   MSVLLETSLGDIVIDLLVDESPKACENFLKLCKVKYYNFSPVHSVQKNFTFQTGDPLGPD 60

Query: 61  T----GGRSVYE------DRFFVDEIRADLKHDKVGTVGMASAGRD------LNASQFYI 104
           +    GG S++        R F  ++   LKH + GTV MA+          L ASQF +
Sbjct: 61  SPESDGGSSIWGLLEGPVKRTFSLKLSPKLKHTERGTVSMATVPSSHDPDERLAASQFIV 120

Query: 105 TLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY-----PP 159
           TL DNL YLD K  IFG+V EG + L +IN A +D++ RP + I I+ T +L      PP
Sbjct: 121 TLEDNLDYLDGKAAIFGKVVEGFDVLEKINGAFIDDQGRPLKDIRIRHTVILDDPYDDPP 180

Query: 160 EL---ADDSIP------------EGEPKDELEPPLNEQLSSEKEAHSRAVALECIGDIPD 204
            L   A+  +P            + E  D ++    E+L  E+EA ++A+ LE +GD+P 
Sbjct: 181 GLVVPAESPLPSKAQLATVRIADDEELDDNMDEEAMEKLRREREARAQALTLEMVGDLPF 240

Query: 205 ADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKRE 264
           A+VKPP+NVLFVC+LNPVT+DEDL +IFS+FG ++S E++RD RTG+SL YAF+EFE ++
Sbjct: 241 AEVKPPENVLFVCKLNPVTQDEDLQLIFSRFGPILSCEVIRDKRTGDSLQYAFIEFENQK 300

Query: 265 ACEQAYFKMNNALIDDRRICVDFSQSVSKI---WKKS 298
            CEQAYFKM   LIDD RI VDFSQSVSK+   W+ +
Sbjct: 301 DCEQAYFKMQGVLIDDHRIHVDFSQSVSKLSESWRNA 337

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 =  291 bits (745), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 162/337 (48%), Positives = 215/337 (63%), Gaps = 39/337 (11%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           MSVL+ETSLGDIVIDL VD+CP+   NFL+ CK KYYN    H++ K+F  QTGDP G  
Sbjct: 1   MSVLLETSLGDIVIDLLVDECPKACENFLKLCKVKYYNFSPVHSVQKNFTFQTGDPLGPD 60

Query: 61  T----------GGRSVYEDRFFVDEIRADLKHDKVGTVGMASA------GRDLNASQFYI 104
           +          G       R F  E    LKHD+ GTV MA+        + + ASQF +
Sbjct: 61  SSESDGGSSIWGLLEGPPKRTFSLEPPPKLKHDERGTVSMATVPSPHDPDQRIAASQFIV 120

Query: 105 TLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY-----PP 159
           TL +NL YLD K  IFG+V EG + L ++N+A +D+  RP + I I+ T +L      PP
Sbjct: 121 TLGENLDYLDGKAVIFGKVVEGFDVLEKVNEAFIDDRGRPLKDIRIRHTVILDDPFDDPP 180

Query: 160 EL---ADDSIP------------EGEPKDELEPPLNEQLSSEKEAHSRAVALECIGDIPD 204
            L   A+  +P            + E  D ++    E+L  E+EA ++A+ LE +GD+P 
Sbjct: 181 GLVAPAESPLPSKAQLATVRIADDEELDDNMDEESMEKLRREREARAQALTLEMVGDLPF 240

Query: 205 ADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKRE 264
           A+VKPP+NVLFVC+LNPVT+DEDLH+IFS+FGT++S E++RD RTG+SL YAF+EFE ++
Sbjct: 241 AEVKPPENVLFVCKLNPVTQDEDLHLIFSRFGTILSCEVIRDKRTGDSLQYAFIEFENQK 300

Query: 265 ACEQAYFKMNNALIDDRRICVDFSQSVSKI---WKKS 298
            CEQAYFKM   LIDD RI VDFSQSVSK+   W+ +
Sbjct: 301 DCEQAYFKMQGVLIDDHRIHVDFSQSVSKLSESWRNA 337

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

 Score =  285 bits (728), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 163/325 (50%), Positives = 212/325 (65%), Gaps = 32/325 (9%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTG-T 59
           MSVLIET++GD+VIDLFV + P+T  NFL+ CK KYYN C F+NI  ++  QTGDP G T
Sbjct: 1   MSVLIETTVGDLVIDLFVKEAPKTCENFLKLCKLKYYNFCPFYNIQHNYTCQTGDPLGPT 60

Query: 60  GTGGRSVYE-----DRFFVDEIRADLKHDKVGTVGMASA---GRD----LNASQFYITLR 107
           G GGR V+       RFF  E    L H+K+G V M++A    RD    +  SQF ITL 
Sbjct: 61  GDGGRCVWNVLNKGTRFFKAEFNPSLVHNKMGLVSMSTATISSRDDKLLVCGSQFIITLS 120

Query: 108 DNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY-----PPELA 162
           DNL  LDE++ I+G+VAEG +TL +IN A+ DEE +P + I IK T +L      PP+L 
Sbjct: 121 DNLEGLDERYPIYGQVAEGFDTLLKINDAICDEEGQPYRDIRIKHTIILDDPFEDPPDLV 180

Query: 163 D---DSIPEGEPKDELEPPLNEQLSSEKE-----------AHSRAVALECIGDIPDADVK 208
           +      P  E    +    NEQ+ SE             A + AV LE IGD+P A V 
Sbjct: 181 EPLRSPSPTPEQLATVRIGENEQIESETSEDKLQREKEMEAEAEAVTLEMIGDLPFAHVA 240

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
           PP+NVLFVC+LNPVT+DEDL +IFS+FG ++S +++RD  TG+SL YAF+EF+ +E+ E+
Sbjct: 241 PPENVLFVCKLNPVTQDEDLELIFSRFGKIISCQVIRDKETGDSLQYAFIEFDNKESVEK 300

Query: 269 AYFKMNNALIDDRRICVDFSQSVSK 293
           AYFKM N LIDD RI VDFSQSV++
Sbjct: 301 AYFKMQNVLIDDSRIHVDFSQSVAR 325

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|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 =  282 bits (722), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 159/343 (46%), Positives = 211/343 (61%), Gaps = 55/343 (16%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           MSVL+ETSLGDIVIDL VD+ P+   NFL+ CK KYYN   F+++ K+F  QTGDP G  
Sbjct: 1   MSVLLETSLGDIVIDLLVDESPKACENFLKLCKVKYYNFSPFYSVQKNFSFQTGDPIGPD 60

Query: 61  T----GGRSVY------EDRFFVDEIRADLKHDKVGTVGMASAGRD------LNASQFYI 104
           +    GG S++        +     +   LKHD+ GTV MA+          L  SQF +
Sbjct: 61  SPDSNGGSSIWGLLEGPSKQAVPLALPPKLKHDEKGTVSMAAVPSPHDPDLRLVTSQFIV 120

Query: 105 TLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPPELADD 164
           TL DNL YLD K  IFG+V EG + L ++N+A +D+  RP + I I+ T +L      DD
Sbjct: 121 TLGDNLDYLDGKAVIFGKVVEGFDVLEKVNEAFIDDRGRPLKDIRIRHTVIL------DD 174

Query: 165 SIPEGEPKDELEPPLN----------------------------EQLSSEKEAHSRAVAL 196
             P  +P   +EPP +                            E+L  E+EA ++A+ L
Sbjct: 175 --PFDDPPGLVEPPESPLPTKAQLATVRIADDEDLGDDMDEASMEKLRREREARAQALTL 232

Query: 197 ECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYA 256
           E +GD+P A+VKPP+NVLFVC+LNPVT+DEDL +IFS+FG ++S E++RD RTG+SL YA
Sbjct: 233 EMVGDLPFAEVKPPENVLFVCKLNPVTQDEDLELIFSRFGKILSCEVIRDKRTGDSLQYA 292

Query: 257 FVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVSKI---WK 296
           F+EFE ++ CEQAYFKM   LIDD RI VDFSQSVSK+   W+
Sbjct: 293 FIEFESQKDCEQAYFKMQGVLIDDHRIHVDFSQSVSKLSESWR 335

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|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 =  266 bits (679), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 157/347 (45%), Positives = 204/347 (58%), Gaps = 58/347 (16%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGT- 59
           MSVL+ETS GDIVIDL VD  P+   NFL+ CK KYYN    H++ K+F  QTGDP G  
Sbjct: 1   MSVLLETSAGDIVIDLLVDHAPKLCENFLKLCKVKYYNFSPVHSVQKNFSFQTGDPLGPL 60

Query: 60  ---GTGGRSVY-------EDRFFVDEIRADLKHDKVGTVGMASAGRD------LNASQFY 103
                GG S++        +R F       LKH + GTV MA+A         +  SQF 
Sbjct: 61  SKDSDGGSSIWGHLSGDPSERTFPAFFHPKLKHLERGTVSMATAPLQSDPDVRVAGSQFI 120

Query: 104 ITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY-----P 158
           ITL  +  +LD K  IFG+V EG E L +IN+A+VDE+  P   I IK T +L      P
Sbjct: 121 ITLGQDTDFLDGKAAIFGKVVEGFEALDKINEAIVDEKGHPLIDIRIKHTVILDDPYADP 180

Query: 159 PELADDSIPEGEPKDELEPPLNEQLSSEK-------------------------EAHSRA 193
           P L +   P   P     PP ++QL + +                         EA ++A
Sbjct: 181 PGLRE---PSTSP-----PPTDQQLKTVRIADEAALHEDDNVDEEELERRRRNREAQAQA 232

Query: 194 VALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESL 253
           + LE +GD+P A+VKPP+NVLFVC+LNPVT DEDL +IF +FG ++S E++RD +TG+SL
Sbjct: 233 LTLEMMGDLPFAEVKPPENVLFVCKLNPVTGDEDLELIFGRFGKILSCEVIRDQKTGDSL 292

Query: 254 CYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVSK---IWKK 297
            YAF+E+E + +CE AYFKM   LIDDRRI VDFSQSVSK   +W+K
Sbjct: 293 QYAFIEYEDKASCEAAYFKMQGVLIDDRRIHVDFSQSVSKLSDVWRK 339

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

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	299
359494535	627	PREDICTED: peptidyl-prolyl cis-trans iso	0.986	0.470	0.668	1e-120
296082685	633	unnamed protein product [Vitis vinifera]	0.986	0.466	0.668	1e-120
224083978	542	predicted protein [Populus trichocarpa]	0.993	0.547	0.658	1e-117
22330231	506	cyclophilin 59 [Arabidopsis thaliana] gi	0.993	0.586	0.640	1e-115
16648909	441	Unknown protein [Arabidopsis thaliana]	0.993	0.673	0.640	1e-115
357500333	621	Peptidyl-prolyl cis-trans isomerase-like	0.986	0.475	0.653	1e-115
297847776	508	hypothetical protein ARALYDRAFT_474506 [	0.993	0.584	0.643	1e-114
449444256	491	PREDICTED: peptidyl-prolyl cis-trans iso	0.993	0.604	0.685	1e-113
449531281	376	PREDICTED: peptidyl-prolyl cis-trans iso	0.993	0.789	0.679	1e-112
357121886	546	PREDICTED: peptidyl-prolyl cis-trans iso	0.986	0.540	0.627	1e-110

>gi|359494535|ref|XP_002266085.2| PREDICTED: peptidyl-prolyl cis-trans isomerase-like 4-like [Vitis vinifera]

 Score =  437 bits (1124), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 218/326 (66%), Positives = 253/326 (77%), Gaps = 31/326 (9%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           MSVLI TSLGDIV+DL+ D+CP T+ NFL+ CK KYYNGCLFH + KDF AQTGDPT TG
Sbjct: 1   MSVLIVTSLGDIVVDLYTDRCPLTSKNFLKLCKIKYYNGCLFHMVQKDFTAQTGDPTATG 60

Query: 61  TGGRSVY------EDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLD 114
           TGG S+Y      + RFF DE+  DLKH K GTV MASAG +LNASQFY TLRD+L YLD
Sbjct: 61  TGGDSIYKFLYGDQARFFNDEVHLDLKHSKTGTVAMASAGENLNASQFYFTLRDDLDYLD 120

Query: 115 EKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPP--------ELADDSI 166
            KHT+FGEVAEGLETLTRIN+A VD++ RP + I IK TY+L  P        EL  D+ 
Sbjct: 121 GKHTVFGEVAEGLETLTRINEAYVDDKGRPYKNIRIKHTYILDDPFGDPSQLTELIPDAS 180

Query: 167 PEGEPKDELEP---------PLNEQLSSE--------KEAHSRAVALECIGDIPDADVKP 209
           PEG+PKDE++          PL+EQL +         KEAHSRAV LE IGDIPDA++KP
Sbjct: 181 PEGKPKDEVDDDVRLEDDWVPLDEQLDTSELEELIRSKEAHSRAVVLESIGDIPDAEIKP 240

Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           PDNVLFVC+LNPVTEDEDLH IFS+FGTV+SAEI+RD++TG+SLCYAF+EFE  EACEQA
Sbjct: 241 PDNVLFVCKLNPVTEDEDLHTIFSRFGTVISAEIIRDFKTGDSLCYAFIEFETNEACEQA 300

Query: 270 YFKMNNALIDDRRICVDFSQSVSKIW 295
           YFKM+NALIDDRRI VDFSQSVSK+W
Sbjct: 301 YFKMDNALIDDRRIHVDFSQSVSKLW 326

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296082685|emb|CBI21690.3| unnamed protein product [Vitis vinifera]

 Score =  436 bits (1122), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 218/326 (66%), Positives = 253/326 (77%), Gaps = 31/326 (9%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           MSVLI TSLGDIV+DL+ D+CP T+ NFL+ CK KYYNGCLFH + KDF AQTGDPT TG
Sbjct: 1   MSVLIVTSLGDIVVDLYTDRCPLTSKNFLKLCKIKYYNGCLFHMVQKDFTAQTGDPTATG 60

Query: 61  TGGRSVY------EDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLD 114
           TGG S+Y      + RFF DE+  DLKH K GTV MASAG +LNASQFY TLRD+L YLD
Sbjct: 61  TGGDSIYKFLYGDQARFFNDEVHLDLKHSKTGTVAMASAGENLNASQFYFTLRDDLDYLD 120

Query: 115 EKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPP--------ELADDSI 166
            KHT+FGEVAEGLETLTRIN+A VD++ RP + I IK TY+L  P        EL  D+ 
Sbjct: 121 GKHTVFGEVAEGLETLTRINEAYVDDKGRPYKNIRIKHTYILDDPFGDPSQLTELIPDAS 180

Query: 167 PEGEPKDELEP---------PLNEQLSSE--------KEAHSRAVALECIGDIPDADVKP 209
           PEG+PKDE++          PL+EQL +         KEAHSRAV LE IGDIPDA++KP
Sbjct: 181 PEGKPKDEVDDDVRLEDDWVPLDEQLDTSELEELIRSKEAHSRAVVLESIGDIPDAEIKP 240

Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           PDNVLFVC+LNPVTEDEDLH IFS+FGTV+SAEI+RD++TG+SLCYAF+EFE  EACEQA
Sbjct: 241 PDNVLFVCKLNPVTEDEDLHTIFSRFGTVISAEIIRDFKTGDSLCYAFIEFETNEACEQA 300

Query: 270 YFKMNNALIDDRRICVDFSQSVSKIW 295
           YFKM+NALIDDRRI VDFSQSVSK+W
Sbjct: 301 YFKMDNALIDDRRIHVDFSQSVSKLW 326

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224083978|ref|XP_002307193.1| predicted protein [Populus trichocarpa] gi|222856642|gb|EEE94189.1| predicted protein [Populus trichocarpa]

 Score =  428 bits (1101), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 216/328 (65%), Positives = 252/328 (76%), Gaps = 31/328 (9%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           MSVLI TSLGDIV+DL+ DKCP T  NFL+ CK KYYNGCLFH I KDF AQTGDPTGTG
Sbjct: 1   MSVLIVTSLGDIVVDLYADKCPLTCKNFLKLCKIKYYNGCLFHTIQKDFTAQTGDPTGTG 60

Query: 61  TGGRSVY------EDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLD 114
            GG SVY      + RFF DEI  DLKH K+GTV MASAG +LNASQFY TLRD+L YLD
Sbjct: 61  AGGDSVYKFLYGDQARFFGDEIHLDLKHSKMGTVAMASAGENLNASQFYFTLRDDLDYLD 120

Query: 115 EKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPP--------ELADDSI 166
            KHT+FGE+AEGLETLTRIN+A VDE+NRP + I IK  Y+L  P        EL  ++ 
Sbjct: 121 GKHTVFGEIAEGLETLTRINEAYVDEKNRPFKNIRIKHAYILDDPFDDPSQLAELIPEAS 180

Query: 167 PEGEPKDELEP---------PLNEQLSSE--------KEAHSRAVALECIGDIPDADVKP 209
           PEG+PKDE++          P++EQL +         KEAHS AV LE IGDIP+A+ KP
Sbjct: 181 PEGKPKDEVDGDVRLEDDWVPMDEQLGTAELEEVLRAKEAHSSAVVLESIGDIPEAETKP 240

Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           PDNVLFVC+LNPVTEDEDLH IFS+FGTV+SA+I+RDY+TG+SLCYAF+EFE +EACE A
Sbjct: 241 PDNVLFVCKLNPVTEDEDLHTIFSRFGTVISADIIRDYKTGDSLCYAFIEFETKEACELA 300

Query: 270 YFKMNNALIDDRRICVDFSQSVSKIWKK 297
           YFKM+NALIDDRRI VDFSQSV+K+W +
Sbjct: 301 YFKMDNALIDDRRIHVDFSQSVAKLWSQ 328

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22330231|ref|NP_175776.2| cyclophilin 59 [Arabidopsis thaliana] gi|45680880|gb|AAS75309.1| multidomain cyclophilin type peptidyl-prolyl cis-trans isomerase [Arabidopsis thaliana] gi|332194868|gb|AEE32989.1| cyclophilin 59 [Arabidopsis thaliana]

 Score =  419 bits (1078), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 210/328 (64%), Positives = 253/328 (77%), Gaps = 31/328 (9%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           MSVLI TSLGDIVIDL  DKCP T  NFL+ CK KYYNGCLFH + KDF AQTGDPTGTG
Sbjct: 1   MSVLIVTSLGDIVIDLHSDKCPLTCKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60

Query: 61  TGGRSVY------EDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLD 114
            GG S+Y      + RF+ DEI  DLKH K GTV MAS G +LNASQFY TLRD+L YLD
Sbjct: 61  AGGDSIYKFLYGEQARFYKDEIHLDLKHSKTGTVAMASGGENLNASQFYFTLRDDLDYLD 120

Query: 115 EKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY-----PPELAD---DSI 166
            KHT+FG++AEG +TLTRIN+A VD +NRP + I IK T++L      PP+LA+   D+ 
Sbjct: 121 GKHTVFGQIAEGFDTLTRINEAYVDPKNRPYKNIRIKHTHILDDPFDDPPQLAEMMPDAS 180

Query: 167 PEGEPKDELEP---------PLNEQLSS--------EKEAHSRAVALECIGDIPDADVKP 209
           PEG+PK+E++          P++E+L +        EK AHS AV LE IGDIP+A+VKP
Sbjct: 181 PEGKPKEEVKDDVRLEDDWVPMDEELGAQELEEVIREKAAHSSAVVLESIGDIPEAEVKP 240

Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           PDNVLFVC+LNPVTEDEDLH IFS+FGTVVSA+++RD++TG+SLCYAF+EFE +E+CEQA
Sbjct: 241 PDNVLFVCKLNPVTEDEDLHTIFSRFGTVVSADVIRDFKTGDSLCYAFIEFENKESCEQA 300

Query: 270 YFKMNNALIDDRRICVDFSQSVSKIWKK 297
           YFKM+NALIDDRRI VDFSQSVSK+W +
Sbjct: 301 YFKMDNALIDDRRIHVDFSQSVSKLWSQ 328

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|16648909|gb|AAL24306.1| Unknown protein [Arabidopsis thaliana]

 Score =  419 bits (1077), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 210/328 (64%), Positives = 253/328 (77%), Gaps = 31/328 (9%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           MSVLI TSLGDIVIDL  DKCP T  NFL+ CK KYYNGCLFH + KDF AQTGDPTGTG
Sbjct: 1   MSVLIVTSLGDIVIDLHSDKCPLTCKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60

Query: 61  TGGRSVY------EDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLD 114
            GG S+Y      + RF+ DEI  DLKH K GTV MAS G +LNASQFY TLRD+L YLD
Sbjct: 61  AGGDSIYKFLYGEQARFYKDEIHLDLKHSKTGTVAMASGGENLNASQFYFTLRDDLDYLD 120

Query: 115 EKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY-----PPELAD---DSI 166
            KHT+FG++AEG +TLTRIN+A VD +NRP + I IK T++L      PP+LA+   D+ 
Sbjct: 121 GKHTVFGQIAEGFDTLTRINEAYVDPKNRPYKNIRIKHTHILDDPFDDPPQLAEMMPDAS 180

Query: 167 PEGEPKDELEP---------PLNEQLSS--------EKEAHSRAVALECIGDIPDADVKP 209
           PEG+PK+E++          P++E+L +        EK AHS AV LE IGDIP+A+VKP
Sbjct: 181 PEGKPKEEVKDDVRLEDDWVPMDEELGAQELEEVIREKAAHSSAVVLESIGDIPEAEVKP 240

Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           PDNVLFVC+LNPVTEDEDLH IFS+FGTVVSA+++RD++TG+SLCYAF+EFE +E+CEQA
Sbjct: 241 PDNVLFVCKLNPVTEDEDLHTIFSRFGTVVSADVIRDFKTGDSLCYAFIEFENKESCEQA 300

Query: 270 YFKMNNALIDDRRICVDFSQSVSKIWKK 297
           YFKM+NALIDDRRI VDFSQSVSK+W +
Sbjct: 301 YFKMDNALIDDRRIHVDFSQSVSKLWSQ 328

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357500333|ref|XP_003620455.1| Peptidyl-prolyl cis-trans isomerase-like protein [Medicago truncatula] gi|355495470|gb|AES76673.1| Peptidyl-prolyl cis-trans isomerase-like protein [Medicago truncatula]

 Score =  419 bits (1076), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 213/326 (65%), Positives = 249/326 (76%), Gaps = 31/326 (9%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           MSVL+ TSLGD+VIDL   KCP T  NFL+ CK KYYNGCLFH + KDF AQTGDPTGTG
Sbjct: 18  MSVLMVTSLGDMVIDLHTQKCPLTCKNFLKLCKIKYYNGCLFHTVLKDFTAQTGDPTGTG 77

Query: 61  TGGRSVY------EDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLD 114
           T G S+Y      + RFF DEI  DLKH K GTV MASAG +LNASQFYITLRD+L YLD
Sbjct: 78  TAGDSIYKFLYGDQARFFNDEIHIDLKHSKTGTVAMASAGENLNASQFYITLRDDLDYLD 137

Query: 115 EKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY-----PPELAD---DSI 166
            KHT+FGEVAEG ETLTRIN+A  D + RP + I IK TY+L      PP+L +   ++ 
Sbjct: 138 GKHTVFGEVAEGFETLTRINEAYADGKGRPFKNIRIKHTYILEDPFDDPPQLPEFIPEAS 197

Query: 167 PEGEPKDELEP---------PLNEQLS--------SEKEAHSRAVALECIGDIPDADVKP 209
           P+G+PKDE++          P++EQL+          KEAHSRAV LE IGDIPDA+VKP
Sbjct: 198 PDGKPKDEVDDEVRLEDDWVPMDEQLNPGELEEVIRSKEAHSRAVVLESIGDIPDAEVKP 257

Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           PDNVLFVC+LNPVTEDEDLH IFS+FGTV SAEI+RD++TG+SLCYAF+EFE + ACEQA
Sbjct: 258 PDNVLFVCKLNPVTEDEDLHTIFSRFGTVSSAEIIRDHKTGDSLCYAFIEFEDKLACEQA 317

Query: 270 YFKMNNALIDDRRICVDFSQSVSKIW 295
           YFKM+NALIDDRRI VDFSQSV+K+W
Sbjct: 318 YFKMDNALIDDRRIHVDFSQSVAKLW 343

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297847776|ref|XP_002891769.1| hypothetical protein ARALYDRAFT_474506 [Arabidopsis lyrata subsp. lyrata] gi|297337611|gb|EFH68028.1| hypothetical protein ARALYDRAFT_474506 [Arabidopsis lyrata subsp. lyrata]

 Score =  419 bits (1076), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 211/328 (64%), Positives = 251/328 (76%), Gaps = 31/328 (9%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           MSVLI TSLGDIVIDL+ +KCP T  NFL+ CK KYYNGCLFH +  DF AQTGDPTGTG
Sbjct: 1   MSVLIVTSLGDIVIDLYPNKCPLTCKNFLKLCKIKYYNGCLFHTVQNDFTAQTGDPTGTG 60

Query: 61  TGGRSVY------EDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLD 114
            GG S+Y      + RFF DEI  DLKH K GTV MAS G +LNASQFY TLRD+L YLD
Sbjct: 61  AGGDSIYKFLYGEQARFFRDEIHLDLKHSKTGTVAMASGGENLNASQFYFTLRDDLDYLD 120

Query: 115 EKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY-----PPELAD---DSI 166
            KHT+FGE+AEG +TLTRIN+A VD +NRP + I IK  ++L      PP+LA+   D+ 
Sbjct: 121 GKHTVFGEIAEGFDTLTRINEAYVDAKNRPYKNIRIKHIHILEDPFDDPPQLAEMIPDAS 180

Query: 167 PEGEPKDELEP---------PLNEQLS--------SEKEAHSRAVALECIGDIPDADVKP 209
           PEG+PK+E+E          P++E+L          EK AHS AV LE IGDIP+A+VKP
Sbjct: 181 PEGKPKEEVEDDVRLEDDWVPMDEELGVQELEEVIREKAAHSSAVVLESIGDIPEAEVKP 240

Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           PDNVLFVC+LNPVTEDEDLH IFS+FGTVVSA+++RD++TG+SLCYAF+EFE +EACEQA
Sbjct: 241 PDNVLFVCKLNPVTEDEDLHTIFSRFGTVVSADVIRDFKTGDSLCYAFIEFENKEACEQA 300

Query: 270 YFKMNNALIDDRRICVDFSQSVSKIWKK 297
           YFKM+NALIDDRRI VDFSQSVSK+W +
Sbjct: 301 YFKMDNALIDDRRIHVDFSQSVSKLWSQ 328

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449444256|ref|XP_004139891.1| PREDICTED: peptidyl-prolyl cis-trans isomerase-like 4-like [Cucumis sativus]

 Score =  412 bits (1060), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 225/328 (68%), Positives = 258/328 (78%), Gaps = 31/328 (9%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           MSVLI TSLGDIVIDL  D CP T+ NFL+ CK KYYNGCLFH I KDF AQTGDPTGTG
Sbjct: 1   MSVLIVTSLGDIVIDLHTDICPLTSKNFLKLCKIKYYNGCLFHTIQKDFTAQTGDPTGTG 60

Query: 61  TGGRSVY------EDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLD 114
           TGG S+Y      + RFF DEIR DLKH K GTV MASAG +LNASQFY TLRD+L YLD
Sbjct: 61  TGGDSIYKFLYGDQARFFSDEIRLDLKHSKTGTVAMASAGENLNASQFYFTLRDDLEYLD 120

Query: 115 EKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY-----PPELAD---DSI 166
            KHT+FGEVAEGL+TLTRIN+A  DE+ RP + I IK TY+L      PP+LA+   DS 
Sbjct: 121 GKHTVFGEVAEGLDTLTRINEAYADEKGRPYKNIRIKHTYILDDPFDDPPQLAELIPDSS 180

Query: 167 PEGEPKDE------LEP---PLNEQLSSE--------KEAHSRAVALECIGDIPDADVKP 209
           P+G+PKDE      LE    PL+EQL +E        KEAHSRAV LE IGDIPDA++KP
Sbjct: 181 PDGKPKDEVVDEVRLEDDWVPLDEQLGAEELEEVFRAKEAHSRAVVLETIGDIPDAEIKP 240

Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           PDNVLFVC+LNPVTEDEDLH IFS+FGTV+SAE++RDY+TG+SLCYAF+EFE +EACEQA
Sbjct: 241 PDNVLFVCKLNPVTEDEDLHTIFSRFGTVLSAEVIRDYKTGDSLCYAFIEFETKEACEQA 300

Query: 270 YFKMNNALIDDRRICVDFSQSVSKIWKK 297
           YFKM+NALIDDRRI VDFSQSV+K+W +
Sbjct: 301 YFKMDNALIDDRRIHVDFSQSVAKLWSQ 328

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449531281|ref|XP_004172615.1| PREDICTED: peptidyl-prolyl cis-trans isomerase-like 4-like, partial [Cucumis sativus]

 Score =  411 bits (1056), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 223/328 (67%), Positives = 257/328 (78%), Gaps = 31/328 (9%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           MSVLI TSLGDIVIDL  D CP T+ NFL+ CK KYYNGCLFH I KDF AQTGDPTGTG
Sbjct: 1   MSVLIVTSLGDIVIDLHTDICPLTSKNFLKLCKIKYYNGCLFHTIQKDFTAQTGDPTGTG 60

Query: 61  TGGRSVY------EDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLD 114
           TGG S+Y      + RFF DEIR DLKH K GTV MASAG +LNASQFY TLRD+L YLD
Sbjct: 61  TGGDSIYKFLYGDQARFFSDEIRLDLKHSKTGTVAMASAGENLNASQFYFTLRDDLEYLD 120

Query: 115 EKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY-----PPELAD---DSI 166
            KHT+FGEVAEGL+TLTRIN+A  DE+ RP + I IK TY+L      PP+LA+   DS 
Sbjct: 121 GKHTVFGEVAEGLDTLTRINEAYADEKGRPYKNIRIKHTYILDDPFDDPPQLAELIPDSS 180

Query: 167 PEGEPKDEL---------EPPLNEQLSSE--------KEAHSRAVALECIGDIPDADVKP 209
           P+G+PKDE+           PL+EQL +E        KEAHSRAV LE IGDIPDA++KP
Sbjct: 181 PDGKPKDEVVDEVRLEDDWVPLDEQLGAEELEEVFRAKEAHSRAVVLETIGDIPDAEIKP 240

Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           PDNVLFVC+LNPVTEDEDLH IFS+FGTV+SAE++RDY+TG+SLCYAF+EFE +EACEQA
Sbjct: 241 PDNVLFVCKLNPVTEDEDLHTIFSRFGTVLSAEVIRDYKTGDSLCYAFIEFETKEACEQA 300

Query: 270 YFKMNNALIDDRRICVDFSQSVSKIWKK 297
           YFKM+NALIDDRRI VDFSQSV+K+W +
Sbjct: 301 YFKMDNALIDDRRIHVDFSQSVAKLWSQ 328

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357121886|ref|XP_003562648.1| PREDICTED: peptidyl-prolyl cis-trans isomerase-like 4-like [Brachypodium distachyon]

 Score =  404 bits (1039), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 204/325 (62%), Positives = 248/325 (76%), Gaps = 30/325 (9%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           MSVLI TS+GDI +DL  D CP TT NFL+ CK KYYNGCLFH + KDF+AQ+GDPTGTG
Sbjct: 1   MSVLIVTSVGDIELDLHTDLCPLTTKNFLKLCKMKYYNGCLFHKVEKDFLAQSGDPTGTG 60

Query: 61  TGGRSVY------EDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLD 114
           +GG SVY      + RFF DEIR +L+H K GTV MASAG + NASQFYITLRD + YLD
Sbjct: 61  SGGDSVYKFLYGDQARFFNDEIRPELRHSKTGTVAMASAGENCNASQFYITLRDEVDYLD 120

Query: 115 EKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY-----PPELAD---DSI 166
           +KHT+FG VAEG +TLT+IN+A VD++ RP + I IK TY+L      PP+LA+   D+ 
Sbjct: 121 DKHTVFGTVAEGFDTLTKINEAYVDDKGRPFKNIRIKHTYILDDPFDDPPQLAELIPDNS 180

Query: 167 PEGEPKDELEP--------PLNEQLSSE--------KEAHSRAVALECIGDIPDADVKPP 210
           P G+P DE+          PL+E +  E        KEAH+ AV LE +GDIPDA+VKPP
Sbjct: 181 PLGKPHDEVAEERLEDSWVPLDETVDPEQLEEMIRSKEAHANAVILESVGDIPDAEVKPP 240

Query: 211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
           DNVLFVC+LNPVT+DEDL+ IFS+FGTV SAEI+RD++TG+SLCYAF+EFE +EACE+AY
Sbjct: 241 DNVLFVCKLNPVTQDEDLYTIFSRFGTVTSAEIIRDFKTGDSLCYAFIEFEVKEACERAY 300

Query: 271 FKMNNALIDDRRICVDFSQSVSKIW 295
           FKM+N LIDDRRI VDFSQSVSK+W
Sbjct: 301 FKMDNCLIDDRRIHVDFSQSVSKLW 325

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	299
TAIR|locus:2024852	506	CYP59 "cyclophilin 59" [Arabid	0.588	0.347	0.573	5.2e-102
UNIPROTKB|E1C3R0	478	PPIL4 "Uncharacterized protein	0.434	0.271	0.637	1.9e-81
UNIPROTKB|G4N9S1	505	MGG_10681 "Peptidyl-prolyl cis	0.438	0.259	0.577	2.9e-50
ZFIN|ZDB-GENE-030131-6251	454	ppil4 "peptidylprolyl isomeras	0.441	0.290	0.661	6.4e-44
MGI|MGI:1914668	492	Ppil4 "peptidylprolyl isomeras	0.551	0.335	0.532	4.5e-43
RGD|1311051	492	Ppil4 "peptidylprolyl isomeras	0.551	0.335	0.532	4.5e-43
UNIPROTKB|F1P661	526	PPIL4 "Uncharacterized protein	0.551	0.313	0.532	5.7e-43
UNIPROTKB|F1N6W2	492	PPIL4 "Uncharacterized protein	0.551	0.335	0.532	5.7e-43
UNIPROTKB|Q8WUA2	492	PPIL4 "Peptidyl-prolyl cis-tra	0.551	0.335	0.532	5.7e-43
UNIPROTKB|I3LGX0	471	PPIL4 "Uncharacterized protein	0.551	0.350	0.526	4e-42

TAIR|locus:2024852 CYP59 "cyclophilin 59" [Arabidopsis thaliana (taxid:3702)]

 Score = 529 (191.3 bits), Expect = 5.2e-102, Sum P(2) = 5.2e-102
 Identities = 109/190 (57%), Positives = 132/190 (69%)

Query:     1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQXXXXXXXX 60
             MSVLI TSLGDIVIDL  DKCP T  NFL+ CK KYYNGCLFH + KDF AQ        
Sbjct:     1 MSVLIVTSLGDIVIDLHSDKCPLTCKNFLKLCKIKYYNGCLFHTVQKDFTAQTGDPTGTG 60

Query:    61 XXXRSVY------EDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLD 114
                 S+Y      + RF+ DEI  DLKH K GTV MAS G +LNASQFY TLRD+L YLD
Sbjct:    61 AGGDSIYKFLYGEQARFYKDEIHLDLKHSKTGTVAMASGGENLNASQFYFTLRDDLDYLD 120

Query:   115 EKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY-----PPELAD---DSI 166
              KHT+FG++AEG +TLTRIN+A VD +NRP + I IK T++L      PP+LA+   D+ 
Sbjct:   121 GKHTVFGQIAEGFDTLTRINEAYVDPKNRPYKNIRIKHTHILDDPFDDPPQLAEMMPDAS 180

Query:   167 PEGEPKDELE 176
             PEG+PK+E++
Sbjct:   181 PEGKPKEEVK 190

GO:0000166 "nucleotide binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0006457 "protein folding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005829 "cytosol" evidence=IDA

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

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

 Score = 460 (167.0 bits), Expect = 1.9e-81, Sum P(2) = 1.9e-81
 Identities = 88/138 (63%), Positives = 112/138 (81%)

Query:   162 ADDSIPE--GEPKDELEPPLNEQLSSEKEAHSRAVALECIGDIPDADVKPPDNVLFVCQL 219
             AD+ I +  G   DE+E     ++ +EKEA +RA+ LE +GD+PDA+VKPP+NVLFVC+L
Sbjct:   193 ADEEIDDMKGRSADEIE-----EVQAEKEAKTRAILLEMVGDLPDAEVKPPENVLFVCKL 247

Query:   220 NPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID 279
             NPVT DEDL +IFS+FG + S E++RD++TGESLCYAF+EFEK E CE+AYFKM+N LID
Sbjct:   248 NPVTTDEDLEIIFSRFGPIKSCEVIRDWKTGESLCYAFIEFEKEEDCEKAYFKMDNVLID 307

Query:   280 DRRICVDFSQSVSKI-WK 296
             DRRI VDFSQSV+KI WK
Sbjct:   308 DRRIHVDFSQSVAKIKWK 325

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|G4N9S1 MGG_10681 "Peptidyl-prolyl cis-trans isomerase-like 4" [Magnaporthe oryzae 70-15 (taxid:242507)]

 Score = 391 (142.7 bits), Expect = 2.9e-50, Sum P(2) = 2.9e-50
 Identities = 78/135 (57%), Positives = 103/135 (76%)

Query:   160 ELADDSIPEGEPKDELEPPLNEQLSSEKEAHSRAVALECIGDIPDADVKPPDNVLFVCQL 219
             +LA++   EG   DE      E+   E+EA ++A+ LE +GD+P A+VKPP+NVLFVC+L
Sbjct:   209 KLAEEDA-EG---DEDRAAAAEKQRREREAKAQALTLEMMGDLPFAEVKPPENVLFVCKL 264

Query:   220 NPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID 279
             NPVT+D DL +IFS+FG ++S E++RD +TG+SL YAF+EFE + ACE AYFKM   LID
Sbjct:   265 NPVTQDADLELIFSRFGKILSCEVIRDSKTGDSLQYAFIEFEDKAACETAYFKMQGVLID 324

Query:   280 DRRICVDFSQSVSKI 294
             DRRI VDFSQSVSK+
Sbjct:   325 DRRIHVDFSQSVSKL 339

GO:0043581 "mycelium development" evidence=IEP

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

 Score = 463 (168.0 bits), Expect = 6.4e-44, P = 6.4e-44
 Identities = 90/136 (66%), Positives = 112/136 (82%)

Query:   162 ADDSIPEGEPKDELEPPLNEQLSSEKEAHSRAVALECIGDIPDADVKPPDNVLFVCQLNP 221
             AD++I + E KD  E  L+E L  +KEA ++A+ LE +GD+PDAD+KPP+NVLFVC+LNP
Sbjct:   193 ADEAINDDEGKDPEE--LDE-LIKDKEAKTQAILLEMVGDLPDADIKPPENVLFVCKLNP 249

Query:   222 VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDR 281
             VT DEDL +IFS+FG +   EI+RD++TGESLCYAF+EFEK E CE+AYFKM+N LIDDR
Sbjct:   250 VTTDEDLEIIFSRFGLIKCCEIIRDWKTGESLCYAFIEFEKEEDCEKAYFKMDNVLIDDR 309

Query:   282 RICVDFSQSVSKI-WK 296
             RI VDFSQSVSKI WK
Sbjct:   310 RIHVDFSQSVSKIKWK 325

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

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

 Score = 455 (165.2 bits), Expect = 4.5e-43, P = 4.5e-43
 Identities = 91/171 (53%), Positives = 123/171 (71%)

Query:   132 RINQAVV--DEENRPPQQIIIKQTYVLYPPELADDSIPEGEPKDELEPPLNEQ---LSSE 186
             RIN  V+  D  + PP  +I  ++      +L    I   E  D+ +    E+   + +E
Sbjct:   155 RINHTVILDDPFDDPPDLLIPDRSPEPTKEQLDSGRIGADEEIDDFKGRSAEEVEEIKAE 214

Query:   187 KEAHSRAVALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRD 246
             KEA ++A+ LE +GD+PDAD+KPP+NVLFVC+LNPVT DEDL +IFS+FG + S E++RD
Sbjct:   215 KEAKTQAILLEMVGDLPDADIKPPENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRD 274

Query:   247 YRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVSKI-WK 296
             ++TGESLCYAF+EFEK E CE+A+FKM+N LIDDRRI VDFSQSV+K+ WK
Sbjct:   275 WKTGESLCYAFIEFEKEEDCEKAFFKMDNVLIDDRRIHVDFSQSVAKVKWK 325

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 = 455 (165.2 bits), Expect = 4.5e-43, P = 4.5e-43
 Identities = 91/171 (53%), Positives = 123/171 (71%)

Query:   132 RINQAVV--DEENRPPQQIIIKQTYVLYPPELADDSIPEGEPKDELEPPLNEQ---LSSE 186
             RIN  V+  D  + PP  +I  ++      +L    I   E  D+ +    E+   + +E
Sbjct:   155 RINHTVILDDPFDDPPDLLIPDRSPEPTKEQLDSGRIGADEEIDDFKGRSAEEVEEIKAE 214

Query:   187 KEAHSRAVALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRD 246
             KEA ++A+ LE +GD+PDAD+KPP+NVLFVC+LNPVT DEDL +IFS+FG + S E++RD
Sbjct:   215 KEAKTQAILLEMVGDLPDADIKPPENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRD 274

Query:   247 YRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVSKI-WK 296
             ++TGESLCYAF+EFEK E CE+A+FKM+N LIDDRRI VDFSQSV+K+ WK
Sbjct:   275 WKTGESLCYAFIEFEKEEDCEKAFFKMDNVLIDDRRIHVDFSQSVAKVKWK 325

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 = 454 (164.9 bits), Expect = 5.7e-43, P = 5.7e-43
 Identities = 91/171 (53%), Positives = 123/171 (71%)

Query:   132 RINQAVV--DEENRPPQQIIIKQTYVLYPPELADDSIPEGEPKDELEPPLNEQ---LSSE 186
             RIN  V+  D  + PP  +I  ++      +L    I   E  D+ +    E+   + +E
Sbjct:   189 RINHTVILDDPFDDPPDLLIPDRSPEPTREQLDSGRIGADEEIDDFKGRSAEEVEEIKAE 248

Query:   187 KEAHSRAVALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRD 246
             KEA ++A+ LE +GD+PDAD+KPP+NVLFVC+LNPVT DEDL +IFS+FG + S E++RD
Sbjct:   249 KEAKTQAILLEMVGDLPDADIKPPENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRD 308

Query:   247 YRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVSKI-WK 296
             ++TGESLCYAF+EFEK E CE+A+FKM+N LIDDRRI VDFSQSV+K+ WK
Sbjct:   309 WKTGESLCYAFIEFEKEEDCEKAFFKMDNVLIDDRRIHVDFSQSVAKVKWK 359

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

 Score = 454 (164.9 bits), Expect = 5.7e-43, P = 5.7e-43
 Identities = 91/171 (53%), Positives = 123/171 (71%)

Query:   132 RINQAVV--DEENRPPQQIIIKQTYVLYPPELADDSIPEGEPKDELEPPLNEQ---LSSE 186
             RIN  V+  D  + PP  +I  ++      +L    I   E  D+ +    E+   + +E
Sbjct:   155 RINHTVILDDPFDDPPDLLIPDRSPEPTREQLDSGRIGADEEIDDFKGRSAEEVEEIKAE 214

Query:   187 KEAHSRAVALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRD 246
             KEA ++A+ LE +GD+PDAD+KPP+NVLFVC+LNPVT DEDL +IFS+FG + S E++RD
Sbjct:   215 KEAKTQAILLEMVGDLPDADIKPPENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRD 274

Query:   247 YRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVSKI-WK 296
             ++TGESLCYAF+EFEK E CE+A+FKM+N LIDDRRI VDFSQSV+K+ WK
Sbjct:   275 WKTGESLCYAFIEFEKEEDCEKAFFKMDNVLIDDRRIHVDFSQSVAKVKWK 325

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 = 454 (164.9 bits), Expect = 5.7e-43, P = 5.7e-43
 Identities = 91/171 (53%), Positives = 123/171 (71%)

Query:   132 RINQAVV--DEENRPPQQIIIKQTYVLYPPELADDSIPEGEPKDELEPPLNEQ---LSSE 186
             RIN  V+  D  + PP  +I  ++      +L    I   E  D+ +    E+   + +E
Sbjct:   155 RINHTVILDDPFDDPPDLLIPDRSPEPTREQLDSGRIGADEEIDDFKGRSAEEVEEIKAE 214

Query:   187 KEAHSRAVALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRD 246
             KEA ++A+ LE +GD+PDAD+KPP+NVLFVC+LNPVT DEDL +IFS+FG + S E++RD
Sbjct:   215 KEAKTQAILLEMVGDLPDADIKPPENVLFVCKLNPVTTDEDLEIIFSRFGPIRSCEVIRD 274

Query:   247 YRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVSKI-WK 296
             ++TGESLCYAF+EFEK E CE+A+FKM+N LIDDRRI VDFSQSV+K+ WK
Sbjct:   275 WKTGESLCYAFIEFEKEEDCEKAFFKMDNVLIDDRRIHVDFSQSVAKVKWK 325

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

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

 Score = 446 (162.1 bits), Expect = 4.0e-42, P = 4.0e-42
 Identities = 90/171 (52%), Positives = 122/171 (71%)

Query:   132 RINQAVV--DEENRPPQQIIIKQTYVLYPPELADDSIPEGEPKDELEPPLNEQ---LSSE 186
             RIN  V+  D  + PP  +I  ++      +L    I   E  D+ +    E+   + +E
Sbjct:   132 RINHTVILDDPFDDPPDLLIPDRSPEPTREQLDSGRIGADEEIDDFKGRSAEEVEEIKAE 191

Query:   187 KEAHSRAVALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRD 246
             KEA ++A+ LE +GD+PDAD+KPP+NVLFVC+LN VT DEDL +IFS+FG + S E++RD
Sbjct:   192 KEAKTQAILLEMVGDLPDADIKPPENVLFVCKLNSVTPDEDLEIIFSRFGPIRSCEVIRD 251

Query:   247 YRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVSKI-WK 296
             ++TGESLCYAF+EFEK E CE+A+FKM+N LIDDRRI VDFSQSV+K+ WK
Sbjct:   252 WKTGESLCYAFIEFEKEEDCEKAFFKMDNVLIDDRRIHVDFSQSVAKVKWK 302

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

---

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)
Q9UUE4	PPIL4_SCHPO	5, ., 2, ., 1, ., 8	0.5015	0.9799	0.6782	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	5.2.1	0.766
4th Layer	5.2.1.8	0.824

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00035738001 RecName- Full=Peptidyl-prolyl cis-trans isomerase; EC=5.2.1.8; (627 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	299
cd01921	166	cd01921, cyclophilin_RRM, cyclophilin_RRM: cycloph	5e-78
cd01928	153	cd01928, Cyclophilin_PPIL3_like, Cyclophilin_PPIL3	6e-56
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	1e-54
pfam00160	144	pfam00160, Pro_isomerase, Cyclophilin type peptidy	1e-54
cd01927	148	cd01927, cyclophilin_WD40, cyclophilin_WD40: cyclo	1e-51
cd01923	159	cd01923, cyclophilin_RING, cyclophilin_RING: cyclo	7e-51
cd00317	146	cd00317, cyclophilin, cyclophilin: cyclophilin-typ	1e-49
COG0652	158	COG0652, PpiB, Peptidyl-prolyl cis-trans isomerase	6e-49
cd01925	171	cd01925, cyclophilin_CeCYP16-like, cyclophilin_CeC	8e-49
cd01922	146	cd01922, cyclophilin_SpCYP2_like, cyclophilin_SpCY	6e-44
cd01926	164	cd01926, cyclophilin_ABH_like, cyclophilin_ABH_lik	9e-35
PTZ00060	183	PTZ00060, PTZ00060, cyclophilin; Provisional	1e-27
PLN03149	186	PLN03149, PLN03149, peptidyl-prolyl isomerase H (c	2e-25
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	5e-20
cd01920	155	cd01920, cyclophilin_EcCYP_like, cyclophilin_EcCYP	1e-19
smart00360	73	smart00360, RRM, RNA recognition motif	6e-19
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	5e-16
PRK10791	164	PRK10791, PRK10791, peptidyl-prolyl cis-trans isom	2e-15
PRK10903	190	PRK10903, PRK10903, peptidyl-prolyl cis-trans isom	4e-14
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	1e-13
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-13
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	9e-13
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-12
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-12
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	6e-12
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	6e-12
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	7e-12
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-11
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-11
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-11
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	3e-11
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-10
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	2e-10
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	3e-10
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	3e-10
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-10
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	8e-10
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	9e-10
cd01924	176	cd01924, cyclophilin_TLP40_like, cyclophilin_TLP40	2e-09
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-09
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	4e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-09
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	5e-09
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	5e-09
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	5e-09
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	5e-09
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	7e-09
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	8e-09
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	9e-09
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	1e-08
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	1e-08
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	1e-08
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	1e-08
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	1e-08
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	2e-08
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	2e-08
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-08
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	3e-08
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	4e-08
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	4e-08
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	4e-08
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	4e-08
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	5e-08
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	5e-08
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	6e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	6e-08
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	6e-08
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	7e-08
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	7e-08
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	7e-08
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	8e-08
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-07
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	1e-07
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	2e-07
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-07
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	2e-07
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-07
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	4e-07
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	4e-07
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	5e-07
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	5e-07
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	5e-07
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	7e-07
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	8e-07
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	8e-07
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	8e-07
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	9e-07
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	9e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-06
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	1e-06
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	1e-06
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-06
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	1e-06
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	1e-06
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-06
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-06
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	2e-06
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	2e-06
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	2e-06
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-06
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	3e-06
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	3e-06
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	3e-06
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	3e-06
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	4e-06
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	5e-06
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	6e-06
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	6e-06
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	7e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	7e-06
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	8e-06
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	9e-06
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	9e-06
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	9e-06
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	1e-05
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	1e-05
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	1e-05
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	1e-05
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	1e-05
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	1e-05
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-05
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	2e-05
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-05
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	2e-05
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	2e-05
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	2e-05
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	2e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	3e-05
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	3e-05
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	3e-05
PLN03121	243	PLN03121, PLN03121, nucleic acid binding protein;	4e-05
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	4e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	5e-05
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	5e-05
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	5e-05
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	6e-05
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	6e-05
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	6e-05
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	6e-05
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	6e-05
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	7e-05
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	7e-05
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	7e-05
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	7e-05
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	7e-05
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	7e-05
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	8e-05
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	8e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	9e-05
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	9e-05
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	1e-04
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	1e-04
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	1e-04
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	1e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	1e-04
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-04
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	2e-04
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	2e-04
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	2e-04
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	2e-04
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-04
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	2e-04
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	2e-04
cd12467	78	cd12467, RRM_Srp1p_like, RNA recognition motif 1 i	3e-04
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	3e-04
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	3e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	3e-04
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	4e-04
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	4e-04
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	4e-04
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	5e-04
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	5e-04
cd12303	86	cd12303, RRM_spSet1p_like, RNA recognition motif i	6e-04
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	6e-04
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	7e-04
cd12269	69	cd12269, RRM_Vip1_like, RNA recognition motif in a	7e-04
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	7e-04
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	7e-04
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	0.001
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	0.001
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	0.001
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	0.001
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	0.001
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	0.001
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	0.001
PRK06134	581	PRK06134, PRK06134, putative FAD-binding dehydroge	0.001
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	0.001
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	0.002
cd12422	85	cd12422, RRM2_PTBP1_hnRNPL_like, RNA recognition m	0.002
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	0.002
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	0.002
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	0.002
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	0.002
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	0.002
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	0.003
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	0.003
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	0.003
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	0.004
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	0.004
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	0.004
cd12289	93	cd12289, RRM_LARP6, RNA recognition motif in La-re	0.004
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	0.004
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	0.004
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	0.004

>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 =  234 bits (598), Expect = 5e-78
 Identities = 96/162 (59%), Positives = 117/162 (72%), Gaps = 6/162 (3%)

Query: 4   LIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGG 63
           L+ET+LGD+VIDLF D+CP    NFL+ CK KYYN CLF+N+ KDFIAQTGDPTGTG GG
Sbjct: 1   LLETTLGDLVIDLFTDECPLACLNFLKLCKLKYYNFCLFYNVQKDFIAQTGDPTGTGAGG 60

Query: 64  RSVYED------RFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKH 117
            S+Y        RFF  EI   LKH K GTV M +AG +LN SQFYITL +NL YLD KH
Sbjct: 61  ESIYSQLYGRQARFFEPEILPLLKHSKKGTVSMVNAGDNLNGSQFYITLGENLDYLDGKH 120

Query: 118 TIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPP 159
           T+FG+V EG + L +IN A+VD++ RP + I IK T++L  P
Sbjct: 121 TVFGQVVEGFDVLEKINDAIVDDDGRPLKDIRIKHTHILDDP 162

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|238909 cd01928, Cyclophilin_PPIL3_like, Cyclophilin_PPIL3_like

 Score =  177 bits (451), Expect = 6e-56
 Identities = 77/155 (49%), Positives = 101/155 (65%), Gaps = 2/155 (1%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           MSV + T+LGDI I+LF D CP+   NFL  C + YYNGC+FH   K F+ QTGDPTGTG
Sbjct: 1   MSVTLHTNLGDIKIELFCDDCPKACENFLALCASGYYNGCIFHRNIKGFMVQTGDPTGTG 60

Query: 61  TGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIF 120
            GG S++  + F DE R  LKHD  G V MA+ G + N SQF+IT     H LD K+T+F
Sbjct: 61  KGGESIWG-KKFEDEFRETLKHDSRGVVSMANNGPNTNGSQFFITYAKQPH-LDGKYTVF 118

Query: 121 GEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYV 155
           G+V +G ETL  + +  VD++ RP ++I IK   +
Sbjct: 119 GKVIDGFETLDTLEKLPVDKKYRPLEEIRIKDVTI 153

Proteins similar to Human cyclophilin-like peptidylprolyl cis- trans isomerase (PPIL3). Members of this family lack a key residue important for cyclosporin binding: the tryptophan residue corresponding to W121 in human hCyP-18a; most members have a histidine at this position. The exact function of the protein is not known. Length = 153

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

 Score =  172 bits (437), Expect = 1e-54
 Identities = 59/83 (71%), Positives = 72/83 (86%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
           PP+NVLFVC+LNPVT DEDL +IFS+FG + S E++RD +TG+SL YAF+EFE +E CE+
Sbjct: 1   PPENVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEE 60

Query: 269 AYFKMNNALIDDRRICVDFSQSV 291
           AYFKM+N LIDDRRI VDFSQSV
Sbjct: 61  AYFKMDNVLIDDRRIHVDFSQSV 83

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|215759 pfam00160, Pro_isomerase, Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD

 Score =  173 bits (442), Expect = 1e-54
 Identities = 63/151 (41%), Positives = 90/151 (59%), Gaps = 8/151 (5%)

Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTG 62
           + I T+LG IVI+LF D+ P+T  NFL  CK  +Y+G +FH +   F+ Q GDPTG GTG
Sbjct: 2   LDITTNLGRIVIELFGDEAPKTVENFLSLCKKGFYDGTIFHRVIPGFMIQGGDPTGPGTG 61

Query: 63  GRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGE 122
           G      R   DE  + LKH + GT+ MA +G +   SQF+ITL D   +LD  +T+FG 
Sbjct: 62  G-----KRSIPDEFVSKLKHKR-GTLSMARSGPNSAGSQFFITLGDA-PHLDGGYTVFGR 114

Query: 123 VAEGLETLTRINQAVVDEENRPPQQIIIKQT 153
           V EG++ + +I +   D + RP + + I   
Sbjct: 115 VVEGMDVVEKIEKVETDGD-RPLKDVKITSC 144

The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyze peptidyl-prolyl isomerisation during which the peptide bond preceding proline (the peptidyl-prolyl bond) is stabilised in the cis conformation. Mammalian cyclophilin A (CypA) is a major cellular target for the immunosuppressive drug cyclosporin A (CsA). Other roles for cyclophilins may include chaperone and cell signalling function. Length = 144

>gnl|CDD|238908 cd01927, cyclophilin_WD40, cyclophilin_WD40: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a WD40 domain

 Score =  166 bits (421), Expect = 1e-51
 Identities = 67/147 (45%), Positives = 93/147 (63%), Gaps = 2/147 (1%)

Query: 4   LIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGG 63
           +I T+ GDI I LF ++ P+T  NF  H +N YYN  +FH + K F+ QTGDPTG GTGG
Sbjct: 1   IIHTTKGDIHIRLFPEEAPKTVENFTTHARNGYYNNTIFHRVIKGFMIQTGDPTGDGTGG 60

Query: 64  RSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEV 123
            S++  + F DE    LKHD+  T+ MA+AG + N SQF+IT      +LD KHT+FG V
Sbjct: 61  ESIW-GKEFEDEFSPSLKHDRPYTLSMANAGPNTNGSQFFITT-VATPWLDNKHTVFGRV 118

Query: 124 AEGLETLTRINQAVVDEENRPPQQIII 150
            +G++ + RI     D+ +RP + I I
Sbjct: 119 VKGMDVVQRIENVKTDKNDRPYEDIKI 145

This group consists of several hypothetical and putative eukaryotic and bacterial proteins which have a cyclophilin domain and a WD40 domain. Function of the protein is not known. Length = 148

>gnl|CDD|238904 cd01923, cyclophilin_RING, cyclophilin_RING: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a modified RING finger domain

 Score =  164 bits (418), Expect = 7e-51
 Identities = 66/157 (42%), Positives = 97/157 (61%), Gaps = 2/157 (1%)

Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTG 62
           V + T+ GD+ ++L  DK P+   NF++ CK  YY+G +FH   ++F+ Q GDPTGTG G
Sbjct: 2   VRLHTNKGDLNLELHCDKAPKACENFIKLCKKGYYDGTIFHRSIRNFMIQGGDPTGTGRG 61

Query: 63  GRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGE 122
           G S++  + F DE + +L HD  G + MA++G + N SQF+IT R +  +LD KHT+FG 
Sbjct: 62  GESIW-GKPFKDEFKPNLSHDGRGVLSMANSGPNTNGSQFFITYR-SCKHLDGKHTVFGR 119

Query: 123 VAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPP 159
           V  GLETL  +        +RP ++I I+ T V   P
Sbjct: 120 VVGGLETLEAMENVPDPGTDRPKEEIKIEDTSVFVDP 156

This group includes the nuclear proteins, Human hCyP-60 and Caenorhabditis elegans MOG-6 which, compared to the archetypal cyclophilin Human cyclophilin A exhibit reduced peptidylprolyl cis- trans isomerase activity and lack a residue important for cyclophilin binding. Human hCyP-60 has been shown to physically interact with the proteinase inhibitor peptide eglin c and; C. elegans MOG-6 to physically interact with MEP-1, a nuclear zinc finger protein. MOG-6 has been shown to function in germline sex determination. Length = 159

>gnl|CDD|238194 cd00317, cyclophilin, cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases

 Score =  161 bits (409), Expect = 1e-49
 Identities = 59/146 (40%), Positives = 86/146 (58%), Gaps = 3/146 (2%)

Query: 5   IETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGR 64
           ++T+ G IVI+L+ D+ P+T  NFL   +  +Y+G  FH +   F+ Q GDPTGTG GG 
Sbjct: 2   LDTTKGRIVIELYGDEAPKTVENFLSLARGGFYDGTTFHRVIPGFMIQGGDPTGTGGGG- 60

Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
                  F DE      H + GT+ MA+AG + N SQF+IT      +LD KHT+FG+V 
Sbjct: 61  -SGPGYKFPDENFPLKYHHRRGTLSMANAGPNTNGSQFFITTAPT-PHLDGKHTVFGKVV 118

Query: 125 EGLETLTRINQAVVDEENRPPQQIII 150
           EG++ + +I +   DE  RP + + I
Sbjct: 119 EGMDVVDKIERGDTDENGRPIKPVTI 144

This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA). Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin. PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system; human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing. . Length = 146

>gnl|CDD|223725 COG0652, PpiB, Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family [Posttranslational modification, protein turnover, chaperones]

 Score =  159 bits (405), Expect = 6e-49
 Identities = 64/162 (39%), Positives = 93/162 (57%), Gaps = 12/162 (7%)

Query: 2   SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGT-G 60
           +V++ET+ GDI I+L+ DK P+T  NFLQ  K  +Y+G +FH +   F+ Q GDPTG  G
Sbjct: 1   TVILETNKGDITIELYPDKAPKTVANFLQLVKEGFYDGTIFHRVIPGFMIQGGDPTGGDG 60

Query: 61  TGGRSVYEDRFFVDEIRADLKH-DKVGTVGMASAG-RDLNASQFYITLRDNLHYLDEKHT 118
           TGG        F DE  A      K GT+ MA AG  + N SQF+IT+ DN  +LD K+T
Sbjct: 61  TGGPG----PPFKDENFALNGDRHKRGTLSMARAGDPNSNGSQFFITVVDN-PFLDGKYT 115

Query: 119 IFGEVAEGLETLTRINQAVVDEE----NRPPQQIIIKQTYVL 156
           +FG+V EG++ + +I     D+     + P   + I    ++
Sbjct: 116 VFGQVVEGMDVVDKIKNGDTDDSGYVQDVPADPVKILSVKIV 157

Length = 158

>gnl|CDD|238906 cd01925, cyclophilin_CeCYP16-like, cyclophilin_CeCYP16-like: cyclophilin-type peptidylprolyl cis- trans isomerase) (PPIase) domain similar to Caenorhabditis elegans cyclophilin 16

 Score =  159 bits (405), Expect = 8e-49
 Identities = 68/167 (40%), Positives = 98/167 (58%), Gaps = 5/167 (2%)

Query: 2   SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGT 61
            V+++T+ GDI I+L+  + P+   NF+Q C   YY+  +FH +   FI Q GDPTGTGT
Sbjct: 7   KVILKTTAGDIDIELWSKEAPKACRNFIQLCLEGYYDNTIFHRVVPGFIIQGGDPTGTGT 66

Query: 62  GGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFG 121
           GG S+Y    F DE  + L+ ++ G VGMA+AG D N SQF+ TL D    L+ KHT+FG
Sbjct: 67  GGESIYG-EPFKDEFHSRLRFNRRGLVGMANAGDDSNGSQFFFTL-DKADELNNKHTLFG 124

Query: 122 EVA-EGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPPELADDSIP 167
           +V  + +  L ++ +   D++ RP     I    VL  P   DD +P
Sbjct: 125 KVTGDTIYNLLKLAEVETDKDERPVYPPKITSVEVLENP--FDDIVP 169

C. elegans CeCYP-16, compared to the archetypal cyclophilin Human cyclophilin A has, a reduced peptidylprolyl cis- trans isomerase activity, is cyclosporin insensitive and shows an altered substrate preference favoring, hydrophobic, acidic or amide amino acids. Most members of this subfamily have a glutamate residue in the active site at the position equivalent to a tryptophan (W121 in Human cyclophilin A), which has been shown to be important for cyclophilin binding. Length = 171

>gnl|CDD|238903 cd01922, cyclophilin_SpCYP2_like, cyclophilin_SpCYP2_like: cyclophilin 2-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to Schizosaccharomyces pombe cyp-2

 Score =  146 bits (370), Expect = 6e-44
 Identities = 66/150 (44%), Positives = 93/150 (62%), Gaps = 6/150 (4%)

Query: 4   LIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGG 63
            +ET++G+I ++L+ +  P+T  NF +  K  YYNG +FH + KDF+ Q GDPTGTG GG
Sbjct: 1   TLETTMGEITLELYWNHAPKTCKNFYELAKRGYYNGTIFHRLIKDFMIQGGDPTGTGRGG 60

Query: 64  RSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEV 123
            S+Y  + F DEI  +LKH   G + MA+AG + N SQF+ITL      LD KHTIFG V
Sbjct: 61  ASIYGKK-FEDEIHPELKHTGAGILSMANAGPNTNGSQFFITLAPTPW-LDGKHTIFGRV 118

Query: 124 AEGLETLTRINQAVVD-EENRPPQQI-IIK 151
           ++G       N   V  + +RP  ++ I+K
Sbjct: 119 SKG--MKVIENMVEVQTQTDRPIDEVKILK 146

These proteins bind their respective SNW chromatin binding protein in autologous systems, in a CsA independent manner indicating interaction with a surface outside the PPIase active site. SNW proteins play a basic and broad range role in signaling. Length = 146

>gnl|CDD|238907 cd01926, cyclophilin_ABH_like, cyclophilin_ABH_like: Cyclophilin A, B and H-like cyclophilin-type peptidylprolyl cis- trans isomerase (PPIase) domain

 Score =  123 bits (311), Expect = 9e-35
 Identities = 59/155 (38%), Positives = 85/155 (54%), Gaps = 13/155 (8%)

Query: 7   TSLGDIVIDLFVDKCPRTTNNFLQHC--------KNKYYNGCLFHNIHKDFIAQTGDPT- 57
              G IV++LF D  P+T  NF   C        K   Y G  FH +  DF+ Q GD T 
Sbjct: 12  EPAGRIVMELFADVVPKTAENFRALCTGEKGKGGKPFGYKGSTFHRVIPDFMIQGGDFTR 71

Query: 58  GTGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKH 117
           G GTGG+S+Y ++F  DE    LKH   G + MA+AG + N SQF+IT      +LD KH
Sbjct: 72  GNGTGGKSIYGEKF-PDE-NFKLKHTGPGLLSMANAGPNTNGSQFFITTVKT-PWLDGKH 128

Query: 118 TIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQ 152
            +FG+V EG++ + +I + V     +P ++++I  
Sbjct: 129 VVFGKVVEGMDVVKKI-ENVGSGNGKPKKKVVIAD 162

This family represents the archetypal cystolic cyclophilin similar to human cyclophilins A, B and H. PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. These enzymes have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. As cyclophilins, Human hCyP-A, human cyclophilin-B (hCyP-19), S. cerevisiae Cpr1 and C. elegans Cyp-3, are inhibited by the immunosuppressive drug cyclopsporin A (CsA). CsA binds to the PPIase active site. Cyp-3. S. cerevisiae Cpr1 interacts with the Rpd3 - Sin3 complex and in addition is a component of the Set3 complex. S. cerevisiae Cpr1 has also been shown to have a role in Zpr1p nuclear transport. Human cyclophilin H associates with the [U4/U6.U5] tri-snRNP particles of the splicesome. Length = 164

>gnl|CDD|240249 PTZ00060, PTZ00060, cyclophilin; Provisional

 Score =  105 bits (264), Expect = 1e-27
 Identities = 58/136 (42%), Positives = 76/136 (55%), Gaps = 13/136 (9%)

Query: 10  GDIVIDLFVDKCPRTTNNFLQHC---------KNKYYNGCLFHNIHKDFIAQTGDPT-GT 59
           G IV +LF D  P+T  NF   C         KN +Y G +FH I   F+ Q GD T   
Sbjct: 30  GRIVFELFSDVTPKTAENFRALCIGDKVGSSGKNLHYKGSIFHRIIPQFMCQGGDITNHN 89

Query: 60  GTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTI 119
           GTGG S+Y  R F DE    LKHD+ G + MA+AG + N SQF+IT      +LD KH +
Sbjct: 90  GTGGESIY-GRKFTDE-NFKLKHDQPGLLSMANAGPNTNGSQFFITTVP-CPWLDGKHVV 146

Query: 120 FGEVAEGLETLTRINQ 135
           FG+V EG+E +  + +
Sbjct: 147 FGKVIEGMEVVRAMEK 162

Length = 183

>gnl|CDD|178694 PLN03149, PLN03149, peptidyl-prolyl isomerase H (cyclophilin H); Provisional

 Score =   99 bits (249), Expect = 2e-25
 Identities = 55/153 (35%), Positives = 77/153 (50%), Gaps = 13/153 (8%)

Query: 10  GDIVIDLFVDKCPRTTNNFLQHCKNKY--------YNGCLFHNIHKDFIAQTGD-PTGTG 60
           G I ++LF D  P+T  NF Q C  ++        Y GC FH + KDF+ Q GD   G G
Sbjct: 33  GRIKMELFADIAPKTAENFRQFCTGEFRKAGLPQGYKGCQFHRVIKDFMIQGGDFLKGDG 92

Query: 61  TGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIF 120
           TG  S+Y  +F  +   A  KH   G + MA++G + N  QF+IT      +LD KH +F
Sbjct: 93  TGCVSIYGSKFEDENFIA--KHTGPGLLSMANSGPNTNGCQFFITCA-KCDWLDNKHVVF 149

Query: 121 GEV-AEGLETLTRINQAVVDEENRPPQQIIIKQ 152
           G V  +GL  + +I        NRP    +I +
Sbjct: 150 GRVLGDGLLVVRKIENVATGPNNRPKLACVISE 182

Length = 186

>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 = 82.3 bits (204), Expect = 5e-20
 Identities = 30/81 (37%), Positives = 44/81 (54%)

Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           P   LFV +L+  T +E L  +FS++G +    ++RD  TG S  YAFVE+E      +A
Sbjct: 2   PYLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRA 61

Query: 270 YFKMNNALIDDRRICVDFSQS 290
           Y   +  +ID   I VDF + 
Sbjct: 62  YRDAHKLVIDGSEIFVDFERE 82

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|238901 cd01920, cyclophilin_EcCYP_like, cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E

 Score = 83.3 bits (206), Expect = 1e-19
 Identities = 50/158 (31%), Positives = 80/158 (50%), Gaps = 15/158 (9%)

Query: 4   LIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGG 63
             +TSLGDIV++L+ DK P T  NFL + +  +Y+  +FH +   F+ Q G   G     
Sbjct: 1   EFQTSLGDIVVELYDDKAPITVENFLAYVRKGFYDNTIFHRVISGFVIQGG---GFTPDL 57

Query: 64  RSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNA-SQFYITLRDNLHYLDEK-----H 117
                 +   +E    L + + GT+ MA      +A SQF+I L+DN   LD +     +
Sbjct: 58  AQKETLKPIKNEAGNGLSNTR-GTIAMARTNAPDSATSQFFINLKDNA-SLDYQNEQWGY 115

Query: 118 TIFGEVAEGLETLTRINQAVVDE----ENRPPQQIIIK 151
           T+FGEV EG++ + +I           ++ P Q +II+
Sbjct: 116 TVFGEVTEGMDVVDKIAGVETYSFGSYQDVPVQDVIIE 153

coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these have reduced affinity for cyclosporin A. E. coli cyclophilin A has a similar peptidylprolyl cis- trans isomerase activity to the human cyclophilin A. Most members of this subfamily contain a phenylalanine residue at the position equivalent to Human cyclophilin W121, where a tyrptophan has been shown to be important for cyclophilin binding. Length = 155

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

 Score = 78.8 bits (195), Expect = 6e-19
 Identities = 31/71 (43%), Positives = 43/71 (60%)

Query: 213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
            LFV  L P T +E+L  +FS+FG V S  ++RD  TG+S  +AFVEFE  E  E+A   
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 273 MNNALIDDRRI 283
           +N   +D R +
Sbjct: 61  LNGKELDGRPL 71

Length = 73

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

 Score = 70.8 bits (174), Expect = 5e-16
 Identities = 32/73 (43%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  L P T +EDL  +FS+FG + S  I+RD + G+S  +AFVEFE  E  E+A   +
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEAL 59

Query: 274 NNALIDDRRICVD 286
           N   +D R++ V 
Sbjct: 60  NGKELDGRKLKVS 72

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

>gnl|CDD|182734 PRK10791, PRK10791, peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional

 Score = 72.6 bits (178), Expect = 2e-15
 Identities = 46/139 (33%), Positives = 70/139 (50%), Gaps = 12/139 (8%)

Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTG 62
           V   T+ GDIVI  F DK P T  NFL +C+  +YN  +FH +   F+ Q G   G   G
Sbjct: 2   VTFHTNHGDIVIKTFDDKAPETVKNFLDYCREGFYNNTIFHRVINGFMIQGG---GFEPG 58

Query: 63  GRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNAS-QFYITLRDN--LHYLDEK--- 116
            +         +E    LK+ + GT+ MA      +A+ QF+I + DN  L++  E    
Sbjct: 59  MKQKATKEPIKNEANNGLKNTR-GTLAMARTQAPHSATAQFFINVVDNDFLNFSGESLQG 117

Query: 117 --HTIFGEVAEGLETLTRI 133
             + +F EV EG++ + +I
Sbjct: 118 WGYCVFAEVVEGMDVVDKI 136

Length = 164

>gnl|CDD|182824 PRK10903, PRK10903, peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional

 Score = 69.1 bits (169), Expect = 4e-14
 Identities = 45/171 (26%), Positives = 80/171 (46%), Gaps = 29/171 (16%)

Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTG 62
           VL+ TS G+I ++L   K P +  NF+ +  + +YN   FH +   F+ Q G  T     
Sbjct: 31  VLLTTSAGNIELELNSQKAPVSVKNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTE---- 86

Query: 63  GRSVYEDRFFVDEIRADLKHD-------KVGTVGMA-SAGRDLNASQFYITLRDNLHYLD 114
                  +    +    +K++         GT+ MA +A +D   SQF+I + DN  +LD
Sbjct: 87  -------QMQQKKPNPPIKNEADNGLRNTRGTIAMARTADKDSATSQFFINVADNA-FLD 138

Query: 115 E-----KHTIFGEVAEGLETLTRINQAVVDE----ENRPPQQIIIKQTYVL 156
                  + +FG+V +G++   +I+Q    +    +N P + ++I    VL
Sbjct: 139 HGQRDFGYAVFGKVVKGMDVADKISQVPTHDVGPYQNVPSKPVVILSAKVL 189

Length = 190

>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 = 64.6 bits (158), Expect = 1e-13
 Identities = 25/72 (34%), Positives = 42/72 (58%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LF+  L     D+DL+ +F+ FG V+SA++  D  TG+S C+ FV ++  E+ + A   M
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 274 NNALIDDRRICV 285
           N   +  +R+ V
Sbjct: 61  NGFQVGGKRLKV 72

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

 Score = 69.2 bits (168), Expect = 2e-13
 Identities = 32/91 (35%), Positives = 50/91 (54%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
           K  +N LFV  L     +EDL  +F +FG V    ++RD  TG+S  +AFVEFE  E+ E
Sbjct: 112 KEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAE 171

Query: 268 QAYFKMNNALIDDRRICVDFSQSVSKIWKKS 298
           +A  ++N   ++ R + V  +Q  S+   + 
Sbjct: 172 KAIEELNGKELEGRPLRVQKAQPASQPRSEL 202

Length = 306

>gnl|CDD|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 62.2 bits (152), Expect = 9e-13
 Identities = 27/75 (36%), Positives = 42/75 (56%)

Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
           N LFV  L+  T +++L  +FS+FG V    +++D  TGES  + FV FE  E  + A  
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 272 KMNNALIDDRRICVD 286
            +N   ++ R I V+
Sbjct: 62  DLNGKELEGRVIKVE 76

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 61.5 bits (150), Expect = 1e-12
 Identities = 31/70 (44%), Positives = 41/70 (58%), Gaps = 1/70 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  L P T +EDL  +FS+FG + S  I+RD  TG S  +AFVEFE  E  E+A   +
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 274 NNALIDDRRI 283
           N   +  R +
Sbjct: 60  NGKELGGREL 69

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

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

 Score = 61.9 bits (151), Expect = 2e-12
 Identities = 27/75 (36%), Positives = 40/75 (53%)

Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
             LFV +LN  T +  L   F ++G +    ++RD +TG+   YAF+EFE     + AY 
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYK 61

Query: 272 KMNNALIDDRRICVD 286
             +   ID RR+ VD
Sbjct: 62  YADGKKIDGRRVLVD 76

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

 Score = 59.9 bits (146), Expect = 6e-12
 Identities = 28/76 (36%), Positives = 44/76 (57%)

Query: 213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
            L V  L+  T + DL  +FS++G +   +++ D +TG S  + FV FE  E  ++A  +
Sbjct: 1   CLGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKER 60

Query: 273 MNNALIDDRRICVDFS 288
           +N   ID RRI VD+S
Sbjct: 61  LNGMEIDGRRIRVDYS 76

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

 Score = 60.0 bits (146), Expect = 6e-12
 Identities = 22/76 (28%), Positives = 37/76 (48%)

Query: 213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           +L V  L     DE    + S FG V    ++    TGES  Y FVE+  + +  +A  +
Sbjct: 1   LLCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQ 60

Query: 273 MNNALIDDRRICVDFS 288
           ++   I  R++ VD++
Sbjct: 61  LDGKQIGGRKLQVDWA 76

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

 Score = 59.7 bits (145), Expect = 7e-12
 Identities = 26/70 (37%), Positives = 38/70 (54%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L+P  + E L   F+ FG +  A +++D +TG+S  Y FV F K+E  E A   M
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 274 NNALIDDRRI 283
           N   +  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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 58.9 bits (143), Expect = 1e-11
 Identities = 31/75 (41%), Positives = 43/75 (57%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  L+   +DE L   F +FGTVV A ++ D  TG S  + +V+FE  E  ++A   M
Sbjct: 2   LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAM 61

Query: 274 NNALIDDRRICVDFS 288
           +   +D R I VDFS
Sbjct: 62  DGKELDGRPINVDFS 76

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

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

 Score = 58.9 bits (143), Expect = 2e-11
 Identities = 21/76 (27%), Positives = 37/76 (48%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  +   T  +DL  +F ++G +V   I  D+ T     +A+V+FE     E A + +
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 274 NNALIDDRRICVDFSQ 289
           +      R I + F+Q
Sbjct: 63  DRTRFLGREIEIQFAQ 78

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

 Score = 58.8 bits (143), Expect = 2e-11
 Identities = 27/72 (37%), Positives = 35/72 (48%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L     +EDL  +F QFG V SA ++ D  TG S  + FVE E  E    A  K+
Sbjct: 2   LYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKL 61

Query: 274 NNALIDDRRICV 285
           N      R + V
Sbjct: 62  NGTDFGGRTLTV 73

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

 Score = 58.3 bits (142), Expect = 3e-11
 Identities = 27/76 (35%), Positives = 41/76 (53%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L+P   +  L+ IFS  G V+S  + RD  T  SL YA+V F+     E+A   +
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 274 NNALIDDRRICVDFSQ 289
           N  +I  + I + +SQ
Sbjct: 62  NFDVIKGKPIRIMWSQ 77

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

 Score = 56.6 bits (137), Expect = 1e-10
 Identities = 20/63 (31%), Positives = 35/63 (55%)

Query: 225 DEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC 284
            E+L  +F   G + S +I+RD  TG+SL Y FV++      ++A   +N   I ++R+ 
Sbjct: 14  QEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRLK 73

Query: 285 VDF 287
           V +
Sbjct: 74  VSY 76

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

 Score = 56.3 bits (136), Expect = 2e-10
 Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
           + LFV  L      E+L  +F + G V S  ++   R+G+    A+VE+E   +  QA  
Sbjct: 3   HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLV-TNRSGKPKGLAYVEYENESSASQAVL 61

Query: 272 KMNNALIDDRRICVDFS 288
           KM+   I ++ I V  S
Sbjct: 62  KMDGTEIKEKTISVAIS 78

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

 Score = 55.3 bits (134), Expect = 3e-10
 Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 5/66 (7%)

Query: 222 VTEDEDLHV--IFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID 279
           V +D   H+  IFS +GTV   ++  D        YA+VEFE  E  E+A   M+   ID
Sbjct: 10  VNKD---HLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDGGQID 66

Query: 280 DRRICV 285
            + + V
Sbjct: 67  GQEVTV 72

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

 Score = 55.4 bits (134), Expect = 3e-10
 Identities = 25/76 (32%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSA-EILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           LF+  L+P  +++ L+  FS FG ++   +I+RD  TG S  +AF+ ++  EA + A   
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 273 MNNALIDDRRICVDFS 288
           MN   + +R I V ++
Sbjct: 64  MNGQYLCNRPITVSYA 79

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

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

 Score = 59.8 bits (145), Expect = 5e-10
 Identities = 25/72 (34%), Positives = 43/72 (59%), Gaps = 1/72 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L+   +++ L   FS+FG ++S ++  D   G+S  Y FV FEK E+ + A  K+
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKV 149

Query: 274 NNALIDDRRICV 285
           N  L++D+ + V
Sbjct: 150 NGMLLNDKEVYV 161

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|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 = 54.1 bits (130), Expect = 8e-10
 Identities = 23/76 (30%), Positives = 40/76 (52%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LF+  L+  T ++ L  +FS++G +    +++D  T  S  + FV FE  +  + A   M
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 274 NNALIDDRRICVDFSQ 289
           N   +D R+I VD + 
Sbjct: 63  NGKSVDGRQIRVDQAG 78

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

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

 Score = 53.8 bits (130), Expect = 9e-10
 Identities = 28/69 (40%), Positives = 41/69 (59%), Gaps = 1/69 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L   T D+ L   FSQFG +  A ++ D +TG+S  Y FV F+ +E+ E+A  K 
Sbjct: 3   IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERA-CKD 61

Query: 274 NNALIDDRR 282
            N +ID R+
Sbjct: 62  PNPIIDGRK 70

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|238905 cd01924, cyclophilin_TLP40_like, cyclophilin_TLP40_like: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) similar ot the Spinach thylakoid lumen protein TLP40

 Score = 55.5 bits (134), Expect = 2e-09
 Identities = 43/155 (27%), Positives = 64/155 (41%), Gaps = 36/155 (23%)

Query: 12  IVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTG--------- 62
           IV+D +    P T  NF+   +  +Y+G  FH +   F+ QTGDP G   G         
Sbjct: 11  IVLDGY--NAPVTAGNFVDLVERGFYDGMEFHRVEGGFVVQTGDPQGKNPGFPDPETGKS 68

Query: 63  ------------GRSVY----EDRFFVDEIRADLKHDKVGTVGMASAGRDLNA--SQFYI 104
                        + VY    E+    DE      +   G + MA    D N+  SQF+ 
Sbjct: 69  RTIPLEIKPEGQKQPVYGKTLEEAGRYDEQPVLPFNAF-GAIAMARTEFDPNSASSQFFF 127

Query: 105 TLRDNLH------YLDEKHTIFGEVAEGLETLTRI 133
            L+DN         LD ++ +FG V +GL+ L  +
Sbjct: 128 LLKDNELTPSRNNVLDGRYAVFGYVTDGLDILREL 162

Compared to the archetypal cyclophilin Human cyclophilin A, these proteins have similar peptidylprolyl cis- trans isomerase activity and reduced affinity for cyclosporin A. Spinach TLP40 has been shown to have a dual function as a folding catalyst and regulator of dephosphorylation. Length = 176

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

 Score = 52.3 bits (126), Expect = 3e-09
 Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 1/66 (1%)

Query: 223 TEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRR 282
             + DL  +FS FG V    I R    G+   +AFV+F  +   E+A   +N   I  R 
Sbjct: 11  CTEADLKKLFSPFGFVWEVTIPRK-PDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKGRP 69

Query: 283 ICVDFS 288
           + VD++
Sbjct: 70  VAVDWA 75

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

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

 Score = 52.1 bits (125), Expect = 4e-09
 Identities = 25/76 (32%), Positives = 36/76 (47%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  L      EDL   FS    +  A ++ D  TGES  Y FV F   E  ++A  K+
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 274 NNALIDDRRICVDFSQ 289
            N  +  R + +D ++
Sbjct: 62  KNKKLHGRILRLDIAE 77

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

 Score = 56.7 bits (137), Expect = 5e-09
 Identities = 25/76 (32%), Positives = 39/76 (51%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L+P   +  L+ +F  FG V+S  + RD  T  SL Y +V F+     E+A   M
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 274 NNALIDDRRICVDFSQ 289
           N   +  + I + +SQ
Sbjct: 63  NFKRLGGKPIRIMWSQ 78

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|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 = 51.9 bits (125), Expect = 5e-09
 Identities = 26/67 (38%), Positives = 34/67 (50%), Gaps = 1/67 (1%)

Query: 222 VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDR 281
            TE E L  IFS+ G VVS  ++ D  TG+   Y F EFE  E    A   +N    + R
Sbjct: 10  ATE-EQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGYEFNGR 68

Query: 282 RICVDFS 288
            + VDF+
Sbjct: 69  ALRVDFA 75

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

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

 Score = 51.9 bits (124), Expect = 5e-09
 Identities = 22/62 (35%), Positives = 35/62 (56%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L      ++L  +FSQ+G ++++ ILRD  TG S    F+ F+KR   E+A   +
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGL 62

Query: 274 NN 275
           N 
Sbjct: 63  NG 64

This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

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

 Score = 51.8 bits (125), Expect = 5e-09
 Identities = 21/59 (35%), Positives = 33/59 (55%)

Query: 216 VCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMN 274
           V  L+   +++DL  +F  FG +    + +D  TG+S  +AFV F  RE  E+A  K+N
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|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins

 Score = 51.8 bits (125), Expect = 5e-09
 Identities = 24/72 (33%), Positives = 42/72 (58%), Gaps = 1/72 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +F+  L+   +++ L+  FS FG ++S ++  D   G S  Y FV FE  EA  +A  K+
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATD-ENGGSKGYGFVHFETEEAAVRAIEKV 63

Query: 274 NNALIDDRRICV 285
           N  L++D+++ V
Sbjct: 64  NGMLLNDKKVFV 75

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

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

 Score = 51.4 bits (124), Expect = 7e-09
 Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 2/74 (2%)

Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
           NV +V  L    +DE L  +F ++G + SA++++D   G+S  + FV FE  EA ++A  
Sbjct: 3   NV-YVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVE 60

Query: 272 KMNNALIDDRRICV 285
           ++N   ++ +++ V
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|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 51.0 bits (123), Expect = 8e-09
 Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LF+  L+  T +E L   FS++G VV   I++D  TG S  + FV F    + ++     
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKV-LAA 59

Query: 274 NNALIDDRRI 283
              ++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|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 51.1 bits (122), Expect = 9e-09
 Identities = 26/70 (37%), Positives = 41/70 (58%)

Query: 219 LNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALI 278
           L+  T + DL  +FS++G +    ++ D RTG S  +AFV FE+ +  ++A    N   +
Sbjct: 7   LSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANGMEL 66

Query: 279 DDRRICVDFS 288
           D RRI VD+S
Sbjct: 67  DGRRIRVDYS 76

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

 Score = 55.0 bits (132), Expect = 1e-08
 Identities = 26/67 (38%), Positives = 35/67 (52%)

Query: 211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
           D  L+V  L     D+ L  IF ++G +V   ILRD  TG     AFV F KRE  ++A 
Sbjct: 193 DTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAI 252

Query: 271 FKMNNAL 277
             +NN +
Sbjct: 253 SALNNVI 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|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 51.0 bits (122), Expect = 1e-08
 Identities = 23/70 (32%), Positives = 34/70 (48%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L+P   D  L   FS F +   A ++ D ++G S  Y FV F  ++  E A  +M
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 274 NNALIDDRRI 283
           N   +  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|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins

 Score = 51.2 bits (122), Expect = 1e-08
 Identities = 28/79 (35%), Positives = 44/79 (55%)

Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           P+  L V  L+  T + DL  +FS++G +    I+ D ++  S  +AFV FE  +  ++A
Sbjct: 8   PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 67

Query: 270 YFKMNNALIDDRRICVDFS 288
             + N   +D RRI VDFS
Sbjct: 68  KERANGMELDGRRIRVDFS 86

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

 Score = 50.7 bits (122), Expect = 1e-08
 Identities = 25/72 (34%), Positives = 36/72 (50%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L    +++ LH  F  FG +   +I  DY T +   +AFVEFE+ E    A   M
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 274 NNALIDDRRICV 285
           N + +  R I V
Sbjct: 61  NESELFGRTIRV 72

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

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

 Score = 50.7 bits (122), Expect = 1e-08
 Identities = 27/80 (33%), Positives = 43/80 (53%), Gaps = 5/80 (6%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREA----CEQA 269
           +F+  L     +E+L  +FSQFG V  A I++D  TG S   AFV+F+ +E+     E A
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 270 Y-FKMNNALIDDRRICVDFS 288
              + +   +D RR+ V  +
Sbjct: 63  DNAEDSGLSLDGRRLIVTLA 82

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

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

 Score = 50.5 bits (121), Expect = 2e-08
 Identities = 22/66 (33%), Positives = 38/66 (57%), Gaps = 1/66 (1%)

Query: 223 TEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRR 282
           T+DE +  +FS  G + S +++RD  TG+SL Y FV +   E  E+A   +N   + ++ 
Sbjct: 14  TQDE-IRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNKT 72

Query: 283 ICVDFS 288
           I V ++
Sbjct: 73  IKVSYA 78

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|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 50.5 bits (121), Expect = 2e-08
 Identities = 20/66 (30%), Positives = 38/66 (57%)

Query: 225 DEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC 284
           DE+   +F   G V + +I+RD RTG S  + FV+++  E  ++A   +N   + ++RI 
Sbjct: 14  DEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRIK 73

Query: 285 VDFSQS 290
           V +++ 
Sbjct: 74  VAYARP 79

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

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 30/76 (39%), Positives = 41/76 (53%), Gaps = 3/76 (3%)

Query: 213 VLFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
            L V  L+  VTE EDL  +F + G V   +I  D R+G S   A V FEKRE  E+A  
Sbjct: 2   RLRVSNLHYDVTE-EDLEELFGRVGEVKKVKINYD-RSGRSEGTADVVFEKREDAERAIK 59

Query: 272 KMNNALIDDRRICVDF 287
           + N  L+D + + V+ 
Sbjct: 60  QFNGVLLDGQPMQVEL 75

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|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 49.9 bits (119), Expect = 3e-08
 Identities = 26/69 (37%), Positives = 34/69 (49%), Gaps = 5/69 (7%)

Query: 226 EDLHVIFSQFGTVVSAEILRDYRTGESLC-YAFVEFEKREACEQAYFKMNNALIDDRRIC 284
             L  IF ++G V  A I R    G  LC +AFV  +KR+  E A    N   ID R + 
Sbjct: 16  VKLKKIFGRYGKVREATIPRK--RGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVA 73

Query: 285 VDFSQSVSK 293
           VD+  +V K
Sbjct: 74  VDW--AVQK 80

This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

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

 Score = 49.5 bits (119), Expect = 4e-08
 Identities = 26/84 (30%), Positives = 42/84 (50%), Gaps = 5/84 (5%)

Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEI--LRDYRTGESLCYAFVEFEKREACE 267
           P N L +  L+ +T +ED+    S   +V   ++  +RD  TG S  +AFVEF   E   
Sbjct: 1   PTNTLILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDAT 60

Query: 268 Q---AYFKMNNALIDDRRICVDFS 288
           Q   A   ++  +ID R + V ++
Sbjct: 61  QWMDALNNLDPFVIDGRVVRVSYA 84

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

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

 Score = 48.7 bits (117), Expect = 4e-08
 Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 5/61 (8%)

Query: 228 LHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF 287
           L+ +FS FG V   ++L+         +AFVEF   EA E+A   +N  L   R + VD+
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKP-----GFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

Query: 288 S 288
           S
Sbjct: 56  S 56

(a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. Length = 56

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

 Score = 49.5 bits (119), Expect = 4e-08
 Identities = 21/75 (28%), Positives = 42/75 (56%)

Query: 213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           ++FV  ++   ++ED+H  F++FG + +  +  D RTG    YA +E+E ++  + A   
Sbjct: 8   IIFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEG 67

Query: 273 MNNALIDDRRICVDF 287
           +N   +  + I VD+
Sbjct: 68  LNGKELLGQTISVDW 82

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

 Score = 49.1 bits (118), Expect = 4e-08
 Identities = 24/52 (46%), Positives = 31/52 (59%)

Query: 232 FSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRI 283
           FSQFGTV    + R  +TG+S  YAFVEFE  E  +     MNN L+ +R +
Sbjct: 20  FSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLL 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|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE

 Score = 49.2 bits (118), Expect = 5e-08
 Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 2/72 (2%)

Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
           N +FV  + P T +E+L   FS+FG+V   +I+ D R G S  Y FV FE +E  E+   
Sbjct: 3   NRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKI-L 60

Query: 272 KMNNALIDDRRI 283
            M N     +++
Sbjct: 61  AMGNLNFRGKKL 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|240789 cd12343, RRM1_2_CoAA_like, RNA recognition motif 1 and 2 in RRM-containing coactivator activator/modulator (CoAA) and similar proteins

 Score = 48.8 bits (117), Expect = 5e-08
 Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  L   T  E+L  +F ++GTV   +++++        Y FV  E+ E  E A   +
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDVVKN--------YGFVHMEEEEDAEDAIKAL 53

Query: 274 NNALIDDRRICV 285
           N      +RI V
Sbjct: 54  NGYEFMGKRINV 65

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

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

 Score = 48.9 bits (117), Expect = 6e-08
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L P   +E+    FSQFG VV A++++D+ TG S  + FV F+   A E   F  
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVE-RVFSA 60

Query: 274 NNALIDDRRICV 285
               +  +++ V
Sbjct: 61  GMLELGGKQVEV 72

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

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

 Score = 48.8 bits (117), Expect = 6e-08
 Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 4/75 (5%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESL---CYAFVEFEKREACEQAY 270
           ++V  L+   +++DL  IFS+FG V S  I +     +      +AFV F+   + E A 
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA- 61

Query: 271 FKMNNALIDDRRICV 285
            ++N   +  R+I V
Sbjct: 62  LQLNGTELGGRKISV 76

This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

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

 Score = 49.2 bits (118), Expect = 6e-08
 Identities = 22/64 (34%), Positives = 37/64 (57%), Gaps = 1/64 (1%)

Query: 223 TEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRR 282
           TE  D+  +FSQ+G +V   ++RD +TG+S  +AF+ +E + +   A   +N   +  R 
Sbjct: 22  TEG-DILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNLNGIKLLGRT 80

Query: 283 ICVD 286
           I VD
Sbjct: 81  IRVD 84

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

 Score = 48.8 bits (117), Expect = 7e-08
 Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 5/81 (6%)

Query: 213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILR-----DYRTGESLCYAFVEFEKREACE 267
            LFV  LN  T +E L   F + G V S  I +           S+ Y FVEF+ +EA +
Sbjct: 2   TLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQ 61

Query: 268 QAYFKMNNALIDDRRICVDFS 288
           +A  ++   ++D   + +  S
Sbjct: 62  KALKRLQGTVLDGHALELKLS 82

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

 Score = 48.4 bits (116), Expect = 7e-08
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 8/73 (10%)

Query: 213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           VL+V  L   T +E L  +FS++G V   + ++DY        AFV FE+R+   +A  +
Sbjct: 3   VLYVRNLPLSTTEEQLRELFSEYGEVERVKKIKDY--------AFVHFEERDDAVKAMEE 54

Query: 273 MNNALIDDRRICV 285
           MN   ++   I V
Sbjct: 55  MNGKELEGSPIEV 67

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

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

 Score = 48.5 bits (116), Expect = 7e-08
 Identities = 20/62 (32%), Positives = 33/62 (53%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L      ++L  +FS +G ++++ IL D  TG S    F+ F+KR   E+A   +
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 274 NN 275
           N 
Sbjct: 63  NG 64

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

 Score = 48.5 bits (116), Expect = 8e-08
 Identities = 21/57 (36%), Positives = 31/57 (54%)

Query: 227 DLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRI 283
           DLH IFS++G VV   I++D  T +S   AF+ F  RE   +    +NN  +  R +
Sbjct: 17  DLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNNKELFGRTL 73

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|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 = 47.9 bits (115), Expect = 1e-07
 Identities = 24/63 (38%), Positives = 36/63 (57%), Gaps = 2/63 (3%)

Query: 214 LFVCQLNPVTEDE-DLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           LFV QL P T  E D+  +F ++G +    I+RD  TG+S   AFV+F  RE  ++A   
Sbjct: 2   LFVGQL-PKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 273 MNN 275
           ++ 
Sbjct: 61  LHG 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|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 47.7 bits (114), Expect = 1e-07
 Identities = 21/73 (28%), Positives = 38/73 (52%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L+  T+  DL  +FS++G VV A+I+ + R+  + C+ FV     E   +    +
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 274 NNALIDDRRICVD 286
           +   +  R I V+
Sbjct: 62  HRTELHGRVISVE 74

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

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

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 7/78 (8%)

Query: 210 PDNVLFVCQLNPVTEDEDLHVI----FSQFGTVVSAEILRDYRTGESLCYAFVEFEKREA 265
           P   +FV  L     D++L       FS++GT+V  ++LRD+R      YAFV+F   + 
Sbjct: 1   PSACVFVASLPASKSDDELEAAVTEHFSKYGTLVFVKVLRDWR---QRPYAFVQFTNDDD 57

Query: 266 CEQAYFKMNNALIDDRRI 283
            + A  K    ++D R I
Sbjct: 58  AKNALAKGQGTILDGRHI 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|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 24/77 (31%), Positives = 35/77 (45%), Gaps = 2/77 (2%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  L+   E +DL   F + G VV   I +D   G S  +  VEF   E  ++A  + 
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDD-DGRSKGFGHVEFATEEGAQKA-LEK 59

Query: 274 NNALIDDRRICVDFSQS 290
           +   +  R I VD +  
Sbjct: 60  SGEELLGREIRVDLATE 76

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

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 22/56 (39%), Positives = 31/56 (55%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           LFV  L     +EDL   FSQ+G V S EI+ D  TG+   +AFV F+  +  ++ 
Sbjct: 2   LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKI 57

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

 Score = 47.1 bits (112), Expect = 2e-07
 Identities = 24/73 (32%), Positives = 38/73 (52%)

Query: 213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           V+++  L     +++L   FSQFGTV +  + R  +TG S  Y F++F   E    A   
Sbjct: 1   VIYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKS 60

Query: 273 MNNALIDDRRICV 285
           MNN L+  + + V
Sbjct: 61  MNNYLLMGKVLQV 73

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

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

 Score = 51.3 bits (123), Expect = 3e-07
 Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 1/67 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L+P   ++ L  +F++FG + SA +++D  +G S  +AFV FEK E   +A  +M
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKD-GSGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 274 NNALIDD 280
           N   I  
Sbjct: 240 NGKKIGL 246

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

 Score = 46.5 bits (111), Expect = 4e-07
 Identities = 23/55 (41%), Positives = 33/55 (60%), Gaps = 1/55 (1%)

Query: 225 DED-LHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALI 278
           DE  ++  F++ G V S +I+R+ +TG+S  Y FVEF   EA EQA   +N   I
Sbjct: 12  DEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGKPI 66

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

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

 Score = 46.1 bits (110), Expect = 4e-07
 Identities = 20/54 (37%), Positives = 30/54 (55%), Gaps = 1/54 (1%)

Query: 221 PVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMN 274
            +TED DL  IF  FG +   ++ RD  TG S  Y F++F   E  ++A  ++N
Sbjct: 9   NITED-DLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 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|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 46.4 bits (110), Expect = 5e-07
 Identities = 25/65 (38%), Positives = 35/65 (53%), Gaps = 2/65 (3%)

Query: 214 LFVCQL-NPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           L+V  L   +TEDE L  IF  +G +V   +LRD  TG     AFV ++KRE  + A   
Sbjct: 3   LYVTNLPRQLTEDE-LRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISS 61

Query: 273 MNNAL 277
           +N  +
Sbjct: 62  LNGTI 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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 46.6 bits (111), Expect = 5e-07
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
           PP++ LF+     VTED DL   F+ FG +    +++D +T ES   A+V+F K  +  +
Sbjct: 1   PPNSRLFIVCGKSVTED-DLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAAR 59

Query: 269 AYFKMNNALIDDR 281
           A  +MN   +   
Sbjct: 60  AMEEMNGKCLGGD 72

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|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 = 46.4 bits (110), Expect = 5e-07
 Identities = 24/72 (33%), Positives = 37/72 (51%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LF+  L     D +L  +F  FG V+SA++  D  T +S C+ FV F+   + + A   M
Sbjct: 7   LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66

Query: 274 NNALIDDRRICV 285
           N   I  +R+ V
Sbjct: 67  NGFQIGMKRLKV 78

This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 79

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

 Score = 46.0 bits (109), Expect = 7e-07
 Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIF-SQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           +FV  L+P   + DL  +F S+F +  SA+I+ D  TG S  Y FV F      ++A  +
Sbjct: 4   IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIE 63

Query: 273 MNNALIDDR 281
           M       R
Sbjct: 64  MQGVYCGGR 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|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 45.7 bits (109), Expect = 8e-07
 Identities = 23/73 (31%), Positives = 44/73 (60%), Gaps = 2/73 (2%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L+    +++L  +FS+ G +    ++++Y+ G+S  YA+VEFE  E+ ++A  K+
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEA-LKL 59

Query: 274 NNALIDDRRICVD 286
           +  LI  R + V 
Sbjct: 60  DRELIKGRPMFVS 72

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

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

 Score = 45.7 bits (109), Expect = 8e-07
 Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 2/66 (3%)

Query: 222 VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDR 281
           VTED  L   F   G V   +++R  R G+S  + FV F+  E  +QA    N   ID  
Sbjct: 12  VTEDR-LREHFESKGEVTDVKVMRT-RDGKSRRFGFVGFKSEEDAQQAVKYFNKTFIDTS 69

Query: 282 RICVDF 287
           +I V+ 
Sbjct: 70  KISVEL 75

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

 Score = 45.7 bits (108), Expect = 8e-07
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 3/72 (4%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK- 272
           +F+  LN  T D+ L   F QFG V    ++RD  TG S  + F+ F+K ++  +   K 
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 273 --MNNALIDDRR 282
             ++  +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|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 45.6 bits (109), Expect = 9e-07
 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 215 FVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMN 274
           FV  L    E+E+L   F   G V +  I+RD +TG    + +V F+ +++   A  K+N
Sbjct: 3   FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALA-LKLN 61

Query: 275 NALIDDRRI 283
              +  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|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins

 Score = 45.4 bits (108), Expect = 9e-07
 Identities = 21/70 (30%), Positives = 33/70 (47%), Gaps = 6/70 (8%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L+P   +++L  +F  FG +V  +I      G      FV+F  R A E A  ++
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGCG------FVQFVHRAAAEAAIQQL 57

Query: 274 NNALIDDRRI 283
              +I   RI
Sbjct: 58  QGTIIGGSRI 67

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

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

 Score = 49.0 bits (117), Expect = 1e-06
 Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L+    DE L  +FS+ G + SA+++ D   G S  + FV F   E   +A  +M
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEM 346

Query: 274 NNALIDDRRICVDFSQ 289
           +  ++  + + V  +Q
Sbjct: 347 HGRMLGGKPLYVALAQ 362

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

 Score = 45.5 bits (107), Expect = 1e-06
 Identities = 23/70 (32%), Positives = 35/70 (50%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L+P    ED+   F+ FG +  A +++D  TG+S  Y FV F  +   E A   M
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 274 NNALIDDRRI 283
               +  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 = 45.0 bits (107), Expect = 1e-06
 Identities = 25/73 (34%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
            LFV  L      ++L   FSQFG V S  +  D  TG S  Y FV F  R+  E A  K
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 273 MNNALIDDRRICV 285
               +++  ++ V
Sbjct: 61  -QKHILEGNKLQV 72

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

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

 Score = 47.0 bits (111), Expect = 1e-06
 Identities = 25/73 (34%), Positives = 38/73 (52%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LF+  L+  T+D  L   F+ FG VV A+++ D  TG S  + FV F    A   A  +M
Sbjct: 37  LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEM 96

Query: 274 NNALIDDRRICVD 286
           +   ++ R I V+
Sbjct: 97  DGKELNGRHIRVN 109

Length = 144

>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 = 25/77 (32%), Positives = 38/77 (49%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
           P    LF+  L     D DL   F  FG V+SA++  D +T  S C+ FV ++  ++ + 
Sbjct: 2   PEGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQA 61

Query: 269 AYFKMNNALIDDRRICV 285
           A   MN   I  +R+ V
Sbjct: 62  AIQAMNGFQIGTKRLKV 78

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

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

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L+   +DE L   FS FGT+ SA+++ D + G S  + FV F   E   +A  +M
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEK-GRSKGFGFVCFSSPEEATKAVTEM 62

Query: 274 NNALIDDRRICVDFSQ 289
           N  +I  + + V  +Q
Sbjct: 63  NGRIIGGKPLYVALAQ 78

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|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 = 25/65 (38%), Positives = 35/65 (53%), Gaps = 2/65 (3%)

Query: 223 TEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEF-EKREACEQAYFKMNNALIDDR 281
           T  +DL  +F ++G V    I RD  T ES  +AFV F +KR+A E A   M+   +D R
Sbjct: 10  TTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDA-EDAMDAMDGKELDGR 68

Query: 282 RICVD 286
            + V 
Sbjct: 69  ELRVQ 73

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

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

 Score = 44.8 bits (107), Expect = 1e-06
 Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L P   +EDL   FS +G V    ++R+        +AFVEF   E  E A  K+
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRN--KDRPRGFAFVEFASPEDAEAALKKL 58

Query: 274 NNALIDDRRI 283
           N  ++D R +
Sbjct: 59  NGLVLDGRTL 68

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

>gnl|CDD|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 48.5 bits (115), Expect = 2e-06
 Identities = 20/66 (30%), Positives = 38/66 (57%)

Query: 224 EDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRI 283
            D +L+ +F   G + +  I+RDY+TG S  YAFV+F      ++A   +N   + ++R+
Sbjct: 120 TDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRL 179

Query: 284 CVDFSQ 289
            V +++
Sbjct: 180 KVSYAR 185

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

 Score = 45.4 bits (107), Expect = 2e-06
 Identities = 27/82 (32%), Positives = 41/82 (50%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
           P    LF+  L     D+DL  +F  FG VVSA++  D +T  S C+ FV ++   + + 
Sbjct: 5   PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQA 64

Query: 269 AYFKMNNALIDDRRICVDFSQS 290
           A   MN   I  +R+ V   +S
Sbjct: 65  AIQAMNGFQIGMKRLKVQLKRS 86

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|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 22/60 (36%), Positives = 28/60 (46%), Gaps = 2/60 (3%)

Query: 221 PVTEDE-DLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID 279
           P+  DE DL  +   +G V+S  ILRD   G+S    F   E RE CE    K N   + 
Sbjct: 9   PLHMDEQDLETMLKPYGQVISTRILRD-SKGQSRGVGFARMESREKCEDIISKFNGKYLK 67

This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 79

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

 Score = 48.0 bits (114), Expect = 2e-06
 Identities = 22/80 (27%), Positives = 38/80 (47%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L+P T++  L  +F  FG V + +I+RD  T +   Y FV     +    A   +
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 274 NNALIDDRRICVDFSQSVSK 293
           N   + +R + V F  + + 
Sbjct: 332 NGYTLGNRVLQVSFKTNKAY 351

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

 Score = 44.4 bits (105), Expect = 3e-06
 Identities = 27/82 (32%), Positives = 44/82 (53%), Gaps = 3/82 (3%)

Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
           N +FV  ++  T + DL   FSQ+GTV   +I+ D R G S  Y FV FE +E  ++   
Sbjct: 3   NRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQKILQ 61

Query: 272 KMNNALIDDRRICVDFSQSVSK 293
           + N     D+++  +  Q++ K
Sbjct: 62  EANRLCFRDKKL--NIGQAIRK 81

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

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

 Score = 44.2 bits (105), Expect = 3e-06
 Identities = 22/74 (29%), Positives = 34/74 (45%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L P  ++  L  +FS FG V + +++RD  T +   Y FV     E    A   +
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 274 NNALIDDRRICVDF 287
           N   +  R + V F
Sbjct: 64  NGYRLGGRVLQVSF 77

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

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

 Score = 44.2 bits (105), Expect = 3e-06
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 3/76 (3%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEIL---RDYRTGESLCYAFVEFEKREACEQAY 270
           L++  L+    +  L  +FS++G +   + L        G+   Y FV FE +E  E+A 
Sbjct: 2   LWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKAL 61

Query: 271 FKMNNALIDDRRICVD 286
             +N      +++ V 
Sbjct: 62  KSLNGKTALGKKLVVR 77

This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear. . Length = 80

>gnl|CDD|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 44.0 bits (104), Expect = 3e-06
 Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 9/75 (12%)

Query: 214 LFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           LFV   +P  T +ED+  +F  FG +V  +I + +        AFVEFE  E   +A   
Sbjct: 2   LFVVGFDPGTTREEDIEKLFEPFGPLVRCDIRKTF--------AFVEFEDSEDATKALEA 53

Query: 273 MNNALIDDRRICVDF 287
           ++ + ID   + V+F
Sbjct: 54  LHGSRIDGSVLTVEF 68

This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus. Length = 70

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

 Score = 43.9 bits (103), Expect = 4e-06
 Identities = 22/70 (31%), Positives = 36/70 (51%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L+P    +D+   F+ FG +  A +++D  TG+S  Y FV F  +   E A  +M
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 274 NNALIDDRRI 283
               +  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|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 42.9 bits (101), Expect = 5e-06
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 8/73 (10%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  ++     ++L  +F +FG VV  + ++D        YAFV  E+ E    A   +
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRVVECDKVKD--------YAFVHMEREEEALAAIEAL 54

Query: 274 NNALIDDRRICVD 286
           N   +  RRI V+
Sbjct: 55  NGKEVKGRRINVE 67

This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 68

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

 Score = 43.5 bits (103), Expect = 6e-06
 Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 2/79 (2%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLC-YAFVEFEKREACEQAYFK 272
           ++V  L      E L  +FS++GTVV   + R Y+    +  +AF+EFE  E  ++A   
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPR-YKHTGDIKGFAFIEFETPEEAQKACKH 60

Query: 273 MNNALIDDRRICVDFSQSV 291
           +NN           F ++V
Sbjct: 61  LNNPPETATDKPGKFPKTV 79

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

 Score = 43.3 bits (103), Expect = 6e-06
 Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 5/78 (6%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEI--LRDYRTGESLCYAFVEFEKREACEQAYF 271
           L+V    P  +  D+  +F Q+G ++S     LR +      CY  V+F   E+   A  
Sbjct: 3   LWVTNFPPSFDQSDIRDLFEQYGEILSIRFPSLR-FNKTRRFCY--VQFTSPESAAAAVA 59

Query: 272 KMNNALIDDRRICVDFSQ 289
            +N  L +  ++ V  S 
Sbjct: 60  LLNGKLGEGYKLVVKISD 77

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

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

 Score = 43.0 bits (102), Expect = 7e-06
 Identities = 20/76 (26%), Positives = 36/76 (47%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  L   T DE L   FS+ G +    +++D  + +   + +V F   E  ++A  + 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 274 NNALIDDRRICVDFSQ 289
                  R+I V+F++
Sbjct: 62  KKTKFGGRKIHVEFAK 77

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

 Score = 43.0 bits (102), Expect = 7e-06
 Identities = 18/64 (28%), Positives = 34/64 (53%)

Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
           N ++V  ++P   ++D+  +F  FG + S  +  D  TG+   Y F+E+E  ++ + A  
Sbjct: 1   NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 272 KMNN 275
            MN 
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|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 43.0 bits (101), Expect = 8e-06
 Identities = 21/56 (37%), Positives = 32/56 (57%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           LFV  L     + DL   FSQFG V  AE++ D +TG+   + FV F+  ++ ++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|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 = 43.2 bits (102), Expect = 9e-06
 Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 208 KPPDNV-LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREAC 266
           K  D + LFV Q+    E++DL  +F QFG +    +L+D  TG     AF+ +  RE+ 
Sbjct: 1   KDDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESA 60

Query: 267 EQA 269
            +A
Sbjct: 61  LKA 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|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 42.7 bits (101), Expect = 9e-06
 Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 215 FVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMN 274
           FV  ++  T  E+L   F   GT+    IL D  TG+   +A++EF  + + E A   +N
Sbjct: 3   FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENA-LLLN 61

Query: 275 NALIDDRRICV 285
            +    R+I V
Sbjct: 62  ESEFRGRQIKV 72

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

>gnl|CDD|240867 cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition motif in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins

 Score = 42.6 bits (101), Expect = 9e-06
 Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 10/81 (12%)

Query: 213 VLFVCQL-NPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ--A 269
           VL +  L   VTE  DL  + S FG V +  +LR          A VE +  E+ +    
Sbjct: 1   VLHLRNLPPDVTE-SDLIALVSPFGKVTNVLLLRGKNQ------ALVEMDSVESAKSMVD 53

Query: 270 YFKMNNALIDDRRICVDFSQS 290
           Y+    ALI  RR+ + +S  
Sbjct: 54  YYLTVPALIRGRRVYIQYSNH 74

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

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

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 21/78 (26%), Positives = 33/78 (42%), Gaps = 1/78 (1%)

Query: 210 PDNV-LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
           PD+  LFV  L     +++L   F +FG V+   I      G    + FV F+  EA ++
Sbjct: 1   PDSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQK 60

Query: 269 AYFKMNNALIDDRRICVD 286
                      D R+ V+
Sbjct: 61  ILANKPIYFRGDHRLNVE 78

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

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 3/62 (4%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LF+  L+  T D+ L   FSQ+G +    +++D  T  S  + FV F      + A   M
Sbjct: 2   LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAA---M 58

Query: 274 NN 275
           N 
Sbjct: 59  NA 60

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

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

 Score = 42.3 bits (99), Expect = 1e-05
 Identities = 21/64 (32%), Positives = 35/64 (54%)

Query: 211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
           D  L+V  L      +++  +FSQ+G ++++ IL D  TG S    F+ F+KR   E+A 
Sbjct: 1   DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAI 60

Query: 271 FKMN 274
             +N
Sbjct: 61  KGLN 64

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

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 1/71 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQ-FGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           +FV  L P   D  L   F   + +V  A+++ D  TG S  Y FV F   +  ++A  +
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 273 MNNALIDDRRI 283
           MN      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|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 21/62 (33%), Positives = 29/62 (46%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           ++V  L+    +E L  +F Q G VV+  I +D  T     Y FVEF   E  + A   M
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 274 NN 275
           N 
Sbjct: 61  NM 62

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

 Score = 41.8 bits (99), Expect = 1e-05
 Identities = 20/55 (36%), Positives = 28/55 (50%)

Query: 215 FVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           FV QL+    + DL+  FS+ G V    I+RD  +  S   A+VEF   E+   A
Sbjct: 3   FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLA 57

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|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 = 41.9 bits (99), Expect = 2e-05
 Identities = 21/68 (30%), Positives = 33/68 (48%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  L   T +E+L  +F  FG +    +  D  T  S  +AFV F   E   +AY ++
Sbjct: 2   LFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSEL 61

Query: 274 NNALIDDR 281
           + ++   R
Sbjct: 62  DGSIFQGR 69

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

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

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 29/75 (38%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
            +LFV  L   T  EDL   F   G   S  +L D +TG+S   AFVEF+  EA  +A  
Sbjct: 1   FILFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKA-L 59

Query: 272 KMNNALIDDRRICVD 286
           K+++ L+  R+I V+
Sbjct: 60  KLHHTLLKGRKINVE 74

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

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

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 19/76 (25%), Positives = 45/76 (59%), Gaps = 2/76 (2%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV QL+P    E+L+  FS+ G ++   +++  R   +  +AF++FE+ +A  +A    
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLIK--RANHTNAFAFIKFEREQAAARAVESE 63

Query: 274 NNALIDDRRICVDFSQ 289
           N++++ ++ + V + +
Sbjct: 64  NHSMLKNKTMHVQYKE 79

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

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

 Score = 42.0 bits (98), Expect = 2e-05
 Identities = 22/64 (34%), Positives = 35/64 (54%)

Query: 211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
           D  L+V  L      ++L  +FSQ+G ++++ IL D  TG S    F+ F+KR   E+A 
Sbjct: 2   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 61

Query: 271 FKMN 274
             +N
Sbjct: 62  KGLN 65

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|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 5/82 (6%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEIL----RDYRTGESLCYAFVEFEKREACEQA 269
           L+V  LNP   +E L   F +FG + S +I+     + R     C  FV F  R   E+A
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNC-GFVAFMNRADAERA 62

Query: 270 YFKMNNALIDDRRICVDFSQSV 291
             +++   +    + + + ++V
Sbjct: 63  LDELDGKDVMGYELKLGWGKAV 84

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

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

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L V  L+    D+D+  +F++FG +  A +  D R+G SL  A V FE+R    +A  + 
Sbjct: 3   LLVSNLDFGVSDDDIKELFAEFGALKKAAVHYD-RSGRSLGTADVVFERRADALKAMKQY 61

Query: 274 NNALIDDR 281
           N   +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|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 28/76 (36%), Positives = 40/76 (52%), Gaps = 2/76 (2%)

Query: 209 PPDNVLFVCQL-NPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
             D  +FV  L N VT DE L   FS++ +   A+++RD RTG+S  Y FV F       
Sbjct: 4   ENDFRIFVGDLGNEVT-DEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYL 62

Query: 268 QAYFKMNNALIDDRRI 283
           +A  +MN   + +R I
Sbjct: 63  KAMKEMNGKYVGNRPI 78

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 = 44.9 bits (106), Expect = 3e-05
 Identities = 21/71 (29%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 222 VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDR 281
           +T++E +  +F+  G + S +++RD  TG+SL Y FV + + E  E+A   +N   + ++
Sbjct: 15  MTQEE-IRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNK 73

Query: 282 RICVDFSQSVS 292
            I V +++  S
Sbjct: 74  TIKVSYARPSS 84

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

 Score = 41.0 bits (97), Expect = 3e-05
 Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 8/77 (10%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L P T   +L   F +FG +    I  DY  G +  YA++E+E  EA + A   +
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAI--RRI--DYDPGRN--YAYIEYESIEAAQAAKEAL 54

Query: 274 NNALI--DDRRICVDFS 288
               +    RR+ VDF+
Sbjct: 55  RGFPLGGPGRRLRVDFA 71

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

 Score = 41.7 bits (97), Expect = 3e-05
 Identities = 22/64 (34%), Positives = 35/64 (54%)

Query: 211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
           D  L+V  L      ++L  +FSQ+G ++++ IL D  TG S    F+ F+KR   E+A 
Sbjct: 5   DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 64

Query: 271 FKMN 274
             +N
Sbjct: 65  KGLN 68

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|215589 PLN03121, PLN03121, nucleic acid binding protein; Provisional

 Score = 43.6 bits (103), Expect = 4e-05
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 4/70 (5%)

Query: 216 VCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNN 275
           V  L+P   ++D++  FS  G +   EI+   R+GE  C A+V F+   A E A   ++ 
Sbjct: 10  VTNLSPKATEKDVYDFFSHCGAIEHVEII---RSGEYACTAYVTFKDAYALETAVL-LSG 65

Query: 276 ALIDDRRICV 285
           A I D+R+C+
Sbjct: 66  ATIVDQRVCI 75

Length = 243

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

 Score = 40.8 bits (96), Expect = 4e-05
 Identities = 21/70 (30%), Positives = 38/70 (54%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  L    +++DL  +FS+FG +    +  D ++G+S  +A+V F   E   +AY ++
Sbjct: 5   LFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKEL 64

Query: 274 NNALIDDRRI 283
           +  +   R I
Sbjct: 65  DGKVFQGRLI 74

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

>gnl|CDD|241004 cd12560, RRM_SRSF12, RNA recognition motif in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins

 Score = 40.8 bits (95), Expect = 5e-05
 Identities = 23/80 (28%), Positives = 39/80 (48%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  +   T  EDL   F ++G +V   +  D+ T     +A+++FE     E A + +
Sbjct: 3   LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62

Query: 274 NNALIDDRRICVDFSQSVSK 293
           N   +  R+I + F+Q   K
Sbjct: 63  NRKWVCGRQIEIQFAQGDRK 82

This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 40.9 bits (95), Expect = 5e-05
 Identities = 20/77 (25%), Positives = 36/77 (46%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L P  ++  L  +F  FG V + +++RD+ T +   + FV     +    A   +
Sbjct: 6   IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 274 NNALIDDRRICVDFSQS 290
           N   + DR + V F  +
Sbjct: 66  NGYRLGDRVLQVSFKTN 82

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

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

 Score = 40.8 bits (95), Expect = 5e-05
 Identities = 23/68 (33%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 222 VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDR 281
           +T+DE L  +FS  G V SA+++RD   G SL Y FV +   +  E+A   +N   +  +
Sbjct: 13  MTQDE-LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLNGLRLQSK 71

Query: 282 RICVDFSQ 289
            I V +++
Sbjct: 72  TIKVSYAR 79

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

 Score = 44.1 bits (104), Expect = 6e-05
 Identities = 32/114 (28%), Positives = 53/114 (46%), Gaps = 6/114 (5%)

Query: 178 PLNEQLSSEKEAHSRAVALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGT 237
           P+  Q S  ++  +   A    GDIP   +K     L+V  L+    +++L  IF  FG 
Sbjct: 159 PIIVQSSQAEKNRAAKAATHQPGDIP-NFLK-----LYVGNLHFNITEQELRQIFEPFGD 212

Query: 238 VVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSV 291
           +   ++ RD  TG S  + F++F   E  ++A   MN   +  R I V ++Q  
Sbjct: 213 IEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDS 266

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

>gnl|CDD|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins

 Score = 40.3 bits (94), Expect = 6e-05
 Identities = 16/62 (25%), Positives = 33/62 (53%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  +     ++++  +F + G V+   I++D RTG      FV++  R+  ++A   +
Sbjct: 2   LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAIRAL 61

Query: 274 NN 275
           +N
Sbjct: 62  HN 63

This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

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

 Score = 40.0 bits (94), Expect = 6e-05
 Identities = 17/73 (23%), Positives = 35/73 (47%), Gaps = 4/73 (5%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREA----CEQA 269
           +FV  L+P T +E +   F +FG +V  E+  D +T +   + F+ F+  E      E  
Sbjct: 2   IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILETQ 61

Query: 270 YFKMNNALIDDRR 282
           +  +    ++ ++
Sbjct: 62  FHVIGGKKVEVKK 74

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|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 40.5 bits (94), Expect = 6e-05
 Identities = 21/73 (28%), Positives = 37/73 (50%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L+  T   DL  +FS++G VV A+++ + R+  + CY FV     E   +    +
Sbjct: 4   LWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCINHL 63

Query: 274 NNALIDDRRICVD 286
           +   +  R I V+
Sbjct: 64  HRTELHGRMISVE 76

This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1. Length = 76

>gnl|CDD|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp

 Score = 40.1 bits (94), Expect = 6e-05
 Identities = 17/73 (23%), Positives = 27/73 (36%), Gaps = 4/73 (5%)

Query: 213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
            ++           D+  +F   G V    +L          +AF+ FE  EA + A   
Sbjct: 1   TVYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQP----HAFITFENLEAAQLAIET 56

Query: 273 MNNALIDDRRICV 285
           +N A +D   I V
Sbjct: 57  LNGASVDGNCIKV 69

This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. . Length = 71

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

 Score = 40.7 bits (96), Expect = 7e-05
 Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 2/75 (2%)

Query: 214 LFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           LFV +L     +   L  +FSQ G     ++      G+   +AFVE+   E  E+A   
Sbjct: 5   LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIA-PNGQPRGFAFVEYATAEDAEEAQQA 63

Query: 273 MNNALIDDRRICVDF 287
           +N   +    I V F
Sbjct: 64  LNGHSLQGSPIRVSF 78

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

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

 Score = 43.9 bits (103), Expect = 7e-05
 Identities = 15/63 (23%), Positives = 30/63 (47%)

Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
           N ++V  ++P   + D+  +F  FG +V  ++ R         Y F+E+   ++  +A  
Sbjct: 205 NRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIA 264

Query: 272 KMN 274
            MN
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|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins

 Score = 40.1 bits (94), Expect = 7e-05
 Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 223 TEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRR 282
           T ++DL   FS FG ++  ++ +D +TG+S  + FV F   E   +    ++   + D R
Sbjct: 11  TTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKV---LSQRHMIDGR 67

Query: 283 IC 284
            C
Sbjct: 68  WC 69

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|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 = 40.3 bits (95), Expect = 7e-05
 Identities = 18/74 (24%), Positives = 36/74 (48%)

Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
           N +F+  L     ++ +  +   FG + +  +++D  TG S  YAF E+      +QA  
Sbjct: 1   NKIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIA 60

Query: 272 KMNNALIDDRRICV 285
            +N   + D+++ V
Sbjct: 61  GLNGMQLGDKKLTV 74

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

>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 40.0 bits (93), Expect = 7e-05
 Identities = 26/71 (36%), Positives = 36/71 (50%), Gaps = 8/71 (11%)

Query: 213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           VLFV  L     +E L   FS+FG +   + L+DY        AFV FE+R+A  +A  +
Sbjct: 3   VLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDY--------AFVHFEERDAAVRAMDE 54

Query: 273 MNNALIDDRRI 283
           MN   I+   I
Sbjct: 55  MNGKEIEGEEI 65

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. . Length = 72

>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 40.3 bits (94), Expect = 7e-05
 Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 3/76 (3%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  L+  T +E L      F   ++A I+ D  TG S  + FV+F   E  + A   M
Sbjct: 3   LFVKGLSEDTTEETLK---ESFDGSIAARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAM 59

Query: 274 NNALIDDRRICVDFSQ 289
            +  ID  ++ +DF++
Sbjct: 60  EDGEIDGNKVTLDFAK 75

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

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

 Score = 40.1 bits (94), Expect = 8e-05
 Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 2/62 (3%)

Query: 225 DEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC 284
           D DL  +F QFG ++  EI+ + R   S  + FV F      ++A  K++  +++ R+I 
Sbjct: 14  DPDLRQMFGQFGPILDVEIIFNERG--SKGFGFVTFANSADADRAREKLHGTVVEGRKIE 71

Query: 285 VD 286
           V+
Sbjct: 72  VN 73

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

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

 Score = 40.4 bits (95), Expect = 8e-05
 Identities = 25/80 (31%), Positives = 39/80 (48%), Gaps = 4/80 (5%)

Query: 215 FVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMN 274
           +V  L+P T  + L   FSQ G V    +  D    +   YAFVEF ++ +   A  K+N
Sbjct: 8   YVGNLDPTTTADQLLEFFSQAGEVKYVRMAGD--ETQPTRYAFVEFAEQTSVINA-LKLN 64

Query: 275 NALIDDRRICVDFS-QSVSK 293
            A+   R + V+ S  ++ K
Sbjct: 65  GAMFGGRPLKVNHSNNAIVK 84

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

 Score = 43.0 bits (101), Expect = 9e-05
 Identities = 21/61 (34%), Positives = 33/61 (54%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L       +L  IFS FG ++++ IL D  TG S    F+ F+KR+  ++A   +
Sbjct: 92  LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTL 151

Query: 274 N 274
           N
Sbjct: 152 N 152

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

 Score = 40.1 bits (93), Expect = 9e-05
 Identities = 21/77 (27%), Positives = 37/77 (48%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L+P  ++  L  +F  FG V + +++RD+ T +   + FV     +    A   +
Sbjct: 4   IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 274 NNALIDDRRICVDFSQS 290
           N   + DR + V F  S
Sbjct: 64  NGYRLGDRVLQVSFKTS 80

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

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

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 12/79 (15%)

Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTV--VSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           N L+V     +TE+  L   FS FG +  +S E  ++       C  FV FEK E+ ++A
Sbjct: 5   NTLYVHGYG-LTEEI-LKKAFSPFGNIINISMEKEKN-------C-GFVTFEKMESADRA 54

Query: 270 YFKMNNALIDDRRICVDFS 288
             ++N   +   ++ V  +
Sbjct: 55  IAELNGTTVQGVQLKVSLA 73

This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. . Length = 75

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

 Score = 40.0 bits (93), Expect = 1e-04
 Identities = 20/61 (32%), Positives = 34/61 (55%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L++  L      +D+  +FS+FG ++++ +L D  TG S   AF+ F+KR   E+A    
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 274 N 274
           N
Sbjct: 63  N 63

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

 Score = 40.1 bits (93), Expect = 1e-04
 Identities = 20/74 (27%), Positives = 37/74 (50%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L+P +++  L  +F  FG V + +++RD+ T +   + FV     +    A   +
Sbjct: 6   IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 274 NNALIDDRRICVDF 287
           N   + DR + V F
Sbjct: 66  NGYRLGDRVLQVSF 79

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

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

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 4/73 (5%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE----QA 269
           +F+  L+  T  +DL   FS+FG VV   +  D  TG S  + FV F++ E+ +    Q 
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 270 YFKMNNALIDDRR 282
             K+N  +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|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 43.1 bits (101), Expect = 1e-04
 Identities = 29/93 (31%), Positives = 43/93 (46%), Gaps = 10/93 (10%)

Query: 203 PDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQF--GTVVSAEILRDYRTGESLCYAFVEF 260
            D DV     +L+V  L   T +E +   FS+F  G V   + +RDY        AFV F
Sbjct: 225 VDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRDY--------AFVHF 276

Query: 261 EKREACEQAYFKMNNALIDDRRICVDFSQSVSK 293
           E RE   +A  ++N   ++   I V  ++ V K
Sbjct: 277 EDREDAVKAMDELNGKELEGSEIEVTLAKPVDK 309

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

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

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 21/64 (32%), Positives = 35/64 (54%)

Query: 225 DEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC 284
           +E L  IFS+ G VVS  ++ D  TG+   Y F E++ +E    A   +N   ++ R++ 
Sbjct: 12  EEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNGYELNGRQLR 71

Query: 285 VDFS 288
           VD +
Sbjct: 72  VDNA 75

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

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

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  L+    + D+ ++F+ FG++    +LRD + G+S   AFV F  R+    A   M
Sbjct: 4   LFVGMLSKKCNENDVRIMFAPFGSIEECTVLRD-QNGQSRGCAFVTFASRQCALNAIKAM 62

Query: 274 N 274
           +
Sbjct: 63  H 63

This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 81

>gnl|CDD|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 = 17/54 (31%), Positives = 29/54 (53%), Gaps = 7/54 (12%)

Query: 224 EDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKR-------EACEQAY 270
            +EDL   F +FG +    I++D  TGES  + +V+F K        E C++++
Sbjct: 13  TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVALENCDKSF 66

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

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 24/74 (32%), Positives = 38/74 (51%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L+  T +E ++ +FS+ G +    +  D  T     + FVE+  RE  E A   +
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 274 NNALIDDRRICVDF 287
           N   +DDR I VD+
Sbjct: 61  NGTKLDDRIIRVDW 74

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

>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 8/75 (10%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  ++  T  E+L  +F  +G V+S  ++R         +AFV      A ++A  ++
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ--------FAFVHLRGEAAADRAIEEL 54

Query: 274 NNALIDDRRICVDFS 288
           N   +  R++ V+ S
Sbjct: 55  NGRELHGRKLVVEHS 69

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

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

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 19/56 (33%), Positives = 32/56 (57%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           +++  L P T DEDL  +   FG ++S + + D +T +   Y FV+F+  EA  +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|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 39.1 bits (91), Expect = 2e-04
 Identities = 23/81 (28%), Positives = 36/81 (44%), Gaps = 5/81 (6%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRD---YRTGE--SLCYAFVEFEKREACEQ 268
           LFV  LN  T ++ L   F      V A +       R G+  S+ + FV F+ +E  + 
Sbjct: 3   LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 269 AYFKMNNALIDDRRICVDFSQ 289
           A   M+  ++D   + V FS 
Sbjct: 63  ALKAMDGFVLDGHTLVVKFSH 83

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

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 6/78 (7%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVS-AEILRDYRTGESLCYAFVEFEKREACEQA--Y 270
           L V  L     + +L   FS+ G  ++  ++LR    G+S   AF+ ++  E  ++A  Y
Sbjct: 3   LIVKNLPASLTEAELKEHFSKHGGEITDVKLLRT-EDGKSRRIAFIGYKTEEEAQKAKDY 61

Query: 271 FKMNNALIDDRRICVDFS 288
           F  NN  I+  +I V+F+
Sbjct: 62  F--NNTYINTSKISVEFA 77

This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 77

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

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 1/69 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V      T   DL   F ++G +V  +I    RT +S  +AFVE+E     E AY +M
Sbjct: 2   LYVTGFGAETRARDLAYEFERYGRLVRCDI-PPPRTFQSRPFAFVEYESHRDAEDAYEEM 60

Query: 274 NNALIDDRR 282
           +     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|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 38.3 bits (89), Expect = 3e-04
 Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 4/73 (5%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE----QA 269
           +FV  L+  T  +DL   FS+FG VV   I  D  TG S  + FV F+   + E    Q 
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 270 YFKMNNALIDDRR 282
             K++  +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|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 38.7 bits (91), Expect = 3e-04
 Identities = 20/86 (23%), Positives = 32/86 (37%), Gaps = 15/86 (17%)

Query: 215 FVCQLNPVTED------------EDLHVIFSQFGTVVSAEILR---DYRTGESLCYAFVE 259
            +C LN VT +            ED+     ++G V+S  I R   +      +   FVE
Sbjct: 3   VLCLLNMVTPEELEDDEEYEEILEDVKEECGKYGKVLSVVIPRPEAEGVDVPGVGKVFVE 62

Query: 260 FEKREACEQAYFKMNNALIDDRRICV 285
           F   E  ++A   +     D R +  
Sbjct: 63  FADVEDAQKAQLALAGRKFDGRTVVA 88

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

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

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 5/75 (6%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           ++V  L P     +L   F ++G + S  + R+   G    +AFVEFE     E A   +
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARN-PPG----FAFVEFEDPRDAEDAVRAL 56

Query: 274 NNALIDDRRICVDFS 288
           +   I   R+ V+ S
Sbjct: 57  DGRRICGNRVRVELS 71

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

 Score = 38.2 bits (89), Expect = 4e-04
 Identities = 16/58 (27%), Positives = 27/58 (46%)

Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
             LFV  LN  T D  L   F+++G +    ++ D  T  S  + F+ F   +  ++A
Sbjct: 3   CKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA 60

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

 Score = 37.8 bits (88), Expect = 4e-04
 Identities = 22/70 (31%), Positives = 38/70 (54%), Gaps = 4/70 (5%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREA----CEQA 269
           +FV  L+  T ++D+   FSQFG V  A ++ D +T     + FV FE  +     CE  
Sbjct: 2   IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEIH 61

Query: 270 YFKMNNALID 279
           + ++NN +++
Sbjct: 62  FHEINNKMVE 71

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|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 2/65 (3%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQ-FGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           LFV  L P  +D  L+  FS+ + +   A+++ D + G S  Y FV F      ++A  +
Sbjct: 4   LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLD-QNGNSRGYGFVRFSDESEQKRALTE 62

Query: 273 MNNAL 277
           M  A 
Sbjct: 63  MQGAS 67

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

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

 Score = 37.8 bits (87), Expect = 5e-04
 Identities = 22/76 (28%), Positives = 38/76 (50%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L V  L      E+L  +F   G + S +++RD  TG+SL Y FV +   +  E+A   +
Sbjct: 7   LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 66

Query: 274 NNALIDDRRICVDFSQ 289
           N   +  + I V +++
Sbjct: 67  NGLRLQTKTIKVSYAR 82

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|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 38.4 bits (90), Expect = 5e-04
 Identities = 20/84 (23%), Positives = 35/84 (41%), Gaps = 18/84 (21%)

Query: 223 TEDEDLHVIFSQFGT---------VVSAEILRD------YRTGESLCYAFVEFEKREACE 267
            +++ L  +F +  +         +   +I+RD         G+S  Y FVEF   E   
Sbjct: 12  VDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFTNHEHAL 71

Query: 268 QAYFKMNN---ALIDDRRICVDFS 288
           +A   +NN       D+R  V+F+
Sbjct: 72  KALRALNNNPEIFGPDKRPIVEFA 95

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

>gnl|CDD|240749 cd12303, RRM_spSet1p_like, RNA recognition motif in fission yeast Schizosaccharomyces pombe SET domain-containing protein 1 (spSet1p) and similar proteins

 Score = 37.7 bits (88), Expect = 6e-04
 Identities = 15/50 (30%), Positives = 26/50 (52%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKR 263
           + +  L+P+T  + + + F  FG +  +E+  D RTG+SL    V F   
Sbjct: 1   ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTFRGD 50

This subfamily corresponds to the RRM of spSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, or Set1 complex component, is encoded by SET1 from the fission yeast S. pombe. It is essential for the H3 lysine-4 methylation. in vivo, and plays an important role in telomere maintenance and DNA repair in an ATM kinase Rad3-dependent pathway. spSet1p is the homology counterpart of Saccharomyces cerevisiae Set1p (scSet1p). However, it is more closely related to Set1 found in mammalian. Moreover, unlike scSet1p, spSet1p is not required for heterochromatin assembly in fission yeast. spSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. . Length = 86

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

 Score = 37.6 bits (88), Expect = 6e-04
 Identities = 20/76 (26%), Positives = 33/76 (43%), Gaps = 5/76 (6%)

Query: 213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
            LFV  +N   EDE+L  +F QFG     +I   Y   +   +  V +    A  +A   
Sbjct: 3   TLFVRNINSNVEDEELRALFEQFG-----DIRTLYTACKHRGFIMVSYYDIRAARRAKRA 57

Query: 273 MNNALIDDRRICVDFS 288
           +    +  R++ + FS
Sbjct: 58  LQGTELGGRKLDIHFS 73

This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. . Length = 77

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

 Score = 37.6 bits (87), Expect = 7e-04
 Identities = 19/81 (23%), Positives = 39/81 (48%), Gaps = 1/81 (1%)

Query: 211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
           +  LF+  L+    + DL   F +FG +   +I R  R G++  Y F++FE  +   +A 
Sbjct: 7   NRTLFLGNLDITVTETDLRRAFDRFGVITEVDIKRPGR-GQTSTYGFLKFENLDMAHRAK 65

Query: 271 FKMNNALIDDRRICVDFSQSV 291
             M+  ++    I + + ++ 
Sbjct: 66  LAMSGKVLRRNPIKIGYGKAT 86

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

>gnl|CDD|240715 cd12269, RRM_Vip1_like, RNA recognition motif in a group of uncharacterized plant proteins similar to fission yeast Vip1

 Score = 37.0 bits (86), Expect = 7e-04
 Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 4/70 (5%)

Query: 216 VCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNN 275
           V  L+P   + D++  FS  G +   EI R    GE    A+V F+  +A E A   ++ 
Sbjct: 3   VTNLSPKATERDIYDFFSFSGDIEYVEIQRS---GEQSQTAYVTFKDPQAQETALL-LSG 58

Query: 276 ALIDDRRICV 285
           A I D+ + +
Sbjct: 59  ATIVDQSVTI 68

This subfamily corresponds to the Vip1-like, uncharacterized proteins found in plants. Although their biological roles remain unclear, these proteins show high sequence similarity to the fission yeast Vip1. Like Vip1 protein, members in this family contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 69

>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 37.6 bits (87), Expect = 7e-04
 Identities = 24/80 (30%), Positives = 38/80 (47%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  +   T  EDL   F ++G +V   +  D+ T     +A+V+FE     E A   +
Sbjct: 3   LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62

Query: 274 NNALIDDRRICVDFSQSVSK 293
           +   I  R+I + F+Q   K
Sbjct: 63  DRKWICGRQIEIQFAQGDRK 82

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

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

 Score = 37.0 bits (86), Expect = 7e-04
 Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 8/56 (14%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           L+V    P T +  +  IFS +G V   +++ +        +AFVEFE  E+  +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|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 20/61 (32%), Positives = 33/61 (54%)

Query: 225 DEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC 284
           ++ +   FS FG + S ++  D  T +   +AFVE+E  EA + A  +MN  ++  R I 
Sbjct: 14  EDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNGVMLGGRNIK 73

Query: 285 V 285
           V
Sbjct: 74  V 74

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

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

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 4/66 (6%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE----QA 269
           +FV  +   TE+  L   F Q+G +   EI+ D  +G+   +AFV F+  ++ +    Q 
Sbjct: 3   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 62

Query: 270 YFKMNN 275
           Y  +N 
Sbjct: 63  YHTVNG 68

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 77

>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 20/68 (29%), Positives = 31/68 (45%), Gaps = 6/68 (8%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           ++V  L     +E+L   FS FG +    + +D   G    YAFV F+  EA   A   +
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD--KG----YAFVRFDTHEAAATAIVAV 56

Query: 274 NNALIDDR 281
           N   I+ +
Sbjct: 57  NGTSINGQ 64

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

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

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 19/67 (28%), Positives = 35/67 (52%)

Query: 226 EDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV 285
           E+   +F   G + S +++RD  TG+SL Y FV +   +  E+A   +N   +  + I V
Sbjct: 17  EEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKV 76

Query: 286 DFSQSVS 292
            +++  S
Sbjct: 77  SYARPSS 83

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|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 8/77 (10%)

Query: 213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           VLFV  L     +E L   F QFG +   + L+D        YAF+ F++R+   +A  +
Sbjct: 3   VLFVRNLANTVTEEILEKAFGQFGKLERVKKLKD--------YAFIHFDERDGAVKAMEE 54

Query: 273 MNNALIDDRRICVDFSQ 289
           MN   ++   I + F++
Sbjct: 55  MNGKELEGENIEIVFAK 71

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 21/56 (37%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           L V  L+P   +E L   FSQFG V  A ++ D R G S     VEF ++   + A
Sbjct: 2   LRVKNLSPFVSNELLEQAFSQFGEVERAVVIVDDR-GRSTGEGIVEFSRKPGAQAA 56

This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 80

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

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 2/57 (3%)

Query: 214 LFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           +FV  L P VTE  DL   FSQFGTV    ++ D+       + F+ FE  ++ +Q 
Sbjct: 5   IFVGGLPPNVTET-DLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQV 60

This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 80

>gnl|CDD|180419 PRK06134, PRK06134, putative FAD-binding dehydrogenase; Reviewed

 Score = 39.7 bits (93), Expect = 0.001
 Identities = 27/92 (29%), Positives = 39/92 (42%), Gaps = 13/92 (14%)

Query: 14  IDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFV 73
           ID F++  P     F +H   ++ +G    + H       GD  G  TGGRS+    F  
Sbjct: 95  IDAFLEAGPHMVAFFERHTALRFADGNAIPDYH-------GDTPGAATGGRSLIAAPFDG 147

Query: 74  DEIRADLKH-----DKVGTVGMA-SAGRDLNA 99
            E+ A L+       +   +GM   AG DL A
Sbjct: 148 RELGALLERLRKPLRETSFMGMPIMAGADLAA 179

Length = 581

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

 Score = 36.7 bits (84), Expect = 0.001
 Identities = 18/56 (32%), Positives = 32/56 (57%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           L++  L+P T D+DL  +   +G +VS + + D  T +   Y FV+F+   A ++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|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 23/73 (31%), Positives = 31/73 (42%), Gaps = 5/73 (6%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L V  L+    D++L  +FSQFG V     +R+     S    FVEF    A E A   +
Sbjct: 4   LLVFNLDSPISDQELRSLFSQFGEVKD---IRETPLRPSQK--FVEFYDIRAAEAALDAL 58

Query: 274 NNALIDDRRICVD 286
           N       R+ V 
Sbjct: 59  NGRPFLGGRLKVK 71

This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. . Length = 71

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 24/71 (33%), Positives = 32/71 (45%), Gaps = 8/71 (11%)

Query: 213 VLFVCQLN---PVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           VL V   N   PVT D  LH +FS +G V    I   +     +  A V+F+  E+ E A
Sbjct: 1   VLLVTISNLLYPVTVDV-LHQVFSPYGAVEKILI---FEKNTGVQ-ALVQFDSVESAENA 55

Query: 270 YFKMNNALIDD 280
              +N   I D
Sbjct: 56  KKALNGRNIYD 66

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

>gnl|CDD|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 1/61 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV     VT+++ LH +F     +   ++ RD  TG+S  +A+V +    +   A  K+
Sbjct: 3   LFVVVSKSVTQEQ-LHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASAIYAKEKL 61

Query: 274 N 274
           N
Sbjct: 62  N 62

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

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 4/73 (5%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKRE----ACEQA 269
           +FV  L+  T  ED+   F QFG V  A ++ D  T     + FV FE  +     CE  
Sbjct: 2   IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 270 YFKMNNALIDDRR 282
           + ++NN +++ ++
Sbjct: 62  FHEINNKMVECKK 74

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 36.3 bits (83), Expect = 0.002
 Identities = 18/56 (32%), Positives = 31/56 (55%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           L++  L P T D+DL  +   +G +VS + + D  T +   Y FV+F+   A ++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|241050 cd12606, RRM1_RBM4, RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 35.6 bits (82), Expect = 0.002
 Identities = 17/71 (23%), Positives = 37/71 (52%), Gaps = 13/71 (18%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA---- 269
           LFV  L P   ++++  +F Q+G V+  +I+++        Y FV  + + A ++A    
Sbjct: 3   LFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN--------YGFVHMDDKTAADEAIRNL 54

Query: 270 -YFKMNNALID 279
            ++K++   I+
Sbjct: 55  HHYKLHGVAIN 65

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

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 2/60 (3%)

Query: 227 DLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD 286
           DL  IF    +V S  ++RD  T +   + +VEFE  E+ ++A  + + AL DDR + VD
Sbjct: 17  DLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEA-LEYDGALFDDRSLRVD 74

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|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 35.5 bits (82), Expect = 0.003
 Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  L     +E+L   F ++G V   +I R  R G+   YAFV+F   +   +A   M
Sbjct: 5   LFVGNLEITITEEELRRAFERYGVVEDVDIKRPPR-GQGNAYAFVKFLNLDMAHRAKVAM 63

Query: 274 NNALI 278
           +   I
Sbjct: 64  SGQYI 68

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

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

 Score = 35.5 bits (81), Expect = 0.003
 Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 222 VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDR 281
           +T++E    +F   G + S +++RD  TG+SL Y FV +      ++A   +N   +  +
Sbjct: 15  MTQEE-FKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQTK 73

Query: 282 RICVDFSQSVS 292
            I V +++  S
Sbjct: 74  TIKVSYARPSS 84

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|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 35.4 bits (81), Expect = 0.003
 Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 1/66 (1%)

Query: 211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
           D  LF+  ++    + D+ V+FS FG +    ILR    G S   AFV F  R   + A 
Sbjct: 1   DRKLFIGMVSKKCNENDIRVMFSPFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAI 59

Query: 271 FKMNNA 276
             M+ A
Sbjct: 60  KAMHQA 65

This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 81

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

 Score = 38.5 bits (89), Expect = 0.004
 Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 1/67 (1%)

Query: 226 ED-LHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC 284
           ED +   F  FG + S  +  D  TG+   +AFVE+E  EA + A  +MN  ++  R I 
Sbjct: 121 EDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIK 180

Query: 285 VDFSQSV 291
           V    ++
Sbjct: 181 VGRPSNM 187

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

>gnl|CDD|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 4/65 (6%)

Query: 214 LFVCQLNPVTEDE-DLHVIFSQFGTVVSAEILRDYRTG--ESLCYAFVEFEKREACEQAY 270
           +FV Q+ P +  E DL  +F Q+G V    +LRD      +S    FV F  R+A  +A 
Sbjct: 4   MFVGQI-PRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 62

Query: 271 FKMNN 275
             ++N
Sbjct: 63  NALHN 67

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 84

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 35.3 bits (81), Expect = 0.004
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
           D  LFV  L+P   +E +  +F Q G V+  +I +D + G+   +AFV F+   +   A 
Sbjct: 1   DRTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKD-KDGKPKQFAFVNFKHEVSVPYAM 59

Query: 271 FKMNNALIDDRRI 283
             +N   +  R +
Sbjct: 60  NLLNGIKLYGRPL 72

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

>gnl|CDD|240735 cd12289, RRM_LARP6, RNA recognition motif in La-related protein 6 (LARP6) and similar proteins

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 20/60 (33%), Positives = 24/60 (40%), Gaps = 16/60 (26%)

Query: 226 EDLHVIFSQFGTVVSAEILRDYRT---------------GESLCYAFVEFEKREACEQAY 270
           E +  +FS  G +    ILR  RT               G   C A VEFEK EA  +A 
Sbjct: 16  ESVLELFSTCGVIALIRILRPGRTIPPDLKRYSSRHPQLGTKEC-AVVEFEKLEAARKAV 74

This subfamily corresponds to the RRM of LARP6, also termed Acheron (Achn), a novel member of the lupus antigen (La) family. It is expressed predominantly in neurons and muscle in vertebrates. LARP6 functions as a key regulatory protein that may play a role in mediating a variety of developmental and homeostatic processes in animals, including myogenesis, neurogenesis and possibly metastasis. LARP6 binds to Ca2+/calmodulin-dependent serine protein kinase (CASK), and forms a complex with inhibitor of differentiation transcription factors. It is structurally related to the La autoantigen and contains a La motif (LAM), nuclear localization and export (NLS and NES) signals, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 93

>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 35.5 bits (81), Expect = 0.004
 Identities = 20/65 (30%), Positives = 29/65 (44%), Gaps = 1/65 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L++  L    ++++L  +   FG V+S  ILRD  +G S    F   E  E CE      
Sbjct: 3   LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVISHF 61

Query: 274 NNALI 278
           N   I
Sbjct: 62  NGKFI 66

This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 85

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

 Score = 35.2 bits (81), Expect = 0.004
 Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 3/76 (3%)

Query: 214 LFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           L+V  L+P VTED  L  IF   G V + +I+ D +  + + Y FVE+ +    E A   
Sbjct: 1   LYVGNLDPRVTEDI-LKQIFQVGGPVQNVKIIPD-KNNKGVNYGFVEYHQSHDAEIALQT 58

Query: 273 MNNALIDDRRICVDFS 288
           +N   I++  I V+++
Sbjct: 59  LNGRQIENNEIRVNWA 74

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

 Score = 35.4 bits (81), Expect = 0.004
 Identities = 20/79 (25%), Positives = 36/79 (45%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +F+  L    ++  L  +F  FG V + +++RD+ T +   + FV     E    A   +
Sbjct: 4   IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASL 63

Query: 274 NNALIDDRRICVDFSQSVS 292
           N   + D+ + V F  S S
Sbjct: 64  NGYRLGDKILQVSFKTSKS 82

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	299
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	100.0
KOG0881	164	consensus Cyclophilin type peptidyl-prolyl cis-tra	100.0
KOG0546	372	consensus HSP90 co-chaperone CPR7/Cyclophilin [Pos	100.0
cd01928	153	Cyclophilin_PPIL3_like Cyclophilin_PPIL3_like. Pro	100.0
KOG0884	161	consensus Similar to cyclophilin-type peptidyl-pro	100.0
cd01923	159	cyclophilin_RING cyclophilin_RING: cyclophilin-typ	100.0
cd01921	166	cyclophilin_RRM cyclophilin_RRM: cyclophilin-type	100.0
KOG0883	518	consensus Cyclophilin type, U box-containing pepti	100.0
KOG0880	217	consensus Peptidyl-prolyl cis-trans isomerase [Pos	100.0
COG0652	158	PpiB Peptidyl-prolyl cis-trans isomerase (rotamase	100.0
cd01927	148	cyclophilin_WD40 cyclophilin_WD40: cyclophilin-typ	100.0
cd01922	146	cyclophilin_SpCYP2_like cyclophilin_SpCYP2_like: c	100.0
KOG0879	177	consensus U-snRNP-associated cyclophilin type pept	100.0
KOG0882	558	consensus Cyclophilin-related peptidyl-prolyl cis-	100.0
cd01925	171	cyclophilin_CeCYP16-like cyclophilin_CeCYP16-like:	100.0
PLN03149	186	peptidyl-prolyl isomerase H (cyclophilin H); Provi	100.0
PRK10903	190	peptidyl-prolyl cis-trans isomerase A (rotamase A)	100.0
PTZ00221	249	cyclophilin; Provisional	100.0
PRK10791	164	peptidyl-prolyl cis-trans isomerase B (rotamase B)	100.0
KOG0885	439	consensus Peptidyl-prolyl cis-trans isomerase [Pos	100.0
cd01926	164	cyclophilin_ABH_like cyclophilin_ABH_like: Cycloph	100.0
PTZ00060	183	cyclophilin; Provisional	100.0
cd01920	155	cyclophilin_EcCYP_like cyclophilin_EcCYP_like: cyc	100.0
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	100.0
cd00317	146	cyclophilin cyclophilin: cyclophilin-type peptidyl	100.0
PF00160	155	Pro_isomerase: Cyclophilin type peptidyl-prolyl ci	100.0
cd01924	176	cyclophilin_TLP40_like cyclophilin_TLP40_like: cyc	100.0
KOG0865	167	consensus Cyclophilin type peptidyl-prolyl cis-tra	99.97
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.75
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.67
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.62
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.62
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.61
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.61
KOG0122	270	consensus Translation initiation factor 3, subunit	99.61
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.55
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.53
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.53
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.52
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.52
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.52
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.51
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.5
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.49
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.49
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.48
PLN03120	260	nucleic acid binding protein; Provisional	99.46
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.45
PLN03213	759	repressor of silencing 3; Provisional	99.45
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.45
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.44
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.44
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.43
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.42
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.42
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.42
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.41
smart00362	72	RRM_2 RNA recognition motif.	99.38
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.38
PLN03121	243	nucleic acid binding protein; Provisional	99.37
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.37
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.36
smart00360	71	RRM RNA recognition motif.	99.35
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.34
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.33
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.32
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.32
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.32
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.31
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.29
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.29
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.28
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.26
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.25
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.25
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.24
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.23
smart00361	70	RRM_1 RNA recognition motif.	99.22
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.21
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.2
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.2
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.18
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.17
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.17
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.15
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.15
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.07
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.06
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.99
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.98
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.94
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.93
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.9
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.88
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.87
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.78
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.77
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.77
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.77
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.75
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.7
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.68
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.66
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.65
KOG0226	290	consensus RNA-binding proteins [General function p	98.64
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.61
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.52
KOG0151	877	consensus Predicted splicing regulator, contains R	98.46
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.39
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.35
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.28
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.25
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.07
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.01
KOG0882	558	consensus Cyclophilin-related peptidyl-prolyl cis-	98.01
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	97.86
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.86
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.83
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.79
KOG4210	285	consensus Nuclear localization sequence binding pr	97.76
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.69
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.68
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.67
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	97.6
KOG3152	278	consensus TBP-binding protein, activator of basal	97.59
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.55
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.43
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.42
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.39
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.27
KOG2314	698	consensus Translation initiation factor 3, subunit	97.27
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.15
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.99
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	96.87
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	96.81
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.79
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	96.72
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.69
TIGR03268	503	methan_mark_3 putative methanogenesis marker prote	96.65
PRK00969	508	hypothetical protein; Provisional	96.55
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.47
PRK00969	508	hypothetical protein; Provisional	96.47
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.38
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.37
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.35
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.25
TIGR03268	503	methan_mark_3 putative methanogenesis marker prote	96.22
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.08
KOG1855	484	consensus Predicted RNA-binding protein [General f	95.96
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	95.83
KOG1996	378	consensus mRNA splicing factor [RNA processing and	95.81
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	95.44
COG4070	512	Predicted peptidyl-prolyl cis-trans isomerase (rot	95.16
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	95.16
KOG2068	327	consensus MOT2 transcription factor [Transcription	95.12
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.12
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	94.88
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	94.53
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	94.51
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	94.5
PF12903	147	DUF3830: Protein of unknown function (DUF3830); In	94.4
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	93.96
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	93.95
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	93.88
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	93.27
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	92.43
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	91.72
KOG4210	285	consensus Nuclear localization sequence binding pr	91.5
KOG4660	549	consensus Protein Mei2, essential for commitment t	90.17
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	89.83
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	89.62
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	89.32
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	89.31
COG4070	512	Predicted peptidyl-prolyl cis-trans isomerase (rot	87.39
PF04126	120	Cyclophil_like: Cyclophilin-like; InterPro: IPR007	86.64
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	85.45
KOG2135	526	consensus Proteins containing the RNA recognition	85.45
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	83.44

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.9e-63  Score=424.68  Aligned_cols=294  Identities=63%  Similarity=1.009  Sum_probs=269.7

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCC------Cccccc
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYE------DRFFVD   74 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~------~~~~~~   74 (299)
                      |+|+|+|++|+|+|.||.+++|.+|.|||+||+-.||+.|.||-|..+|++|.||++++|.||.++|+      ..||..
T Consensus         1 MsVlieTtlGDlvIDLf~~erP~~clNFLKLCk~KYYN~clfh~vq~~f~aQTGDPtGtG~GG~si~~~lyG~q~rffea   80 (479)
T KOG0415|consen    1 MSVLIETTLGDLVIDLFVKERPRTCLNFLKLCKIKYYNFCLFHTVQRDFTAQTGDPTGTGDGGESIYGVLYGEQARFFEA   80 (479)
T ss_pred             CcEEEEeecccEEeeeecccCcHHHHHHHHHHhHhhcccceeeeccccceeecCCCCCCCCCcceeeeecccccchhhhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999984      357899


Q ss_pred             ccccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEE
Q 046966           75 EIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTY  154 (299)
Q Consensus        75 e~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~  154 (299)
                      |+.+.++|.+.|+|||++.|.|.+||||||||++++.+||++|+|||+|++||++|.+|+..-++.+++|.++|.|+.+.
T Consensus        81 E~~p~l~Hsk~G~vsmvs~g~n~~gSQF~iTlgenLdyLDg~htvfGqV~EG~dtl~kiNea~vD~~~rPykdIRI~HTi  160 (479)
T KOG0415|consen   81 EFLPKLKHSKMGTVSMVSAGENLNGSQFFITLGENLDYLDGKHTVFGQVAEGFDTLTKINEAIVDPKNRPYKDIRIKHTI  160 (479)
T ss_pred             hhcccccccccceEEeecCCcccccceEEEEccccccccccccceeeehhhhHHHHHHHHHHhcCCCCCcccceeeeeeE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEC-CCCC-----CCCCCCCCCCCC--CCC--CCC------------ccccchhHHhhhhhhhccccCCCCCCCCCCCCc
Q 046966          155 VLY-PPEL-----ADDSIPEGEPKD--ELE--PPL------------NEQLSSEKEAHSRAVALECIGDIPDADVKPPDN  212 (299)
Q Consensus       155 v~~-p~~~-----~p~~~p~~~~~~--~~~--~~~------------~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~  212 (299)
                      |++ |.+-     .|.-+|+|.++.  ..+  ..+            -+++.+|++++..|...+.+++.|+++..||..
T Consensus       161 iLdDPFddpp~l~~p~rspsPt~e~l~~g~i~~de~~d~~~g~saeel~e~~~e~ea~~~A~iLEmvGDlpdAd~~PPeN  240 (479)
T KOG0415|consen  161 ILDDPFDDPPDLAEPMRSPSPTPEQLVKGRIRLDEDEDDDEGLSAEELEEVLAEKEAKAQAVILEMVGDLPDADVKPPEN  240 (479)
T ss_pred             EecCCCCCchhhccCCCCCCCCHHHhhccccccCcccccccccCHHHHHHHHHHHHHHhhHhHHHHhcCCcccccCCCcc
Confidence            997 3322     444555555443  212  111            123567888899999999999999999999999


Q ss_pred             eEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCCcc
Q 046966          213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVS  292 (299)
Q Consensus       213 ~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~~~  292 (299)
                      .|||..|.+.++.++|.-+|+.||.|.+|.+++|..||.+..||||+|.+.+++++|.-.|++..|.+++|+|.|+.+.+
T Consensus       241 VLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQSVs  320 (479)
T KOG0415|consen  241 VLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQSVS  320 (479)
T ss_pred             eEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhhhhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             cc
Q 046966          293 KI  294 (299)
Q Consensus       293 ~~  294 (299)
                      +.
T Consensus       321 k~  322 (479)
T KOG0415|consen  321 KV  322 (479)
T ss_pred             hh
Confidence            63

>KOG0881 consensus Cyclophilin type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.5e-50  Score=296.31  Aligned_cols=152  Identities=47%  Similarity=0.852  Sum_probs=147.4

Q ss_pred             EEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCC
Q 046966            2 SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLK   81 (299)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~   81 (299)
                      -|+++|+.|.|++|||-+.||+||.||.+|++.|||+|+.||||+++|+|||||++++|.||.|||+.+ |.||.+.+|+
T Consensus        11 ~V~LeTsmG~i~~ElY~kHaP~TC~NF~eLarrgYYn~v~FHRii~DFmiQGGDPTGTGRGGaSIYG~k-F~DEi~~dLk   89 (164)
T KOG0881|consen   11 NVTLETSMGKITLELYWKHAPRTCQNFAELARRGYYNGVIFHRIIKDFMIQGGDPTGTGRGGASIYGDK-FEDEIHSDLK   89 (164)
T ss_pred             eEEEeecccceehhhhhhcCcHHHHHHHHHHhcccccceeeeehhhhheeecCCCCCCCCCccccccch-hhhhhhhhhc
Confidence            389999999999999999999999999999999999999999999999999999999999999999988 5999999999


Q ss_pred             CCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEE
Q 046966           82 HDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYV  155 (299)
Q Consensus        82 ~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v  155 (299)
                      |..+|.|+|||.|||+|+|||||||.+ .+|||++|++||||..||+|+.++....++..++|..+++|.+..+
T Consensus        90 hTGAGILsMANaGPnTNgSQFFiTLAP-t~~LDGKHTIFGRV~~Gm~vikr~G~v~Td~~DRPi~~~kIika~~  162 (164)
T KOG0881|consen   90 HTGAGILSMANAGPNTNGSQFFITLAP-TQWLDGKHTIFGRVCSGMEVIKRMGMVETDNSDRPIDEVKIIKAYP  162 (164)
T ss_pred             ccchhhhhhhccCCCCCCceEEEEecC-ccccCCcceeehhhhhhHHHHHhhcceecCCCCCCccceeeEeeec
Confidence            999999999999999999999999999 7999999999999999999999999999999999999999988754

>KOG0546 consensus HSP90 co-chaperone CPR7/Cyclophilin [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=3e-49  Score=341.48  Aligned_cols=150  Identities=39%  Similarity=0.667  Sum_probs=142.3

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhCC-----------CcCCceeeEeecCcEEEecCCC-CCCCCCCCCCCCccccc
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKNK-----------YYNGCLFHNIHKDFIAQTGDPT-GTGTGGRSVYEDRFFVD   74 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~~-----------~y~~~~f~ri~~~~~iq~G~~~-~~~~~~~~~~~~~~~~~   74 (299)
                      -+.|||+||||.|.||+||+||+.||+|.           .|+|+.||||+++|||||||++ ++|+||.|||++. |+|
T Consensus        20 e~~GRIvfeLf~dv~PKTaENFraLCtGE~G~~~~~gk~L~YKG~~FHRViK~FMiQgGDfs~gnGtGGeSIYG~~-FdD   98 (372)
T KOG0546|consen   20 EPAGRIVFELFNDVVPKTAENFRALCTGEKGGGLTTGKPLHYKGSRFHRVIKNFMIQGGDFSEGNGTGGESIYGEK-FDD   98 (372)
T ss_pred             cccceEEEEeecccCchhHHHHHHHhccccCCCCCCCCeeeecCchhheeeecceeeccccccCCCCCcccccccc-ccc
Confidence            56799999999999999999999999763           4999999999999999999965 6799999999987 699


Q ss_pred             ccccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEE
Q 046966           75 EIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTY  154 (299)
Q Consensus        75 e~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~  154 (299)
                      | ++.++|+++++|||||.|||+||||||||+.+ +|||||+|+|||+||.|++||+.|+.+.++..++|..+|.|.+||
T Consensus        99 E-nF~lKHdrpflLSMAN~GpNTNgSQFFITT~p-~PHLdGkHVVFGqVI~G~~VVr~IEn~~~d~~skP~~dV~I~dCG  176 (372)
T KOG0546|consen   99 E-NFELKHDRPFLLSMANRGPNTNGSQFFITTVP-TPHLDGKHVVFGQVIKGKEVVREIENLETDEESKPLADVVISDCG  176 (372)
T ss_pred             c-cceeccCcchhhhhhcCCCCCCCcceEEeCCC-CCCcCCceeEEeeEeechhHHHHHhccccccCCCCccceEecccc
Confidence            9 89999999999999999999999999999998 899999999999999999999999999999999999999999999


Q ss_pred             EECCC
Q 046966          155 VLYPP  159 (299)
Q Consensus       155 v~~p~  159 (299)
                      ++...
T Consensus       177 el~~~  181 (372)
T KOG0546|consen  177 ELVKK  181 (372)
T ss_pred             ccccc
Confidence            99854

>cd01928 Cyclophilin_PPIL3_like Cyclophilin_PPIL3_like

Probab=100.00  E-value=1.6e-47  Score=306.56  Aligned_cols=153  Identities=50%  Similarity=0.876  Sum_probs=144.7

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCC
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADL   80 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~   80 (299)
                      |||+|+|+.|+|+||||++.||+||+||++||++++|+|+.|||++++|++||||+.+++.++.++|+.. +++|....+
T Consensus         1 m~v~l~T~~G~i~ieL~~~~aP~t~~nF~~L~~~g~Y~~~~f~rv~~~f~iq~Gd~~~~g~g~~~~~~~~-~~~e~~~~~   79 (153)
T cd01928           1 MSVTLHTNLGDIKIELFCDDCPKACENFLALCASGYYNGCIFHRNIKGFMVQTGDPTGTGKGGESIWGKK-FEDEFRETL   79 (153)
T ss_pred             CEEEEEEccccEEEEEcCCCCcHHHHHHHHHHhcCccCCcEEEEeCCCCEEEccccCCCCCCCCccCCCc-cccccccCC
Confidence            9999999999999999999999999999999999999999999999999999999988888888888754 688877778


Q ss_pred             CCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEE
Q 046966           81 KHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYV  155 (299)
Q Consensus        81 ~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v  155 (299)
                      +|+++|+|+|++.++++++|||||++++ .++||++|+|||+|++||+||++|++.+++++++|..+|+|.+|.+
T Consensus        80 ~~~~~G~v~ma~~~~~~~~SqFfI~~~~-~~~Ld~~~tvFG~V~~G~dvl~~I~~~~~~~~~~P~~~i~I~~~~~  153 (153)
T cd01928          80 KHDSRGVVSMANNGPNTNGSQFFITYAK-QPHLDGKYTVFGKVIDGFETLDTLEKLPVDKKYRPLEEIRIKDVTI  153 (153)
T ss_pred             CcCCCcEEEEeeCCCCCcccEEEEEeCC-CcccCCCceEEEEEEeCHHHHHHHHcCCCCCCCCCcCCeEEEEeEC
Confidence            9999999999999999999999999998 6999999999999999999999999999999999999999999853

Proteins similar to Human cyclophilin-like peptidylprolyl cis- trans isomerase (PPIL3). Members of this family lack a key residue important for cyclosporin binding: the tryptophan residue corresponding to W121 in human hCyP-18a; most members have a histidine at this position. The exact function of the protein is not known.

>KOG0884 consensus Similar to cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.7e-47  Score=278.62  Aligned_cols=155  Identities=45%  Similarity=0.776  Sum_probs=149.9

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCC
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADL   80 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~   80 (299)
                      |||+++|+.|+|.||||++.+|++|+||+.||...||++|.|||-+++|++|+||++..|.||.+||+++ |+||+...|
T Consensus         1 msvtlht~~gdikiev~~e~tpktce~~l~~~~~~~~n~~~~~~~~~~f~v~~~~~~~tgrgg~siwg~~-fede~~~~l   79 (161)
T KOG0884|consen    1 MSVTLHTDVGDIKIEVFCERTPKTCENFLALCASDYYNGCIFHRNIKGFMVQTGDPTHTGRGGNSIWGKK-FEDEYSEYL   79 (161)
T ss_pred             CeEEEeeccCcEEEEEEecCChhHHHHHHHHhhhhhccceeecCCCCCcEEEeCCCCCCCCCCccccCCc-chHHHHHHH
Confidence            8999999999999999999999999999999999999999999999999999999999999999999987 699999999


Q ss_pred             CCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCC-CCCceeEEEEEEEEEC
Q 046966           81 KHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEE-NRPPQQIIIKQTYVLY  157 (299)
Q Consensus        81 ~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~-~~p~~~v~I~~~~v~~  157 (299)
                      +|+.||+||||+.|||+|+||||||.+. .+|||-+|++||+||+|+++|+.|+..++++. -+|+.++.|.++.|..
T Consensus        80 kh~~rg~vsmanngp~tn~sqffity~k-q~hldmkytvfgkvidg~etldele~l~v~~ktyrpl~~~~ik~itiha  156 (161)
T KOG0884|consen   80 KHNVRGVVSMANNGPNTNGSQFFITYGK-QPHLDMKYTVFGKVIDGLETLDELEKLPVNEKTYRPLNDVHIKDITIHA  156 (161)
T ss_pred             hhccceeEEcccCCCCCCCceEEEEecC-CCccceeEeeeeeeccchhhHHHHhhcccCccccccchheeeeeeEEec
Confidence            9999999999999999999999999998 59999999999999999999999999999876 6999999999999865

>cd01923 cyclophilin_RING cyclophilin_RING: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a modified RING finger domain

Probab=100.00  E-value=2.4e-46  Score=301.84  Aligned_cols=153  Identities=42%  Similarity=0.778  Sum_probs=145.8

Q ss_pred             EEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCCC
Q 046966            3 VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKH   82 (299)
Q Consensus         3 v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~~   82 (299)
                      |+|+|+.|+|+||||++.||+||+||++||+.++|+|+.||||+|++++||||+.+++.++.++|+.. +++|....++|
T Consensus         2 v~~~T~~G~i~ieL~~~~aP~t~~nF~~L~~~g~Y~~~~f~rv~~~~~iq~Gd~~~~g~~~~~~~g~~-~~~E~~~~~~h   80 (159)
T cd01923           2 VRLHTNKGDLNLELHCDKAPKACENFIKLCKKGYYDGTIFHRSIRNFMIQGGDPTGTGRGGESIWGKP-FKDEFKPNLSH   80 (159)
T ss_pred             EEEEEccccEEEEEeCCCChHHHHHHHHHHhcCccCCcEEEEEeCCcEEEecccCCCCCCCccccCCc-cCcccccCcCc
Confidence            78999999999999999999999999999999999999999999999999999998888888888755 68887778899


Q ss_pred             CCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEEC
Q 046966           83 DKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY  157 (299)
Q Consensus        83 ~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~~  157 (299)
                      +++|+|+|++.++++++|||||++++ .++||++|+|||+|++||++|++|++.+++++++|+.+|+|.+|+|+.
T Consensus        81 ~~~G~v~ma~~~~~s~~sqFfIt~~~-~~~Ld~~~~vFG~V~~G~~vl~~I~~~~~~~~~~P~~~i~I~~~~i~~  154 (159)
T cd01923          81 DGRGVLSMANSGPNTNGSQFFITYRS-CKHLDGKHTVFGRVVGGLETLEAMENVPDPGTDRPKEEIKIEDTSVFV  154 (159)
T ss_pred             CCCcEEEEeeCCCCCcccEEEEECCC-CcccCCCccEEEEEEcCHHHHHHHHcCCCCCCCCCCCCeEEEEeEEEe
Confidence            99999999999999999999999998 799999999999999999999999999998899999999999999987

This group includes the nuclear proteins, Human hCyP-60 and Caenorhabditis elegans MOG-6 which, compared to the archetypal cyclophilin Human cyclophilin A exhibit reduced peptidylprolyl cis- trans isomerase activity and lack a residue important for cyclophilin binding. Human hCyP-60 has been shown to physically interact with the proteinase inhibitor peptide eglin c and; C. elegans MOG-6 to physically interact with MEP-1, a nuclear zinc finger protein. MOG-6 has been shown to function in germline sex determination.

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

Probab=100.00  E-value=5.2e-46  Score=302.16  Aligned_cols=154  Identities=62%  Similarity=1.029  Sum_probs=143.3

Q ss_pred             EEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCC------cccccccc
Q 046966            4 LIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYED------RFFVDEIR   77 (299)
Q Consensus         4 ~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~------~~~~~e~~   77 (299)
                      +|+|+.|+|+||||++.||+||+||++||+.++|+|+.||||+++++|||||+..++.++.++++.      .++.+|..
T Consensus         1 ll~Ts~G~i~ieL~~~~aP~t~~nF~~L~~~~~Y~g~~fhrvi~~f~iQgGd~~~~g~~~~~~~~~~~~~~~~~~~~e~~   80 (166)
T cd01921           1 LLETTLGDLVIDLFTDECPLACLNFLKLCKLKYYNFCLFYNVQKDFIAQTGDPTGTGAGGESIYSQLYGRQARFFEPEIL   80 (166)
T ss_pred             CcEeccCCEEEEEcCCCCCHHHHHHHHHHhcCCcCCCEEEEEeCCceEEECCcCCCCCCCcccccccccccCcccCcccC
Confidence            479999999999999999999999999999999999999999999999999998888888777642      34677767


Q ss_pred             cCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEEC
Q 046966           78 ADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY  157 (299)
Q Consensus        78 ~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~~  157 (299)
                      ..++|+.+|+|+||+.++++++|||||++.+++++||++|+|||+|++||+||++|++.+++.+++|..+|+|.+|+|+.
T Consensus        81 ~~~~h~~~G~l~ma~~~~~~~~SQFfIt~~~~~~~Ldg~~tvFG~Vi~G~dvv~~I~~~~~~~~~~P~~~i~I~~~~i~~  160 (166)
T cd01921          81 PLLKHSKKGTVSMVNAGDNLNGSQFYITLGENLDYLDGKHTVFGQVVEGFDVLEKINDAIVDDDGRPLKDIRIKHTHILD  160 (166)
T ss_pred             CccccCCceEEEEeECCCCCccceEEEEcCCCCcccCCCccEEEEEEcCHHHHHHHHcCCCCCCCCCCCCeEEEEEEEEC
Confidence            78899999999999999999999999999865799999999999999999999999999999999999999999999997

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.

>KOG0883 consensus Cyclophilin type, U box-containing peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=5.6e-47  Score=327.26  Aligned_cols=153  Identities=44%  Similarity=0.777  Sum_probs=149.7

Q ss_pred             EEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCCC
Q 046966            3 VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKH   82 (299)
Q Consensus         3 v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~~   82 (299)
                      |.|.|+.|.|.|||++|.+|++|+||+.||+.|||+|+.|||.+.+|||||||++++|.||.|||+.+ |.||+.+.+.|
T Consensus       280 vrl~Tn~G~lNlELhcd~~P~aceNFI~lc~~gYYnnt~FHRsIrnFmiQGGDPTGTG~GGeSiWgKp-FkDEf~~~l~H  358 (518)
T KOG0883|consen  280 VRLVTNHGPLNLELHCDYAPRACENFITLCKNGYYNNTIFHRSIRNFMIQGGDPTGTGRGGESIWGKP-FKDEFCSNLSH  358 (518)
T ss_pred             EEEeccCCceeeEeecCcchHHHHHHHHHHhcccccchHHHHHHHHHeeeCCCCCCCCCCCccccCCc-cccccCCCCCc
Confidence            78999999999999999999999999999999999999999999999999999999999999999976 69999999999


Q ss_pred             CCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEEC
Q 046966           83 DKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY  157 (299)
Q Consensus        83 ~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~~  157 (299)
                      +.||+|||||+|||+|||||||+..+ +.|||++|++||+||.|+++|.+|+++++++.++|+.+|+|.++.|..
T Consensus       359 ~gRGvlSMANsGpnTNgSQFFItyrs-ckhLd~KHTIFGrvVGGldtL~amEnve~d~~DrP~e~I~i~~~~VFV  432 (518)
T KOG0883|consen  359 DGRGVLSMANSGPNTNGSQFFITYRS-CKHLDNKHTIFGRVVGGLDTLTAMENVETDEKDRPKEEIKIEDAIVFV  432 (518)
T ss_pred             CCcceEeeccCCCCCCCceEEEEecc-hhhccccceeeeeeeccHHHHHHHhcCCCCCCCCcccceEEeeeEEee
Confidence            99999999999999999999999998 899999999999999999999999999999999999999999999975

>KOG0880 consensus Peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.4e-46  Score=298.18  Aligned_cols=148  Identities=40%  Similarity=0.692  Sum_probs=139.9

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhCC----CcCCceeeEeecCcEEEecCCCC-CCCCCCCCCCCcccccccccCCC
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKNK----YYNGCLFHNIHKDFIAQTGDPTG-TGTGGRSVYEDRFFVDEIRADLK   81 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~~----~y~~~~f~ri~~~~~iq~G~~~~-~~~~~~~~~~~~~~~~e~~~~~~   81 (299)
                      -+.|||+|+||+..+|+||+||.+||.++    .|.|++||||+|+|||||||.+. +|.||.++|+.+ |+|| ++.|+
T Consensus        51 ~~~grIvigLfG~~vPKTV~NF~~l~~~~~~~~gY~gS~FhRVi~nfmIQGGd~t~g~gtGg~SIyG~~-F~DE-Nf~Lk  128 (217)
T KOG0880|consen   51 EPVGRIVIGLFGKVVPKTVENFRALATSGEKGYGYKGSKFHRVIPNFMIQGGDFTKGDGTGGKSIYGEK-FPDE-NFKLK  128 (217)
T ss_pred             EeccEEEEEeccccchHHHHHHHHHHccCCCCcccCCceeeeeecCceeecCccccCCCCCCeEeecCC-CCCc-cceee
Confidence            56799999999999999999999999843    49999999999999999999775 599999999988 5999 79999


Q ss_pred             CCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEEC
Q 046966           82 HDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY  157 (299)
Q Consensus        82 ~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~~  157 (299)
                      |+++|.||||+.|||+||||||||+.. ++||||+|+|||+|++||++|.+|+..+++++++|.++++|.+|+-+.
T Consensus       129 H~rpG~lSMAn~GpDtNGsQFfItT~~-t~wLDGkhVVFGqVl~Gmdvv~~Ie~~~TD~~dkP~e~v~I~~~g~l~  203 (217)
T KOG0880|consen  129 HDRPGRLSMANAGPDTNGSQFFITTVK-TPWLDGKHVVFGQVLEGMDVVRKIENVKTDERDKPLEDVVIANCGELP  203 (217)
T ss_pred             cCCCceEeeeccCCCCCCceEEEEecC-CccccCceeEEeeehhhHHHHHHHHhcccCCCCCccccEEEeecCccc
Confidence            999999999999999999999999997 799999999999999999999999999999999999999999999765

>COG0652 PpiB Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=5e-46  Score=293.64  Aligned_cols=149  Identities=43%  Similarity=0.745  Sum_probs=132.0

Q ss_pred             EEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCC-CCCCCCCCCCcccccccccCC
Q 046966            2 SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGT-GTGGRSVYEDRFFVDEIRADL   80 (299)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~-~~~~~~~~~~~~~~~e~~~~~   80 (299)
                      +|+++|++|+|+||||++.||+||+||++||+.++|+|+.||||+++|||||||+.+. +.+|.+    ..+++|+.. .
T Consensus         1 ~v~~~t~~G~I~ieL~~~~aP~Tv~NF~~l~~~g~Ydg~~FHRVi~~FmiQgGd~~~~~g~gg~~----~~f~~E~~~-~   75 (158)
T COG0652           1 TVILETNKGDITIELYPDKAPKTVANFLQLVKEGFYDGTIFHRVIPGFMIQGGDPTGGDGTGGPG----PPFKDENFA-L   75 (158)
T ss_pred             CceeeccCCCEEEEECCCcCcHHHHHHHHHHHcCCCCCceEEEeecCceeecCCCCCCCCCCCCC----CCCcccccc-c
Confidence            4789999999999999999999999999999999999999999999999999999887 777766    447888443 3


Q ss_pred             CCCC--ceEEEEEcCC-CCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCC----CCCceeEEEEEE
Q 046966           81 KHDK--VGTVGMASAG-RDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEE----NRPPQQIIIKQT  153 (299)
Q Consensus        81 ~~~~--~G~l~~~~~~-~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~----~~p~~~v~I~~~  153 (299)
                      .|++  +|+|||||.+ ||+++|||||++.+ .+|||++|+|||+|++||++|++|++..+...    +.|..+++|...
T Consensus        76 ~~~~~~~G~lsMA~~g~P~t~~SQFFI~~~~-~~~Ld~~ytVFG~Vv~GmdvvdkI~~~~~~~~~~~~~~~~~~~~i~~~  154 (158)
T COG0652          76 NGDRHKRGTLSMARAGDPNSNGSQFFITVVD-NPFLDGKYTVFGQVVEGMDVVDKIKNGDTDDSGYVQDVPADPVKILSV  154 (158)
T ss_pred             ccccCCcceEeEcccCCcCCccCeEEEEecC-CcccCCCCcEEEEEehhHHHHHHHHcCCccCCCcccCCCCCCeEEeee
Confidence            4445  9999999999 99999999999998 69999999999999999999999999888754    356678888887


Q ss_pred             EEE
Q 046966          154 YVL  156 (299)
Q Consensus       154 ~v~  156 (299)
                      .++
T Consensus       155 ~~~  157 (158)
T COG0652         155 KIV  157 (158)
T ss_pred             eee
Confidence            664

>cd01927 cyclophilin_WD40 cyclophilin_WD40: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a WD40 domain

Probab=100.00  E-value=1.6e-45  Score=293.49  Aligned_cols=147  Identities=46%  Similarity=0.808  Sum_probs=138.9

Q ss_pred             EEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCCCC
Q 046966            4 LIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKHD   83 (299)
Q Consensus         4 ~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~~~   83 (299)
                      +|+|+.|+|+||||.+.||++|+||++||+.++|+++.||||+|+|++||||+.+++.++.++|+.. +++|..+.++|+
T Consensus         1 ~i~T~~G~i~ieL~~~~aP~t~~nF~~L~~~g~Y~~~~f~Rvi~~f~iq~Gd~~~~g~g~~~~~~~~-~~~e~~~~~~h~   79 (148)
T cd01927           1 IIHTTKGDIHIRLFPEEAPKTVENFTTHARNGYYNNTIFHRVIKGFMIQTGDPTGDGTGGESIWGKE-FEDEFSPSLKHD   79 (148)
T ss_pred             CeEeccccEEEEEeCCCCcHHHHHHHHHhhcCCcCCcEEEEEcCCcEEEecccCCCCCCCCcccCCc-cccccccccCcC
Confidence            4899999999999999999999999999999999999999999999999999988888888888754 688877789999


Q ss_pred             CceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEE
Q 046966           84 KVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQ  152 (299)
Q Consensus        84 ~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~  152 (299)
                      ++|+|+|++.++++++|||||++.+ +++||++|+|||+|++||+||++|++.+++++++|..+|+|.+
T Consensus        80 ~~G~l~ma~~~~~s~~SqFfIt~~~-~p~Ldg~~tvFG~V~~G~dvl~~I~~~~~~~~~~P~~~i~I~~  147 (148)
T cd01927          80 RPYTLSMANAGPNTNGSQFFITTVA-TPWLDNKHTVFGRVVKGMDVVQRIENVKTDKNDRPYEDIKIIN  147 (148)
T ss_pred             CCeEEEEeeCCCCCCCceEEEEcCC-CcccCCCceEEEEEEcCHHHHHHHHcCCCCCCCCCcCCeEEEe
Confidence            9999999999999999999999998 7999999999999999999999999999998999999999986

This group consists of several hypothetical and putative eukaryotic and bacterial proteins which have a cyclophilin domain and a WD40 domain. Function of the protein is not known.

>cd01922 cyclophilin_SpCYP2_like cyclophilin_SpCYP2_like: cyclophilin 2-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to Schizosaccharomyces pombe cyp-2

Probab=100.00  E-value=1.3e-44  Score=287.52  Aligned_cols=145  Identities=43%  Similarity=0.824  Sum_probs=136.5

Q ss_pred             EEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCCCC
Q 046966            4 LIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKHD   83 (299)
Q Consensus         4 ~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~~~   83 (299)
                      +|+|+.|+|+||||.+.||++|+||++||+.++|+++.|||++|+|++||||+.+++.++.++|+.. +++|....++|+
T Consensus         1 ~i~T~~G~i~ieL~~~~aP~t~~nF~~L~~~g~Y~~~~f~Rvi~~f~iq~Gd~~~~g~~~~~~~~~~-~~~e~~~~~~h~   79 (146)
T cd01922           1 TLETTMGEITLELYWNHAPKTCKNFYELAKRGYYNGTIFHRLIKDFMIQGGDPTGTGRGGASIYGKK-FEDEIHPELKHT   79 (146)
T ss_pred             CeEeccccEEEEEcCCCCcHHHHHHHHHHhcCCcCCcEEEEEcCCcEEEecccCCCCCCcccccCCC-cccccccCcCCC
Confidence            4799999999999999999999999999999999999999999999999999988888888888754 688877889999


Q ss_pred             CceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEE
Q 046966           84 KVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIK  151 (299)
Q Consensus        84 ~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~  151 (299)
                      ++|+|+|++.++++++|||||++++ .++||++|+|||+|++||+||++|++.+++ +++|..+|+|.
T Consensus        80 ~~G~l~ma~~~~~s~~sqFfIt~~~-~p~Ld~~~tvFG~V~~G~dvl~~I~~~~~~-~~~P~~~I~I~  145 (146)
T cd01922          80 GAGILSMANAGPNTNGSQFFITLAP-TPWLDGKHTIFGRVSKGMKVIENMVEVQTQ-TDRPIDEVKIL  145 (146)
T ss_pred             CCeEEEEeeCCCCCCccEEEEEcCC-CcccCCCCCEEEEEEcCHHHHHHHHhCCCC-CCCcCCCeEEe
Confidence            9999999999999999999999998 699999999999999999999999999998 88999999986

These proteins bind their respective SNW chromatin binding protein in autologous systems, in a CsA independent manner indicating interaction with a surface outside the PPIase active site. SNW proteins play a basic and broad range role in signaling.

>KOG0879 consensus U-snRNP-associated cyclophilin type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.8e-45  Score=273.84  Aligned_cols=146  Identities=40%  Similarity=0.716  Sum_probs=139.2

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhCCC--------cCCceeeEeecCcEEEecCC-CCCCCCCCCCCCCcccccccc
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKNKY--------YNGCLFHNIHKDFIAQTGDP-TGTGTGGRSVYEDRFFVDEIR   77 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~--------y~~~~f~ri~~~~~iq~G~~-~~~~~~~~~~~~~~~~~~e~~   77 (299)
                      ++.|||.||||++.+|+|++||+++|++.+        |+++.|||++++|||||||. .++|+|..+||+.. |+|| +
T Consensus        22 ~~~GrikieLFadivPkTAENFRQFCTGE~r~~g~PiGYK~~tFHRvIkdFMiQgGDFv~gDGtG~~sIy~~~-F~DE-N   99 (177)
T KOG0879|consen   22 RPIGRIKIELFADIVPKTAENFRQFCTGEYRKDGVPIGYKNSTFHRVIKDFMIQGGDFVNGDGTGVASIYGST-FPDE-N   99 (177)
T ss_pred             EEcceEEEEEeeccChhhHHHHHhhcccccccCCccccccccchHHHhhhheeccCceecCCCceEEEEcCCC-CCCc-c
Confidence            678999999999999999999999999865        99999999999999999995 56799999999986 6999 7


Q ss_pred             cCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEE
Q 046966           78 ADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYV  155 (299)
Q Consensus        78 ~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v  155 (299)
                      +.++|+.+|+||||++|+++||.|||||... +.|||++|+|||+|++|+.++++|+..++..+++|+.+|.|..|+.
T Consensus       100 FtlkH~~PGlLSMANsG~~tNGCQFFITcak-cdfLD~KHVVFGrvldGlli~rkIEnvp~G~NnkPKl~v~i~qCGe  176 (177)
T KOG0879|consen  100 FTLKHDGPGLLSMANSGKDTNGCQFFITCAK-CDFLDGKHVVFGRVLDGLLIMRKIENVPTGPNNKPKLPVVIVQCGE  176 (177)
T ss_pred             eeeecCCCceeeccccCCCCCCceEEEEecc-cccccCceEEEeeeehhhhhhhhhhcCCCCCCCCCCCcEEEeeccc
Confidence            8999999999999999999999999999997 9999999999999999999999999999999999999999999974

>KOG0882 consensus Cyclophilin-related peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=3.1e-45  Score=322.30  Aligned_cols=152  Identities=44%  Similarity=0.780  Sum_probs=148.3

Q ss_pred             EEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCC
Q 046966            2 SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLK   81 (299)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~   81 (299)
                      .++|||+.|+|.|.||+++||+||+||-..|++|||+|..||||++|||||+||+.++|+||.|||++. |+||+++.|+
T Consensus       406 ~aiihtt~gdi~~kl~p~ecpktvenf~th~rngyy~~~~fhriik~fmiqtgdp~g~gtggesiwg~d-fedefh~~lr  484 (558)
T KOG0882|consen  406 AAIIHTTQGDIHIKLYPEECPKTVENFTTHSRNGYYDNHTFHRIIKGFMIQTGDPLGDGTGGESIWGKD-FEDEFHPNLR  484 (558)
T ss_pred             ceEEEecccceEEEecccccchhhhhhhccccCccccCcchHHhhhhheeecCCCCCCCCCCccccccc-chhhcCcccc
Confidence            478999999999999999999999999999999999999999999999999999999999999999987 6999999999


Q ss_pred             CCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEE
Q 046966           82 HDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYV  155 (299)
Q Consensus        82 ~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v  155 (299)
                      |+++-+|||||.|||+||||||||+-+ +||||++|+|||||+.||+|+++|+++.++.+++|.+++.|.++.|
T Consensus       485 hdrpft~smanag~ntngsqffit~~~-tpwld~khtvfgrv~~gm~vvqri~~v~t~k~drp~e~v~iinisv  557 (558)
T KOG0882|consen  485 HDRPFTVSMANAGPNTNGSQFFITTVP-TPWLDGKHTVFGRVTAGMDVVQRIEQVKTDKYDRPYEDVKIINISV  557 (558)
T ss_pred             cCCCceEEecccCCCCCCceEEEEecC-ccccCCcceeEEEEecchhHHhHhhhcccCcCCCCCCceeEEEEec
Confidence            999999999999999999999999998 7999999999999999999999999999999999999999999876

>cd01925 cyclophilin_CeCYP16-like cyclophilin_CeCYP16-like: cyclophilin-type peptidylprolyl cis- trans isomerase) (PPIase) domain similar to Caenorhabditis elegans cyclophilin 16

Probab=100.00  E-value=8e-44  Score=290.27  Aligned_cols=154  Identities=41%  Similarity=0.737  Sum_probs=145.5

Q ss_pred             EEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCC
Q 046966            2 SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLK   81 (299)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~   81 (299)
                      +|+|+|++|+|+||||++.||+||+||++||+.++|+|+.|||++|+|++||||+.++|.++.++|+.. +++|....++
T Consensus         7 ~v~i~Ts~G~i~ieL~~~~~P~t~~nF~~L~~~~~Y~~~~f~Rvi~~f~iQgGd~~~~g~g~~s~~g~~-~~~E~~~~~~   85 (171)
T cd01925           7 KVILKTTAGDIDIELWSKEAPKACRNFIQLCLEGYYDNTIFHRVVPGFIIQGGDPTGTGTGGESIYGEP-FKDEFHSRLR   85 (171)
T ss_pred             EEEEEEccccEEEEEeCCCChHHHHHHHHHHhcCCCCCCEEEEEcCCcEEEccccCCCCccCcccCCCc-cCcccccCcC
Confidence            689999999999999999999999999999999999999999999999999999998899999988755 6888777888


Q ss_pred             CCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeec-CHHHHHHHHhcccCCCCCCceeEEEEEEEEEC
Q 046966           82 HDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAE-GLETLTRINQAVVDEENRPPQQIIIKQTYVLY  157 (299)
Q Consensus        82 ~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~-G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~~  157 (299)
                      |+++|+|+|++.++++++|||||++++ .++||++|+|||+|++ ++++|++|++.+++++++|..+|.|.+|+|+.
T Consensus        86 ~~~~G~l~ma~~g~~s~~sqFfIt~~~-~~~ldg~~tvFG~V~g~~~~~v~~i~~~~~~~~~~P~~~i~I~~~~i~~  161 (171)
T cd01925          86 FNRRGLVGMANAGDDSNGSQFFFTLDK-ADELNNKHTLFGKVTGDTIYNLLKLAEVETDKDERPVYPPKITSVEVLE  161 (171)
T ss_pred             CCCCcEEEECcCCCCCcccEEEEEcCC-CcccCCCceEEEEEEECcHHHHHHHhcCCcCCCCCcCCCeEEEEEEEEc
Confidence            999999999999999999999999998 7999999999999994 68899999999999999999999999999987

C. elegans CeCYP-16, compared to the archetypal cyclophilin Human cyclophilin A has, a reduced peptidylprolyl cis- trans isomerase activity, is cyclosporin insensitive and shows an altered substrate preference favoring, hydrophobic, acidic or amide amino acids. Most members of this subfamily have a glutamate residue in the active site at the position equivalent to a tryptophan (W121 in Human cyclophilin A), which has been shown to be important for cyclophilin binding.

>PLN03149 peptidyl-prolyl isomerase H (cyclophilin H); Provisional

Probab=100.00  E-value=9.4e-42  Score=280.88  Aligned_cols=147  Identities=38%  Similarity=0.698  Sum_probs=134.0

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhCCC--------cCCceeeEeecCcEEEecCCC-CCCCCCCCCCCCcccccccc
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKNKY--------YNGCLFHNIHKDFIAQTGDPT-GTGTGGRSVYEDRFFVDEIR   77 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~--------y~~~~f~ri~~~~~iq~G~~~-~~~~~~~~~~~~~~~~~e~~   77 (299)
                      ++.|+|+||||.+.||+||+||++||++.+        |+++.||||+++++|||||+. +++.++.++|+.. +++| .
T Consensus        30 ~~~G~i~ieL~~~~aP~t~~NF~~Lc~g~~~~~g~~~~Y~~~~fhrVi~~f~iqgGd~~~~~g~g~~~~~g~~-f~~e-~  107 (186)
T PLN03149         30 IPAGRIKMELFADIAPKTAENFRQFCTGEFRKAGLPQGYKGCQFHRVIKDFMIQGGDFLKGDGTGCVSIYGSK-FEDE-N  107 (186)
T ss_pred             cccccEEEEEcCCCCcHHHHHHHHHHhhhccccCcccccCCcEEEEEcCCcEEEcCCcccCCCCCcccccCCc-cCCc-c
Confidence            367999999999999999999999998654        999999999999999999964 6688888888765 5667 3


Q ss_pred             cCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEee-cCHHHHHHHHhcccCCCCCCceeEEEEEEEEE
Q 046966           78 ADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA-EGLETLTRINQAVVDEENRPPQQIIIKQTYVL  156 (299)
Q Consensus        78 ~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~-~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~  156 (299)
                      ..++|+++|+|+|++.++++++|||||++.+ +++||++|+|||+|+ +||+||++|++.+++.+++|..+|+|.+|+++
T Consensus       108 ~~~~h~~~G~lsma~~g~~s~~sqFfIt~~~-~p~Ldg~~tVFG~Vi~eG~dvl~~I~~~~~~~~~~P~~~i~I~~cG~~  186 (186)
T PLN03149        108 FIAKHTGPGLLSMANSGPNTNGCQFFITCAK-CDWLDNKHVVFGRVLGDGLLVVRKIENVATGPNNRPKLACVISECGEM  186 (186)
T ss_pred             cccccCCCCEEEEeeCCCCCcccEEEEECCC-CCccCCCceEEEEEEECcHHHHHHHHcCCCCCCCCCcCCeEEEeCEeC
Confidence            5678989999999999999999999999998 799999999999999 79999999999999999999999999999974

>PRK10903 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional

Probab=100.00  E-value=2.9e-41  Score=278.69  Aligned_cols=150  Identities=29%  Similarity=0.502  Sum_probs=130.0

Q ss_pred             EEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCC
Q 046966            2 SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLK   81 (299)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~   81 (299)
                      +|+|+|+.|+|+||||++.||+||+||++||+.+||+|+.|||++|+|++|||++.....+.  .++ ..+.+|....+ 
T Consensus        30 ~v~l~T~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Ydg~~FhRvi~~f~iQgG~~~~~~~~~--~~~-~~~~~e~~~~l-  105 (190)
T PRK10903         30 HVLLTTSAGNIELELNSQKAPVSVKNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQK--KPN-PPIKNEADNGL-  105 (190)
T ss_pred             EEEEEeccccEEEEEeCCCCcHHHHHHHHHHhcCCcCCcEEEEEeCCceEEeCCcCCCCCCC--CCC-CcccCcccccC-
Confidence            68999999999999999999999999999999999999999999999999999976542211  122 23567754444 


Q ss_pred             CCCceEEEEEcCC-CCCCcceEEEEecCCCCCCCC-----CceEEEEeecCHHHHHHHHhcccCC----CCCCceeEEEE
Q 046966           82 HDKVGTVGMASAG-RDLNASQFYITLRDNLHYLDE-----KHTIFGEVAEGLETLTRINQAVVDE----ENRPPQQIIIK  151 (299)
Q Consensus        82 ~~~~G~l~~~~~~-~~~~~s~FfI~~~~~~~~ld~-----~~~vfG~V~~G~~vl~~i~~~~~~~----~~~p~~~v~I~  151 (299)
                      |+.+|+|+||+.+ +++++|||||++.+ .++||+     +|+|||+|++||+||++|++.+++.    +++|..+|+|.
T Consensus       106 ~~~~G~lama~~~~~~sn~SQFfIt~~~-~~~ld~~~~dg~ytvFG~V~eG~dvl~~I~~~~~~~~~~~~~~P~~~v~I~  184 (190)
T PRK10903        106 RNTRGTIAMARTADKDSATSQFFINVAD-NAFLDHGQRDFGYAVFGKVVKGMDVADKISQVPTHDVGPYQNVPSKPVVIL  184 (190)
T ss_pred             cCCCcEEEeCCCCCCCCcccEEEEECcC-cccccCCccCCCccEEEEEecCHHHHHHHHcCCCCCCCCCCCcccCCeEEE
Confidence            4589999999865 89999999999998 588884     8999999999999999999999976    57999999999


Q ss_pred             EEEEE
Q 046966          152 QTYVL  156 (299)
Q Consensus       152 ~~~v~  156 (299)
                      +|+|+
T Consensus       185 ~~~v~  189 (190)
T PRK10903        185 SAKVL  189 (190)
T ss_pred             EEEEe
Confidence            99885

>PTZ00221 cyclophilin; Provisional

Probab=100.00  E-value=3.2e-41  Score=285.67  Aligned_cols=151  Identities=25%  Similarity=0.339  Sum_probs=134.1

Q ss_pred             EEEEEEc-----ceeEEEEecCCCChHHHHHHHHhhhCC-----------CcCCceeeEeecC-cEEEecCCCCCCCCCC
Q 046966            2 SVLIETS-----LGDIVIDLFVDKCPRTTNNFLQHCKNK-----------YYNGCLFHNIHKD-FIAQTGDPTGTGTGGR   64 (299)
Q Consensus         2 ~v~~~T~-----~G~i~ieL~~~~~P~~~~nF~~l~~~~-----------~y~~~~f~ri~~~-~~iq~G~~~~~~~~~~   64 (299)
                      .|.|+|+     .|+|+||||.+.||+||+||++||++.           .|+|+.||||+++ ++||+||+...   +.
T Consensus        54 rVfldisig~~~~GrIvIELf~d~aP~T~eNF~~Lc~g~~g~~~~~g~k~~Y~gt~FhRVi~~~f~iqgGD~~~~---g~  130 (249)
T PTZ00221         54 RAFLDISIGDVLAGRLVFELFEDVVPETVENFRALITGSCGIDTNTGVKLDYLYTPVHHVDRNNNIIVLGELDSF---NV  130 (249)
T ss_pred             EEEEEEeeCCeecceEEEEEeCCCCcHHHHHHHHHhhcccccccccCcccccCCCEEEEEeCCCCEEEeCCCCCC---Cc
Confidence            3666666     578999999999999999999999753           3999999999986 89999997643   33


Q ss_pred             CCCCCcccccccccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCC
Q 046966           65 SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRP  144 (299)
Q Consensus        65 ~~~~~~~~~~e~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p  144 (299)
                      ++++. .+.+| ...++|+++|+|+|++.++++++||||||+.+ +++||++|+|||+|++||+||++|++.+++..++|
T Consensus       131 s~~G~-~f~dE-~~~~~h~~~G~LsMan~GpntngSQFfITl~~-~p~LDgk~vVFGrVveGmdVv~kIe~v~~d~~grP  207 (249)
T PTZ00221        131 SSTGT-PIADE-GYRHRHTERGLLTMISEGPHTSGSVFGITLGP-SPSLDFKQVVFGKAVDDLSLLEKLESLPLDDVGRP  207 (249)
T ss_pred             cCCCC-cccCc-cccccCCCCCEEEeCcCCCCCccceEEEECCC-CCccCCCceEEEEEEeCHHHHHHHHcCCcCCCCCC
Confidence            45654 46888 56789999999999999999999999999998 69999999999999999999999999999889999


Q ss_pred             ceeEEEEEEEEECC
Q 046966          145 PQQIIIKQTYVLYP  158 (299)
Q Consensus       145 ~~~v~I~~~~v~~p  158 (299)
                      ..+|+|.+|+++..
T Consensus       208 ~~~V~I~~Cgvl~~  221 (249)
T PTZ00221        208 LLPVTVSFCGALTG  221 (249)
T ss_pred             CCCeEEEECeEecC
Confidence            99999999999983

>PRK10791 peptidyl-prolyl cis-trans isomerase B (rotamase B); Provisional

Probab=100.00  E-value=3.5e-41  Score=272.26  Aligned_cols=149  Identities=30%  Similarity=0.532  Sum_probs=127.4

Q ss_pred             EEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCCC
Q 046966            3 VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKH   82 (299)
Q Consensus         3 v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~~   82 (299)
                      |+|+|+.|+|+|+||++.||+||+||++||+.+||+++.||||+|+|+||||++... .+. ..++ ..+.+|....++|
T Consensus         2 v~~~T~~G~i~ieL~~~~aP~t~~nF~~L~~~g~Yd~~~fhRvi~~f~iQgGd~~~~-~~~-~~~~-~~~~~e~~~~~~~   78 (164)
T PRK10791          2 VTFHTNHGDIVIKTFDDKAPETVKNFLDYCREGFYNNTIFHRVINGFMIQGGGFEPG-MKQ-KATK-EPIKNEANNGLKN   78 (164)
T ss_pred             EEEEEccccEEEEEeCCCCcHHHHHHHHHHhcCCcCCcEEEEEecCcEEEeCCcCCC-CCc-CCCC-CCcCCcccccccC
Confidence            689999999999999999999999999999999999999999999999999986532 111 1122 2356675556665


Q ss_pred             CCceEEEEEcCC-CCCCcceEEEEecCCCCCCC-------C-CceEEEEeecCHHHHHHHHhcccCC----CCCCceeEE
Q 046966           83 DKVGTVGMASAG-RDLNASQFYITLRDNLHYLD-------E-KHTIFGEVAEGLETLTRINQAVVDE----ENRPPQQII  149 (299)
Q Consensus        83 ~~~G~l~~~~~~-~~~~~s~FfI~~~~~~~~ld-------~-~~~vfG~V~~G~~vl~~i~~~~~~~----~~~p~~~v~  149 (299)
                       .+|+||||+.+ |++++|||||++.+ .++||       + +|+|||+|++||+||++|++.+++.    +++|..+|+
T Consensus        79 -~~G~lsma~~~~p~s~~SQFfI~~~~-~~~ld~~~~~~d~~~~tvFG~V~eG~dvl~~I~~~~~~~~~~~~~~P~~~v~  156 (164)
T PRK10791         79 -TRGTLAMARTQAPHSATAQFFINVVD-NDFLNFSGESLQGWGYCVFAEVVEGMDVVDKIKGVATGRSGMHQDVPKEDVI  156 (164)
T ss_pred             -CCcEEEECCCCCcCCccceEEEEecC-chhhcccccccCCCCccEEEEEecCHHHHHHHHcCcCCCCCccCCCcCCCeE
Confidence             79999999875 89999999999998 47665       3 7999999999999999999999976    369999999


Q ss_pred             EEEEEEE
Q 046966          150 IKQTYVL  156 (299)
Q Consensus       150 I~~~~v~  156 (299)
                      |.+|.|.
T Consensus       157 I~~~~i~  163 (164)
T PRK10791        157 IESVTVS  163 (164)
T ss_pred             EEEEEEe
Confidence            9999875

>KOG0885 consensus Peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.7e-42  Score=297.11  Aligned_cols=155  Identities=43%  Similarity=0.771  Sum_probs=150.3

Q ss_pred             EEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCC
Q 046966            2 SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLK   81 (299)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~   81 (299)
                      .|++.|+.|.|.||||+.+||++|.||++||..|||+|+.|||++|||++||||++++|+||.+||+.. |.+|++++|.
T Consensus        14 kvil~TT~G~I~iELW~kE~P~acrnFiqKOGegyy~nt~fhrlvp~f~~Qggdp~~~gtGgesiyg~~-fadE~h~Rlr   92 (439)
T KOG0885|consen   14 KVILKTTKGDIDIELWAKECPKACRNFIQLCLEGYYDNTEFHRLVPGFLVQGGDPTGTGTGGESIYGRP-FADEFHPRLR   92 (439)
T ss_pred             eEEEEeccCceeeeehhhhhhHHHHHHHHHHHhccccCceeeeeccchhcccCCCCCCCCCcccccccc-chhhcCccee
Confidence            589999999999999999999999999999999999999999999999999999999999999999987 6999999999


Q ss_pred             CCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeec-CHHHHHHHHhcccCCCCCCceeEEEEEEEEECC
Q 046966           82 HDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAE-GLETLTRINQAVVDEENRPPQQIIIKQTYVLYP  158 (299)
Q Consensus        82 ~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~-G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~~p  158 (299)
                      +.++|+|+||+.+.+.||||||+||++ +++|+++|++||+|+. .++.+.+|..+.++.+.+|..+..|.+|.|+.+
T Consensus        93 f~rrGlvgmana~~~~ngsqFfftl~~-~~el~nk~tiFGKVtGdtIYn~lri~e~eida~~Rp~~p~kI~s~EV~~n  169 (439)
T KOG0885|consen   93 FNRRGLVGMANAGNDDNGSQFFFTLGD-TPELNNKHTIFGKVTGDTIYNMLRISEVEIDADDRPVDPPKIKSVEVLIN  169 (439)
T ss_pred             eeccceeeecccCCCCCCceEEEEecC-ChHhcccCceeeeecchhhhhhhhhcccccccccCCCCccceeeeEeecC
Confidence            999999999999999999999999998 8999999999999997 899999999999999999999999999999983

>cd01926 cyclophilin_ABH_like cyclophilin_ABH_like: Cyclophilin A, B and H-like cyclophilin-type peptidylprolyl cis- trans isomerase (PPIase) domain

Probab=100.00  E-value=6.6e-41  Score=271.84  Aligned_cols=144  Identities=40%  Similarity=0.731  Sum_probs=132.6

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhC--C------CcCCceeeEeecCcEEEecCCC-CCCCCCCCCCCCcccccccc
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKN--K------YYNGCLFHNIHKDFIAQTGDPT-GTGTGGRSVYEDRFFVDEIR   77 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~--~------~y~~~~f~ri~~~~~iq~G~~~-~~~~~~~~~~~~~~~~~e~~   77 (299)
                      ++.|+|+||||.+.||+||+||++||++  +      +|+++.||||+|+|+|||||+. .++.++.++|+.. +++| .
T Consensus        12 ~~~G~i~ieL~~~~aP~~~~nF~~L~~~~~g~~~~~~~Y~~~~f~Rv~~~~~iq~Gd~~~~~g~~~~~~~g~~-~~~e-~   89 (164)
T cd01926          12 EPAGRIVMELFADVVPKTAENFRALCTGEKGKGGKPFGYKGSTFHRVIPDFMIQGGDFTRGNGTGGKSIYGEK-FPDE-N   89 (164)
T ss_pred             eeceeEEEEEeCCCCCHHHHHHHHHhcccCCCcccccccCCCEEEEEeCCcEEEcCCccCCCCCCCCcccCCc-cCCC-C
Confidence            6899999999999999999999999984  4      7999999999999999999965 5677888888765 5677 5


Q ss_pred             cCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEE
Q 046966           78 ADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTY  154 (299)
Q Consensus        78 ~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~  154 (299)
                      ..++|+++|+|+|++.++++++|||||++++ +++||++|+|||+|++||+||++|++.+++ +++|..+|+|.+|+
T Consensus        90 ~~~~h~~~G~lsma~~~~~~~~sqFfIt~~~-~~~Ld~~~tvFG~V~~G~dvl~~i~~~~~~-~~~P~~~i~I~~cG  164 (164)
T cd01926          90 FKLKHTGPGLLSMANAGPNTNGSQFFITTVK-TPWLDGKHVVFGKVVEGMDVVKKIENVGSG-NGKPKKKVVIADCG  164 (164)
T ss_pred             ccccCCCccEEEeeECCCCCcccEEEEEeCC-CCccCCcccEEEEEEEcHHHHHHHHcCCCC-CCCCcCCeEEEECC
Confidence            6789999999999999999999999999998 799999999999999999999999999998 89999999999996

This family represents the archetypal cystolic cyclophilin similar to human cyclophilins A, B and H. PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. These enzymes have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. As cyclophilins, Human hCyP-A, human cyclophilin-B (hCyP-19), S. cerevisiae Cpr1 and C. elegans Cyp-3, are inhibited by the immunosuppressive drug cyclopsporin A (CsA). CsA binds to the PPIase active site. Cyp-3. S. cerevisiae Cpr1 interacts with the Rpd3 - Sin3 complex and in addition is a component of the Set3 complex. S. cerevisiae Cpr1 has also been shown to have a role in Zpr1p nuclear transport. Human cyclophilin H associates with the [U4/U6.U5] tri-snRNP particles of the spl

>PTZ00060 cyclophilin; Provisional

Probab=100.00  E-value=1.6e-40  Score=273.28  Aligned_cols=146  Identities=40%  Similarity=0.700  Sum_probs=132.7

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhh---------CCCcCCceeeEeecCcEEEecCCC-CCCCCCCCCCCCccccccc
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCK---------NKYYNGCLFHNIHKDFIAQTGDPT-GTGTGGRSVYEDRFFVDEI   76 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~---------~~~y~~~~f~ri~~~~~iq~G~~~-~~~~~~~~~~~~~~~~~e~   76 (299)
                      |+.|+|+||||.+.||++|+||++||+         .++|+|+.||||+|+++|||||+. ..+.++.++|+.. +++| 
T Consensus        27 ~~~G~ivIeL~~d~aP~t~~nF~~L~~g~~~~~~g~~~~Y~~~~fhRvi~~~~iqgGd~~~~~g~~g~~~~g~~-~~~e-  104 (183)
T PTZ00060         27 APAGRIVFELFSDVTPKTAENFRALCIGDKVGSSGKNLHYKGSIFHRIIPQFMCQGGDITNHNGTGGESIYGRK-FTDE-  104 (183)
T ss_pred             EeCceEEEEEcCCCCcHHHHHHHHHhcCCcccccCcccccCCeEEEEEcCCCeEEeCCccCCCCCCCCcccccc-cCCc-
Confidence            678999999999999999999999997         458999999999999999999976 4577888888654 5677 


Q ss_pred             ccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEE
Q 046966           77 RADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVL  156 (299)
Q Consensus        77 ~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~  156 (299)
                      ...++|+.+|+|+|++.++++++|||||++.+ .++||++|+|||+|++||+||++|++..+ .+++|..+|+|.+|+++
T Consensus       105 ~~~~~h~~~G~lsma~~g~~~~~sqFfIt~~~-~~~Ldg~~tvFG~Vi~G~dvl~~I~~~~~-~~~~P~~~v~I~~cg~~  182 (183)
T PTZ00060        105 NFKLKHDQPGLLSMANAGPNTNGSQFFITTVP-CPWLDGKHVVFGKVIEGMEVVRAMEKEGT-QSGYPKKPVVVTDCGEL  182 (183)
T ss_pred             cccccCCCCCEEEeccCCCCCCcceEEEEeCC-CcccCCCccEEEEEEccHHHHHHHHccCC-CCCCCcCCeEEEEeEEc
Confidence            56788989999999999999999999999998 69999999999999999999999998877 57899999999999986

>cd01920 cyclophilin_EcCYP_like cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E

Probab=100.00  E-value=8e-40  Score=262.73  Aligned_cols=143  Identities=34%  Similarity=0.542  Sum_probs=122.9

Q ss_pred             EEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCCCCC
Q 046966            5 IETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKHDK   84 (299)
Q Consensus         5 ~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~   84 (299)
                      |+|+.|+|+||||++.||+||+||++||+.++|+++.||||+|+|++|||++...+.+..  ++ ..+.+|....+ |+.
T Consensus         2 l~T~~G~i~ieL~~~~aP~t~~nF~~L~~~g~Yd~~~fhRvi~~f~iQ~Gd~~~~~~~~~--~~-~~~~~e~~~~~-~~~   77 (155)
T cd01920           2 FQTSLGDIVVELYDDKAPITVENFLAYVRKGFYDNTIFHRVISGFVIQGGGFTPDLAQKE--TL-KPIKNEAGNGL-SNT   77 (155)
T ss_pred             cEecceeEEEEEeCCCCcHHHHHHHHHHhcCCCCCCEEEEEeCCcEEEeCCCCCCCCccc--cC-CcccCcccccc-cCC
Confidence            789999999999999999999999999999999999999999999999999876543321  22 23566644444 458


Q ss_pred             ceEEEEEcCC-CCCCcceEEEEecCCCCCCCC-----CceEEEEeecCHHHHHHHHhcccCCC----CCCceeEEEEE
Q 046966           85 VGTVGMASAG-RDLNASQFYITLRDNLHYLDE-----KHTIFGEVAEGLETLTRINQAVVDEE----NRPPQQIIIKQ  152 (299)
Q Consensus        85 ~G~l~~~~~~-~~~~~s~FfI~~~~~~~~ld~-----~~~vfG~V~~G~~vl~~i~~~~~~~~----~~p~~~v~I~~  152 (299)
                      +|+|+||+.+ +++++|||||++.+ .++||+     +|+|||+|++||+||++|++.+++..    +.|..+|.|.+
T Consensus        78 ~G~v~ma~~~~~~s~~SqFfI~~~~-~~~ld~~~~~~~ytvFG~V~eG~dvl~~I~~~~~~~~~~~~~~p~~~v~i~~  154 (155)
T cd01920          78 RGTIAMARTNAPDSATSQFFINLKD-NASLDYQNEQWGYTVFGEVTEGMDVVDKIAGVETYSFGSYQDVPVQDVIIES  154 (155)
T ss_pred             ceEEEECCCCCCCCccceEEEECCC-chhcCCcccCCCccEEEEEecCHHHHHHHHcCCccCCCCcCCCcCCCeEEEE
Confidence            9999999875 89999999999998 688985     79999999999999999999999764    68988888875

coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these have reduced affinity for cyclosporin A. E. coli cyclophilin A has a similar peptidylprolyl cis- trans isomerase activity to the human cyclophilin A. Most members of this subfamily contain a phenylalanine residue at the position equivalent to Human cyclophilin W121, where a tyrptophan has been shown to be important for cyclophilin binding.

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1e-39  Score=262.88  Aligned_cols=147  Identities=37%  Similarity=0.629  Sum_probs=135.8

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhCC---CcCCceeeEeecCcEEEecCCCC-CCCCCCCCCCCcccccccccCCCC
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKNK---YYNGCLFHNIHKDFIAQTGDPTG-TGTGGRSVYEDRFFVDEIRADLKH   82 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~~---~y~~~~f~ri~~~~~iq~G~~~~-~~~~~~~~~~~~~~~~e~~~~~~~   82 (299)
                      -..|||+++|..+..|+|++||..||++.   -|+|++||||+|.||+||||.+. +|+||.|||+.+ |.|| ++.|+|
T Consensus       148 ~~~Gri~~~lrtdv~Pmtaenfr~Lctge~gfgykgssfhriip~fmcqggdftn~ngtggksiygkk-fdde-nf~lkh  225 (298)
T KOG0111|consen  148 DRAGRIVMLLRTDVVPMTAENFRCLCTGEAGFGYKGSSFHRIIPKFMCQGGDFTNGNGTGGKSIYGKK-FDDE-NFTLKH  225 (298)
T ss_pred             cccceEEEeecccCChhhhhhhhhhccccCccCccccchhhhhhhhhccCCccccCCCCCCccccccc-cccc-ceeeec
Confidence            45799999999999999999999999763   39999999999999999999874 599999999988 5888 889999


Q ss_pred             CCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEEC
Q 046966           83 DKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY  157 (299)
Q Consensus        83 ~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~~  157 (299)
                      ..+|+||||++|+|+||||||||+.. ..|||++|+|||.|++||+||+++++. ..++|+|.+.|+|..|+.++
T Consensus       226 t~pgtlsmansgantngsqffict~k-tdwldgkhvvfghv~eg~~vvrq~e~q-gsksgkp~qkv~i~~cge~~  298 (298)
T KOG0111|consen  226 TMPGTLSMANSGANTNGSQFFICTEK-TDWLDGKHVVFGHVVEGMNVVRQVEQQ-GSKSGKPQQKVKIVECGEIE  298 (298)
T ss_pred             CCCceeeccccCCCCCCceEEEEecc-cccccCceeEEeeecchHHHHHHHHhc-cCCCCCcceEEEEEeccccC
Confidence            99999999999999999999999986 799999999999999999999999665 45899999999999998753

>cd00317 cyclophilin cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases

Probab=100.00  E-value=1.4e-38  Score=254.53  Aligned_cols=146  Identities=41%  Similarity=0.684  Sum_probs=131.8

Q ss_pred             EEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCCCC
Q 046966            4 LIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKHD   83 (299)
Q Consensus         4 ~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~~~   83 (299)
                      +++|+.|+|+|+||++.||++|+||++||++++|+++.|||++|++++|||++...+..+ +.++ ..+++|......|+
T Consensus         1 ~~~T~~G~i~IeL~~~~~P~~~~nF~~l~~~~~Y~~~~f~rv~~~~~iq~Gd~~~~~~~~-~~~~-~~~~~E~~~~~~~~   78 (146)
T cd00317           1 TLDTTKGRIVIELYGDEAPKTVENFLSLARGGFYDGTTFHRVIPGFMIQGGDPTGTGGGG-SGPG-YKFPDENFPLKYHH   78 (146)
T ss_pred             CeEeccCcEEEEEcCCCChHHHHHHHHHHhcCCcCCCEEEEEeCCCeEEECCCCCCCCCC-CcCC-CccCCccccCcCcC
Confidence            478999999999999999999999999999999999999999999999999987664432 2233 34788877777688


Q ss_pred             CceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEE
Q 046966           84 KVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQ  152 (299)
Q Consensus        84 ~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~  152 (299)
                      ++|+|+|++.++++++|||||++.+ .++||++|+|||+|++||++|++|+..+++++++|..+|+|..
T Consensus        79 ~~G~v~~~~~~~~~~~sqF~Itl~~-~~~ld~~~~vfG~V~~G~~vl~~I~~~~~~~~~~P~~~i~I~~  146 (146)
T cd00317          79 RRGTLSMANAGPNTNGSQFFITTAP-TPHLDGKHTVFGKVVEGMDVVDKIERGDTDENGRPIKPVTISD  146 (146)
T ss_pred             CCcEEEEeeCCCCCcccEEEEECCC-CcccCCCceEEEEEeCCHHHHHHHHcCCCCCCCcCcCceEEeC
Confidence            9999999999999999999999998 7999999999999999999999999999999999999999863

This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA). Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin. PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system; human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP

>PF00160 Pro_isomerase: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD; InterPro: IPR002130 Cyclophilin [] is the major high-affinity binding protein in vertebrates for the immunosuppressive drug cyclosporin A (CSA), but is also found in other organisms

Probab=100.00  E-value=6.7e-38  Score=253.09  Aligned_cols=150  Identities=47%  Similarity=0.729  Sum_probs=130.5

Q ss_pred             EEEEEEc-ceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCC-CCCCCccccccccc-
Q 046966            2 SVLIETS-LGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGR-SVYEDRFFVDEIRA-   78 (299)
Q Consensus         2 ~v~~~T~-~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~-~~~~~~~~~~e~~~-   78 (299)
                      .|.|+|+ +|+|+||||++.||++|+||++||+.++|+|+.|||++|++++|+|++...+..+. ....+..+++|... 
T Consensus         1 ~~~i~t~~~G~i~ieL~~~~aP~~~~nF~~l~~~~~y~g~~f~ri~~~~~i~~G~~~~~~~~~~~~~~~~~~~~~E~~~~   80 (155)
T PF00160_consen    1 FVDIETSGLGRIVIELFGDEAPKTVENFLRLCTSGFYDGTKFHRIIPNFVIQGGDPTGNGGYGREDSTGGEPIPDEFNPS   80 (155)
T ss_dssp             EEEEEETTEEEEEEEEETTTSHHHHHHHHHHHHTTSSTTEBEEEEETTTEEEESSTTTSSSSTSEEBTTBSCBSSSGBTT
T ss_pred             CEEEEeCCccCEEEEEeCCCCcHHHHhhehhhcccccCCceeecccccceeeeeeccCCCCcccccccCccccccccccc
Confidence            3789997 99999999999999999999999999999999999999999999999876544211 11122347888653 


Q ss_pred             CCCCCCceEEEEEcCC--CCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEE
Q 046966           79 DLKHDKVGTVGMASAG--RDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYV  155 (299)
Q Consensus        79 ~~~~~~~G~l~~~~~~--~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v  155 (299)
                      .+.| .+|+|+|++.+  +++++|||||+|.+ .++||++|+|||+|++||++|++|++.+++.  +|.++|+|.+|+|
T Consensus        81 ~~~~-~~G~v~~~~~~~~~~~~~sqF~I~l~~-~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~--~p~~~v~I~~cgv  155 (155)
T PF00160_consen   81 LLKH-RRGLVSMARSGKDPNSNGSQFFITLSD-APHLDGKYTVFGRVIEGMDVLDKIEAGPTDE--RPKQDVTISSCGV  155 (155)
T ss_dssp             SSSS-STTEEEEEBSSSSTTEBSSEEEEESSC-GGGGTTTSEEEEEEEEHHHHHHHHHTSBBTT--EBSSTEEEEEEEE
T ss_pred             cccc-cceeeeecccccCCCCCCceEEeeccC-CCccccceeeeeEEehhHHHHHHHHCCCCCC--ccCCCeEEEEeEC
Confidence            4555 99999999986  78899999999998 6899999999999999999999999998876  9999999999997

It exhibits a peptidyl-prolyl cis-trans isomerase activity (5.2.1.8 from EC) (PPIase or rotamase). PPIase is an enzyme that accelerates protein folding by catalysing the cis-trans isomerisation of proline imidic peptide bonds in oligopeptides []. It is probable that CSA mediates some of its effects via an forming a tight complex with cyclophilin that inhibits the phosphatase activity of calcineurin [], []. Cyclophilin A is a cytosolic and highly abundant protein. The protein belongs to a family of isozymes, including cyclophilins B and C, and natural killer cell cyclophilin-related protein [, , ]. Major isoforms have been found throughout the cell, including the ER, and some are even secreted. The sequences of the different forms of cyclophilin-type PPIases are well conserved. Note: FKBP's, a family of proteins that bind the immunosuppressive drug FK506, are also PPIases, but their sequence is not at all related to that of cyclophilin (see IPR001179 from INTERPRO).; GO: 0003755 peptidyl-prolyl cis-trans isomerase activity, 0006457 protein folding; PDB: 1Z81_A 1IHG_A 1IIP_A 3PMP_B 3O7T_A 2B71_A 1QNG_A 1QNH_A 2HQJ_A 2RMC_G ....

>cd01924 cyclophilin_TLP40_like cyclophilin_TLP40_like: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) similar ot the Spinach thylakoid lumen protein TLP40

Probab=100.00  E-value=4.7e-37  Score=250.78  Aligned_cols=131  Identities=31%  Similarity=0.535  Sum_probs=110.3

Q ss_pred             EEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCC---------------------CC
Q 046966            6 ETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTG---------------------GR   64 (299)
Q Consensus         6 ~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~---------------------~~   64 (299)
                      .|++|+|+|+||++.||+||+||++||+.++|+++.||||+++|++||||+...+.+                     +.
T Consensus         3 ~T~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Ydg~~FhRVi~~fviQgGdp~~~~~~~~~~~~~~~~~~p~e~~~~~~~~   82 (176)
T cd01924           3 ATDNGTITIVLDGYNAPVTAGNFVDLVERGFYDGMEFHRVEGGFVVQTGDPQGKNPGFPDPETGKSRTIPLEIKPEGQKQ   82 (176)
T ss_pred             ccccceEEEEEcCCCCCHHHHHHHHHHHhCCcCCCEEEEecCCcEEEecCCCCCCCCcccccccccccccceecccCCCC
Confidence            589999999999999999999999999999999999999999999999998765322                     22


Q ss_pred             CCCCCccc---ccccccCCCCCCceEEEEEcCC--CCCCcceEEEEecC------CCCCCCCCceEEEEeecCHHHHHHH
Q 046966           65 SVYEDRFF---VDEIRADLKHDKVGTVGMASAG--RDLNASQFYITLRD------NLHYLDEKHTIFGEVAEGLETLTRI  133 (299)
Q Consensus        65 ~~~~~~~~---~~e~~~~~~~~~~G~l~~~~~~--~~~~~s~FfI~~~~------~~~~ld~~~~vfG~V~~G~~vl~~i  133 (299)
                      ++|+..+.   .++....+.|+.+|+|+||+.+  +++++|||||++++      .+++||++|+|||+|++||+||++|
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~G~laMa~~~~~~ns~~SQFfI~~~~~~~~~~~~~~Ldg~ytVFG~VveG~dvl~~I  162 (176)
T cd01924          83 PVYGKTLEEAGRYDEQPVLPFNAFGAIAMARTEFDPNSASSQFFFLLKDNELTPSRNNVLDGRYAVFGYVTDGLDILREL  162 (176)
T ss_pred             CccCcccccccccccccccccCCCCeEEEccCCCCCCCccceEEEEeccccccCCCCCccCCCceEEEEEecCHHHHHhh
Confidence            34432211   0222455778899999999987  69999999999994      4799999999999999999999999


Q ss_pred             Hhc
Q 046966          134 NQA  136 (299)
Q Consensus       134 ~~~  136 (299)
                      +..
T Consensus       163 ~~g  165 (176)
T cd01924         163 KVG  165 (176)
T ss_pred             cCC
Confidence            644

Compared to the archetypal cyclophilin Human cyclophilin A, these proteins have similar peptidylprolyl cis- trans isomerase activity and reduced affinity for cyclosporin A. Spinach TLP40 has been shown to have a dual function as a folding catalyst and regulator of dephosphorylation.

>KOG0865 consensus Cyclophilin type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.97  E-value=1.2e-31  Score=213.57  Aligned_cols=146  Identities=39%  Similarity=0.685  Sum_probs=132.7

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhCC---CcCCceeeE---eecCcEEEecCCC-CCCCCCCCCCCCcccccccccC
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKNK---YYNGCLFHN---IHKDFIAQTGDPT-GTGTGGRSVYEDRFFVDEIRAD   79 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~~---~y~~~~f~r---i~~~~~iq~G~~~-~~~~~~~~~~~~~~~~~e~~~~   79 (299)
                      +++|++.++||.+..|+|++||..||++.   -|++..|||   .+++|++||||.+ .++++|.++|+++| +|| ++.
T Consensus        15 ~p~gr~~~~l~ad~~Pktaenf~al~tgekg~~yk~s~fhr~~~~~~~fm~qggDft~hngtggkSiy~ekF-~De-nFi   92 (167)
T KOG0865|consen   15 EPLGRIVFELFADKIPKTAENFRALCTGEKGFGYKGSCFHRLIPIIPGFMCQGGDFTCHNGTGGKSIYGEKF-DDE-NFI   92 (167)
T ss_pred             ccccccceecccccCcchHhhhhhcccCCCccccccchhhhccccccceeeccCcccccCCccceEeccccc-CCc-CcE
Confidence            78999999999999999999999999853   399999999   3457999999975 55999999999885 888 899


Q ss_pred             CCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEE
Q 046966           80 LKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVL  156 (299)
Q Consensus        80 ~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~  156 (299)
                      ++|..+|+|+|||.+||+|+||||||+.. ..|||++|+|||+|.+||+++++|+. -..+++++..+|.|.+|+.+
T Consensus        93 lkhtgpGiLSmaNagpntngsqffictak-tewLdgkhVVfGkv~eGm~iv~a~e~-~gs~~gk~~~~i~i~dcg~l  167 (167)
T KOG0865|consen   93 LKHTGPGILSMANAGPNTNGSQFFICTAK-TEWLDGKHVVFGKVKEGMDIVEAMER-FGSRNGKTSKKITIADCGQL  167 (167)
T ss_pred             EecCCCCeeehhhcCCCccccEEEEEccc-cccccCceeEcCceEcccchhhhhhc-cCCcCCcccccEEEecCCcC
Confidence            99999999999999999999999999997 59999999999999999999999966 55678999999999999853

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

Probab=99.75  E-value=1.4e-17  Score=132.02  Aligned_cols=85  Identities=29%  Similarity=0.436  Sum_probs=80.8

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ....++|||+|||+++++++|+++|++||.|.++.++.++.+++++|||||+|.+.++|++|++.||+..|+|+.|+|++
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            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCcc
Q 046966          288 SQSVS  292 (299)
Q Consensus       288 a~~~~  292 (299)
                      +.++.
T Consensus       111 a~~~~  115 (144)
T PLN03134        111 ANDRP  115 (144)
T ss_pred             CCcCC
Confidence            98664

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.67  E-value=5.1e-16  Score=141.62  Aligned_cols=84  Identities=26%  Similarity=0.476  Sum_probs=79.9

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      .+.+|||+|||+.+++++|+++|++||.|.++++++++.++.++|||||+|.+.++|.+|+..|||..++||.|+|.|+.
T Consensus       268 ~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~  347 (352)
T TIGR01661       268 AGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKT  347 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcc
Confidence            34579999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             Cccc
Q 046966          290 SVSK  293 (299)
Q Consensus       290 ~~~~  293 (299)
                      ++.+
T Consensus       348 ~~~~  351 (352)
T TIGR01661       348 NKAY  351 (352)
T ss_pred             CCCC
Confidence            8754

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.62  E-value=2.2e-15  Score=137.43  Aligned_cols=83  Identities=28%  Similarity=0.495  Sum_probs=79.6

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      +..+|||+|||+.+++++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|++|++.|||..+.|+.|.|.+++
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            46899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             Ccc
Q 046966          290 SVS  292 (299)
Q Consensus       290 ~~~  292 (299)
                      +..
T Consensus        82 ~~~   84 (352)
T TIGR01661        82 PSS   84 (352)
T ss_pred             ccc
Confidence            764

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

>PF00076 RRM_1: RNA recognition motif

Probab=99.62  E-value=4.9e-15  Score=102.59  Aligned_cols=70  Identities=41%  Similarity=0.685  Sum_probs=67.3

Q ss_pred             EEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 046966          214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC  284 (299)
Q Consensus       214 v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~  284 (299)
                      |||+|||+++++++|+++|++||.+..+.+..+ .++..+|+|||+|.+.++|++|++.|+|..++|+.|+
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 6899999999999999999999999999999999985

(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 ....

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.61  E-value=4e-15  Score=126.04  Aligned_cols=91  Identities=34%  Similarity=0.532  Sum_probs=85.3

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .|-+||||+.|+++++|..|+..|+.||.|+.++|+.+..||+++|||||+|.+..+.+.|.+..+|..|+|+.|.|++.
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            67889999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCc-ccccccCC
Q 046966          289 QSV-SKIWKKSY  299 (299)
Q Consensus       289 ~~~-~~~~~~~~  299 (299)
                      +.+ -+.|..+|
T Consensus       179 RgRTvkgW~PRR  190 (335)
T KOG0113|consen  179 RGRTVKGWLPRR  190 (335)
T ss_pred             cccccccccccc
Confidence            876 35677654

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.61  E-value=3.7e-15  Score=134.41  Aligned_cols=84  Identities=27%  Similarity=0.504  Sum_probs=80.2

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ....++|||+|||+++++++|+++|+.||.|.+|+|+.++.+++++|||||+|.+.++|++|++.|++..+.+++|+|.+
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            45689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCc
Q 046966          288 SQSV  291 (299)
Q Consensus       288 a~~~  291 (299)
                      +++.
T Consensus       184 a~p~  187 (346)
T TIGR01659       184 ARPG  187 (346)
T ss_pred             cccc
Confidence            8764

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).

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.61  E-value=4.1e-15  Score=122.72  Aligned_cols=84  Identities=27%  Similarity=0.437  Sum_probs=80.8

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ....++|-|.||+.+++|++|+++|.+||.|.++.|.+|+.||.++|||||.|.+.++|.+|+..|||+-++.-.|+|+|
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEw  265 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEW  265 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEe
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCc
Q 046966          288 SQSV  291 (299)
Q Consensus       288 a~~~  291 (299)
                      ++|+
T Consensus       266 skP~  269 (270)
T KOG0122|consen  266 SKPS  269 (270)
T ss_pred             cCCC
Confidence            9986

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.55  E-value=7.7e-15  Score=120.68  Aligned_cols=78  Identities=35%  Similarity=0.492  Sum_probs=72.2

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      -++||||+|+|.+..+.|+++|++||+|+++.++.|+.+|+++|||||+|.+.++|.+|++. ..-.|+||+..+.+|-
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            46899999999999999999999999999999999999999999999999999999999976 4567999998888765

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.53  E-value=2.1e-14  Score=108.07  Aligned_cols=82  Identities=26%  Similarity=0.406  Sum_probs=78.4

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .-.++.|||.+++..++++++.+.|..||+|+.+.+..|+.||..+|||+|+|.+.+.|++|+..|||..|.|+.|.|+|
T Consensus        69 SVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw  148 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDW  148 (170)
T ss_pred             ceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEE
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cC
Q 046966          288 SQ  289 (299)
Q Consensus       288 a~  289 (299)
                      +=
T Consensus       149 ~F  150 (170)
T KOG0130|consen  149 CF  150 (170)
T ss_pred             EE
Confidence            65

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.53  E-value=1.4e-13  Score=95.55  Aligned_cols=70  Identities=34%  Similarity=0.624  Sum_probs=64.8

Q ss_pred             EEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 046966          214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC  284 (299)
Q Consensus       214 v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~  284 (299)
                      |||+|||+++++++|.++|+.||.|..+.+..++. +..+|+|||+|.+.++|.+|+..+++..++|+.|+
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            79999999999999999999999999999999866 89999999999999999999999999999999875

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.52  E-value=3.9e-14  Score=121.49  Aligned_cols=81  Identities=23%  Similarity=0.407  Sum_probs=75.7

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ..+++|+|+|+|+...+-||+.+|++||.|.+|.|+.+  ..-+||||||+|++.++|++|-+.|||..+.||+|.|..|
T Consensus        94 ~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~A  171 (376)
T KOG0125|consen   94 DTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNA  171 (376)
T ss_pred             CCCceeEeecCCccccCccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEecc
Confidence            45789999999999999999999999999999999997  3458999999999999999999999999999999999999


Q ss_pred             CCc
Q 046966          289 QSV  291 (299)
Q Consensus       289 ~~~  291 (299)
                      ..+
T Consensus       172 Tar  174 (376)
T KOG0125|consen  172 TAR  174 (376)
T ss_pred             chh
Confidence            875

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

Probab=99.52  E-value=5e-14  Score=117.28  Aligned_cols=89  Identities=26%  Similarity=0.442  Sum_probs=83.0

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ......+.|..||.++++++++.+|+..|+|++|++++|+.+|++.|||||.|-++++|++|+..|||..+..+.|+|.|
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            34567799999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCcccccc
Q 046966          288 SQSVSKIWK  296 (299)
Q Consensus       288 a~~~~~~~~  296 (299)
                      |+|.+..++
T Consensus       118 ARPSs~~Ik  126 (360)
T KOG0145|consen  118 ARPSSDSIK  126 (360)
T ss_pred             ccCChhhhc
Confidence            999765443

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.52  E-value=7.6e-14  Score=125.94  Aligned_cols=84  Identities=33%  Similarity=0.554  Sum_probs=78.0

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEe
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDD--RRICVDF  287 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g--~~l~v~~  287 (299)
                      ..++|||+|||+.+++++|+++|++||.|..++++.++.+++++|||||+|.+.++|++|++.||+..+.+  ++|.|++
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            35789999999999999999999999999999999998899999999999999999999999999998875  7899999


Q ss_pred             cCCccc
Q 046966          288 SQSVSK  293 (299)
Q Consensus       288 a~~~~~  293 (299)
                      +....+
T Consensus       272 a~~~~~  277 (346)
T TIGR01659       272 AEEHGK  277 (346)
T ss_pred             CCcccc
Confidence            987543

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).

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

Probab=99.51  E-value=4.8e-14  Score=134.16  Aligned_cols=82  Identities=26%  Similarity=0.364  Sum_probs=77.7

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ...++|||+|||+.+++++|+++|.+||.|.+|++++|+.+++++|||||+|.+.++|++|++.|||..++||.|+|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999875


Q ss_pred             CC
Q 046966          289 QS  290 (299)
Q Consensus       289 ~~  290 (299)
                      ..
T Consensus       185 ~~  186 (612)
T TIGR01645       185 SN  186 (612)
T ss_pred             cc
Confidence            53

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=99.50  E-value=9.9e-14  Score=132.01  Aligned_cols=81  Identities=20%  Similarity=0.341  Sum_probs=78.0

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      .++|||+|||+++++++|+++|+.||.|.++++.+++.+++++|||||+|.+.++|.+|++.||+..++|+.|+|.++.+
T Consensus       204 ~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~  283 (612)
T TIGR01645       204 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  283 (612)
T ss_pred             cceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCC
Confidence            57899999999999999999999999999999999988999999999999999999999999999999999999999885


Q ss_pred             c
Q 046966          291 V  291 (299)
Q Consensus       291 ~  291 (299)
                      +
T Consensus       284 p  284 (612)
T TIGR01645       284 P  284 (612)
T ss_pred             C
Confidence            4

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

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

Probab=99.49  E-value=1.1e-13  Score=123.13  Aligned_cols=88  Identities=23%  Similarity=0.378  Sum_probs=82.6

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC-CeEEEEEe
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID-DRRICVDF  287 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~-g~~l~v~~  287 (299)
                      +.+|.||||.||.++.|++|..+|++.|.|-.++|+.|+.+|.+||||||.|.+.+.|+.|++.||+++|. |+.|.|+.
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            56889999999999999999999999999999999999999999999999999999999999999999986 99999999


Q ss_pred             cCCcccccc
Q 046966          288 SQSVSKIWK  296 (299)
Q Consensus       288 a~~~~~~~~  296 (299)
                      +....|+..
T Consensus       161 Svan~RLFi  169 (506)
T KOG0117|consen  161 SVANCRLFI  169 (506)
T ss_pred             eeecceeEe
Confidence            887776643

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.49  E-value=1.2e-13  Score=108.74  Aligned_cols=81  Identities=26%  Similarity=0.399  Sum_probs=74.2

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .+..++||||||+..+++.+|+..|..||.+.++.|-..     ..|||||+|++..+|+.|+..|+|..|.|..|+|++
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            355899999999999999999999999999999987654     468999999999999999999999999999999999


Q ss_pred             cCCccc
Q 046966          288 SQSVSK  293 (299)
Q Consensus       288 a~~~~~  293 (299)
                      ++...+
T Consensus        82 S~G~~r   87 (195)
T KOG0107|consen   82 STGRPR   87 (195)
T ss_pred             ecCCcc
Confidence            987654

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.48  E-value=1e-13  Score=103.56  Aligned_cols=81  Identities=23%  Similarity=0.359  Sum_probs=76.7

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      .+++||||||++.++|++|.++|+++|.|..+-+=.|+.+....||+||+|.+.++|..|++.++++.++.+.|+++|.-
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            47999999999999999999999999999999888888888899999999999999999999999999999999999865


Q ss_pred             C
Q 046966          290 S  290 (299)
Q Consensus       290 ~  290 (299)
                      .
T Consensus       115 G  115 (153)
T KOG0121|consen  115 G  115 (153)
T ss_pred             c
Confidence            3

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.46  E-value=3.3e-13  Score=114.70  Aligned_cols=76  Identities=18%  Similarity=0.277  Sum_probs=70.6

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      .++|||+|||+.+++++|+++|+.||.|.++.|+.++.   .+|||||+|.+.++|+.|+ .|+|..|.|+.|.|..+..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~Al-lLnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETAL-LLSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHH-HhcCCeeCCceEEEEeccC
Confidence            57999999999999999999999999999999998853   4689999999999999999 5999999999999999873

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.45  E-value=8.3e-14  Score=112.29  Aligned_cols=81  Identities=31%  Similarity=0.414  Sum_probs=77.4

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      .-..|-|-||.+-++.++|..+|++||.|-.|.|++|+.|+.++|||||-|....+|+.|+.+|+|.+|+|+.|.|++|+
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             C
Q 046966          290 S  290 (299)
Q Consensus       290 ~  290 (299)
                      -
T Consensus        92 y   92 (256)
T KOG4207|consen   92 Y   92 (256)
T ss_pred             c
Confidence            3

>PLN03213 repressor of silencing 3; Provisional

Probab=99.45  E-value=3e-13  Score=121.74  Aligned_cols=79  Identities=23%  Similarity=0.368  Sum_probs=73.2

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCH--HHHHHHHHHhCCceeCCeEEEEE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKR--EACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~--~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ....+||||||++.+++++|...|+.||.|.++.|++  .+|  ||||||+|...  .++.+|+..|||..+.|+.|+|.
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            3468999999999999999999999999999999994  577  89999999987  68999999999999999999999


Q ss_pred             ecCCc
Q 046966          287 FSQSV  291 (299)
Q Consensus       287 ~a~~~  291 (299)
                      .|++.
T Consensus        84 KAKP~   88 (759)
T PLN03213         84 KAKEH   88 (759)
T ss_pred             eccHH
Confidence            99985

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

Probab=99.45  E-value=1.7e-13  Score=114.72  Aligned_cols=82  Identities=33%  Similarity=0.564  Sum_probs=77.9

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      -.-+||+-|...++-++|++.|.+||+|.++++++|..|++++|||||.|.+.++|++||..|||..|++|.|+-.||.-
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            35699999999999999999999999999999999999999999999999999999999999999999999999999875


Q ss_pred             cc
Q 046966          291 VS  292 (299)
Q Consensus       291 ~~  292 (299)
                      +.
T Consensus       142 Kp  143 (321)
T KOG0148|consen  142 KP  143 (321)
T ss_pred             Cc
Confidence            43

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.44  E-value=7.2e-14  Score=113.63  Aligned_cols=84  Identities=27%  Similarity=0.417  Sum_probs=80.7

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ...++||||+|...+++.-|...|-+||.|..+.++.|..++++||||||+|...++|.+|+..||+.+|.||.|+|.+|
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcc
Q 046966          289 QSVS  292 (299)
Q Consensus       289 ~~~~  292 (299)
                      +|.+
T Consensus        88 kP~k   91 (298)
T KOG0111|consen   88 KPEK   91 (298)
T ss_pred             CCcc
Confidence            9864

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

Probab=99.44  E-value=4.1e-13  Score=127.56  Aligned_cols=86  Identities=23%  Similarity=0.343  Sum_probs=77.6

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC-CeEEEEEe
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID-DRRICVDF  287 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~-g~~l~v~~  287 (299)
                      ...++|||+|||++++|++|+++|++||.|.+++|++| .+|+++|||||+|.+.++|++|++.||+..+. |+.|.|..
T Consensus        56 ~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~  134 (578)
T TIGR01648        56 GRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCI  134 (578)
T ss_pred             CCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccc
Confidence            34689999999999999999999999999999999999 79999999999999999999999999999985 88888887


Q ss_pred             cCCccccc
Q 046966          288 SQSVSKIW  295 (299)
Q Consensus       288 a~~~~~~~  295 (299)
                      +....+++
T Consensus       135 S~~~~rLF  142 (578)
T TIGR01648       135 SVDNCRLF  142 (578)
T ss_pred             cccCceeE
Confidence            76544443

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.

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

Probab=99.43  E-value=7.4e-13  Score=128.15  Aligned_cols=78  Identities=32%  Similarity=0.494  Sum_probs=75.4

Q ss_pred             eEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       213 ~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      +|||+|||+++++++|+++|++||.|.+|++.+|..+++++|||||+|.+.++|++|+..||+..+.|+.|+|.|+..
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~~   79 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQR   79 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccc
Confidence            699999999999999999999999999999999998999999999999999999999999999999999999999763

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

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

Probab=99.42  E-value=1.1e-12  Score=125.39  Aligned_cols=83  Identities=18%  Similarity=0.338  Sum_probs=78.7

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .+..+|||+|||+.+++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|..|+..|+|..|+|+.|.|.++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             CCc
Q 046966          289 QSV  291 (299)
Q Consensus       289 ~~~  291 (299)
                      ...
T Consensus       373 ~~~  375 (509)
T TIGR01642       373 CVG  375 (509)
T ss_pred             ccC
Confidence            754

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

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

Probab=99.42  E-value=1.1e-12  Score=123.96  Aligned_cols=80  Identities=29%  Similarity=0.439  Sum_probs=77.1

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ..++|||+|||..+++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|.+|+..|+|..|.|+.|.|.++.
T Consensus       185 ~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            37899999999999999999999999999999999998889999999999999999999999999999999999999976

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.

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

Probab=99.42  E-value=8e-13  Score=127.93  Aligned_cols=83  Identities=27%  Similarity=0.452  Sum_probs=78.9

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ....+|||+||++.+++++|+++|++||.|.+++++.+ .+|+++|||||.|.+.++|.+|+..|||..++|++|.|.+|
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 68999999999999999999999999999999999999999


Q ss_pred             CCcc
Q 046966          289 QSVS  292 (299)
Q Consensus       289 ~~~~  292 (299)
                      ..+.
T Consensus       362 ~~k~  365 (562)
T TIGR01628       362 QRKE  365 (562)
T ss_pred             cCcH
Confidence            9764

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

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.41  E-value=5.2e-14  Score=111.26  Aligned_cols=80  Identities=28%  Similarity=0.436  Sum_probs=76.0

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      .+.-|||||||+..||.||.-+|++||+|+.+.+++|+.||+++||||+-|.+-.+---|+..|||..|.||.|+|++.-
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            46789999999999999999999999999999999999999999999999999988888999999999999999999754

>smart00362 RRM_2 RNA recognition motif

Probab=99.38  E-value=2.9e-12  Score=88.21  Aligned_cols=72  Identities=40%  Similarity=0.636  Sum_probs=67.1

Q ss_pred             eEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       213 ~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      +|||+|||..+++++|+++|.+||.+..+.+..++  +.++|+|||+|.+.++|++|++.+++..+.|+.|.|+
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            58999999999999999999999999999988775  7788999999999999999999999999999998873

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

Probab=99.38  E-value=3.7e-12  Score=106.23  Aligned_cols=84  Identities=24%  Similarity=0.450  Sum_probs=79.7

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ..+++|||-||.++++|.-|+.+|++||.|..+++++|..|.+++|||||.+.+.++|..|+..|||+.+++|.|.|.|.
T Consensus       276 ~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFK  355 (360)
T KOG0145|consen  276 GGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFK  355 (360)
T ss_pred             CCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEe
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCcc
Q 046966          289 QSVS  292 (299)
Q Consensus       289 ~~~~  292 (299)
                      .++.
T Consensus       356 tnk~  359 (360)
T KOG0145|consen  356 TNKA  359 (360)
T ss_pred             cCCC
Confidence            7653

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.37  E-value=3.9e-12  Score=106.53  Aligned_cols=76  Identities=30%  Similarity=0.440  Sum_probs=69.6

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      .+++|||+||++.+++++|+++|+.||.|.+|+|+++.   ..+|||||+|.+.++++.|+ .|+|..|.+++|.|....
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAV-LLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEEeCc
Confidence            46899999999999999999999999999999999884   44579999999999999999 789999999999998744

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

Probab=99.37  E-value=3.7e-12  Score=120.28  Aligned_cols=81  Identities=30%  Similarity=0.385  Sum_probs=76.4

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .+.++|||+|||+.+++++|+++|++||.|..|+++.++.+++++|||||+|.+.++|.+|+. |+|..+.|++|.|..+
T Consensus        87 ~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~  165 (457)
T TIGR01622        87 RDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSS  165 (457)
T ss_pred             cCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeec
Confidence            457899999999999999999999999999999999999999999999999999999999995 8999999999999987


Q ss_pred             CC
Q 046966          289 QS  290 (299)
Q Consensus       289 ~~  290 (299)
                      ..
T Consensus       166 ~~  167 (457)
T TIGR01622       166 QA  167 (457)
T ss_pred             ch
Confidence            64

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.

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

Probab=99.36  E-value=9.3e-13  Score=104.35  Aligned_cols=82  Identities=29%  Similarity=0.365  Sum_probs=78.6

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .....+|||+||+..++++.|.++|-+.|+|..+.+++|+.++..+||||++|.+.++|+-|++.||...+.||+|+|..
T Consensus         6 rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~k   85 (203)
T KOG0131|consen    6 RNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNK   85 (203)
T ss_pred             cCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEe
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cC
Q 046966          288 SQ  289 (299)
Q Consensus       288 a~  289 (299)
                      +.
T Consensus        86 as   87 (203)
T KOG0131|consen   86 AS   87 (203)
T ss_pred             cc
Confidence            77

>smart00360 RRM RNA recognition motif

Probab=99.35  E-value=4.3e-12  Score=87.01  Aligned_cols=71  Identities=39%  Similarity=0.617  Sum_probs=66.5

Q ss_pred             EEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          216 VCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       216 v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      |+|||..+++++|+.+|++||.+..+.+..++.++.++|+|||+|.+.++|.+|+..|++..++|+.|.|+
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            57899999999999999999999999999887788999999999999999999999999999999998873

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

Probab=99.34  E-value=5.5e-12  Score=105.81  Aligned_cols=79  Identities=25%  Similarity=0.482  Sum_probs=73.5

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ..+.+++||+||++.-++|++|++.|++||.|.+|++.++      +||+||.|.+.++|.+||..||+.+++|+.+++.
T Consensus       160 ssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCs  233 (321)
T KOG0148|consen  160 SSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCS  233 (321)
T ss_pred             CCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEe
Confidence            3467899999999999999999999999999999999887      4899999999999999999999999999999999


Q ss_pred             ecCCc
Q 046966          287 FSQSV  291 (299)
Q Consensus       287 ~a~~~  291 (299)
                      |-+..
T Consensus       234 WGKe~  238 (321)
T KOG0148|consen  234 WGKEG  238 (321)
T ss_pred             ccccC
Confidence            97753

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

Probab=99.33  E-value=1.4e-12  Score=109.15  Aligned_cols=86  Identities=29%  Similarity=0.477  Sum_probs=82.6

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ..+.+|.|||-.||.+..+.+|..+|-.||.|.+.++..|+.|.++++||||.|.+..+++.||..|||+.|+-++|+|+
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQ  360 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ  360 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhh
Confidence            34779999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCcc
Q 046966          287 FSQSVS  292 (299)
Q Consensus       287 ~a~~~~  292 (299)
                      +.+|+.
T Consensus       361 LKRPkd  366 (371)
T KOG0146|consen  361 LKRPKD  366 (371)
T ss_pred             hcCccc
Confidence            999875

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.32  E-value=3.5e-12  Score=116.97  Aligned_cols=81  Identities=28%  Similarity=0.471  Sum_probs=78.9

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCCc
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSV  291 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~~  291 (299)
                      +.+||||+|+++++++|..+|+..|.|.+++++.|+.||+.+||||++|.+.+.|.+|++.|||.++.||+|+|.|+...
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            89999999999999999999999999999999999999999999999999999999999999999999999999998865


Q ss_pred             c
Q 046966          292 S  292 (299)
Q Consensus       292 ~  292 (299)
                      +
T Consensus        99 ~   99 (435)
T KOG0108|consen   99 K   99 (435)
T ss_pred             c
Confidence            4

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

Probab=99.32  E-value=7.7e-12  Score=114.01  Aligned_cols=83  Identities=31%  Similarity=0.468  Sum_probs=77.0

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      +.++|.|.|||+.+.+.+|+.+|+.||.|..+.|++.+ .|+.+|||||+|....+|..|++.+|+.+|+||+|.|+||-
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~-dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV  194 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKK-DGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAV  194 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCC-CCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeec
Confidence            47899999999999999999999999999999999775 55666999999999999999999999999999999999999


Q ss_pred             Cccc
Q 046966          290 SVSK  293 (299)
Q Consensus       290 ~~~~  293 (299)
                      ++..
T Consensus       195 ~Kd~  198 (678)
T KOG0127|consen  195 DKDT  198 (678)
T ss_pred             cccc
Confidence            8753

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.32  E-value=8.2e-12  Score=108.83  Aligned_cols=79  Identities=38%  Similarity=0.584  Sum_probs=76.7

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      .++|||+|||+.+++++|.++|.+||.+..+.+..++.+++++|||||.|.+.++|..|+..+++..+.|++|.|.++.
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~  193 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQ  193 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccc
Confidence            6999999999999999999999999999999999998899999999999999999999999999999999999999965

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.31  E-value=2e-11  Score=87.98  Aligned_cols=80  Identities=21%  Similarity=0.306  Sum_probs=72.6

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ...+.|||.|||+.++.++..++|++||.|..+++=..   ...+|-|||.|++..+|.+|+..|+|+-+.++.|.|-+.
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~---k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyy   92 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNT---KETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYY   92 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCc---cCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEec
Confidence            45778999999999999999999999999999988443   456899999999999999999999999999999999998


Q ss_pred             CCc
Q 046966          289 QSV  291 (299)
Q Consensus       289 ~~~  291 (299)
                      .+-
T Consensus        93 q~~   95 (124)
T KOG0114|consen   93 QPE   95 (124)
T ss_pred             CHH
Confidence            764

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

Probab=99.29  E-value=1.7e-11  Score=116.65  Aligned_cols=77  Identities=32%  Similarity=0.489  Sum_probs=70.4

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccC--CCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQF--GTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~--G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ....+|||+||++++++++|+++|++|  |.|.+|++++        +||||+|.+.++|++|++.||+..|+|+.|+|+
T Consensus       231 ~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r--------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~  302 (578)
T TIGR01648       231 AKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR--------DYAFVHFEDREDAVKAMDELNGKELEGSEIEVT  302 (578)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec--------CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            345789999999999999999999999  9999987653        599999999999999999999999999999999


Q ss_pred             ecCCccc
Q 046966          287 FSQSVSK  293 (299)
Q Consensus       287 ~a~~~~~  293 (299)
                      +++++.+
T Consensus       303 ~Akp~~~  309 (578)
T TIGR01648       303 LAKPVDK  309 (578)
T ss_pred             EccCCCc
Confidence            9998643

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

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

Probab=99.29  E-value=1.8e-11  Score=116.12  Aligned_cols=79  Identities=19%  Similarity=0.258  Sum_probs=72.5

Q ss_pred             CCCCceEEEEcCCC-CCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          208 KPPDNVLFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       208 ~~~~~~v~v~nL~~-~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      .+++++|||+||++ .+++++|+.+|++||.|.+|+++.++     +|||||+|.+.++|..|+..|||..|.|+.|+|.
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            34678999999998 69999999999999999999998862     5899999999999999999999999999999999


Q ss_pred             ecCCc
Q 046966          287 FSQSV  291 (299)
Q Consensus       287 ~a~~~  291 (299)
                      +++..
T Consensus       347 ~s~~~  351 (481)
T TIGR01649       347 PSKQQ  351 (481)
T ss_pred             Ecccc
Confidence            98653

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).

>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=99.28  E-value=4.2e-11  Score=82.78  Aligned_cols=74  Identities=43%  Similarity=0.653  Sum_probs=68.3

Q ss_pred             eEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       213 ~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      +|+|+|||+.+++++|+.+|+.+|.+..+.+..++.+ ..+|+|||+|.+.++|..|+..+++..+.|+.+.|.+
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            4899999999999999999999999999999887544 7789999999999999999999999999999998864

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).

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

Probab=99.26  E-value=1.2e-11  Score=98.28  Aligned_cols=79  Identities=22%  Similarity=0.373  Sum_probs=71.4

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ..++|||+|||.++.+.+|+++|-+||.|..|.|...   ....+||||+|++..+|+.|+..-+|+.++|.+|+|++++
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            4789999999999999999999999999999987443   2346799999999999999999999999999999999998


Q ss_pred             Cc
Q 046966          290 SV  291 (299)
Q Consensus       290 ~~  291 (299)
                      .-
T Consensus        82 gg   83 (241)
T KOG0105|consen   82 GG   83 (241)
T ss_pred             CC
Confidence            64

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

Probab=99.25  E-value=2.6e-11  Score=110.63  Aligned_cols=83  Identities=31%  Similarity=0.412  Sum_probs=76.3

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHh-----CC-ceeCCeEE
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM-----NN-ALIDDRRI  283 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l-----~~-~~i~g~~l  283 (299)
                      ...+|||.|||+++++++|...|++||.|..+.++.++.|+.++|.|||.|.+..+|+.||...     .| ..|.||.|
T Consensus       291 ~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~L  370 (678)
T KOG0127|consen  291 EGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLL  370 (678)
T ss_pred             ccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEE
Confidence            4589999999999999999999999999999999999999999999999999999999999876     23 67889999


Q ss_pred             EEEecCCcc
Q 046966          284 CVDFSQSVS  292 (299)
Q Consensus       284 ~v~~a~~~~  292 (299)
                      .|..|.++.
T Consensus       371 kv~~Av~Rk  379 (678)
T KOG0127|consen  371 KVTLAVTRK  379 (678)
T ss_pred             eeeeccchH
Confidence            999988753

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

Probab=99.25  E-value=5.6e-12  Score=109.73  Aligned_cols=79  Identities=27%  Similarity=0.384  Sum_probs=76.0

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      -|+||||.+.+...|+.|+..|..||.|+++.+.||+.|++++|||||+|+-++.|+-|++.|||.+++||.|+|....
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCC
Confidence            5899999999999999999999999999999999999999999999999999999999999999999999999998544

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

Probab=99.24  E-value=6e-12  Score=111.76  Aligned_cols=83  Identities=29%  Similarity=0.476  Sum_probs=76.1

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCce-eC--CeEEEEE
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNAL-ID--DRRICVD  286 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~-i~--g~~l~v~  286 (299)
                      ..++||||-|+..++|.+++++|++||.|++|.|++| ..+.+||||||.|.+.+-|..|++.|||.. +.  ..+|.|+
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd-~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVk  201 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRD-PDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVK  201 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheec-ccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEE
Confidence            4789999999999999999999999999999999999 579999999999999999999999999964 44  5789999


Q ss_pred             ecCCccc
Q 046966          287 FSQSVSK  293 (299)
Q Consensus       287 ~a~~~~~  293 (299)
                      ||++.+.
T Consensus       202 FADtqkd  208 (510)
T KOG0144|consen  202 FADTQKD  208 (510)
T ss_pred             ecccCCC
Confidence            9998754

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

Probab=99.23  E-value=3.6e-11  Score=114.06  Aligned_cols=76  Identities=25%  Similarity=0.272  Sum_probs=69.2

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHh--CCceeCCeEEEEEe
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM--NNALIDDRRICVDF  287 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l--~~~~i~g~~l~v~~  287 (299)
                      |+++|||+|||+.+++++|+++|++||.|.++.++.+      +|||||+|.+.++|++|++.|  ++..+.|++|.|.+
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 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNY   74 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEe
Confidence            4689999999999999999999999999999998754      479999999999999999864  77899999999999


Q ss_pred             cCCc
Q 046966          288 SQSV  291 (299)
Q Consensus       288 a~~~  291 (299)
                      +..+
T Consensus        75 s~~~   78 (481)
T TIGR01649        75 STSQ   78 (481)
T ss_pred             cCCc
Confidence            8754

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).

>smart00361 RRM_1 RNA recognition motif

Probab=99.22  E-value=5.7e-11  Score=82.35  Aligned_cols=62  Identities=27%  Similarity=0.419  Sum_probs=55.4

Q ss_pred             HHHHHHhcc----cCCCeEEEE-EeecCCC--CCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          225 DEDLHVIFS----QFGTVVSAE-ILRDYRT--GESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       225 e~~L~~~f~----~~G~i~~~~-~~~~~~~--g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      +++|+++|+    +||.|.++. ++.++.+  +.++|||||.|.+.++|.+|++.|||..+.|+.|.++
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            578888888    999999995 7776666  8999999999999999999999999999999999863

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.21  E-value=4.5e-11  Score=106.36  Aligned_cols=82  Identities=24%  Similarity=0.344  Sum_probs=75.5

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcc-cCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFS-QFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~-~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ....+.+||+|+|+++.+.+|+++|. +.|+|..|.+..| .+|++||+|.|+|++++.+++|++.||.+.+.||.|.|+
T Consensus        41 ~~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vK  119 (608)
T KOG4212|consen   41 AARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVK  119 (608)
T ss_pred             ccccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEe
Confidence            34456799999999999999999995 6899999999999 699999999999999999999999999999999999998


Q ss_pred             ecCC
Q 046966          287 FSQS  290 (299)
Q Consensus       287 ~a~~  290 (299)
                      -...
T Consensus       120 Ed~d  123 (608)
T KOG4212|consen  120 EDHD  123 (608)
T ss_pred             ccCc
Confidence            7654

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

Probab=99.20  E-value=2.6e-11  Score=107.72  Aligned_cols=84  Identities=23%  Similarity=0.447  Sum_probs=76.2

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCce-eC--CeEEEEE
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNAL-ID--DRRICVD  286 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~-i~--g~~l~v~  286 (299)
                      ..-++|||.+|..++|.||+.+|++||.|.+|.|++|+.|+.++||+||.|.+.++|.+|+.+||+.. |-  ..+|.|+
T Consensus        33 ~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk  112 (510)
T KOG0144|consen   33 SAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVK  112 (510)
T ss_pred             hhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeec
Confidence            45689999999999999999999999999999999999999999999999999999999999999865 33  5789999


Q ss_pred             ecCCccc
Q 046966          287 FSQSVSK  293 (299)
Q Consensus       287 ~a~~~~~  293 (299)
                      +|+..+.
T Consensus       113 ~Ad~E~e  119 (510)
T KOG0144|consen  113 YADGERE  119 (510)
T ss_pred             ccchhhh
Confidence            9987543

>PF13893 RRM_5: RNA recognition motif

Probab=99.20  E-value=9.4e-11  Score=77.50  Aligned_cols=56  Identities=30%  Similarity=0.519  Sum_probs=50.5

Q ss_pred             HHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          228 LHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       228 L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      |.++|++||.|.++.+..+.     +++|||+|.+.++|.+|++.|||..+.|++|+|+||
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            67899999999999887652     589999999999999999999999999999999986

(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 ....

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

Probab=99.18  E-value=4.7e-11  Score=106.58  Aligned_cols=76  Identities=36%  Similarity=0.519  Sum_probs=71.3

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      .-..|||.||+.++|++.|+++|++||.|.+|+.++|        ||||-|.+.++|.+|++.+||+.|+|..|.|.+|+
T Consensus       258 ~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAK  329 (506)
T KOG0117|consen  258 KVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAK  329 (506)
T ss_pred             heeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecC
Confidence            3467999999999999999999999999999988776        99999999999999999999999999999999999


Q ss_pred             Cccc
Q 046966          290 SVSK  293 (299)
Q Consensus       290 ~~~~  293 (299)
                      |..+
T Consensus       330 P~~k  333 (506)
T KOG0117|consen  330 PVDK  333 (506)
T ss_pred             Chhh
Confidence            8754

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

Probab=99.17  E-value=3.7e-11  Score=109.92  Aligned_cols=79  Identities=25%  Similarity=0.395  Sum_probs=74.4

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      -..+|||||++++++++|+..|++||.|..+.+.+|..||+++|||||+|.+.++|.+|+..|||..|-|+.|+|..-.
T Consensus       278 ~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~  356 (549)
T KOG0147|consen  278 MRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVT  356 (549)
T ss_pred             hhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEee
Confidence            3349999999999999999999999999999999998899999999999999999999999999999999999988644

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.17  E-value=1.5e-10  Score=93.85  Aligned_cols=84  Identities=31%  Similarity=0.398  Sum_probs=76.4

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccC-CCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQF-GTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~-G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ......+|+..+|..+.+.++..+|.+| |.+...++.+++.||.++|||||+|.+.+.|+-|-+.||++.+.++.|.|.
T Consensus        46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~  125 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECH  125 (214)
T ss_pred             cCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeE
Confidence            3456789999999999999999999998 777788888999999999999999999999999999999999999999998


Q ss_pred             ecCCc
Q 046966          287 FSQSV  291 (299)
Q Consensus       287 ~a~~~  291 (299)
                      +=-|-
T Consensus       126 vmppe  130 (214)
T KOG4208|consen  126 VMPPE  130 (214)
T ss_pred             EeCch
Confidence            85543

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

Probab=99.15  E-value=4.8e-11  Score=101.19  Aligned_cols=75  Identities=29%  Similarity=0.512  Sum_probs=70.9

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCCc
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSV  291 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~~  291 (299)
                      .++||||||..+++.+|+.+|++||.|.+|.|+++        ||||-.++...++.|+..||++.|+|..|.|+-++++
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            57999999999999999999999999999999987        9999999999999999999999999999999999988


Q ss_pred             ccc
Q 046966          292 SKI  294 (299)
Q Consensus       292 ~~~  294 (299)
                      ++.
T Consensus        75 sk~   77 (346)
T KOG0109|consen   75 SKA   77 (346)
T ss_pred             CCC
Confidence            543

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

Probab=99.15  E-value=1.1e-10  Score=95.98  Aligned_cols=86  Identities=24%  Similarity=0.424  Sum_probs=76.6

Q ss_pred             CCCceEEEEcCCCCCCHHHHHH----hcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHV----IFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC  284 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~----~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~  284 (299)
                      ++..++||.||+..+..++|+.    +|++||.|..|...   .+.+.||.|||.|.+.+.|-.|+..|+|..+.|+.++
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~---kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mr   83 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF---KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMR   83 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec---CCCCccCceEEEecChhHHHHHHHHhcCCcccCchhh
Confidence            4556999999999999998887    99999999988764   3678999999999999999999999999999999999


Q ss_pred             EEecCCccccccc
Q 046966          285 VDFSQSVSKIWKK  297 (299)
Q Consensus       285 v~~a~~~~~~~~~  297 (299)
                      |+||++.+....+
T Consensus        84 iqyA~s~sdii~~   96 (221)
T KOG4206|consen   84 IQYAKSDSDIIAQ   96 (221)
T ss_pred             eecccCccchhhc
Confidence            9999998765443

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

Probab=99.07  E-value=1.6e-10  Score=91.77  Aligned_cols=83  Identities=30%  Similarity=0.476  Sum_probs=76.7

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEE-EEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVS-AEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~-~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+..+||+||.+.++|..|.+.|+.||.+.. .++++++.||.++||||+.|.+.+.+.+|+..|||..+.++++.|.+
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            34689999999999999999999999999874 58899999999999999999999999999999999999999999999


Q ss_pred             cCCc
Q 046966          288 SQSV  291 (299)
Q Consensus       288 a~~~  291 (299)
                      +.-+
T Consensus       174 a~k~  177 (203)
T KOG0131|consen  174 AFKK  177 (203)
T ss_pred             EEec
Confidence            8754

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=99.06  E-value=6.2e-10  Score=102.14  Aligned_cols=82  Identities=24%  Similarity=0.462  Sum_probs=77.3

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ..++.+||.+|...+...+|+.+|++||.|+-.+++.+..+.-.+||+||++.+..+|.+||..||.+.|.|+.|.|..+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            45678999999999999999999999999999999999888888999999999999999999999999999999999988


Q ss_pred             CC
Q 046966          289 QS  290 (299)
Q Consensus       289 ~~  290 (299)
                      +.
T Consensus       483 KN  484 (940)
T KOG4661|consen  483 KN  484 (940)
T ss_pred             cc
Confidence            74

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.99  E-value=1.3e-09  Score=103.44  Aligned_cols=77  Identities=22%  Similarity=0.391  Sum_probs=71.3

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      --++|||||+|+.++++.+|..+|+.||.|.++.++-.      +|+|||.+...++|.+|+..|+.+.+.++.|+|.|+
T Consensus       419 V~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa  492 (894)
T KOG0132|consen  419 VCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWA  492 (894)
T ss_pred             EeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeee
Confidence            34689999999999999999999999999999987654      689999999999999999999999999999999999


Q ss_pred             CCc
Q 046966          289 QSV  291 (299)
Q Consensus       289 ~~~  291 (299)
                      ..+
T Consensus       493 ~g~  495 (894)
T KOG0132|consen  493 VGK  495 (894)
T ss_pred             ccC
Confidence            864

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

Probab=98.98  E-value=9.3e-10  Score=96.08  Aligned_cols=80  Identities=20%  Similarity=0.353  Sum_probs=75.8

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      -.+|||..++++.+++||+..|+.||+|++|.+-+++..+.++||||++|.+..+...|+..||-+.++|+-|+|-.+..
T Consensus       210 fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vT  289 (544)
T KOG0124|consen  210 FNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  289 (544)
T ss_pred             hheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccC
Confidence            46899999999999999999999999999999999998889999999999999999999999999999999999987653

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

Probab=98.94  E-value=1.1e-09  Score=91.90  Aligned_cols=84  Identities=25%  Similarity=0.421  Sum_probs=75.3

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC---CeEEEEE
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID---DRRICVD  286 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~---g~~l~v~  286 (299)
                      .++++|||.|...-.|+|++.+|..||.+.+|.+.+.+ .|.++|+|||.|.+..+|+.||..|||..-.   ...|.|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            67899999999999999999999999999999999984 7899999999999999999999999996533   5679999


Q ss_pred             ecCCcccc
Q 046966          287 FSQSVSKI  294 (299)
Q Consensus       287 ~a~~~~~~  294 (299)
                      |++..+.+
T Consensus        97 ~ADTdkER  104 (371)
T KOG0146|consen   97 FADTDKER  104 (371)
T ss_pred             eccchHHH
Confidence            99976533

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

Probab=98.93  E-value=3.1e-09  Score=96.74  Aligned_cols=76  Identities=30%  Similarity=0.577  Sum_probs=71.4

Q ss_pred             EEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCCcc
Q 046966          214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVS  292 (299)
Q Consensus       214 v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~~~  292 (299)
                      +||.||+++++..+|.++|+.||.|++|++..+ ..| ++|| ||+|.+.++|++|+..|||..+.|++|.|.....+.
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~-~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~  154 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATD-ENG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKE  154 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEc-CCC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchh
Confidence            999999999999999999999999999999999 456 9999 999999999999999999999999999998877653

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

Probab=98.90  E-value=1.4e-09  Score=95.84  Aligned_cols=82  Identities=29%  Similarity=0.397  Sum_probs=75.8

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ..+++||++|+|.++++.|+++|.+||.|..|.+++|+.+++++||+||+|.+.+...+++.. ..+.|.|+.|.+.-|.
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 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceecc
Confidence            579999999999999999999999999999999999999999999999999999988888843 5678999999999988


Q ss_pred             Ccc
Q 046966          290 SVS  292 (299)
Q Consensus       290 ~~~  292 (299)
                      |+.
T Consensus        84 ~r~   86 (311)
T KOG4205|consen   84 SRE   86 (311)
T ss_pred             Ccc
Confidence            875

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

Probab=98.88  E-value=6.6e-09  Score=97.94  Aligned_cols=79  Identities=34%  Similarity=0.468  Sum_probs=70.7

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCC---CCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRT---GESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~---g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .+++||.||++.++.++|...|...|.|.++.|...+..   -.+.|||||+|.+.++|++|++.|+|+.|.|+.|.|++
T Consensus       515 ~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~  594 (725)
T KOG0110|consen  515 ETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKI  594 (725)
T ss_pred             chhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEe
Confidence            344999999999999999999999999999988765422   13569999999999999999999999999999999999


Q ss_pred             cC
Q 046966          288 SQ  289 (299)
Q Consensus       288 a~  289 (299)
                      +.
T Consensus       595 S~  596 (725)
T KOG0110|consen  595 SE  596 (725)
T ss_pred             cc
Confidence            98

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

Probab=98.87  E-value=3.3e-09  Score=90.19  Aligned_cols=75  Identities=28%  Similarity=0.564  Sum_probs=71.3

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ...+++|+|+.+.++..+|+..|.+||.+.+|.|+++        |+||-|...++|..|++.|++.++.|++++|+.+.
T Consensus        77 ~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~st  148 (346)
T KOG0109|consen   77 ASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQLST  148 (346)
T ss_pred             CccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccceeeeeeec
Confidence            5688999999999999999999999999999999887        99999999999999999999999999999999998


Q ss_pred             Ccc
Q 046966          290 SVS  292 (299)
Q Consensus       290 ~~~  292 (299)
                      ++-
T Consensus       149 srl  151 (346)
T KOG0109|consen  149 SRL  151 (346)
T ss_pred             ccc
Confidence            864

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

Probab=98.78  E-value=6.2e-09  Score=98.13  Aligned_cols=82  Identities=16%  Similarity=0.375  Sum_probs=76.3

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      ...|+|.|+|+..+..+++.+|..||.+.+|+|+.-...+.++|||||+|-++.+|.+|+.+|.++.+.||+|.++||..
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            56899999999999999999999999999999988756677899999999999999999999999999999999999987


Q ss_pred             cc
Q 046966          291 VS  292 (299)
Q Consensus       291 ~~  292 (299)
                      ..
T Consensus       693 d~  694 (725)
T KOG0110|consen  693 DN  694 (725)
T ss_pred             ch
Confidence            53

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

Probab=98.77  E-value=1.8e-08  Score=91.70  Aligned_cols=74  Identities=34%  Similarity=0.449  Sum_probs=69.1

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCCc
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSV  291 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~~  291 (299)
                      ..+|||   +++++..|.+.|+++|.+.++++.+|. |  +.|||||.|.++.+|.+|+..||...+.|++|++.|+.-.
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            368898   899999999999999999999999996 5  9999999999999999999999999999999999998643

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

Probab=98.77  E-value=2.6e-08  Score=87.88  Aligned_cols=83  Identities=23%  Similarity=0.376  Sum_probs=76.8

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ...++||++||.++++++++++|.+||.|..+.++.|..+.+.+||+||.|.+.+++.+++. ..-+.|+++.+.|..|.
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            46789999999999999999999999999999999999999999999999999999999984 47788999999999999


Q ss_pred             Cccc
Q 046966          290 SVSK  293 (299)
Q Consensus       290 ~~~~  293 (299)
                      |+.-
T Consensus       175 pk~~  178 (311)
T KOG4205|consen  175 PKEV  178 (311)
T ss_pred             chhh
Confidence            8753

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

Probab=98.77  E-value=2.9e-08  Score=95.05  Aligned_cols=82  Identities=23%  Similarity=0.348  Sum_probs=69.1

Q ss_pred             CCCceEEEEcCCCCC----------CHHHHHHhcccCCCeEEEEEeec---CCCCCeeeEEEEEecCHHHHHHHHHHhCC
Q 046966          209 PPDNVLFVCQLNPVT----------EDEDLHVIFSQFGTVVSAEILRD---YRTGESLCYAFVEFEKREACEQAYFKMNN  275 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~----------~e~~L~~~f~~~G~i~~~~~~~~---~~~g~~~g~afv~f~~~~~a~~al~~l~~  275 (299)
                      .+..+|++.|+...-          ..++|+++|++||.|..|.|+++   ..++.+.|++||+|.+.++|++|+..|||
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            356889999996421          12578999999999999999875   23456789999999999999999999999


Q ss_pred             ceeCCeEEEEEecCC
Q 046966          276 ALIDDRRICVDFSQS  290 (299)
Q Consensus       276 ~~i~g~~l~v~~a~~  290 (299)
                      ..++|+.|.|.|...
T Consensus       487 r~~~gr~v~~~~~~~  501 (509)
T TIGR01642       487 RKFNDRVVVAAFYGE  501 (509)
T ss_pred             CEECCeEEEEEEeCH
Confidence            999999999999764

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

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.75  E-value=4.4e-08  Score=89.67  Aligned_cols=83  Identities=27%  Similarity=0.397  Sum_probs=71.0

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .....|||.|||.+++..+|+++|.+||.|+...|......++..+||||+|.+..+++.|+++ +-..+++++|.|+-.
T Consensus       286 ~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek  364 (419)
T KOG0116|consen  286 ADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEK  364 (419)
T ss_pred             ecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEec
Confidence            3455699999999999999999999999999888766433355559999999999999999987 678899999999988


Q ss_pred             CCcc
Q 046966          289 QSVS  292 (299)
Q Consensus       289 ~~~~  292 (299)
                      ++..
T Consensus       365 ~~~~  368 (419)
T KOG0116|consen  365 RPGF  368 (419)
T ss_pred             cccc
Confidence            8754

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.70  E-value=4.1e-08  Score=85.51  Aligned_cols=75  Identities=29%  Similarity=0.434  Sum_probs=66.1

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHH-HhCCceeCCeEEEEEec
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF-KMNNALIDDRRICVDFS  288 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~-~l~~~~i~g~~l~v~~a  288 (299)
                      .-.+|||++|...+++.+|++.|-+||+|.++.+...      +++|||+|.+.++|+.|.+ .++...|+|++|.|.|.
T Consensus       227 ~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg  300 (377)
T KOG0153|consen  227 SIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWG  300 (377)
T ss_pred             ceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEEEEeC
Confidence            3568999999999999999999999999999988765      3599999999999998875 45556789999999999


Q ss_pred             CC
Q 046966          289 QS  290 (299)
Q Consensus       289 ~~  290 (299)
                      ++
T Consensus       301 ~~  302 (377)
T KOG0153|consen  301 RP  302 (377)
T ss_pred             CC
Confidence            98

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

Probab=98.68  E-value=1.4e-07  Score=77.55  Aligned_cols=87  Identities=16%  Similarity=0.165  Sum_probs=72.2

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeec-CCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC---CeEEE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRD-YRTGESLCYAFVEFEKREACEQAYFKMNNALID---DRRIC  284 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~-~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~---g~~l~  284 (299)
                      ..-++|||.+||.++...+|..+|..|-..+.+.+... +.....+-+||+.|.+.+.|.+|++.|||..++   +..|+
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLh  111 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLH  111 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeE
Confidence            34689999999999999999999999977776655433 222345689999999999999999999999987   88899


Q ss_pred             EEecCCccccc
Q 046966          285 VDFSQSVSKIW  295 (299)
Q Consensus       285 v~~a~~~~~~~  295 (299)
                      +++|++..|+.
T Consensus       112 iElAKSNtK~k  122 (284)
T KOG1457|consen  112 IELAKSNTKRK  122 (284)
T ss_pred             eeehhcCcccc
Confidence            99999876553

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.66  E-value=9.5e-08  Score=81.20  Aligned_cols=83  Identities=30%  Similarity=0.403  Sum_probs=76.0

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ....+|+|.|||+.+.++||+++|..||.+..+.+..+ .+|++.|.|-|.|...++|.+|++.+|+..++|+.+++...
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~-~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i  159 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYD-RAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEII  159 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccC-CCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEe
Confidence            44588999999999999999999999999999999898 58999999999999999999999999999999999999886


Q ss_pred             CCcc
Q 046966          289 QSVS  292 (299)
Q Consensus       289 ~~~~  292 (299)
                      .+.+
T Consensus       160 ~~~~  163 (243)
T KOG0533|consen  160 SSPS  163 (243)
T ss_pred             cCcc
Confidence            6543

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=98.65  E-value=5.2e-08  Score=87.19  Aligned_cols=75  Identities=27%  Similarity=0.290  Sum_probs=68.6

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ...|+|||.|||.++|++.|++-|..||.|..+.|+.   .|+++|  .|.|.++++|++|+..|++..+.||.|.|.|.
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            4578999999999999999999999999999988843   577877  79999999999999999999999999999874

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.64  E-value=2.1e-08  Score=83.78  Aligned_cols=86  Identities=29%  Similarity=0.397  Sum_probs=78.4

Q ss_pred             CCCCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 046966          205 ADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC  284 (299)
Q Consensus       205 ~~~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~  284 (299)
                      .+....+.+||.|-|.-+++.+-|...|.+|-.....++++++.||+++||+||.|.+..++.+|+..|+|..++.|+|+
T Consensus       184 ~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpik  263 (290)
T KOG0226|consen  184 AEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIK  263 (290)
T ss_pred             ccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhH
Confidence            34455678999999999999999999999999888999999999999999999999999999999999999999999998


Q ss_pred             EEecCC
Q 046966          285 VDFSQS  290 (299)
Q Consensus       285 v~~a~~  290 (299)
                      ++-+..
T Consensus       264 lRkS~w  269 (290)
T KOG0226|consen  264 LRKSEW  269 (290)
T ss_pred             hhhhhH
Confidence            876543

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

Probab=98.61  E-value=1.9e-07  Score=81.35  Aligned_cols=80  Identities=18%  Similarity=0.285  Sum_probs=72.8

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeE--------EEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCe
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVV--------SAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDR  281 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~--------~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~  281 (299)
                      .+..|||+|||.++|-+++.++|+++|.|.        .|++.++ ..|..+|=|.+.|...+++.-|++.|++..+.|+
T Consensus       133 ~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd-~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~  211 (382)
T KOG1548|consen  133 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRD-NQGKLKGDALCCYIKRESVELAIKILDEDELRGK  211 (382)
T ss_pred             cCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEec-CCCCccCceEEEeecccHHHHHHHHhCcccccCc
Confidence            356699999999999999999999999885        4788888 4699999999999999999999999999999999


Q ss_pred             EEEEEecCC
Q 046966          282 RICVDFSQS  290 (299)
Q Consensus       282 ~l~v~~a~~  290 (299)
                      .|+|+.|+=
T Consensus       212 ~~rVerAkf  220 (382)
T KOG1548|consen  212 KLRVERAKF  220 (382)
T ss_pred             EEEEehhhh
Confidence            999998863

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.52  E-value=2.4e-07  Score=78.85  Aligned_cols=83  Identities=19%  Similarity=0.309  Sum_probs=76.5

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ......+||+|+.+.++.+++...|+.||.+..+.++.++.++.++||+||+|.+.+.++.++. |++..|.|+.+.|.+
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVTL  176 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceeee
Confidence            3457899999999999999999999999999999999998888999999999999999999997 999999999999998


Q ss_pred             cCCc
Q 046966          288 SQSV  291 (299)
Q Consensus       288 a~~~  291 (299)
                      .+-.
T Consensus       177 ~r~~  180 (231)
T KOG4209|consen  177 KRTN  180 (231)
T ss_pred             eeee
Confidence            7643

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.46  E-value=3.1e-07  Score=86.80  Aligned_cols=83  Identities=23%  Similarity=0.422  Sum_probs=73.9

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecC---CCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDY---RTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~---~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      |..+.+||+||++.++++.|...|+.||++.++++++.+   ...+.+-+|||.|-+..+|++|++.|+|..+.++.+++
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            345679999999999999999999999999999998864   22456779999999999999999999999999999999


Q ss_pred             EecCCc
Q 046966          286 DFSQSV  291 (299)
Q Consensus       286 ~~a~~~  291 (299)
                      -|+++.
T Consensus       252 gWgk~V  257 (877)
T KOG0151|consen  252 GWGKAV  257 (877)
T ss_pred             cccccc
Confidence            998653

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.39  E-value=3.1e-06  Score=61.84  Aligned_cols=79  Identities=18%  Similarity=0.232  Sum_probs=68.5

Q ss_pred             ceEEEEcCCCCCCHHHHHHhccc--CCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC----CeEEEE
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQ--FGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID----DRRICV  285 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~--~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~----g~~l~v  285 (299)
                      +||.|.|+|...+.++|.+++..  .|....+-++.|..++-+.|||||.|.+.+.|.+-.+.++|..+.    .+.+.|
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            68999999999999999988854  366678889999889999999999999999999999999998865    566778


Q ss_pred             EecCC
Q 046966          286 DFSQS  290 (299)
Q Consensus       286 ~~a~~  290 (299)
                      .+|+-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            88763

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.35  E-value=1.9e-07  Score=76.59  Aligned_cols=82  Identities=20%  Similarity=0.173  Sum_probs=73.6

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .+..++|||+|+...++|+-|.++|-+-|.|.++.|..++ .+..+ ||||.|.++.+..-|++.|||..+.++.+.+.+
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~   83 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTL   83 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhccc
Confidence            3457899999999999999999999999999999998874 45566 999999999999999999999999999999988


Q ss_pred             cCCc
Q 046966          288 SQSV  291 (299)
Q Consensus       288 a~~~  291 (299)
                      ....
T Consensus        84 r~G~   87 (267)
T KOG4454|consen   84 RCGN   87 (267)
T ss_pred             ccCC
Confidence            6654

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

Probab=98.28  E-value=7.1e-07  Score=74.33  Aligned_cols=72  Identities=18%  Similarity=0.407  Sum_probs=65.5

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCCc
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSV  291 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~~  291 (299)
                      ..+||++||+.+.+.+|..+|..||.+..+.+.        .||+||.|.+..+|..|+..+|+..++|-.+.|.+++..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            468999999999999999999999999888663        358999999999999999999999999999999999853

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.25  E-value=6.2e-07  Score=82.83  Aligned_cols=70  Identities=26%  Similarity=0.332  Sum_probs=64.1

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC  284 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~  284 (299)
                      +..+|+|.|||..+++++|..+|+.||+|..++.     +...+|..||+|.+..+|++|+++|++..+.|+.|.
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            4689999999999999999999999999998654     455678999999999999999999999999999988

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.07  E-value=3.1e-06  Score=78.74  Aligned_cols=86  Identities=21%  Similarity=0.361  Sum_probs=79.6

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ....+.+||++||...++.++.+++..||.+..-.++.+..+|.++||||.+|.+......|+..|||..++++.|.|+.
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~  365 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQR  365 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeeh
Confidence            34578899999999999999999999999999999999988899999999999999999999999999999999999999


Q ss_pred             cCCccc
Q 046966          288 SQSVSK  293 (299)
Q Consensus       288 a~~~~~  293 (299)
                      |....+
T Consensus       366 A~~g~~  371 (500)
T KOG0120|consen  366 AIVGAS  371 (500)
T ss_pred             hhccch
Confidence            886543

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

Probab=98.01  E-value=2.6e-05  Score=69.68  Aligned_cols=76  Identities=20%  Similarity=0.350  Sum_probs=68.6

Q ss_pred             CceEEEEcCCC-CCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          211 DNVLFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       211 ~~~v~v~nL~~-~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      +..|.|.||.. .+|.+.|..+|+.||.|.+++|..++.     --|.|+|.+...|+-|++.|+|..+.|++|+|.+++
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            57888998865 589999999999999999999998743     479999999999999999999999999999999988


Q ss_pred             Cc
Q 046966          290 SV  291 (299)
Q Consensus       290 ~~  291 (299)
                      -.
T Consensus       372 H~  373 (492)
T KOG1190|consen  372 HT  373 (492)
T ss_pred             Cc
Confidence            54

>KOG0882 consensus Cyclophilin-related peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.01  E-value=6.8e-06  Score=74.35  Aligned_cols=153  Identities=18%  Similarity=0.247  Sum_probs=122.1

Q ss_pred             EEEEEcce----eEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCC-CCCCCC-CCCCc----cc
Q 046966            3 VLIETSLG----DIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGT-GTGGRS-VYEDR----FF   72 (299)
Q Consensus         3 v~~~T~~G----~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~-~~~~~~-~~~~~----~~   72 (299)
                      +.+.|..|    -|.|+|+.+-.|.-++.|..+|.-+++++..|.+|...+++|.||.... ..+|.- .|.+.    +.
T Consensus       101 a~wv~skGd~~s~IAVs~~~sg~i~VvD~~~d~~q~~~fkklH~sPV~~i~y~qa~Ds~vSiD~~gmVEyWs~e~~~qfP  180 (558)
T KOG0882|consen  101 AEWVTSKGDKISLIAVSLFKSGKIFVVDGFGDFCQDGYFKKLHFSPVKKIRYNQAGDSAVSIDISGMVEYWSAEGPFQFP  180 (558)
T ss_pred             eEEecCCCCeeeeEEeecccCCCcEEECCcCCcCccceecccccCceEEEEeeccccceeeccccceeEeecCCCcccCc
Confidence            56778899    8999999999999999999999999999999999999999999995433 323321 11111    33


Q ss_pred             ccccccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEE
Q 046966           73 VDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQ  152 (299)
Q Consensus        73 ~~e~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~  152 (299)
                      ..+.+..++|. .-++.+.+......+-+|++.-.. -+-++.+..|||++..|-++++.|.+..++....|..++.|..
T Consensus       181 r~~l~~~~K~e-TdLy~f~K~Kt~pts~Efsp~g~q-istl~~DrkVR~F~~KtGklvqeiDE~~t~~~~q~ks~y~l~~  258 (558)
T KOG0882|consen  181 RTNLNFELKHE-TDLYGFPKAKTEPTSFEFSPDGAQ-ISTLNPDRKVRGFVFKTGKLVQEIDEVLTDAQYQPKSPYGLMH  258 (558)
T ss_pred             ccccccccccc-chhhcccccccCccceEEccccCc-ccccCcccEEEEEEeccchhhhhhhccchhhhhccccccccce
Confidence            44457778884 466677666555566788888876 5778889999999999999999999999998889999888888


Q ss_pred             EEEEC
Q 046966          153 TYVLY  157 (299)
Q Consensus       153 ~~v~~  157 (299)
                      +....
T Consensus       259 VelgR  263 (558)
T KOG0882|consen  259 VELGR  263 (558)
T ss_pred             eehhh
Confidence            87754

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

Probab=97.86  E-value=5.5e-06  Score=76.54  Aligned_cols=80  Identities=24%  Similarity=0.318  Sum_probs=74.6

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ..+++|+-.|+...++-+|.++|+.+|.|..++++.|+.+++++|.+||+|.+.++...|+ .|.|..+.|.+|.|+.+.
T Consensus       178 d~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq~sE  256 (549)
T KOG0147|consen  178 DQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQLSE  256 (549)
T ss_pred             hHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEecccH
Confidence            4578999999999999999999999999999999999999999999999999999999999 789999999999998765


Q ss_pred             C
Q 046966          290 S  290 (299)
Q Consensus       290 ~  290 (299)
                      .
T Consensus       257 a  257 (549)
T KOG0147|consen  257 A  257 (549)
T ss_pred             H
Confidence            3

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

Probab=97.86  E-value=6.1e-05  Score=68.96  Aligned_cols=79  Identities=25%  Similarity=0.277  Sum_probs=66.3

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .....|-+.+|||++|+++|.++|+.++ |.++.+.+  .+|+..|=|||+|.+.+++++|++. +...++.|-|.|--+
T Consensus         8 ~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf~~   83 (510)
T KOG4211|consen    8 STAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR--RNGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVFTA   83 (510)
T ss_pred             CcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEec--cCCCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEEcc
Confidence            3456788899999999999999999985 56644444  5899999999999999999999975 777888999999877


Q ss_pred             CCc
Q 046966          289 QSV  291 (299)
Q Consensus       289 ~~~  291 (299)
                      .+.
T Consensus        84 ~~~   86 (510)
T KOG4211|consen   84 GGA   86 (510)
T ss_pred             CCc
Confidence            554

>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=97.83  E-value=5.9e-05  Score=52.80  Aligned_cols=68  Identities=26%  Similarity=0.360  Sum_probs=46.9

Q ss_pred             ceEEEEcCCCCCCHHH----HHHhcccCC-CeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          212 NVLFVCQLNPVTEDED----LHVIFSQFG-TVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~----L~~~f~~~G-~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ..|+|.|||.+.+...    |+.++..+| .|..+          +.+-|++-|.+.+.|.+|.+.|+|-.+.|++|.|+
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            4689999999888654    556666776 45443          12589999999999999999999999999999999


Q ss_pred             ecC
Q 046966          287 FSQ  289 (299)
Q Consensus       287 ~a~  289 (299)
                      |+.
T Consensus        73 ~~~   75 (90)
T PF11608_consen   73 FSP   75 (90)
T ss_dssp             SS-
T ss_pred             EcC
Confidence            974

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

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

Probab=97.79  E-value=2e-05  Score=65.08  Aligned_cols=65  Identities=22%  Similarity=0.390  Sum_probs=53.9

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID  279 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~  279 (299)
                      -.++||.||.++++|++|+.+|+.|.....++|-.    ....+.||++|++.+.|..|+..|+|..|.
T Consensus       210 cstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~----~~g~~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  210 CSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA----RGGMPVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             hhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec----CCCcceEeecHHHHHHHHHHHHHhhcceec
Confidence            45799999999999999999999998766655522    223468999999999999999999998754

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.76  E-value=1.9e-05  Score=69.49  Aligned_cols=84  Identities=23%  Similarity=0.364  Sum_probs=76.1

Q ss_pred             CCCceEE-EEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          209 PPDNVLF-VCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       209 ~~~~~v~-v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .+..++| +++|+.++++++|+..|..+|.|..+++..++.++.++|||++.|.....+..++.. +...+.++.+.+.+
T Consensus       182 ~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~  260 (285)
T KOG4210|consen  182 GPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEE  260 (285)
T ss_pred             CccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCccccccc
Confidence            3456666 999999999999999999999999999999999999999999999999999999877 78889999999999


Q ss_pred             cCCccc
Q 046966          288 SQSVSK  293 (299)
Q Consensus       288 a~~~~~  293 (299)
                      ..++..
T Consensus       261 ~~~~~~  266 (285)
T KOG4210|consen  261 DEPRPK  266 (285)
T ss_pred             CCCCcc
Confidence            887743

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.69  E-value=0.00015  Score=63.37  Aligned_cols=82  Identities=17%  Similarity=0.421  Sum_probs=63.0

Q ss_pred             CCceEEEEcCCCCCCHHH----H--HHhcccCCCeEEEEEeecCCCC-Ceee-EE-EEEecCHHHHHHHHHHhCCceeCC
Q 046966          210 PDNVLFVCQLNPVTEDED----L--HVIFSQFGTVVSAEILRDYRTG-ESLC-YA-FVEFEKREACEQAYFKMNNALIDD  280 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~----L--~~~f~~~G~i~~~~~~~~~~~g-~~~g-~a-fv~f~~~~~a~~al~~l~~~~i~g  280 (299)
                      ...-+||-+|++.+..++    |  .++|++||.|.++-+.+...+- ...+ +| ||+|.+.++|.+|+...+|..++|
T Consensus       113 QKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DG  192 (480)
T COG5175         113 QKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDG  192 (480)
T ss_pred             ecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccC
Confidence            356799999988876554    3  4789999999988775532111 1122 22 999999999999999999999999


Q ss_pred             eEEEEEecCCc
Q 046966          281 RRICVDFSQSV  291 (299)
Q Consensus       281 ~~l~v~~a~~~  291 (299)
                      |.|+..|-..+
T Consensus       193 r~lkatYGTTK  203 (480)
T COG5175         193 RVLKATYGTTK  203 (480)
T ss_pred             ceEeeecCchH
Confidence            99999986643

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.68  E-value=3.6e-05  Score=67.46  Aligned_cols=78  Identities=19%  Similarity=0.196  Sum_probs=67.0

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCC--CeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFG--TVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G--~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ....++|||||-|+++++||.+.+...|  .+..++...++.+|+++|||++...+..+.++.++.|-...|.|+.=.|-
T Consensus        78 Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   78 GRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             CceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            3456899999999999999998888766  45677778888999999999999999999999999999999998765544

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.67  E-value=5e-05  Score=67.03  Aligned_cols=85  Identities=21%  Similarity=0.205  Sum_probs=76.3

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeE--------EEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVV--------SAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID  279 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~--------~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~  279 (299)
                      .....++||-+||..+++++|.++|.++|.|.        .+.+-+++.|+..+|-|.|.|.+...|+.|+..+++..+.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            34567899999999999999999999999885        3567788899999999999999999999999999999999


Q ss_pred             CeEEEEEecCCcc
Q 046966          280 DRRICVDFSQSVS  292 (299)
Q Consensus       280 g~~l~v~~a~~~~  292 (299)
                      +..|+|..|..+.
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999999887554

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

Probab=97.60  E-value=0.00028  Score=58.62  Aligned_cols=78  Identities=24%  Similarity=0.404  Sum_probs=68.5

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC-CeEEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID-DRRICV  285 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~-g~~l~v  285 (299)
                      ..++...+|+.|||..++.+.|..+|.+|.....++++...     .+.|||+|.+...+..|...+++..|- ...+.|
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            35778899999999999999999999999999999987652     469999999999999999999999887 777888


Q ss_pred             EecC
Q 046966          286 DFSQ  289 (299)
Q Consensus       286 ~~a~  289 (299)
                      .+++
T Consensus       217 ~~a~  220 (221)
T KOG4206|consen  217 TFAK  220 (221)
T ss_pred             cccC
Confidence            7764

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.59  E-value=6.7e-05  Score=63.23  Aligned_cols=73  Identities=21%  Similarity=0.354  Sum_probs=60.8

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCC--------CCeeeE----EEEEecCHHHHHHHHHHhCCce
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRT--------GESLCY----AFVEFEKREACEQAYFKMNNAL  277 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~--------g~~~g~----afv~f~~~~~a~~al~~l~~~~  277 (299)
                      ....||++++|+.+...-|+.+|+.||.|-.+.+.....+        |.+..+    |+|+|.+...|.++...||+..
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            4568999999999999999999999999988877654333        222222    6799999999999999999999


Q ss_pred             eCCeE
Q 046966          278 IDDRR  282 (299)
Q Consensus       278 i~g~~  282 (299)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99976

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

Probab=97.55  E-value=0.0002  Score=65.71  Aligned_cols=79  Identities=28%  Similarity=0.274  Sum_probs=64.6

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEE-EEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVS-AEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~-~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .....|-+.+||+.++++||.++|+..--+.. +.++.+ ..+++.|=|||+|.+.+.|++|+.. |...|+.|-|.|.-
T Consensus       101 ~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d-~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~  178 (510)
T KOG4211|consen  101 ANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMD-QRGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFR  178 (510)
T ss_pred             CCCceEEecCCCccCcHHHHHHHhcCCcccccceeeecc-CCCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeeh
Confidence            35678999999999999999999987654444 556666 4678999999999999999999965 77778888888865


Q ss_pred             cC
Q 046966          288 SQ  289 (299)
Q Consensus       288 a~  289 (299)
                      +.
T Consensus       179 Ss  180 (510)
T KOG4211|consen  179 SS  180 (510)
T ss_pred             hH
Confidence            43

>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=97.43  E-value=0.00046  Score=51.50  Aligned_cols=70  Identities=29%  Similarity=0.456  Sum_probs=43.2

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCc-----eeCCeEEEEE
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNA-----LIDDRRICVD  286 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~-----~i~g~~l~v~  286 (299)
                      +.|.+.+++..++.++|++.|++||.|..|.+...    .  .-|||-|.+.+.|++|+..+...     .+.+..+.++
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G----~--~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG----D--TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC----C--CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            57889999999999999999999999998877543    1  37899999999999999766544     4556555555


Q ss_pred             e
Q 046966          287 F  287 (299)
Q Consensus       287 ~  287 (299)
                      .
T Consensus        76 v   76 (105)
T PF08777_consen   76 V   76 (105)
T ss_dssp             -
T ss_pred             E
Confidence            4

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

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

Probab=97.42  E-value=0.00032  Score=62.96  Aligned_cols=80  Identities=26%  Similarity=0.395  Sum_probs=67.4

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC-CeEEEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID-DRRICVD  286 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~-g~~l~v~  286 (299)
                      -++..++.+.|+|.+++|++|+..|..-|...+....    -++.+-+|++++.+.+.|-.|+..++.+.++ +..|+|.
T Consensus       411 ~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkf----f~kd~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvS  486 (492)
T KOG1190|consen  411 FPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKF----FQKDRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVS  486 (492)
T ss_pred             CCchhheeeccCCcccchhHHHHhhhcCCceEEeeee----cCCCcceeecccCChhHhhhhccccccccCCCCceEEEE
Confidence            4678899999999999999999999988876655432    2345569999999999999999999999988 4589999


Q ss_pred             ecCCc
Q 046966          287 FSQSV  291 (299)
Q Consensus       287 ~a~~~  291 (299)
                      |+++.
T Consensus       487 FSks~  491 (492)
T KOG1190|consen  487 FSKST  491 (492)
T ss_pred             eeccc
Confidence            98863

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

Probab=97.39  E-value=0.0001  Score=61.59  Aligned_cols=71  Identities=28%  Similarity=0.371  Sum_probs=62.1

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ..+.+.+.+++..+.+.+|.+.|.++|.+....+        ..+++||+|...+++.+|+..|++..+.++.|.+...
T Consensus        98 s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen   98 THFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             ccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeeeccc
Confidence            4678999999999999999999999999854333        3469999999999999999999999999999999543

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

Probab=97.27  E-value=0.0026  Score=56.11  Aligned_cols=81  Identities=19%  Similarity=0.263  Sum_probs=63.9

Q ss_pred             CCCceEEEEcCCC----CCC-------HHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCce
Q 046966          209 PPDNVLFVCQLNP----VTE-------DEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNAL  277 (299)
Q Consensus       209 ~~~~~v~v~nL~~----~~~-------e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~  277 (299)
                      ...++|.+.|+=.    ..+       +++|.+-..+||.|.++.+.-.    .+.|.+-|.|.+.+.|..|++.|+|..
T Consensus       263 r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~----hPdGvvtV~f~n~eeA~~ciq~m~GR~  338 (382)
T KOG1548|consen  263 RADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDR----HPDGVVTVSFRNNEEADQCIQTMDGRW  338 (382)
T ss_pred             cCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEecc----CCCceeEEEeCChHHHHHHHHHhcCee
Confidence            4577888888721    222       3566677889999999876432    256899999999999999999999999


Q ss_pred             eCCeEEEEEecCCccc
Q 046966          278 IDDRRICVDFSQSVSK  293 (299)
Q Consensus       278 i~g~~l~v~~a~~~~~  293 (299)
                      ++||.|.......+.+
T Consensus       339 fdgRql~A~i~DG~t~  354 (382)
T KOG1548|consen  339 FDGRQLTASIWDGKTK  354 (382)
T ss_pred             ecceEEEEEEeCCcce
Confidence            9999999998776543

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.27  E-value=0.00065  Score=63.34  Aligned_cols=78  Identities=24%  Similarity=0.304  Sum_probs=63.4

Q ss_pred             CCCceEEEEcCCCCCC------HHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC-Ce
Q 046966          209 PPDNVLFVCQLNPVTE------DEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID-DR  281 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~------e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~-g~  281 (299)
                      .-...|+|.|.|---.      ..-|..+|+++|.+....++.+..+| ++||.|++|.+..+|+.|++.|||+.++ .+
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknH  134 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNH  134 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccc
Confidence            3467899999986432      23467889999999999998886555 9999999999999999999999999887 66


Q ss_pred             EEEEEe
Q 046966          282 RICVDF  287 (299)
Q Consensus       282 ~l~v~~  287 (299)
                      ...|..
T Consensus       135 tf~v~~  140 (698)
T KOG2314|consen  135 TFFVRL  140 (698)
T ss_pred             eEEeeh
Confidence            666654

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

Probab=97.15  E-value=0.0036  Score=55.72  Aligned_cols=81  Identities=23%  Similarity=0.313  Sum_probs=66.6

Q ss_pred             CCCCCceEEEEcC--CCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC--CeE
Q 046966          207 VKPPDNVLFVCQL--NPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID--DRR  282 (299)
Q Consensus       207 ~~~~~~~v~v~nL--~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~--g~~  282 (299)
                      ...++..|.+.-|  -+.++-+-|..+....|.|.++-|.+.  +|.   .|.|+|.+.+.|++|.++|||..|.  -..
T Consensus       116 s~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ngV---QAmVEFdsv~~AqrAk~alNGADIYsGCCT  190 (494)
T KOG1456|consen  116 SATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NGV---QAMVEFDSVEVAQRAKAALNGADIYSGCCT  190 (494)
T ss_pred             CCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cce---eeEEeechhHHHHHHHhhccccccccccee
Confidence            3445666665544  456889999999999999999988764  554   7899999999999999999999875  678


Q ss_pred             EEEEecCCcc
Q 046966          283 ICVDFSQSVS  292 (299)
Q Consensus       283 l~v~~a~~~~  292 (299)
                      |+|+||+|.+
T Consensus       191 LKIeyAkP~r  200 (494)
T KOG1456|consen  191 LKIEYAKPTR  200 (494)
T ss_pred             EEEEecCcce
Confidence            9999999875

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=96.99  E-value=0.0024  Score=59.14  Aligned_cols=65  Identities=25%  Similarity=0.244  Sum_probs=60.1

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcc-cCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHH
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFS-QFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK  272 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~-~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~  272 (299)
                      -.+.+|||||+||.-++-++|..+|. -||.|..+.|-.|++-+..+|-|-|+|.+-.+-.+||.+
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            35788999999999999999999998 799999999999988889999999999999999999865

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

Probab=96.87  E-value=0.008  Score=53.61  Aligned_cols=79  Identities=23%  Similarity=0.274  Sum_probs=69.3

Q ss_pred             CCCCCceEEEEcCCCC-CCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          207 VKPPDNVLFVCQLNPV-TEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~-~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      ...+++.+.|-+|... ++-+.|..+|-.||.|.+++.++.+     .|-|.|++.+..+.++|+..||+..+-|.+|.|
T Consensus       283 g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v  357 (494)
T KOG1456|consen  283 GGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNV  357 (494)
T ss_pred             CCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEE
Confidence            3457889999999775 5667899999999999999998863     367999999999999999999999999999999


Q ss_pred             EecCC
Q 046966          286 DFSQS  290 (299)
Q Consensus       286 ~~a~~  290 (299)
                      .+++.
T Consensus       358 ~~SkQ  362 (494)
T KOG1456|consen  358 CVSKQ  362 (494)
T ss_pred             eeccc
Confidence            98874

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

Probab=96.81  E-value=0.0045  Score=49.96  Aligned_cols=64  Identities=23%  Similarity=0.302  Sum_probs=57.1

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID  279 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~  279 (299)
                      .+...|.|.+||++.++++|++...+-|.+....+.+|       |++.|+|...++.+-|+..|....+.
T Consensus       113 rSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  113 RSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             ccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhcccccc
Confidence            45678999999999999999999999999999988877       48899999999999999998887654

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.79  E-value=0.0086  Score=46.87  Aligned_cols=74  Identities=23%  Similarity=0.457  Sum_probs=52.0

Q ss_pred             CCCCceEEEEcCCC------CCCH---HHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCcee
Q 046966          208 KPPDNVLFVCQLNP------VTED---EDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALI  278 (299)
Q Consensus       208 ~~~~~~v~v~nL~~------~~~e---~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i  278 (299)
                      .|+..+|.|.-+.+      ...+   .+|.+.|..||.+.-++.+-+        --+|+|.+.++|.+|+ .|+|..+
T Consensus        24 GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaal-s~dg~~v   94 (146)
T PF08952_consen   24 GPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAAL-SLDGIQV   94 (146)
T ss_dssp             --TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHH-HGCCSEE
T ss_pred             CCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHH-ccCCcEE
Confidence            46788888876662      2222   256778889998877776544        3589999999999999 5799999


Q ss_pred             CCeEEEEEecCC
Q 046966          279 DDRRICVDFSQS  290 (299)
Q Consensus       279 ~g~~l~v~~a~~  290 (299)
                      +|+.|+|+...|
T Consensus        95 ~g~~l~i~LKtp  106 (146)
T PF08952_consen   95 NGRTLKIRLKTP  106 (146)
T ss_dssp             TTEEEEEEE---
T ss_pred             CCEEEEEEeCCc
Confidence            999999998665

; PDB: 1UFW_A 2DNR_A.

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=96.72  E-value=0.005  Score=57.79  Aligned_cols=66  Identities=24%  Similarity=0.337  Sum_probs=53.6

Q ss_pred             HHHHHhcccCCCeEEEEEeec-C--CCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCCc
Q 046966          226 EDLHVIFSQFGTVVSAEILRD-Y--RTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSV  291 (299)
Q Consensus       226 ~~L~~~f~~~G~i~~~~~~~~-~--~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~~  291 (299)
                      ++++.-+++||.|..|.++++ .  ...-..|--||+|.+.+++++|.++|+|..+.||.+...|-...
T Consensus       424 Edvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeD  492 (500)
T KOG0120|consen  424 EDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDED  492 (500)
T ss_pred             HHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHH
Confidence            345566789999999998876 2  22234566799999999999999999999999999999987643

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=96.69  E-value=0.0044  Score=40.03  Aligned_cols=52  Identities=21%  Similarity=0.412  Sum_probs=40.0

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHH
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY  270 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al  270 (299)
                      +.|-|.+.++...+. +...|.+||+|..+.+..      ..-..++.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPE------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCC------CCcEEEEEECCHHHHHhhC
Confidence            456788888776644 555888999999987752      2348899999999999985

>TIGR03268 methan_mark_3 putative methanogenesis marker protein 3

Probab=96.65  E-value=0.0094  Score=55.42  Aligned_cols=99  Identities=18%  Similarity=0.312  Sum_probs=65.7

Q ss_pred             eEEEEecCCCChHHHHHHHHhhhCCCc----CCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCCCCCce
Q 046966           11 DIVIDLFVDKCPRTTNNFLQHCKNKYY----NGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKHDKVG   86 (299)
Q Consensus        11 ~i~ieL~~~~~P~~~~nF~~l~~~~~y----~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~G   86 (299)
                      .+.+||. ..+|.++++|+.+.+.|.+    .-.+|-+   ...+|                +...+.| +  +....+|
T Consensus       202 y~evE~~-~~~p~s~EH~la~~~~G~~~Vd~~tsTfi~---d~~L~----------------g~~~p~E-n--~~~R~rG  258 (503)
T TIGR03268       202 YVEVELD-PNAPVSVEHFLALMEDGTFRVDYRTSTFIS---DDSLR----------------GLDKPEE-N--IEKRRRG  258 (503)
T ss_pred             EEEEEEc-CCCChhHHHHHHHHhCCeEEEeeeecceEe---ccccc----------------CccCCcc-c--cCcccce
Confidence            4667765 5789999999999999853    2222211   11111                1123444 2  2234789


Q ss_pred             EEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhc
Q 046966           87 TVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQA  136 (299)
Q Consensus        87 ~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~  136 (299)
                      +|.+.+.|..  ...-||.-.+-++  .-.|+|+|+|+.||++++--+..
T Consensus       259 tVTVRn~G~G--~G~VYIYredr~s--s~sHtvVG~V~~GiELid~a~~G  304 (503)
T TIGR03268       259 AVTVRNSGVG--EGRVYIYREDRPS--SLSHNVVGHVTRGIELIDIAQEG  304 (503)
T ss_pred             eEEEEeeccC--ceeEEEEcCCCCC--CcccceeEEEecceeeeecccCC
Confidence            9999998753  3578998887433  34699999999999999876544

A single member of this protein family is found in each of the first ten complete genome sequences of archaeal methanogens, and nowhere else. This protein family was detected by the method of partial phylogenetic profiling (see Haft, et al., 2006). The functions of proteins in this family are unknown, but their role is likely one essential to methanogenesis.

>PRK00969 hypothetical protein; Provisional

Probab=96.55  E-value=0.01  Score=55.27  Aligned_cols=99  Identities=22%  Similarity=0.344  Sum_probs=65.5

Q ss_pred             eEEEEecCCCChHHHHHHHHhhhCCCc----CCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCCCCCce
Q 046966           11 DIVIDLFVDKCPRTTNNFLQHCKNKYY----NGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKHDKVG   86 (299)
Q Consensus        11 ~i~ieL~~~~~P~~~~nF~~l~~~~~y----~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~G   86 (299)
                      .+.+||. ..+|.++++|+.+.+.|.+    .-.+|-+   ...+|               + ...+.| +  +....+|
T Consensus       205 y~eve~~-~~~p~s~EH~la~~~~G~f~Vd~~tstfI~---d~~L~---------------g-~~~p~E-n--~~~R~~G  261 (508)
T PRK00969        205 YVEVELD-PGAPKSVEHFLALLEDGTFEVDFETSTFIA---DDRLQ---------------G-LKIPEE-N--FEPRRRG  261 (508)
T ss_pred             EEEEEEc-CCCCchHHHHHHHHhCCeEEEeeeecceEe---ecccc---------------C-ccCCcc-c--cCccccc
Confidence            3566776 4689999999999999853    2222211   11111               1 123444 2  2233789


Q ss_pred             EEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhc
Q 046966           87 TVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQA  136 (299)
Q Consensus        87 ~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~  136 (299)
                      +|.+.+.|.+  ...-||.-.+-++  .-.|+|+|+|+.||++++--...
T Consensus       262 tVTVRt~G~g--~G~vYIyredr~s--s~sHtvVG~V~~GiELi~~a~~G  307 (508)
T PRK00969        262 TVTVRTAGVG--VGKVYIYREDRPS--SLSHTVVGRVTHGIELIDFAKEG  307 (508)
T ss_pred             eEEEEeeccC--ceeEEEECCCCCC--CccceeEEEEecceeeeecccCC
Confidence            9999998753  4578999887433  34699999999999999876544

>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=96.47  E-value=0.017  Score=42.58  Aligned_cols=79  Identities=16%  Similarity=0.272  Sum_probs=51.0

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEE-EeecC------CCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCe-E
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAE-ILRDY------RTGESLCYAFVEFEKREACEQAYFKMNNALIDDR-R  282 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~-~~~~~------~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~-~  282 (299)
                      .+-|.|-+.|+. .-..+.+.|++||.|.+.. +.++.      ........-.|.|.++.+|.+||.. ||..++|. .
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            456888899887 4466788999999998764 11100      0011234778999999999999965 99999875 5


Q ss_pred             EEEEecCCc
Q 046966          283 ICVDFSQSV  291 (299)
Q Consensus       283 l~v~~a~~~  291 (299)
                      +-|.++++.
T Consensus        84 vGV~~~~~~   92 (100)
T PF05172_consen   84 VGVKPCDPA   92 (100)
T ss_dssp             EEEEE-HHH
T ss_pred             EEEEEcHHh
Confidence            558877543

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.

>PRK00969 hypothetical protein; Provisional

Probab=96.47  E-value=0.03  Score=52.31  Aligned_cols=116  Identities=18%  Similarity=0.253  Sum_probs=74.4

Q ss_pred             EEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCC
Q 046966            2 SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLK   81 (299)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~   81 (299)
                      ...|.|+.|.|+|||.  ....++.-|+..++.  |.|...+=..+ .-+.+|-...+            +...  ..-.
T Consensus        52 ~y~IkTtkG~i~Iel~--~~~~~~~~w~e~yk~--~e~~~i~W~s~-~~vAfGp~~s~------------l~p~--~~~~  112 (508)
T PRK00969         52 KYRIKTTKGEIVIELT--EENESVDFWLENYKE--FEGKSLRWTSR-SAVAFGPFESD------------LEPS--REEY  112 (508)
T ss_pred             eEEEEccCceEEEEEc--cCcchhhHHHHhHHh--hcCCceEeccc-cceeEcccccC------------cccc--cCcc
Confidence            3578999999999999  555667777777765  56666654323 33334432211            1111  1111


Q ss_pred             CCCceEEEEEcCCCCCCcceEEEEecCCCCCCCC-CceEEEEeecCHHHHHHHHhc
Q 046966           82 HDKVGTVGMASAGRDLNASQFYITLRDNLHYLDE-KHTIFGEVAEGLETLTRINQA  136 (299)
Q Consensus        82 ~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~-~~~vfG~V~~G~~vl~~i~~~  136 (299)
                      ...++-|.+.-.|-+...+.+.|+..+....+.- .--+||+||.|..+|+++...
T Consensus       113 ~y~r~DV~lg~~G~dp~~thLIfsk~~h~a~YG~p~~gv~grVi~Gk~vl~~L~~~  168 (508)
T PRK00969        113 EYERWDVVLSLSGFDPSETHLIFSKRDHSADYGAPNDGVIGRVVGGKRVLDRLTDG  168 (508)
T ss_pred             eeecccEEEEccCCCCCCceEEEEecchhhhhCCCCCCceEEEccchhhHhhccCC
Confidence            2256788888888777778888887764222221 128999999999999999654

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=96.38  E-value=0.018  Score=53.51  Aligned_cols=66  Identities=18%  Similarity=0.248  Sum_probs=49.6

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCC---CCCeee---EEEEEecCHHHHHHHHHHhC
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYR---TGESLC---YAFVEFEKREACEQAYFKMN  274 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~---~g~~~g---~afv~f~~~~~a~~al~~l~  274 (299)
                      ..-.++||||+||++++|+.|...|..||.+. +.++....   --..+|   |+|+.|+++.++..-+.+..
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~  327 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACS  327 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHh
Confidence            34578999999999999999999999999853 44542111   112356   99999999988887766543

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=96.37  E-value=0.0026  Score=57.53  Aligned_cols=77  Identities=22%  Similarity=0.313  Sum_probs=59.5

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCc-eeCCeEEEEEecCC
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNA-LIDDRRICVDFSQS  290 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~-~i~g~~l~v~~a~~  290 (299)
                      ..+|++||.+.++..+|..+|+.----.+-.++      ...||+||.+.+..+|.+|++.++|. .+.|+++.+.++-+
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 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFL------VKSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCccee------eecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            368999999999999999999743100011111      12479999999999999999999996 47899999999888


Q ss_pred             cccc
Q 046966          291 VSKI  294 (299)
Q Consensus       291 ~~~~  294 (299)
                      ++++
T Consensus        76 kkqr   79 (584)
T KOG2193|consen   76 KKQR   79 (584)
T ss_pred             HHHH
Confidence            7543

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.35  E-value=0.013  Score=56.37  Aligned_cols=75  Identities=21%  Similarity=0.285  Sum_probs=65.3

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeE-EEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVV-SAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~-~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      +.|-+.|+|+.++-+||-++|..|-.+- +|.+-++ ..|+..|-+-|.|++.++|.+|...|++..|..|.+.+.+
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n-d~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            3788899999999999999999996554 5555554 6799999999999999999999999999999999998864

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=96.25  E-value=0.0059  Score=54.60  Aligned_cols=79  Identities=19%  Similarity=0.191  Sum_probs=65.5

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCe-E--EEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTV-V--SAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i-~--~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      +..+|.+.+||+..+.++|-.+|..|..- .  -+.++.+ ..|+..|-|||+|.+.++|..|....+.+....|-|.|-
T Consensus       279 ~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N-~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvf  357 (508)
T KOG1365|consen  279 SKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN-GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVF  357 (508)
T ss_pred             CCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc-CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEe
Confidence            35689999999999999999999988642 2  3667776 678999999999999999999998888777778888876


Q ss_pred             ecC
Q 046966          287 FSQ  289 (299)
Q Consensus       287 ~a~  289 (299)
                      -+.
T Consensus       358 p~S  360 (508)
T KOG1365|consen  358 PCS  360 (508)
T ss_pred             ecc
Confidence            543

>TIGR03268 methan_mark_3 putative methanogenesis marker protein 3

Probab=96.22  E-value=0.06  Score=50.24  Aligned_cols=116  Identities=15%  Similarity=0.191  Sum_probs=74.2

Q ss_pred             EEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCC
Q 046966            2 SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLK   81 (299)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~   81 (299)
                      ...|.|+.|.|+|+|-.  ...+++-|+..++.  |-|...+=..+. -+.+|-...+            +...  ..-.
T Consensus        48 ~y~IkTtkG~i~iel~~--~~~~~~~w~e~y~~--~e~~~i~W~s~~-~vAfGp~~sd------------l~p~--~~~~  108 (503)
T TIGR03268        48 EYLIKTTKGEVVIELTP--NTEAGKFWSEIYKE--LEGKQIRWTTPQ-EVAFGPFPSD------------LEPS--REPS  108 (503)
T ss_pred             eEEEEccCceEEEEecC--CchHHHHHHHHHHh--hcCCceeecchh-heeeCcccCC------------cccc--CCcc
Confidence            35789999999999993  55577777777665  455555433222 2333322211            1111  1111


Q ss_pred             CCCceEEEEEcCCCCCCcceEEEEecCCCCCCC--CCceEEEEeecCHHHHHHHHhc
Q 046966           82 HDKVGTVGMASAGRDLNASQFYITLRDNLHYLD--EKHTIFGEVAEGLETLTRINQA  136 (299)
Q Consensus        82 ~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld--~~~~vfG~V~~G~~vl~~i~~~  136 (299)
                      ...++-|.+.-+|-+...+.+.|+..+....+.  ...-+||+||.|..+|+++...
T Consensus       109 ~y~r~DV~lg~~G~d~~~thLIfsk~~h~~~YG~p~~~gvigrvi~Gk~vl~~L~~~  165 (503)
T TIGR03268       109 EYERWDVILSLSGFDPDETHIIFSKKRHAAEYGVPDENGIIARVVGGKRVIDRLSDG  165 (503)
T ss_pred             eeecccEEEEccCCCCCCceEEEEecchhhhhCCCCCCCEEEEEccchhhHhhccCC
Confidence            235678888888877778888888876432221  1468999999999999999654

A single member of this protein family is found in each of the first ten complete genome sequences of archaeal methanogens, and nowhere else. This protein family was detected by the method of partial phylogenetic profiling (see Haft, et al., 2006). The functions of proteins in this family are unknown, but their role is likely one essential to methanogenesis.

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.08  E-value=0.0065  Score=59.83  Aligned_cols=77  Identities=26%  Similarity=0.413  Sum_probs=66.9

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC--CeEEEEE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID--DRRICVD  286 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~--g~~l~v~  286 (299)
                      .+.+.+|+++|++++....|...|..||.|..+.+-.    |  .-||+|+|.+...++.|++.|.|..|+  .++++|.
T Consensus       453 t~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h----g--q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvd  526 (975)
T KOG0112|consen  453 TPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH----G--QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVD  526 (975)
T ss_pred             ccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc----C--CcceeeecccCccchhhHHHHhcCcCCCCCcccccc
Confidence            4567899999999999999999999999998876522    2  249999999999999999999999998  4779999


Q ss_pred             ecCCc
Q 046966          287 FSQSV  291 (299)
Q Consensus       287 ~a~~~  291 (299)
                      |+.+.
T Consensus       527 la~~~  531 (975)
T KOG0112|consen  527 LASPP  531 (975)
T ss_pred             cccCC
Confidence            98864

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=95.96  E-value=0.0074  Score=54.75  Aligned_cols=68  Identities=26%  Similarity=0.300  Sum_probs=56.1

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeec---CCC--CC--------eeeEEEEEecCHHHHHHHHHHhCC
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRD---YRT--GE--------SLCYAFVEFEKREACEQAYFKMNN  275 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~---~~~--g~--------~~g~afv~f~~~~~a~~al~~l~~  275 (299)
                      -+.++|.+-|||.+-.-+-|.++|+.+|.|..|+|...   +.+  +.        .+-+|+|+|...+.|.+|.+.|+.
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            47899999999999888999999999999999998765   222  11        245789999999999999988765


Q ss_pred             c
Q 046966          276 A  276 (299)
Q Consensus       276 ~  276 (299)
                      .
T Consensus       309 e  309 (484)
T KOG1855|consen  309 E  309 (484)
T ss_pred             h
Confidence            3

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=95.83  E-value=0.0038  Score=61.09  Aligned_cols=80  Identities=16%  Similarity=0.130  Sum_probs=71.2

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      ...++|.|+|+..|.+.|+.++..+|.+.+.+++.. ..|+.+|.|++.|.+..++.+++..+....+.-+.+.|..++|
T Consensus       736 K~~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  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTV-RAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhh-hccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            567999999999999999999999999999998887 5899999999999999999999988777777777788888666


Q ss_pred             c
Q 046966          291 V  291 (299)
Q Consensus       291 ~  291 (299)
                      .
T Consensus       815 ~  815 (881)
T KOG0128|consen  815 E  815 (881)
T ss_pred             c
Confidence            3

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=95.81  E-value=0.027  Score=48.75  Aligned_cols=65  Identities=22%  Similarity=0.304  Sum_probs=53.4

Q ss_pred             HHHHHHhcccCCCeEEEEEeecCCCCCeeeE-EEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          225 DEDLHVIFSQFGTVVSAEILRDYRTGESLCY-AFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       225 e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~-afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ++++++-+++||.|..|-|...+......-. -||+|...++|.+|+-.|||..++||.++..|-+
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            3567788899999999988776544433333 4999999999999999999999999999988765

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=95.44  E-value=0.0059  Score=51.82  Aligned_cols=62  Identities=19%  Similarity=0.351  Sum_probs=49.2

Q ss_pred             HHHHhcc-cCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          227 DLHVIFS-QFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       227 ~L~~~f~-~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ++...|+ +||+|+++.+-.+ ..-...|-.||.|...++|++|+..||+..+.|++|...++-
T Consensus        84 d~f~E~~~kygEiee~~Vc~N-l~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDN-LGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhcc-cchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            3333444 8999998765544 233457888999999999999999999999999999988754

>COG4070 Predicted peptidyl-prolyl cis-trans isomerase (rotamase), cyclophilin family [Posttranslational modification, protein turnover, chaperones]

Probab=95.16  E-value=0.059  Score=48.62  Aligned_cols=99  Identities=22%  Similarity=0.340  Sum_probs=64.2

Q ss_pred             eEEEEecCCCChHHHHHHHHhhhCCCc----CCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCCCCCce
Q 046966           11 DIVIDLFVDKCPRTTNNFLQHCKNKYY----NGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKHDKVG   86 (299)
Q Consensus        11 ~i~ieL~~~~~P~~~~nF~~l~~~~~y----~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~G   86 (299)
                      .+.+||- ..+|+++++|+.|.+.|.+    .-.+|.-.   ..+|               . ..++.| +..+  ..+|
T Consensus       204 y~eve~s-~nsP~saEH~lalmedG~lri~~~tntfis~---~~lq---------------~-~~~~~e-n~d~--RerG  260 (512)
T COG4070         204 YFEVELS-RNSPKSAEHFLALMEDGTLRIDVTTNTFISD---DTLQ---------------E-EKVPEE-NFDL--RERG  260 (512)
T ss_pred             EEEEEeC-CCCchhHHHHHHHhhcceEEEEEeccceeec---cccc---------------c-ccCChh-hhhh--hhcc
Confidence            4667776 4579999999999998742    22222111   0011               1 113444 3333  3689


Q ss_pred             EEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhc
Q 046966           87 TVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQA  136 (299)
Q Consensus        87 ~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~  136 (299)
                      .++..|.|-+  ...-||.-.+-.+.+  .|.+.|+|+.||+.+|-..++
T Consensus       261 ~iTvRn~Gvg--eGrvYIyRedR~ss~--sHnvVGrV~eGiELid~a~eG  306 (512)
T COG4070         261 AITVRNVGVG--EGRVYIYREDRPSSL--SHNVVGRVIEGIELIDLAEEG  306 (512)
T ss_pred             eEEEEeeecc--cceEEEEecCCCCcc--ccceeeeeecceEEEEecccC
Confidence            9999988753  357888887744443  589999999999999876444

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=95.16  E-value=0.03  Score=52.93  Aligned_cols=82  Identities=20%  Similarity=0.283  Sum_probs=64.6

Q ss_pred             CCCCCCCCCceEEEEcCCCCCCHHHHHHhccc-CCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCcee---
Q 046966          203 PDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQ-FGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALI---  278 (299)
Q Consensus       203 ~~~~~~~~~~~v~v~nL~~~~~e~~L~~~f~~-~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i---  278 (299)
                      ++.......+.|||.||-.-+|.-+|+.+++. .|.|... || |    +-+..+||.|.+.++|-....+|||..+   
T Consensus       436 pSPsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-Wm-D----kIKShCyV~yss~eEA~atr~AlhnV~WP~s  509 (718)
T KOG2416|consen  436 PSPSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WM-D----KIKSHCYVSYSSVEEAAATREALHNVQWPPS  509 (718)
T ss_pred             CCCCCCCccceEeeecccccchHHHHHHHHhhccCchHHH-HH-H----HhhcceeEecccHHHHHHHHHHHhccccCCC
Confidence            34445567889999999999999999999985 4555554 33 2    2345789999999999999999999764   


Q ss_pred             CCeEEEEEecCC
Q 046966          279 DDRRICVDFSQS  290 (299)
Q Consensus       279 ~g~~l~v~~a~~  290 (299)
                      +++.|.+.|...
T Consensus       510 NPK~L~adf~~~  521 (718)
T KOG2416|consen  510 NPKHLIADFVRA  521 (718)
T ss_pred             CCceeEeeecch
Confidence            578899998764

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=95.12  E-value=0.012  Score=52.04  Aligned_cols=81  Identities=19%  Similarity=0.339  Sum_probs=62.3

Q ss_pred             CceEEEEcCCCCCCHH-HHH--HhcccCCCeEEEEEeecCC--CC-CeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 046966          211 DNVLFVCQLNPVTEDE-DLH--VIFSQFGTVVSAEILRDYR--TG-ESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC  284 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~-~L~--~~f~~~G~i~~~~~~~~~~--~g-~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~  284 (299)
                      ...+||-+|+.....+ .|+  +.|++||.|.++.+..++.  .+ ....-++|+|...++|.+||...+|..+.|+.++
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            4678888898776544 443  6799999999998877652  11 1123379999999999999999999999999988


Q ss_pred             EEecCCc
Q 046966          285 VDFSQSV  291 (299)
Q Consensus       285 v~~a~~~  291 (299)
                      ..+...+
T Consensus       157 a~~gttk  163 (327)
T KOG2068|consen  157 ASLGTTK  163 (327)
T ss_pred             HhhCCCc
Confidence            8877654

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=95.12  E-value=0.18  Score=35.57  Aligned_cols=57  Identities=21%  Similarity=0.385  Sum_probs=43.0

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNN  275 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~  275 (299)
                      ..+..+|+ .|..+...||..+|+.||.| .|.++.|.       -|||...+.+.|..++..+..
T Consensus         8 RdHVFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    8 RDHVFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             GCCEEEEE---TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEECCCHHHHHHHHHHTT
T ss_pred             cceEEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEeecHHHHHHHHHHhcc
Confidence            35666776 99999999999999999986 46666662       799999999999999887753

; 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.

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=94.88  E-value=0.0019  Score=63.17  Aligned_cols=68  Identities=28%  Similarity=0.314  Sum_probs=58.0

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID  279 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~  279 (299)
                      .++|+.||++.+.+.+|...|..+|.+..+++.-...+++.+|+||+.|...+.+.+|+....++.++
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            46899999999999999999999999888777655568899999999999999999999665544443

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=94.53  E-value=0.062  Score=48.40  Aligned_cols=75  Identities=16%  Similarity=0.338  Sum_probs=59.7

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecC---CCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDY---RTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~---~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ...|.|.||.+.++.++++.+|+..|.|..++|.-..   .-....-.+||.|.+...+..|. .|.++.+-++.|.|-
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdraliv~   84 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDRALIVR   84 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeeeeEEEE
Confidence            3489999999999999999999999999998876532   22344568999999999999996 567777666666554

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=94.51  E-value=0.047  Score=49.00  Aligned_cols=70  Identities=21%  Similarity=0.158  Sum_probs=51.8

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccC----CCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQF----GTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRI  283 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~----G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l  283 (299)
                      -.|...+||+++++.++.++|.+-    |....+..+.. -.|+..|=|||.|..+++|+.|+.. |...++-|-|
T Consensus       162 vivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYI  235 (508)
T KOG1365|consen  162 VIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYI  235 (508)
T ss_pred             eEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHH
Confidence            356678999999999999999632    23345544444 4788999999999999999999965 4444444433

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=94.50  E-value=0.22  Score=33.12  Aligned_cols=55  Identities=16%  Similarity=0.297  Sum_probs=44.3

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccC---CCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHh
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQF---GTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM  273 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~---G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l  273 (299)
                      ..+|+|.++. +++.++++.+|..|   .....+.|+-|.       -+-|.|.+.+.|.+||.+|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            5689999986 47788999999988   234688888873       4679999999999999764

>PF12903 DUF3830: Protein of unknown function (DUF3830); InterPro: IPR024532 This is a family of bacterial and archaeal proteins

Probab=94.40  E-value=0.34  Score=38.15  Aligned_cols=116  Identities=17%  Similarity=0.083  Sum_probs=57.9

Q ss_pred             EEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCc--EEEecCCCCCCCCCCCCCCCcccccccccCCCC
Q 046966            5 IETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDF--IAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKH   82 (299)
Q Consensus         5 ~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~--~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~~   82 (299)
                      |+..--.++.+|..+.||+||+.|.++.   =|.+..+|-...|.  ++.-++...           .....|+.+..+ 
T Consensus         3 ~~~~g~~~~A~l~~d~AP~Tcaa~~~~L---P~~~~~~HarwSG~ei~~~l~~~~~-----------~~~~~EN~T~~P-   67 (147)
T PF12903_consen    3 LTKRGVSFTARLLDDKAPKTCAAFWEAL---PLKGKVIHARWSGEEIWIPLPDFDP-----------FEPGRENHTVTP-   67 (147)
T ss_dssp             ETTTTEEEEEEE-TTTSHHHHHHHHHH-----EEEE-EE-SSSSSEEEEEEE--SS-----------S---S-SEESS--
T ss_pred             EecCCeEEEEEEcccCChHHHHHHHHhC---CCCCcEEEEEEECcEEEEECCCcCc-----------CCCCCCcCcccC-
Confidence            3334457899999999999999999987   34455555433332  233333221           112334344433 


Q ss_pred             CCceEEEEEc---CCCC--CC-cceEEEEecCCCCCCCCC-----ceEEEEeecCHHHHHHHHhc
Q 046966           83 DKVGTVGMAS---AGRD--LN-ASQFYITLRDNLHYLDEK-----HTIFGEVAEGLETLTRINQA  136 (299)
Q Consensus        83 ~~~G~l~~~~---~~~~--~~-~s~FfI~~~~~~~~ld~~-----~~vfG~V~~G~~vl~~i~~~  136 (299)
                       .+|-|.+.=   ...+  .. -++.-|.++-+.-.+.++     -.+|++|++|++-+.++.+.
T Consensus        68 -~pGdi~~~y~~~~~~~~~pg~~~e~~i~yg~g~~~f~~~~G~l~GN~FatI~egle~la~~~~~  131 (147)
T PF12903_consen   68 -IPGDILLYYEPGSAWGGNPGGISETEIFYGYGNLLFASKMGWLPGNHFATITEGLEELAEACRD  131 (147)
T ss_dssp             --TTEEEEE-----------E-EEEEEEE-SSS---EETTTEE--EEEEEEEEESHHHHHHHHHH
T ss_pred             -CCCcEEEEecCCccccCCCcceEEEEEEEeeCceEecCCccccceeEEEEEcCCHHHHHHHHHH
Confidence             457777761   0001  11 245555555332222211     36999999999988887553

The structure of one of family members, A0JVT3 from SWISSPROT, has been characterised and shown to contain a cyclophilin-like fold.; PDB: 3KOP_B.

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=93.96  E-value=0.041  Score=53.02  Aligned_cols=80  Identities=25%  Similarity=0.054  Sum_probs=65.6

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEE-EEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVS-AEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~-~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ...+..|||..||..+++.++..+|...-.|+. |.|...+ +++.++-|||.|...+++..|...-+.+.++.|.|+|+
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            345779999999999999999999987666665 6666653 67888999999999888888887667777888999987


Q ss_pred             ec
Q 046966          287 FS  288 (299)
Q Consensus       287 ~a  288 (299)
                      -.
T Consensus       510 si  511 (944)
T KOG4307|consen  510 SI  511 (944)
T ss_pred             ch
Confidence            53

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=93.95  E-value=0.073  Score=45.34  Aligned_cols=62  Identities=24%  Similarity=0.324  Sum_probs=54.7

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhC
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMN  274 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~  274 (299)
                      ..|||.||..-++.+.|...|+.||.+....+..| ..++..+=++|.|...-.+.+|+..++
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHhc
Confidence            67999999999999999999999999997766666 568888899999999999999987763

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=93.88  E-value=0.015  Score=57.35  Aligned_cols=82  Identities=20%  Similarity=0.298  Sum_probs=67.5

Q ss_pred             CCCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          206 DVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       206 ~~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      +....+.+||+|||+..+++.+|+..|..+|.+.++.+-..+ -+...-|||+.|.+.+.+.+|...+.+..|..-.+++
T Consensus       367 DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~  445 (975)
T KOG0112|consen  367 DDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRI  445 (975)
T ss_pred             cchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCcccc
Confidence            334457899999999999999999999999999998876542 3444569999999999999999999998887656666


Q ss_pred             Eec
Q 046966          286 DFS  288 (299)
Q Consensus       286 ~~a  288 (299)
                      .+.
T Consensus       446 glG  448 (975)
T KOG0112|consen  446 GLG  448 (975)
T ss_pred             ccc
Confidence            655

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=93.27  E-value=0.31  Score=39.89  Aligned_cols=81  Identities=12%  Similarity=0.150  Sum_probs=50.0

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhccc-CCCe---EEEE--EeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCC---
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQ-FGTV---VSAE--ILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDD---  280 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~-~G~i---~~~~--~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g---  280 (299)
                      ...+|.|.+||++.+++++.+.+.. ++.-   ....  ..........-.-|||.|.+.+++..-...++|+.+.+   
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            4678999999999999999997776 6654   2222  11111111223568999999999999999999987642   


Q ss_pred             --eEEEEEecCC
Q 046966          281 --RRICVDFSQS  290 (299)
Q Consensus       281 --~~l~v~~a~~  290 (299)
                        .+..|.+|--
T Consensus        86 ~~~~~~VE~Apy   97 (176)
T PF03467_consen   86 NEYPAVVEFAPY   97 (176)
T ss_dssp             -EEEEEEEE-SS
T ss_pred             CCcceeEEEcch
Confidence              3455666554

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.

>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=92.43  E-value=2.1  Score=32.11  Aligned_cols=65  Identities=15%  Similarity=0.248  Sum_probs=47.2

Q ss_pred             eEEEEcCCCCCCHHHHHHhcccC-CCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC
Q 046966          213 VLFVCQLNPVTEDEDLHVIFSQF-GTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID  279 (299)
Q Consensus       213 ~v~v~nL~~~~~e~~L~~~f~~~-G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~  279 (299)
                      .+.+...|+.++-++|..+.+.+ ..|..++++++  ...++-.+.+.|.+.++|..-...+||+.++
T Consensus        15 ~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird--~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   15 LCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRD--GTPNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             EEEEEeCcccccHHHHHHhhhcccccEEEEEEeeC--CCCceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            34444455555556676555555 35668888887  3346778899999999999999999998866

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=91.72  E-value=0.84  Score=35.62  Aligned_cols=73  Identities=22%  Similarity=0.279  Sum_probs=53.8

Q ss_pred             CCCCceEEEEcCCCCCCH-HHHHH---hcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 046966          208 KPPDNVLFVCQLNPVTED-EDLHV---IFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRI  283 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e-~~L~~---~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l  283 (299)
                      .++-.+|.|.=|..++.. +||+.   .++.||+|.++.+.     |+  --|.|.|.+..+|-+|+.+++. ..-|..+
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----Gr--qsavVvF~d~~SAC~Av~Af~s-~~pgtm~  154 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----GR--QSAVVVFKDITSACKAVSAFQS-RAPGTMF  154 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----CC--ceEEEEehhhHHHHHHHHhhcC-CCCCceE
Confidence            456778888877776653 45554   45789999998763     32  3689999999999999999876 4566677


Q ss_pred             EEEec
Q 046966          284 CVDFS  288 (299)
Q Consensus       284 ~v~~a  288 (299)
                      .+.|-
T Consensus       155 qCsWq  159 (166)
T PF15023_consen  155 QCSWQ  159 (166)
T ss_pred             Eeecc
Confidence            76663

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=91.50  E-value=0.22  Score=44.05  Aligned_cols=82  Identities=17%  Similarity=0.086  Sum_probs=66.6

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ...++.|++++.+.+.+.+...++...|....+..........++|++++.|...+.+..|+.....+.+.++.+...+.
T Consensus        86 ~~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~  165 (285)
T KOG4210|consen   86 GSSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLN  165 (285)
T ss_pred             cccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCccc
Confidence            35788999999999999988899999998877777665577889999999999999999999765555666766665554


Q ss_pred             CC
Q 046966          289 QS  290 (299)
Q Consensus       289 ~~  290 (299)
                      ..
T Consensus       166 ~~  167 (285)
T KOG4210|consen  166 TR  167 (285)
T ss_pred             cc
Confidence            43

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=90.17  E-value=0.47  Score=44.79  Aligned_cols=61  Identities=18%  Similarity=0.241  Sum_probs=47.9

Q ss_pred             CCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCce---eC-CeEEEEEecCCccccc
Q 046966          235 FGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNAL---ID-DRRICVDFSQSVSKIW  295 (299)
Q Consensus       235 ~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~---i~-g~~l~v~~a~~~~~~~  295 (299)
                      .|.-..+.++.|-.+....|||||.|-+.+++.++.+++||+.   ++ .+.+.+.||+...+.|
T Consensus       413 ~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itYArIQGk~~  477 (549)
T KOG4660|consen  413 KGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITYARIQGKEA  477 (549)
T ss_pred             cCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeehhhhhchHH
Confidence            5555667777776777788999999999999999999999986   33 4556788888665543

>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=89.83  E-value=1  Score=31.03  Aligned_cols=58  Identities=17%  Similarity=0.281  Sum_probs=33.9

Q ss_pred             CCCHHHHHHhcccCCCe-----EEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          222 VTEDEDLHVIFSQFGTV-----VSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       222 ~~~e~~L~~~f~~~G~i-----~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .++..+|..++..-+.+     -.+.+..+        |+||+-.. +.|..++..|++..+.|++++|+.|
T Consensus        12 g~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   12 GLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             T--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             CCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            46777887777655433     46666444        88999874 5888999999999999999999865

; PDB: 2G0C_A 3MOJ_B.

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=89.62  E-value=0.22  Score=47.89  Aligned_cols=74  Identities=23%  Similarity=0.292  Sum_probs=62.8

Q ss_pred             CCCCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 046966          205 ADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC  284 (299)
Q Consensus       205 ~~~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~  284 (299)
                      ....++..++||+|+...+..+-++.++..+|.|.++....         |||..|.......+|+..++...++|..+.
T Consensus        34 ~~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~  104 (668)
T KOG2253|consen   34 FQPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLI  104 (668)
T ss_pred             ccCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhh
Confidence            34456788999999999999999999999999887764322         999999999999999999999889888876


Q ss_pred             EEe
Q 046966          285 VDF  287 (299)
Q Consensus       285 v~~  287 (299)
                      +..
T Consensus       105 ~~~  107 (668)
T KOG2253|consen  105 ENV  107 (668)
T ss_pred             ccc
Confidence            654

>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=89.32  E-value=0.95  Score=37.31  Aligned_cols=62  Identities=23%  Similarity=0.316  Sum_probs=44.2

Q ss_pred             CHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhC--CceeCCeEEEEEecCCc
Q 046966          224 EDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMN--NALIDDRRICVDFSQSV  291 (299)
Q Consensus       224 ~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~--~~~i~g~~l~v~~a~~~  291 (299)
                      ..+.|+++|..++.+.....+..      -+-..|.|.+.+.|.+|...|+  +..+.|..+++-|+...
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~s------FrRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKS------FRRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETT------TTEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCC------CCEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            34789999999998887665543      2245799999999999999999  99999999999998644

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=89.31  E-value=1.7  Score=29.34  Aligned_cols=55  Identities=20%  Similarity=0.360  Sum_probs=42.3

Q ss_pred             CCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          222 VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       222 ~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      .++-++++.-+..|+-   .++..+ .+|    | ||.|.+..+|++|....++..+.+..|.+
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 GVTVEDFKKRLRKYRW---DRIRDD-RTG----F-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCc---ceEEec-CCE----E-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            3567889999999863   234444 233    3 89999999999999999999988877654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>COG4070 Predicted peptidyl-prolyl cis-trans isomerase (rotamase), cyclophilin family [Posttranslational modification, protein turnover, chaperones]

Probab=87.39  E-value=6.1  Score=36.13  Aligned_cols=116  Identities=18%  Similarity=0.213  Sum_probs=69.9

Q ss_pred             EEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCCC
Q 046966            3 VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKH   82 (299)
Q Consensus         3 v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~~   82 (299)
                      -.|.|+.|.|.|+|-...  .+...|...|+.  |-|+.++-..|.-+.. |-..              ..-|....-..
T Consensus        53 ~~IktttG~i~ielt~~~--~e~k~~~e~yke--l~~~~i~Wts~~eva~-Gp~~--------------~dle~s~e~~e  113 (512)
T COG4070          53 YRIKTTTGEIRIELTDES--VEGKRWAEHYKE--LEGTYIRWTSPEEVAF-GPFE--------------ADLEPSRETGE  113 (512)
T ss_pred             EEEEccCCcEEEEecccc--chhHHHHHHHHh--ccCceEEecChhHccc-cccc--------------ccccccccccc
Confidence            468899999999999633  356778888877  6677666554443332 2111              11111111111


Q ss_pred             CCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcc
Q 046966           83 DKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAV  137 (299)
Q Consensus        83 ~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~  137 (299)
                      ..+-.+.|.-+|-+...+-|.|+-....-.+.-.--..|+|+.|-.+++++....
T Consensus       114 f~~~dvvl~l~g~dpdethiiiskkr~~~~Yg~~~d~~G~Vv~Gr~lidrL~~gd  168 (512)
T COG4070         114 FEAFDVVLSLSGFDPDETHIIISKKRHVAEYGAPEDIHGRVVGGRNLIDRLSRGD  168 (512)
T ss_pred             cccceEEEEccCCCCCcceEEEEecceeeEecCCccccceEecchhhhhHhccCC
Confidence            2334566666665656677888776532222222345689999999999996653

>PF04126 Cyclophil_like: Cyclophilin-like; InterPro: IPR007256 Proteins of this family have no known function

Probab=86.64  E-value=4.2  Score=30.98  Aligned_cols=102  Identities=15%  Similarity=0.191  Sum_probs=58.6

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhh----hCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccc-cc
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHC----KNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFV-DE   75 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~----~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~-~e   75 (299)
                      |.+.|+-....+.++|+..   .|++.|++..    +-..|.+-.++.. |-.                      .+ ++
T Consensus         1 mkI~i~i~~~~~~a~L~d~---~ta~~~~~~LPlt~~~~~~g~E~y~~~-p~~----------------------l~~~~   54 (120)
T PF04126_consen    1 MKIKITIGGQEIEAELNDS---PTARAFAAQLPLTVTMNDWGNEKYFSL-PLK----------------------LPTEE   54 (120)
T ss_dssp             EEEEEEETTEEEEEEEETT---HHHHHHHHC-SEEEEEEECTTEEEEE--S---------------------------SS
T ss_pred             CeEEEEECCEEEEEEECCC---HHHHHHHHhCCeEEEHHHCCceEEEeC-CCC----------------------CCccc
Confidence            7788888989999999977   7899998876    1122422222221 110                      01 11


Q ss_pred             cccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCC-------CCCCCceEEEEeecCHHHHHHHHhc
Q 046966           76 IRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLH-------YLDEKHTIFGEVAEGLETLTRINQA  136 (299)
Q Consensus        76 ~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~-------~ld~~~~vfG~V~~G~~vl~~i~~~  136 (299)
                       ..+- ....|.|+.-..+     ..|.|-+++ .+       .+-....++|+|++|.+.+..+...
T Consensus        55 -~~~~-~~~~GDi~Yw~pg-----~~l~ifyg~-~p~S~~~~~~~~~~v~~lG~i~~~~~~l~~~~~~  114 (120)
T PF04126_consen   55 -NPRS-SVEAGDIAYWPPG-----GALAIFYGD-TPISEGGEIRPASPVNVLGRIVSDLENLKEVKGG  114 (120)
T ss_dssp             -SEES-SB-TTEEEEECCC-----TEEEEESS---TT--TTSB--SSSEEEEEEEEC-GGGGGG--TT
T ss_pred             -Cccc-cccCceEEEeCCC-----CEEEEEecC-cccccccccccCCcceEEEEECCCHHHHhhCCCC
Confidence             1111 1256888886543     358888876 33       3445688999999999999888443

; PDB: 2KA0_A 1ZX8_C 2NNZ_A.

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=85.45  E-value=0.57  Score=46.47  Aligned_cols=75  Identities=21%  Similarity=0.221  Sum_probs=61.7

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC--CeEEEEEec
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID--DRRICVDFS  288 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~--g~~l~v~~a  288 (299)
                      ..+.++.|.+-+.+-..|..+|..||.+.+++..++-      -.|.|.|...+.|-.|+.+|+|.++.  |-+.+|.+|
T Consensus       298 qp~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~a  371 (1007)
T KOG4574|consen  298 QPKQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFA  371 (1007)
T ss_pred             cchhhhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEec
Confidence            3455556666677888899999999999998776663      37899999999999999999998754  888999998


Q ss_pred             CCc
Q 046966          289 QSV  291 (299)
Q Consensus       289 ~~~  291 (299)
                      +.-
T Consensus       372 k~~  374 (1007)
T KOG4574|consen  372 KTL  374 (1007)
T ss_pred             ccc
Confidence            864

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=85.45  E-value=0.51  Score=43.79  Aligned_cols=68  Identities=22%  Similarity=0.278  Sum_probs=53.2

Q ss_pred             EEcCCCCC-CHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          216 VCQLNPVT-EDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       216 v~nL~~~~-~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      +.-.|+.. +-++|...|.+||.|..|.+-..      .--|.|+|.+..+|-.|. ..++..|++|.|+|.|-++
T Consensus       377 lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~-~s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  377 LEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAY-ASHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             hhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchh-ccccceecCceeEEEEecC
Confidence            33344444 34789999999999999876443      236889999999997776 4589999999999999776

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=83.44  E-value=6.2  Score=34.75  Aligned_cols=69  Identities=20%  Similarity=0.280  Sum_probs=48.3

Q ss_pred             EEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEE-EEEecCC
Q 046966          214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRI-CVDFSQS  290 (299)
Q Consensus       214 v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l-~v~~a~~  290 (299)
                      |-|.++|+.-. .-+-.+|.+||.|++....   .+|   .+-+|.|.+..+|++||. .+|..|+|-.+ -|.-+..
T Consensus       200 VTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~---~ng---NwMhirYssr~~A~KALs-kng~ii~g~vmiGVkpCtD  269 (350)
T KOG4285|consen  200 VTVFGFPPGQV-SIVLNLFSRCGEVVKHVTP---SNG---NWMHIRYSSRTHAQKALS-KNGTIIDGDVMIGVKPCTD  269 (350)
T ss_pred             EEEeccCccch-hHHHHHHHhhCeeeeeecC---CCC---ceEEEEecchhHHHHhhh-hcCeeeccceEEeeeecCC
Confidence            44557776533 4566789999999876432   223   377999999999999995 49999887653 3555443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	299
1xwn_A	174	Solution Structure Of Cyclophilin Like 1(Ppil1) And		7e-26
2x7k_A	166	The Crystal Structure Of Ppil1 In Complex With Cycl		8e-26
2k7n_A	203	Solution Structure Of The Ppil1 Bound To A Fragment		8e-26
2a2n_A	176	Crystal Structure Of The Peptidylprolyl Isomerase D		1e-25
2oju_A	167	X-Ray Structure Of Complex Of Human Cyclophilin J W		7e-25
1xyh_A	161	Crystal Structure Of Recombinant Human Cyclophilin		8e-25
1zkc_A	197	Crystal Structure Of The Cyclophiln_ring Domain Of		4e-23
2fu0_A	160	Plasmodium Falciparum Cyclophilin Pfe0505w Putative		5e-21
2poe_A	185	Crystal Structure Of Cryptosporidium Parvum Cycloph		9e-21
2hq6_A	185	Structure Of The Cyclophilin_cecyp16-like Domain Of		1e-19
2b71_A	196	Plasmodium Yoelii Cyclophilin-Like Protein Length =		3e-18
1h0p_A	182	Cyclophilin_5 From C. Elegans Length = 182		4e-18
3ich_A	188	Crystal Structure Of Cyclophilin B At 1.2 A Resolut		2e-17
1cyn_A	178	Cyclophilin B Complexed With [d-(Cholinylester)ser8		2e-17
4fru_A	185	Crystal Structure Of Horse Wild-Type Cyclophilin B		3e-17
4frv_A	185	Crystal Structure Of Mutated Cyclophilin B That Cau		3e-17
3k2c_A	193	Crystal Structure Of Peptidyl-Prolyl Cis-Trans Isom		6e-17
2rmc_A	182	Crystal Structure Of Murine Cyclophilin C Complexed		1e-16
2gw2_A	198	Crystal Structure Of The Peptidyl-Prolyl Isomerase		1e-16
2wfj_A	179	Atomic Resolution Crystal Structure Of The Ppiase D		2e-16
3bkp_A	232	Crystal Structure Of The Toxoplasma Gondii Cyclophi		4e-16
2esl_A	190	Human Cyclophilin C In Complex With Cyclosporin A L		5e-16
1ihg_A	370	Bovine Cyclophilin 40, Monoclinic Form Length = 370		9e-16
1qoi_A	177	U4U6 SNRNP-Specific Cyclophilin Snucyp-20 Length =		1e-15
1c5f_A	177	Crystal Structure Of The Cyclophilin-Like Domain Fr		1e-15
2wfi_A	179	Atomic Resolution Crystal Structure Of The Ppiase D		4e-15
2haq_A	172	Crystal Structure Of Cyclophilin A From Leishmania		4e-15
1xo7_A	166	Crystal Structure Of Cyclophilin From Trypanosoma C		5e-15
3bt8_A	172	Crystal Structure Of Mutant Cyclophilin (R147a) Fro		7e-15
2c3b_A	172	The Crystal Structure Of Aspergillus Fumigatus Cycl		7e-15
1qng_A	170	Plasmodium Falciparum Cyclophilin Complexed With Cy		1e-14
1qnh_A	170	Plasmodium Falciparum Cyclophilin (Double Mutant) C		3e-14
2he9_A	192	Structure Of The Peptidylprolyl Isomerase Domain Of		3e-14
2cfe_A	162	The 1.5 A Crystal Structure Of The Malassezia Sympo		3e-14
1w74_A	191	X-Ray Structure Of Peptidyl-Prolyl Cis-Trans Isomer		4e-14
2bit_X	165	Crystal Structure Of Human Cyclophilin D At 1.7 A R		5e-14
3r49_A	166	Human Cyclophilin D Complexed With Quinolin-8-Amine		6e-14
3qyu_A	164	Crystal Structure Of Human Cyclophilin D At 1.54 A		6e-14
2z6w_A	165	Crystal Structure Of Human Cyclophilin D In Complex		6e-14
2r99_A	173	Crystal Structure Of Cyclophilin Abh-Like Domain Of		6e-14
4i9y_A	167	Structure Of The C-terminal Domain Of Nup358 Length		7e-14
1zmf_A	165	C Domain Of Human Cyclophilin-33(Hcyp33) Length = 1		8e-14
1ist_A	162	Crystal Structure Of Yeast Cyclophilin A, Cpr1 Leng		1e-12
3bo7_A	201	Crystal Structure Of Toxoplasma Gondii Peptidyl-Pro		2e-12
3uch_A	174	Crystal Structure Of A Hypotherical Peptidyl-Prolyl		2e-12
2xgy_B	173	Complex Of Rabbit Endogenous Lentivirus (Relik)caps		3e-12
3pmp_A	164	Crystal Structure Of Cyclophilin A From Moniliophth		4e-12
3k0r_A	165	Cryogenic Structure Of Cypa Mutant Arg55lys Length		4e-12
4dgd_A	165	Trimcyp Cyclophilin Domain From Macaca Mulatta: H70		4e-12
2plu_A	186	Crystal Structure Of Cryptosporidium Parvum Cycloph		4e-12
2rma_A	165	Crystal Structures Of Cyclophilin A Complexed With		5e-12
2wlw_A	165	Structure Of The N-Terminal Capsid Domain Of Hiv-2		5e-12
3o7t_A	164	Crystal Structure Of Cyclophilin A From Moniliophth		5e-12
1bck_A	165	Human Cyclophilin A Complexed With 2-Thr Cyclospori		5e-12
5cyh_A	164	Cyclophilin A Complexed With Dipeptide Gly-Pro Leng		5e-12
1m9e_A	164	X-Ray Crystal Structure Of Cyclophilin AHIV-1 Ca N-		5e-12
1z81_A	229	Crystal Structure Of Cyclophilin From Plasmodium Yo		5e-12
3rdd_A	184	Human Cyclophilin A Complexed With An Inhibitor Len		6e-12
2ck1_A	172	The Structure Of Oxidised Cyclophilin A From S. Man		6e-12
3k0o_A	165	Room Temperature Structure Of Cypa Mutant Ser99thr		7e-12
2x83_B	163	Evolutionary Basis Of Hiv Restriction By The Antire		7e-12
2alf_A	164	Crystal Structure Of Human Cypa Mutant K131a Length		8e-12
2x2c_K	165	Acetyl-Cypa:cyclosporine Complex Length = 165		2e-11
2x2a_A	165	Free Acetyl-Cypa Trigonal Form Length = 165		2e-11
2x25_B	169	Free Acetyl-Cypa Orthorhombic Form Length = 169		6e-11
1dyw_A	173	Biochemical And Structural Characterization Of A Di		9e-11
1aws_A	164	Secypa Complexed With Hagpia (Pseudo-Symmetric Mono		2e-10
3t1u_A	163	Crystal Structure Of The Complex Of Cyclophilin-a E		2e-10
2hqj_A	183	Cyclophilin From Leishmania Major Length = 183		2e-10
1j2a_A	166	Structure Of E. Coli Cyclophilin B K163t Mutant Len		1e-09
1clh_A	166	Three-Dimensional Solution Structure Of Escherichia		1e-09
2nul_A	164	Peptidylprolyl Isomerase From E. Coli Length = 164		1e-09
1lop_A	164	Cyclophilin A Complexed With Succinyl-Ala-Pro-Ala-P		2e-09
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		2e-07
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		2e-07
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		2e-07
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		3e-07
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		4e-07
1sxl_A	97	Resonance Assignments And Solution Structure Of The		7e-07
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		1e-06
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		1e-06
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		1e-06
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		1e-06
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		1e-06
3s6m_A	167	The Structure Of A Peptidyl-Prolyl Cis-Trans Isomer		2e-06
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		2e-06
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		2e-06
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		3e-06
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		4e-06
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		5e-06
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		8e-06
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		1e-05
2sxl_A	88	Sex-Lethal Rbd1, Nmr, Minimized Average Structure L		1e-05
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		2e-05
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		2e-05
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		2e-05
2khc_A	118	Bruno Rrm3+ Length = 118		2e-05
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		4e-05
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		4e-05
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		5e-05
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		6e-05
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		7e-05
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		8e-05
2fc8_A	102	Solution Structure Of The Rrm_1 Domain Of Ncl Prote		1e-04
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		1e-04
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		1e-04
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		2e-04
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		2e-04
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		2e-04
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		2e-04
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		2e-04
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		2e-04
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		3e-04
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		3e-04
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		5e-04
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		5e-04
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		7e-04
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		8e-04
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		9e-04

>pdb|1XWN|A Chain A, Solution Structure Of Cyclophilin Like 1(Ppil1) And Insights Into Its Interaction With Skip Length = 174

Iteration: 1
 Score =  114 bits (285), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 58/153 (37%), Positives = 85/153 (55%), Gaps = 2/153 (1%)
Query: 2   SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQXXXXXXXXX 61
           +V +ETS+G IV++L+    P+T  NF +  +  YYNG  FH I KDF+ Q         
Sbjct: 13  NVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGR 72
Query: 62  XXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFG 121
              S+Y  + F DE+  DLK    G + MA+AG D N SQF++TL     +LD KHTIFG
Sbjct: 73  GGASIYGKQ-FEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPT-QWLDGKHTIFG 130
Query: 122 EVAEGLETLTRINQAVVDEENRPPQQIIIKQTY 154
            V +G+  + R+     + ++RP   + I + Y
Sbjct: 131 RVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAY 163

>pdb|2X7K|A Chain A, The Crystal Structure Of Ppil1 In Complex With Cyclosporine A Suggests A Binding Mode For Skip Length = 166

Iteration: 1
 Score =  114 bits (284), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 58/153 (37%), Positives = 85/153 (55%), Gaps = 2/153 (1%)
Query: 2   SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQXXXXXXXXX 61
           +V +ETS+G IV++L+    P+T  NF +  +  YYNG  FH I KDF+ Q         
Sbjct: 13  NVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGR 72
Query: 62  XXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFG 121
              S+Y  + F DE+  DLK    G + MA+AG D N SQF++TL     +LD KHTIFG
Sbjct: 73  GGASIYGKQ-FEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPT-QWLDGKHTIFG 130
Query: 122 EVAEGLETLTRINQAVVDEENRPPQQIIIKQTY 154
            V +G+  + R+     + ++RP   + I + Y
Sbjct: 131 RVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAY 163

>pdb|2K7N|A Chain A, Solution Structure Of The Ppil1 Bound To A Fragment Of Skip Length = 203

Iteration: 1
 Score =  114 bits (284), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 58/153 (37%), Positives = 85/153 (55%), Gaps = 2/153 (1%)
Query: 2   SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQXXXXXXXXX 61
           +V +ETS+G IV++L+    P+T  NF +  +  YYNG  FH I KDF+ Q         
Sbjct: 13  NVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGR 72
Query: 62  XXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFG 121
              S+Y  + F DE+  DLK    G + MA+AG D N SQF++TL     +LD KHTIFG
Sbjct: 73  GGASIYGKQ-FEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPT-QWLDGKHTIFG 130
Query: 122 EVAEGLETLTRINQAVVDEENRPPQQIIIKQTY 154
            V +G+  + R+     + ++RP   + I + Y
Sbjct: 131 RVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAY 163

>pdb|2A2N|A Chain A, Crystal Structure Of The Peptidylprolyl Isomerase Domain Of Human Ppwd1 Length = 176

Iteration: 1
 Score =  113 bits (283), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 58/144 (40%), Positives = 82/144 (56%), Gaps = 2/144 (1%)
Query: 2   SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQXXXXXXXXX 61
           S +I TS+GDI   LF  +CP+T  NF  H +N YYNG  FH I K F+ Q         
Sbjct: 23  SAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNGYYNGHTFHRIIKGFMIQTGDPTGTGM 82
Query: 62  XXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFG 121
              S++    F DE  + L+HD+  T+ MA+AG + N SQF+IT+     +LD KHT+FG
Sbjct: 83  GGESIWGGE-FEDEFHSTLRHDRPYTLSMANAGSNTNGSQFFITVVPTP-WLDNKHTVFG 140
Query: 122 EVAEGLETLTRINQAVVDEENRPP 145
            V +G+E + RI+   V+ +   P
Sbjct: 141 RVTKGMEVVQRISNVKVNPKTDKP 164

>pdb|2OJU|A Chain A, X-Ray Structure Of Complex Of Human Cyclophilin J With Cyclosporin A Length = 167

Iteration: 1
 Score =  110 bits (276), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 63/160 (39%), Positives = 90/160 (56%), Gaps = 3/160 (1%)
Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQXXXXXXXX 60
           MSV + T +GDI I++F ++ P+T  NFL  C + YYNGC+FH   K F+ Q        
Sbjct: 7   MSVTLHTDVGDIKIEVFCERTPKTCENFLALCASNYYNGCIFHRNIKGFMVQTGDPTGTG 66
Query: 61  XXXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIF 120
               S++  + F DE    LKH+  G V MA+ G + N SQF+IT     H LD K+T+F
Sbjct: 67  RGGNSIWGKK-FEDEYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGKQPH-LDMKYTVF 124
Query: 121 GEVAEGLETLTRINQAVVDEEN-RPPQQIIIKQTYVLYPP 159
           G+V +GLETL  + +  V+E+  RP   + IK   +   P
Sbjct: 125 GKVIDGLETLDELEKLPVNEKTYRPLNDVHIKDITIHANP 164

>pdb|1XYH|A Chain A, Crystal Structure Of Recombinant Human Cyclophilin J Length = 161

Iteration: 1
 Score =  110 bits (276), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 63/160 (39%), Positives = 90/160 (56%), Gaps = 3/160 (1%)
Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQXXXXXXXX 60
           MSV + T +GDI I++F ++ P+T  NFL  C + YYNGC+FH   K F+ Q        
Sbjct: 1   MSVTLHTDVGDIKIEVFCERTPKTCENFLALCASNYYNGCIFHRNIKGFMVQTGDPTGTG 60
Query: 61  XXXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIF 120
               S++  + F DE    LKH+  G V MA+ G + N SQF+IT     H LD K+T+F
Sbjct: 61  RGGNSIWGKK-FEDEYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGKQPH-LDMKYTVF 118
Query: 121 GEVAEGLETLTRINQAVVDEEN-RPPQQIIIKQTYVLYPP 159
           G+V +GLETL  + +  V+E+  RP   + IK   +   P
Sbjct: 119 GKVIDGLETLDELEKLPVNEKTYRPLNDVHIKDITIHANP 158

>pdb|1ZKC|A Chain A, Crystal Structure Of The Cyclophiln_ring Domain Of Human Peptidylprolyl Isomerase (Cyclophilin)-Like 2 Isoform B Length = 197

Iteration: 1
 Score =  105 bits (261), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 66/176 (37%), Positives = 97/176 (55%), Gaps = 5/176 (2%)
Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQXXXXXXXXXX 62
           V + T+ GD+ ++L  D  P+T  NF++ CK  YY+G +FH   ++F+ Q          
Sbjct: 22  VRLHTNKGDLNLELHCDLTPKTCENFIRLCKKHYYDGTIFHRSIRNFVIQGGDPTGTGTG 81
Query: 63  XRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGE 122
             S Y  + F DE R +L H   G + MA++G + N SQF+IT R +  YLD+KHTIFG 
Sbjct: 82  GES-YWGKPFKDEFRPNLSHTGRGILSMANSGPNSNRSQFFITFR-SCAYLDKKHTIFGR 139
Query: 123 VAEGLETLTRINQAVVD-EENRPPQQIIIKQTYVLYPP-ELADDSIPEGEPKDELE 176
           V  G + LT +     D + +RP ++I I  T V   P E AD  I + E K +L+
Sbjct: 140 VVGGFDVLTAMENVESDPKTDRPKEEIRIDATTVFVDPYEEADAQIAQ-ERKTQLK 194

>pdb|2FU0|A Chain A, Plasmodium Falciparum Cyclophilin Pfe0505w Putative Cyclosporin- Binding Domain Length = 160

Iteration: 1
 Score = 98.2 bits (243), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 55/149 (36%), Positives = 80/149 (53%), Gaps = 2/149 (1%)
Query: 2   SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQXXXXXXXXX 61
           S +I T++GDI I LF  +C +T  NF  H  N YYN C+FH + K F+ Q         
Sbjct: 7   SAIIYTTMGDIHISLFYKECKKTVQNFSVHSINGYYNNCIFHRVIKHFMVQTGDPSGDGT 66
Query: 62  XXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFG 121
              S++ +  F DE    L H K   V MA+ G + N SQF+IT      +LD KHT+FG
Sbjct: 67  GGESIWGNE-FEDEFFDHLNHSKPFMVSMANCGPNTNGSQFFITTVP-CPWLDFKHTVFG 124
Query: 122 EVAEGLETLTRINQAVVDEENRPPQQIII 150
           +V +G + +  I +   D+ ++P + I I
Sbjct: 125 KVTQGSKIVLDIEKVRTDKRDKPLEDIKI 153

>pdb|2POE|A Chain A, Crystal Structure Of Cryptosporidium Parvum Cyclophilin Type Peptidyl-Prolyl Cis-Trans Isomerase Cgd2_1660 Length = 185

Iteration: 1
 Score = 97.4 bits (241), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 60/169 (35%), Positives = 90/169 (53%), Gaps = 7/169 (4%)
Query: 2   SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQXXXXXXXXX 61
            V I T+ GD+  +LF  +CP+   NFL    + YY   +FH   K FI Q         
Sbjct: 18  GVRIITNYGDLKFELFCSQCPKACKNFLALSASGYYKNTIFHKNIKGFIIQGGDPTGTGK 77
Query: 62  XXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGR----DLNASQFYITLRDNLHYLDEKH 117
              S+Y  R+F DEI  +LK+D+ G + MAS G     + N SQF+IT   +L  L+ ++
Sbjct: 78  GGESIY-GRYFDDEIYPELKYDRRGILSMASKGASKKPNTNGSQFFITY-SSLPQLNGEY 135
Query: 118 TIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPPELADDSI 166
            IFG++ +G ETL  +     D+ ++P  +IIIK   V++   +AD  I
Sbjct: 136 VIFGKLIDGFETLNTLENCPSDKSHKPIDEIIIKDI-VIHSNPIADQEI 183

>pdb|2HQ6|A Chain A, Structure Of The Cyclophilin_cecyp16-like Domain Of The Serologically Defined Colon Cancer Antigen 10 From Homo Sapiens Length = 185

Iteration: 1
 Score = 94.0 bits (232), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 55/158 (34%), Positives = 85/158 (53%), Gaps = 3/158 (1%)
Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQXXXXXXXXXX 62
           VL++T+ GDI I+L+  + P+   NF+Q C   YY+  +FH +   FI Q          
Sbjct: 27  VLLKTTAGDIDIELWSKEAPKACRNFIQLCLEAYYDNTIFHRVVPGFIVQGGDPTGTGSG 86
Query: 63  XRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGE 122
             S+Y    F DE  + L+ ++ G V MA+AG   N SQF+ TL      L+ KHTIFG+
Sbjct: 87  GESIYGAP-FKDEFHSRLRFNRRGLVAMANAGSHDNGSQFFFTL-GRADELNNKHTIFGK 144
Query: 123 V-AEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPP 159
           V  + +  + R+++  +D++ RP     IK   VL+ P
Sbjct: 145 VTGDTVYNMLRLSEVDIDDDERPHNPHKIKSCEVLFNP 182

>pdb|2B71|A Chain A, Plasmodium Yoelii Cyclophilin-Like Protein Length = 196

Iteration: 1
 Score = 89.0 bits (219), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 47/142 (33%), Positives = 77/142 (54%), Gaps = 2/142 (1%)
Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQXXXXXXXXXX 62
           + I T+LGD  ++L+    P+T  NF   C+  +Y+  +FH +  +F+ Q          
Sbjct: 41  ITIYTNLGDFEVELYWYHSPKTCLNFYTLCEMGFYDNTIFHRVIPNFVIQGGDPTGTGKG 100
Query: 63  XRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGE 122
            +S+Y + +F DEI  +LKH   G + M++ G + N+SQF+ITL   L +LD KHTIF  
Sbjct: 101 GKSIYGE-YFEDEINKELKHTGAGILSMSNNGPNTNSSQFFITLAP-LPHLDGKHTIFAR 158
Query: 123 VAEGLETLTRINQAVVDEENRP 144
           V++ +  +  I        N+P
Sbjct: 159 VSKNMTCIENIASVQTTATNKP 180

>pdb|1H0P|A Chain A, Cyclophilin_5 From C. Elegans Length = 182

Iteration: 1
 Score = 88.6 bits (218), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 51/146 (34%), Positives = 77/146 (52%), Gaps = 7/146 (4%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHCK---NKYYNGCLFHNIHKDFIAQXXXXXXX-XXXXR 64
           +G IVI LF    P+T  NF++  K    + Y G  FH +  DF+ Q            R
Sbjct: 20  IGRIVIGLFGKTVPKTATNFIELAKKPKGEGYPGSKFHRVIADFMIQGGDFTRGDGTGGR 79
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  +  +  LKH   G + MA+AG D N SQF+IT      +LD +H +FG++ 
Sbjct: 80  SIYGEKFADENFK--LKHYGAGWLSMANAGADTNGSQFFITTVKT-PWLDGRHVVFGKIL 136
Query: 125 EGLETLTRINQAVVDEENRPPQQIII 150
           EG++ + +I Q      +RP Q +II
Sbjct: 137 EGMDVVRKIEQTEKLPGDRPKQDVII 162

>pdb|3ICH|A Chain A, Crystal Structure Of Cyclophilin B At 1.2 A Resolution Length = 188

Iteration: 1
 Score = 86.3 bits (212), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 49/146 (33%), Positives = 76/146 (52%), Gaps = 7/146 (4%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXXX-XXXXXXXXR 64
           +G ++  LF    P+T +NF+      K   Y    FH + KDF+ Q            +
Sbjct: 29  VGRVIFGLFGKTVPKTVDNFVALATGEKGFGYKNSKFHRVIKDFMIQGGDFTRGDGTGGK 88
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y +RF  +  +  LKH   G V MA+AG+D N SQF+IT      +LD KH +FG+V 
Sbjct: 89  SIYGERFPDENFK--LKHYGPGWVSMANAGKDTNGSQFFITTVKTA-WLDGKHVVFGKVL 145
Query: 125 EGLETLTRINQAVVDEENRPPQQIII 150
           EG+E + ++     D  ++P + +II
Sbjct: 146 EGMEVVRKVESTKTDSRDKPLKDVII 171

>pdb|1CYN|A Chain A, Cyclophilin B Complexed With [d-(Cholinylester)ser8]-Cyclosporin Length = 178

Iteration: 1
 Score = 85.9 bits (211), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 49/146 (33%), Positives = 76/146 (52%), Gaps = 7/146 (4%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXXXXXXX-XXXXR 64
           +G ++  LF    P+T +NF+      K   Y    FH + KDF+ Q            +
Sbjct: 19  VGRVIFGLFGKTVPKTVDNFVALATGEKGFGYKNSKFHRVIKDFMIQGGDFTRGDGTGGK 78
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y +RF  +  +  LKH   G V MA+AG+D N SQF+IT      +LD KH +FG+V 
Sbjct: 79  SIYGERFPDENFK--LKHYGPGWVSMANAGKDTNGSQFFITTVKTA-WLDGKHVVFGKVL 135
Query: 125 EGLETLTRINQAVVDEENRPPQQIII 150
           EG+E + ++     D  ++P + +II
Sbjct: 136 EGMEVVRKVESTKTDSRDKPLKDVII 161

>pdb|4FRU|A Chain A, Crystal Structure Of Horse Wild-Type Cyclophilin B Length = 185

Iteration: 1
 Score = 85.5 bits (210), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 50/146 (34%), Positives = 76/146 (52%), Gaps = 7/146 (4%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXXX-XXXXXXXXR 64
           +G +VI LF    P+T +NF+      K   Y    FH + KDF+ Q            +
Sbjct: 26  IGRVVIGLFGKTVPKTVDNFVALATGEKGFGYKDSKFHRVIKDFMIQGGDFTRGDGTGGK 85
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y +RF  +  +  LKH   G V MA+AG+D N SQF+IT      +LD KH +FG+V 
Sbjct: 86  SIYGERFPDENFK--LKHYGPGWVSMANAGKDTNGSQFFITTV-KTAWLDGKHVVFGKVL 142
Query: 125 EGLETLTRINQAVVDEENRPPQQIII 150
           EG+E + ++     D  ++P + + I
Sbjct: 143 EGMEVVRKVETTKTDGRDKPLKDVTI 168

>pdb|4FRV|A Chain A, Crystal Structure Of Mutated Cyclophilin B That Causes Hyperelastosis Cutis In The American Quarter Horse Length = 185

Iteration: 1
 Score = 85.5 bits (210), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 50/146 (34%), Positives = 76/146 (52%), Gaps = 7/146 (4%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXXX-XXXXXXXXR 64
           +G +VI LF    P+T +NF+      K   Y    FH + KDF+ Q            +
Sbjct: 26  IGRVVIGLFGKTVPKTVDNFVALATGEKGFGYKDSKFHRVIKDFMIQGGDFTRGDGTGGK 85
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y +RF  +  +  LKH   G V MA+AG+D N SQF+IT      +LD KH +FG+V 
Sbjct: 86  SIYGERFPDENFK--LKHYGPGWVSMANAGKDTNGSQFFITTVKTA-WLDGKHVVFGKVL 142
Query: 125 EGLETLTRINQAVVDEENRPPQQIII 150
           EG+E + ++     D  ++P + + I
Sbjct: 143 EGMEVVRKVETTKTDGRDKPLKDVTI 168

>pdb|3K2C|A Chain A, Crystal Structure Of Peptidyl-Prolyl Cis-Trans Isomerase From Encephalitozoon Cuniculi At 1.9 A Resolution Length = 193

Iteration: 1
 Score = 84.7 bits (208), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 54/132 (40%), Positives = 71/132 (53%), Gaps = 7/132 (5%)
Query: 6   ETSLGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXX 61
           E SLG IV+ L  D  P+T  NF   C   K + Y G  FH I   F+ Q          
Sbjct: 38  EESLGRIVMKLEDDIVPKTAKNFRTLCERPKGEGYKGSTFHRIIPGFMVQGGDYTAHNGT 97
Query: 62  XXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFG 121
             RS+Y ++F  DE   +LKH K G + MA+ G   N SQF+ITL     +LDEKH +FG
Sbjct: 98  GGRSIYGEKF-PDE-NFELKHTKEGILSMANCGAHTNGSQFFITL-GKTQWLDEKHVVFG 154
Query: 122 EVAEGLETLTRI 133
           EV EG++ + +I
Sbjct: 155 EVVEGMDVVHKI 166

>pdb|2RMC|A Chain A, Crystal Structure Of Murine Cyclophilin C Complexed With Immunosuppressive Drug Cyclosporin A Length = 182

Iteration: 1
 Score = 83.6 bits (205), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 51/140 (36%), Positives = 72/140 (51%), Gaps = 7/140 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXXXXXXX-XXXXR 64
           +G IVI LF +  P+T  NF+      K   Y G +FH + KDF+ Q             
Sbjct: 21  VGRIVIGLFGNVVPKTVENFVALATGEKGYGYKGSIFHRVIKDFMIQGGDFTARDGTGGM 80
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y + F  +  +  LKH  +G V MA+AG D N SQF+ITL     +LD KH +FG+V 
Sbjct: 81  SIYGETFPDENFK--LKHYGIGWVSMANAGPDTNGSQFFITLTKPT-WLDGKHVVFGKVL 137
Query: 125 EGLETLTRINQAVVDEENRP 144
           +G+  +  I     D  +RP
Sbjct: 138 DGMTVVHSIELQATDGHDRP 157

>pdb|2GW2|A Chain A, Crystal Structure Of The Peptidyl-Prolyl Isomerase Domain Of Human Cyclophilin G Length = 198

Iteration: 1
 Score = 83.6 bits (205), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 52/160 (32%), Positives = 73/160 (45%), Gaps = 13/160 (8%)
Query: 10  GDIVIDLFVDKCPRTTNNFLQHCKNK-----------YYNGCLFHNIHKDFIAQXXXXXX 58
           G +V +LF D CP+T  NF   C  +           +Y  CLFH + KDF+ Q      
Sbjct: 41  GRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSE 100
Query: 59  XXXXXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHT 118
                       FF DE  A +KH+    + MA+ G+D N SQF+IT +   H LD  H 
Sbjct: 101 GNGRGGESIYGGFFEDESFA-VKHNAAFLLSMANRGKDTNGSQFFITTKPTPH-LDGHHV 158
Query: 119 IFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYP 158
           +FG+V  G E +  I     D  ++P  ++ I     L P
Sbjct: 159 VFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGELIP 198

>pdb|2WFJ|A Chain A, Atomic Resolution Crystal Structure Of The Ppiase Domain Of Human Cyclophilin G In Complex With Cyclosporin A Length = 179

Iteration: 1
 Score = 83.2 bits (204), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 51/152 (33%), Positives = 72/152 (47%), Gaps = 13/152 (8%)
Query: 10  GDIVIDLFVDKCPRTTNNFLQHCKNK-----------YYNGCLFHNIHKDFIAQXXXXXX 58
           G +V +LF D CP+T  NF   C  +           +Y  CLFH + KDF+ Q      
Sbjct: 24  GRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSE 83
Query: 59  XXXXXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHT 118
                       FF DE  A +KH+K   + MA+ G+D N SQF+IT +   H LD  H 
Sbjct: 84  GNGRGGESIYGGFFEDESFA-VKHNKEFLLSMANRGKDTNGSQFFITTKPTPH-LDGHHV 141
Query: 119 IFGEVAEGLETLTRINQAVVDEENRPPQQIII 150
           +FG+V  G E +  I     D  ++P  ++ I
Sbjct: 142 VFGQVISGQEVVREIENQKTDAASKPFAEVRI 173

>pdb|3BKP|A Chain A, Crystal Structure Of The Toxoplasma Gondii Cyclophilin, 49.m03261 Length = 232

Iteration: 1
 Score = 82.0 bits (201), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 61/192 (31%), Positives = 90/192 (46%), Gaps = 21/192 (10%)
Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQXX-XXXXXXX 61
           V++ TSLGD+ ++L+  +CP    NF+Q C   YY   +FH + KDFI Q          
Sbjct: 24  VVLHTSLGDLDVELWARECPLACRNFVQLCLEGYYVNTIFHRVVKDFIVQGGDPTGTGRG 83
Query: 62  XXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRD--------------LNASQFYITLR 107
              + ++ + F  E    LK    G VG+A+ GR                N +QF+ITL 
Sbjct: 84  GADTTFDGKPFDVETHPRLKFRYRGLVGVANLGRSSKDAENDERGRSLGTNGNQFFITL- 142
Query: 108 DNLHYLDEKHTIFGEV-AEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPP--ELADD 164
                L+  +T+FG+V    L  L + N   V +E+RP     IK   VL+ P  +L   
Sbjct: 143 ARADVLNNAYTLFGKVTGHTLYNLMKFNDLEVGKEDRPMTPPFIKSVDVLWNPFEDLVPR 202
Query: 165 SIPEGEP--KDE 174
            +P+  P  KDE
Sbjct: 203 RLPDAPPAQKDE 214

>pdb|2ESL|A Chain A, Human Cyclophilin C In Complex With Cyclosporin A Length = 190

Iteration: 1
 Score = 81.3 bits (199), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 51/140 (36%), Positives = 70/140 (50%), Gaps = 7/140 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXXXXXXXXXXXR- 64
           +G IVI LF    P+T  NF+      K   Y G  FH + KDF+ Q             
Sbjct: 29  VGRIVIGLFGKVVPKTVENFVALATGEKGYGYKGSKFHRVIKDFMIQGGDITTGDGTGGV 88
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y + F  +  +  LKH  +G V MA+AG D N SQF+ITL     +LD KH +FG+V 
Sbjct: 89  SIYGETFPDENFK--LKHYGIGWVSMANAGPDTNGSQFFITLTKPT-WLDGKHVVFGKVI 145
Query: 125 EGLETLTRINQAVVDEENRP 144
           +G+  +  I     D  +RP
Sbjct: 146 DGMTVVHSIELQATDGHDRP 165

>pdb|1IHG|A Chain A, Bovine Cyclophilin 40, Monoclinic Form Length = 370

Iteration: 1
 Score = 80.9 bits (198), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 54/180 (30%), Positives = 89/180 (49%), Gaps = 24/180 (13%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHCKNK-----------YYNGCLFHNIHKDFIAQXXX-X 56
           +G IV++LF D  P+T  NF   C  +           ++ GC FH I K F+ Q     
Sbjct: 29  VGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFS 88
Query: 57  XXXXXXXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEK 116
                   S+Y ++F  ++     KHDK G + MA+AG + N SQF+IT     H LD K
Sbjct: 89  NQNGTGGESIYGEKF--EDENFHYKHDKEGLLSMANAGSNTNGSQFFITTVPTPH-LDGK 145
Query: 117 HTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQT--------YVLYPPELADDSIPE 168
           H +FG+V +G+  + +I + V  +  +P +  +I +         + ++P + + DS P+
Sbjct: 146 HVVFGQVIKGM-GVAKILENVEVKGEKPAKLCVIAECGELKEGDDWGIFPKDGSGDSHPD 204

>pdb|1QOI|A Chain A, U4U6 SNRNP-Specific Cyclophilin Snucyp-20 Length = 177

Iteration: 1
 Score = 80.5 bits (197), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 46/153 (30%), Positives = 72/153 (47%), Gaps = 12/153 (7%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHCKNKY--------YNGCLFHNIHKDFIAQXXXXXXX- 59
           +G + I+LF D  P+T  NF Q C  ++        Y G  FH + KDF+ Q        
Sbjct: 24  VGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRVIKDFMIQGGDFVNGD 83
Query: 60  XXXXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTI 119
                S+Y   F  +  +  L+H   G + MA++G   N  QF+IT      +LD KH +
Sbjct: 84  GTGVASIYRGPFADENFK--LRHSAPGLLSMANSGPSTNGCQFFITC-SKCDWLDGKHVV 140
Query: 120 FGEVAEGLETLTRINQAVVDEENRPPQQIIIKQ 152
           FG++ +GL  + +I        N+P   ++I Q
Sbjct: 141 FGKIIDGLLVMRKIENVPTGPNNKPKLPVVISQ 173

>pdb|1C5F|A Chain A, Crystal Structure Of The Cyclophilin-Like Domain From Brugia Malayi Complexed With Cyclosporin A Length = 177

Iteration: 1
 Score = 80.1 bits (196), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 55/163 (33%), Positives = 81/163 (49%), Gaps = 16/163 (9%)
Query: 1   MSVLIETSL-GDIVIDLFVDKCPRTTNNFLQHC-----------KNKYYNGCLFHNIHKD 48
           + V I+ +L G IV++L+ D  PRT NNFL  C           K  +Y G  FH + K+
Sbjct: 11  LDVTIDGNLAGRIVMELYNDIAPRTCNNFLMLCTGMAGTGKISGKPLHYKGSTFHRVIKN 70
Query: 49  FIAQXXXXXXX-XXXXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLR 107
           F+ Q             S+Y   F  D+    +KHD+   V MA+ G + N SQF+IT  
Sbjct: 71  FMIQGGDFTKGDGTGGESIYGGMF--DDEEFVMKHDEPFVVSMANKGPNTNGSQFFITTT 128
Query: 108 DNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIII 150
              H L+  H +FG+V  G E +T+I     + +NRP   ++I
Sbjct: 129 PAPH-LNNIHVVFGKVVSGQEVVTKIEYLKTNSKNRPLADVVI 170

>pdb|2WFI|A Chain A, Atomic Resolution Crystal Structure Of The Ppiase Domain Of Human Cyclophilin G Length = 179

Iteration: 1
 Score = 78.6 bits (192), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 50/152 (32%), Positives = 71/152 (46%), Gaps = 13/152 (8%)
Query: 10  GDIVIDLFVDKCPRTTNNFLQHCKNK-----------YYNGCLFHNIHKDFIAQXXXXXX 58
           G +V +LF D CP+T  NF   C  +           +Y   LFH + KDF+ Q      
Sbjct: 24  GRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSXLFHRVVKDFMVQGGDFSE 83
Query: 59  XXXXXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHT 118
                       FF DE  A +KH+K   + MA+ G+D N SQF+IT +   H LD  H 
Sbjct: 84  GNGRGGESIYGGFFEDESFA-VKHNKEFLLSMANRGKDTNGSQFFITTKPTPH-LDGHHV 141
Query: 119 IFGEVAEGLETLTRINQAVVDEENRPPQQIII 150
           +FG+V  G E +  I     D  ++P  ++ I
Sbjct: 142 VFGQVISGQEVVREIENQKTDAASKPFAEVRI 173

>pdb|2HAQ|A Chain A, Crystal Structure Of Cyclophilin A From Leishmania Donovani Length = 172

Iteration: 1
 Score = 78.6 bits (192), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 51/153 (33%), Positives = 84/153 (54%), Gaps = 9/153 (5%)
Query: 3   VLIETS-LGDIVIDLFVDKCPRTTNNFLQHCKNKY---YNGCLFHNIHKDFIAQXXXXXX 58
           V+I++  LG I I LF    P TT NF Q C  ++   Y   +FH + ++F+ Q      
Sbjct: 18  VMIDSEPLGRITIGLFGKDAPLTTENFRQLCTGEHGFGYKDSIFHRVIQNFMIQGGDFTN 77
Query: 59  X-XXXXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKH 117
                 +S+Y ++F  DE   ++KH  VG + MA+AG + N SQF+IT      +LD +H
Sbjct: 78  FDGTGGKSIYGEKF-ADE-NLNVKH-FVGALSMANAGPNTNGSQFFITTAPT-PWLDGRH 133
Query: 118 TIFGEVAEGLETLTRINQAVVDEENRPPQQIII 150
            +FG+V +G++ + RI +   +  +RP + + I
Sbjct: 134 VVFGKVLDGMDVVLRIEKTKTNSHDRPVKPVKI 166

>pdb|1XO7|A Chain A, Crystal Structure Of Cyclophilin From Trypanosoma Cruzi Length = 166

Iteration: 1
 Score = 78.2 bits (191), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 48/152 (31%), Positives = 80/152 (52%), Gaps = 8/152 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNF--LQHCKNKY-YNGCLFHNIHKDFIAQXXXXXXX-XXXXR 64
           +G +VI LF +  P+T  NF  L   +N + Y G +FH + ++F+ Q            +
Sbjct: 19  VGRVVIGLFGNDVPKTVENFKQLASGENGFGYKGSIFHRVIRNFMIQGGDFTNFDGTGGK 78
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y  RF  D+    +KH  VG V MA+AG + N SQF++T      +LD +H +FG+V 
Sbjct: 79  SIYGTRF--DDENLKIKH-FVGAVSMANAGPNSNGSQFFVTTAPT-PWLDGRHVVFGKVV 134
Query: 125 EGLETLTRINQAVVDEENRPPQQIIIKQTYVL 156
           EG++ + ++        ++P + + I    VL
Sbjct: 135 EGMDVVKKVENTKTGLNDKPKKAVKINDCGVL 166

>pdb|3BT8|A Chain A, Crystal Structure Of Mutant Cyclophilin (R147a) From Leishmania Donovani Length = 172

Iteration: 1
 Score = 77.8 bits (190), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 51/153 (33%), Positives = 83/153 (54%), Gaps = 9/153 (5%)
Query: 3   VLIETS-LGDIVIDLFVDKCPRTTNNFLQHCKNKY---YNGCLFHNIHKDFIAQXXXXXX 58
           V+I++  LG I I LF    P TT NF Q C  ++   Y   +FH + ++F+ Q      
Sbjct: 18  VMIDSEPLGRITIGLFGKDAPLTTENFRQLCTGEHGFGYKDSIFHRVIQNFMIQGGDFTN 77
Query: 59  X-XXXXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKH 117
                 +S+Y ++F  DE   ++KH  VG + MA+AG + N SQF+IT      +LD  H
Sbjct: 78  FDGTGGKSIYGEKF-ADE-NLNVKH-FVGALSMANAGPNTNGSQFFITTAPT-PWLDGAH 133
Query: 118 TIFGEVAEGLETLTRINQAVVDEENRPPQQIII 150
            +FG+V +G++ + RI +   +  +RP + + I
Sbjct: 134 VVFGKVLDGMDVVLRIEKTKTNSHDRPVKPVKI 166

>pdb|2C3B|A Chain A, The Crystal Structure Of Aspergillus Fumigatus Cyclophilin Reveals 3d Domain Swapping Of A Central Element Length = 172

Iteration: 1
 Score = 77.8 bits (190), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 50/124 (40%), Positives = 66/124 (53%), Gaps = 7/124 (5%)
Query: 6   ETSLGDIVIDLFVDKCPRTTNNFLQHCK---NKYYNGCLFHNIHKDFIAQXX-XXXXXXX 61
           ET +G IV +LF    P+T  NF + CK    + Y    FH I  +F+ Q          
Sbjct: 18  ETKVGRIVFNLFDKDVPKTAKNFRELCKRPAGEGYRESTFHRIIPNFMIQGGDFTRGNGT 77
Query: 62  XXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFG 121
             RS+Y D+F  DE     KHDK G + MA+AG + N SQF+IT      +LD KH +FG
Sbjct: 78  GGRSIYGDKF-ADE-NFSRKHDKKGILSMANAGPNTNGSQFFITTAVT-SWLDGKHVVFG 134
Query: 122 EVAE 125
           EVA+
Sbjct: 135 EVAD 138

>pdb|1QNG|A Chain A, Plasmodium Falciparum Cyclophilin Complexed With Cyclosporin A Length = 170

Iteration: 1
 Score = 77.0 bits (188), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 47/133 (35%), Positives = 67/133 (50%), Gaps = 11/133 (8%)
Query: 7   TSLGDIVIDLFVDKCPRTTNNFLQHC---------KNKYYNGCLFHNIHKDFIAQXXXXX 57
           ++ G I+ +LF D  PRT  NF   C         KN +Y   +FH I   F+ Q     
Sbjct: 15  SNAGRIIFELFSDITPRTCENFRALCTGEKIGSRGKNLHYKNSIFHRIIPQFMCQGGDIT 74
Query: 58  XXXXXXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKH 117
                       R F DE   ++KHD+ G + MA+AG + N+SQF+ITL     +LD KH
Sbjct: 75  NGNGSGGESIYGRSFTDE-NFNMKHDQPGLLSMANAGPNTNSSQFFITLVP-CPWLDGKH 132
Query: 118 TIFGEVAEGLETL 130
            +FG+V EG+  +
Sbjct: 133 VVFGKVIEGMNVV 145

>pdb|1QNH|A Chain A, Plasmodium Falciparum Cyclophilin (Double Mutant) Complexed With Cyclosporin A Length = 170

Iteration: 1
 Score = 75.9 bits (185), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 47/133 (35%), Positives = 66/133 (49%), Gaps = 11/133 (8%)
Query: 7   TSLGDIVIDLFVDKCPRTTNNFLQHC---------KNKYYNGCLFHNIHKDFIAQXXXXX 57
           ++ G I+ +LF D  PRT  NF   C         KN +Y   +FH I   F+ Q     
Sbjct: 15  SNAGRIIFELFSDITPRTCENFRALCTGEKIGSRGKNLHYKNSIFHRIIPQFMCQGGDIT 74
Query: 58  XXXXXXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKH 117
                       R F DE   ++KHD+ G + MA+AG + N+SQF ITL     +LD KH
Sbjct: 75  NGNGSGGESIYGRSFTDE-NFNMKHDQPGLLSMANAGPNTNSSQFLITLVP-CPWLDGKH 132
Query: 118 TIFGEVAEGLETL 130
            +FG+V EG+  +
Sbjct: 133 VVFGKVIEGMNVV 145

>pdb|2HE9|A Chain A, Structure Of The Peptidylprolyl Isomerase Domain Of The Human Nk-Tumour Recognition Protein Length = 192

Iteration: 1
 Score = 75.9 bits (185), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 51/159 (32%), Positives = 70/159 (44%), Gaps = 13/159 (8%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC-----------KNKYYNGCLFHNIHKDFIAQXXXXX 57
           +G I+  LF D CP+T  NFL  C           K   Y G  FH + K+F+ Q     
Sbjct: 33  VGRIMFQLFSDICPKTCKNFLCLCSGEKGLGKTTGKKLCYKGSTFHRVVKNFMIQGGDFS 92
Query: 58  XXXXXXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKH 117
                        +F DE    LKHD+   + MA+ G+  N SQF+IT +   H LD  H
Sbjct: 93  EGNGKGGESIYGGYFKDE-NFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPH-LDGVH 150
Query: 118 TIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVL 156
            +FG V  G E + +I     D  +RP   + +    VL
Sbjct: 151 VVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDCGVL 189

>pdb|2CFE|A Chain A, The 1.5 A Crystal Structure Of The Malassezia Sympodialis Mala S 6 Allergen, A Member Of The Cyclophilin Pan- Allergen Family Length = 162

Iteration: 1
 Score = 75.5 bits (184), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 54/151 (35%), Positives = 74/151 (49%), Gaps = 8/151 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXXXXR 64
           LG I   LF D  P+T  NF   C   K   Y G  FH +  DF+ Q            +
Sbjct: 15  LGTIKFKLFDDVVPKTAANFRALCTGEKGFGYAGSHFHRVIPDFMLQGGDFTAGNGTGGK 74
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y  +F  DE    LKH+K G + MA+AG + N SQF+IT      +LD KH +FGEV 
Sbjct: 75  SIYGAKF-ADE-NFQLKHNKPGLLSMANAGPNTNGSQFFITTVVT-SWLDGKHVVFGEVI 131
Query: 125 EGLETLTRINQAVVDEENRPPQQIIIKQTYV 155
           +G+  +  I +A      +P  +I I +  V
Sbjct: 132 DGMNVVKAI-EAEGSGSGKPRSRIEIAKCGV 161

>pdb|1W74|A Chain A, X-Ray Structure Of Peptidyl-Prolyl Cis-Trans Isomerase A, Ppia, Rv0009, From Mycobacterium Tuberculosis. Length = 191

Iteration: 1
 Score = 75.1 bits (183), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 50/171 (29%), Positives = 80/171 (46%), Gaps = 22/171 (12%)
Query: 2   SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNK---------------YYNGCLFHNIH 46
           +  + T+ GDI I LF +  P+T  NF+   +                 +Y+G +FH + 
Sbjct: 25  TATLHTNRGDIKIALFGNHAPKTVANFVGLAQGTKDYSTQNASGGPSGPFYDGAVFHRVI 84
Query: 47  KDFIAQXXXXXXXXXXXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITL 106
           + F+ Q              Y+   F DE   +L+ DK   + MA+AG   N SQF+IT+
Sbjct: 85  QGFMIQGGDPTGTGRG-GPGYK---FADEFHPELQFDKPYLLAMANAGPGTNGSQFFITV 140
Query: 107 RDNLHYLDEKHTIFGEV--AEGLETLTRINQAVVDEENRPPQQIIIKQTYV 155
               H L+ +HTIFGEV  AE    +  I++   D  +RP   ++I+   +
Sbjct: 141 GKTPH-LNRRHTIFGEVIDAESQRVVEAISKTATDGNDRPTDPVVIESITI 190

>pdb|2BIT|X Chain X, Crystal Structure Of Human Cyclophilin D At 1.7 A Resolution Length = 165

Iteration: 1
 Score = 74.7 bits (182), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 50/147 (34%), Positives = 77/147 (52%), Gaps = 10/147 (6%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXXXXR 64
           LG +V++L  D  P+T  NF   C   K   Y G  FH +   F+ Q            +
Sbjct: 17  LGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGK 76
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYI-TLRDNLHYLDEKHTIFGEV 123
           S+Y  RF  DE    LKH   G + MA+AG + N SQF+I T++ +  +LD KH +FG V
Sbjct: 77  SIYGSRF-PDE-NFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTD--WLDGKHVVFGHV 132
Query: 124 AEGLETLTRINQAVVDEENRPPQQIII 150
            EG++ + +I ++   +  R  ++I+I
Sbjct: 133 IEGMDVVKKI-ESFGSKSGRTSKKIVI 158

>pdb|3R49|A Chain A, Human Cyclophilin D Complexed With Quinolin-8-Amine Length = 166

Iteration: 1
 Score = 74.7 bits (182), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 50/147 (34%), Positives = 77/147 (52%), Gaps = 10/147 (6%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXXXXR 64
           LG +V++L  D  P+T  NF   C   K   Y G  FH +   F+ Q            +
Sbjct: 18  LGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGK 77
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYI-TLRDNLHYLDEKHTIFGEV 123
           S+Y  RF  DE    LKH   G + MA+AG + N SQF+I T++ +  +LD KH +FG V
Sbjct: 78  SIYGSRF-PDE-NFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTD--WLDGKHVVFGHV 133
Query: 124 AEGLETLTRINQAVVDEENRPPQQIII 150
            EG++ + +I ++   +  R  ++I+I
Sbjct: 134 IEGMDVVKKI-ESFGSKSGRTSKKIVI 159

>pdb|3QYU|A Chain A, Crystal Structure Of Human Cyclophilin D At 1.54 A Resolution At Room Temperature Length = 164

Iteration: 1
 Score = 74.7 bits (182), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 50/147 (34%), Positives = 77/147 (52%), Gaps = 10/147 (6%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXXXXR 64
           LG +V++L  D  P+T  NF   C   K   Y G  FH +   F+ Q            +
Sbjct: 16  LGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGK 75
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYI-TLRDNLHYLDEKHTIFGEV 123
           S+Y  RF  DE    LKH   G + MA+AG + N SQF+I T++ +  +LD KH +FG V
Sbjct: 76  SIYGSRF-PDE-NFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTD--WLDGKHVVFGHV 131
Query: 124 AEGLETLTRINQAVVDEENRPPQQIII 150
            EG++ + +I ++   +  R  ++I+I
Sbjct: 132 IEGMDVVKKI-ESFGSKSGRTSKKIVI 157

>pdb|2Z6W|A Chain A, Crystal Structure Of Human Cyclophilin D In Complex With Cyclosporin A Length = 165

Iteration: 1
 Score = 74.7 bits (182), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 50/147 (34%), Positives = 77/147 (52%), Gaps = 10/147 (6%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXXXXR 64
           LG +V++L  D  P+T  NF   C   K   Y G  FH +   F+ Q            +
Sbjct: 17  LGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGK 76
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYI-TLRDNLHYLDEKHTIFGEV 123
           S+Y  RF  DE    LKH   G + MA+AG + N SQF+I T++ +  +LD KH +FG V
Sbjct: 77  SIYGSRF-PDE-NFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTD--WLDGKHVVFGHV 132
Query: 124 AEGLETLTRINQAVVDEENRPPQQIII 150
            EG++ + +I ++   +  R  ++I+I
Sbjct: 133 IEGMDVVKKI-ESFGSKSGRTSKKIVI 158

>pdb|2R99|A Chain A, Crystal Structure Of Cyclophilin Abh-Like Domain Of Human Peptidylprolyl Isomerase E Isoform 1 Length = 173

Iteration: 1
 Score = 74.7 bits (182), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 51/145 (35%), Positives = 74/145 (51%), Gaps = 8/145 (5%)
Query: 10  GDIVIDLFVDKCPRTTNNF---LQHCKNKYYNGCLFHNIHKDFIAQXXX-XXXXXXXXRS 65
           G I + L  D  P T  NF     H K   + G  FH I   F+ Q            +S
Sbjct: 26  GRIQMLLRSDVVPMTAENFRCLCTHEKGFGFKGSSFHRIIPQFMCQGGDFTNHNGTGGKS 85
Query: 66  VYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAE 125
           +Y  +F  D+    LKH   G + MA++G + N SQF++T  D   +LD KH +FGEV E
Sbjct: 86  IYGKKF--DDENFILKHTGPGLLSMANSGPNTNGSQFFLTC-DKTDWLDGKHVVFGEVTE 142
Query: 126 GLETLTRINQAVVDEENRPPQQIII 150
           GL+ L +I +A   ++ +P Q++II
Sbjct: 143 GLDVLRQI-EAQGSKDGKPKQKVII 166

>pdb|4I9Y|A Chain A, Structure Of The C-terminal Domain Of Nup358 Length = 167

Iteration: 1
 Score = 74.3 bits (181), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 46/129 (35%), Positives = 70/129 (54%), Gaps = 7/129 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXXXXXXX-XXXXR 64
           LG I ++LF +  PRT  NF   C   K   +   +FH +  DF+ Q            +
Sbjct: 20  LGRITMELFSNIVPRTAENFRALCTGEKGFGFKNSIFHRVIPDFVCQGGDITKHDGTGGQ 79
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y D+F  ++   D+KH   G + MA+ G++ N SQF ITL+   H LD KH +FG V 
Sbjct: 80  SIYGDKF--EDENFDVKHTGPGLLSMANQGQNTNNSQFVITLKKAEH-LDFKHVVFGFVK 136
Query: 125 EGLETLTRI 133
           +G++T+ +I
Sbjct: 137 DGMDTVKKI 145

>pdb|1ZMF|A Chain A, C Domain Of Human Cyclophilin-33(Hcyp33) Length = 165

Iteration: 1
 Score = 74.3 bits (181), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 51/145 (35%), Positives = 74/145 (51%), Gaps = 8/145 (5%)
Query: 10  GDIVIDLFVDKCPRTTNNF---LQHCKNKYYNGCLFHNIHKDFIAQXXX-XXXXXXXXRS 65
           G I + L  D  P T  NF     H K   + G  FH I   F+ Q            +S
Sbjct: 18  GRIQMLLRSDVVPMTAENFRCLCTHEKGFGFKGSSFHRIIPQFMCQGGDFTNHNGTGGKS 77
Query: 66  VYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAE 125
           +Y  +F  D+    LKH   G + MA++G + N SQF++T  D   +LD KH +FGEV E
Sbjct: 78  IYGKKF--DDENFILKHTGPGLLSMANSGPNTNGSQFFLTC-DKTDWLDGKHVVFGEVTE 134
Query: 126 GLETLTRINQAVVDEENRPPQQIII 150
           GL+ L +I +A   ++ +P Q++II
Sbjct: 135 GLDVLRQI-EAQGSKDGKPKQKVII 158

>pdb|1IST|A Chain A, Crystal Structure Of Yeast Cyclophilin A, Cpr1 Length = 162

Iteration: 1
 Score = 70.5 bits (171), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 42/129 (32%), Positives = 65/129 (50%), Gaps = 7/129 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXXXXR 64
           +G +V  L+ D  P+T  NF   C   K   Y G  FH +  DF+ Q            +
Sbjct: 15  IGRVVFKLYNDIVPKTAENFRALCTGEKGFGYAGSPFHRVIPDFMLQGGDFTAGNGTGGK 74
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y  +F  +  +    HD+ G + MA+AG + N SQF+IT      +LD KH +FGEV 
Sbjct: 75  SIYGGKFPDENFKK--HHDRPGLLSMANAGPNTNGSQFFITTVP-CPWLDGKHVVFGEVV 131
Query: 125 EGLETLTRI 133
           +G + + ++
Sbjct: 132 DGYDIVKKV 140

>pdb|3BO7|A Chain A, Crystal Structure Of Toxoplasma Gondii Peptidyl-Prolyl Cis-Trans Isomerase, 541.M00136 Length = 201

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 43/137 (31%), Positives = 66/137 (48%), Gaps = 12/137 (8%)
Query: 5   IETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQXXXXXXXXXXXR 64
           I T+ G + I+L  D  PR  ++FL+ C  KY++  +FH   ++F+ Q           +
Sbjct: 11  IVTTQGSLNIELHADMAPRACDSFLRLCAVKYFDDTIFHRCIRNFMIQGGRAELRQPSKK 70
Query: 65  SVYEDR-----------FFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYL 113
              +              F DE    L H  +G + MA+ G+  N S+F+IT +   H L
Sbjct: 71  KEVQQSPRSISGFPGGAPFEDEFDNRLVHQGIGVLSMANDGKHSNLSEFFITFKSCEH-L 129
Query: 114 DEKHTIFGEVAEGLETL 130
           + KHTIFG V  GL+ L
Sbjct: 130 NNKHTIFGRVVGGLDVL 146

>pdb|3UCH|A Chain A, Crystal Structure Of A Hypotherical Peptidyl-Prolyl Cis-Trans Isomerase E (Ppie) From Homo Sapiens At 2.50 A Resolution Length = 174

Iteration: 1
 Score = 69.7 bits (169), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 50/145 (34%), Positives = 71/145 (48%), Gaps = 8/145 (5%)
Query: 10  GDIVIDLFVDKCPRTTNNF---LQHCKNKYYNGCLFHNIHKDFIAQXXX-XXXXXXXXRS 65
           G I   L  D  P T  NF     H K   + G  FH I   F  Q            +S
Sbjct: 27  GRIQXLLRSDVVPXTAENFRCLCTHEKGFGFKGSSFHRIIPQFXCQGGDFTNHNGTGGKS 86
Query: 66  VYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAE 125
           +Y  +F  D+    LKH   G +  A++G + N SQF++T  D   +LD KH +FGEV E
Sbjct: 87  IYGKKF--DDENFILKHTGPGLLSXANSGPNTNGSQFFLTC-DKTDWLDGKHVVFGEVTE 143
Query: 126 GLETLTRINQAVVDEENRPPQQIII 150
           GL+ L +I +A   ++ +P Q++II
Sbjct: 144 GLDVLRQI-EAQGSKDGKPKQKVII 167

>pdb|2XGY|B Chain B, Complex Of Rabbit Endogenous Lentivirus (Relik)capsid With Cyclophilin A Length = 173

Iteration: 1
 Score = 68.9 bits (167), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 43/123 (34%), Positives = 61/123 (49%), Gaps = 7/123 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXXXXR 64
           LG +  +LF DK P+T  NF       K   Y G  FH I   F+ Q            +
Sbjct: 25  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGK 84
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  ++    LKH   G + MA+AG + N SQF+I       +LD KH +FG+V 
Sbjct: 85  SIYGEKF--EDENFILKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVVFGKVK 141
Query: 125 EGL 127
           EG+
Sbjct: 142 EGM 144

>pdb|3PMP|A Chain A, Crystal Structure Of Cyclophilin A From Moniliophthora Perniciosa In Complex With Cyclosporin A Length = 164

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 43/128 (33%), Positives = 67/128 (52%), Gaps = 7/128 (5%)
Query: 10  GDIVIDLFVDKCPRTTNNFLQHCKNKY---YNGCLFHNIHKDFIAQXX-XXXXXXXXXRS 65
           G IV  L+ +  P+T  NF +    ++   Y   +FH +   F+ Q            +S
Sbjct: 17  GRIVFKLYDEAVPKTAKNFRELATGQHGFGYKDSIFHRVIPQFMLQGGDFTRHNGTGGKS 76
Query: 66  VYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAE 125
           +Y ++F  DE    +KH K G + MA+AG + N SQF+IT      +LD KH +FGEV E
Sbjct: 77  IYGEKF-ADE-NFQVKHTKPGLLSMANAGANTNGSQFFITTVPT-SWLDGKHVVFGEVIE 133
Query: 126 GLETLTRI 133
           GL+ + ++
Sbjct: 134 GLDIVRKV 141

>pdb|3K0R|A Chain A, Cryogenic Structure Of Cypa Mutant Arg55lys Length = 165

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 43/123 (34%), Positives = 61/123 (49%), Gaps = 7/123 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXXXXR 64
           LG +  +LF DK P+T  NF       K   Y G  FH I   F+ Q            +
Sbjct: 17  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHKIIPGFMCQGGDFTRHNGTGGK 76
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  ++    LKH   G + MA+AG + N SQF+I       +LD KH +FG+V 
Sbjct: 77  SIYGEKF--EDENFILKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVVFGKVK 133
Query: 125 EGL 127
           EG+
Sbjct: 134 EGM 136

>pdb|4DGD|A Chain A, Trimcyp Cyclophilin Domain From Macaca Mulatta: H70c Mutant Length = 165

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 43/123 (34%), Positives = 61/123 (49%), Gaps = 7/123 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXXXXXX-XXXXXR 64
           LG +  +LF DK P+T  NF       K   Y G  FH I   F+ Q            +
Sbjct: 17  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGNFTHCNGTGGK 76
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  ++    LKH   G + MA+AG + N SQF+I       +LD KH +FG+V 
Sbjct: 77  SIYGEKF--EDENFILKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVVFGKVK 133
Query: 125 EGL 127
           EG+
Sbjct: 134 EGM 136

>pdb|2PLU|A Chain A, Crystal Structure Of Cryptosporidium Parvum Cyclophilin Type Peptidyl-Prolyl Cis-Trans Isomerase Cgd2_4120 Length = 186

Iteration: 1
 Score = 68.6 bits (166), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 50/161 (31%), Positives = 72/161 (44%), Gaps = 15/161 (9%)
Query: 6   ETSLGDIVIDLFVDKCPRTTNNFLQHCKNKY----------YNGCLFHNIHKDFIAQXXX 55
           +T  G I ++LF DK P T  NF   C  +           Y G  FH I   F+ Q   
Sbjct: 30  QTPAGRITMELFADKVPITAENFRALCTGEKGMGQSGKPLCYTGSFFHRIIPQFMIQGGD 89
Query: 56  XXXX-XXXXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLD 114
                     S+Y  +F  DE      HD    + MA+AG + N SQF+IT      +LD
Sbjct: 90  FTRGDGTGGESIYGSKF-RDE-NFVYTHDAPFLLSMANAGPNTNGSQFFITTVP-CPWLD 146
Query: 115 EKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYV 155
            KH +FG+V EG+E +  I +    +  +P + + I  + V
Sbjct: 147 GKHVVFGKVLEGMEVVKSIEKC-GSQNGKPTKSVCITASGV 186

>pdb|2RMA|A Chain A, Crystal Structures Of Cyclophilin A Complexed With Cyclosporin A And N-Methyl-4-[(E)-2-Butenyl]-4,4-Dimethylthreonine Cyclosporin A Length = 165

Iteration: 1
 Score = 68.6 bits (166), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 43/123 (34%), Positives = 61/123 (49%), Gaps = 7/123 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXXXXR 64
           LG +  +LF DK P+T  NF       K   Y G  FH I   F+ Q            +
Sbjct: 17  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGK 76
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  ++    LKH   G + MA+AG + N SQF+I       +LD KH +FG+V 
Sbjct: 77  SIYGEKF--EDENFILKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVVFGKVK 133
Query: 125 EGL 127
           EG+
Sbjct: 134 EGM 136

>pdb|2WLW|A Chain A, Structure Of The N-Terminal Capsid Domain Of Hiv-2 Length = 165

Iteration: 1
 Score = 68.2 bits (165), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 43/123 (34%), Positives = 61/123 (49%), Gaps = 7/123 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXXX-XXXXXXXXR 64
           LG +  +LF DK P+T  NF       K   Y G  FH I   F+ Q            +
Sbjct: 17  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGNFTHHNGTGGK 76
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  ++    LKH   G + MA+AG + N SQF+I       +LD KH +FG+V 
Sbjct: 77  SIYGEKF--EDENFILKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVVFGKVK 133
Query: 125 EGL 127
           EG+
Sbjct: 134 EGM 136

>pdb|3O7T|A Chain A, Crystal Structure Of Cyclophilin A From Moniliophthora Perniciosa Length = 164

Iteration: 1
 Score = 68.2 bits (165), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 43/128 (33%), Positives = 67/128 (52%), Gaps = 7/128 (5%)
Query: 10  GDIVIDLFVDKCPRTTNNFLQHCKNKY---YNGCLFHNIHKDFIAQXX-XXXXXXXXXRS 65
           G IV  L+ +  P+T  NF +    ++   Y   +FH +   F+ Q            +S
Sbjct: 18  GRIVFKLYDEAVPKTAKNFRELATGQHGFGYKDSIFHRVIPQFMLQGGDFTRHNGTGGKS 77
Query: 66  VYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAE 125
           +Y ++F  DE    +KH K G + MA+AG + N SQF+IT      +LD KH +FGEV E
Sbjct: 78  IYGEKF-ADE-NFQVKHTKPGLLSMANAGANTNGSQFFITTVPT-SWLDGKHVVFGEVIE 134
Query: 126 GLETLTRI 133
           GL+ + ++
Sbjct: 135 GLDIVRKV 142

>pdb|1BCK|A Chain A, Human Cyclophilin A Complexed With 2-Thr Cyclosporin Length = 165

Iteration: 1
 Score = 68.2 bits (165), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 43/123 (34%), Positives = 61/123 (49%), Gaps = 7/123 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXXXXR 64
           LG +  +LF DK P+T  NF       K   Y G  FH I   F+ Q            +
Sbjct: 17  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGK 76
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  ++    LKH   G + MA+AG + N SQF+I       +LD KH +FG+V 
Sbjct: 77  SIYGEKF--EDENFILKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVVFGKVK 133
Query: 125 EGL 127
           EG+
Sbjct: 134 EGM 136

>pdb|5CYH|A Chain A, Cyclophilin A Complexed With Dipeptide Gly-Pro Length = 164

Iteration: 1
 Score = 68.2 bits (165), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 43/123 (34%), Positives = 61/123 (49%), Gaps = 7/123 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXXXXR 64
           LG +  +LF DK P+T  NF       K   Y G  FH I   F+ Q            +
Sbjct: 16  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGK 75
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  ++    LKH   G + MA+AG + N SQF+I       +LD KH +FG+V 
Sbjct: 76  SIYGEKF--EDENFILKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVVFGKVK 132
Query: 125 EGL 127
           EG+
Sbjct: 133 EGM 135

>pdb|1M9E|A Chain A, X-Ray Crystal Structure Of Cyclophilin AHIV-1 Ca N- Terminal Domain (1-146) M-Type H87a Complex. Length = 164

Iteration: 1
 Score = 68.2 bits (165), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 43/123 (34%), Positives = 61/123 (49%), Gaps = 7/123 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXXXXR 64
           LG +  +LF DK P+T  NF       K   Y G  FH I   F+ Q            +
Sbjct: 17  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGK 76
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  ++    LKH   G + MA+AG + N SQF+I       +LD KH +FG+V 
Sbjct: 77  SIYGEKF--EDENFILKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVVFGKVK 133
Query: 125 EGL 127
           EG+
Sbjct: 134 EGM 136

>pdb|1Z81|A Chain A, Crystal Structure Of Cyclophilin From Plasmodium Yoelii Length = 229

Iteration: 1
 Score = 68.2 bits (165), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 40/126 (31%), Positives = 65/126 (51%), Gaps = 12/126 (9%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHCKNKY--------YNGCLFHNIHKDFIAQXXXXXXXX 60
           LG    +LF +  P+T+ NF Q C  +Y        Y   +FH + K+F+ Q        
Sbjct: 73  LGKFKFELFQNIVPKTSENFRQFCTGEYKVNNLPVGYKNTIFHRVIKEFMIQGGDFINHN 132
Query: 61  XXXR-SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTI 119
                S+Y ++F  D+   D+KHDK G + MA++G + N  QF+IT +    +LD K+ +
Sbjct: 133 GSGSLSIYGEKF--DDENFDIKHDKEGLLSMANSGPNTNGCQFFITTKK-CEWLDGKNVV 189
Query: 120 FGEVAE 125
           FG + +
Sbjct: 190 FGRIID 195

>pdb|3RDD|A Chain A, Human Cyclophilin A Complexed With An Inhibitor Length = 184

Iteration: 1
 Score = 68.2 bits (165), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 43/123 (34%), Positives = 61/123 (49%), Gaps = 7/123 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXXXXR 64
           LG +  +LF DK P+T  NF       K   Y G  FH I   F+ Q            +
Sbjct: 36  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGK 95
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  ++    LKH   G + MA+AG + N SQF+I       +LD KH +FG+V 
Sbjct: 96  SIYGEKF--EDENFILKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVVFGKVK 152
Query: 125 EGL 127
           EG+
Sbjct: 153 EGM 155

>pdb|2CK1|A Chain A, The Structure Of Oxidised Cyclophilin A From S. Mansoni Length = 172

Iteration: 1
 Score = 67.8 bits (164), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 43/147 (29%), Positives = 73/147 (49%), Gaps = 8/147 (5%)
Query: 10  GDIVIDLFVDKCPRTTNNFLQHCKNKY---YNGCLFHNIHKDFIAQXXXXXXX-XXXXRS 65
           G IV++L  D  PRT  NF   C  +    Y+ C FH +   F+ Q            +S
Sbjct: 25  GRIVMELRSDIVPRTAENFRALCTGERGFGYHNCCFHRVIPQFMCQGGDFVKGDGTGGKS 84
Query: 66  VYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAE 125
           +Y  +F  D+    L+H+  G + MA++G + N SQF+I       +LD KH +FG V +
Sbjct: 85  IYGRKF--DDENFQLRHEGFGVLSMANSGPNTNGSQFFICT-TKCDWLDGKHVVFGRVVD 141
Query: 126 GLETLTRINQAVVDEENRPPQQIIIKQ 152
           G   + ++ ++V  +  +  + +II +
Sbjct: 142 GQNVVKKM-ESVGSKSGKVKEPVIISR 167

>pdb|3K0O|A Chain A, Room Temperature Structure Of Cypa Mutant Ser99thr Length = 165

Iteration: 1
 Score = 67.8 bits (164), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 43/123 (34%), Positives = 61/123 (49%), Gaps = 7/123 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXXXXR 64
           LG +  +LF DK P+T  NF       K   Y G  FH I   F+ Q            +
Sbjct: 17  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGK 76
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  ++    LKH   G + MA+AG + N SQF+I       +LD KH +FG+V 
Sbjct: 77  SIYGEKF--EDENFILKHTGPGILTMANAGPNTNGSQFFICTAKT-EWLDGKHVVFGKVK 133
Query: 125 EGL 127
           EG+
Sbjct: 134 EGM 136

>pdb|2X83|B Chain B, Evolutionary Basis Of Hiv Restriction By The Antiretroviral Trimcyp Length = 163

Iteration: 1
 Score = 67.8 bits (164), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 43/123 (34%), Positives = 61/123 (49%), Gaps = 7/123 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXXXXR 64
           LG +  +LF DK P+T  NF       K   Y G  FH I   F+ Q            +
Sbjct: 16  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTHHNGTGGK 75
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  ++    LKH   G + MA+AG + N SQF+I       +LD KH +FG+V 
Sbjct: 76  SIYGEKF--EDENFILKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGKHVVFGKVK 132
Query: 125 EGL 127
           EG+
Sbjct: 133 EGM 135

>pdb|2ALF|A Chain A, Crystal Structure Of Human Cypa Mutant K131a Length = 164

Iteration: 1
 Score = 67.8 bits (164), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 43/123 (34%), Positives = 60/123 (48%), Gaps = 7/123 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXXXXR 64
           LG +  +LF DK P+T  NF       K   Y G  FH I   F+ Q            +
Sbjct: 16  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGK 75
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  ++    LKH   G + MA+AG + N SQF+I       +LD KH +FG V 
Sbjct: 76  SIYGEKF--EDENFILKHTGPGILSMANAGPNTNGSQFFICTAKT-KWLDGKHVVFGAVK 132
Query: 125 EGL 127
           EG+
Sbjct: 133 EGM 135

>pdb|2X2C|K Chain K, Acetyl-Cypa:cyclosporine Complex Length = 165

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 42/123 (34%), Positives = 60/123 (48%), Gaps = 7/123 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXXXXR 64
           LG +  +LF DK P+T  NF       K   Y G  FH I   F+ Q            +
Sbjct: 17  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGK 76
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  ++    LKH   G + MA+AG + N SQF+I       +LD  H +FG+V 
Sbjct: 77  SIYGEKF--EDENFILKHTGPGILSMANAGPNTNGSQFFICTAKT-EWLDGXHVVFGKVK 133
Query: 125 EGL 127
           EG+
Sbjct: 134 EGM 136

>pdb|2X2A|A Chain A, Free Acetyl-Cypa Trigonal Form Length = 165

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 42/123 (34%), Positives = 60/123 (48%), Gaps = 7/123 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXXXXR 64
           LG +  +LF DK P+T  NF       K   Y G  FH I   F+ Q            +
Sbjct: 17  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGK 76
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  ++    LKH   G + MA+AG + N SQF+I       +LD  H +FG+V 
Sbjct: 77  SIYGEKF--EDENFILKHTGPGILSMANAGPNTNGSQFFICTAKT-KWLDGXHVVFGKVK 133
Query: 125 EGL 127
           EG+
Sbjct: 134 EGM 136

>pdb|2X25|B Chain B, Free Acetyl-Cypa Orthorhombic Form Length = 169

Iteration: 1
 Score = 64.7 bits (156), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 42/123 (34%), Positives = 60/123 (48%), Gaps = 7/123 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXXXXR 64
           LG +  +LF DK P+T  NF       K   Y G  FH I   F+ Q            +
Sbjct: 21  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGK 80
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  ++    LKH   G + MA+AG + N SQF+I       +LD  H +FG+V 
Sbjct: 81  SIYGEKF--EDENFILKHTGPGILSMANAGPNTNGSQFFICTAKT-KWLDGXHVVFGKVK 137
Query: 125 EGL 127
           EG+
Sbjct: 138 EGM 140

>pdb|1DYW|A Chain A, Biochemical And Structural Characterization Of A Divergent Loop Cyclophilin From Caenorhabditis Elegans Length = 173

Iteration: 1
 Score = 63.9 bits (154), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 43/153 (28%), Positives = 75/153 (49%), Gaps = 17/153 (11%)
Query: 10  GDIVIDLFVDKCPRTTNNFLQHCKNK----------YYNGCLFHNIHKDFIAQXX-XXXX 58
           G IV++L+ D  P+T  NF   C  +          ++ G  FH I  +F+ Q       
Sbjct: 18  GRIVMELYDDVVPKTAGNFRALCTGENGIGKSGKPLHFKGSKFHRIIPNFMIQGGDFTRG 77
Query: 59  XXXXXRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYI-TLRDNLHYLDEKH 117
                 S+Y ++F  +  +   KH   G + MA+AG + N SQF++ T++    +LD KH
Sbjct: 78  NGTGGESIYGEKFPDENFKE--KHTGPGVLSMANAGPNTNGSQFFLCTVK--TEWLDGKH 133
Query: 118 TIFGEVAEGLETLTRINQAVVDEENRPPQQIII 150
            +FG V EGL+ +  + ++   +  +P +  +I
Sbjct: 134 VVFGRVVEGLDVVKAV-ESNGSQSGKPVKDCMI 165

>pdb|1AWS|A Chain A, Secypa Complexed With Hagpia (Pseudo-Symmetric Monomer) Length = 164

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 42/122 (34%), Positives = 58/122 (47%), Gaps = 7/122 (5%)
Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQXX-XXXXXXXXXR 64
           LG +  +LF DK P+T  NF       K   Y G  FH I   F  Q            +
Sbjct: 16  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFXCQGGDFTRHNGTGGK 75
Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  ++    LKH   G +  A+AG + N SQF+I       +LD KH +FG+V 
Sbjct: 76  SIYGEKF--EDENFILKHTGPGILSXANAGPNTNGSQFFICTAKT-EWLDGKHVVFGKVK 132
Query: 125 EG 126
           EG
Sbjct: 133 EG 134

>pdb|3T1U|A Chain A, Crystal Structure Of The Complex Of Cyclophilin-a Enzyme From Azotobacter Vinelandii With Sucafpfpna Peptide Length = 163

Iteration: 1
 Score = 62.8 bits (151), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 45/148 (30%), Positives = 71/148 (47%), Gaps = 28/148 (18%)
Query: 2   SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQXXXXXXXXX 61
           S+ ++T+ G I + LF DK P T  NF Q+ K+ +Y+G +FH +   F+ Q         
Sbjct: 1   SIKLQTNHGTITLKLFADKAPETAANFEQYVKDGHYDGTIFHRVIDGFMIQGGG------ 54
Query: 62  XXRSVYEDRFFVDEIRADLKH-------DKVGTVGMASAGRDLNAS-QFYITLRDNLHYL 113
                +E        RA +K+       +K  T+ MA      +AS QF+I ++DN  +L
Sbjct: 55  -----FEPGMKQKSTRAPIKNEANNGLSNKKYTIAMARTPDPHSASAQFFINVKDNA-FL 108
Query: 114 DE--------KHTIFGEVAEGLETLTRI 133
           D          + +FGEV EG + + RI
Sbjct: 109 DHTAPTAHGWGYAVFGEVVEGTDVVDRI 136

>pdb|2HQJ|A Chain A, Cyclophilin From Leishmania Major Length = 183

Iteration: 1
 Score = 62.8 bits (151), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 38/140 (27%), Positives = 65/140 (46%), Gaps = 13/140 (9%)
Query: 8   SLGDIVIDLFVDKCPRTTNNFLQHCKNK----------YYNGCLFHNIHKDFIAQXXX-X 56
           + G IV++L+ D  P+T  NF   C  +          +Y   +FH +  +F+ Q     
Sbjct: 20  AAGRIVMELYADTVPKTAENFRALCTGEKGKGRSGKPLHYKSSVFHRVIPNFMIQGGDFT 79
Query: 57  XXXXXXXRSVYEDRFFVDEIRADL-KHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDE 115
                   S+Y   F  +       +H  +G + MA+AG + N SQF+I       +LD 
Sbjct: 80  RGNGTGGESIYGTTFRDESFSGKAGRHTGLGCLSMANAGPNTNGSQFFICTAAT-PWLDG 138
Query: 116 KHTIFGEVAEGLETLTRINQ 135
           KH +FG V +GL+ + ++ +
Sbjct: 139 KHVVFGRVIDGLDVVKKVER 158

>pdb|1J2A|A Chain A, Structure Of E. Coli Cyclophilin B K163t Mutant Length = 166

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 45/164 (27%), Positives = 80/164 (48%), Gaps = 15/164 (9%)
Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQXXXXXXXXXX 62
           VL+ TS G+I ++L   K P +  NF+ +  + +YN   FH +   F+ Q          
Sbjct: 7   VLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQ 66
Query: 63  XRSVYEDRFFVDEIRADLKHDKVGTVGMA-SAGRDLNASQFYITLRDNLHYLDE-----K 116
            +    +    +E    L++ + GT+ MA +A +D   SQF+I + DN  +LD       
Sbjct: 67  KK---PNPPIKNEADNGLRNTR-GTIAMARTADKDSATSQFFINVADNA-FLDHGQRDFG 121
Query: 117 HTIFGEVAEGLETLTRINQA----VVDEENRPPQQIIIKQTYVL 156
           + +FG+V +G++   +I+Q     V   +N P + ++I    VL
Sbjct: 122 YAVFGKVVKGMDVADKISQVPTHDVGPYQNVPSKPVVILSATVL 165

>pdb|1CLH|A Chain A, Three-Dimensional Solution Structure Of Escherichia Coli Periplasmic Cyclophilin Length = 166

Iteration: 1
 Score = 60.5 bits (145), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 45/164 (27%), Positives = 80/164 (48%), Gaps = 15/164 (9%)
Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQXXXXXXXXXX 62
           VL+ TS G+I ++L   K P +  NF+ +  + +YN   FH +   F+ Q          
Sbjct: 7   VLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQ 66
Query: 63  XRSVYEDRFFVDEIRADLKHDKVGTVGMA-SAGRDLNASQFYITLRDNLHYLDE-----K 116
            +    +    +E    L++ + GT+ MA +A +D   SQF+I + DN  +LD       
Sbjct: 67  KK---PNPPIKNEADNGLRNTR-GTIAMARTADKDSATSQFFINVADNA-FLDHGQRDFG 121
Query: 117 HTIFGEVAEGLETLTRINQA----VVDEENRPPQQIIIKQTYVL 156
           + +FG+V +G++   +I+Q     V   +N P + ++I    VL
Sbjct: 122 YAVFGKVVKGMDVADKISQVPTHDVGPYQNVPSKPVVILSAKVL 165

>pdb|2NUL|A Chain A, Peptidylprolyl Isomerase From E. Coli Length = 164

Iteration: 1
 Score = 60.1 bits (144), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 46/165 (27%), Positives = 77/165 (46%), Gaps = 16/165 (9%)
Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQXXXXXXXXXX 62
           V   T+ GDIVI  F DK P T  NFL +C+  +YN  +FH +   F+ Q          
Sbjct: 2   VTFHTNHGDIVIKTFDDKAPETVKNFLDYCREGFYNNTIFHRVINGFMIQGGGFEPGMKQ 61
Query: 63  XRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNAS-QFYITLRDN--LHYLDEK--- 116
             +    +   +E    LK+ + GT+ MA      +A+ QF+I + DN  L++  E    
Sbjct: 62  KATKEPIK---NEANNGLKNTR-GTLAMARTQAPHSATAQFFINVVDNDFLNFSGESLQG 117
Query: 117 --HTIFGEVAEGLETLTRINQAVVD----EENRPPQQIIIKQTYV 155
             + +F EV +G++ + +I           ++ P + +II+   V
Sbjct: 118 WGYCVFAEVVDGMDVVDKIKGVATGRSGMHQDVPKEDVIIESVTV 162

>pdb|1LOP|A Chain A, Cyclophilin A Complexed With Succinyl-Ala-Pro-Ala-P-Nitroanilide Length = 164

Iteration: 1
 Score = 59.7 bits (143), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 46/165 (27%), Positives = 77/165 (46%), Gaps = 16/165 (9%)
Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQXXXXXXXXXX 62
           V   T+ GDIVI  F DK P T  NFL +C+  +YN  +FH +   F+ Q          
Sbjct: 2   VTFHTNHGDIVIKTFDDKAPETVKNFLDYCREGFYNNTIFHRVINGFMIQGGGFEPGMKQ 61
Query: 63  XRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNAS-QFYITLRDN--LHYLDEK--- 116
             +    +   +E    LK+ + GT+ MA      +A+ QF+I + DN  L++  E    
Sbjct: 62  KATKEPIK---NEANNGLKNTR-GTLAMARTQAPHSATAQFFINVVDNDFLNFSGESLQG 117
Query: 117 --HTIFGEVAEGLETLTRINQAVVDE----ENRPPQQIIIKQTYV 155
             + +F EV +G++ + +I           ++ P + +II+   V
Sbjct: 118 WGYCVFAEVVDGMDEVDKIKGVATGRSGMHQDVPKEDVIIESVTV 162

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 24/84 (28%), Positives = 43/84 (51%)
Query: 206 DVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREA 265
           D +  +  L V  L     D +L+ +F   G + +  I RDY+TG S  YAFV+F     
Sbjct: 9   DPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXD 68
Query: 266 CEQAYFKMNNALIDDRRICVDFSQ 289
            ++A   +N   + ++R+ V +++
Sbjct: 69  SQRAIKVLNGITVRNKRLKVSYAR 92

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 25/67 (37%), Positives = 36/67 (53%)
Query: 211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
           D  L+V  L     D+ L  IF ++G++V   ILRD  TG     AFV + KRE  ++A 
Sbjct: 89  DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148
Query: 271 FKMNNAL 277
             +NN +
Sbjct: 149 SALNNVI 155

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 32/111 (28%), Positives = 53/111 (47%), Gaps = 3/111 (2%)
Query: 178 PLNEQLSSEKEAHSRAVALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGT 237
           P    ++S             +G+  + D   P+  L V  L+  T + DL  +FS++G 
Sbjct: 16  PRGSHMASMTGGQQMGRGSRHVGNRANPD---PNCCLGVFGLSLYTTERDLREVFSKYGP 72
Query: 238 VVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS 288
           +    I+ D ++  S  +AFV FE  +  ++A  + N   +D RRI VDFS
Sbjct: 73  IADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS 123

>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 = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 39/75 (52%)
Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L+P    ED+   F+ FG +  A +++D  TG+S  Y FV F  +   E A  +M
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 274 NNALIDDRRICVDFS 288
               +  R+I  +++
Sbjct: 78  GGQWLGGRQIRTNWA 92

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 52.0 bits (123), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 38/75 (50%)
Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L+P    ED+   F+ FG +  A +++D  TG+S  Y FV F  +   E A   M
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 274 NNALIDDRRICVDFS 288
               +  R+I  +++
Sbjct: 78  GGQWLGGRQIRTNWA 92

>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 = 51.2 bits (121), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 25/67 (37%), Positives = 36/67 (53%)
Query: 211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
           D  L+V  L     D+ L  IF ++G++V   ILRD  TG     AFV + KRE  ++A 
Sbjct: 13  DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
Query: 271 FKMNNAL 277
             +NN +
Sbjct: 73  SALNNVI 79

>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 = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 42/80 (52%)
Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           P   L+V  L+P   +  L+  FS  G ++S  + RD  T  SL YA+V F++    E+A
Sbjct: 14  PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 73
Query: 270 YFKMNNALIDDRRICVDFSQ 289
              MN  +I  + + + +SQ
Sbjct: 74  LDTMNFDVIKGKPVRIMWSQ 93

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 44/72 (61%), Gaps = 2/72 (2%)
Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +F+  L+   +++ L+  FS FG ++S +++ D     S  Y FV FE +EA E+A  KM
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKM 65
Query: 274 NNALIDDRRICV 285
           N  L++DR++ V
Sbjct: 66  NGMLLNDRKVFV 77

>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 = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 30/103 (29%), Positives = 47/103 (45%)
Query: 188 EAHSRAVALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDY 247
            + S  +  + IG        P    LF+  L     D+DL  +F  FG VVSA++  D 
Sbjct: 2   SSGSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDK 61
Query: 248 RTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS 290
           +T  S C+ FV ++   + + A   MN   I  +R+ V   +S
Sbjct: 62  QTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRS 104

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 44/79 (55%)
Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           P+  L V  L+  T + DL  +FS++G +    I+ D ++  S  +AFV FE  +  ++A
Sbjct: 11  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 70
Query: 270 YFKMNNALIDDRRICVDFS 288
             + N   +D RRI VDFS
Sbjct: 71  KERANGMELDGRRIRVDFS 89

>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 = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 42/80 (52%)
Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           P   L+V  L+P   +  L+  FS  G ++S  + RD  T  SL YA+V F++    E+A
Sbjct: 9   PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERA 68
Query: 270 YFKMNNALIDDRRICVDFSQ 289
              MN  +I  + + + +SQ
Sbjct: 69  LDTMNFDVIKGKPVRIMWSQ 88

>pdb|3S6M|A Chain A, The Structure Of A Peptidyl-Prolyl Cis-Trans Isomerase From Burkholderia Pseudomallei Length = 167

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 39/140 (27%), Positives = 66/140 (47%), Gaps = 14/140 (10%)
Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQXXXXXXXXXX 62
           V + T+ G I ++L   K P+T  NFL + K  +Y+G +FH +   F+ Q          
Sbjct: 6   VELHTNHGVIKLELDEAKAPKTVENFLNYVKKGHYDGTIFHRVINGFMIQGGGFEPGLKQ 65
Query: 63  XRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNAS-QFYITLRDNLHYLDEK----- 116
             +   D    +E    LK+D   T+ MA      +A+ QF+I + DN  +L+       
Sbjct: 66  KPT---DAPIANEANNGLKNDTY-TIAMARTNDPHSATAQFFINVNDN-EFLNHSSPTPQ 120
Query: 117 ---HTIFGEVAEGLETLTRI 133
              + +FG+V EG + + +I
Sbjct: 121 GWGYAVFGKVVEGQDIVDKI 140

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/79 (35%), Positives = 44/79 (55%)
Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           P+  L V  L+  T + DL  +FS++G +    I+ D ++  S  +AFV FE  +  ++A
Sbjct: 14  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73
Query: 270 YFKMNNALIDDRRICVDFS 288
             + N   +D RRI VDFS
Sbjct: 74  KERANGMELDGRRIRVDFS 92

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/72 (34%), Positives = 44/72 (61%), Gaps = 2/72 (2%)
Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +F+  L+   +++ L+  FS FG ++S +++ D    +   Y FV FE +EA E+A  KM
Sbjct: 14  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG--YGFVHFETQEAAERAIEKM 71
Query: 274 NNALIDDRRICV 285
           N  L++DR++ V
Sbjct: 72  NGMLLNDRKVFV 83

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/84 (29%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
            LFV ++N  T +  L   F  +G +    ++   R+G+   YAF+E+E       AY  
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 273 MNNALIDDRRICVDFSQSVS-KIW 295
            +   ID RR+ VD  +  + K W
Sbjct: 164 ADGKKIDGRRVLVDVERGRTVKGW 187

>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 = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 36/63 (57%)
Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
           N ++V  ++    D+D+  +F  FG + SA + RD  TG+   Y F+E+EK ++ + A  
Sbjct: 126 NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS 185
Query: 272 KMN 274
            MN
Sbjct: 186 SMN 188

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 48.5 bits (114), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 39/73 (53%)
Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  L+  T ++ L  +FS++G +    +++D  T  S  + FV FE  +  + A   M
Sbjct: 15  LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 274 NNALIDDRRICVD 286
           N   +D R+I VD
Sbjct: 75  NGKSVDGRQIRVD 87

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 47.8 bits (112), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 25/85 (29%), Positives = 40/85 (47%), Gaps = 1/85 (1%)
Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
             LFV ++N  T +  L   F  +G +    ++   R+G+   YAF+E+E       AY 
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 272 KMNNALIDDRRICVDFSQSVS-KIW 295
             +   ID RR+ VD  +  + K W
Sbjct: 163 HADGKKIDGRRVLVDVERGRTVKGW 187

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 25/76 (32%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVV-SAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           +F+  L+P  +++ L+  FS FG ++ + +I+RD  TG S  YAF+ F   +A + A   
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67
Query: 273 MNNALIDDRRICVDFS 288
           MN   + +R I V ++
Sbjct: 68  MNGQYLCNRPITVSYA 83

>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure Length = 88

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 20/65 (30%), Positives = 38/65 (58%)
Query: 225 DEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC 284
           D +L+ +F   G + +  I+RDY+TG S  YAFV+F      ++A   +N   + ++R+ 
Sbjct: 17  DRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLK 76
Query: 285 VDFSQ 289
           V +++
Sbjct: 77  VSYAR 81

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/92 (31%), Positives = 48/92 (52%), Gaps = 3/92 (3%)
Query: 202 IPDADVKPPDNVLFVCQLN--PVTEDE-DLHVIFSQFGTVVSAEILRDYRTGESLCYAFV 258
           IP   + P  +VL    +N  P T DE  L  +F ++G + S +I+ D  T +S  Y FV
Sbjct: 30  IPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFV 89
Query: 259 EFEKREACEQAYFKMNNALIDDRRICVDFSQS 290
           +F+   + +QA   +N   I ++R+ V  + S
Sbjct: 90  KFQSGSSAQQAIAGLNGFNILNKRLKVALAAS 121

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 222 VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDR 281
           +T+DE L  +FS  G V SA+++RD   G SL Y FV +   +  E+A   +N   +  +
Sbjct: 14  MTQDE-LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSK 72
Query: 282 RICVDFSQSVSKIWK 296
            I V +++  S++ K
Sbjct: 73  TIKVSYARPSSEVIK 87

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 222 VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDR 281
           +T+DE L  +FS  G V SA+++RD   G SL Y FV +   +  E+A   +N   +  +
Sbjct: 14  MTQDE-LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSK 72
Query: 282 RICVDFSQSVSKIWK 296
            I V +++  S++ K
Sbjct: 73  TIKVSYARPSSEVIK 87

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 37/72 (51%)
Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LF+  L     D DL   F  FG V+SA++  D +T  S C+ FV F+  ++ + A   M
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 274 NNALIDDRRICV 285
           N   +  +R+ V
Sbjct: 103 NGFQVGTKRLKV 114

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 35/63 (55%)
Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
           N ++V  ++    D+D+  +F  FG + S  + RD  TG+   Y F+E+EK ++ + A  
Sbjct: 111 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 170
Query: 272 KMN 274
            MN
Sbjct: 171 SMN 173

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 38/75 (50%)
Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  LN   +DE L   F  F + +S  ++ D +TG S  Y FV F  ++  + A   M
Sbjct: 90  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 274 NNALIDDRRICVDFS 288
               ++ R + ++++
Sbjct: 150 QGQDLNGRPLRINWA 164

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 35/65 (53%)
Query: 211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
           D  L+V  L      +++  +FSQ+G ++++ IL D  TG S    F+ F+KR   E+A 
Sbjct: 90  DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 149
Query: 271 FKMNN 275
             +N 
Sbjct: 150 KGLNG 154

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 39/77 (50%)
Query: 213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           VL+V  L    +D+ LH  F  FG +   +I  DY T +   +AFVEFE  E    A   
Sbjct: 14  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73
Query: 273 MNNALIDDRRICVDFSQ 289
           MN + +  R I V+ ++
Sbjct: 74  MNESELFGRTIRVNLAK 90

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 44.7 bits (104), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 35/65 (53%)
Query: 211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
           D  L+V  L      ++L  +FSQ+G ++++ IL D  TG S    F+ F+KR   E+A 
Sbjct: 88  DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 147
Query: 271 FKMNN 275
             +N 
Sbjct: 148 KGLNG 152

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L   T D  L   F  FG +  A ++ D +TG+S  Y FV    R A E+A  K 
Sbjct: 20  IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA-CKD 78
Query: 274 NNALIDDRRICVDFS 288
            N +ID R+  V+ +
Sbjct: 79  PNPIIDGRKANVNLA 93

>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein Length = 102

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 3/80 (3%)
Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           P   LFV  L+  T +E L      F   V A I+ D  TG S  + FV+F   E  + A
Sbjct: 14  PSKTLFVKGLSEDTTEETLK---ESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAA 70
Query: 270 YFKMNNALIDDRRICVDFSQ 289
              M +  ID  ++ +D+++
Sbjct: 71  KEAMEDGEIDGNKVTLDWAK 90

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/76 (32%), Positives = 41/76 (53%)
Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           P+  L V  L+  T + DL  +FS++G +    I+ D ++  S  +AFV FE  +  ++A
Sbjct: 14  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73
Query: 270 YFKMNNALIDDRRICV 285
             + N   +D RRI V
Sbjct: 74  KERANGMELDGRRIRV 89

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 5/72 (6%)
Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  + P    ++    FSQ+GT++ A+++ D  TG+S  + FV ++  +A ++     
Sbjct: 90  IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRV---C 146
Query: 274 NNALID--DRRI 283
            N  ID  DR+I
Sbjct: 147 QNKFIDFKDRKI 158

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 27/77 (35%), Positives = 39/77 (50%)
Query: 213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           VL+V  L    +D+ LH  F  FG +   +I  DY T +   +AFVEFE  E    A   
Sbjct: 9   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 68
Query: 273 MNNALIDDRRICVDFSQ 289
           MN + +  R I V+ ++
Sbjct: 69  MNESELFGRTIRVNLAK 85

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 38/76 (50%)
Query: 213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           VL+V  L    +D+ LH  F  FG +   +I  DY T +   +AFVEFE  E    A   
Sbjct: 4   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 63
Query: 273 MNNALIDDRRICVDFS 288
           MN + +  R I V+ +
Sbjct: 64  MNESELFGRTIRVNLA 79

>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 = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 19/63 (30%), Positives = 34/63 (53%)
Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
           N ++V  ++    D+D+  +F  FG + S  + RD  TG+   Y F+E+EK ++ + A  
Sbjct: 110 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 169
Query: 272 KMN 274
             N
Sbjct: 170 SXN 172

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L+   +DE L   FS FGT+ SA+++ +   G S  + FV F   E   +A  +M
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75
Query: 274 NNALIDDRRICVDFSQ 289
           N  ++  + + V  +Q
Sbjct: 76  NGRIVATKPLYVALAQ 91

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 27/77 (35%), Positives = 39/77 (50%)
Query: 213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           VL+V  L    +D+ LH  F  FG +   +I  DY T +   +AFVEFE  E    A   
Sbjct: 7   VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 66
Query: 273 MNNALIDDRRICVDFSQ 289
           MN + +  R I V+ ++
Sbjct: 67  MNESELFGRTIRVNLAK 83

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/64 (32%), Positives = 35/64 (54%)
Query: 211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
           D  L+V  L      +++  +FSQ+G ++++ IL D  TG S    F+ F+KR   E+A 
Sbjct: 1   DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAI 60
Query: 271 FKMN 274
             +N
Sbjct: 61  KGLN 64

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/93 (26%), Positives = 45/93 (48%)
Query: 195 ALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLC 254
           ++E  GD P         +LFV  ++    +ED+H  F+++G + +  +  D RTG    
Sbjct: 7   SVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG 66
Query: 255 YAFVEFEKREACEQAYFKMNNALIDDRRICVDF 287
           Y  VE+E  +  + A   +N   +  + I VD+
Sbjct: 67  YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 99

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/93 (26%), Positives = 45/93 (48%)
Query: 195 ALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLC 254
           ++E  GD P         +LFV  ++    +ED+H  F+++G + +  +  D RTG    
Sbjct: 6   SVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG 65
Query: 255 YAFVEFEKREACEQAYFKMNNALIDDRRICVDF 287
           Y  VE+E  +  + A   +N   +  + I VD+
Sbjct: 66  YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98

>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 = 42.0 bits (97), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 23/68 (33%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 222 VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDR 281
           +T+DE L  +FS  G V SA+++RD   G SL Y FV +   +  E+A   +N   +  +
Sbjct: 16  MTQDE-LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSK 74
Query: 282 RICVDFSQ 289
            I V +++
Sbjct: 75  TIKVSYAR 82

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 22/75 (29%), Positives = 38/75 (50%)
Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  LN   +DE L   F  F + +S  ++ D +TG S  Y FV F  ++  + A   M
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 274 NNALIDDRRICVDFS 288
               ++ R + ++++
Sbjct: 64  QGQDLNGRPLRINWA 78

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 38/76 (50%)
Query: 213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           VL+V  L    +D+ LH  F  FG +   +I  DY T +   +AFVEFE  E    A   
Sbjct: 65  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 124
Query: 273 MNNALIDDRRICVDFS 288
           MN + +  R I V+ +
Sbjct: 125 MNESELFGRTIRVNLA 140

>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 = 41.2 bits (95), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 23/67 (34%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 223 TEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRR 282
           T+DE L  +FS  G V SA+++RD   G SL Y FV +   +  E+A   +N   +  + 
Sbjct: 32  TQDE-LRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKT 90
Query: 283 ICVDFSQ 289
           I V +++
Sbjct: 91  IKVSYAR 97

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 40.8 bits (94), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 25/70 (35%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  L+  T  E L   FSQ+G VV   I++D  T +S  + FV+F K   C       
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF-KDPNCVGTVLAS 77
Query: 274 NNALIDDRRI 283
               +D R I
Sbjct: 78  RPHTLDGRNI 87

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	299
2ok3_A	161	Peptidyl-prolyl CIS-trans isomerase-like 3; beta-b	1e-78
3bkp_A	232	Cyclophilin; malaria, isomerase, structural GENO s	2e-77
2hq6_A	185	Serologically defined colon cancer antigen 10; pro	7e-77
2poe_A	185	Cyclophilin-like protein, putative; cryptosporidiu	3e-76
1zkc_A	197	Peptidyl-prolyl CIS-trans isomerase like 2; CIS-tr	4e-76
3bo7_A	201	Peptidyl-prolyl CIS-trans isomerase cyclophilin-T;	5e-75
2b71_A	196	Cyclophilin-like protein; structural genomics, str	2e-69
2fu0_A	160	Cyclophilin, putative; PFE0505W, cyclosporin-bindi	3e-69
2x7k_A	166	Peptidyl-prolyl CIS-trans isomerase-like 1; isomer	5e-69
2k7n_A	203	Peptidyl-prolyl CIS-trans isomerase-like 1; beta b	8e-69
2a2n_A	176	Peptidylprolyl isomerase domain and WD repeat CON;	2e-66
1w74_A	191	Peptidyl-prolyl CIS-trans isomerase A; cyclophilin	1e-56
1lop_A	164	Cyclophilin A; rotamase, isomerase-isomerase inhib	1e-42
3s6m_A	167	Peptidyl-prolyl CIS-trans isomerase; seattle struc	4e-42
1v9t_A	166	Cyclophilin B; beta barrel, isomerase-isomerase in	7e-42
2wfi_A	179	Peptidyl-prolyl CIS-trans isomerase G; phosphoprot	5e-41
1a58_A	177	Cyclophilin; isomerase, ppiase; 1.95A {Brugia mala	1e-40
2he9_A	192	NK-tumor recognition protein; cyclosporin, isomera	3e-40
1mzw_A	177	Cyclophilin H, U-snRNP-ASSOCIATED cyclophilin; cyc	5e-39
2ose_A	234	Probable peptidyl-prolyl CIS-trans isomerase; cycl	2e-38
3ich_A	188	Peptidyl-prolyl CIS-trans isomerase B; beta sandwi	6e-37
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	1e-36
2poy_A	186	Peptidyl-prolyl CIS-trans isomerase; isomerase-imm	2e-36
2igv_A	173	Peptidyl-prolyl CIS-trans isomerase 3; rotamase; 1	2e-36
2haq_A	172	Cyclophilin; rotamase, proline, isomerase, CIS-tra	3e-36
2cmt_A	172	Peptidyl-prolyl CIS-trans isomerase E; rotamase ac	4e-36
1qng_A	170	Peptidyl-prolyl CIS-trans isomerase; isomerase-imm	5e-36
1z81_A	229	Cyclophilin; structural genomics, structural genom	5e-36
2r99_A	173	Peptidyl-prolyl CIS-trans isomerase E; CIS-trans i	6e-36
2z6w_A	165	Peptidyl-prolyl CIS-trans isomerase; isomerase-imm	7e-36
3pmp_A	164	Cyclophilin A; peptidyl prolyl isomerase, isomeras	9e-36
3k2c_A	193	Peptidyl-prolyl CIS-trans isomerase; ssgcid, NIH,	2e-35
3rdd_A	184	Peptidyl-prolyl CIS-trans isomerase A; beta barrel	3e-35
2c3b_A	172	Ppiase, cyclophilin; isomerase, 3D domain swapping	7e-34
3rfy_A	369	Peptidyl-prolyl CIS-trans isomerase CYP38, chloro;	6e-31
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	7e-29
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-28
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	3e-23
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	3e-21
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-21
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-14
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-10
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	7e-21
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	8e-21
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-19
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-20
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-18
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	3e-20
1x5o_A	114	RNA binding motif, single-stranded interacting pro	5e-20
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	8e-20
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-19
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-19
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-19
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-19
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-19
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-17
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	4e-19
1x4e_A	85	RNA binding motif, single-stranded interacting pro	5e-19
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	6e-19
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	8e-19
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	9e-19
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-18
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-18
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-13
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-18
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-18
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-18
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-18
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-18
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-16
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-18
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	4e-18
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	6e-18
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-18
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	8e-18
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-17
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	1e-17
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-11
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-17
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-17
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-17
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-17
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	2e-17
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-17
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	3e-17
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-17
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-17
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-17
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	6e-17
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-11
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	6e-17
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	7e-17
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	7e-17
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	8e-17
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	9e-17
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-16
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-16
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-16
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-16
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-16
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-16
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-15
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	3e-16
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-16
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	5e-16
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	5e-16
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	5e-16
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	7e-16
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-15
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-15
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-15
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	6e-15
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-11
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-15
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-15
2div_A	99	TRNA selenocysteine associated protein; structural	4e-15
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-15
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	9e-15
1x5p_A	97	Negative elongation factor E; structure genomics,	6e-15
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-15
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-12
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	8e-15
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	6e-07
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-14
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-14
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-14
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-14
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	2e-14
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-14
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	2e-14
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	2e-14
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	3e-14
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-14
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	8e-12
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	4e-14
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	4e-14
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	5e-14
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	5e-14
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	5e-14
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	5e-14
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-14
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	6e-14
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	7e-14
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	7e-14
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-13
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-13
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-13
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-13
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-13
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	3e-13
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	3e-13
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	3e-13
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	5e-13
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-13
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-12
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	7e-13
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	9e-13
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-12
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-12
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-12
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-12
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-12
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	2e-12
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-12
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	8e-12
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-12
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-12
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	3e-12
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	3e-12
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-12
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	7e-12
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	4e-12
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	4e-12
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	5e-12
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	6e-12
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	7e-12
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	8e-12
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-11
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-11
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-11
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	2e-11
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	4e-11
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	7e-11
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	7e-11
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	8e-11
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-10
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-10
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-10
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-10
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	3e-10
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	4e-10
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	6e-10
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	6e-10
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-09
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-09
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-09
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-09
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	3e-09
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-09
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	5e-09
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	7e-09
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	1e-08
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-08
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-08
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-08
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	2e-08
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	3e-08
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-08
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	5e-08
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	5e-08
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	7e-08
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	9e-08
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	4e-07
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	8e-07
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	9e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-07
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-06
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	3e-06
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	3e-06
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	5e-06
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	7e-06
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-05
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-05
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	2e-04
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-04
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	5e-04

>2ok3_A Peptidyl-prolyl CIS-trans isomerase-like 3; beta-barrel, helix, disulfide bridge; 2.00A {Homo sapiens} SCOP: b.62.1.1 PDB: 1xyh_A 2oju_A* Length = 161

 Score =  234 bits (600), Expect = 1e-78
 Identities = 73/160 (45%), Positives = 100/160 (62%), Gaps = 3/160 (1%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           MSV + T +GDI I++F ++ P+T  NFL  C + YYNGC+FH   K F+ QTGDPTGTG
Sbjct: 1   MSVTLHTDVGDIKIEVFCERTPKTCENFLALCASNYYNGCIFHRNIKGFMVQTGDPTGTG 60

Query: 61  TGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIF 120
            GG S++  + F DE    LKH+  G V MA+ G + N SQF+IT     H LD K+T+F
Sbjct: 61  RGGNSIW-GKKFEDEYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGKQPH-LDMKYTVF 118

Query: 121 GEVAEGLETLTRINQAVVDEEN-RPPQQIIIKQTYVLYPP 159
           G+V +GLETL  + +  V+E+  RP   + IK   +   P
Sbjct: 119 GKVIDGLETLDELEKLPVNEKTYRPLNDVHIKDITIHANP 158

>3bkp_A Cyclophilin; malaria, isomerase, structural GENO structural genomics consortium, SGC; 1.80A {Toxoplasma gondii} Length = 232

 Score =  234 bits (599), Expect = 2e-77
 Identities = 68/207 (32%), Positives = 96/207 (46%), Gaps = 19/207 (9%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
             V++ TSLGD+ ++L+  +CP    NF+Q C   YY   +FH + KDFI Q GDPTGTG
Sbjct: 22  GKVVLHTSLGDLDVELWARECPLACRNFVQLCLEGYYVNTIFHRVVKDFIVQGGDPTGTG 81

Query: 61  TGGRSVYED-RFFVDEIRADLKHDKVGTVGMASAGRDL--------------NASQFYIT 105
            GG     D + F  E    LK    G VG+A+ GR                N +QF+IT
Sbjct: 82  RGGADTTFDGKPFDVETHPRLKFRYRGLVGVANLGRSSKDAENDERGRSLGTNGNQFFIT 141

Query: 106 LRDNLHYLDEKHTIFGEVA-EGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPPELADD 164
           L      L+  +T+FG+V    L  L + N   V +E+RP     IK   VL+ P   +D
Sbjct: 142 L-ARADVLNNAYTLFGKVTGHTLYNLMKFNDLEVGKEDRPMTPPFIKSVDVLWNP--FED 198

Query: 165 SIPEGEPKDELEPPLNEQLSSEKEAHS 191
            +P   P          + +      +
Sbjct: 199 LVPRRLPDAPPAQKDERKRARAAGGRT 225

>2hq6_A Serologically defined colon cancer antigen 10; protein folding, peptidyl-prolyl CIS-trans isomerase, struct genomics; 1.75A {Homo sapiens} Length = 185

 Score =  231 bits (592), Expect = 7e-77
 Identities = 64/160 (40%), Positives = 95/160 (59%), Gaps = 3/160 (1%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
             VL++T+ GDI I+L+  + P+   NF+Q C   YY+  +FH +   FI Q GDPTGTG
Sbjct: 25  GKVLLKTTAGDIDIELWSKEAPKACRNFIQLCLEAYYDNTIFHRVVPGFIVQGGDPTGTG 84

Query: 61  TGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIF 120
           +GG S+Y    F DE  + L+ ++ G V MA+AG   N SQF+ TL      L+ KHTIF
Sbjct: 85  SGGESIY-GAPFKDEFHSRLRFNRRGLVAMANAGSHDNGSQFFFTL-GRADELNNKHTIF 142

Query: 121 GEVA-EGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPP 159
           G+V  + +  + R+++  +D++ RP     IK   VL+ P
Sbjct: 143 GKVTGDTVYNMLRLSEVDIDDDERPHNPHKIKSCEVLFNP 182

>2poe_A Cyclophilin-like protein, putative; cryptosporidium parvum cyclophilin isomerase, structural genomics; 2.01A {Cryptosporidium parvum iowa II} PDB: 2qer_A Length = 185

 Score =  229 bits (587), Expect = 3e-76
 Identities = 65/162 (40%), Positives = 92/162 (56%), Gaps = 6/162 (3%)

Query: 2   SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGT 61
            V I T+ GD+  +LF  +CP+   NFL    + YY   +FH   K FI Q GDPTGTG 
Sbjct: 18  GVRIITNYGDLKFELFCSQCPKACKNFLALSASGYYKNTIFHKNIKGFIIQGGDPTGTGK 77

Query: 62  GGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGR----DLNASQFYITLRDNLHYLDEKH 117
           GG S+Y  R+F DEI  +LK+D+ G + MAS G     + N SQF+IT       L+ ++
Sbjct: 78  GGESIY-GRYFDDEIYPELKYDRRGILSMASKGASKKPNTNGSQFFITYSSLPQ-LNGEY 135

Query: 118 TIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPP 159
            IFG++ +G ETL  +     D+ ++P  +IIIK   +   P
Sbjct: 136 VIFGKLIDGFETLNTLENCPSDKSHKPIDEIIIKDIVIHSNP 177

>1zkc_A Peptidyl-prolyl CIS-trans isomerase like 2; CIS-trans isomerization, peptidylprolyl isomerase, protein- folding, structural genomics consortium; 1.65A {Homo sapiens} SCOP: b.62.1.1 Length = 197

 Score =  229 bits (587), Expect = 4e-76
 Identities = 70/178 (39%), Positives = 102/178 (57%), Gaps = 5/178 (2%)

Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTG 62
           V + T+ GD+ ++L  D  P+T  NF++ CK  YY+G +FH   ++F+ Q GDPTGTGTG
Sbjct: 22  VRLHTNKGDLNLELHCDLTPKTCENFIRLCKKHYYDGTIFHRSIRNFVIQGGDPTGTGTG 81

Query: 63  GRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGE 122
           G S +  + F DE R +L H   G + MA++G + N SQF+IT R   + LD+KHTIFG 
Sbjct: 82  GESYW-GKPFKDEFRPNLSHTGRGILSMANSGPNSNRSQFFITFRSCAY-LDKKHTIFGR 139

Query: 123 VAEGLETLTRINQAVVDEEN-RPPQQIIIKQTYVLYPP--ELADDSIPEGEPKDELEP 177
           V  G + LT +     D +  RP ++I I  T V   P  E       E + + ++ P
Sbjct: 140 VVGGFDVLTAMENVESDPKTDRPKEEIRIDATTVFVDPYEEADAQIAQERKTQLKVAP 197

>3bo7_A Peptidyl-prolyl CIS-trans isomerase cyclophilin-T; isomerase-immunosuppressant complex, immunosuppressant, cyclophilin, structural G structural genomics consortium, SGC; HET: BMT; 2.35A {Toxoplasma gondii} Length = 201

 Score =  227 bits (581), Expect = 5e-75
 Identities = 54/191 (28%), Positives = 93/191 (48%), Gaps = 14/191 (7%)

Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTG-----DPT 57
           + I T+ G + I+L  D  PR  ++FL+ C  KY++  +FH   ++F+ Q G      P+
Sbjct: 9   LRIVTTQGSLNIELHADMAPRACDSFLRLCAVKYFDDTIFHRCIRNFMIQGGRAELRQPS 68

Query: 58  GTGTGGRSVYED------RFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLH 111
                 +S            F DE    L H  +G + MA+ G+  N S+F+IT +   H
Sbjct: 69  KKKEVQQSPRSISGFPGGAPFEDEFDNRLVHQGIGVLSMANDGKHSNLSEFFITFKSCEH 128

Query: 112 YLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPPELADDSIPEGEP 171
            L+ KHTIFG V  GL+ L +  +   D++++P +   +++  V   P   +D+  E E 
Sbjct: 129 -LNNKHTIFGRVVGGLDVLRQWEKLETDKKDKPLKPPKVEEIIVFKNPF--EDARKEMED 185

Query: 172 KDELEPPLNEQ 182
           +   E    ++
Sbjct: 186 EKREEEEKEKK 196

>2b71_A Cyclophilin-like protein; structural genomics, structural genomics consortium, SGC, isomerase; 2.50A {Plasmodium yoelii} SCOP: b.62.1.1 Length = 196

 Score =  212 bits (543), Expect = 2e-69
 Identities = 58/155 (37%), Positives = 88/155 (56%), Gaps = 2/155 (1%)

Query: 2   SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGT 61
            + I T+LGD  ++L+    P+T  NF   C+  +Y+  +FH +  +F+ Q GDPTGTG 
Sbjct: 40  YITIYTNLGDFEVELYWYHSPKTCLNFYTLCEMGFYDNTIFHRVIPNFVIQGGDPTGTGK 99

Query: 62  GGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFG 121
           GG+S+Y   +F DEI  +LKH   G + M++ G + N+SQF+ITL    H LD KHTIF 
Sbjct: 100 GGKSIY-GEYFEDEINKELKHTGAGILSMSNNGPNTNSSQFFITLAPLPH-LDGKHTIFA 157

Query: 122 EVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVL 156
            V++ +  +  I        N+P   + I +T   
Sbjct: 158 RVSKNMTCIENIASVQTTATNKPIFDLKILRTSTA 192

>2fu0_A Cyclophilin, putative; PFE0505W, cyclosporin-binding domain, structura genomics, structural genomics consortium, SGC, unknown FUNC; 1.80A {Plasmodium falciparum} SCOP: b.62.1.1 Length = 160

 Score =  210 bits (538), Expect = 3e-69
 Identities = 64/154 (41%), Positives = 90/154 (58%), Gaps = 2/154 (1%)

Query: 2   SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGT 61
           S +I T++GDI I LF  +C +T  NF  H  N YYN C+FH + K F+ QTGDP+G GT
Sbjct: 7   SAIIYTTMGDIHISLFYKECKKTVQNFSVHSINGYYNNCIFHRVIKHFMVQTGDPSGDGT 66

Query: 62  GGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFG 121
           GG S++ +  F DE    L H K   V MA+ G + N SQF+IT       LD KHT+FG
Sbjct: 67  GGESIWGNE-FEDEFFDHLNHSKPFMVSMANCGPNTNGSQFFITTVPCPW-LDFKHTVFG 124

Query: 122 EVAEGLETLTRINQAVVDEENRPPQQIIIKQTYV 155
           +V +G + +  I +   D+ ++P + I I    +
Sbjct: 125 KVTQGSKIVLDIEKVRTDKRDKPLEDIKILNIKI 158

>2x7k_A Peptidyl-prolyl CIS-trans isomerase-like 1; isomerase-immunosuppressant complex, immunosuppressant; HET: MLE MVA BMT ABA SAR; 1.15A {Homo sapiens} PDB: 1xwn_A Length = 166

 Score =  210 bits (538), Expect = 5e-69
 Identities = 67/155 (43%), Positives = 93/155 (60%), Gaps = 2/155 (1%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
            +V +ETS+G IV++L+    P+T  NF +  +  YYNG  FH I KDF+ Q GDPTGTG
Sbjct: 12  PNVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTG 71

Query: 61  TGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIF 120
            GG S+Y  + F DE+  DLK    G + MA+AG D N SQF++TL      LD KHTIF
Sbjct: 72  RGGASIYGKQ-FEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPTQW-LDGKHTIF 129

Query: 121 GEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYV 155
           G V +G+  + R+     + ++RP   + I + Y 
Sbjct: 130 GRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYP 164

>2k7n_A Peptidyl-prolyl CIS-trans isomerase-like 1; beta barrel, disorder-order transition, HOOK-like, mRNA processing, mRNA splicing, rotamase; NMR {Homo sapiens} Length = 203

 Score =  211 bits (540), Expect = 8e-69
 Identities = 68/165 (41%), Positives = 94/165 (56%), Gaps = 2/165 (1%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
            +V +ETS+G IV++L+    P+T  NF +  +  YYNG  FH I KDF+ Q GDPTGTG
Sbjct: 12  PNVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTG 71

Query: 61  TGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIF 120
            GG S+Y  + F DE+  DLK    G + MA+AG D N SQF++TL      LD KHTIF
Sbjct: 72  RGGASIYGKQ-FEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPTQW-LDGKHTIF 129

Query: 121 GEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPPELADDS 165
           G V +G+  + R+     + ++RP   + I + Y          S
Sbjct: 130 GRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYPSGGGGSGGGS 174

>2a2n_A Peptidylprolyl isomerase domain and WD repeat CON; CIS-trans isomerization, protein-folding, peptidylprolyl ISO structural genomics; 1.65A {Homo sapiens} SCOP: b.62.1.1 Length = 176

 Score =  204 bits (522), Expect = 2e-66
 Identities = 70/155 (45%), Positives = 96/155 (61%), Gaps = 3/155 (1%)

Query: 2   SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGT 61
           S +I TS+GDI   LF  +CP+T  NF  H +N YYNG  FH I K F+ QTGDPTGTG 
Sbjct: 23  SAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNGYYNGHTFHRIIKGFMIQTGDPTGTGM 82

Query: 62  GGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFG 121
           GG S++    F DE  + L+HD+  T+ MA+AG + N SQF+IT+      LD KHT+FG
Sbjct: 83  GGESIWGGE-FEDEFHSTLRHDRPYTLSMANAGSNTNGSQFFITVVPTPW-LDNKHTVFG 140

Query: 122 EVAEGLETLTRINQAVVDEEN-RPPQQIIIKQTYV 155
            V +G+E + RI+   V+ +  +P + + I    V
Sbjct: 141 RVTKGMEVVQRISNVKVNPKTDKPYEDVSIINITV 175

>1w74_A Peptidyl-prolyl CIS-trans isomerase A; cyclophilin, ppiase, RV0009, rotamase, structural proteomics in europe, spine; 2.6A {Mycobacterium tuberculosis} SCOP: b.62.1.1 Length = 191

 Score =  180 bits (458), Expect = 1e-56
 Identities = 58/172 (33%), Positives = 87/172 (50%), Gaps = 22/172 (12%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKN---------------KYYNGCLFHNI 45
            +  + T+ GDI I LF +  P+T  NF+   +                 +Y+G +FH +
Sbjct: 24  ATATLHTNRGDIKIALFGNHAPKTVANFVGLAQGTKDYSTQNASGGPSGPFYDGAVFHRV 83

Query: 46  HKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYIT 105
            + F+ Q GDPTGTG GG        F DE   +L+ DK   + MA+AG   N SQF+IT
Sbjct: 84  IQGFMIQGGDPTGTGRGG----PGYKFADEFHPELQFDKPYLLAMANAGPGTNGSQFFIT 139

Query: 106 LRDNLHYLDEKHTIFGEV--AEGLETLTRINQAVVDEENRPPQQIIIKQTYV 155
           +    H L+ +HTIFGEV  AE    +  I++   D  +RP   ++I+   +
Sbjct: 140 VGKTPH-LNRRHTIFGEVIDAESQRVVEAISKTATDGNDRPTDPVVIESITI 190

>1lop_A Cyclophilin A; rotamase, isomerase-isomerase inhibitor complex; HET: NIT; 1.80A {Escherichia coli} SCOP: b.62.1.1 PDB: 2nul_A 2rs4_A Length = 164

 Score =  143 bits (362), Expect = 1e-42
 Identities = 44/166 (26%), Positives = 72/166 (43%), Gaps = 16/166 (9%)

Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTG 62
           V   T+ GDIVI  F DK P T  NFL +C+  +YN  +FH +   F+ Q G        
Sbjct: 2   VTFHTNHGDIVIKTFDDKAPETVKNFLDYCREGFYNNTIFHRVINGFMIQGGGFEPGMKQ 61

Query: 63  GRSVYEDRFFVDEIRADLKHDKVGTVGMA-SAGRDLNASQFYITLRDNLHY-------LD 114
             +        +E    LK+ + GT+ MA +       +QF+I + DN            
Sbjct: 62  KAT---KEPIKNEANNGLKNTR-GTLAMARTQAPHSATAQFFINVVDNDFLNFSGESLQG 117

Query: 115 EKHTIFGEVAEGLETLTRINQAVVDE----ENRPPQQIIIKQTYVL 156
             + +F EV +G++ + +I           ++ P + +II+   V 
Sbjct: 118 WGYCVFAEVVDGMDEVDKIKGVATGRSGMHQDVPKEDVIIESVTVS 163

>3s6m_A Peptidyl-prolyl CIS-trans isomerase; seattle structural genomics center for infectious disease; 1.65A {Burkholderia pseudomallei} PDB: 3t1u_A* Length = 167

 Score =  141 bits (359), Expect = 4e-42
 Identities = 42/167 (25%), Positives = 76/167 (45%), Gaps = 18/167 (10%)

Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTG 62
           V + T+ G I ++L   K P+T  NFL + K  +Y+G +FH +   F+ Q G        
Sbjct: 6   VELHTNHGVIKLELDEAKAPKTVENFLNYVKKGHYDGTIFHRVINGFMIQGGGFEPGLKQ 65

Query: 63  GRSVYEDRFFVDEIRADLKHDKVGTVGMA-SAGRDLNASQFYITLRDNLHYLDEK----- 116
             +   D    +E    LK+D   T+ MA +       +QF+I + DN  +L+       
Sbjct: 66  KPT---DAPIANEANNGLKNDT-YTIAMARTNDPHSATAQFFINVNDN-EFLNHSSPTPQ 120

Query: 117 ---HTIFGEVAEGLETLTRINQAVVDE----ENRPPQQIIIKQTYVL 156
              + +FG+V EG + + +I           ++ P   ++I++  V+
Sbjct: 121 GWGYAVFGKVVEGQDIVDKIKAVKTGSKGFHQDVPNDDVVIEKAVVV 167

>1v9t_A Cyclophilin B; beta barrel, isomerase-isomerase inhibitor complex; HET: NIT; 1.70A {Escherichia coli} SCOP: b.62.1.1 PDB: 1j2a_A* 1vai_A* 1clh_A Length = 166

 Score =  141 bits (357), Expect = 7e-42
 Identities = 46/164 (28%), Positives = 81/164 (49%), Gaps = 15/164 (9%)

Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTG 62
           VL+ TS G+I ++L   K P +  NF+ +  + +YN   FH +   F+ Q G  T     
Sbjct: 7   VLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQ 66

Query: 63  GRSVYEDRFFVDEIRADLKHDKVGTVGMA-SAGRDLNASQFYITLRDNLHYLDE-----K 116
            +         +E    L++ + GT+ MA +A +D   SQF+I + DN  +LD       
Sbjct: 67  KKPNP---PIKNEADNGLRNTR-GTIAMARTADKDSATSQFFINVADN-AFLDHGQRDFG 121

Query: 117 HTIFGEVAEGLETLTRINQAVVDE----ENRPPQQIIIKQTYVL 156
           + +FG+V +G++   +I+Q    +    +N P + ++I    VL
Sbjct: 122 YAVFGKVVKGMDVADKISQVPTHDVGPYQNVPSKPVVILSATVL 165

>2wfi_A Peptidyl-prolyl CIS-trans isomerase G; phosphoprotein, PRE-mRNA splicing, alternative splicing, nucleus, rotamase, cyclosporin; HET: OCS; 0.75A {Homo sapiens} PDB: 2wfj_A* 2gw2_A Length = 179

 Score =  139 bits (353), Expect = 5e-41
 Identities = 58/154 (37%), Positives = 80/154 (51%), Gaps = 15/154 (9%)

Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC-----------KNKYYNGCLFHNIHKDFIAQTGDPT 57
            G +V +LF D CP+T  NF   C           K  +Y  CLFH + KDF+ Q GD +
Sbjct: 23  AGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFS 82

Query: 58  -GTGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEK 116
            G G GG S+Y   F  DE    +KH+K   + MA+ G+D N SQF+IT +   H LD  
Sbjct: 83  EGNGRGGESIYGGFF-EDE-SFAVKHNKEFLLSMANRGKDTNGSQFFITTKPTPH-LDGH 139

Query: 117 HTIFGEVAEGLETLTRINQAVVDEENRPPQQIII 150
           H +FG+V  G E +  I     D  ++P  ++ I
Sbjct: 140 HVVFGQVISGQEVVREIENQKTDAASKPFAEVRI 173

>1a58_A Cyclophilin; isomerase, ppiase; 1.95A {Brugia malayi} SCOP: b.62.1.1 PDB: 1a33_A 1c5f_A* Length = 177

 Score =  138 bits (351), Expect = 1e-40
 Identities = 61/154 (39%), Positives = 83/154 (53%), Gaps = 15/154 (9%)

Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC-----------KNKYYNGCLFHNIHKDFIAQTGDPT 57
            G IV++L+ D  PRT NNFL  C           K  +Y G  FH + K+F+ Q GD T
Sbjct: 20  AGRIVMELYNDIAPRTCNNFLMLCTGMAGTGKISGKPLHYKGSTFHRVIKNFMIQGGDFT 79

Query: 58  -GTGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEK 116
            G GTGG S+Y   F  DE    +KHD+   V MA+ G + N SQF+IT     H L+  
Sbjct: 80  KGDGTGGESIYGGMF-DDE-EFVMKHDEPFVVSMANKGPNTNGSQFFITTTPAPH-LNNI 136

Query: 117 HTIFGEVAEGLETLTRINQAVVDEENRPPQQIII 150
           H +FG+V  G E +T+I     + +NRP   ++I
Sbjct: 137 HVVFGKVVSGQEVVTKIEYLKTNSKNRPLADVVI 170

>2he9_A NK-tumor recognition protein; cyclosporin, isomerase, membrane, repeat, rotamase, peptidylprolyl isomerase, structural genomics; 2.00A {Homo sapiens} Length = 192

 Score =  138 bits (349), Expect = 3e-40
 Identities = 57/154 (37%), Positives = 77/154 (50%), Gaps = 15/154 (9%)

Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC-----------KNKYYNGCLFHNIHKDFIAQTGDPT 57
           +G I+  LF D CP+T  NFL  C           K   Y G  FH + K+F+ Q GD +
Sbjct: 33  VGRIMFQLFSDICPKTCKNFLCLCSGEKGLGKTTGKKLCYKGSTFHRVVKNFMIQGGDFS 92

Query: 58  -GTGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEK 116
            G G GG S+Y   F  DE    LKHD+   + MA+ G+  N SQF+IT +   H LD  
Sbjct: 93  EGNGKGGESIYGGYF-KDE-NFILKHDRAFLLSMANRGKHTNGSQFFITTKPAPH-LDGV 149

Query: 117 HTIFGEVAEGLETLTRINQAVVDEENRPPQQIII 150
           H +FG V  G E + +I     D  +RP   + +
Sbjct: 150 HVVFGLVISGFEVIEQIENLKTDAASRPYADVRV 183

>1mzw_A Cyclophilin H, U-snRNP-ASSOCIATED cyclophilin; cyclophilin, peptidyl-prolyl-CIS/trans isomerase, spliceosome, U4/U6-60K protein, WD protein; 2.00A {Homo sapiens} SCOP: b.62.1.1 PDB: 1qoi_A Length = 177

 Score =  134 bits (339), Expect = 5e-39
 Identities = 53/151 (35%), Positives = 74/151 (49%), Gaps = 12/151 (7%)

Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC--------KNKYYNGCLFHNIHKDFIAQTGDPT-GT 59
           +G + I+LF D  P+T  NF Q C            Y G  FH + KDF+ Q GD   G 
Sbjct: 24  VGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRVIKDFMIQGGDFVNGD 83

Query: 60  GTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTI 119
           GTG  S+Y   F  DE    L+H   G + MA++G   N  QF+IT       LD KH +
Sbjct: 84  GTGVASIYRGPF-ADE-NFKLRHSAPGLLSMANSGPSTNGCQFFITCSKCDW-LDGKHVV 140

Query: 120 FGEVAEGLETLTRINQAVVDEENRPPQQIII 150
           FG++ +GL  + +I        N+P   ++I
Sbjct: 141 FGKIIDGLLVMRKIENVPTGPNNKPKLPVVI 171

>2ose_A Probable peptidyl-prolyl CIS-trans isomerase; cyclophilin; 2.04A {Mimivirus} Length = 234

 Score =  134 bits (339), Expect = 2e-38
 Identities = 45/198 (22%), Positives = 66/198 (33%), Gaps = 33/198 (16%)

Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC--------------------KNKYYNGCLFHNIHKD 48
           +G + I LF D  P    NF+Q                       N+ Y GC FHN+  +
Sbjct: 28  IGRLQIKLFRDAFPAGVENFVQLTNGKTYRVNSNGTGKYKYNRHINRTYEGCKFHNVLHN 87

Query: 49  FIAQTGDPT-GTGTGGRSVYEDRFFVDEIRAD--LKHDKVGTVGMAS----AGRDLNASQ 101
               +GD     G+   +VY D      +  D    H+  G + +      +G     S 
Sbjct: 88  NYIVSGDIYNSNGSSAGTVYCDEPI-PPVFGDYFYPHESKGLLSLVPYTDESGNRYYDST 146

Query: 102 FYITLRDNLH-----YLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVL 156
           F ITL D         LD    + G+V  GL+ L +IN  +     R      I +    
Sbjct: 147 FMITLDDIRPSNVLDELDRDQVVIGQVYGGLDVLDKINSMIKPYAGRKYPTFSIGKCGAY 206

Query: 157 YPPELADDSIPEGEPKDE 174
                A    P      +
Sbjct: 207 LDSSQAQRKRPVNVNGTK 224

>3ich_A Peptidyl-prolyl CIS-trans isomerase B; beta sandwich, cyclosporin, endoplasmic reticulum, glycoprot isomerase, rotamase; 1.20A {Homo sapiens} PDB: 3ici_A* 1cyn_A* 2esl_A* 2rmc_A* 1h0p_A 1xo7_A 1xq7_A* Length = 188

 Score =  129 bits (326), Expect = 6e-37
 Identities = 59/146 (40%), Positives = 83/146 (56%), Gaps = 7/146 (4%)

Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQTGDPT-GTGTGGR 64
           +G ++  LF    P+T +NF+      K   Y    FH + KDF+ Q GD T G GTGG+
Sbjct: 29  VGRVIFGLFGKTVPKTVDNFVALATGEKGFGYKNSKFHRVIKDFMIQGGDFTRGDGTGGK 88

Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y +RF  DE    LKH   G V MA+AG+D N SQF+IT       LD KH +FG+V 
Sbjct: 89  SIYGERF-PDE-NFKLKHYGPGWVSMANAGKDTNGSQFFITTVKTAW-LDGKHVVFGKVL 145

Query: 125 EGLETLTRINQAVVDEENRPPQQIII 150
           EG+E + ++     D  ++P + +II
Sbjct: 146 EGMEVVRKVESTKTDSRDKPLKDVII 171

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A Length = 370

 Score =  133 bits (336), Expect = 1e-36
 Identities = 62/194 (31%), Positives = 98/194 (50%), Gaps = 24/194 (12%)

Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC-----------KNKYYNGCLFHNIHKDFIAQTGDPT 57
           +G IV++LF D  P+T  NF   C           K  ++ GC FH I K F+ Q GD +
Sbjct: 29  VGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFS 88

Query: 58  -GTGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEK 116
              GTGG S+Y ++F  DE     KHDK G + MA+AG + N SQF+IT     H LD K
Sbjct: 89  NQNGTGGESIYGEKF-EDE-NFHYKHDKEGLLSMANAGSNTNGSQFFITTVPTPH-LDGK 145

Query: 117 HTIFGEVAEGLETLTRINQAVVDEENRPPQQIII--------KQTYVLYPPELADDSIPE 168
           H +FG+V +G+     + + V  +  +P +  +I           + ++P + + DS P+
Sbjct: 146 HVVFGQVIKGMGVAKIL-ENVEVKGEKPAKLCVIAECGELKEGDDWGIFPKDGSGDSHPD 204

Query: 169 GEPKDELEPPLNEQ 182
                +++    ++
Sbjct: 205 FPEDADVDLKDVDK 218

>2poy_A Peptidyl-prolyl CIS-trans isomerase; isomerase-immunosuppressant complex, immunosuppressant, cyclophilin, isomerase, S genomics, structural genomics consortium; HET: BMT; 1.80A {Cryptosporidium parvum iowa II} PDB: 2plu_A* Length = 186

 Score =  128 bits (323), Expect = 2e-36
 Identities = 57/153 (37%), Positives = 75/153 (49%), Gaps = 15/153 (9%)

Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC----------KNKYYNGCLFHNIHKDFIAQTGDPT- 57
            G I ++LF DK P T  NF   C          K   Y G  FH I   F+ Q GD T 
Sbjct: 33  AGRITMELFADKVPITAENFRALCTGEKGMGQSGKPLCYTGSFFHRIIPQFMIQGGDFTR 92

Query: 58  GTGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKH 117
           G GTGG S+Y  +F  DE      HD    + MA+AG + N SQF+IT       LD KH
Sbjct: 93  GDGTGGESIYGSKF-RDE-NFVYTHDAPFLLSMANAGPNTNGSQFFITTVPCPW-LDGKH 149

Query: 118 TIFGEVAEGLETLTRINQAVVDEENRPPQQIII 150
            +FG+V EG+E +  I +    +  +P + + I
Sbjct: 150 VVFGKVLEGMEVVKSI-EKCGSQNGKPTKSVCI 181

>2igv_A Peptidyl-prolyl CIS-trans isomerase 3; rotamase; 1.67A {Caenorhabditis elegans} SCOP: b.62.1.1 PDB: 1e3b_A 1e8k_A 1dyw_A 2igw_A 2hqj_A Length = 173

 Score =  127 bits (322), Expect = 2e-36
 Identities = 53/153 (34%), Positives = 79/153 (51%), Gaps = 15/153 (9%)

Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC----------KNKYYNGCLFHNIHKDFIAQTGDPT- 57
            G IV++L+ D  P+T  NF   C          K  ++ G  FH I  +F+ Q GD T 
Sbjct: 17  SGRIVMELYDDVVPKTAGNFRALCTGENGIGKSGKPLHFKGSKFHRIIPNFMIQGGDFTR 76

Query: 58  GTGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKH 117
           G GTGG S+Y ++F  DE     KH   G + MA+AG + N SQF++        LD KH
Sbjct: 77  GNGTGGESIYGEKF-PDE-NFKEKHTGPGVLSMANAGPNTNGSQFFLCTVKTEW-LDGKH 133

Query: 118 TIFGEVAEGLETLTRINQAVVDEENRPPQQIII 150
            +FG V EGL+ +  + ++   +  +P +  +I
Sbjct: 134 VVFGRVVEGLDVVKAV-ESNGSQSGKPVKDCMI 165

>2haq_A Cyclophilin; rotamase, proline, isomerase, CIS-trans, protozoa, KAla-AZAR.; 1.97A {Leishmania donovani} PDB: 3eov_A* 3bt8_A Length = 172

 Score =  126 bits (320), Expect = 3e-36
 Identities = 55/146 (37%), Positives = 82/146 (56%), Gaps = 8/146 (5%)

Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQTGDPT-GTGTGGR 64
           LG I I LF    P TT NF Q C       Y   +FH + ++F+ Q GD T   GTGG+
Sbjct: 25  LGRITIGLFGKDAPLTTENFRQLCTGEHGFGYKDSIFHRVIQNFMIQGGDFTNFDGTGGK 84

Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  DE   ++KH   G + MA+AG + N SQF+IT       LD +H +FG+V 
Sbjct: 85  SIYGEKF-ADE-NLNVKHFV-GALSMANAGPNTNGSQFFITTAPTPW-LDGRHVVFGKVL 140

Query: 125 EGLETLTRINQAVVDEENRPPQQIII 150
           +G++ + RI +   +  +RP + + I
Sbjct: 141 DGMDVVLRIEKTKTNSHDRPVKPVKI 166

>2cmt_A Peptidyl-prolyl CIS-trans isomerase E; rotamase activity, rotamase, RNA-binding, cyclosporin, cyclophilin, beta-barrel; 1.50A {Schistosoma mansoni} PDB: 2ck1_A Length = 172

 Score =  126 bits (319), Expect = 4e-36
 Identities = 51/146 (34%), Positives = 78/146 (53%), Gaps = 8/146 (5%)

Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQTGDPT-GTGTGGR 64
            G IV++L  D  PRT  NF   C   +   Y+ C FH +   F+ Q GD   G GTGG+
Sbjct: 24  AGRIVMELRSDIVPRTAENFRALCTGERGFGYHNCCFHRVIPQFMCQGGDFVKGDGTGGK 83

Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y  +F  DE    L+H+  G + MA++G + N SQF+I        LD KH +FG V 
Sbjct: 84  SIYGRKF-DDE-NFQLRHEGFGVLSMANSGPNTNGSQFFICTTKCDW-LDGKHVVFGRVV 140

Query: 125 EGLETLTRINQAVVDEENRPPQQIII 150
           +G   + ++ ++V  +  +  + +II
Sbjct: 141 DGQNVVKKM-ESVGSKSGKVKEPVII 165

>1qng_A Peptidyl-prolyl CIS-trans isomerase; isomerase-immunosuppressant complex, cyclophilin-cyclosporin complex, immunosuppressant, cyclophilin; HET: BMT; 2.1A {Plasmodium falciparum} SCOP: b.62.1.1 PDB: 1qnh_A* Length = 170

 Score =  126 bits (318), Expect = 5e-36
 Identities = 56/153 (36%), Positives = 82/153 (53%), Gaps = 14/153 (9%)

Query: 8   SLGDIVIDLFVDKCPRTTNNFLQHC---------KNKYYNGCLFHNIHKDFIAQTGDPT- 57
           + G I+ +LF D  PRT  NF   C         KN +Y   +FH I   F+ Q GD T 
Sbjct: 16  NAGRIIFELFSDITPRTCENFRALCTGEKIGSRGKNLHYKNSIFHRIIPQFMCQGGDITN 75

Query: 58  GTGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKH 117
           G G+GG S+Y   F  DE   ++KHD+ G + MA+AG + N+SQF+ITL      LD KH
Sbjct: 76  GNGSGGESIYGRSF-TDE-NFNMKHDQPGLLSMANAGPNTNSSQFFITLVPCPW-LDGKH 132

Query: 118 TIFGEVAEGLETLTRINQAVVDEENRPPQQIII 150
            +FG+V EG+  +  + +    +     + ++I
Sbjct: 133 VVFGKVIEGMNVVREM-EKEGAKSGYVKRSVVI 164

>1z81_A Cyclophilin; structural genomics, structural genomics consortium, SGC, isomerase; 2.80A {Plasmodium yoelii yoelii} SCOP: b.62.1.1 Length = 229

 Score =  127 bits (322), Expect = 5e-36
 Identities = 51/156 (32%), Positives = 79/156 (50%), Gaps = 15/156 (9%)

Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC--------KNKYYNGCLFHNIHKDFIAQTGDPT-GT 59
           LG    +LF +  P+T+ NF Q C            Y   +FH + K+F+ Q GD     
Sbjct: 73  LGKFKFELFQNIVPKTSENFRQFCTGEYKVNNLPVGYKNTIFHRVIKEFMIQGGDFINHN 132

Query: 60  GTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTI 119
           G+G  S+Y ++F  DE   D+KHDK G + MA++G + N  QF+IT +     LD K+ +
Sbjct: 133 GSGSLSIYGEKF-DDE-NFDIKHDKEGLLSMANSGPNTNGCQFFITTKKCEW-LDGKNVV 189

Query: 120 FGEV--AEGLETLTRI-NQAVVDEENRPPQQIIIKQ 152
           FG +   + L  L +I N +V     +P   I + +
Sbjct: 190 FGRIIDNDSLLLLKKIENVSVTPYIYKPKIPINVVE 225

>2r99_A Peptidyl-prolyl CIS-trans isomerase E; CIS-trans isomerization, structural genomics consortium, SGC, alternative splicing, mRNA processing; 1.61A {Homo sapiens} SCOP: b.62.1.1 PDB: 3uch_A 1zmf_A Length = 173

 Score =  126 bits (318), Expect = 6e-36
 Identities = 58/146 (39%), Positives = 79/146 (54%), Gaps = 8/146 (5%)

Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQTGDPT-GTGTGGR 64
            G I + L  D  P T  NF   C   K   + G  FH I   F+ Q GD T   GTGG+
Sbjct: 25  AGRIQMLLRSDVVPMTAENFRCLCTHEKGFGFKGSSFHRIIPQFMCQGGDFTNHNGTGGK 84

Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y  +F  DE    LKH   G + MA++G + N SQF++T       LD KH +FGEV 
Sbjct: 85  SIYGKKF-DDE-NFILKHTGPGLLSMANSGPNTNGSQFFLTCDKTDW-LDGKHVVFGEVT 141

Query: 125 EGLETLTRINQAVVDEENRPPQQIII 150
           EGL+ L +I +A   ++ +P Q++II
Sbjct: 142 EGLDVLRQI-EAQGSKDGKPKQKVII 166

>2z6w_A Peptidyl-prolyl CIS-trans isomerase; isomerase-immunosuppressant complex, immunosuppressant, cyclophilin D; HET: BMT MLE CIT; 0.96A {Homo sapiens} SCOP: b.62.1.1 PDB: 3rcg_A* 3r49_A* 3r54_A 3r56_A* 3r57_A* 3r59_A* 3rcf_A* 3r4g_A* 3rci_X* 3rck_X* 3rcl_A* 3rd9_X* 3rda_X* 3rdb_A* 3rdc_A* 2bit_X 2biu_X 3qyu_A 3k0m_A 1ak4_A* ... Length = 165

 Score =  125 bits (317), Expect = 7e-36
 Identities = 56/146 (38%), Positives = 79/146 (54%), Gaps = 8/146 (5%)

Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQTGDPT-GTGTGGR 64
           LG +V++L  D  P+T  NF   C   K   Y G  FH +   F+ Q GD T   GTGG+
Sbjct: 17  LGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGK 76

Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y  RF  DE    LKH   G + MA+AG + N SQF+I        LD KH +FG V 
Sbjct: 77  SIYGSRF-PDE-NFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDW-LDGKHVVFGHVI 133

Query: 125 EGLETLTRINQAVVDEENRPPQQIII 150
           EG++ + +I ++   +  R  ++I+I
Sbjct: 134 EGMDVVKKI-ESFGSKSGRTSKKIVI 158

>3pmp_A Cyclophilin A; peptidyl prolyl isomerase, isomerase-immunosuppressant compl; HET: BMT; 1.47A {Moniliophthora perniciosa} PDB: 3o7t_A Length = 164

 Score =  125 bits (316), Expect = 9e-36
 Identities = 52/146 (35%), Positives = 75/146 (51%), Gaps = 8/146 (5%)

Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQTGDPT-GTGTGGR 64
            G IV  L+ +  P+T  NF +         Y   +FH +   F+ Q GD T   GTGG+
Sbjct: 16  EGRIVFKLYDEAVPKTAKNFRELATGQHGFGYKDSIFHRVIPQFMLQGGDFTRHNGTGGK 75

Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  DE    +KH K G + MA+AG + N SQF+IT       LD KH +FGEV 
Sbjct: 76  SIYGEKF-ADE-NFQVKHTKPGLLSMANAGANTNGSQFFITTVPTSW-LDGKHVVFGEVI 132

Query: 125 EGLETLTRINQAVVDEENRPPQQIII 150
           EGL+ + ++ +       +    I I
Sbjct: 133 EGLDIVRKV-EGKGSASGKTNATIKI 157

>3k2c_A Peptidyl-prolyl CIS-trans isomerase; ssgcid, NIH, niaid, SBRI, UW, decode, cytoplasm, rotamase, structural genomics; HET: PG5; 1.95A {Encephalitozoon cuniculi} Length = 193

 Score =  125 bits (316), Expect = 2e-35
 Identities = 61/147 (41%), Positives = 80/147 (54%), Gaps = 8/147 (5%)

Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQTGDPT-GTGTGGR 64
           LG IV+ L  D  P+T  NF   C   K + Y G  FH I   F+ Q GD T   GTGGR
Sbjct: 41  LGRIVMKLEDDIVPKTAKNFRTLCERPKGEGYKGSTFHRIIPGFMVQGGDYTAHNGTGGR 100

Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  DE   +LKH K G + MA+ G   N SQF+ITL      LDEKH +FGEV 
Sbjct: 101 SIYGEKF-PDE-NFELKHTKEGILSMANCGAHTNGSQFFITLGKTQW-LDEKHVVFGEVV 157

Query: 125 EGLETLTRI-NQAVVDEENRPPQQIII 150
           EG++ + +I        + +   +I I
Sbjct: 158 EGMDVVHKIAKYGSESGQVKKGYRIEI 184

>3rdd_A Peptidyl-prolyl CIS-trans isomerase A; beta barrel, cytosolic, inhibito isomerase-isomerase inhibitor complex; HET: EA4; 2.14A {Homo sapiens} Length = 184

 Score =  125 bits (315), Expect = 3e-35
 Identities = 54/146 (36%), Positives = 75/146 (51%), Gaps = 8/146 (5%)

Query: 9   LGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQTGDPT-GTGTGGR 64
           LG +  +LF DK P+T  NF       K   Y G  FH I   F+ Q GD T   GTGG+
Sbjct: 36  LGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGK 95

Query: 65  SVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA 124
           S+Y ++F  DE    LKH   G + MA+AG + N SQF+I        LD KH +FG+V 
Sbjct: 96  SIYGEKF-EDE-NFILKHTGPGILSMANAGPNTNGSQFFICTAKTEW-LDGKHVVFGKVK 152

Query: 125 EGLETLTRINQAVVDEENRPPQQIII 150
           EG+  +  + +       +  ++I I
Sbjct: 153 EGMNIVEAM-ERFGSRNGKTSKKITI 177

>2c3b_A Ppiase, cyclophilin; isomerase, 3D domain swapping, misfolding, Asp F 11, allergen, rotamase; 1.85A {Aspergillus fumigatus} SCOP: b.62.1.1 Length = 172

 Score =  120 bits (304), Expect = 7e-34
 Identities = 57/150 (38%), Positives = 74/150 (49%), Gaps = 10/150 (6%)

Query: 8   SLGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQTGDPT-GTGTGG 63
            +G IV +LF    P+T  NF + C     + Y    FH I  +F+ Q GD T G GTGG
Sbjct: 20  KVGRIVFNLFDKDVPKTAKNFRELCKRPAGEGYRESTFHRIIPNFMIQGGDFTRGNGTGG 79

Query: 64  RSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEV 123
           RS+Y D+F  DE     KHDK G + MA+AG + N SQF+IT       LD KH +FGEV
Sbjct: 80  RSIYGDKF-ADE-NFSRKHDKKGILSMANAGPNTNGSQFFITTAVTSW-LDGKHVVFGEV 136

Query: 124 --AEGLETLTRI-NQAVVDEENRPPQQIII 150
              +    +  I          R   +  I
Sbjct: 137 ADEKSYSVVKEIEALGSSSGSVRSNTRPKI 166

>3rfy_A Peptidyl-prolyl CIS-trans isomerase CYP38, chloro; cyclophilin, peptidyl prolyl isomerase, ppiase, TLP,; 2.39A {Arabidopsis thaliana} Length = 369

 Score =  118 bits (296), Expect = 6e-31
 Identities = 32/163 (19%), Positives = 55/163 (33%), Gaps = 33/163 (20%)

Query: 5   IETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGR 64
                    I L     P T  NF+   +  +Y+G         F+ QTGDP G   G  
Sbjct: 183 PNIEDCVFRIVLDGYNAPVTAGNFVDLVERHFYDGMEIQRS-DGFVVQTGDPEGPAEGFI 241

Query: 65  SVY--EDRFFVDEIRA----------------------DLKHDKVGTVGMASAGRDLNA- 99
                + R    EI                         +  +  GT+ MA    + ++ 
Sbjct: 242 DPSTEKTRTVPLEIMVTGEKTPFYGSTLEELGLYKAQVVIPFNAFGTMAMAREEFENDSG 301

Query: 100 -SQFYITLRDN------LHYLDEKHTIFGEVAEGLETLTRINQ 135
            SQ +  L+++       + LD ++ +FG V +  + L  +  
Sbjct: 302 SSQVFWLLKESELTPSNSNILDGRYAVFGYVTDNEDFLADLKV 344

>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 =  113 bits (283), Expect = 7e-29
 Identities = 35/141 (24%), Positives = 53/141 (37%), Gaps = 4/141 (2%)

Query: 157 YPPELADDSIPEGEPKDELEPPLNEQLSSEK-EAHSRAVALECIGDIPDADVKP---PDN 212
           Y  E  D        + E      E+   EK E   + V  E     P  D         
Sbjct: 44  YIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFK 103

Query: 213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
            LFV ++N  T +  L   F  +G +    ++   R+G+   YAF+E+E       AY  
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163

Query: 273 MNNALIDDRRICVDFSQSVSK 293
            +   ID RR+ VD  +  + 
Sbjct: 164 ADGKKIDGRRVLVDVERGRTV 184

>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 =  104 bits (262), Expect = 1e-28
 Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 8/84 (9%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
            P   L+V  L P T    L   F +FG++ + + ++         +A++++E  +A + 
Sbjct: 15  NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYIQYESLDAAQA 68

Query: 269 AYFKMNNALID--DRRICVDFSQS 290
           A  KM    +   DRR+ VDF++S
Sbjct: 69  ACAKMRGFPLGGPDRRLRVDFAKS 92

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 90.9 bits (226), Expect = 3e-23
 Identities = 16/86 (18%), Positives = 29/86 (33%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
            P   +   +LN    +  L  +  ++G V   EIL   RT + L  A V F      ++
Sbjct: 4   IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKE 63

Query: 269 AYFKMNNALIDDRRICVDFSQSVSKI 294
               ++   +    I         + 
Sbjct: 64  TVKNLHLTSVMGNIIHAQLDIKGQQR 89

>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 = 86.3 bits (214), Expect = 3e-21
 Identities = 28/87 (32%), Positives = 45/87 (51%)

Query: 203 PDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEK 262
            +     P+  L V  L+  T + DL  +FS++G +    I+ D ++  S  +AFV FE 
Sbjct: 38  GNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 97

Query: 263 REACEQAYFKMNNALIDDRRICVDFSQ 289
            +  ++A  + N   +D RRI VDFS 
Sbjct: 98  VDDAKEAKERANGMELDGRRIRVDFSI 124

>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 = 90.0 bits (224), Expect = 4e-21
 Identities = 19/82 (23%), Positives = 38/82 (46%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
           P D +L V  L P    +    +   FG++    ++   RTG+S  Y F E+ K+++  +
Sbjct: 93  PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152

Query: 269 AYFKMNNALIDDRRICVDFSQS 290
           A   +    +  R + V ++ +
Sbjct: 153 AKSDLLGKPLGPRTLYVHWTDA 174

>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 = 71.2 bits (175), Expect = 2e-14
 Identities = 16/92 (17%), Positives = 32/92 (34%), Gaps = 8/92 (8%)

Query: 205 ADVKPPD------NVLFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAF 257
            D             L V +L P   + + L    S   +    ++    + G+   +A 
Sbjct: 172 TDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACG-QDGQLKGFAV 230

Query: 258 VEFEKREACEQAYFKMNNALIDDRRICVDFSQ 289
           +E+E  E  E+A  + +   +    + V F  
Sbjct: 231 LEYETAEMAEEAQQQADGLSLGGSHLRVSFCA 262

>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 = 58.1 bits (141), Expect = 5e-10
 Identities = 12/81 (14%), Positives = 30/81 (37%), Gaps = 7/81 (8%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           + +  L     ++++H + S +        L+     +    AFV     E  E A    
Sbjct: 25  ILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAAINAF 77

Query: 274 NNALIDDRRICVDFSQSVSKI 294
           + + + +R + V    + + +
Sbjct: 78  HQSRLRERELSVQLQPTDALL 98

>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 = 84.2 bits (209), Expect = 7e-21
 Identities = 26/82 (31%), Positives = 42/82 (51%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
            P+  L V  L+  T + DL  +FS++G +    I+ D ++  S  +AFV FE  +  ++
Sbjct: 13  DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72

Query: 269 AYFKMNNALIDDRRICVDFSQS 290
           A  + N   +D RRI V    S
Sbjct: 73  AKERANGMELDGRRIRVSGPSS 94

>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 = 86.1 bits (214), Expect = 8e-21
 Identities = 23/76 (30%), Positives = 41/76 (53%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L V  L     D +L+ +F   G + +  I+RDY+TG S  YAFV+F      ++A   +
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65

Query: 274 NNALIDDRRICVDFSQ 289
           N   + ++R+ V +++
Sbjct: 66  NGITVRNKRLKVSYAR 81

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 82.2 bits (204), Expect = 3e-19
 Identities = 27/87 (31%), Positives = 42/87 (48%), Gaps = 3/87 (3%)

Query: 203 PDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEK 262
           P  +     N L+V  L     D+ L  IF ++G++V   ILRD  TG     AFV + K
Sbjct: 82  PGGESIKDTN-LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNK 140

Query: 263 REACEQAYFKMNNALID--DRRICVDF 287
           RE  ++A   +NN + +   + + V  
Sbjct: 141 REEAQEAISALNNVIPEGGSQPLSVRL 167

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 85.3 bits (212), Expect = 2e-20
 Identities = 21/76 (27%), Positives = 37/76 (48%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L V  L      E+   +F   G + S +++RD  TG+SL Y FV +   +  E+A   +
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 274 NNALIDDRRICVDFSQ 289
           N   +  + I V +++
Sbjct: 65  NGLRLQTKTIKVSYAR 80

>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 = 80.3 bits (199), Expect = 1e-18
 Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 2/76 (2%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L      ++L  +FSQ+G ++++ IL D  TG S    F+ F+KR   E+A   +
Sbjct: 91  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150

Query: 274 NNALID--DRRICVDF 287
           N          I V F
Sbjct: 151 NGQKPSGATEPITVKF 166

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 82.4 bits (204), Expect = 3e-20
 Identities = 18/98 (18%), Positives = 41/98 (41%), Gaps = 10/98 (10%)

Query: 199 IGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGT--VVSAEILRDYRTGESLCYA 256
           +G           + + +  + P T  + +    S + +  V +  +++D +T ++  +A
Sbjct: 1   MGHHHH----HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFA 56

Query: 257 FVEFEKREACEQAYFKMNNA----LIDDRRICVDFSQS 290
           FV+        Q    + +      ID + I VDF++S
Sbjct: 57  FVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS 94

>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 = 82.3 bits (204), Expect = 5e-20
 Identities = 20/76 (26%), Positives = 31/76 (40%), Gaps = 1/76 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L++  L    ++++L  +   FG V+S  ILRD  +G S    F   E  E CE      
Sbjct: 28  LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHF 86

Query: 274 NNALIDDRRICVDFSQ 289
           N   I         ++
Sbjct: 87  NGKFIKTPPGVSAPTE 102

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 82.0 bits (203), Expect = 8e-20
 Identities = 25/82 (30%), Positives = 39/82 (47%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
            P    LF+  L     D DL   F  FG V+SA++  D +T  S C+ FV F+  ++ +
Sbjct: 37  GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQ 96

Query: 268 QAYFKMNNALIDDRRICVDFSQ 289
            A   MN   +  +R+ V   +
Sbjct: 97  VAIKAMNGFQVGTKRLKVQLKK 118

>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 = 81.2 bits (201), Expect = 1e-19
 Identities = 23/90 (25%), Positives = 45/90 (50%), Gaps = 4/90 (4%)

Query: 205 ADVKPPDNV-LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKR 263
           + +K  D + LF+ Q+    +++DL  +F +FG +    +L+D  TG     AF+ + +R
Sbjct: 6   SGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCER 65

Query: 264 EACEQAYFKMNNALI---DDRRICVDFSQS 290
           E+  +A   ++        +R I V  + S
Sbjct: 66  ESALKAQSALHEQKTLPGMNRPIQVKPADS 95

>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 = 81.6 bits (202), Expect = 1e-19
 Identities = 26/82 (31%), Positives = 40/82 (48%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
            P    LF+  L     D+DL  +F  FG VVSA++  D +T  S C+ FV ++   + +
Sbjct: 22  GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQ 81

Query: 268 QAYFKMNNALIDDRRICVDFSQ 289
            A   MN   I  +R+ V   +
Sbjct: 82  AAIQSMNGFQIGMKRLKVQLKR 103

>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 = 82.5 bits (204), Expect = 2e-19
 Identities = 28/117 (23%), Positives = 48/117 (41%), Gaps = 8/117 (6%)

Query: 174 ELEPPLNEQLSSEKEAHSRAVALECIGDIPDADVK-PPDNVLFVCQLNPVTEDEDLHVIF 232
            L      +LS  ++ H R       GD  + +        L+V  L+  T +E ++ +F
Sbjct: 8   ALRSDSYVELSQYRDQHFR-------GDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELF 60

Query: 233 SQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ 289
           S+ G +    +  D     +  + FVE+  R   E A   +N   +DDR I  D+  
Sbjct: 61  SKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA 117

>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 = 80.7 bits (200), Expect = 2e-19
 Identities = 20/81 (24%), Positives = 41/81 (50%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
             +  + V  L+  T + DL  +F  FG++    + +D  TG+S  +AF+ F +RE   +
Sbjct: 13  DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 72

Query: 269 AYFKMNNALIDDRRICVDFSQ 289
           A   ++    D   + V++++
Sbjct: 73  AIAGVSGFGYDHLILNVEWAK 93

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 83.5 bits (207), Expect = 2e-19
 Identities = 20/77 (25%), Positives = 39/77 (50%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           ++V  +     ++ +   F+ FG + S ++  D  T +   +AFVE+E  EA + A  +M
Sbjct: 31  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90

Query: 274 NNALIDDRRICVDFSQS 290
           N+ ++  R I V    +
Sbjct: 91  NSVMLGGRNIKVGRPSN 107

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 77.0 bits (190), Expect = 5e-17
 Identities = 23/91 (25%), Positives = 45/91 (49%), Gaps = 1/91 (1%)

Query: 199 IGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFV 258
           I D    + +  + + +V  ++    D+D+  +F  FG + SA + RD  TG+   Y F+
Sbjct: 114 IIDQLAEEARAFNRI-YVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFI 172

Query: 259 EFEKREACEQAYFKMNNALIDDRRICVDFSQ 289
           E+EK ++ + A   MN   +  + + V  + 
Sbjct: 173 EYEKAQSSQDAVSSMNLFDLGGQYLRVGKAV 203

>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 = 80.1 bits (198), Expect = 4e-19
 Identities = 22/85 (25%), Positives = 41/85 (48%), Gaps = 2/85 (2%)

Query: 205 ADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKRE 264
            +   P   LF+  LN  T ++ L  +F + G +    +++D RT +S  +AF+ FE   
Sbjct: 2   VEADHPGK-LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPA 59

Query: 265 ACEQAYFKMNNALIDDRRICVDFSQ 289
             + A   MN   +  + I V+ ++
Sbjct: 60  DAKNAAKDMNGKSLHGKAIKVEQAK 84

>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 = 79.1 bits (196), Expect = 5e-19
 Identities = 18/70 (25%), Positives = 35/70 (50%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L++  L P T D+DL  +   +G +VS + + D  T +   Y FV+F+   A ++A   +
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67

Query: 274 NNALIDDRRI 283
             + +  +  
Sbjct: 68  KASGVQAQMA 77

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 78.7 bits (195), Expect = 6e-19
 Identities = 21/80 (26%), Positives = 37/80 (46%)

Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
               +FV  L+P      +   F+ FG +  A +++D  TG+S  Y FV F  +   E A
Sbjct: 5   SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENA 64

Query: 270 YFKMNNALIDDRRICVDFSQ 289
             +M    +  R+I  +++ 
Sbjct: 65  IQQMGGQWLGGRQIRTNWAT 84

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 79.8 bits (197), Expect = 8e-19
 Identities = 29/113 (25%), Positives = 45/113 (39%), Gaps = 3/113 (2%)

Query: 177 PPLNEQLSSEKEAHSRAVALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFG 236
           P  +   S          ++      PD +       L V  L   T  + L  +F ++G
Sbjct: 16  PRGSHMASMTGGQQMGRGSMSYGRPPPDVE---GMTSLKVDNLTYRTSPDTLRRVFEKYG 72

Query: 237 TVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ 289
            V    I RD  T ES  +AFV F  +   E A   M+ A++D R + V  ++
Sbjct: 73  RVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMAR 125

>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 = 79.3 bits (196), Expect = 9e-19
 Identities = 20/82 (24%), Positives = 38/82 (46%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
            P+ VL++  L+P   + DL  +F++F       I     TG     AF+ F  +E   Q
Sbjct: 23  EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 82

Query: 269 AYFKMNNALIDDRRICVDFSQS 290
           A   +N   +  + + ++F ++
Sbjct: 83  ALHLVNGYKLYGKILVIEFGKN 104

>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 = 78.5 bits (194), Expect = 1e-18
 Identities = 22/91 (24%), Positives = 35/91 (38%), Gaps = 4/91 (4%)

Query: 203 PDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEK 262
                   D  LFV  LN    +ED+  +F  FG +    +LR    G S   AFV+F  
Sbjct: 7   GSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFVKFSS 65

Query: 263 REACEQAYFKMNNALIDD---RRICVDFSQS 290
               + A   ++ +         + V F+ +
Sbjct: 66  HTEAQAAIHALHGSQTMPGASSSLVVKFADT 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 = 80.0 bits (198), Expect = 2e-18
 Identities = 18/83 (21%), Positives = 34/83 (40%), Gaps = 2/83 (2%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
                 LF+  LNP     +L V  S+        ++   RTG +  + +V+FE  E  E
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLE 68

Query: 268 QAYFKMNNALIDDRRICVDFSQS 290
           +A  ++    +    I ++  + 
Sbjct: 69  KAL-ELTGLKVFGNEIKLEKPKG 90

>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 = 66.1 bits (162), Expect = 2e-13
 Identities = 17/87 (19%), Positives = 34/87 (39%), Gaps = 6/87 (6%)

Query: 203 PDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEK 262
               V+     L    L+    +++L  +F         EI    + G+S   A++EF+ 
Sbjct: 92  DSKKVRAART-LLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIEFKS 145

Query: 263 REACEQAYFKMNNALIDDRRICVDFSQ 289
               E+   +   A ID R + + ++ 
Sbjct: 146 EADAEKNLEEKQGAEIDGRSVSLYYTG 172

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 79.0 bits (195), Expect = 2e-18
 Identities = 21/77 (27%), Positives = 40/77 (51%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L V  +    ++  L  +F ++G + S +I+ D  T +S  Y FV+F+   + +QA   +
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104

Query: 274 NNALIDDRRICVDFSQS 290
           N   I ++R+ V  + S
Sbjct: 105 NGFNILNKRLKVALAAS 121

>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 = 79.5 bits (197), Expect = 3e-18
 Identities = 16/77 (20%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L+    ++ L   F   G + + +I+ D +  +++ YAFVE+ +      A   +
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTL 61

Query: 274 NNALIDDRRICVDFSQS 290
           N   I++  + ++++  
Sbjct: 62  NGKQIENNIVKINWAFQ 78

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 79.1 bits (196), Expect = 3e-18
 Identities = 22/82 (26%), Positives = 38/82 (46%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
                 LFV  LN   +DE L   F  F + +S  ++ D +TG S  Y FV F  ++  +
Sbjct: 84  SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQ 143

Query: 268 QAYFKMNNALIDDRRICVDFSQ 289
            A   M    ++ R + ++++ 
Sbjct: 144 NAMDSMQGQDLNGRPLRINWAA 165

>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 = 77.3 bits (191), Expect = 3e-18
 Identities = 22/76 (28%), Positives = 34/76 (44%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L V  L   T  + L  +F ++G V    I R+  T     +AFV F  R   + A   M
Sbjct: 16  LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAM 75

Query: 274 NNALIDDRRICVDFSQ 289
           + A +D R + V  ++
Sbjct: 76  DGAELDGRELRVQVAR 91

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 80.4 bits (199), Expect = 3e-18
 Identities = 28/88 (31%), Positives = 44/88 (50%), Gaps = 1/88 (1%)

Query: 203 PDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEK 262
           P A    P   L+V  L+P   +  L+  FS  G ++S  + RD  T  SL YA+V F++
Sbjct: 8   PSAP-SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ 66

Query: 263 REACEQAYFKMNNALIDDRRICVDFSQS 290
               E+A   MN  +I  + + + +SQ 
Sbjct: 67  PADAERALDTMNFDVIKGKPVRIMWSQR 94

>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 = 76.2 bits (188), Expect = 1e-16
 Identities = 28/83 (33%), Positives = 47/83 (56%), Gaps = 2/83 (2%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
           K     +F+  L+   +++ L+  FS FG ++S +++ D     S  Y FV FE +EA E
Sbjct: 100 KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAE 157

Query: 268 QAYFKMNNALIDDRRICVDFSQS 290
           +A  KMN  L++DR++ V   +S
Sbjct: 158 RAIEKMNGMLLNDRKVFVGRFKS 180

>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 = 77.7 bits (192), Expect = 3e-18
 Identities = 27/77 (35%), Positives = 46/77 (59%), Gaps = 2/77 (2%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +F+  L+   +++ L+  FS FG ++S +++ D     S  Y FV FE +EA E+A  KM
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 65

Query: 274 NNALIDDRRICVDFSQS 290
           N  L++DR++ V   +S
Sbjct: 66  NGMLLNDRKVFVGRFKS 82

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 76.9 bits (190), Expect = 4e-18
 Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 3/79 (3%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGE---SLCYAFVEFEKREACEQAY 270
           LF+  LN  T +E L  +FS+ G + S  I +         S+ + FVE++K E  ++A 
Sbjct: 8   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67

Query: 271 FKMNNALIDDRRICVDFSQ 289
            ++    +D  ++ V  S+
Sbjct: 68  KQLQGHTVDGHKLEVRISE 86

>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 = 77.0 bits (190), Expect = 6e-18
 Identities = 23/76 (30%), Positives = 39/76 (51%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L+P    ED+   F+ FG +  A +++D  TG+S  Y FV F  +   E A  +M
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77

Query: 274 NNALIDDRRICVDFSQ 289
               +  R+I  +++ 
Sbjct: 78  GGQWLGGRQIRTNWAT 93

>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 = 75.6 bits (187), Expect = 8e-18
 Identities = 22/76 (28%), Positives = 38/76 (50%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  LN   +DE L   F  F + +S  ++ D +TG S  Y FV F  ++  + A   M
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63

Query: 274 NNALIDDRRICVDFSQ 289
               ++ R + ++++ 
Sbjct: 64  QGQDLNGRPLRINWAA 79

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 76.0 bits (187), Expect = 8e-18
 Identities = 21/92 (22%), Positives = 31/92 (33%), Gaps = 8/92 (8%)

Query: 201 DIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEF 260
           +  D    P   V+ +  L     + DL     +FG +    ++   R       A VEF
Sbjct: 11  NYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKR------QALVEF 64

Query: 261 EKREACEQA--YFKMNNALIDDRRICVDFSQS 290
           E       A  Y   N   I      V++S S
Sbjct: 65  EDVLGACNAVNYAADNQIYIAGHPAFVNYSTS 96

>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 = 75.8 bits (187), Expect = 1e-17
 Identities = 26/90 (28%), Positives = 38/90 (42%), Gaps = 1/90 (1%)

Query: 200 GDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVE 259
           G           + +FV  L+     + L  +FS  G VV A+IL D + G+S     V 
Sbjct: 4   GSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVT 62

Query: 260 FEKREACEQAYFKMNNALIDDRRICVDFSQ 289
           FE+     QA    N  L+ DR + V   +
Sbjct: 63  FEQSIEAVQAISMFNGQLLFDRPMHVKMDE 92

>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 = 78.1 bits (193), Expect = 1e-17
 Identities = 20/87 (22%), Positives = 39/87 (44%)

Query: 203 PDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEK 262
               V    + LF+  L     D+ +  + + FG + +  +++D  TG S  YAF E+  
Sbjct: 106 VSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVD 165

Query: 263 REACEQAYFKMNNALIDDRRICVDFSQ 289
               +QA   +N   + D+++ V  + 
Sbjct: 166 INVTDQAIAGLNGMQLGDKKLLVQRAS 192

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 60.4 bits (147), Expect = 4e-11
 Identities = 10/81 (12%), Positives = 27/81 (33%), Gaps = 6/81 (7%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVS-----AEILRDYRTGESLCYAFVEFEKREACEQ 268
           L+V  +     +E +   F+    +          +   +  +   +AF+EF   +   Q
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 269 AYFKMNNALIDDRRICVDFSQ 289
           A    +  +   + + +    
Sbjct: 67  A-MAFDGIIFQGQSLKIRRPH 86

>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 = 77.2 bits (190), Expect = 1e-17
 Identities = 23/88 (26%), Positives = 40/88 (45%)

Query: 203 PDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEK 262
           P         +LFV  ++   +++++   F  +G + +  +  D RTG S  YA VE+E 
Sbjct: 64  PGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYET 123

Query: 263 REACEQAYFKMNNALIDDRRICVDFSQS 290
            +    A   +N A I  + I VD+   
Sbjct: 124 HKQALAAKEALNGAEIMGQTIQVDWCFV 151

>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 = 74.9 bits (185), Expect = 2e-17
 Identities = 25/78 (32%), Positives = 43/78 (55%), Gaps = 1/78 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVS-AEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           +F+  L+P  +++ L+  FS FG ++   +I+RD  TG S  YAF+ F   +A + A   
Sbjct: 8   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 67

Query: 273 MNNALIDDRRICVDFSQS 290
           MN   + +R I V ++  
Sbjct: 68  MNGQYLCNRPITVSYAFK 85

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 75.0 bits (185), Expect = 2e-17
 Identities = 22/84 (26%), Positives = 41/84 (48%)

Query: 205 ADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKRE 264
             + P  + ++V  L     + DL+ IFS++G VV   I++D  T +S   AF+ F  ++
Sbjct: 10  GGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKD 69

Query: 265 ACEQAYFKMNNALIDDRRICVDFS 288
           + +     +NN  +  R I    +
Sbjct: 70  SAQNCTRAINNKQLFGRVIKASIA 93

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 77.2 bits (190), Expect = 2e-17
 Identities = 24/88 (27%), Positives = 39/88 (44%), Gaps = 1/88 (1%)

Query: 203 PDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEK 262
              +       L V  L+    D D+  +F++FGT+  A +  D R+G SL  A V FE+
Sbjct: 80  GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFER 138

Query: 263 REACEQAYFKMNNALIDDRRICVDFSQS 290
           R    +A  +     +D R + +    S
Sbjct: 139 RADALKAMKQYKGVPLDGRPMDIQLVAS 166

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 74.6 bits (184), Expect = 2e-17
 Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 1/82 (1%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
              + LF+  L      E+L  I    GTV    ++ + R G+    A+VE+E      Q
Sbjct: 15  LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEYENESQASQ 73

Query: 269 AYFKMNNALIDDRRICVDFSQS 290
           A  KM+   I +  I V  S S
Sbjct: 74  AVMKMDGMTIKENIIKVAISNS 95

>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 = 75.5 bits (186), Expect = 3e-17
 Identities = 24/90 (26%), Positives = 42/90 (46%)

Query: 200 GDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVE 259
           GD P         +LFV  ++    +ED+H  F+++G + +  +  D RTG    Y  VE
Sbjct: 11  GDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVE 70

Query: 260 FEKREACEQAYFKMNNALIDDRRICVDFSQ 289
           +E  +  + A   +N   +  + I VD+  
Sbjct: 71  YETYKEAQAAMEGLNGQDLMGQPISVDWCF 100

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 75.0 bits (185), Expect = 3e-17
 Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 1/83 (1%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
                 L V  L+    D D+  +F++FGT+  A +  D R+G SL  A V FE++    
Sbjct: 26  VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADAL 84

Query: 268 QAYFKMNNALIDDRRICVDFSQS 290
           +A  + N   +D R + +    S
Sbjct: 85  KAMKQYNGVPLDGRPMNIQLVTS 107

>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 = 76.4 bits (188), Expect = 3e-17
 Identities = 31/132 (23%), Positives = 47/132 (35%)

Query: 158 PPELADDSIPEGEPKDELEPPLNEQLSSEKEAHSRAVALECIGDIPDADVKPPDNVLFVC 217
             E  D +  E   K        +   +  +A       E                L V 
Sbjct: 17  TTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVD 76

Query: 218 QLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNAL 277
            L   T  + L  +F ++G V    I RD  T ES  +AFV F  +   E A   M+ A+
Sbjct: 77  NLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAV 136

Query: 278 IDDRRICVDFSQ 289
           +D R + V  ++
Sbjct: 137 LDGRELRVQMAR 148

>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 = 74.6 bits (184), Expect = 3e-17
 Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 2/76 (2%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L+   +DE L   FS FGT+ SA+++ +   G S  + FV F   E   +A  +M
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75

Query: 274 NNALIDDRRICVDFSQ 289
           N  ++  + + V  +Q
Sbjct: 76  NGRIVATKPLYVALAQ 91

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 75.6 bits (186), Expect = 3e-17
 Identities = 31/114 (27%), Positives = 44/114 (38%), Gaps = 1/114 (0%)

Query: 175 LEPPLNEQLSSEKEAHSRAVALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQ 234
              P +   +       R V     G            VL+V  L    +D+ LH  F  
Sbjct: 28  SNLPESVAYT-CVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIP 86

Query: 235 FGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS 288
           FG +   +I  DY T +   +AFVEFE  E    A   MN + +  R I V+ +
Sbjct: 87  FGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140

>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 = 75.7 bits (187), Expect = 6e-17
 Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 1/85 (1%)

Query: 202 IPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFE 261
                +      LF+  L     D+ +  + + FG + +  +++D  TG S  YAF E+ 
Sbjct: 86  HDYQPLPGAHK-LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYV 144

Query: 262 KREACEQAYFKMNNALIDDRRICVD 286
                +QA   +N   + D+++ V 
Sbjct: 145 DINVTDQAIAGLNGMQLGDKKLLVQ 169

>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 = 59.6 bits (145), Expect = 4e-11
 Identities = 10/81 (12%), Positives = 27/81 (33%), Gaps = 6/81 (7%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVS-----AEILRDYRTGESLCYAFVEFEKREACEQ 268
           L+V  +     +E +   F+    +          +   +  +   +AF+EF   +   Q
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 269 AYFKMNNALIDDRRICVDFSQ 289
           A    +  +   + + +    
Sbjct: 67  A-MAFDGIIFQGQSLKIRRPH 86

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 73.8 bits (182), Expect = 6e-17
 Identities = 25/91 (27%), Positives = 44/91 (48%)

Query: 200 GDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVE 259
           G    + +   +  LFV  L+  T ++ L  +FS++G +    +++D  T  S  + FV 
Sbjct: 1   GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVT 60

Query: 260 FEKREACEQAYFKMNNALIDDRRICVDFSQS 290
           FE  +  + A   MN   +D R+I VD +  
Sbjct: 61  FENIDDAKDAMMAMNGKSVDGRQIRVDQAGK 91

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 73.4 bits (181), Expect = 7e-17
 Identities = 20/80 (25%), Positives = 39/80 (48%)

Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           P  V+++  +     +E +  + S  G V++ +++ D +TG S  YAF+EF   E+   A
Sbjct: 1   PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASA 60

Query: 270 YFKMNNALIDDRRICVDFSQ 289
              +N   +  R +   +S 
Sbjct: 61  VRNLNGYQLGSRFLKCGYSS 80

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 73.4 bits (181), Expect = 7e-17
 Identities = 23/86 (26%), Positives = 36/86 (41%), Gaps = 2/86 (2%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
                 +FV  L      + L   F++ G V+ A+I  +   G+S     V+FE  E  E
Sbjct: 5   SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAE 62

Query: 268 QAYFKMNNALIDDRRICVDFSQSVSK 293
           +A   MN   +  R I V   ++ S 
Sbjct: 63  RACRMMNGMKLSGREIDVRIDRNASG 88

>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 = 74.3 bits (183), Expect = 8e-17
 Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 1/87 (1%)

Query: 204 DADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKR 263
             +       L V  L+    D D+  +F++FGT+  A +  D R+G SL  A V FE+R
Sbjct: 28  GGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERR 86

Query: 264 EACEQAYFKMNNALIDDRRICVDFSQS 290
               +A  +     +D R + +    S
Sbjct: 87  ADALKAMKQYKGVPLDGRPMDIQLVAS 113

>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 = 73.5 bits (181), Expect = 9e-17
 Identities = 23/87 (26%), Positives = 40/87 (45%)

Query: 203 PDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEK 262
           P         +LFV  ++   +++++   F  +G + +  +  D RTG S  YA VE+E 
Sbjct: 18  PGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYET 77

Query: 263 REACEQAYFKMNNALIDDRRICVDFSQ 289
            +    A   +N A I  + I VD+  
Sbjct: 78  HKQALAAKEALNGAEIMGQTIQVDWCF 104

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 73.4 bits (181), Expect = 1e-16
 Identities = 25/95 (26%), Positives = 45/95 (47%)

Query: 195 ALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLC 254
           ++E  GD P         +LFV  ++    +ED+H  F+++G + +  +  D RTG    
Sbjct: 7   SVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKG 66

Query: 255 YAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ 289
           Y  VE+E  +  + A   +N   +  + I VD+  
Sbjct: 67  YTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCF 101

>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 = 73.1 bits (180), Expect = 1e-16
 Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 8/90 (8%)

Query: 204 DADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKR 263
            +       VLFV  L     +E L   FSQFG +   + L+DY        AF+ F++R
Sbjct: 4   GSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDY--------AFIHFDER 55

Query: 264 EACEQAYFKMNNALIDDRRICVDFSQSVSK 293
           +   +A  +MN   ++   I + F++   +
Sbjct: 56  DGAVKAMEEMNGKDLEGENIEIVFAKPPDQ 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 = 72.3 bits (178), Expect = 2e-16
 Identities = 23/83 (27%), Positives = 36/83 (43%), Gaps = 1/83 (1%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
           +  D  +FV  L     +E L+ +F Q G +    I +D R G+   + FV F+  E+  
Sbjct: 13  EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVCFKHPESVS 71

Query: 268 QAYFKMNNALIDDRRICVDFSQS 290
            A   +N   +  R I V    S
Sbjct: 72  YAIALLNGIRLYGRPINVSGPSS 94

>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 = 72.7 bits (179), Expect = 2e-16
 Identities = 18/88 (20%), Positives = 38/88 (43%), Gaps = 2/88 (2%)

Query: 203 PDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEK 262
              +       L+V  L+    +  +  +FSQ G   S +++ ++ + +   Y FVEF +
Sbjct: 7   GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYE 64

Query: 263 REACEQAYFKMNNALIDDRRICVDFSQS 290
                 A   MN   I  + + V+++ +
Sbjct: 65  HRDAAAALAAMNGRKILGKEVKVNWATT 92

>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 = 72.3 bits (178), Expect = 2e-16
 Identities = 27/85 (31%), Positives = 41/85 (48%)

Query: 205 ADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKRE 264
           + +     VL+V  L    +D+ LH  F  FG +   +I  DY T +   +AFVEFE  E
Sbjct: 6   SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 65

Query: 265 ACEQAYFKMNNALIDDRRICVDFSQ 289
               A   MN + +  R I V+ ++
Sbjct: 66  DAAAAIDNMNESELFGRTIRVNLAK 90

>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 = 74.2 bits (183), Expect = 2e-16
 Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 2/72 (2%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGE--SLCYAFVEFEKREACEQAYF 271
           +FV Q+     ++DL  +F Q+G V    +LRD       S    FV F  R+A  +A  
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65

Query: 272 KMNNALIDDRRI 283
            ++N  +     
Sbjct: 66  ALHNMKVLPGMH 77

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 71.9 bits (177), Expect = 2e-15
 Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 1/65 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LF+  ++    + D+ V+FS FG +    ILR    G S   AFV F  R   + A   M
Sbjct: 98  LFIGMISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAM 156

Query: 274 NNALI 278
           + A  
Sbjct: 157 HQAQT 161

>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 = 71.9 bits (177), Expect = 3e-16
 Identities = 22/82 (26%), Positives = 38/82 (46%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
           +  D  ++V  L+    +  L  +F Q G VV+  + +D  TG+   Y FVEF   E  +
Sbjct: 12  RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD 71

Query: 268 QAYFKMNNALIDDRRICVDFSQ 289
            A   M+   +  + I V+ + 
Sbjct: 72  YAIKIMDMIKLYGKPIRVNKAS 93

>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 = 71.9 bits (177), Expect = 3e-16
 Identities = 22/82 (26%), Positives = 36/82 (43%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
                 LFV  L+  + +EDL  +FS +G +       D  T +   +AFV F   E   
Sbjct: 5   SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAV 64

Query: 268 QAYFKMNNALIDDRRICVDFSQ 289
           +AY +++  +   R + V  S 
Sbjct: 65  KAYAEVDGQVFQGRMLHVLPST 86

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 71.4 bits (175), Expect = 5e-16
 Identities = 17/90 (18%), Positives = 32/90 (35%), Gaps = 8/90 (8%)

Query: 203 PDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEK 262
                     V+ V  L     + DL     +FGT+    ++   R       A VEFE 
Sbjct: 7   GSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEFEN 60

Query: 263 REACEQA--YFKMNNALIDDRRICVDFSQS 290
            ++ ++   +       I  ++   ++S S
Sbjct: 61  IDSAKECVTFAADVPVYIAGQQAFFNYSTS 90

>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 = 71.2 bits (175), Expect = 5e-16
 Identities = 25/96 (26%), Positives = 38/96 (39%), Gaps = 10/96 (10%)

Query: 200 GDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEI--LRDYRTGESLCYAF 257
           G   D D      +L+V  L   T +E +   F+         +  +RDY        AF
Sbjct: 4   GSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDY--------AF 55

Query: 258 VEFEKREACEQAYFKMNNALIDDRRICVDFSQSVSK 293
           V F  RE   +A   +N  ++D   I V  ++ V K
Sbjct: 56  VHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK 91

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 70.6 bits (174), Expect = 5e-16
 Identities = 27/81 (33%), Positives = 39/81 (48%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
               VL+V  L    +D+ LH  F  FG +   +I  DY T +   +AFVEFE  E    
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64

Query: 269 AYFKMNNALIDDRRICVDFSQ 289
           A   MN + +  R I V+ ++
Sbjct: 65  AIDNMNESELFGRTIRVNLAK 85

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 70.6 bits (174), Expect = 7e-16
 Identities = 18/82 (21%), Positives = 33/82 (40%), Gaps = 1/82 (1%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRD-YRTGESLCYAFVEFEKREACE 267
                + + +L      + +  IFS +G +   ++  +      S  YA+VEFE  +  E
Sbjct: 2   MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAE 61

Query: 268 QAYFKMNNALIDDRRICVDFSQ 289
           +A   M+   ID + I      
Sbjct: 62  KALKHMDGGQIDGQEITATAVL 83

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 69.9 bits (172), Expect = 1e-15
 Identities = 20/81 (24%), Positives = 36/81 (44%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
              + L+V  L+    ++ L  IF  FG + +  +++D  TG S  Y F+ F   E   +
Sbjct: 3   SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62

Query: 269 AYFKMNNALIDDRRICVDFSQ 289
           A  ++N   +  R + V    
Sbjct: 63  ALEQLNGFELAGRPMRVGHVT 83

>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 = 70.0 bits (172), Expect = 2e-15
 Identities = 22/87 (25%), Positives = 43/87 (49%), Gaps = 2/87 (2%)

Query: 204 DADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKR 263
           +++ K     L V  +     D DL  +F QFG ++  EI+ +     S  + FV FE  
Sbjct: 8   NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENS 65

Query: 264 EACEQAYFKMNNALIDDRRICVDFSQS 290
              ++A  K++  +++ R+I V+ + +
Sbjct: 66  ADADRAREKLHGTVVEGRKIEVNNATA 92

>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 = 74.3 bits (183), Expect = 2e-15
 Identities = 13/80 (16%), Positives = 28/80 (35%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L++    P     ++  +      V  +  L   R   S  +A+++   +E       K+
Sbjct: 120 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 179

Query: 274 NNALIDDRRICVDFSQSVSK 293
           N   I+   +    S  + K
Sbjct: 180 NGLKIEGYTLVTKVSNPLEK 199

>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 = 72.7 bits (179), Expect = 6e-15
 Identities = 19/79 (24%), Positives = 39/79 (49%), Gaps = 3/79 (3%)

Query: 214 LFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYR-TGESLCYAFVEFEKREACEQAYF 271
           + +  L+  + ++  L   F  FG++    I    +    + C AF+ FE +++ E+A  
Sbjct: 213 IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA-L 271

Query: 272 KMNNALIDDRRICVDFSQS 290
           +MN +L+ +R I V  +  
Sbjct: 272 QMNRSLLGNREISVSLADK 290

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 62.3 bits (152), Expect = 2e-11
 Identities = 10/72 (13%), Positives = 26/72 (36%), Gaps = 3/72 (4%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           + V  L        ++  F   G ++  ++       ++  +A +EF + +    A    
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAA-ITK 100

Query: 274 NNALIDDRRICV 285
            + ++    I V
Sbjct: 101 THKVVGQNEIIV 112

>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 = 69.2 bits (170), Expect = 2e-15
 Identities = 19/82 (23%), Positives = 34/82 (41%), Gaps = 2/82 (2%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
                LF+  LNP     +L V  S+        +  D RTG +  + +V+FE  E  E+
Sbjct: 15  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAV-VDVRTGTNRKFGYVDFESAEDLEK 73

Query: 269 AYFKMNNALIDDRRICVDFSQS 290
           A  ++    +    I ++  + 
Sbjct: 74  A-LELTGLKVFGNEIKLEKPKG 94

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 69.7 bits (171), Expect = 3e-15
 Identities = 25/100 (25%), Positives = 45/100 (45%), Gaps = 2/100 (2%)

Query: 190 HSRAVALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRT 249
           H  +  L   G   + + K     L V  +     D DL  +F QFG ++  EI+ +   
Sbjct: 8   HHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--E 65

Query: 250 GESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ 289
             S  + FV FE     ++A  K++  +++ R+I V+ + 
Sbjct: 66  RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT 105

>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 = 68.9 bits (169), Expect = 4e-15
 Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFG-TVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           L++  L P  ++  +   F+  G TV+S +I+R+  TG    Y FVEF      E+   K
Sbjct: 12  LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71

Query: 273 MNNALIDDRRICVDF 287
           +N   +        F
Sbjct: 72  INGKPLPGATPAKRF 86

>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 = 72.4 bits (178), Expect = 5e-15
 Identities = 19/92 (20%), Positives = 35/92 (38%), Gaps = 6/92 (6%)

Query: 203 PDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEK 262
           P          LFV  L     +ED   +F ++G      I RD        + F+  E 
Sbjct: 14  PGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLES 67

Query: 263 REACEQAYFKMNNALIDDRRICVDFSQSVSKI 294
           R   E A  +++  ++  R + + F+   + +
Sbjct: 68  RTLAEIAKAELDGTILKSRPLRIRFATHGAAL 99

>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 = 71.6 bits (176), Expect = 9e-15
 Identities = 21/74 (28%), Positives = 30/74 (40%), Gaps = 1/74 (1%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
                L V  L+PV  +E L   FSQFG V  A ++ D   G +    FVEF  +    +
Sbjct: 94  THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARK 152

Query: 269 AYFKMNNALIDDRR 282
           A  +  +       
Sbjct: 153 ALERCGDGAFLLTT 166

>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 = 68.1 bits (167), Expect = 6e-15
 Identities = 21/91 (23%), Positives = 40/91 (43%), Gaps = 8/91 (8%)

Query: 200 GDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVE 259
           G   +       N L+V   + +T    L   FS FG ++   +    R       AFV 
Sbjct: 4   GSSGERRAPRKGNTLYVYGED-MTP-TLLRGAFSPFGNIIDLSMDPP-R-----NCAFVT 55

Query: 260 FEKREACEQAYFKMNNALIDDRRICVDFSQS 290
           +EK E+ +QA  ++N   ++  ++ V+ ++ 
Sbjct: 56  YEKMESADQAVAELNGTQVESVQLKVNIARK 86

>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 = 71.2 bits (174), Expect = 8e-15
 Identities = 18/92 (19%), Positives = 36/92 (39%), Gaps = 6/92 (6%)

Query: 208 KPPDNVLFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREAC 266
              ++VL V  LNP     + L ++F  +G V   +IL + +       A V+       
Sbjct: 31  GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQA 85

Query: 267 EQAYFKMNNALIDDRRICVDFSQSVSKIWKKS 298
           + A   +N   +  + I +  S+  +    + 
Sbjct: 86  QLAMSHLNGHKLHGKPIRITLSKHQNVQLPRE 117

>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 = 64.2 bits (156), Expect = 2e-12
 Identities = 23/87 (26%), Positives = 37/87 (42%), Gaps = 5/87 (5%)

Query: 205 ADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKRE 264
            ++ PP   L +  + P   +EDL V+FS  G VV                A ++    E
Sbjct: 145 QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK----MALIQMGSVE 200

Query: 265 ACEQAYFKMNNA-LIDDRRICVDFSQS 290
              QA   ++N  L ++  + V FS+S
Sbjct: 201 EAVQALIDLHNHDLGENHHLRVSFSKS 227

>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 = 72.2 bits (176), Expect = 8e-15
 Identities = 23/93 (24%), Positives = 46/93 (49%), Gaps = 7/93 (7%)

Query: 209 PPDNVLFVCQLNP-VTEDE---DLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKRE 264
            P++ +++  LN  + +DE    L+ IFSQFG ++   + R   + +    AFV F++  
Sbjct: 7   RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVS 63

Query: 265 ACEQAYFKMNNALIDDRRICVDFSQSVSKIWKK 297
           +   A   M      D+ + + ++++ S I  K
Sbjct: 64  SATNALRSMQGFPFYDKPMRIQYAKTDSDIIAK 96

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 48.7 bits (115), Expect = 6e-07
 Identities = 17/82 (20%), Positives = 35/82 (42%), Gaps = 6/82 (7%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
           PP+++LF+  L   T +  L ++F+QF       ++           AFVEF+       
Sbjct: 205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHD-----IAFVEFDNEVQAGA 259

Query: 269 AYFKMNNA-LIDDRRICVDFSQ 289
           A   +    +  +  + + F++
Sbjct: 260 ARDALQGFKITQNNAMKISFAK 281

>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 = 68.1 bits (167), Expect = 1e-14
 Identities = 21/77 (27%), Positives = 31/77 (40%), Gaps = 1/77 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +F  QL       DL   FS  G V    I+ D  +  S   A+VEF + ++   A   +
Sbjct: 28  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA-IGL 86

Query: 274 NNALIDDRRICVDFSQS 290
               +    I V  SQ+
Sbjct: 87  TGQRLLGVPIIVQASQA 103

>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 = 67.7 bits (166), Expect = 1e-14
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 6/83 (7%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
               + LFV  L P   +E++  +F ++G      I +D        + F+  E R   E
Sbjct: 12  FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAE 65

Query: 268 QAYFKMNNALIDDRRICVDFSQS 290
            A  +++N  +  +++ V F+  
Sbjct: 66  IAKVELDNMPLRGKQLRVRFACH 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 = 70.5 bits (172), Expect = 1e-14
 Identities = 19/132 (14%), Positives = 40/132 (30%), Gaps = 4/132 (3%)

Query: 160 ELADDSIPEGEPKDELEPPLNEQLSSEKEAHSRAVALECIGDIPDADVKPPDNVLFVCQL 219
           +L DD I       +  P   + + +        V      ++           L++  L
Sbjct: 19  DLYDDVISPSANNGD-APEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGKRIA-LYIGNL 76

Query: 220 NPVTEDEDLHVIFSQFGT--VVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNAL 277
              T DEDL       G   ++  +   +   G+S  +A V      + ++    +    
Sbjct: 77  TWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRE 136

Query: 278 IDDRRICVDFSQ 289
           +  +   V    
Sbjct: 137 LHGQNPVVTPVN 148

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 68.0 bits (166), Expect = 2e-14
 Identities = 13/99 (13%), Positives = 37/99 (37%), Gaps = 7/99 (7%)

Query: 203 PDADVKPPDNVLFVCQLNP-VTEDE---DLHVIFSQFGTVVSAEILRDYRTGESLCYAFV 258
                  P  V+ +  +NP V +++    L+ + S  G ++    +    + ++   A++
Sbjct: 21  STPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILD---IVVDLSDDNSGKAYI 77

Query: 259 EFEKREACEQAYFKMNNALIDDRRICVDFSQSVSKIWKK 297
            F  +E+ +               + + FS++      +
Sbjct: 78  VFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAE 116

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 67.1 bits (164), Expect = 2e-14
 Identities = 16/88 (18%), Positives = 32/88 (36%), Gaps = 3/88 (3%)

Query: 200 GDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVE 259
           G       +     L +  + P  + E L  +  Q+G V S E +             V 
Sbjct: 4   GSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV---VNVT 60

Query: 260 FEKREACEQAYFKMNNALIDDRRICVDF 287
           +  ++   QA  K+N   +++  + V +
Sbjct: 61  YSSKDQARQALDKLNGFQLENFTLKVAY 88

>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 = 66.9 bits (164), Expect = 2e-14
 Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 4/86 (4%)

Query: 204 DADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKR 263
           ++        L +  L+    +E L  +F +   +     +   + G+S  YAF+EF   
Sbjct: 8   NSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASF 63

Query: 264 EACEQAYFKMNNALIDDRRICVDFSQ 289
           E  ++A    N   I+ R I ++   
Sbjct: 64  EDAKEALNSCNKREIEGRAIRLELQG 89

>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 = 66.9 bits (164), Expect = 2e-14
 Identities = 18/84 (21%), Positives = 41/84 (48%), Gaps = 5/84 (5%)

Query: 202 IPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFE 261
           +P+  + P  N +FV  ++   ++ ++   F+++G+V   +I+ D RTG S  Y FV F 
Sbjct: 2   LPEGKIMP--NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFY 58

Query: 262 KREACEQAYFKMNNALIDDRRICV 285
                ++     +      +++ +
Sbjct: 59  NDVDVQKI--VESQINFHGKKLKL 80

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 66.5 bits (163), Expect = 3e-14
 Identities = 25/81 (30%), Positives = 38/81 (46%), Gaps = 3/81 (3%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
            P   LFV  L+  T +E L   F      V A I+ D  TG S  + FV+F   E  + 
Sbjct: 13  QPSKTLFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFVDFNSEEDAKA 69

Query: 269 AYFKMNNALIDDRRICVDFSQ 289
           A   M +  ID  ++ +D+++
Sbjct: 70  AKEAMEDGEIDGNKVTLDWAK 90

>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 = 68.8 bits (168), Expect = 3e-14
 Identities = 18/79 (22%), Positives = 33/79 (41%), Gaps = 6/79 (7%)

Query: 211 DNVLFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           ++VL V  LNP     + L ++F  +G V   +IL + +       A V+       + A
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK-----ENALVQMADGNQAQLA 57

Query: 270 YFKMNNALIDDRRICVDFS 288
              +N   +  + I +  S
Sbjct: 58  MSHLNGHKLHGKPIRITLS 76

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 62.2 bits (151), Expect = 8e-12
 Identities = 23/87 (26%), Positives = 37/87 (42%), Gaps = 5/87 (5%)

Query: 205 ADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKRE 264
            ++ PP   L +  + P   +EDL V+FS  G VV                A ++    E
Sbjct: 114 QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRK----MALIQMGSVE 169

Query: 265 ACEQAYFKMNNA-LIDDRRICVDFSQS 290
              QA   ++N  L ++  + V FS+S
Sbjct: 170 EAVQALIDLHNHDLGENHHLRVSFSKS 196

>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 = 66.6 bits (163), Expect = 4e-14
 Identities = 14/81 (17%), Positives = 36/81 (44%), Gaps = 3/81 (3%)

Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
            + +L++  L      E+++ IF ++G +    +     T E+   A+V +E     + A
Sbjct: 7   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNA 63

Query: 270 YFKMNNALIDDRRICVDFSQS 290
              ++   + +R + V +  +
Sbjct: 64  VDHLSGFNVSNRYLVVLYYNA 84

>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 = 66.1 bits (162), Expect = 4e-14
 Identities = 26/87 (29%), Positives = 39/87 (44%)

Query: 204 DADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKR 263
           D  V      +FV  +     +E L  IFS+ G VVS  ++ D  TG+   Y F E++ +
Sbjct: 1   DPAVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQ 60

Query: 264 EACEQAYFKMNNALIDDRRICVDFSQS 290
           E    A   +N      R + VD + S
Sbjct: 61  ETALSAMRNLNGREFSGRALRVDNAAS 87

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 66.2 bits (162), Expect = 5e-14
 Identities = 20/85 (23%), Positives = 41/85 (48%), Gaps = 8/85 (9%)

Query: 206 DVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREA 265
           + +  +  LFV       ++ +L+ IF  FG +   +IL  +        AFVEFE+ E+
Sbjct: 26  EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNGF--------AFVEFEEAES 77

Query: 266 CEQAYFKMNNALIDDRRICVDFSQS 290
             +A  +++     ++ + V +S+ 
Sbjct: 78  AAKAIEEVHGKSFANQPLEVVYSKL 102

>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 = 65.7 bits (161), Expect = 5e-14
 Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 8/80 (10%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  ++     ++L  +F + G V+  ++++D        YAFV  EK    + A  ++
Sbjct: 12  IFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQL 63

Query: 274 NNALIDDRRICVDFSQSVSK 293
           N   +  +RI V+ S    K
Sbjct: 64  NGKEVKGKRINVELSTKGQK 83

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 66.0 bits (161), Expect = 5e-14
 Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 8/84 (9%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
            P  V+ + +L     + ++  +   FG V +  +L+          AF+E    EA   
Sbjct: 14  VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAANT 67

Query: 269 A--YFKMNNALIDDRRICVDFSQS 290
              Y+     ++  + I + FS  
Sbjct: 68  MVNYYTSVTPVLRGQPIYIQFSNH 91

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 66.2 bits (162), Expect = 5e-14
 Identities = 21/76 (27%), Positives = 36/76 (47%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L+    ++ L  IF  FG + S +++ D  TG S  Y F+ F   E  ++A  ++
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88

Query: 274 NNALIDDRRICVDFSQ 289
           N   +  R + V    
Sbjct: 89  NGFELAGRPMKVGHVT 104

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 65.8 bits (161), Expect = 6e-14
 Identities = 11/83 (13%), Positives = 28/83 (33%), Gaps = 7/83 (8%)

Query: 209 PPDNV-LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
           PP     ++  +     + DL  +F  FG ++  +   +          F++++  E   
Sbjct: 24  PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKG------CCFIKYDTHEQAA 77

Query: 268 QAYFKMNNALIDDRRICVDFSQS 290
                + N     R +   + + 
Sbjct: 78  VCIVALANFPFQGRNLRTGWGKE 100

>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 = 65.7 bits (161), Expect = 6e-14
 Identities = 22/90 (24%), Positives = 45/90 (50%), Gaps = 7/90 (7%)

Query: 209 PPDNVLFVCQLNP-VTEDE---DLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKRE 264
            P++ +++  LN  + +DE    LH IFS+FG ++   + R   + +    AFV F++  
Sbjct: 6   RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVS 62

Query: 265 ACEQAYFKMNNALIDDRRICVDFSQSVSKI 294
           +   A   M      D+ + + ++++ S I
Sbjct: 63  SATNALRSMQGFPFYDKPMRIQYAKTDSDI 92

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 64.9 bits (159), Expect = 7e-14
 Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 8/77 (10%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L V  ++P   +++L   F ++G V+  +I++DY        AFV  E+ E   +A   +
Sbjct: 13  LHVGNISPTCTNQELRAKFEEYGPVIECDIVKDY--------AFVHMERAEDAVEAIRGL 64

Query: 274 NNALIDDRRICVDFSQS 290
           +N     +R+ V  S S
Sbjct: 65  DNTEFQGKRMHVQLSTS 81

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 65.8 bits (161), Expect = 7e-14
 Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 6/82 (7%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
           P +  ++   +     D+ +   FS FG ++   +  +        Y+FV F   E+   
Sbjct: 23  PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESAAH 76

Query: 269 AYFKMNNALIDDRRICVDFSQS 290
           A   +N   I+   +   + + 
Sbjct: 77  AIVSVNGTTIEGHVVKCYWGKE 98

>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 = 64.8 bits (158), Expect = 1e-13
 Identities = 16/85 (18%), Positives = 32/85 (37%), Gaps = 8/85 (9%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
             P  VL + +L     + ++  +   FG V +  +L+          AF+E    EA  
Sbjct: 12  GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQAFLELATEEAAI 65

Query: 268 QA--YFKMNNALIDDRRICVDFSQS 290
               Y+      + ++ I + +S  
Sbjct: 66  TMVNYYSAVTPHLRNQPIYIQYSNH 90

>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 = 64.1 bits (157), Expect = 2e-13
 Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           ++V  ++     E+L   F   G+V    IL D  +G    +A++EF  +E+   +   +
Sbjct: 9   IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS-LAL 67

Query: 274 NNALIDDRRICVD 286
           + +L   R+I V 
Sbjct: 68  DESLFRGRQIKVI 80

>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 = 64.7 bits (158), Expect = 2e-13
 Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 6/83 (7%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +F+  L+  +E+E L  +  QFG +    ++    T  S   AF +F  +EA ++     
Sbjct: 18  VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 77

Query: 274 NNAL------IDDRRICVDFSQS 290
           +         +D R++ VD + +
Sbjct: 78  SLEAEGGGLKLDGRQLKVDLAVT 100

>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 = 64.2 bits (157), Expect = 2e-13
 Identities = 15/89 (16%), Positives = 41/89 (46%), Gaps = 2/89 (2%)

Query: 204 DADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYR-TGESLCYAFVEFEK 262
               K   + + V  +       ++  +FS FG + +  + +    TG    + FV+F  
Sbjct: 8   QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 67

Query: 263 REACEQAYFKMNNAL-IDDRRICVDFSQS 290
           ++  ++A+  + ++  +  RR+ ++++ S
Sbjct: 68  KQDAKKAFNALCHSTHLYGRRLVLEWADS 96

>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 = 64.6 bits (157), Expect = 2e-13
 Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 8/84 (9%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
            P  V+ + +L     + ++  +   FG V +  +L+          AF+E    EA   
Sbjct: 29  VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAANT 82

Query: 269 A--YFKMNNALIDDRRICVDFSQS 290
              Y+     ++  + I + FS  
Sbjct: 83  MVNYYTSVTPVLRGQPIYIQFSNH 106

>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 = 65.3 bits (159), Expect = 3e-13
 Identities = 19/81 (23%), Positives = 33/81 (40%), Gaps = 5/81 (6%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
           P D  ++V  L       +L   F  +G + S  + R+        +AFVEFE       
Sbjct: 71  PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP-----GFAFVEFEDPRDAAD 125

Query: 269 AYFKMNNALIDDRRICVDFSQ 289
           A  +++   +   R+ V+ S 
Sbjct: 126 AVRELDGRTLCGCRVRVELSN 146

>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 = 63.8 bits (156), Expect = 3e-13
 Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 1/77 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  +     + +L   F +FG V    ++ D        + F+ FE  ++ +QA   M
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQA-VNM 71

Query: 274 NNALIDDRRICVDFSQS 290
           +   I  +++ V  ++ 
Sbjct: 72  HFHDIMGKKVEVKRAEP 88

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 65.3 bits (159), Expect = 3e-13
 Identities = 19/116 (16%), Positives = 39/116 (33%), Gaps = 7/116 (6%)

Query: 177 PPLNEQLSSEKEAHSRAVALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFG 236
           PP   Q  S K  +     L     + +         ++V   +  T D+ L  +    G
Sbjct: 26  PPPVRQEPSPKPNNKTPAILYTYSGLRNRRAA-----VYVGSFSWWTTDQQLIQVIRSIG 80

Query: 237 T--VVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS 290
              VV  +   +   G+S  YA V      +  +    +   +++  ++ V  +  
Sbjct: 81  VYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATR 136

>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 = 64.0 bits (156), Expect = 5e-13
 Identities = 27/128 (21%), Positives = 44/128 (34%), Gaps = 21/128 (16%)

Query: 159 PELADDSIPEGEPKDELEPPLNEQLSSEKEAHSRAVALECIGDIPDADVKPPDNVLFVCQ 218
           P +               PP       +KE   R+V                    +V  
Sbjct: 4   PCMQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKRSV--------------------YVGN 43

Query: 219 LNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALI 278
           ++  +  +DL   FS  G++    IL D  +G    YA++EF +R +   A   M+  + 
Sbjct: 44  VDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNS-VDAAVAMDETVF 102

Query: 279 DDRRICVD 286
             R I V 
Sbjct: 103 RGRTIKVL 110

>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 = 65.9 bits (160), Expect = 5e-13
 Identities = 13/113 (11%), Positives = 34/113 (30%)

Query: 180 NEQLSSEKEAHSRAVALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVV 239
           +   S +  + SR              ++ P NVL          +E+   I  + G   
Sbjct: 92  DGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKR 151

Query: 240 SAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVS 292
              +       E      +E++ +    +    +N+  + +      ++  + 
Sbjct: 152 PTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC 204

>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 = 64.3 bits (156), Expect = 2e-12
 Identities = 17/81 (20%), Positives = 32/81 (39%), Gaps = 6/81 (7%)

Query: 209 PPDNVLFVCQLNPVTEDED-LHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
               VL V  L+    + D +  +F  +G V   + ++          A VE     A +
Sbjct: 2   ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPG-----AAMVEMADGYAVD 56

Query: 268 QAYFKMNNALIDDRRICVDFS 288
           +A   +NN  +  +++ V  S
Sbjct: 57  RAITHLNNNFMFGQKMNVCVS 77

>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 = 63.1 bits (154), Expect = 7e-13
 Identities = 27/73 (36%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L   T D  L   F  FG +  A ++ D +TG+S  Y FV    R A E+A  K 
Sbjct: 20  IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA-CKD 78

Query: 274 NNALIDDRRICVD 286
            N +ID R+  V+
Sbjct: 79  PNPIIDGRKANVN 91

>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 = 62.2 bits (152), Expect = 9e-13
 Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 1/76 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           ++V  L      E +  +FSQFG V + +++ D  T +   + FVE ++     +A  K+
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESV-SEAIAKL 62

Query: 274 NNALIDDRRICVDFSQ 289
           +N     R I V  + 
Sbjct: 63  DNTDFMGRTIRVTEAN 78

>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 = 63.3 bits (154), Expect = 1e-12
 Identities = 25/136 (18%), Positives = 53/136 (38%), Gaps = 12/136 (8%)

Query: 167 PEGEPKDELEPPLNEQLSSEKEAHSRAVALECIGDIP---DADVKPPDNVLFVCQLNPVT 223
           P G   DE+      +  S +E     ++ E +  +      +   P+  ++V  L    
Sbjct: 2   PLGSDSDEM----PSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHV 57

Query: 224 EDEDLHVIFSQFGTVVSAEI-----LRDYRTGESLCYAFVEFEKREACEQAYFKMNNALI 278
           +++DL  IF ++    S        +R  + G     AF+     +A  +A  + N  ++
Sbjct: 58  QEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVL 117

Query: 279 DDRRICVDFSQSVSKI 294
             + + V F++S    
Sbjct: 118 FGKPMVVQFARSARPK 133

>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 = 62.1 bits (151), Expect = 1e-12
 Identities = 15/80 (18%), Positives = 34/80 (42%), Gaps = 4/80 (5%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVV-SAEILRDYR-TGESLCYAFVEFEKREACEQAYF 271
           LF+  +  + + E++    ++    V    +        ++  +AFVE+E   A   A  
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

Query: 272 KMNNA--LIDDRRICVDFSQ 289
           K+      +   +I VD+++
Sbjct: 71  KLMPGRIQLWGHQIAVDWAE 90

>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 = 61.9 bits (151), Expect = 1e-12
 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 5/82 (6%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
                L    L+    +++L  +F         EI    + G+S   A++EF+     E+
Sbjct: 14  RAARTLLAKNLSFNITEDELKEVFEDAL-----EIRLVSQDGKSKGIAYIEFKSEADAEK 68

Query: 269 AYFKMNNALIDDRRICVDFSQS 290
              +   A ID R + + ++  
Sbjct: 69  NLEEKQGAEIDGRSVSLYYTGE 90

>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 = 62.0 bits (151), Expect = 1e-12
 Identities = 17/86 (19%), Positives = 37/86 (43%), Gaps = 9/86 (10%)

Query: 206 DVKPPDNVLFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKRE 264
           D K  ++ +F+  LN  + +  D+  IFS++G V    + + Y        AFV++    
Sbjct: 22  DPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGY--------AFVQYSNER 73

Query: 265 ACEQAYFKMNNALIDDRRICVDFSQS 290
               A    N  ++  + + ++ +  
Sbjct: 74  HARAAVLGENGRVLAGQTLDINMAGE 99

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 61.5 bits (150), Expect = 2e-12
 Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 5/77 (6%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           ++V  L       +L   FS +G + +  I R+        +AFVEFE     E A   +
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPP-----GFAFVEFEDPRDAEDAVRGL 57

Query: 274 NNALIDDRRICVDFSQS 290
           +  +I   R+ V+ S  
Sbjct: 58  DGKVICGSRVRVELSTG 74

>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 = 62.0 bits (151), Expect = 2e-12
 Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 3/82 (3%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
             D  ++V  L P    +D+  +F ++G +   ++           +AFVEFE     E 
Sbjct: 20  NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG---GPPFAFVEFEDPRDAED 76

Query: 269 AYFKMNNALIDDRRICVDFSQS 290
           A +  +    D  R+ V+F +S
Sbjct: 77  AVYGRDGYDYDGYRLRVEFPRS 98

>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 = 63.9 bits (156), Expect = 2e-12
 Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 1/77 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LF+  L+  T DE L   F Q+GT+    ++RD  T  S  + FV +   E  + A    
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA-MNA 74

Query: 274 NNALIDDRRICVDFSQS 290
               +D R +    + S
Sbjct: 75  RPHKVDGRVVEPKRAVS 91

>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 = 62.3 bits (152), Expect = 8e-12
 Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 1/77 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  +   TE+  L   F Q+G +   EI+ D  +G+   +AFV F+  ++ ++     
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKI-VIQ 165

Query: 274 NNALIDDRRICVDFSQS 290
               ++     V  + S
Sbjct: 166 KYHTVNGHNCEVRKALS 182

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 60.9 bits (149), Expect = 2e-12
 Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L+  T  ED+   F QFG V  A ++ D  T     + FV FE  +  E+   ++
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV-CEI 60

Query: 274 NNALIDDRRI 283
           +   I+++ +
Sbjct: 61  HFHEINNKMV 70

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 61.1 bits (149), Expect = 3e-12
 Identities = 18/86 (20%), Positives = 38/86 (44%), Gaps = 9/86 (10%)

Query: 209 PPDNVLFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
           PP + LF+  L       EDL  IFS +G ++   I   +         F++F+  ++  
Sbjct: 8   PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAF--------GFIQFDNPQSVR 59

Query: 268 QAYFKMNNALIDDRRICVDFSQSVSK 293
            A    +  +   +++ ++ S S ++
Sbjct: 60  DAIECESQEMNFGKKLILEVSSSNAR 85

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 60.7 bits (148), Expect = 3e-12
 Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 8/80 (10%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LF+  L     ++++  +F Q+G V+  +I+++Y         FV  E + A E A   +
Sbjct: 11  LFIGNLPREATEQEIRSLFEQYGKVLECDIIKNY--------GFVHIEDKTAAEDAIRNL 62

Query: 274 NNALIDDRRICVDFSQSVSK 293
           ++  +    I V+ S++ SK
Sbjct: 63  HHYKLHGVNINVEASKNKSK 82

>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 = 60.7 bits (148), Expect = 3e-12
 Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 2/70 (2%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L V  L   T ++DL   FS FG V+  ++ +D +TG S  + FV F + E   +   + 
Sbjct: 18  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 77

Query: 274 NNALIDDRRI 283
           +   ID R  
Sbjct: 78  HM--IDGRWC 85

>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 = 62.5 bits (153), Expect = 3e-12
 Identities = 21/89 (23%), Positives = 44/89 (49%), Gaps = 2/89 (2%)

Query: 202 IPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFE 261
           IP  +      + FV  + P    ++    FSQ+GT++ A+++ D  TG+S  + FV ++
Sbjct: 79  IPRDEQDKTGKI-FVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYD 137

Query: 262 KREACEQAYFKMNNALIDDRRICVDFSQS 290
             +A ++   +       DR+I +  ++ 
Sbjct: 138 SADAVDRV-CQNKFIDFKDRKIEIKRAEP 165

>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 = 61.4 bits (150), Expect = 7e-12
 Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +F+  LN  T +++L   F ++GTV   +I++D  TG S  + F+ FEK  + ++     
Sbjct: 6   MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQ 65

Query: 274 NNALIDDRRICVDFSQS 290
           +   +D + I    +  
Sbjct: 66  HI--LDGKVIDPKRAIP 80

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 61.0 bits (148), Expect = 4e-12
 Identities = 18/83 (21%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 212 NVLFVCQLNPVTEDEDL---HVIFSQFGTVVSAEILRDYRTGES---LCYAFVEFEKREA 265
           N++FV  L+    D ++      F +FG +    I        S      A+V + + E 
Sbjct: 16  NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 75

Query: 266 CEQAYFKMNNALIDDRRICVDFS 288
             +A   +NN ++D R +     
Sbjct: 76  ALRAIQCVNNVVVDGRTLKASLG 98

>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 = 59.8 bits (146), Expect = 4e-12
 Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L+P T +E +   F  FG V S E+  D +T +   + F+ F++ E  ++   + 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI-MEK 60

Query: 274 NNALIDDRRI 283
               +   + 
Sbjct: 61  KYHNVGLSKC 70

>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 = 60.0 bits (146), Expect = 5e-12
 Identities = 17/88 (19%), Positives = 33/88 (37%)

Query: 203 PDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEK 262
             +  KP   V+ V  +      +++   F  +  +  +  L+    G     A V FE 
Sbjct: 7   GSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFES 66

Query: 263 REACEQAYFKMNNALIDDRRICVDFSQS 290
           R+    A   +N+  I  R++ +    S
Sbjct: 67  RDEATAAVIDLNDRPIGSRKVKLSGPSS 94

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 60.0 bits (146), Expect = 6e-12
 Identities = 17/90 (18%), Positives = 39/90 (43%), Gaps = 11/90 (12%)

Query: 206 DVKPPDNVLFVCQLNP--VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKR 263
                 + LF+  L    V++ EDL  IFS +G ++   I   +         F++F+  
Sbjct: 17  RGSHMKSRLFIGNLPLKNVSK-EDLFRIFSPYGHIMQINIKNAF--------GFIQFDNP 67

Query: 264 EACEQAYFKMNNALIDDRRICVDFSQSVSK 293
           ++   A    +  +   +++ ++ S S ++
Sbjct: 68  QSVRDAIEXESQEMNFGKKLILEVSSSNAR 97

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 60.0 bits (146), Expect = 7e-12
 Identities = 22/90 (24%), Positives = 43/90 (47%), Gaps = 6/90 (6%)

Query: 200 GDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVE 259
            ++P      P    +V  L   T   D+  IF     + S  ++RD  T +   + +VE
Sbjct: 8   KELPT----EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVE 62

Query: 260 FEKREACEQAYFKMNNALIDDRRICVDFSQ 289
           F++ ++ ++A    + AL+ DR + VD ++
Sbjct: 63  FDEVDSLKEA-LTYDGALLGDRSLRVDIAE 91

>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 = 59.6 bits (145), Expect = 8e-12
 Identities = 15/81 (18%), Positives = 31/81 (38%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
           KP   ++ V  +      +++   F  +  +  +  L+    G     A V FE R+   
Sbjct: 12  KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 71

Query: 268 QAYFKMNNALIDDRRICVDFS 288
            A   +N+  I  R++ +   
Sbjct: 72  AAVIDLNDRPIGSRKVKLVLG 92

>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 = 58.8 bits (143), Expect = 1e-11
 Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 7/71 (9%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L     + DL   F QFG + +  +++  +       AF++F  R+A E A  K 
Sbjct: 15  LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ------CAFIQFATRQAAEVAAEKS 68

Query: 274 -NNALIDDRRI 283
            N  +++ RR+
Sbjct: 69  FNKLIVNGRRL 79

>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 = 58.7 bits (143), Expect = 1e-11
 Identities = 14/79 (17%), Positives = 28/79 (35%), Gaps = 2/79 (2%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGT--VVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
           L++  L   T DEDL       G   ++  +   +   G+S  +A V      + ++   
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 272 KMNNALIDDRRICVDFSQS 290
            +    +  +   V  S  
Sbjct: 64  LLPKRELHGQNPVVTPSNK 82

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 57.5 bits (140), Expect = 2e-11
 Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 1/70 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +F+  L+  T  E L   F QFG V    ++RD  T  S  + FV F  +   ++     
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV-LAQ 61

Query: 274 NNALIDDRRI 283
           +   +D + I
Sbjct: 62  SRHELDSKTI 71

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 58.2 bits (141), Expect = 2e-11
 Identities = 14/73 (19%), Positives = 28/73 (38%)

Query: 211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
           +    +         + L  +FS+ G VV+ E   D  TG++  + FVE       ++  
Sbjct: 12  NGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKII 71

Query: 271 FKMNNALIDDRRI 283
              +   +D +  
Sbjct: 72  KSFHGKRLDLKHR 84

>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 = 58.0 bits (141), Expect = 4e-11
 Identities = 23/70 (32%), Positives = 32/70 (45%), Gaps = 1/70 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  L+  T  E L   FSQ+G VV   I++D  T +S  + FV+F+            
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV-LAS 77

Query: 274 NNALIDDRRI 283
               +D R I
Sbjct: 78  RPHTLDGRNI 87

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 56.8 bits (138), Expect = 7e-11
 Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L+  T  +DL   F++FG VV   I  D  TG S  + F+ F+   + E+     
Sbjct: 14  MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKV-LDQ 72

Query: 274 NNALIDDRRI 283
               +D R I
Sbjct: 73  KEHRLDGRVI 82

>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 = 57.3 bits (139), Expect = 7e-11
 Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 1/70 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LF+  L+  T +E L   + Q+G +    ++RD  +  S  + FV F      + A    
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA-MAA 88

Query: 274 NNALIDDRRI 283
               ID R +
Sbjct: 89  RPHSIDGRVV 98

>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 = 57.3 bits (139), Expect = 8e-11
 Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 1/70 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +F+  L+  T  E L   F QFG V    ++RD  T  S  + FV F  +   ++     
Sbjct: 28  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV-LAQ 86

Query: 274 NNALIDDRRI 283
           +   +D + I
Sbjct: 87  SRHELDSKTI 96

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 56.6 bits (137), Expect = 1e-10
 Identities = 18/90 (20%), Positives = 31/90 (34%), Gaps = 8/90 (8%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAE--------ILRDYRTGESLCYAFVE 259
              +N +FV  L      E +   F Q G + + +        +  D  TG+    A V 
Sbjct: 4   NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVS 63

Query: 260 FEKREACEQAYFKMNNALIDDRRICVDFSQ 289
           F+   + + A    +        I V F+ 
Sbjct: 64  FDDPPSAKAAIDWFDGKEFSGNPIKVSFAT 93

>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 = 56.2 bits (136), Expect = 2e-10
 Identities = 19/97 (19%), Positives = 32/97 (32%), Gaps = 8/97 (8%)

Query: 199 IGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAE--------ILRDYRTG 250
           +G          +N +FV  L      E +   F Q G + + +        +  D  TG
Sbjct: 1   MGHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETG 60

Query: 251 ESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF 287
           +    A V F+   + + A    +        I V F
Sbjct: 61  KLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 55.7 bits (135), Expect = 2e-10
 Identities = 20/92 (21%), Positives = 40/92 (43%), Gaps = 6/92 (6%)

Query: 200 GDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQ-FGTVVSAEILRDYRTGESLCYAFV 258
           G    +    P+  LFV  L P  +D  L+  F + + +    +++ D +TG S  Y FV
Sbjct: 1   GSSGSSG---PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFV 56

Query: 259 EFEKREACEQAYFKMNNA-LIDDRRICVDFSQ 289
           +F      ++A  +   A  +  + + +  + 
Sbjct: 57  KFTDELEQKRALTECQGAVGLGSKPVRLSVAI 88

>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 = 56.3 bits (136), Expect = 2e-10
 Identities = 21/98 (21%), Positives = 34/98 (34%), Gaps = 8/98 (8%)

Query: 200 GDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTV--------VSAEILRDYRTGE 251
           G   D D    ++ ++V  LN     +DL   F Q G V            I  D  TG+
Sbjct: 4   GSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGK 63

Query: 252 SLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ 289
               A V +E     + A    +       ++ V  ++
Sbjct: 64  PKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLAR 101

>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 = 55.7 bits (135), Expect = 3e-10
 Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 3/84 (3%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESL-CYAFVEFEKREAC 266
           K P    F+  L     +E +   F     + +  + R+    E L  + + EFE  ++ 
Sbjct: 12  KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSL 70

Query: 267 EQAYFKMNNALIDDRRICVDFSQS 290
             A   +N   + ++RI VD +  
Sbjct: 71  LSA-LSLNEESLGNKRIRVDVADQ 93

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 54.3 bits (131), Expect = 4e-10
 Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 8/79 (10%)

Query: 211 DNVLFVCQLNPVTED------EDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKRE 264
           D+V+ V  +  V  D        +H IFS+FG + +     +   G++  Y F+E+    
Sbjct: 1   DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPA 58

Query: 265 ACEQAYFKMNNALIDDRRI 283
               A    +   +D +  
Sbjct: 59  HAVDAVKNADGYKLDKQHT 77

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 54.6 bits (132), Expect = 6e-10
 Identities = 16/80 (20%), Positives = 33/80 (41%), Gaps = 7/80 (8%)

Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
           N L++  L+P    +DL  +F      +        +      YAFV++  +    +A  
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIE 62

Query: 272 KMN-NALIDDRRICVDFSQS 290
            ++    +  + + VD+S S
Sbjct: 63  TLSGKVELHGKIMEVDYSVS 82

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 54.7 bits (132), Expect = 6e-10
 Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 8/79 (10%)

Query: 211 DNVLFVCQLNPVTED------EDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKRE 264
           D+V+ V  +  V  D        +H IFS+FG + +     +   G++  Y F+E+    
Sbjct: 15  DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPA 72

Query: 265 ACEQAYFKMNNALIDDRRI 283
               A    +   +D +  
Sbjct: 73  HAVDAVKNADGYKLDKQHT 91

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 53.5 bits (129), Expect = 1e-09
 Identities = 17/72 (23%), Positives = 25/72 (34%), Gaps = 6/72 (8%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV       +   L   F  FG V  A ++ D   G    +A VE     A E      
Sbjct: 11  VFVSGFPRGVDSAQLSEYFLAFGPV--ASVVMDKDKG---VFAIVEMGDVGAREAV-LSQ 64

Query: 274 NNALIDDRRICV 285
           +   +   R+ V
Sbjct: 65  SQHSLGGHRLRV 76

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 53.2 bits (128), Expect = 2e-09
 Identities = 8/72 (11%), Positives = 25/72 (34%), Gaps = 2/72 (2%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +++         +D+       G V++ ++ R           FV F+  E+ ++   + 
Sbjct: 14  VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKF-VET 71

Query: 274 NNALIDDRRICV 285
                 +  + +
Sbjct: 72  PGQKYKETDLLI 83

>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 = 52.6 bits (127), Expect = 2e-09
 Identities = 15/73 (20%), Positives = 31/73 (42%), Gaps = 7/73 (9%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV +      +++L   FSQ+G V+   I + +R      +AFV F   +  +      
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQIAQSLC--G 60

Query: 274 NNALIDDRRICVD 286
            + +I    + + 
Sbjct: 61  EDLIIKGISVHIS 73

>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 = 53.0 bits (128), Expect = 2e-09
 Identities = 19/84 (22%), Positives = 34/84 (40%), Gaps = 4/84 (4%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESL-CYAFVEFEKREAC 266
            PP    F+  L     +E +   F     + +  + R+    E L  + + EFE  ++ 
Sbjct: 17  SPPY-TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSL 74

Query: 267 EQAYFKMNNALIDDRRICVDFSQS 290
             A   +N   + +RRI VD +  
Sbjct: 75  LSA-LSLNEESLGNRRIRVDVADQ 97

>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 = 52.8 bits (127), Expect = 3e-09
 Identities = 22/89 (24%), Positives = 34/89 (38%), Gaps = 1/89 (1%)

Query: 200 GDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVE 259
           G   ++     D  + +  L      E++   FS    V +   L     G S   AFV+
Sbjct: 4   GSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQ 63

Query: 260 FEKREACEQAYFKMNNALIDDRRICVDFS 288
           F  +E  E+A  K +   I  R I +  S
Sbjct: 64  FASQEIAEKA-LKKHKERIGHRYIEIFKS 91

>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 = 52.5 bits (126), Expect = 5e-09
 Identities = 13/77 (16%), Positives = 29/77 (37%), Gaps = 6/77 (7%)

Query: 211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
             V+    L   T   ++   FS+FG++    +       E    A VEF +     +A+
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKAF 63

Query: 271 FKMNNALIDDRRICVDF 287
             +  +      + +++
Sbjct: 64  RHLAYSKFHHVPLYLEW 80

>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 = 52.4 bits (126), Expect = 5e-09
 Identities = 11/85 (12%), Positives = 28/85 (32%), Gaps = 1/85 (1%)

Query: 204 DADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKR 263
           + DV        +  +       D+           +A  +     G+ L  A V+F+  
Sbjct: 8   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 67

Query: 264 EACEQAYFKMNNALIDDRRICVDFS 288
           +   ++  +++   ++ R   V   
Sbjct: 68  DDARKS-ERLHRKKLNGREAFVHVV 91

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 51.7 bits (124), Expect = 7e-09
 Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 7/80 (8%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
           +  +N + V  L P    +DL     + G V  A++ RD           VEF ++E   
Sbjct: 12  RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-------TGVVEFVRKEDMT 64

Query: 268 QAYFKMNNALIDDRRICVDF 287
            A  K++N           +
Sbjct: 65  YAVRKLDNTKFRSHEGETAY 84

>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 = 50.7 bits (122), Expect = 1e-08
 Identities = 16/73 (21%), Positives = 29/73 (39%), Gaps = 7/73 (9%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV +       E+L   F Q+G VV   I + +R      +AFV F   +  +      
Sbjct: 14  VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFR-----AFAFVTFADDKVAQSLC--G 66

Query: 274 NNALIDDRRICVD 286
            + +I    + + 
Sbjct: 67  EDLIIKGISVHIS 79

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 51.1 bits (122), Expect = 1e-08
 Identities = 16/89 (17%), Positives = 31/89 (34%), Gaps = 9/89 (10%)

Query: 209 PPDNVLFVCQL-NPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
               V+ +  L +    D  +  +   +G + +  ++R          AF+E E RE   
Sbjct: 23  ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKS------QAFIEMETREDAM 76

Query: 268 QA--YFKMNNALIDDRRICVDFSQSVSKI 294
               +          R + VD S+   K+
Sbjct: 77  AMVDHCLKKALWFQGRCVKVDLSEKYKKL 105

>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 = 51.4 bits (123), Expect = 1e-08
 Identities = 21/89 (23%), Positives = 33/89 (37%), Gaps = 1/89 (1%)

Query: 200 GDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVE 259
           G   ++     D  + +  L      E++   FS    V +   L     G+    AFV+
Sbjct: 31  GRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQ 90

Query: 260 FEKREACEQAYFKMNNALIDDRRICVDFS 288
           F  +E  E+A    +   I  R I V  S
Sbjct: 91  FASQELAEKA-LGKHKERIGHRYIEVFKS 118

>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 = 50.3 bits (120), Expect = 2e-08
 Identities = 14/78 (17%), Positives = 25/78 (32%), Gaps = 8/78 (10%)

Query: 207 VKPPDNVLFVC--QLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKRE 264
           V      L V    L        L  +  + G V +  +  +        Y+F  +   E
Sbjct: 21  VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTE 74

Query: 265 ACEQAYFKMNNALIDDRR 282
             ++AY  +N   + D  
Sbjct: 75  ESKRAYVTLNGKEVVDDL 92

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 49.7 bits (119), Expect = 2e-08
 Identities = 10/81 (12%), Positives = 26/81 (32%), Gaps = 7/81 (8%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           + V  L   +  +++H +   +        L+      +   AFV     E  + A    
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMF 60

Query: 274 NNALIDDRRICVDFSQSVSKI 294
           +      + + V    + + +
Sbjct: 61  HQYSFRGKDLIVQLQPTDALL 81

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 50.2 bits (120), Expect = 3e-08
 Identities = 18/80 (22%), Positives = 30/80 (37%), Gaps = 7/80 (8%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
           +  +N + V  L P    +DL     + G V  A++ RD           VEF ++E   
Sbjct: 13  RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMT 65

Query: 268 QAYFKMNNALIDDRRICVDF 287
            A  K++N           +
Sbjct: 66  YAVRKLDNTKFRSHEGETAY 85

>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 = 51.3 bits (122), Expect = 3e-08
 Identities = 22/86 (25%), Positives = 37/86 (43%), Gaps = 10/86 (11%)

Query: 209 PPDNVLFVCQLN---PVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREA 265
               VL +   N   PVT D  LH IFS+FGTV+           +    A +++    +
Sbjct: 42  GQSPVLRIIVENLFYPVTLDV-LHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVS 96

Query: 266 CEQAYFKMNNALIDDRR--ICVDFSQ 289
            + A   ++   I +    + +DFS+
Sbjct: 97  AQHAKLSLDGQNIYNACCTLRIDFSK 122

>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 = 49.4 bits (118), Expect = 5e-08
 Identities = 17/82 (20%), Positives = 32/82 (39%), Gaps = 3/82 (3%)

Query: 207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREAC 266
           + P D  + V  +     + D+   F     V +  +L+D   G +     V+F   +  
Sbjct: 12  INPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKD-HVGRNNGNGLVKFLSPQDT 69

Query: 267 EQAYFKMNNALIDDRRICVDFS 288
            +A  K N  L+  R + V  +
Sbjct: 70  FEA-LKRNRMLMIQRYVEVSPA 90

>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 = 49.8 bits (119), Expect = 5e-08
 Identities = 13/86 (15%), Positives = 28/86 (32%), Gaps = 1/86 (1%)

Query: 203 PDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEK 262
                      +++  L    E++ +   F +   V  +  +     G++    FVEF  
Sbjct: 17  RSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRN 76

Query: 263 REACEQAYFKMNNALIDDRRICVDFS 288
               + A    +   + +R I V   
Sbjct: 77  EADYKAA-LCRHKQYMGNRFIQVHPI 101

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 48.7 bits (116), Expect = 7e-08
 Identities = 15/88 (17%), Positives = 29/88 (32%), Gaps = 5/88 (5%)

Query: 203 PDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEK 262
           P  +  P    ++V  L       DL     + G+V      +  R       AF+ +  
Sbjct: 11  PPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPR-----RRAFLHYPD 65

Query: 263 REACEQAYFKMNNALIDDRRICVDFSQS 290
             A +QA   +    +    + V  ++ 
Sbjct: 66  SAAAQQAVSCLQGLRLGTDTLRVALARQ 93

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 49.3 bits (117), Expect = 9e-08
 Identities = 22/86 (25%), Positives = 37/86 (43%), Gaps = 10/86 (11%)

Query: 209 PPDNVLFVCQLN---PVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREA 265
               VL +   N   PVT D  LH IFS+FGTV+           +    A +++    +
Sbjct: 24  GQSPVLRIIVENLFYPVTLDV-LHQIFSKFGTVLKIITFTKNNQFQ----ALLQYADPVS 78

Query: 266 CEQAYFKMNNALIDDR--RICVDFSQ 289
            + A   ++   I +    + +DFS+
Sbjct: 79  AQHAKLSLDGQNIYNACCTLRIDFSK 104

>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 = 46.6 bits (111), Expect = 4e-07
 Identities = 15/89 (16%), Positives = 28/89 (31%), Gaps = 3/89 (3%)

Query: 200 GDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVE 259
           G    +      + + +  L     + D++  FS     +   I      G     A VE
Sbjct: 4   GSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIG-PDGRVTGEADVE 61

Query: 260 FEKREACEQAYFKMNNALIDDRRICVDFS 288
           F   E    A    + A +  R + +  +
Sbjct: 62  FATHEDAVAA-MAKDKANMQHRYVELFLN 89

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 46.0 bits (109), Expect = 8e-07
 Identities = 12/78 (15%), Positives = 24/78 (30%), Gaps = 5/78 (6%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVS-AEILRDYRTGESLCYAFVEFEKREACE 267
                + +  L      +DL  +  +     + + +      G       +EF   E   
Sbjct: 26  AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDG----TGALEFPSEEILV 81

Query: 268 QAYFKMNNALIDDRRICV 285
           +A  ++NN       I V
Sbjct: 82  EALERLNNIEFRGSVITV 99

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 102

 Score = 45.6 bits (108), Expect = 9e-07
 Identities = 17/86 (19%), Positives = 28/86 (32%), Gaps = 9/86 (10%)

Query: 208 KPPDNVLFVCQL-NPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREAC 266
                V+ +            L  +   FG + +  IL           AF+E    E  
Sbjct: 12  VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN------EAFIEMATTEDA 65

Query: 267 EQA--YFKMNNALIDDRRICVDFSQS 290
           + A  Y+    AL+  + + V  SQ 
Sbjct: 66  QAAVDYYTTTPALVFGKPVRVHLSQK 91

>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 = 49.5 bits (117), Expect = 9e-07
 Identities = 45/359 (12%), Positives = 93/359 (25%), Gaps = 100/359 (27%)

Query: 2   SVLIETSLGDIV------------IDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDF 49
           S+L +  +  I+                + K       F++      Y   L   I    
Sbjct: 44  SILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINY-KFLMSPIKT-- 100

Query: 50  IAQTGDPTGTGTGGRSVYEDRFF----------------VDEIRADLK----HDKVGTVG 89
             +   P+   T       DR +                  ++R  L        V   G
Sbjct: 101 --EQRQPSMM-TRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDG 157

Query: 90  MASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAV----VDEENRPP 145
           +  +G                     K  +  +V    +   +++  +    +   N P 
Sbjct: 158 VLGSG---------------------KTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPE 196

Query: 146 QQIIIKQT--YVLYPP--ELADDSIPEGEPKDELEPPLNEQLSSEKEAHSRAVALECIGD 201
             + + Q   Y + P     +D S         ++  L   L S+   +     L     
Sbjct: 197 TVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC----L----L 248

Query: 202 IPDADVKPPDNVL----FVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTG------E 251
           +   +V+            C++   T  +   V         +   L  +         +
Sbjct: 249 VLL-NVQNA-KAWNAFNLSCKILLTTRFKQ--VTDFLSAATTTHISLDHHSMTLTPDEVK 304

Query: 252 SLCYAFVEFEK----REACEQAYFKMN--NALIDDRRICVDFSQSV-----SKIWKKSY 299
           SL   +++       RE       +++     I D     D  + V     + I + S 
Sbjct: 305 SLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSL 363

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 47.1 bits (111), Expect = 1e-06
 Identities = 9/93 (9%), Positives = 28/93 (30%), Gaps = 2/93 (2%)

Query: 197 ECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYA 256
                  +      +  +++         +D+       G V++ ++ R           
Sbjct: 95  PLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSI 153

Query: 257 FVEFEKREACEQAYFKMNNALIDDRRICVDFSQ 289
           FV F+  E+ ++   +       +  + + F  
Sbjct: 154 FVVFDSIESAKKF-VETPGQKYKETDLLILFKD 185

>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 = 43.6 bits (103), Expect = 3e-06
 Identities = 11/75 (14%), Positives = 26/75 (34%), Gaps = 6/75 (8%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFG-----TVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
           L+V  +     +E +   F+        T      +   +  +   +AF+EF   +   Q
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 269 AYFKMNNALIDDRRI 283
           A    +  +   + +
Sbjct: 69  A-MAFDGIIFQGQSL 82

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 44.2 bits (104), Expect = 3e-06
 Identities = 15/83 (18%), Positives = 34/83 (40%), Gaps = 13/83 (15%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYR--TGESLCYAFVEFEKREACEQA-- 269
           +FV  L P  +++++   F +FG +V     +           YAF+ F++  + +    
Sbjct: 11  VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALID 70

Query: 270 ---------YFKMNNALIDDRRI 283
                    Y  +++  I D+ +
Sbjct: 71  ACLEEDGKLYLCVSSPTIKDKPV 93

>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 = 44.4 bits (105), Expect = 5e-06
 Identities = 18/89 (20%), Positives = 28/89 (31%), Gaps = 3/89 (3%)

Query: 200 GDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVE 259
           GD          + + +  L     + D++  FS     V   I      G     A VE
Sbjct: 35  GDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIG-PDGRVTGEADVE 92

Query: 260 FEKREACEQAYFKMNNALIDDRRICVDFS 288
           F   E    A    + A +  R I +  +
Sbjct: 93  FATHEEAVAA-MSKDRANMQHRYIELFLN 120

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 43.5 bits (102), Expect = 7e-06
 Identities = 17/85 (20%), Positives = 34/85 (40%), Gaps = 9/85 (10%)

Query: 209 PPDNVLFVCQLNPV--TEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREAC 266
             + VL +   NP+     + L+ + +  G V    I +          A VEFE     
Sbjct: 21  GGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGI-----QAMVEFESVLCA 75

Query: 267 EQAYFKMNNALIDDR--RICVDFSQ 289
           ++A   +N A I      + +++++
Sbjct: 76  QKAKAALNGADIYAGCCTLKIEYAR 100

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 44.0 bits (103), Expect = 2e-05
 Identities = 15/80 (18%), Positives = 27/80 (33%), Gaps = 6/80 (7%)

Query: 211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
           D  L    L P   +  +  +FS+ G +     +       S    FV+F+ +   E A 
Sbjct: 143 DGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAK 196

Query: 271 FKMNNALIDDRRICVDFSQS 290
             M+N  +          + 
Sbjct: 197 EAMSNQTLLLPSDKEWDDRR 216

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 17/81 (20%), Positives = 32/81 (39%), Gaps = 3/81 (3%)

Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
             + + +        ++++    +     V+  I+R+   G    Y FV+F   E  +QA
Sbjct: 9   TCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAH-GNKTGYIFVDFSNEEEVKQA 66

Query: 270 YFKMNNALIDDRRICVDFSQS 290
             K N   +  R I V   +S
Sbjct: 67  -LKCNREYMGGRYIEVFREKS 86

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 39.9 bits (93), Expect = 2e-04
 Identities = 17/84 (20%), Positives = 30/84 (35%), Gaps = 4/84 (4%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAE---ILRDYRTGESLCYAFVEFEKRE 264
           K    ++ +  L      E++   F Q   +   +   +   Y  G     AFV F   E
Sbjct: 20  KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEE 79

Query: 265 ACEQAYFKMNNALIDDRRICVDFS 288
             + A  + +  L+  R I +  S
Sbjct: 80  YAQNA-LRKHKDLLGKRYIELFRS 102

>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 = 39.6 bits (92), Expect = 2e-04
 Identities = 23/126 (18%), Positives = 36/126 (28%), Gaps = 10/126 (7%)

Query: 177 PPLNEQLSSEKEAHSRAVALECIGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFG 236
            P    ++S              G +          V+ +  L      ED+    S   
Sbjct: 15  VPRGSHMASMTGGQQMGR-----GSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCT 69

Query: 237 TVVSAEILR--DYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS--QSVS 292
               A  +     R G     AFVE    +  + A  K +   +  R I V  S    + 
Sbjct: 70  IHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMA-LKKDRESMGHRYIEVFKSHRTEMD 128

Query: 293 KIWKKS 298
            + K S
Sbjct: 129 WVLKHS 134

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 38.4 bits (89), Expect = 5e-04
 Identities = 19/84 (22%), Positives = 27/84 (32%), Gaps = 5/84 (5%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQF---GTVVSAEILRDYRTGESLCYAFVEFEKRE 264
                V+ +  L      ED+    S       V     +   R G     AFVE E  +
Sbjct: 14  GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYT-REGRQSGEAFVELESED 72

Query: 265 ACEQAYFKMNNALIDDRRICVDFS 288
             + A  K +   +  R I V  S
Sbjct: 73  DVKLA-LKKDRESMGHRYIEVFKS 95

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	299
2ok3_A	161	Peptidyl-prolyl CIS-trans isomerase-like 3; beta-b	100.0
2fu0_A	160	Cyclophilin, putative; PFE0505W, cyclosporin-bindi	100.0
2x7k_A	166	Peptidyl-prolyl CIS-trans isomerase-like 1; isomer	100.0
2poe_A	185	Cyclophilin-like protein, putative; cryptosporidiu	100.0
3bo7_A	201	Peptidyl-prolyl CIS-trans isomerase cyclophilin-T;	100.0
2b71_A	196	Cyclophilin-like protein; structural genomics, str	100.0
1zkc_A	197	Peptidyl-prolyl CIS-trans isomerase like 2; CIS-tr	100.0
2a2n_A	176	Peptidylprolyl isomerase domain and WD repeat CON;	100.0
2k7n_A	203	Peptidyl-prolyl CIS-trans isomerase-like 1; beta b	100.0
1w74_A	191	Peptidyl-prolyl CIS-trans isomerase A; cyclophilin	100.0
3bkp_A	232	Cyclophilin; malaria, isomerase, structural GENO s	100.0
1mzw_A	177	Cyclophilin H, U-snRNP-ASSOCIATED cyclophilin; cyc	100.0
2hq6_A	185	Serologically defined colon cancer antigen 10; pro	100.0
2he9_A	192	NK-tumor recognition protein; cyclosporin, isomera	100.0
2wfi_A	179	Peptidyl-prolyl CIS-trans isomerase G; phosphoprot	100.0
1a58_A	177	Cyclophilin; isomerase, ppiase; 1.95A {Brugia mala	100.0
3pmp_A	164	Cyclophilin A; peptidyl prolyl isomerase, isomeras	100.0
2cmt_A	172	Peptidyl-prolyl CIS-trans isomerase E; rotamase ac	100.0
2haq_A	172	Cyclophilin; rotamase, proline, isomerase, CIS-tra	100.0
3ich_A	188	Peptidyl-prolyl CIS-trans isomerase B; beta sandwi	100.0
2igv_A	173	Peptidyl-prolyl CIS-trans isomerase 3; rotamase; 1	100.0
1qng_A	170	Peptidyl-prolyl CIS-trans isomerase; isomerase-imm	100.0
2r99_A	173	Peptidyl-prolyl CIS-trans isomerase E; CIS-trans i	100.0
2z6w_A	165	Peptidyl-prolyl CIS-trans isomerase; isomerase-imm	100.0
3s6m_A	167	Peptidyl-prolyl CIS-trans isomerase; seattle struc	100.0
2poy_A	186	Peptidyl-prolyl CIS-trans isomerase; isomerase-imm	100.0
1lop_A	164	Cyclophilin A; rotamase, isomerase-isomerase inhib	100.0
4fru_A	185	Cyclophilin B, peptidyl-prolyl CIS-trans isomerase	100.0
3rdd_A	184	Peptidyl-prolyl CIS-trans isomerase A; beta barrel	100.0
2c3b_A	172	Ppiase, cyclophilin; isomerase, 3D domain swapping	100.0
1z81_A	229	Cyclophilin; structural genomics, structural genom	100.0
1v9t_A	166	Cyclophilin B; beta barrel, isomerase-isomerase in	100.0
3k2c_A	193	Peptidyl-prolyl CIS-trans isomerase; ssgcid, NIH,	100.0
2ose_A	234	Probable peptidyl-prolyl CIS-trans isomerase; cycl	100.0
1ihg_A	370	Cyclophilin 40; ppiase immunophilin tetratricopept	100.0
3rfy_A	369	Peptidyl-prolyl CIS-trans isomerase CYP38, chloro;	100.0
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.86
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.84
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.81
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.81
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.81
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.81
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.8
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.8
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.8
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.8
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.79
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.79
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.79
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.79
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.79
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.79
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.79
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.79
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.79
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.79
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.79
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.79
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.79
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.78
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.78
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.78
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.78
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.78
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.78
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.78
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.78
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.78
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.78
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.78
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.78
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.77
2div_A	99	TRNA selenocysteine associated protein; structural	99.77
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.77
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.77
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.77
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.76
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.76
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.76
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.76
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.76
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.76
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.76
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.76
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.76
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.76
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.76
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.76
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.76
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.76
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.76
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.76
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.75
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.75
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.75
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.75
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.75
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.75
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.75
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.75
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.75
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.75
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.75
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.75
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.74
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.74
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.74
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.74
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.74
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.74
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.74
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.74
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.74
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.74
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.73
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.73
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.73
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.73
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.73
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.73
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.73
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.73
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.73
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.73
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.73
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.73
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.73
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.72
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.72
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.72
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.72
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.72
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.72
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.72
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.71
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.71
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.71
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.71
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.71
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.7
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.7
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.7
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.7
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.7
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.7
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.7
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.7
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.7
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.7
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.7
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.7
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.53
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.69
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.69
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.69
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.69
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.69
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.69
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.69
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.69
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.68
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.68
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.68
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.68
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.68
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.68
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.67
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.67
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.67
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.67
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.67
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.67
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.67
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.67
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.67
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.66
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.66
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.66
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.66
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.65
1x5p_A	97	Negative elongation factor E; structure genomics,	99.65
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.64
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.64
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.64
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.63
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.63
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.63
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.63
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.63
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.63
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.63
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.63
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.62
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.62
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.62
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.62
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.62
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.62
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.61
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.61
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.6
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.59
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.59
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.59
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.59
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.58
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.57
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	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	99.56
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.56
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.56
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.56
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.55
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.54
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.54
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	99.52
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.51
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.5
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.5
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.5
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.49
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.45
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.45
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.45
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.45
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.45
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.44
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.44
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.43
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.42
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.42
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.42
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.4
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.32
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.32
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.3
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.26
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.22
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.18
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.03
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.98
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.81
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.23
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.25
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.97
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.91
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.9
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.75
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	95.77
3kop_A	188	Uncharacterized protein; protein with A cyclophili	95.33
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	95.23
2nnz_A	153	Hypothetical protein; beta-barrel, structural geno	94.77
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	94.32
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	94.17
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	93.49
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	93.41
1zx8_A	136	Hypothetical protein TM1367; structural genomics,	86.41

>2ok3_A Peptidyl-prolyl CIS-trans isomerase-like 3; beta-barrel, helix, disulfide bridge; 2.00A {Homo sapiens} SCOP: b.62.1.1 PDB: 1xyh_A 2oju_A*

Probab=100.00  E-value=5.8e-51  Score=327.43  Aligned_cols=155  Identities=46%  Similarity=0.794  Sum_probs=149.1

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCC
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADL   80 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~   80 (299)
                      |+|+|+|+.|+|+||||++.||+||+||++||++++|+|+.||||+|+|++||||+.++|.++.++|+.. +++|..+.+
T Consensus         1 m~v~~~T~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Y~g~~fhRvi~~f~iQgGd~~~~g~gg~si~g~~-~~dE~~~~l   79 (161)
T 2ok3_A            1 MSVTLHTDVGDIKIEVFCERTPKTCENFLALCASNYYNGCIFHRNIKGFMVQTGDPTGTGRGGNSIWGKK-FEDEYSEYL   79 (161)
T ss_dssp             CEEEEEETTEEEEEEECTTTCHHHHHHHHHHHHTTTTTTCBCCEEETTTEEEECCTTSSSSCCCCTTSSC-BCCCCCTTC
T ss_pred             CEEEEEeCCccEEEEEcCCCCcHHHHHHHHHhhhcccCCCEEEEEECCCEEecCCCCCCCCCCCcccCCc-cccccCcCc
Confidence            8999999999999999999999999999999999999999999999999999999999999999999875 688977789


Q ss_pred             CCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCC-CCCceeEEEEEEEEEC
Q 046966           81 KHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEE-NRPPQQIIIKQTYVLY  157 (299)
Q Consensus        81 ~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~-~~p~~~v~I~~~~v~~  157 (299)
                      +|+++|+||||+.+|++++|||||++.+ .+|||++|+|||+|++||+||++|++.+++.+ ++|..+|+|.+|.|+.
T Consensus        80 ~h~~~G~lsma~~gp~s~~SQFfI~~~~-~~~Ldg~~tvFG~Vv~G~dvv~~I~~~~~~~~~~~P~~~v~I~~~~i~~  156 (161)
T 2ok3_A           80 KHNVRGVVSMANNGPNTNGSQFFITYGK-QPHLDMKYTVFGKVIDGLETLDELEKLPVNEKTYRPLNDVHIKDITIHA  156 (161)
T ss_dssp             CSCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTCCBCTTTCCBSSCCBEEEEEEEC
T ss_pred             CcCCCeEEEEecCCCCCcceEEEEEcCC-CCccCCCEeEEEEEeCCHHHHHHHHhCCccCCCCCcCCCeEEEEEEEec
Confidence            9999999999999999999999999998 69999999999999999999999999999887 9999999999999997

>2fu0_A Cyclophilin, putative; PFE0505W, cyclosporin-binding domain, structura genomics, structural genomics consortium, SGC, unknown FUNC; 1.80A {Plasmodium falciparum} SCOP: b.62.1.1

Probab=100.00  E-value=4.3e-50  Score=321.44  Aligned_cols=154  Identities=42%  Similarity=0.720  Sum_probs=147.2

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCC
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADL   80 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~   80 (299)
                      ++|+|+|+.|+|+||||++.||+||+||++||+.++|+|+.||||+|+|+|||||+.++|.++.++|+.. +++|..+.+
T Consensus         6 ~~v~~~T~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Y~g~~fhRvi~~f~iQgGd~~~~g~gg~si~g~~-~~dE~~~~l   84 (160)
T 2fu0_A            6 KSAIIYTTMGDIHISLFYKECKKTVQNFSVHSINGYYNNCIFHRVIKHFMVQTGDPSGDGTGGESIWGNE-FEDEFFDHL   84 (160)
T ss_dssp             CEEEEEETTEEEEEEECTTTCHHHHHHHHHHHHTTTTTTCBCCEEETTTEEEECCTTSSSSCCCCTTSSC-BCCCCBTTB
T ss_pred             CEEEEEecCccEEEEEeCCCChHHHHHHHHHhccCccCCCEEEEEECCCEEEeCCcCCCCCCCCcccCCC-ccccccCCc
Confidence            5799999999999999999999999999999999999999999999999999999998999999999866 689977789


Q ss_pred             CCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEE
Q 046966           81 KHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVL  156 (299)
Q Consensus        81 ~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~  156 (299)
                      +|+++|+||||+.+|++++|||||++.+ .+|||++|+|||+|++||+||++|++.+++.+++|..+|+|.+|.|+
T Consensus        85 ~h~~~G~lsmA~~gp~s~~SQFfI~~~~-~~~Ldg~~tvFG~Vv~G~dvv~~I~~~~t~~~~~P~~~v~I~~~~v~  159 (160)
T 2fu0_A           85 NHSKPFMVSMANCGPNTNGSQFFITTVP-CPWLDFKHTVFGKVTQGSKIVLDIEKVRTDKRDKPLEDIKILNIKIN  159 (160)
T ss_dssp             CSSSSSEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTSCBSSCCBEEEEEEC
T ss_pred             ccCCceEEEEecCCCCCcccEEEEECCC-CCccCCCcEEEEEEEcCHHHHHHHHhCCcCCCCCcCCCeEEEEEEEe
Confidence            9999999999999999999999999998 69999999999999999999999999999989999999999999985

>2x7k_A Peptidyl-prolyl CIS-trans isomerase-like 1; isomerase-immunosuppressant complex, immunosuppressant; HET: MLE MVA BMT ABA SAR; 1.15A {Homo sapiens} PDB: 1xwn_A

Probab=100.00  E-value=6.5e-50  Score=322.31  Aligned_cols=154  Identities=44%  Similarity=0.780  Sum_probs=147.5

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCC
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADL   80 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~   80 (299)
                      ++|+|+|+.|+|+||||++.||+||+||++||+.++|+|+.||||+|+|+|||||+.++|.++.++|+.. +++|..+.+
T Consensus        12 ~~v~l~t~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Y~g~~fhRvi~~f~iQgGd~~~~g~gg~si~g~~-~~dE~~~~l   90 (166)
T 2x7k_A           12 PNVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGRGGASIYGKQ-FEDELHPDL   90 (166)
T ss_dssp             SEEEEEETTEEEEEEECTTTCHHHHHHHHHHHHHTTTTTEECCEEETTTEEEECCTTSSSSCCCCTTSSC-BCCCCCTTS
T ss_pred             CEEEEEeCCCcEEEEEccCCCCHHHHHHHHHHhcCCCCCCEEEEEECCCEEEcCCCCCCCCCCCccCCCc-ccccccccc
Confidence            5799999999999999999999999999999999999999999999999999999999999999999866 689977889


Q ss_pred             CCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEE
Q 046966           81 KHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVL  156 (299)
Q Consensus        81 ~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~  156 (299)
                      +|+++|+||||+.+||+++|||||++.+ .+|||++|+|||+|++||+||++|++.+++.+++|..+|+|.+|.|+
T Consensus        91 ~h~~~G~lsmAn~gp~s~gSQFfI~~~~-~~~Ldg~~tvFG~Vv~G~dvv~~I~~~~t~~~~~P~~~i~I~~~~i~  165 (166)
T 2x7k_A           91 KFTGAGILAMANAGPDTNGSQFFVTLAP-TQWLDGKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYPS  165 (166)
T ss_dssp             CCCSTTEEEECBSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHTTSCBCTTSCBSSCCEEEEEEEC
T ss_pred             CCCCCeEEEEeeCCCCCccceEEEECCC-CCccCCCeeEEEEEEcCHHHHHHHHcCCcCCCCCcCCCeEEEEEEEe
Confidence            9988999999999999999999999998 69999999999999999999999999999988999999999999985

>2poe_A Cyclophilin-like protein, putative; cryptosporidium parvum cyclophilin isomerase, structural genomics; 2.01A {Cryptosporidium parvum iowa II} PDB: 2qer_A

Probab=100.00  E-value=1.2e-49  Score=325.63  Aligned_cols=155  Identities=41%  Similarity=0.717  Sum_probs=149.0

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCC
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADL   80 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~   80 (299)
                      |+|+|+|+.|+|+||||++.||+||+||++||+.|+|+|+.||||+|+|+|||||+.++|.++.++|+.. +++|..+.+
T Consensus        17 ~~v~i~t~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Y~g~~FhRvi~~f~iQgGd~~~~g~gg~si~g~~-~~dE~~~~l   95 (185)
T 2poe_A           17 QGVRIITNYGDLKFELFCSQCPKACKNFLALSASGYYKNTIFHKNIKGFIIQGGDPTGTGKGGESIYGRY-FDDEIYPEL   95 (185)
T ss_dssp             CEEEEEETTEEEEEEECTTTCHHHHHHHHHHHHTTTTTTEEEEEECTTSEEEEEETTSSSSCCCBTTBSC-BCCCCCTTS
T ss_pred             eEEEEEecCccEEEEEeCCCCcHHHHHHHHHhccCCCCCCEEEEEECCCEEEcCCCCCCCCCCCccCCCc-ccccccCCC
Confidence            6899999999999999999999999999999999999999999999999999999999999999999865 689977899


Q ss_pred             CCCCceEEEEEcCC----CCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEE
Q 046966           81 KHDKVGTVGMASAG----RDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVL  156 (299)
Q Consensus        81 ~~~~~G~l~~~~~~----~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~  156 (299)
                      +|+++|+||||+.+    |++++|||||++.+ .+|||++|+|||+|++||+||++|++.+++.+++|..+|+|.+|+++
T Consensus        96 ~h~~~G~lsmA~~g~~~~p~s~gSQFFIt~~~-~~~LDg~~tVFG~Vv~Gmdvv~~I~~~~t~~~~~P~~~v~I~~~~i~  174 (185)
T 2poe_A           96 KYDRRGILSMASKGASKKPNTNGSQFFITYSS-LPQLNGEYVIFGKLIDGFETLNTLENCPSDKSHKPIDEIIIKDIVIH  174 (185)
T ss_dssp             CCCSTTEEEECCSCC-CCCSCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHHSCBCTTSCBSSCCEEEEEEEE
T ss_pred             ccCCCeEEEEecCCCCCCCCCccceEEEECCC-CCccCCCeeEEEEEeCCHHHHHHHHhCCcCCCCCcCCCeEEEEEEEE
Confidence            99999999999999    99999999999998 79999999999999999999999999999988999999999999999


Q ss_pred             C
Q 046966          157 Y  157 (299)
Q Consensus       157 ~  157 (299)
                      .
T Consensus       175 ~  175 (185)
T 2poe_A          175 S  175 (185)
T ss_dssp             C
T ss_pred             C
Confidence            7

>3bo7_A Peptidyl-prolyl CIS-trans isomerase cyclophilin-T; isomerase-immunosuppressant complex, immunosuppressant, cyclophilin, structural G structural genomics consortium, SGC; HET: BMT; 2.35A {Toxoplasma gondii}

Probab=100.00  E-value=9.7e-50  Score=331.04  Aligned_cols=155  Identities=31%  Similarity=0.569  Sum_probs=141.4

Q ss_pred             EEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEec-----CCCCCCCCCCCCCC------Cc
Q 046966            2 SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTG-----DPTGTGTGGRSVYE------DR   70 (299)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G-----~~~~~~~~~~~~~~------~~   70 (299)
                      .|+|+|+.|+|+||||++.||+||+||++||+.|||+|+.||||+|+||||||     |+.++|.++.++|.      +.
T Consensus         8 ~v~l~T~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Ydg~~FhRvi~~f~iQgG~~~~~Dp~~~g~gg~si~~~~~~~~g~   87 (201)
T 3bo7_A            8 YLRIVTTQGSLNIELHADMAPRACDSFLRLCAVKYFDDTIFHRCIRNFMIQGGRAELRQPSKKKEVQQSPRSISGFPGGA   87 (201)
T ss_dssp             EEEEEETTEEEEEEECTTTCHHHHHHHHHHHHTTTTTTCBEEEEETTTEEEECCGGGCCC-------CCSSCCCSSTTCC
T ss_pred             EEEEEeCCCCEEEEEcCCCCcHHHHHHHHHHhcCccCCCEEEEeeCCCEEEcCcccccCCCCCCCCCccccccccccCCC
Confidence            68999999999999999999999999999999999999999999999999999     99988999999983      34


Q ss_pred             ccccccccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEE
Q 046966           71 FFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIII  150 (299)
Q Consensus        71 ~~~~e~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I  150 (299)
                      .+++|..+.++|+.+|+||||+.+|++++|||||++.+ .+|||++|+|||+|++||+||++|++.+++.+++|..+|+|
T Consensus        88 ~f~dE~~~~l~h~~~G~lsmA~~gp~s~gSQFFIt~~~-~~~LDg~~tVFG~Vv~Gmdvv~~I~~~~t~~~~~P~~~i~I  166 (201)
T 3bo7_A           88 PFEDEFDNRLVHQGIGVLSMANDGKHSNLSEFFITFKS-CEHLNNKHTIFGRVVGGLDVLRQWEKLETDKKDKPLKPPKV  166 (201)
T ss_dssp             CBCCCCCTTCCCCSTTEEEECCSSTTCBSSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHTTCCBCTTSCBSSCCBE
T ss_pred             cccCcccCCCCcCCCcEEEEeeCCCCCcccEEEEECCC-CcccCCCceEEEEEecCHHHHHHHHhCCcCCCCCcCCCeEE
Confidence            57899888999999999999999999999999999998 79999999999999999999999999999989999999999


Q ss_pred             EEEEEEC
Q 046966          151 KQTYVLY  157 (299)
Q Consensus       151 ~~~~v~~  157 (299)
                      .+|+++.
T Consensus       167 ~~~~v~~  173 (201)
T 3bo7_A          167 EEIIVFK  173 (201)
T ss_dssp             EEEEEEE
T ss_pred             EEEEEEc
Confidence            9999996

>2b71_A Cyclophilin-like protein; structural genomics, structural genomics consortium, SGC, isomerase; 2.50A {Plasmodium yoelii} SCOP: b.62.1.1

Probab=100.00  E-value=1.2e-49  Score=327.53  Aligned_cols=155  Identities=37%  Similarity=0.659  Sum_probs=147.4

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCC
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADL   80 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~   80 (299)
                      ++|+|+|+.|+|+||||++.||+||+||++||+.|+|+|+.||||+|+|+|||||+.++|.++.++|+.. +++|..+.+
T Consensus        39 ~~V~l~T~~G~I~ieL~~~~aP~tv~NF~~L~~~g~Y~g~~FhRVi~~f~iQgGd~~~~g~gg~si~g~~-~~dE~~~~l  117 (196)
T 2b71_A           39 GYITIYTNLGDFEVELYWYHSPKTCLNFYTLCEMGFYDNTIFHRVIPNFVIQGGDPTGTGKGGKSIYGEY-FEDEINKEL  117 (196)
T ss_dssp             CEEEEEETTEEEEEEECTTTSHHHHHHHHHHHHTTTTTTEEEEEEETTTEEEEEETTSSSSCCCBTTBSC-BCCCCCTTC
T ss_pred             cEEEEEeCCCCEEEEEeCCCCcHHHHHHHHHhhcCCcCCCEEEEEeCCcEEEcCCCCCCCCCCCccCCCc-ccccccCCc
Confidence            5799999999999999999999999999999999999999999999999999999999999999999865 688978889


Q ss_pred             CCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEEC
Q 046966           81 KHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY  157 (299)
Q Consensus        81 ~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~~  157 (299)
                      +|+++|+||||+.+|++++|||||++.+ .+|||++|+|||+|++||+||++|++.+++.+++|..+|+|.+|.|+.
T Consensus       118 ~h~~~G~lsMAn~gpns~gSQFFIt~~~-~~~LDg~~tVFG~Vv~Gmdvv~~I~~~~t~~~~~P~~~i~I~~~~i~~  193 (196)
T 2b71_A          118 KHTGAGILSMSNNGPNTNSSQFFITLAP-LPHLDGKHTIFARVSKNMTCIENIASVQTTATNKPIFDLKILRTSTAV  193 (196)
T ss_dssp             CCCSTTEEEECCSSTTCBSSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTCCBSSCCEEEEEEC--
T ss_pred             CcCCCeEEEEccCCCCCcccEEEEECCC-CCccCCCEeEEEEEecCHHHHHHHHhCCcCCCCCCCCCeEEEEEEEec
Confidence            9999999999999999999999999998 799999999999999999999999999999899999999999999986

>1zkc_A Peptidyl-prolyl CIS-trans isomerase like 2; CIS-trans isomerization, peptidylprolyl isomerase, protein- folding, structural genomics consortium; 1.65A {Homo sapiens} SCOP: b.62.1.1

Probab=100.00  E-value=4.8e-49  Score=323.87  Aligned_cols=154  Identities=44%  Similarity=0.788  Sum_probs=147.7

Q ss_pred             EEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCC
Q 046966            2 SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLK   81 (299)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~   81 (299)
                      .|+|+|+.|+|+||||++.||+||+||++||+.|||+|+.||||+|+|||||||+.++|.++.++|+.. +++|..+.++
T Consensus        21 ~v~l~T~~G~I~ieL~~~~aP~tv~NF~~L~~~g~Ydg~~FhRVi~~f~iQgGd~~~~g~Gg~si~g~~-f~dE~~~~l~   99 (197)
T 1zkc_A           21 YVRLHTNKGDLNLELHCDLTPKTCENFIRLCKKHYYDGTIFHRSIRNFVIQGGDPTGTGTGGESYWGKP-FKDEFRPNLS   99 (197)
T ss_dssp             EEEEEETTEEEEEEECTTTSHHHHHHHHHHHHTTTTTTEEEEEEETTTEEEECCTTSSSSCCCBTTBSC-BCCCCCTTCC
T ss_pred             EEEEEeCCccEEEEEcCCCCcHHHHHHHHHHhcCCCCCCEEEEEeCCCEEEcCCCCCCCCCCCccCCCc-cccccCcCcC
Confidence            589999999999999999999999999999999999999999999999999999999999999998765 6899888999


Q ss_pred             CCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCC-CCCceeEEEEEEEEEC
Q 046966           82 HDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEE-NRPPQQIIIKQTYVLY  157 (299)
Q Consensus        82 ~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~-~~p~~~v~I~~~~v~~  157 (299)
                      |+.+|+||||+.+|++++|||||++.+ .++||++|+|||+|++||+||++|++.+++.+ ++|..+|+|.+|+++.
T Consensus       100 h~~~G~lsMAn~gp~sngSQFFIt~~~-~~~LDg~~tVFG~Vv~Gmdvv~~I~~~~t~~~~~~P~~~i~I~~~~v~~  175 (197)
T 1zkc_A          100 HTGRGILSMANSGPNSNRSQFFITFRS-CAYLDKKHTIFGRVVGGFDVLTAMENVESDPKTDRPKEEIRIDATTVFV  175 (197)
T ss_dssp             SCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHHSCBCTTTCCBSSCCEEEEEEEEE
T ss_pred             CCCceEEEEecCCCCCcccEEEEEcCC-CCccCCCccEEEEEEcCHHHHHHHHcCCCCCCCCCcCCCeEEEEEEEEc
Confidence            999999999999999999999999998 79999999999999999999999999999887 9999999999999986

>2a2n_A Peptidylprolyl isomerase domain and WD repeat CON; CIS-trans isomerization, protein-folding, peptidylprolyl ISO structural genomics; 1.65A {Homo sapiens} SCOP: b.62.1.1

Probab=100.00  E-value=9.1e-49  Score=317.99  Aligned_cols=153  Identities=46%  Similarity=0.797  Sum_probs=145.7

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCC
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADL   80 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~   80 (299)
                      +.|+++|+.|+|+||||++.||+||+||++||+.++|+|+.||||+|+|+|||||+.++|.++.++|+.. +++|....+
T Consensus        22 ~~v~~~t~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Y~g~~FhRvi~~f~iQgGd~~~~g~gg~si~g~~-~~dE~~~~l  100 (176)
T 2a2n_A           22 DSAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNGYYNGHTFHRIIKGFMIQTGDPTGTGMGGESIWGGE-FEDEFHSTL  100 (176)
T ss_dssp             SEEEEEETTEEEEEEECTTTCHHHHHHHHHHHHTTTTTTCBCCEEETTTEEEECCTTSSSSCCCCTTSSC-BCCCCCTTC
T ss_pred             CEEEEEecCccEEEEEeCCCChHHHHHHHHHhhcCccCCCEEEEEECCcEEEccCCCCCCCCCCcccCCc-ccccccccc
Confidence            3699999999999999999999999999999999999999999999999999999999999999999866 689977789


Q ss_pred             CCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccC-CCCCCceeEEEEEEEE
Q 046966           81 KHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVD-EENRPPQQIIIKQTYV  155 (299)
Q Consensus        81 ~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~-~~~~p~~~v~I~~~~v  155 (299)
                      +|+++|+||||+.+|++++|||||++.+ .+|||++|+|||+|++||+||++|++.+++ .+++|..+|+|.+|.|
T Consensus       101 ~h~~~G~lsmA~~gp~s~gSQFFIt~~~-~~~LDg~~tVFG~Vv~Gmdvv~~I~~~~t~~~~~~P~~~v~I~~v~v  175 (176)
T 2a2n_A          101 RHDRPYTLSMANAGSNTNGSQFFITVVP-TPWLDNKHTVFGRVTKGMEVVQRISNVKVNPKTDKPYEDVSIINITV  175 (176)
T ss_dssp             CSCSSSEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTTCCBSSCCBEEEEEE
T ss_pred             ccCCceEEEEEeCCCCCcccEEEEECCC-CCccCCCeeEEEEEeCCHHHHHHHHcCCccCCCCccCCCeEEEEEEE
Confidence            9999999999999999999999999998 799999999999999999999999999998 6899999999999986

>2k7n_A Peptidyl-prolyl CIS-trans isomerase-like 1; beta barrel, disorder-order transition, HOOK-like, mRNA processing, mRNA splicing, rotamase; NMR {Homo sapiens}

Probab=100.00  E-value=8.4e-49  Score=323.50  Aligned_cols=155  Identities=43%  Similarity=0.766  Sum_probs=148.7

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCC
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADL   80 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~   80 (299)
                      +.|+|+|++|+|+||||++.||+||+||++||+.+||+|+.||||+|+|+|||||+.+++.++.++|+.. +++|..+.+
T Consensus        12 ~~V~l~T~~G~I~ieL~~d~aP~tv~NF~~L~~~g~Ydg~~FhRVi~~F~iQgGd~~~~g~gg~si~g~~-f~dE~~~~l   90 (203)
T 2k7n_A           12 PNVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGRGGASIYGKQ-FEDELHPDL   90 (203)
T ss_dssp             SEEEEEESSCEEEEEECTTTCTTHHHHHHHHHHHTCGGGCEEEEEETTTEEEEECSSSSSSCCCTTSCSC-BCCCCCCSS
T ss_pred             CEEEEEeCCCcEEEEEccCCCcHHHHHHHHHHhcCccCCCEEEEEeCCcEEEcCCCCCCCCCCCccCCCc-ccccccccc
Confidence            5799999999999999999999999999999999999999999999999999999999999999999766 689977899


Q ss_pred             CCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEEC
Q 046966           81 KHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY  157 (299)
Q Consensus        81 ~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~~  157 (299)
                      +|+++|+|+||+.+||+++|||||++.+ .+|||++|+|||+|++||+||++|++.+++.+++|..+|+|.+|+|++
T Consensus        91 ~h~~~G~lsMAn~gpnsngSQFFIt~~~-~~~LDg~~tVFG~VveGmdvv~kI~~~~t~~~~~P~~~V~I~~~~v~~  166 (203)
T 2k7n_A           91 KFTGAGILAMANAGPDTNGSQFFVTLAP-TQWLDGKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYPSG  166 (203)
T ss_dssp             CCCSSCEEEEEESSTTCEEEEEEEESSC-CCSSTTTSCEEEEEESCHHHHHHHHSCCEEETTEECCCCBEEEEEECC
T ss_pred             cCCCCeEEEEeeCCCCCcccEEEEEcCC-CCccCCCeeEEEEEEcCHHHHHHHHcCCcCCCCCcCCCeEEEEEEEEe
Confidence            9998999999999999999999999998 699999999999999999999999999999889999999999999997

>1w74_A Peptidyl-prolyl CIS-trans isomerase A; cyclophilin, ppiase, RV0009, rotamase, structural proteomics in europe, spine; 2.6A {Mycobacterium tuberculosis} SCOP: b.62.1.1

Probab=100.00  E-value=1.3e-47  Score=314.63  Aligned_cols=151  Identities=36%  Similarity=0.650  Sum_probs=140.9

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhh---------------hCCCcCCceeeEeecCcEEEecCCCCCCCCCCC
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHC---------------KNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRS   65 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~---------------~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~   65 (299)
                      ++|+|+|+.|+|+||||++.||+||+||++||               +.++|+|+.||||+|+|||||||+.++|.++  
T Consensus        24 ~~v~l~t~~G~I~ieL~~~~aP~tv~NF~~L~tG~~~~~~~~~g~~~~~~~Y~g~~FhRVi~~fmiQgGd~~g~G~gg--  101 (191)
T 1w74_A           24 ATATLHTNRGDIKIALFGNHAPKTVANFVGLAQGTKDYSTQNASGGPSGPFYDGAVFHRVIQGFMIQGGDPTGTGRGG--  101 (191)
T ss_dssp             EEEEEEETTEEEEEEECTTTSHHHHHHHHHHHHTCSCCSSCCTTBSSSSCSSTTEEEEEEETTTEEEECCTTSSSSCC--
T ss_pred             eEEEEEecceeEEEEEcCCCChHHHHHHHHHhcCCcccccccccccccCCccCCCEEEEEeCCCEEecCCCCCCCCCC--
Confidence            46999999999999999999999999999999               3579999999999999999999998887777  


Q ss_pred             CCCCcccccccccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeec--CHHHHHHHHhcccCCCCC
Q 046966           66 VYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAE--GLETLTRINQAVVDEENR  143 (299)
Q Consensus        66 ~~~~~~~~~e~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~--G~~vl~~i~~~~~~~~~~  143 (299)
                       ++. .+++|..+.++|+++|+||||+.+||+++|||||++.+ .+|||++|+|||+|++  ||+||++|++.+++.+++
T Consensus       102 -~g~-~f~dE~~~~l~h~~~G~lsMAn~gpntngSQFFIt~~~-~~~LDg~~tVFG~Vv~~~Gmdvv~~I~~~~t~~~~~  178 (191)
T 1w74_A          102 -PGY-KFADEFHPELQFDKPYLLAMANAGPGTNGSQFFITVGK-TPHLNRRHTIFGEVIDAESQRVVEAISKTATDGNDR  178 (191)
T ss_dssp             -SSC-CBCCCCCTTCCSCSSSEEEECCSSTTCBSSCEEEESSC-CGGGTTTSCEEEEECSHHHHHHHHHHHTSCBCTTSC
T ss_pred             -CCC-ccccccccCCCcCCCcEEEEeeCCCCCccceEEEEcCC-CcccCCCeeEEEEEEECCCHHHHHHHHcCCcCCCCC
Confidence             333 47899778999999999999999999999999999998 7999999999999999  999999999999998999


Q ss_pred             CceeEEEEEEEEE
Q 046966          144 PPQQIIIKQTYVL  156 (299)
Q Consensus       144 p~~~v~I~~~~v~  156 (299)
                      |..+|+|.+|+|+
T Consensus       179 P~~~v~I~~~~i~  191 (191)
T 1w74_A          179 PTDPVVIESITIS  191 (191)
T ss_dssp             BSSCCEEEEEEEC
T ss_pred             cCCCeEEEEEEEC
Confidence            9999999999984

>3bkp_A Cyclophilin; malaria, isomerase, structural GENO structural genomics consortium, SGC; 1.80A {Toxoplasma gondii}

Probab=100.00  E-value=2.9e-47  Score=321.32  Aligned_cols=155  Identities=41%  Similarity=0.674  Sum_probs=143.4

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCC-CcccccccccC
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYE-DRFFVDEIRAD   79 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~-~~~~~~e~~~~   79 (299)
                      ..|+|+|++|+|+||||++.||+||+||++||+.|||+|+.||||+|+|||||||+.++|.+|.++|. +..+++|..+.
T Consensus        22 ~~V~l~T~~G~I~ieL~~d~aP~tv~NF~~L~~~g~Ydgt~FhRVi~~FmiQgGdp~~~G~Gg~si~~~g~~f~dE~~~~  101 (232)
T 3bkp_A           22 GKVVLHTSLGDLDVELWARECPLACRNFVQLCLEGYYVNTIFHRVVKDFIVQGGDPTGTGRGGADTTFDGKPFDVETHPR  101 (232)
T ss_dssp             CEEEEEETTEEEEEEEBTTTCHHHHHHHHHHHHHTTTTTCBEEEEETTTEEEECCTTSSSSCCCCCTTTTCCBCCCCCTT
T ss_pred             CEEEEEECCCcEEEEEcCCCCcHHHHHHHHHhhcCccCCCEEEEEeCCCEEEcCCCCCCCCCCCccccCCCccCCccccC
Confidence            36999999999999999999999999999999999999999999999999999999999999999983 34479997778


Q ss_pred             CCCCCceEEEEEcCCC--------------CCCcceEEEEecCCCCCCCCCceEEEEeecCHHH--HHHHHhcccCCCCC
Q 046966           80 LKHDKVGTVGMASAGR--------------DLNASQFYITLRDNLHYLDEKHTIFGEVAEGLET--LTRINQAVVDEENR  143 (299)
Q Consensus        80 ~~~~~~G~l~~~~~~~--------------~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~v--l~~i~~~~~~~~~~  143 (299)
                      ++|+.+|+||||+.++              ++++|||||++.+ .+|||++|+|||+|+ ||++  |++|++.+++.+++
T Consensus       102 l~h~~~G~lsMA~~g~~~~~~~n~e~g~~~~sngSQFFIt~~~-~p~LDg~~tVFG~Vv-g~~v~~v~kI~~~~t~~~~~  179 (232)
T 3bkp_A          102 LKFRYRGLVGVANLGRSSKDAENDERGRSLGTNGNQFFITLAR-ADVLNNAYTLFGKVT-GHTLYNLMKFNDLEVGKEDR  179 (232)
T ss_dssp             CCCCSTTEEEECCCC----------------CBCSCEEEESSC-CGGGTTTSCEEEEEC-GGGHHHHHHHTTSCBCGGGC
T ss_pred             cCcCCCeEEEEeccCCcccccccccccccCCCcCCEEEEECCC-CcccCCCccEEEEEE-eCchHHHHHHHcCCcCCCCC
Confidence            9999999999999997              5999999999998 799999999999999 7765  89999999999999


Q ss_pred             CceeEEEEEEEEEC
Q 046966          144 PPQQIIIKQTYVLY  157 (299)
Q Consensus       144 p~~~v~I~~~~v~~  157 (299)
                      |..+|+|.+|+|+.
T Consensus       180 P~~~i~I~~~~vl~  193 (232)
T 3bkp_A          180 PMTPPFIKSVDVLW  193 (232)
T ss_dssp             BSSCCBEEEEEEEE
T ss_pred             cCCCeEEEEEEEEc
Confidence            99999999999997

>1mzw_A Cyclophilin H, U-snRNP-ASSOCIATED cyclophilin; cyclophilin, peptidyl-prolyl-CIS/trans isomerase, spliceosome, U4/U6-60K protein, WD protein; 2.00A {Homo sapiens} SCOP: b.62.1.1 PDB: 1qoi_A

Probab=100.00  E-value=4.1e-47  Score=309.11  Aligned_cols=147  Identities=37%  Similarity=0.705  Sum_probs=139.1

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhCCC--------cCCceeeEeecCcEEEecCCC-CCCCCCCCCCCCcccccccc
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKNKY--------YNGCLFHNIHKDFIAQTGDPT-GTGTGGRSVYEDRFFVDEIR   77 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~--------y~~~~f~ri~~~~~iq~G~~~-~~~~~~~~~~~~~~~~~e~~   77 (299)
                      |+.|+|+||||++.||+||+||++||++++        |+|+.||||+|+|+|||||+. ++|.++.++|+.. +++| .
T Consensus        22 t~~G~i~ieL~~~~aP~t~~NF~~L~~~~~g~~g~~~~Y~g~~FhRvi~~f~iQgGd~~~~~G~gg~si~g~~-f~dE-~   99 (177)
T 1mzw_A           22 QEVGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRVIKDFMIQGGDFVNGDGTGVASIYRGP-FADE-N   99 (177)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTCCEETTEECSSTTCBCCEEETTTEEEECCTTTSSSCCCCCTTSSC-BCCC-C
T ss_pred             eeceeEEEEEcCCCCcHHHHHHHHHHhcccCCcCccceECCCEEEEEECCCEEEcCCcccCCCCCCCccCCCc-ccCc-c
Confidence            679999999999999999999999999998        999999999999999999985 6789999999866 6888 5


Q ss_pred             cCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEE
Q 046966           78 ADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVL  156 (299)
Q Consensus        78 ~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~  156 (299)
                      ..++|+++|+||||+.+|++++|||||++.+ .+|||++|+|||+|++||+||++|++.+++.+++|..+|+|.+|+++
T Consensus       100 ~~l~h~~~G~lsmAn~gp~tngSQFfIt~~~-~~~LDg~~~VFG~Vv~G~dvv~~I~~~~t~~~~~P~~~v~I~~cG~l  177 (177)
T 1mzw_A          100 FKLRHSAPGLLSMANSGPSTNGCQFFITCSK-CDWLDGKHVVFGKIIDGLLVMRKIENVPTGPNNKPKLPVVISQCGEM  177 (177)
T ss_dssp             CCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCGGGCBSSCEEEEEEEEC
T ss_pred             cccccCCCCEEEEccCCCCCcceEEEEECCC-CCccCCCeeEEEEEeCCHHHHHHHHhCCcCCCCCCCCCEEEEeceeC
Confidence            7899999999999999999999999999998 79999999999999999999999999999999999999999999975

>2hq6_A Serologically defined colon cancer antigen 10; protein folding, peptidyl-prolyl CIS-trans isomerase, struct genomics; 1.75A {Homo sapiens}

Probab=100.00  E-value=5.8e-47  Score=309.47  Aligned_cols=153  Identities=42%  Similarity=0.757  Sum_probs=144.5

Q ss_pred             EEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCC
Q 046966            2 SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLK   81 (299)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~   81 (299)
                      .|+|+|+.|+|+||||++.||+||+||++||+.++|+|+.||||+|+|+|||||+.++|.++.++|+.. +++|....++
T Consensus        26 ~V~l~T~~G~I~ieL~~~~aP~tv~NF~~L~~~g~Y~g~~FhRvi~~f~iQgGd~~~~g~gg~si~g~~-~~dE~~~~l~  104 (185)
T 2hq6_A           26 KVLLKTTAGDIDIELWSKEAPKACRNFIQLCLEAYYDNTIFHRVVPGFIVQGGDPTGTGSGGESIYGAP-FKDEFHSRLR  104 (185)
T ss_dssp             EEEEEETTEEEEEEEBTTTCHHHHHHHHHHHHTTTTTTEECCEEETTTEEEECCTTSSSSCCCCTTSSC-BCCCCBTTBC
T ss_pred             EEEEEeCCccEEEEEeCCCCcHHHHHHHHHhhcCccCCCEEEEEECCCEEEcCCCCCCCCCCCcccCCc-cccccccCcc
Confidence            689999999999999999999999999999999999999999999999999999998899999999866 6889777899


Q ss_pred             CCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHH--HHHHhcccCCCCCCceeEEEEEEEEEC
Q 046966           82 HDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETL--TRINQAVVDEENRPPQQIIIKQTYVLY  157 (299)
Q Consensus        82 ~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl--~~i~~~~~~~~~~p~~~v~I~~~~v~~  157 (299)
                      |+++|+||||+.++++++|||||++.+ .++||++|+|||+|+ ||+++  ++|++.+++.+++|..+|+|.+|++++
T Consensus       105 h~~~G~lsMA~~g~~s~gSQFFIt~~~-~~~LDg~~tVFG~V~-G~~v~~~~~i~~~~~~~~~~P~~~v~I~~~~v~~  180 (185)
T 2hq6_A          105 FNRRGLVAMANAGSHDNGSQFFFTLGR-ADELNNKHTIFGKVT-GDTVYNMLRLSEVDIDDDERPHNPHKIKSCEVLF  180 (185)
T ss_dssp             SCSSSEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEC-GGGHHHHHHTTCSCBCTTSCBSSCCEEEEEEEEE
T ss_pred             cCCCeEEEEccCCCCCccceEEEECCC-CCccCCCceEEEEEE-eCeeehhhHHhhCCcCCCCCCCCCeEEEEEEEeC
Confidence            999999999999999999999999998 699999999999999 88774  688889998899999999999999996

>2he9_A NK-tumor recognition protein; cyclosporin, isomerase, membrane, repeat, rotamase, peptidylprolyl isomerase, structural genomics; 2.00A {Homo sapiens}

Probab=100.00  E-value=5.1e-47  Score=311.59  Aligned_cols=150  Identities=38%  Similarity=0.657  Sum_probs=140.3

Q ss_pred             EEcceeEEEEecCCCChHHHHHHHHhhh-----------CCCcCCceeeEeecCcEEEecCCC-CCCCCCCCCCCCcccc
Q 046966            6 ETSLGDIVIDLFVDKCPRTTNNFLQHCK-----------NKYYNGCLFHNIHKDFIAQTGDPT-GTGTGGRSVYEDRFFV   73 (299)
Q Consensus         6 ~T~~G~i~ieL~~~~~P~~~~nF~~l~~-----------~~~y~~~~f~ri~~~~~iq~G~~~-~~~~~~~~~~~~~~~~   73 (299)
                      +|+.|+|+||||++.||+||+||++||+           .++|+|+.||||+|+|||||||+. ++|.++.++|+.. ++
T Consensus        30 ~t~~G~I~ieL~~~~aP~t~~NF~~L~~g~~g~~~~~~k~~~Y~g~~FhRVi~~fmiQgGd~~~~~G~gg~siyg~~-f~  108 (192)
T 2he9_A           30 REPVGRIMFQLFSDICPKTCKNFLCLCSGEKGLGKTTGKKLCYKGSTFHRVVKNFMIQGGDFSEGNGKGGESIYGGY-FK  108 (192)
T ss_dssp             TEEEEEEEEEECTTTCHHHHHHHHHHHHCTTCBCTTTCSBSCCTTCBEEEEETTTEEEECCTTTSSSSCCCCTTSSC-BC
T ss_pred             CEecceEEEEEcCCCCchHHHHHHHHhcCCCCcccccccCCeECCCEEEEEECCCEEEcCcccCCCCCCCCcccCCc-cc
Confidence            5899999999999999999999999996           468999999999999999999986 6789999999866 68


Q ss_pred             cccccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEE
Q 046966           74 DEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQT  153 (299)
Q Consensus        74 ~e~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~  153 (299)
                      +| ...++|+++|+||||+.+|++++|||||++.+ .+|||++|+|||+|++||+||++|++.+++.+++|..+|+|.+|
T Consensus       109 dE-~~~l~h~~~G~lsMAn~gp~tngSQFFIt~~~-~~~LDg~~tVFG~Vv~Gmdvv~~I~~~~t~~~~~P~~~v~I~~~  186 (192)
T 2he9_A          109 DE-NFILKHDRAFLLSMANRGKHTNGSQFFITTKP-APHLDGVHVVFGLVISGFEVIEQIENLKTDAASRPYADVRVIDC  186 (192)
T ss_dssp             CC-CCCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTSCBSSCEEEEEE
T ss_pred             Cc-cccCCCCCCeEEEEEeCCCCCcceEEEEEcCC-CcccCCCccEEEEEEeCHHHHHHHHcCCcCCCCCCcCCeEEEEe
Confidence            88 57899999999999999999999999999998 69999999999999999999999999999999999999999999


Q ss_pred             EEECC
Q 046966          154 YVLYP  158 (299)
Q Consensus       154 ~v~~p  158 (299)
                      +++.+
T Consensus       187 g~l~~  191 (192)
T 2he9_A          187 GVLAT  191 (192)
T ss_dssp             EECC-
T ss_pred             EEEcc
Confidence            99864

>2wfi_A Peptidyl-prolyl CIS-trans isomerase G; phosphoprotein, PRE-mRNA splicing, alternative splicing, nucleus, rotamase, cyclosporin; HET: OCS; 0.75A {Homo sapiens} PDB: 2wfj_A* 2gw2_A

Probab=100.00  E-value=5.6e-47  Score=308.88  Aligned_cols=148  Identities=39%  Similarity=0.668  Sum_probs=138.8

Q ss_pred             EEcceeEEEEecCCCChHHHHHHHHhhh-----------CCCcCCceeeEeecCcEEEecCCC-CCCCCCCCCCCCcccc
Q 046966            6 ETSLGDIVIDLFVDKCPRTTNNFLQHCK-----------NKYYNGCLFHNIHKDFIAQTGDPT-GTGTGGRSVYEDRFFV   73 (299)
Q Consensus         6 ~T~~G~i~ieL~~~~~P~~~~nF~~l~~-----------~~~y~~~~f~ri~~~~~iq~G~~~-~~~~~~~~~~~~~~~~   73 (299)
                      .|+.|+|+||||++.||+||+||++||+           .++|+|+.||||+|+|+|||||+. ++|.++.++|+.. ++
T Consensus        20 ~t~~G~i~ieL~~~~aP~t~~NF~~L~~g~~g~~~~~~~~~~Y~g~~FhRvi~~f~iQgGd~~~~~g~gg~si~g~~-f~   98 (179)
T 2wfi_A           20 NQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGF-FE   98 (179)
T ss_dssp             TEEEEEEEEEECTTTCHHHHHHHHHHHHCTTCBCTTTCSBSCCTTCBEEEEETTTEEEECCTTTSSSSCCCCTTSSC-BC
T ss_pred             CccceEEEEEEcCCCCChHHHHHHHHhcCCcCcccccccCCeECCCEEEEEECCCEEEcccccCCCCCCCCcccCCc-cc
Confidence            4899999999999999999999999997           468999999999999999999986 6789999999866 68


Q ss_pred             cccccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEE
Q 046966           74 DEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQT  153 (299)
Q Consensus        74 ~e~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~  153 (299)
                      +| ...++|+++|+||||+.+|++++|||||++.+ .+|||++|+|||+|++||+||++|++.+++.+++|..+|+|.+|
T Consensus        99 dE-~~~~~h~~~G~lsMAn~gp~tngSQFfIt~~~-~~~LDg~~tVFG~Vv~G~dvv~~I~~~~t~~~~~P~~~v~I~~~  176 (179)
T 2wfi_A           99 DE-SFAVKHNKEFLLSMANRGKDTNGSQFFITTKP-TPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSC  176 (179)
T ss_dssp             CC-CCCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTCCBCTTSCBSSCEEEEEE
T ss_pred             cc-ccCcCcCCCeEEEEEeCCCCCcceEEEEEcCC-CcccCCCeeEEEEEeCCHHHHHHHHcCCCCCCCCCCCCeEEEeC
Confidence            88 56799999999999999999999999999998 69999999999999999999999999999999999999999999


Q ss_pred             EEE
Q 046966          154 YVL  156 (299)
Q Consensus       154 ~v~  156 (299)
                      +++
T Consensus       177 G~l  179 (179)
T 2wfi_A          177 GEL  179 (179)
T ss_dssp             EEC
T ss_pred             eeC
Confidence            975

>1a58_A Cyclophilin; isomerase, ppiase; 1.95A {Brugia malayi} SCOP: b.62.1.1 PDB: 1a33_A 1c5f_A*

Probab=100.00  E-value=8.5e-47  Score=307.53  Aligned_cols=148  Identities=41%  Similarity=0.649  Sum_probs=138.9

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhC--------C---CcCCceeeEeecCcEEEecCCC-CCCCCCCCCCCCccccc
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKN--------K---YYNGCLFHNIHKDFIAQTGDPT-GTGTGGRSVYEDRFFVD   74 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~--------~---~y~~~~f~ri~~~~~iq~G~~~-~~~~~~~~~~~~~~~~~   74 (299)
                      |+.|+|+||||++.||+||+||++||++        +   +|+|+.||||+|+|+|||||+. ++|.++.++|+.. +++
T Consensus        18 ~~~G~i~ieL~~~~aP~t~~NF~~L~~~~~g~~~~~g~~~~Y~g~~FhRvi~~f~iQgGd~~~~~g~gg~si~g~~-f~d   96 (177)
T 1a58_A           18 NLAGRIVMELYNDIAPRTCNNFLMLCTGMAGTGKISGKPLHYKGSTFHRVIKNFMIQGGDFTKGDGTGGESIYGGM-FDD   96 (177)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHCTTCBCTTTCSBCCCTTCBEEEEETTTEEEECCCSSSSSSCCCCTTSSC-BCC
T ss_pred             EeceeEEEEEcCCCCchHHHHHHHHhcCCcCcccccCCcceeCCCEEEEEECCCEEEeCCccCCCCCCCCcccCCc-ccC
Confidence            7899999999999999999999999985        4   8999999999999999999986 6789999999866 688


Q ss_pred             ccccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEE
Q 046966           75 EIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTY  154 (299)
Q Consensus        75 e~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~  154 (299)
                      | ...++|+++|+||||+.+|++++|||||++.+ .+|||++|+|||+|++||+||++|++.+++.+++|..+|+|.+|+
T Consensus        97 E-~~~~~h~~~G~lsmAn~gp~tngSQFfIt~~~-~~~LDg~~~VFG~Vv~G~dvv~~I~~~~~~~~~~P~~~v~I~~~G  174 (177)
T 1a58_A           97 E-EFVMKHDEPFVVSMANKGPNTNGSQFFITTTP-APHLNNIHVVFGKVVSGQEVVTKIEYLKTNSKNRPLADVVILNCG  174 (177)
T ss_dssp             C-CCCSCCCSSSEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTSCBSSCEEEEEEE
T ss_pred             c-ccCcccCCCeEEEEeeCCCCCceeEEEEECCC-CCccCCCEEEEEEEEcCHHHHHHHHhCCCCCCCcCCCCeEEEEeE
Confidence            8 56889999999999999999999999999998 799999999999999999999999999999999999999999999


Q ss_pred             EEC
Q 046966          155 VLY  157 (299)
Q Consensus       155 v~~  157 (299)
                      ++.
T Consensus       175 ~l~  177 (177)
T 1a58_A          175 ELV  177 (177)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            874

>3pmp_A Cyclophilin A; peptidyl prolyl isomerase, isomerase-immunosuppressant compl; HET: BMT; 1.47A {Moniliophthora perniciosa} SCOP: b.62.1.1 PDB: 3o7t_A

Probab=100.00  E-value=7.5e-47  Score=304.66  Aligned_cols=153  Identities=34%  Similarity=0.627  Sum_probs=141.8

Q ss_pred             CEEEEE-EcceeEEEEecCCCChHHHHHHHHhhh--CCC-cCCceeeEeecCcEEEecC-CCCCCCCCCCCCCCcccccc
Q 046966            1 MSVLIE-TSLGDIVIDLFVDKCPRTTNNFLQHCK--NKY-YNGCLFHNIHKDFIAQTGD-PTGTGTGGRSVYEDRFFVDE   75 (299)
Q Consensus         1 ~~v~~~-T~~G~i~ieL~~~~~P~~~~nF~~l~~--~~~-y~~~~f~ri~~~~~iq~G~-~~~~~~~~~~~~~~~~~~~e   75 (299)
                      |.|.+. |+.|+|+||||++.||+||+||++||+  .++ |+|+.|||++|+|++|||| ...++.++.++|+.. +++|
T Consensus         7 ~di~i~~t~~G~i~ieL~~~~aP~t~~nF~~L~~g~~g~~Y~g~~fhRvi~~f~iQgGd~~~~~g~gg~si~g~~-~~dE   85 (164)
T 3pmp_A            7 FNISINDKPEGRIVFKLYDEAVPKTAKNFRELATGQHGFGYKDSIFHRVIPQFMLQGGDFTRHNGTGGKSIYGEK-FADE   85 (164)
T ss_dssp             EEEEETTEEEEEEEEEECTTTCHHHHHHHHHHHHTTTSCSSTTCBEEEEETTTEEEECCTTTSSSSCCCBTTBSC-BCCC
T ss_pred             EEEEECCEEeeEEEEEEeCCCCcHHHHHHHHHhcccCCCcccCCEEEEEECCCeEEeCCCCCCCCCCCcccCCcc-cccc
Confidence            456776 999999999999999999999999999  678 9999999999999999999 667799999999876 5888


Q ss_pred             cccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEE
Q 046966           76 IRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYV  155 (299)
Q Consensus        76 ~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v  155 (299)
                       ...++|+++|+||||+.+|++++|||||++.+ .+|||++|+|||+|++||+||++|++.+++ +++|..+|+|.+|++
T Consensus        86 -~~~l~h~~~G~lsma~~g~~t~~SQFfIt~~~-~~~Ld~~~~vFG~Vv~G~~vv~~I~~~~~~-~~~P~~~v~I~~cg~  162 (164)
T 3pmp_A           86 -NFQVKHTKPGLLSMANAGANTNGSQFFITTVP-TSWLDGKHVVFGEVIEGLDIVRKVEGKGSA-SGKTNATIKITDCGT  162 (164)
T ss_dssp             -CCCSCCCSTTEEEECBSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTTCCT-TCCCSSCEEEEEEEE
T ss_pred             -ccccCcCCCcEEEEeeCCCCCcccEEEEECCC-ChhhCCCccEEEEEeCCHHHHHHHHhCCCC-CCCcccCEEEEeCeE
Confidence             78899999999999999999999999999998 699999999999999999999999998885 789999999999998


Q ss_pred             EC
Q 046966          156 LY  157 (299)
Q Consensus       156 ~~  157 (299)
                      +.
T Consensus       163 l~  164 (164)
T 3pmp_A          163 VA  164 (164)
T ss_dssp             C-
T ss_pred             EC
Confidence            63

>2cmt_A Peptidyl-prolyl CIS-trans isomerase E; rotamase activity, rotamase, RNA-binding, cyclosporin, cyclophilin, beta-barrel; 1.50A {Schistosoma mansoni} PDB: 2ck1_A

Probab=100.00  E-value=1.5e-46  Score=304.20  Aligned_cols=147  Identities=35%  Similarity=0.675  Sum_probs=137.2

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhC--CC-cCCceeeEeecCcEEEecCCC-CCCCCCCCCCCCcccccccccCCCC
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKN--KY-YNGCLFHNIHKDFIAQTGDPT-GTGTGGRSVYEDRFFVDEIRADLKH   82 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~--~~-y~~~~f~ri~~~~~iq~G~~~-~~~~~~~~~~~~~~~~~e~~~~~~~   82 (299)
                      |+.|+|+||||++.||+||+||++||++  |+ |+|+.||||+|+|+|||||+. ++|.++.++|+.. +++| ...++|
T Consensus        22 t~~G~i~ieL~~~~aP~t~~NF~~L~~~~~g~~Y~g~~FhRvi~~f~iQgGd~~~~~G~gg~si~g~~-f~dE-~~~l~h   99 (172)
T 2cmt_A           22 GDAGRIVMELRSDIVPRTAENFRALCTGERGFGYHNCCFHRVIPQFMCQGGDFVKGDGTGGKSIYGRK-FDDE-NFQLRH   99 (172)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTTTSCSSTTCBEEEEETTTEEEECCTTTSSSSCCCBTTBSC-BCCC-CCCSCC
T ss_pred             eecceEEEEEcCCCCCHHHHHHHHHhccCCCceECCCEEEEEECCCEEEcCCccCCCCCCCCccCCCc-cccc-ccCccc
Confidence            8999999999999999999999999985  77 999999999999999999986 6788999999766 6888 568999


Q ss_pred             CCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEEC
Q 046966           83 DKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY  157 (299)
Q Consensus        83 ~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~~  157 (299)
                      +++|+||||+.+|++++|||||++.+ .+|||++|+|||+|++||+||++|++.++ .+++|..+|+|.+|++++
T Consensus       100 ~~~G~lsmA~~gp~t~gSQFfIt~~~-~~~LDg~~tvFG~Vv~G~dvv~~I~~~~~-~~~~P~~~v~I~~~g~l~  172 (172)
T 2cmt_A          100 EGFGVLSMANSGPNTNGSQFFICTTK-CDWLDGKHVVFGRVVDGQNVVKKMESVGS-KSGKVKEPVIISRCGELI  172 (172)
T ss_dssp             CSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHGGGGCC-TTCCCSSCEEEEEEEEEC
T ss_pred             CCceEEEEeeCCCCCcccEEEEECCC-CCccCCCeeEEEEEEcCHHHHHHHHhCCC-CCCCCCCCEEEEEeEeEC
Confidence            99999999999999999999999998 69999999999999999999999998887 568999999999999974

>2haq_A Cyclophilin; rotamase, proline, isomerase, CIS-trans, protozoa, KAla-AZAR.; 1.97A {Leishmania donovani} PDB: 3eov_A* 3bt8_A

Probab=100.00  E-value=5.4e-47  Score=306.15  Aligned_cols=147  Identities=38%  Similarity=0.719  Sum_probs=138.7

Q ss_pred             EEcceeEEEEecCCCChHHHHHHHHhh--hCCC-cCCceeeEeecCcEEEecC-CCCCCCCCCCCCCCcccccccccCCC
Q 046966            6 ETSLGDIVIDLFVDKCPRTTNNFLQHC--KNKY-YNGCLFHNIHKDFIAQTGD-PTGTGTGGRSVYEDRFFVDEIRADLK   81 (299)
Q Consensus         6 ~T~~G~i~ieL~~~~~P~~~~nF~~l~--~~~~-y~~~~f~ri~~~~~iq~G~-~~~~~~~~~~~~~~~~~~~e~~~~~~   81 (299)
                      .|+.|+|+||||++.||+||+||++||  +.++ |+|+.||||+|+|+||||| +.++|.++.++|+.. +++| .+.++
T Consensus        22 ~t~~G~i~ieL~~~~aP~t~~NF~~L~~g~~g~~Y~g~~FhRvi~~f~iQgGd~~~~~g~gg~si~g~~-f~dE-~~~l~   99 (172)
T 2haq_A           22 SEPLGRITIGLFGKDAPLTTENFRQLCTGEHGFGYKDSIFHRVIQNFMIQGGDFTNFDGTGGKSIYGEK-FADE-NLNVK   99 (172)
T ss_dssp             TEEEEEEEEEECTTTCHHHHHHHHHHHHTTTSCCSTTCBCCEEETTTEEEECCTTTSSSSCCCCSSSSC-BCCC-CCCSC
T ss_pred             CEecceEEEEEeCCCCcHHHHHHHHHhccCCCcccCCCEEEEEECCCEEecCCccCCCCCCCccccCCc-ccCc-CCCcc
Confidence            589999999999999999999999999  6789 9999999999999999999 567789999999866 6888 78899


Q ss_pred             CCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEE
Q 046966           82 HDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVL  156 (299)
Q Consensus        82 ~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~  156 (299)
                      |. +|+||||+.+|++++|||||++.+ .++||++|+|||+|++||+||++|++.+++..++|..+|+|.+|+++
T Consensus       100 h~-~G~lsmAn~gp~tngSQFfIt~~~-~~~LDg~~~vFG~Vv~G~dvv~~I~~~~t~~~~~P~~~v~I~~~g~l  172 (172)
T 2haq_A          100 HF-VGALSMANAGPNTNGSQFFITTAP-TPWLDGRHVVFGKVLDGMDVVLRIEKTKTNSHDRPVKPVKIVASGEL  172 (172)
T ss_dssp             CC-TTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCGGGCBSSCEEEEEEEEC
T ss_pred             cC-ceEEEEccCCCCCcccEEEEECCC-CCccCCCEeEEEEEeCCHHHHHHHHhCCcCCCCcCCCCeEEEEeEEC
Confidence            98 999999999999999999999998 69999999999999999999999999999888899999999999975

>3ich_A Peptidyl-prolyl CIS-trans isomerase B; beta sandwich, cyclosporin, endoplasmic reticulum, glycoprot isomerase, rotamase; 1.20A {Homo sapiens} PDB: 3ici_A* 1cyn_A* 2esl_A* 2rmc_A* 1h0p_A 1xo7_A 1xq7_A*

Probab=100.00  E-value=6.1e-47  Score=310.42  Aligned_cols=148  Identities=39%  Similarity=0.715  Sum_probs=140.0

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhh--CCC-cCCceeeEeecCcEEEecC-CCCCCCCCCCCCCCcccccccccCCCC
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCK--NKY-YNGCLFHNIHKDFIAQTGD-PTGTGTGGRSVYEDRFFVDEIRADLKH   82 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~--~~~-y~~~~f~ri~~~~~iq~G~-~~~~~~~~~~~~~~~~~~~e~~~~~~~   82 (299)
                      |+.|+|+||||++.||+||+||++||+  .|+ |+|+.||||+|+||||||| ..++|.++.++|+.. +++| ...++|
T Consensus        27 t~~G~i~ieL~~~~aP~t~~NF~~L~~g~~g~~Y~g~~FhRvi~~f~iQgGd~~~~~g~gg~si~g~~-f~dE-~~~l~h  104 (188)
T 3ich_A           27 EDVGRVIFGLFGKTVPKTVDNFVALATGEKGFGYKNSKFHRVIKDFMIQGGDFTRGDGTGGKSIYGER-FPDE-NFKLKH  104 (188)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTTTSCSSTTCBCCEEETTTEEEECCTTTSSSSCCCBTTBSC-BCCC-CCCSCC
T ss_pred             EeceeEEEEEcCCCCcHHHHHHHHHhcccCCccccCCEEEEEECCCEEEcCCccCCCCCCCccccCCc-cccc-ccCccc
Confidence            899999999999999999999999996  578 9999999999999999999 667799999999866 6888 788999


Q ss_pred             CCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEEC
Q 046966           83 DKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY  157 (299)
Q Consensus        83 ~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~~  157 (299)
                      +++|+||||+.+|++++|||||++.+ .+|||++|+|||+|++||+||++|++.+++..++|..+|+|.+|+++.
T Consensus       105 ~~~G~lsmAn~gp~tngSQFfIt~~~-~~~LDg~~tVFG~Vv~G~dvv~~I~~~~~~~~~~P~~~v~I~~~~~l~  178 (188)
T 3ich_A          105 YGPGWVSMANAGKDTNGSQFFITTVK-TAWLDGKHVVFGKVLEGMEVVRKVESTKTDSRDKPLKDVIIADCGKIE  178 (188)
T ss_dssp             CSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTSCBSSCEEEEEEEEEE
T ss_pred             CCCeEEEEccCCCCCcccEEEEECCC-CcccCCCeeEEEEEeCCHHHHHHHHhCCcCCCCeECCCEEEEEeEEEe
Confidence            99999999999999999999999998 699999999999999999999999999999888999999999999984

>2igv_A Peptidyl-prolyl CIS-trans isomerase 3; rotamase; 1.67A {Caenorhabditis elegans} SCOP: b.62.1.1 PDB: 1e3b_A 1e8k_A 1dyw_A 2igw_A 2hqj_A

Probab=100.00  E-value=3.4e-46  Score=302.88  Aligned_cols=147  Identities=36%  Similarity=0.650  Sum_probs=136.7

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhC--C--------CcCCceeeEeecCcEEEecCCC-CCCCCCCCCCCCcccccc
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKN--K--------YYNGCLFHNIHKDFIAQTGDPT-GTGTGGRSVYEDRFFVDE   75 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~--~--------~y~~~~f~ri~~~~~iq~G~~~-~~~~~~~~~~~~~~~~~e   75 (299)
                      |+.|+|+||||++.||+||+||++||++  |        +|+|+.||||+|+|||||||+. ++|.++.++|+.. +++|
T Consensus        15 ~~~G~i~ieL~~~~aP~t~~NF~~L~~~~~g~g~~~~~~~Y~g~~FhRvi~~f~iQgGd~~~~~G~gg~siyg~~-f~dE   93 (173)
T 2igv_A           15 KASGRIVMELYDDVVPKTAGNFRALCTGENGIGKSGKPLHFKGSKFHRIIPNFMIQGGDFTRGNGTGGESIYGEK-FPDE   93 (173)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTTTCBCTTSSBSCCTTCBCCEEETTTEEEECCTTTSSSSCCCBTTBSC-BCCC
T ss_pred             EecceEEEEEeCCCCcHHHHHHHHHhcCCCCCCccCccceECCCEEEEEECCCEEEcCCCCCCCCCCCCccCCCc-ccCc
Confidence            4489999999999999999999999987  5        7999999999999999999986 6789999999876 6888


Q ss_pred             cccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEE
Q 046966           76 IRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYV  155 (299)
Q Consensus        76 ~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v  155 (299)
                       ...++|+++|+||||+.+||+++|||||++.+ .+|||++|+|||+|++||+||++|++.++ .+++|..+|+|.+|++
T Consensus        94 -~~~l~h~~~G~lsmAn~gp~tngSQFfIt~~~-~~~LDg~~~vFG~Vv~G~dvv~~I~~~~t-~~~~P~~~v~I~~~g~  170 (173)
T 2igv_A           94 -NFKEKHTGPGVLSMANAGPNTNGSQFFLCTVK-TEWLDGKHVVFGRVVEGLDVVKAVESNGS-QSGKPVKDCMIADCGQ  170 (173)
T ss_dssp             -CCCSCCCSTTEEEECCSSTTCBSSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTTCC-TTSCCSSCEEEEEEEE
T ss_pred             -ccccCCCCCeEEEEeeCCCCCcceEEEEEcCC-ccccCCCeeEEEEEecCHHHHHHHHhCCC-CCCCCCCCEEEEEeEE
Confidence             56899999999999999999999999999998 79999999999999999999999998887 5689999999999999


Q ss_pred             EC
Q 046966          156 LY  157 (299)
Q Consensus       156 ~~  157 (299)
                      ++
T Consensus       171 l~  172 (173)
T 2igv_A          171 LK  172 (173)
T ss_dssp             EC
T ss_pred             Ec
Confidence            85

>1qng_A Peptidyl-prolyl CIS-trans isomerase; isomerase-immunosuppressant complex, cyclophilin-cyclosporin complex, immunosuppressant, cyclophilin; HET: BMT; 2.1A {Plasmodium falciparum} SCOP: b.62.1.1 PDB: 1qnh_A*

Probab=100.00  E-value=2.6e-46  Score=302.74  Aligned_cols=150  Identities=39%  Similarity=0.703  Sum_probs=138.7

Q ss_pred             EEEEEc-----ceeEEEEecCCCChHHHHHHHHhhhC-CC--------cCCceeeEeecCcEEEecCCC-CCCCCCCCCC
Q 046966            3 VLIETS-----LGDIVIDLFVDKCPRTTNNFLQHCKN-KY--------YNGCLFHNIHKDFIAQTGDPT-GTGTGGRSVY   67 (299)
Q Consensus         3 v~~~T~-----~G~i~ieL~~~~~P~~~~nF~~l~~~-~~--------y~~~~f~ri~~~~~iq~G~~~-~~~~~~~~~~   67 (299)
                      |.|+++     .|+|+||||++.||+||+||++||++ ++        |+|+.||||+|+|||||||+. ++|.++.++|
T Consensus         6 v~~di~i~~~~~G~i~ieL~~~~aP~t~~NF~~L~~~~g~g~~~~~~~Y~g~~FhRvi~~f~iQgGd~~~~~g~gg~si~   85 (170)
T 1qng_A            6 VFFDISIDNSNAGRIIFELFSDITPRTCENFRALCTGEKIGSRGKNLHYKNSIFHRIIPQFMCQGGDITNGNGSGGESIY   85 (170)
T ss_dssp             EEEEEEESSSEEEEEEEEECTTTCHHHHHHHHHHHHTCEECTTSSEECCTTCBCCEEETTTEEEECCTTTSSSSCCCBTT
T ss_pred             EEEEEeECCEeceeEEEEEcCCCCCHHHHHHHHHhccCCcCccCccceECCCEEEEEECCCEEEcCCccCCCCCCCcccc
Confidence            555555     89999999999999999999999984 78        999999999999999999985 6788999999


Q ss_pred             CCcccccccccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCcee
Q 046966           68 EDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQ  147 (299)
Q Consensus        68 ~~~~~~~e~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~  147 (299)
                      +.. +++| ...++|+++|+||||+.+||+++|||||++.+ .+|||++|+|||+|++||+||++|++.++ .+++|..+
T Consensus        86 g~~-f~dE-~~~l~h~~~G~lsmAn~gp~tngSQFfIt~~~-~~~Ldg~~~vFG~Vv~G~dvv~~I~~~~t-~~~~P~~~  161 (170)
T 1qng_A           86 GRS-FTDE-NFNMKHDQPGLLSMANAGPNTNSSQFFITLVP-CPWLDGKHVVFGKVIEGMNVVREMEKEGA-KSGYVKRS  161 (170)
T ss_dssp             BSC-BCCC-CCCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTTCC-TTCCCSSC
T ss_pred             CCc-cccc-ccccccCCCCEEEEeecCCCCcccEEEEECCC-CcccCCCeeEEEEEECCHHHHHHHHhCCC-CCCCCCCC
Confidence            866 6888 57899999999999999999999999999998 69999999999999999999999999998 78999999


Q ss_pred             EEEEEEEEE
Q 046966          148 IIIKQTYVL  156 (299)
Q Consensus       148 v~I~~~~v~  156 (299)
                      |+|.+|+++
T Consensus       162 v~I~~cG~l  170 (170)
T 1qng_A          162 VVITDCGEL  170 (170)
T ss_dssp             EEEEEEEEC
T ss_pred             eEEEeceeC
Confidence            999999975

>2r99_A Peptidyl-prolyl CIS-trans isomerase E; CIS-trans isomerization, structural genomics consortium, SGC, alternative splicing, mRNA processing; 1.61A {Homo sapiens} SCOP: b.62.1.1 PDB: 3uch_A 1zmf_A

Probab=100.00  E-value=5.8e-46  Score=301.28  Aligned_cols=147  Identities=38%  Similarity=0.637  Sum_probs=136.5

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhh--CCC-cCCceeeEeecCcEEEecCCC-CCCCCCCCCCCCcccccccccCCCC
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCK--NKY-YNGCLFHNIHKDFIAQTGDPT-GTGTGGRSVYEDRFFVDEIRADLKH   82 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~--~~~-y~~~~f~ri~~~~~iq~G~~~-~~~~~~~~~~~~~~~~~e~~~~~~~   82 (299)
                      |+.|+|+||||++.||+||+||++||+  .++ |+|+.||||+|+|||||||+. ++|.++.++|+.. +++| ...++|
T Consensus        23 t~~G~i~ieL~~~~aP~t~~NF~~L~~g~~g~~Y~g~~FhRvi~~f~iQgGd~~~~~g~gg~si~g~~-f~dE-~~~l~h  100 (173)
T 2r99_A           23 KPAGRIQMLLRSDVVPMTAENFRCLCTHEKGFGFKGSSFHRIIPQFMCQGGDFTNHNGTGGKSIYGKK-FDDE-NFILKH  100 (173)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTTTSCCSTTCBEEEEETTTEEEECCTTTSSSSCCCBTTBSC-BCCC-CCCSCC
T ss_pred             ccceeEEEEECCCCCcHHHHHHHHHhcccCCceecCCEEEEeeCCCEEEeCCcCCCCCCCCCccCCCc-ccCc-ccCccc
Confidence            899999999999999999999999995  577 999999999999999999986 5788999999876 6888 678999


Q ss_pred             CCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEEC
Q 046966           83 DKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY  157 (299)
Q Consensus        83 ~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~~  157 (299)
                      +++|+||||+.+||+++|||||++.+ .+|||++|+|||+|++||+||++|++.+++ +++|..+|+|.+|+++.
T Consensus       101 ~~~G~lsmA~~gp~t~gSQFfIt~~~-~~~LDg~~tVFG~Vv~G~dvv~~I~~~~~~-~~~P~~~v~I~~cG~l~  173 (173)
T 2r99_A          101 TGPGLLSMANSGPNTNGSQFFLTCDK-TDWLDGKHVVFGEVTEGLDVLRQIEAQGSK-DGKPKQKVIIADCGEYV  173 (173)
T ss_dssp             CSSSEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTTCCT-TCCCSSCEEEEEEEECC
T ss_pred             CCCcEEEEccCCCCCcccEEEEECCC-CCccCCCeeEEEEEEcCHHHHHHHHhCCCC-CCCCCCCeEEEEeeeEC
Confidence            99999999999999999999999998 799999999999999999999999988774 68999999999999864

>2z6w_A Peptidyl-prolyl CIS-trans isomerase; isomerase-immunosuppressant complex, immunosuppressant, cyclophilin D; HET: BMT MLE CIT; 0.96A {Homo sapiens} SCOP: b.62.1.1 PDB: 3rcg_A* 3r49_A* 3r54_A 3r56_A* 3r57_A* 3r59_A* 3rcf_A* 3r4g_A* 3rci_X* 3rck_X* 3rcl_A* 3rd9_X* 3rda_X* 3rdb_A* 3rdc_A* 2bit_X 2biu_X 3qyu_A 3k0m_A 1ak4_A* ...

Probab=100.00  E-value=6.3e-46  Score=299.07  Aligned_cols=147  Identities=38%  Similarity=0.680  Sum_probs=137.3

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhh--CCC-cCCceeeEeecCcEEEecCCC-CCCCCCCCCCCCcccccccccCCCC
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCK--NKY-YNGCLFHNIHKDFIAQTGDPT-GTGTGGRSVYEDRFFVDEIRADLKH   82 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~--~~~-y~~~~f~ri~~~~~iq~G~~~-~~~~~~~~~~~~~~~~~e~~~~~~~   82 (299)
                      |+.|+|+||||++.||+||+||++||+  .++ |+|+.||||+|+|++||||+. ++|.++.++|+.. +++| .+.++|
T Consensus        15 t~~G~i~ieL~~~~aP~t~~NF~~L~~g~~g~~Y~g~~fhRvi~~f~iQgGd~~~~~g~gg~si~g~~-f~dE-~~~l~h   92 (165)
T 2z6w_A           15 KPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSR-FPDE-NFTLKH   92 (165)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTTTSCCSTTCBEEEEETTTEEEECCTTTSSSSCCCBTTBSC-BCCC-CCCSCC
T ss_pred             EeeeEEEEEEeCCCCcHHHHHHHHHhccCCCccCcCCEEEEEECCCEEEeCCccCCCCCCCCcccCCc-ccCc-cccccc
Confidence            578999999999999999999999999  889 999999999999999999985 5788899999876 6888 678999


Q ss_pred             CCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEEC
Q 046966           83 DKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY  157 (299)
Q Consensus        83 ~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~~  157 (299)
                      +++|+||||+.+|++++|||||++.+ .+|||++|+|||+|++||+||++|++.++ .+++|..+|+|.+|+++.
T Consensus        93 ~~~G~lsmA~~gp~s~~SQFfI~~~~-~~~Ldg~~~vFG~Vv~G~dvv~~I~~~~~-~~~~P~~~v~I~~~g~l~  165 (165)
T 2z6w_A           93 VGPGVLSMANAGPNTNGSQFFICTIK-TDWLDGKHVVFGHVIEGMDVVKKIESFGS-KSGRTSKKIVITDCGQLS  165 (165)
T ss_dssp             CSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHHTCC-TTSCCSSCEEEEEEEECC
T ss_pred             CCCCEEEEeeCCCCCcccEEEEEcCC-CcccCCCeeEEEEEEcCHHHHHHHHhCCC-CCCCCCCcEEEEEeEEEC
Confidence            98999999999999999999999998 79999999999999999999999998875 689999999999999863

>3s6m_A Peptidyl-prolyl CIS-trans isomerase; seattle structural genomics center for infectious disease; 1.65A {Burkholderia pseudomallei} SCOP: b.62.1.1 PDB: 3t1u_A*

Probab=100.00  E-value=3.6e-46  Score=302.01  Aligned_cols=151  Identities=26%  Similarity=0.450  Sum_probs=136.1

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCC
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADL   80 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~   80 (299)
                      |+|+|+|+.|+|+||||++.||+||+||++||+.++|+|+.||||+|+|||||||+...+.  ...++. .+++|....+
T Consensus         4 ~~v~l~T~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Y~g~~FhRvi~~f~iQgGd~~~~~~--~~~~~~-~~~~E~~~~l   80 (167)
T 3s6m_A            4 SMVELHTNHGVIKLELDEAKAPKTVENFLNYVKKGHYDGTIFHRVINGFMIQGGGFEPGLK--QKPTDA-PIANEANNGL   80 (167)
T ss_dssp             CEEEEEETTEEEEEEECTTTCHHHHHHHHHHHHHTTTTTEECCEEETTTEEEESSEETTTE--ECCCCC-CBCCCGGGCC
T ss_pred             cEEEEEeCCceEEEEEeCCCCcHHHHHHHHHhhhcccCCCEeEEecCCcEEEeccccCCCC--CCCCCC-ccCCcccccc
Confidence            7899999999999999999999999999999999999999999999999999999875432  122333 3678877778


Q ss_pred             CCCCceEEEEEc-CCCCCCcceEEEEecCCCCCCCCC--------ceEEEEeecCHHHHHHHHhcccCC----CCCCcee
Q 046966           81 KHDKVGTVGMAS-AGRDLNASQFYITLRDNLHYLDEK--------HTIFGEVAEGLETLTRINQAVVDE----ENRPPQQ  147 (299)
Q Consensus        81 ~~~~~G~l~~~~-~~~~~~~s~FfI~~~~~~~~ld~~--------~~vfG~V~~G~~vl~~i~~~~~~~----~~~p~~~  147 (299)
                      +| .+|+||||+ .+|++++|||||++.+ .+|||++        |+|||+|++||+||++|++.+++.    +++|..+
T Consensus        81 ~~-~~G~lsmA~~~~p~t~gSQFfI~~~~-~~~Ld~~~~~~~~~~~~VFG~Vv~G~dvv~~I~~~~t~~~~~~~~~P~~~  158 (167)
T 3s6m_A           81 KN-DTYTIAMARTNDPHSATAQFFINVND-NEFLNHSSPTPQGWGYAVFGKVVEGQDIVDKIKAVKTGSKGFHQDVPNDD  158 (167)
T ss_dssp             CC-CTTEEEECCCSSTTCBCSCEEEESSC-CGGGSCCSSSTTTCCCCEEEEEEECHHHHHHHTTSCBBC---CBTCBSSC
T ss_pred             cC-CccEEEEecCCCCCCccceEEEEcCC-chhcCCcccccCCCCceEEEEEEcCHHHHHHHHcCCcCCCcccCCCcCCC
Confidence            77 899999999 6799999999999998 6999998        999999999999999999999987    6899999


Q ss_pred             EEEEEEEEE
Q 046966          148 IIIKQTYVL  156 (299)
Q Consensus       148 v~I~~~~v~  156 (299)
                      |+|.+|.|+
T Consensus       159 v~I~~~~il  167 (167)
T 3s6m_A          159 VVIEKAVVV  167 (167)
T ss_dssp             CEEEEEEEC
T ss_pred             eEEEEEEEC
Confidence            999999885

>2poy_A Peptidyl-prolyl CIS-trans isomerase; isomerase-immunosuppressant complex, immunosuppressant, cyclophilin, isomerase, S genomics, structural genomics consortium; HET: BMT; 1.80A {Cryptosporidium parvum iowa II} PDB: 2plu_A*

Probab=100.00  E-value=2e-45  Score=300.65  Aligned_cols=145  Identities=40%  Similarity=0.679  Sum_probs=134.1

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhh--CCC--------cCCceeeEeecCcEEEecCCC-CCCCCCCCCCCCcccccc
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCK--NKY--------YNGCLFHNIHKDFIAQTGDPT-GTGTGGRSVYEDRFFVDE   75 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~--~~~--------y~~~~f~ri~~~~~iq~G~~~-~~~~~~~~~~~~~~~~~e   75 (299)
                      |+.|+|+||||++.||+||+||++||+  .|+        |+|+.||||+|+|||||||+. ++|.++.++|+.. +++|
T Consensus        31 t~~G~I~ieL~~~~aP~t~~NF~~L~~g~~g~~~~~~~~~Y~g~~FhRVi~~f~iQgGd~~~~~G~gg~si~g~~-f~dE  109 (186)
T 2poy_A           31 TPAGRITMELFADKVPITAENFRALCTGEKGMGQSGKPLCYTGSFFHRIIPQFMIQGGDFTRGDGTGGESIYGSK-FRDE  109 (186)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTTTCBCTTSSBSCCTTCBCCEEETTTEEEECCTTTSSSSCCCCTTC-C-BCCC
T ss_pred             EecccEEEEEeCCCCcHHHHHHHHHhcccCCccccCccceECCCEEEEEeCCCEEEeCCCCCCCCCCCCccCCCc-ccCc
Confidence            459999999999999999999999997  477        999999999999999999975 6789999999866 6888


Q ss_pred             cccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEE
Q 046966           76 IRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYV  155 (299)
Q Consensus        76 ~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v  155 (299)
                       ...++|+++|+||||+.+||+++|||||++.+ .+|||++|+|||+|++||+||++|++.++ .+++|..+|+|.+|++
T Consensus       110 -~~~l~h~~~G~lsMAn~gpntngSQFFIt~~~-~~~LDg~~tVFG~Vv~Gmdvv~~I~~~~t-~~~~P~~~v~I~~cG~  186 (186)
T 2poy_A          110 -NFVYTHDAPFLLSMANAGPNTNGSQFFITTVP-CPWLDGKHVVFGKVLEGMEVVKSIEKCGS-QNGKPTKSVCITASGV  186 (186)
T ss_dssp             -CCCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHHTCC-TTSCCSSCEEEEEEEC
T ss_pred             -ccccccCCCcEEEEeeCCCCCcccEEEEECCC-CcccCCCeeEEEEEecCHHHHHHHHhCCC-CCCCCCCCEEEEeCCC
Confidence             57899999999999999999999999999998 69999999999999999999999999988 6789999999999984

>1lop_A Cyclophilin A; rotamase, isomerase-isomerase inhibitor complex; HET: NIT; 1.80A {Escherichia coli} SCOP: b.62.1.1 PDB: 2nul_A 2rs4_A

Probab=100.00  E-value=5e-46  Score=299.85  Aligned_cols=151  Identities=29%  Similarity=0.523  Sum_probs=135.4

Q ss_pred             EEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCC
Q 046966            2 SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLK   81 (299)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~   81 (299)
                      .|+|+|+.|+|+||||++.||+||+||++||+.|+|+|+.||||+|+|||||||+...  .+.++++.. +++|....++
T Consensus         1 ~v~l~T~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Y~g~~FhRvi~~f~iQgGd~~~~--~g~~~~g~~-~~dE~~~~l~   77 (164)
T 1lop_A            1 MVTFHTNHGDIVIKTFDDKAPETVKNFLDYCREGFYNNTIFHRVINGFMIQGGGFEPG--MKQKATKEP-IKNEANNGLK   77 (164)
T ss_dssp             CEEEEETTEEEEEEECTTTSHHHHHHHHHHHHTTTTTTEECCEEETTTEEEESSEETT--TEECCCCCC-BCCCCCSSCC
T ss_pred             CEEEEeCCCCEEEEEeCCCCcHHHHHHHHHHhcCCCCCCEEEEEeCCceEecCCcccC--CCcCCCCCc-cccccccccc
Confidence            3899999999999999999999999999999999999999999999999999998632  134455544 6889767788


Q ss_pred             CCCceEEEEEcC-CCCCCcceEEEEecCCCCCCCCC--------ceEEEEeecCHHHHHHHHhcccCC----CCCCceeE
Q 046966           82 HDKVGTVGMASA-GRDLNASQFYITLRDNLHYLDEK--------HTIFGEVAEGLETLTRINQAVVDE----ENRPPQQI  148 (299)
Q Consensus        82 ~~~~G~l~~~~~-~~~~~~s~FfI~~~~~~~~ld~~--------~~vfG~V~~G~~vl~~i~~~~~~~----~~~p~~~v  148 (299)
                      | .+|+||||+. +|++++|||||++.+ .+|||++        |+|||+|++||+||++|++.+++.    +++|..+|
T Consensus        78 ~-~~G~lsmA~~~~p~s~gSQFfI~~~~-~~~Ld~~~~~~~~~~~tvFG~Vv~G~dvv~~I~~~~t~~~~~~~~~P~~~v  155 (164)
T 1lop_A           78 N-TRGTLAMARTQAPHSATAQFFINVVD-NDFLNFSGESLQGWGYCVFAEVVDGMDEVDKIKGVATGRSGMHQDVPKEDV  155 (164)
T ss_dssp             C-CTTEEEECCCSSTTCBCSCEEEESSC-CGGGSCCSSSTTTSCCCEEEEEEECHHHHHHHHTSCEEEETTEEEEESSCC
T ss_pred             c-CccEEEEeecCCCCCccceEEEEcCC-ccccCCccccccCCceEEEEEEecCHHHHHHHHhCCcCCccccCCCcCCCe
Confidence            7 6999999974 799999999999998 6999998        999999999999999999999875    57999999


Q ss_pred             EEEEEEEEC
Q 046966          149 IIKQTYVLY  157 (299)
Q Consensus       149 ~I~~~~v~~  157 (299)
                      +|.+|++++
T Consensus       156 ~I~~~~v~~  164 (164)
T 1lop_A          156 IIESVTVSE  164 (164)
T ss_dssp             EEEEEEECC
T ss_pred             EEEEEEEeC
Confidence            999999863

>4fru_A Cyclophilin B, peptidyl-prolyl CIS-trans isomerase; cyclophilin-type ppiase, peptidyl-prolyl CIS-trans isomerase chaperone, foldase; HET: ME2 PEG; 1.10A {Equus caballus} PDB: 4frv_A* 3ich_A 3ici_A* 1cyn_A* 2esl_A* 2rmc_A* 1h0p_A 1xo7_A 1xq7_A*

Probab=100.00  E-value=3.1e-45  Score=300.64  Aligned_cols=148  Identities=40%  Similarity=0.687  Sum_probs=139.1

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhC--C-CcCCceeeEeecCcEEEecCCC-CCCCCCCCCCCCcccccccccCCCC
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKN--K-YYNGCLFHNIHKDFIAQTGDPT-GTGTGGRSVYEDRFFVDEIRADLKH   82 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~--~-~y~~~~f~ri~~~~~iq~G~~~-~~~~~~~~~~~~~~~~~e~~~~~~~   82 (299)
                      |+.|+|+||||++.||+||+||++||++  | +|+|+.||||+|+|+|||||+. ++|.++.++|+.. +++| ...++|
T Consensus        24 ~~~G~i~ieL~~~~aP~t~~NF~~L~~~~~g~~Y~g~~FhRvi~~f~iQgGd~~~~~g~gg~si~g~~-f~de-~~~~~h  101 (185)
T 4fru_A           24 EDIGRVVIGLFGKTVPKTVDNFVALATGEKGFGYKDSKFHRVIKDFMIQGGDFTRGDGTGGKSIYGER-FPDE-NFKLKH  101 (185)
T ss_dssp             EEEEEEEEEECTTTSHHHHHHHHHHHHTTTSCCSTTCBCCEEETTTEEEECCTTTSSSSCCCBTTBSC-BCCC-CCCSCC
T ss_pred             EecceEEEEEeCCCCcHHHHHHHHHHhcCCCCeEcCCEEEEeeCCCeEEECCCCCCCCCCCccccCCc-cCcc-ccccCc
Confidence            5699999999999999999999999986  5 7999999999999999999976 6789999999876 5888 678999


Q ss_pred             CCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEEC
Q 046966           83 DKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY  157 (299)
Q Consensus        83 ~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~~  157 (299)
                      +++|+||||+.++++++|||||++.+ .+|||++|+|||+|++||+||++|++.+++.+++|..+|+|.+|+++.
T Consensus       102 ~~~G~lsma~~gp~t~~SQFfI~~~~-~~~Ld~~~~vFG~Vv~G~dvv~~I~~~~t~~~~~P~~~v~I~~~g~l~  175 (185)
T 4fru_A          102 YGPGWVSMANAGKDTNGSQFFITTVK-TAWLDGKHVVFGKVLEGMEVVRKVETTKTDGRDKPLKDVTIADCGKIE  175 (185)
T ss_dssp             CSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTSCBSSCEEEEEEEEEE
T ss_pred             CCCeEEEEeeCCCCCcceEEEEEeCC-CcccCCCccEEEEEeCCHHHHHHHHhCCCCCCCcCCCCEEEEEceEEe
Confidence            99999999999999999999999998 799999999999999999999999999999999999999999999985

>3rdd_A Peptidyl-prolyl CIS-trans isomerase A; beta barrel, cytosolic, inhibito isomerase-isomerase inhibitor complex; HET: EA4; 2.14A {Homo sapiens}

Probab=100.00  E-value=2.6e-45  Score=300.02  Aligned_cols=152  Identities=36%  Similarity=0.630  Sum_probs=139.1

Q ss_pred             EEEEEEc-----ceeEEEEecCCCChHHHHHHHHhhhCCC---cCCceeeEeecCcEEEecCC-CCCCCCCCCCCCCccc
Q 046966            2 SVLIETS-----LGDIVIDLFVDKCPRTTNNFLQHCKNKY---YNGCLFHNIHKDFIAQTGDP-TGTGTGGRSVYEDRFF   72 (299)
Q Consensus         2 ~v~~~T~-----~G~i~ieL~~~~~P~~~~nF~~l~~~~~---y~~~~f~ri~~~~~iq~G~~-~~~~~~~~~~~~~~~~   72 (299)
                      .|.|+|+     .|+|+||||++.||+||+||++||++++   |+|+.||||+|+|+|||||+ ..+|.++.++|+.. +
T Consensus        24 ~v~~di~i~~~~~G~I~ieL~~~~aP~t~~NF~~L~~~~~g~~Y~g~~FhRvi~~f~iQgGd~~~~~g~gg~si~g~~-~  102 (184)
T 3rdd_A           24 TVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEK-F  102 (184)
T ss_dssp             EEEEEEEETTEEEEEEEEEECTTTSHHHHHHHHHHHHTTTSCSSTTCBCCEEETTTEEEECCTTTSSSSCCCBTTBSC-B
T ss_pred             EEEEEEeECCEeeeEEEEEEeCCCCcHHHHHHHHHhccCcCcccCCCEEEEccCCcEEEeCCCCCCCCCCCcccCCCc-c
Confidence            3677766     9999999999999999999999998755   99999999999999999994 56788999999876 5


Q ss_pred             ccccccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEE
Q 046966           73 VDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQ  152 (299)
Q Consensus        73 ~~e~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~  152 (299)
                      ++| ...++|+.+|+|+||+.+|++++|||||++.+ .++||++|+|||+|++||+||++|++.++ .+++|..+|+|.+
T Consensus       103 ~de-~~~l~h~~~G~lsmA~~gp~s~gSQFfIt~~~-~~~LDg~~tVFG~Vv~G~dvv~~I~~~~~-~~g~P~~~v~I~~  179 (184)
T 3rdd_A          103 EDE-NFILKHTGPGILSMANAGPNTNGSQFFICTAK-TEWLDGKHVVFGKVKEGMNIVEAMERFGS-RNGKTSKKITIAD  179 (184)
T ss_dssp             CCC-CCCSCCCSTTEEEECCSSTTCBSSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTTCC-TTSCCSSCEEEEE
T ss_pred             cCc-ccccccCCCcEEEEEeCCCCCcccEEEEEeCC-chhhCCCceEEEEEecCHHHHHHHHhcCC-CCCCCcCCeEEEe
Confidence            777 57899999999999999999999999999998 69999999999999999999999988876 5789999999999


Q ss_pred             EEEEC
Q 046966          153 TYVLY  157 (299)
Q Consensus       153 ~~v~~  157 (299)
                      |++++
T Consensus       180 cG~l~  184 (184)
T 3rdd_A          180 CGQLE  184 (184)
T ss_dssp             EEECC
T ss_pred             CeEEC
Confidence            99974

>2c3b_A Ppiase, cyclophilin; isomerase, 3D domain swapping, misfolding, Asp F 11, allergen, rotamase; 1.85A {Aspergillus fumigatus} SCOP: b.62.1.1

Probab=100.00  E-value=2.4e-46  Score=303.24  Aligned_cols=147  Identities=41%  Similarity=0.657  Sum_probs=111.4

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhh--CCC-cCCceeeEeecCcEEEecC-CCCCCCCCCCCCCCcccccccccCCCC
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCK--NKY-YNGCLFHNIHKDFIAQTGD-PTGTGTGGRSVYEDRFFVDEIRADLKH   82 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~--~~~-y~~~~f~ri~~~~~iq~G~-~~~~~~~~~~~~~~~~~~~e~~~~~~~   82 (299)
                      |++|+|+||||++.||+||+||++||+  .|+ |+|+.||||+|+|++|||| +.++|.++.++|+.. +++| ...++|
T Consensus        19 T~~G~i~ieL~~~~aP~t~~NF~~L~~g~~g~~Y~g~~fhRvi~~f~iQgGd~~~~~g~gg~si~g~~-f~dE-~~~~~h   96 (172)
T 2c3b_A           19 TKVGRIVFNLFDKDVPKTAKNFRELCKRPAGEGYRESTFHRIIPNFMIQGGDFTRGNGTGGRSIYGDK-FADE-NFSRKH   96 (172)
T ss_dssp             CEEEEEEEEECTTTSHHHHHHHHHHHHSCTTTSSTTCBCCEEETTTEEEECC------------------------CHHH
T ss_pred             cccccEEEEEcCCCCcHHHHHHHHHhccCCCcccCCCEEEEEeCCCEEEeCCcCCCCCCCCcccCCCc-ccCc-cccccc
Confidence            888999999999999999999999999  567 9999999999999999999 777899999999876 6888 678889


Q ss_pred             CCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeec--CHHHHHHHHhcccCCCC-CCceeEEEEEEEEE
Q 046966           83 DKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAE--GLETLTRINQAVVDEEN-RPPQQIIIKQTYVL  156 (299)
Q Consensus        83 ~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~--G~~vl~~i~~~~~~~~~-~p~~~v~I~~~~v~  156 (299)
                      +++|+||||+.+|++++|||||++.+ .+|||++|+|||+|++  ||+||++|++.+++..+ +|..+|+|.+|+++
T Consensus        97 ~~~G~lsmA~~gp~t~gSQFfIt~~~-~~~LDg~~tvFG~Vv~~~G~dvv~~I~~~~t~~~~~~P~~~v~I~~cG~l  172 (172)
T 2c3b_A           97 DKKGILSMANAGPNTNGSQFFITTAV-TSWLDGKHVVFGEVADEKSYSVVKEIEALGSSSGSVRSNTRPKIVNCGEL  172 (172)
T ss_dssp             HHTCEEEEC---------CEEEECSC-CTTCCSCCEEEEEECSHHHHHHHHHHHTTCCTTSCCCSSSCCEEEEEEEC
T ss_pred             CCCeEEEEeeCCCCCcccEEEEECCC-CCccCCCeeEEEEEEecCCHHHHHHHHhCCCCCCCccCCCCeEEEeCeeC
Confidence            99999999999999999999999998 6999999999999999  99999999999997655 99999999999974

>1z81_A Cyclophilin; structural genomics, structural genomics consortium, SGC, isomerase; 2.80A {Plasmodium yoelii yoelii} SCOP: b.62.1.1

Probab=100.00  E-value=2.5e-45  Score=307.81  Aligned_cols=147  Identities=35%  Similarity=0.627  Sum_probs=138.0

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhCC--------CcCCceeeEeecCcEEEecCCC-CCCCCCCCCCCCcccccccc
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKNK--------YYNGCLFHNIHKDFIAQTGDPT-GTGTGGRSVYEDRFFVDEIR   77 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~~--------~y~~~~f~ri~~~~~iq~G~~~-~~~~~~~~~~~~~~~~~e~~   77 (299)
                      |+.|+|+||||++.||+||+||++||+++        +|+|+.||||+|+|+|||||+. ++|.++.++|+.. +++| .
T Consensus        71 t~~G~I~ieL~~d~aP~tv~NF~~L~~~~~g~~g~~~~Y~gt~FHRVi~~FmiQgGD~~~g~G~Gg~siyg~~-f~dE-~  148 (229)
T 1z81_A           71 NFLGKFKFELFQNIVPKTSENFRQFCTGEYKVNNLPVGYKNTIFHRVIKEFMIQGGDFINHNGSGSLSIYGEK-FDDE-N  148 (229)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTCCBSSSSBCSSTTEECCEEETTTEEEECCTTTSSSCCCCBTTBSC-CCCC-C
T ss_pred             eecccEEEEEcCCCCCHHHHHHHHHhhCCCCCcCCCceECCCEEEEEeCCCEEEcCCCcCCCCCCCCccCCCc-cccc-c
Confidence            45999999999999999999999999987        6999999999999999999985 7789999999866 6888 5


Q ss_pred             cCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEee--cCHHHHHHHHhcccCCC-CCCceeEEEEEEE
Q 046966           78 ADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVA--EGLETLTRINQAVVDEE-NRPPQQIIIKQTY  154 (299)
Q Consensus        78 ~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~--~G~~vl~~i~~~~~~~~-~~p~~~v~I~~~~  154 (299)
                      +.++|+++|+||||+.+|++++|||||++.+ .+|||++|+|||+|+  +||+||++|++.+++.+ ++|..+|+|.+|+
T Consensus       149 ~~l~h~~~G~LsMAn~gpntngSQFFIt~~~-~~~LDg~~tVFG~Vv~~eGmdVv~~I~~~~t~~~~~~P~~~V~I~~cG  227 (229)
T 1z81_A          149 FDIKHDKEGLLSMANSGPNTNGCQFFITTKK-CEWLDGKNVVFGRIIDNDSLLLLKKIENVSVTPYIYKPKIPINVVECG  227 (229)
T ss_dssp             CCSCCCSTTEEEECCSSSSCCCSCEEEESSC-CGGGBTTBCEEEEECSHHHHHHHHHHHHSCBCTTTCCBSSCEEEEEEE
T ss_pred             cccccCCCcEEEeccCCCCCcccEEEEECCC-CcccCCCeeEEEEEEecCcHHHHHHHHhCCCCCCCCCCCCCeEEEeCe
Confidence            7899999999999999999999999999998 799999999999999  99999999999999887 9999999999999


Q ss_pred             EE
Q 046966          155 VL  156 (299)
Q Consensus       155 v~  156 (299)
                      ++
T Consensus       228 ~l  229 (229)
T 1z81_A          228 EL  229 (229)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>1v9t_A Cyclophilin B; beta barrel, isomerase-isomerase inhibitor complex; HET: NIT; 1.70A {Escherichia coli} SCOP: b.62.1.1 PDB: 1j2a_A* 1vai_A* 1clh_A

Probab=100.00  E-value=1.8e-45  Score=297.13  Aligned_cols=152  Identities=29%  Similarity=0.484  Sum_probs=134.9

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCC
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADL   80 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~   80 (299)
                      ..|+|+|+.|+|+||||+++||+||+||++||+.++|+|+.||||+|+|||||||+...+.+  ..++. .+++|....+
T Consensus         5 ~~v~~~t~~G~i~ieL~~~~aP~t~~NF~~L~~~g~Y~g~~FhRvi~~f~iQgGd~~~~~~~--~~~g~-~~~dE~~~~l   81 (166)
T 1v9t_A            5 PHVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQ--KKPNP-PIKNEADNGL   81 (166)
T ss_dssp             CEEEEEETTEEEEEEECTTTCHHHHHHHHHHHHTTTTTTCBEEEEETTTEEEESSBCTTCCB--CCCCC-CBCCCGGGSC
T ss_pred             eEEEEEeCCccEEEEEcCCCCcHHHHHHHHHhccCCCCCCEEEEEECCcEEEcCCcCcCCCC--CCCCC-cccccccccc
Confidence            36999999999999999999999999999999999999999999999999999998765332  22333 4688866666


Q ss_pred             CCCCceEEEEEcC-CCCCCcceEEEEecCCCCCCCCC-----ceEEEEeecCHHHHHHHHhcccCC----CCCCceeEEE
Q 046966           81 KHDKVGTVGMASA-GRDLNASQFYITLRDNLHYLDEK-----HTIFGEVAEGLETLTRINQAVVDE----ENRPPQQIII  150 (299)
Q Consensus        81 ~~~~~G~l~~~~~-~~~~~~s~FfI~~~~~~~~ld~~-----~~vfG~V~~G~~vl~~i~~~~~~~----~~~p~~~v~I  150 (299)
                      +| .+|+||||+. +||+++|||||++.+ .+|||++     |+|||+|++||+||++|++.+++.    .++|..+|+|
T Consensus        82 ~~-~~G~lsmA~~~~p~t~gSQFfI~~~~-~~~Ld~~~~~~~~tvFG~Vv~G~dvv~~I~~~~~~~~~~~~~~P~~~v~I  159 (166)
T 1v9t_A           82 RN-TRGTIAMARTADKDSATSQFFINVAD-NAFLDHGQRDFGYAVFGKVVKGMDVADKISQVPTHDVGPYQNVPSKPVVI  159 (166)
T ss_dssp             CC-CTTEEEECCCSSTTCBCSCEEEESSC-CGGGSCCSSCCCCCEEEEEEECHHHHHHHHTSCEEEETTEEEEESSCCBE
T ss_pred             cC-CceEEEEeecCCCCCccceEEEEeCC-ccccCCccCcCCeeEEEEEecCHHHHHHHHhCCCCCCCccCCCcCCCeEE
Confidence            65 7999999997 699999999999998 6999998     999999999999999999999876    4789999999


Q ss_pred             EEEEEEC
Q 046966          151 KQTYVLY  157 (299)
Q Consensus       151 ~~~~v~~  157 (299)
                      .+|.|++
T Consensus       160 ~~~~v~~  166 (166)
T 1v9t_A          160 LSATVLP  166 (166)
T ss_dssp             EEEEECC
T ss_pred             EEEEEeC
Confidence            9999863

>3k2c_A Peptidyl-prolyl CIS-trans isomerase; ssgcid, NIH, niaid, SBRI, UW, decode, cytoplasm, rotamase, structural genomics; HET: PG5; 1.95A {Encephalitozoon cuniculi}

Probab=100.00  E-value=9.2e-45  Score=298.71  Aligned_cols=148  Identities=42%  Similarity=0.695  Sum_probs=137.3

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhh--CCC-cCCceeeEeecCcEEEecC-CCCCCCCCCCCCCCcccccccccCCCC
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCK--NKY-YNGCLFHNIHKDFIAQTGD-PTGTGTGGRSVYEDRFFVDEIRADLKH   82 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~--~~~-y~~~~f~ri~~~~~iq~G~-~~~~~~~~~~~~~~~~~~~e~~~~~~~   82 (299)
                      |+.|+|+||||++.||+||+||++||+  .++ |+|+.||||+|+|++|||| ...++.++.++|+.. +++| ...++|
T Consensus        39 t~~G~I~ieL~~~~aP~tv~NF~~L~~g~~g~~Y~g~~FhRvi~~f~iQgGd~~~~~g~gg~si~g~~-f~dE-~~~l~h  116 (193)
T 3k2c_A           39 ESLGRIVMKLEDDIVPKTAKNFRTLCERPKGEGYKGSTFHRIIPGFMVQGGDYTAHNGTGGRSIYGEK-FPDE-NFELKH  116 (193)
T ss_dssp             EEEEEEEEEECTTTSHHHHHHHHHHHHSCTTSSSTTCBEEEEETTTEEEECCTTTSSSSCCCCTTSSC-BCCC-CCCSCC
T ss_pred             EEeeEEEEEEcCCCChHHHHHHHHHhccccCCcccCCEEEEEeCCCEEEeCCCCCCCCcCCcccCCCc-cccc-cccccc
Confidence            889999999999999999999999998  566 9999999999999999999 556789999999876 5788 778999


Q ss_pred             CCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCc--eeEEEEEEEEECC
Q 046966           83 DKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPP--QQIIIKQTYVLYP  158 (299)
Q Consensus        83 ~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~--~~v~I~~~~v~~p  158 (299)
                      +++|+|+||+.+|++++|||||++.+ .++||++|+|||+|++||+||++|++.+++ +++|.  .+|+|.+|+++.+
T Consensus       117 ~~~G~lsmAn~gp~t~gSQFFIt~~~-~~~LDg~~tVFG~Vv~Gmdvv~~I~~~~t~-~g~P~~~~~v~I~~cG~l~~  192 (193)
T 3k2c_A          117 TKEGILSMANCGAHTNGSQFFITLGK-TQWLDEKHVVFGEVVEGMDVVHKIAKYGSE-SGQVKKGYRIEIRDCGVLGS  192 (193)
T ss_dssp             CSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTTCCT-TCCCCTTCCEEEEEEEECC-
T ss_pred             CCCcEEEEEeCCCCCCccEEEEECCC-CcccCCCccEEEEEeCCHHHHHHHHhcCCC-CCcCccCccEEEEEceEeCC
Confidence            99999999999999999999999998 699999999999999999999999998886 67999  9999999999873

>2ose_A Probable peptidyl-prolyl CIS-trans isomerase; cyclophilin; 2.04A {Mimivirus}

Probab=100.00  E-value=3.4e-45  Score=309.39  Aligned_cols=156  Identities=27%  Similarity=0.449  Sum_probs=136.1

Q ss_pred             EEEEE-EcceeEEEEecCCCChHHHHHHHHhhhC-----------------C--C-cCCceeeEeecCcEEEecC-CCCC
Q 046966            2 SVLIE-TSLGDIVIDLFVDKCPRTTNNFLQHCKN-----------------K--Y-YNGCLFHNIHKDFIAQTGD-PTGT   59 (299)
Q Consensus         2 ~v~~~-T~~G~i~ieL~~~~~P~~~~nF~~l~~~-----------------~--~-y~~~~f~ri~~~~~iq~G~-~~~~   59 (299)
                      .|.|+ |+.|+|+||||++.||+||+||++||++                 |  + |+|+.||||+++||||||| +.++
T Consensus        20 di~i~~t~~G~I~ieL~~d~aP~tv~NF~~L~~g~~~~~~p~~~~~~~~~~G~~~~Y~gt~FHRVi~~FmiQgGd~~~g~   99 (234)
T 2ose_A           20 DIVLNNEIIGRLQIKLFRDAFPAGVENFVQLTNGKTYRVNSNGTGKYKYNRHINRTYEGCKFHNVLHNNYIVSGDIYNSN   99 (234)
T ss_dssp             EEEETTEEEEEEEEEECGGGCHHHHHHHHHHHHTCCCC---------------CCCSTTCBCCEEETTTEEEECCCC---
T ss_pred             EEEECCcccceEEEEEcCCCCcHHHHHHHHHhcCCccccccccccccccccCCceEECCcEEEEEECCCEEEcCCccCCC
Confidence            45555 9999999999999999999999999985                 4  6 9999999999999999999 5778


Q ss_pred             CCCCCCCCCCccccccc-ccCCCCCCceEEEEEc----CCCCCCcceEEEEecCC-----CCCCCCCceEEEEeecCHHH
Q 046966           60 GTGGRSVYEDRFFVDEI-RADLKHDKVGTVGMAS----AGRDLNASQFYITLRDN-----LHYLDEKHTIFGEVAEGLET  129 (299)
Q Consensus        60 ~~~~~~~~~~~~~~~e~-~~~~~~~~~G~l~~~~----~~~~~~~s~FfI~~~~~-----~~~ld~~~~vfG~V~~G~~v  129 (299)
                      |.+|.++|+....+.++ .+.++|+++|+||||+    .+|++++|||||++.+.     ++|||++|+|||+|++||+|
T Consensus       100 G~Gg~siyg~~~~p~~f~~~~l~h~~~G~lsMAn~~~~~gpntngSQFFIt~~~~~~~~g~p~LDg~~tVFG~Vv~GmdV  179 (234)
T 2ose_A          100 GSSAGTVYCDEPIPPVFGDYFYPHESKGLLSLVPYTDESGNRYYDSTFMITLDDIRPSNVLDELDRDQVVIGQVYGGLDV  179 (234)
T ss_dssp             -CCCCCTTTTCCBCCCCCSCCCCSCSTTEEEECCEECTTSCEEBCSCEEEESSCCCTTSSGGGSCTTSEEEEEEEECHHH
T ss_pred             CCCCccccCCccCcccccCcCccCCCCCEEEEecccccCCCCCccceEEEEecCccccCCCcccCCCeeEEEEEeCCHHH
Confidence            99999999876212111 3579999999999999    89999999999999973     59999999999999999999


Q ss_pred             HHHHHhcccCCCCCCceeEEEEEEEEEC
Q 046966          130 LTRINQAVVDEENRPPQQIIIKQTYVLY  157 (299)
Q Consensus       130 l~~i~~~~~~~~~~p~~~v~I~~~~v~~  157 (299)
                      |++|++.+++.+++|..+|+|.+|+++.
T Consensus       180 v~~I~~~~t~~~~~P~~~V~I~~~~~l~  207 (234)
T 2ose_A          180 LDKINSMIKPYAGRKYPTFSIGKCGAYL  207 (234)
T ss_dssp             HHHHHHHTCCCTTCCCCCEEEEEEEECC
T ss_pred             HHHHHhCCcCCCCCccCCEEEEEEEEec
Confidence            9999999999889999999999999987

>1ihg_A Cyclophilin 40; ppiase immunophilin tetratricopeptide, isomerase; 1.80A {Bos taurus} SCOP: a.118.8.1 b.62.1.1 PDB: 1iip_A

Probab=100.00  E-value=2.6e-41  Score=308.79  Aligned_cols=152  Identities=38%  Similarity=0.676  Sum_probs=142.0

Q ss_pred             EEEEEc-----ceeEEEEecCCCChHHHHHHHHhhhC--------C---CcCCceeeEeecCcEEEecCCC-CCCCCCCC
Q 046966            3 VLIETS-----LGDIVIDLFVDKCPRTTNNFLQHCKN--------K---YYNGCLFHNIHKDFIAQTGDPT-GTGTGGRS   65 (299)
Q Consensus         3 v~~~T~-----~G~i~ieL~~~~~P~~~~nF~~l~~~--------~---~y~~~~f~ri~~~~~iq~G~~~-~~~~~~~~   65 (299)
                      |.|+|+     .|+|+||||++.||+||+||+.||++        |   +|+|+.||||+|+|||||||++ ++|+||.+
T Consensus        18 v~~~~~~~~~~~G~i~~~l~~~~~P~t~~nf~~l~~~~~~~~~~~g~~~~y~~~~fhrv~~~f~~q~Gd~~~~~g~g~~~   97 (370)
T 1ihg_A           18 VFFDVDIGGERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGES   97 (370)
T ss_dssp             EEEEEEETTEEEEEEEEEECTTTCHHHHHHHHHHHHCTTCBCTTTSSBSCCTTCBEEEEETTTEEEECCTTTSSSSCCCB
T ss_pred             EEEEEEECCEecccEEEEEcCCCCchHHHHHHHHcCCCcCcCccCCCcceeCCcEeEEEECCcEEECCCCCCCCCCCCCC
Confidence            677776     89999999999999999999999998        6   6999999999999999999988 77999999


Q ss_pred             CCCCcccccccccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCc
Q 046966           66 VYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPP  145 (299)
Q Consensus        66 ~~~~~~~~~e~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~  145 (299)
                      +|+.. |++| ...++|+.+|+||||+.+||+++||||||+.+ .+|||++|+|||+|++||+||++|+..+++. ++|.
T Consensus        98 ~~~~~-~~~e-~~~~~~~~~g~l~ma~~~~~~~~sqffi~~~~-~~~ld~~~~vfG~v~~g~~v~~~i~~~~~~~-~~P~  173 (370)
T 1ihg_A           98 IYGEK-FEDE-NFHYKHDKEGLLSMANAGSNTNGSQFFITTVP-TPHLDGKHVVFGQVIKGMGVAKILENVEVKG-EKPA  173 (370)
T ss_dssp             TTBSC-BCCC-CCCBCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCEET-TEES
T ss_pred             CCCCC-cCCC-cCCcCCCCCeEEEEeeCCCCCCCceEEEeCCC-CcccCCCceEEEEEecCHHHHHHHHcCCCCC-Cccc
Confidence            99876 6888 56899999999999999999999999999998 6999999999999999999999999998876 8999


Q ss_pred             eeEEEEEEEEECC
Q 046966          146 QQIIIKQTYVLYP  158 (299)
Q Consensus       146 ~~v~I~~~~v~~p  158 (299)
                      .+|+|.+|+++..
T Consensus       174 ~~v~I~~~g~l~~  186 (370)
T 1ihg_A          174 KLCVIAECGELKE  186 (370)
T ss_dssp             SCEEEEEEEEECT
T ss_pred             eeEEEEEEEEecc
Confidence            9999999999973

>3rfy_A Peptidyl-prolyl CIS-trans isomerase CYP38, chloro; cyclophilin, peptidyl prolyl isomerase, ppiase, TLP,; 2.39A {Arabidopsis thaliana}

Probab=100.00  E-value=5.1e-38  Score=279.46  Aligned_cols=143  Identities=25%  Similarity=0.391  Sum_probs=122.3

Q ss_pred             EEEEEEc--------ceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCC-----------
Q 046966            2 SVLIETS--------LGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTG-----------   62 (299)
Q Consensus         2 ~v~~~T~--------~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~-----------   62 (299)
                      +|.|+|+        .|+|+|+||++.||+||+||++||+.+||+|+.|||| ++|||||||+.++|.|           
T Consensus       172 ~V~m~t~~~~~~~~~~G~I~IeL~~d~AP~Tv~NFl~L~~~GfYdGt~FHRV-~gFmIQgGDp~g~G~G~~~~~~g~~~~  250 (369)
T 3rfy_A          172 SVDMKVKIKDNPNIEDCVFRIVLDGYNAPVTAGNFVDLVERHFYDGMEIQRS-DGFVVQTGDPEGPAEGFIDPSTEKTRT  250 (369)
T ss_dssp             EEEEEEECCSCSSCSEEEEEEEEETTTCHHHHHHHHHHHHTTTTTTEECEEE-EEEEECCCCCCCCCSCCCSCCCCCCCS
T ss_pred             EEEEEEeccCCCcccceEEEEEEeCCCCcHHHHHHHHHhhcCCcCCCeeeee-CCeeEecCCCCCCCCCccCcccCcCcc
Confidence            5778776        9999999999999999999999999999999999999 9999999999887665           


Q ss_pred             ----------CCCCCCCccccccc----ccCCCCCCceEEEEEcC--CCCCCcceEEEEecC------CCCCCCCCceEE
Q 046966           63 ----------GRSVYEDRFFVDEI----RADLKHDKVGTVGMASA--GRDLNASQFYITLRD------NLHYLDEKHTIF  120 (299)
Q Consensus        63 ----------~~~~~~~~~~~~e~----~~~~~~~~~G~l~~~~~--~~~~~~s~FfI~~~~------~~~~ld~~~~vf  120 (299)
                                +.++|+.. +++|.    .+.++|+.+|+||||+.  +||+++|||||++.+      .++|||++|+||
T Consensus       251 iP~E~~~~G~g~piyg~~-fedegf~~~~~~L~h~~~G~LsMAns~~gPnSngSQFFItl~d~~L~~~~~~~LDgkytVF  329 (369)
T 3rfy_A          251 VPLEIMVTGEKTPFYGST-LEELGLYKAQVVIPFNAFGTMAMAREEFENDSGSSQVFWLLKESELTPSNSNILDGRYAVF  329 (369)
T ss_dssp             SSSSSCSSSSCCSCCCSS-TGGGTEEEEEEEECCCCCCCCCCSSCCCCCCCSSCCCCCCCEEEEECSCCCSSSCSCEEEE
T ss_pred             cCccccccCCCCCcCCCc-cccccccccccccccCCCceEEEeecCCCCCCccceEEEEecccccCCCCCcccCCCeeEE
Confidence                      34555544 35542    45788999999999998  899999999999952      379999999999


Q ss_pred             EEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEEC
Q 046966          121 GEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY  157 (299)
Q Consensus       121 G~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~~  157 (299)
                      |+|++||+||++|++..           .|.++.|+.
T Consensus       330 G~VveGmdVVdkI~~GD-----------~I~sv~I~~  355 (369)
T 3rfy_A          330 GYVTDNEDFLADLKVGD-----------VIESIQVVS  355 (369)
T ss_dssp             EEEEESTTGGGGCCTTC-----------EEEEEEEEE
T ss_pred             EEEecCHHHHHHHhCCC-----------ceEEEEEec
Confidence            99999999999997642           267777765

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.86  E-value=4.2e-21  Score=141.99  Aligned_cols=82  Identities=28%  Similarity=0.448  Sum_probs=79.3

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ..+++|||+|||+++++++|+++|++||.|.++++++++.+|+++|||||+|.+.++|++|++.|||..++|++|+|++|
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~A   96 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA   96 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CC
Q 046966          289 QS  290 (299)
Q Consensus       289 ~~  290 (299)
                      +|
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            87

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.84  E-value=2.2e-20  Score=140.74  Aligned_cols=85  Identities=19%  Similarity=0.187  Sum_probs=81.2

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .++.++|||+|||+++++++|+++|++||.|.+++|++++.+++++|||||+|.+.++|++|++.|||..++|+.|+|.+
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            45688999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCcc
Q 046966          288 SQSVS  292 (299)
Q Consensus       288 a~~~~  292 (299)
                      +....
T Consensus        83 a~~~~   87 (110)
T 3s8s_A           83 DIKGQ   87 (110)
T ss_dssp             CSTTH
T ss_pred             CCCCc
Confidence            98654

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0

Probab=99.81  E-value=2.4e-19  Score=127.86  Aligned_cols=82  Identities=27%  Similarity=0.464  Sum_probs=78.8

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      +++|||+|||+++++++|+++|++||.|.++.++.++.+++++|||||+|.+.++|++|+..|||..++|+.|+|+++++
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            36899999999999999999999999999999999988999999999999999999999999999999999999999998


Q ss_pred             cc
Q 046966          291 VS  292 (299)
Q Consensus       291 ~~  292 (299)
                      +.
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.81  E-value=1.7e-20  Score=136.53  Aligned_cols=84  Identities=19%  Similarity=0.352  Sum_probs=78.0

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCC-CeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhC-CceeCCeEEEEEec
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFG-TVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMN-NALIDDRRICVDFS  288 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G-~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~-~~~i~g~~l~v~~a  288 (299)
                      +.+|||+|||+++++++|+++|++|| .|.++++++++.+|+++|||||+|.+.++|++|++.|+ +..++|++|+|++|
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 79999999999999999999999999999999998874 56799999999999


Q ss_pred             CCcccc
Q 046966          289 QSVSKI  294 (299)
Q Consensus       289 ~~~~~~  294 (299)
                      +++++.
T Consensus        81 ~~~~~~   86 (91)
T 2lxi_A           81 DPKPKI   86 (91)
T ss_dssp             CSCCCC
T ss_pred             CCCCCC
Confidence            988654

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}

Probab=99.81  E-value=2.6e-19  Score=128.88  Aligned_cols=83  Identities=25%  Similarity=0.440  Sum_probs=77.4

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ++.++|||+|||+++++++|+++|++||.|.++.++.++.++.++|||||+|.+.++|++|++.||+..++|+.|+|+++
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            46789999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCc
Q 046966          289 QSV  291 (299)
Q Consensus       289 ~~~  291 (299)
                      +++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            875

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=4.9e-19  Score=131.71  Aligned_cols=88  Identities=23%  Similarity=0.381  Sum_probs=82.8

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ...+.++|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|+..||+..++|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            34568999999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             ecCCcccc
Q 046966          287 FSQSVSKI  294 (299)
Q Consensus       287 ~a~~~~~~  294 (299)
                      +++++.+.
T Consensus        91 ~a~~~~~~   98 (103)
T 2cq0_A           91 WAKPSTNS   98 (103)
T ss_dssp             ESSCCCCS
T ss_pred             ECCCCCCC
Confidence            99987643

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.80  E-value=4e-19  Score=130.50  Aligned_cols=85  Identities=24%  Similarity=0.383  Sum_probs=81.1

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      |+++|||+|||+++++++|+++|++||.|.+++++.++.+|.++|||||+|.+.++|.+|++.|||..++|+.|+|++++
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            46899999999999999999999999999999999998899999999999999999999999999999999999999999


Q ss_pred             Ccccc
Q 046966          290 SVSKI  294 (299)
Q Consensus       290 ~~~~~  294 (299)
                      ++...
T Consensus        81 ~~~~~   85 (96)
T 2x1f_A           81 NSDIS   85 (96)
T ss_dssp             CSSGG
T ss_pred             CCCCC
Confidence            87654

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=7.6e-19  Score=128.57  Aligned_cols=85  Identities=31%  Similarity=0.416  Sum_probs=80.6

Q ss_pred             CCCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          206 DVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       206 ~~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      ...++.++|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++.||+..++|+.|+|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   89 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   89 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34567889999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EecCC
Q 046966          286 DFSQS  290 (299)
Q Consensus       286 ~~a~~  290 (299)
                      +++++
T Consensus        90 ~~a~~   94 (95)
T 2cqc_A           90 SGPSS   94 (95)
T ss_dssp             ECCSC
T ss_pred             EecCC
Confidence            99875

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.80  E-value=1.5e-19  Score=132.35  Aligned_cols=82  Identities=21%  Similarity=0.354  Sum_probs=76.3

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCC--eEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCc----eeCCeE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGT--VVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNA----LIDDRR  282 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~--i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~----~i~g~~  282 (299)
                      ..-.+|||+|||+.+++++|+++|++||.  +.+|++++|+.+|+++|||||+|.+.++|++|++.||+.    .++||+
T Consensus         7 ~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~   86 (95)
T 2lkz_A            7 HHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKT   86 (95)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEE
T ss_pred             CccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEE
Confidence            34578999999999999999999999995  568999999999999999999999999999999999996    599999


Q ss_pred             EEEEecCC
Q 046966          283 ICVDFSQS  290 (299)
Q Consensus       283 l~v~~a~~  290 (299)
                      |.|+||++
T Consensus        87 i~V~~Aks   94 (95)
T 2lkz_A           87 IGVDFAKS   94 (95)
T ss_dssp             EEEEECCC
T ss_pred             EEEEEccC
Confidence            99999986

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.80  E-value=1.2e-18  Score=132.27  Aligned_cols=88  Identities=26%  Similarity=0.441  Sum_probs=82.5

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ...+.++|||+|||+.+++++|+++|++||.|..++++.++.++.++|||||+|.+.++|++|++.||+..++|+.|+|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34568899999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             ecCCcccc
Q 046966          287 FSQSVSKI  294 (299)
Q Consensus       287 ~a~~~~~~  294 (299)
                      +++++...
T Consensus        91 ~a~~~~~~   98 (115)
T 2dgo_A           91 WATRKPPA   98 (115)
T ss_dssp             ESSCCCCC
T ss_pred             EccCCCCC
Confidence            99977543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=1.2e-18  Score=128.94  Aligned_cols=86  Identities=27%  Similarity=0.358  Sum_probs=81.1

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ...+.++|||+|||+++++++|+++|++||.|..+.++.++ +++++|||||+|.+.++|++|++.||+..++|+.|+|.
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   91 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVA   91 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34568899999999999999999999999999999999997 99999999999999999999999999999999999999


Q ss_pred             ecCCccc
Q 046966          287 FSQSVSK  293 (299)
Q Consensus       287 ~a~~~~~  293 (299)
                      +++++.+
T Consensus        92 ~a~~~~~   98 (100)
T 2do4_A           92 ISNSGPS   98 (100)
T ss_dssp             ECCCCSC
T ss_pred             ECCCCCC
Confidence            9998754

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=4.3e-19  Score=132.46  Aligned_cols=89  Identities=26%  Similarity=0.328  Sum_probs=83.4

Q ss_pred             CCCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          206 DVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       206 ~~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      ....+.++|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++.||+..++|+.|+|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   89 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV   89 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            33457899999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EecCCcccc
Q 046966          286 DFSQSVSKI  294 (299)
Q Consensus       286 ~~a~~~~~~  294 (299)
                      .+++++++.
T Consensus        90 ~~a~~~~~~   98 (105)
T 1x5u_A           90 NKASAHNKN   98 (105)
T ss_dssp             EETTTTSCC
T ss_pred             EECCCCCcC
Confidence            999987654

>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=5.4e-19  Score=126.62  Aligned_cols=82  Identities=33%  Similarity=0.476  Sum_probs=78.5

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .++.++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.|||..++|+.|+|++
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            35689999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cC
Q 046966          288 SQ  289 (299)
Q Consensus       288 a~  289 (299)
                      |+
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            85

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=7.8e-19  Score=129.64  Aligned_cols=86  Identities=20%  Similarity=0.313  Sum_probs=80.9

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++ |++..++|+.|.|.+
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            4567999999999999999999999999999999999998899999999999999999999998 999999999999999


Q ss_pred             cCCcccc
Q 046966          288 SQSVSKI  294 (299)
Q Consensus       288 a~~~~~~  294 (299)
                      ++++...
T Consensus        86 a~~~~~~   92 (99)
T 2dgs_A           86 AEPRDSK   92 (99)
T ss_dssp             CCCCCCC
T ss_pred             CCCCccc
Confidence            9987543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.79  E-value=7.5e-19  Score=129.76  Aligned_cols=85  Identities=21%  Similarity=0.257  Sum_probs=80.1

Q ss_pred             CCCCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEE--------EEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCc
Q 046966          205 ADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVS--------AEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNA  276 (299)
Q Consensus       205 ~~~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~--------~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~  276 (299)
                      ....++.++|||+|||+++++++|+++|++||.|..        ++++.++.+|+++|||||+|.+.++|++|++.|||.
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        999999889999999999999999999999999999


Q ss_pred             eeCCeEEEEEecC
Q 046966          277 LIDDRRICVDFSQ  289 (299)
Q Consensus       277 ~i~g~~l~v~~a~  289 (299)
                      .++|+.|+|++|+
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            9999999999985

>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=99.79  E-value=8.7e-19  Score=132.09  Aligned_cols=88  Identities=22%  Similarity=0.314  Sum_probs=82.8

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhC------CceeCC
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMN------NALIDD  280 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~------~~~i~g  280 (299)
                      ...+.++|||+|||+++++++|+++|++||.|..|+++.++.++.++|||||+|.+.++|.+|+..||      +..++|
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            34568899999999999999999999999999999999999899999999999999999999999999      999999


Q ss_pred             eEEEEEecCCcccc
Q 046966          281 RRICVDFSQSVSKI  294 (299)
Q Consensus       281 ~~l~v~~a~~~~~~  294 (299)
                      +.|+|+++.++.+.
T Consensus        91 ~~l~v~~a~~~~~~  104 (111)
T 1x4h_A           91 RQLKVDLAVTRDEA  104 (111)
T ss_dssp             CEEEEECCCCCCCC
T ss_pred             EEEEEEECCCCccC
Confidence            99999999987644

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=5.2e-19  Score=131.29  Aligned_cols=87  Identities=31%  Similarity=0.440  Sum_probs=82.3

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+.+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..++|+.|+|.+
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            45689999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cCCcccc
Q 046966          288 SQSVSKI  294 (299)
Q Consensus       288 a~~~~~~  294 (299)
                      ++++.+.
T Consensus        89 a~~~~~~   95 (102)
T 2cqb_A           89 AKPMRIK   95 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            9987543

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.79  E-value=7e-19  Score=129.84  Aligned_cols=86  Identities=26%  Similarity=0.325  Sum_probs=81.6

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .+.++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..+.|+.|+|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   85 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            46789999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCcccc
Q 046966          289 QSVSKI  294 (299)
Q Consensus       289 ~~~~~~  294 (299)
                      +++...
T Consensus        86 ~~~~~~   91 (99)
T 1whw_A           86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCccc
Confidence            987643

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.79  E-value=7.2e-19  Score=128.72  Aligned_cols=85  Identities=24%  Similarity=0.359  Sum_probs=81.2

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ++.++|||+|||+.+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..++|+.|+|+++
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            46799999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCccc
Q 046966          289 QSVSK  293 (299)
Q Consensus       289 ~~~~~  293 (299)
                      +++..
T Consensus        83 ~~~~~   87 (95)
T 2dnz_A           83 TERLD   87 (95)
T ss_dssp             SCCCC
T ss_pred             ccccC
Confidence            98754

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=8.5e-19  Score=130.66  Aligned_cols=87  Identities=18%  Similarity=0.313  Sum_probs=80.7

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCC-CCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRT-GESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~-g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ..+.++|||+|||+.+++++|+++|++|| |..+.++.++.+ ++++|||||+|.+.++|++|+ .||+..+.|+.|.|.
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            45679999999999999999999999999 999999999887 999999999999999999999 999999999999999


Q ss_pred             ecCCcccccc
Q 046966          287 FSQSVSKIWK  296 (299)
Q Consensus       287 ~a~~~~~~~~  296 (299)
                      +++++....+
T Consensus        90 ~a~~~~~~~~   99 (104)
T 1wi8_A           90 VADQAQDKDS   99 (104)
T ss_dssp             ECCCCCCCCC
T ss_pred             EccCCCCCCC
Confidence            9998765433

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A

Probab=99.79  E-value=9e-19  Score=132.95  Aligned_cols=87  Identities=31%  Similarity=0.486  Sum_probs=82.0

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .++.++|||+|||+++++++|+++|++||.|..++++.++.+++++|||||+|.+.++|++|++.||+..++|+.|+|++
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            35678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cCCcccc
Q 046966          288 SQSVSKI  294 (299)
Q Consensus       288 a~~~~~~  294 (299)
                      ++++.+.
T Consensus       102 a~~~~~~  108 (115)
T 2cpz_A          102 KRSKNDS  108 (115)
T ss_dssp             CCCSCCC
T ss_pred             cCCCCcC
Confidence            9987543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.79  E-value=8.3e-20  Score=135.24  Aligned_cols=85  Identities=21%  Similarity=0.260  Sum_probs=81.1

Q ss_pred             CCceEEEEcCCC------CCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCC-eE
Q 046966          210 PDNVLFVCQLNP------VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDD-RR  282 (299)
Q Consensus       210 ~~~~v~v~nL~~------~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g-~~  282 (299)
                      .+++|||+|||+      ++++++|+++|++||.|.++++++++.||+++|||||+|.+.++|++|++.|||..+.| +.
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            468999999999      99999999999999999999999999999999999999999999999999999999999 99


Q ss_pred             EEEEecCCcccc
Q 046966          283 ICVDFSQSVSKI  294 (299)
Q Consensus       283 l~v~~a~~~~~~  294 (299)
                      |+|.++.++.+.
T Consensus        85 l~V~~a~~~~~~   96 (100)
T 3ns6_A           85 LFLYTMKDVERY   96 (100)
T ss_dssp             CEEEESHHHHHH
T ss_pred             EEEEECchhhhh
Confidence            999999987654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=7.7e-19  Score=131.30  Aligned_cols=85  Identities=25%  Similarity=0.369  Sum_probs=80.7

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|+..|||..++|+.|.|++
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            34578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCcc
Q 046966          288 SQSVS  292 (299)
Q Consensus       288 a~~~~  292 (299)
                      ++++.
T Consensus       100 a~~~~  104 (106)
T 1p27_B          100 CFVRG  104 (106)
T ss_dssp             SEESS
T ss_pred             ecCCC
Confidence            98764

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=5.3e-19  Score=131.49  Aligned_cols=86  Identities=26%  Similarity=0.310  Sum_probs=81.5

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++.||+..++|+.|.|.+
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            45679999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cCCccc
Q 046966          288 SQSVSK  293 (299)
Q Consensus       288 a~~~~~  293 (299)
                      +++..+
T Consensus        90 a~~~~~   95 (103)
T 2dnm_A           90 ARYGRR   95 (103)
T ss_dssp             CSSCCS
T ss_pred             CCcCCC
Confidence            997654

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=1.2e-18  Score=127.21  Aligned_cols=84  Identities=26%  Similarity=0.404  Sum_probs=79.4

Q ss_pred             CCCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          206 DVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       206 ~~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      ...++.++|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++.||+..++|+.|+|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   90 (94)
T 2e5h_A           11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKA   90 (94)
T ss_dssp             SCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            34467889999999999999999999999999999999999888999999999999999999999999999999999999


Q ss_pred             EecC
Q 046966          286 DFSQ  289 (299)
Q Consensus       286 ~~a~  289 (299)
                      ++|+
T Consensus        91 ~~ak   94 (94)
T 2e5h_A           91 SIAI   94 (94)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9985

>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=99.78  E-value=1.9e-18  Score=128.89  Aligned_cols=86  Identities=26%  Similarity=0.394  Sum_probs=80.5

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCC---eEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDD---RRIC  284 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g---~~l~  284 (299)
                      .++.++|||+|||+++++++|+++|++||.|..+.++.++ ++.++|||||+|.+.++|++|++.||+..+.|   +.|+
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            4568999999999999999999999999999999999996 89999999999999999999999999999998   9999


Q ss_pred             EEecCCcccc
Q 046966          285 VDFSQSVSKI  294 (299)
Q Consensus       285 v~~a~~~~~~  294 (299)
                      |.+++++...
T Consensus        91 V~~a~~~~~~  100 (105)
T 2dnh_A           91 VKFADTDKES  100 (105)
T ss_dssp             EEESCSSCCC
T ss_pred             EEECccCccc
Confidence            9999987543

>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=4.3e-19  Score=130.18  Aligned_cols=86  Identities=29%  Similarity=0.478  Sum_probs=81.3

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEE-EEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSA-EILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~-~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .+.++|||+|||+++++++|+++|++||.|..+ +++.++.++.++|||||+|.+.++|++|++.||+..++|+.|+|++
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            467999999999999999999999999999999 9999988999999999999999999999999999999999999999


Q ss_pred             cCCcccc
Q 046966          288 SQSVSKI  294 (299)
Q Consensus       288 a~~~~~~  294 (299)
                      ++++.+.
T Consensus        83 a~~~~~~   89 (96)
T 1x5t_A           83 AFKKDSK   89 (96)
T ss_dssp             SCCCCCC
T ss_pred             ecccCCC
Confidence            9987543

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=1.9e-18  Score=128.43  Aligned_cols=87  Identities=28%  Similarity=0.410  Sum_probs=81.0

Q ss_pred             CCCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          206 DVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       206 ~~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      ....+.++|||+|||+.+++++|+++|++||.|..+.++.+  ++.++|||||+|.+.++|++|++.||+..+.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2d9p_A           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV   87 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            33457899999999999999999999999999999999988  8999999999999999999999999999999999999


Q ss_pred             EecCCcccc
Q 046966          286 DFSQSVSKI  294 (299)
Q Consensus       286 ~~a~~~~~~  294 (299)
                      .+++++.+.
T Consensus        88 ~~a~~~~~~   96 (103)
T 2d9p_A           88 ALAQRKEER   96 (103)
T ss_dssp             EECSSCCCC
T ss_pred             EEecccccC
Confidence            999987644

>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=99.78  E-value=1.1e-18  Score=132.61  Aligned_cols=81  Identities=33%  Similarity=0.514  Sum_probs=75.4

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ...+|||+|||+++++++|+++|++||.|.+|+|+.++  +.++|||||+|.+.++|++|++.|++..++|+.|+|.++.
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~   81 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   81 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESS
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            35789999999999999999999999999999999984  4589999999999999999999999999999999999998


Q ss_pred             Ccc
Q 046966          290 SVS  292 (299)
Q Consensus       290 ~~~  292 (299)
                      ++.
T Consensus        82 ~~~   84 (115)
T 4f25_A           82 SRK   84 (115)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            764

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.78  E-value=1.1e-18  Score=130.92  Aligned_cols=85  Identities=25%  Similarity=0.368  Sum_probs=81.0

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .++.++|||+|||+.+++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|.+|++.|+|..++|+.|+|++
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            45678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cCCcc
Q 046966          288 SQSVS  292 (299)
Q Consensus       288 a~~~~  292 (299)
                      ++++.
T Consensus       103 a~~k~  107 (108)
T 2jrs_A          103 VTERT  107 (108)
T ss_dssp             SCSSC
T ss_pred             cccCC
Confidence            98764

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.78  E-value=1.4e-19  Score=131.29  Aligned_cols=82  Identities=17%  Similarity=0.248  Sum_probs=72.9

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCC--CeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFG--TVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G--~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      .+|||+|||+++++++|+++|++||  .|.+++++.++.+|+++|||||+|.+.++|++|++.|||..++|+.|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            5799999999999999999999999  99999999999999999999999999999999999999999999999999999


Q ss_pred             Cccc
Q 046966          290 SVSK  293 (299)
Q Consensus       290 ~~~~  293 (299)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7653

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.78  E-value=2.9e-18  Score=127.49  Aligned_cols=84  Identities=25%  Similarity=0.443  Sum_probs=79.3

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+++++++|+++|++|| |..++++.++.+++++|||||+|.+.++|++|+ .||+..++|+.|+|.+
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 999999999889999999999999999999999 8999999999999999


Q ss_pred             cCCccc
Q 046966          288 SQSVSK  293 (299)
Q Consensus       288 a~~~~~  293 (299)
                      ++++.+
T Consensus        90 a~~~~~   95 (103)
T 2dng_A           90 AEGRKQ   95 (103)
T ss_dssp             CCCCCC
T ss_pred             ecCCCC
Confidence            998754

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=8.1e-19  Score=130.22  Aligned_cols=87  Identities=29%  Similarity=0.454  Sum_probs=82.1

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|++.||+..++|+.|+|.+
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            45689999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cCCcccc
Q 046966          288 SQSVSKI  294 (299)
Q Consensus       288 a~~~~~~  294 (299)
                      ++++.+.
T Consensus        89 a~~~~~~   95 (102)
T 1x5s_A           89 AGKSSDN   95 (102)
T ss_dssp             EECCCCC
T ss_pred             CCCCCCC
Confidence            9987543

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=1.4e-18  Score=128.02  Aligned_cols=85  Identities=27%  Similarity=0.422  Sum_probs=79.7

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCC---CCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYR---TGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~---~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      .+.++|||+|||+++++++|+++|++||.|..+.++.++.   ++.++|||||+|.+.++|++|++.||+..++|+.|.|
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            4679999999999999999999999999999999998866   6699999999999999999999999999999999999


Q ss_pred             EecCCccc
Q 046966          286 DFSQSVSK  293 (299)
Q Consensus       286 ~~a~~~~~  293 (299)
                      ++++++.+
T Consensus        83 ~~a~~~~~   90 (98)
T 2cpf_A           83 RISERATK   90 (98)
T ss_dssp             ECSSCSSC
T ss_pred             EEccCCCC
Confidence            99998754

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=1.7e-18  Score=129.60  Aligned_cols=88  Identities=17%  Similarity=0.406  Sum_probs=82.1

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeec-CCCCCeeeEEEEEecCHHHHHHHHHHh-CCceeCCeEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRD-YRTGESLCYAFVEFEKREACEQAYFKM-NNALIDDRRIC  284 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~-~~~g~~~g~afv~f~~~~~a~~al~~l-~~~~i~g~~l~  284 (299)
                      ...+.++|||+|||+.+++++|+++|++||.|..++++.+ +.++.++|||||+|.+.++|++|+..| |+..+.|+.|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            3456899999999999999999999999999999999998 779999999999999999999999999 99999999999


Q ss_pred             EEecCCcccc
Q 046966          285 VDFSQSVSKI  294 (299)
Q Consensus       285 v~~a~~~~~~  294 (299)
                      |.+++++...
T Consensus        91 v~~a~~~~~~  100 (107)
T 2cph_A           91 LEWADSEVTV  100 (107)
T ss_dssp             EEECCCCCCC
T ss_pred             EEeCCCCCCC
Confidence            9999987543

>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=131.01  Aligned_cols=85  Identities=26%  Similarity=0.370  Sum_probs=80.7

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
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            35678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cCCcc
Q 046966          288 SQSVS  292 (299)
Q Consensus       288 a~~~~  292 (299)
                      ++++.
T Consensus       103 a~~~~  107 (110)
T 1oo0_B          103 CFVKG  107 (110)
T ss_dssp             SEESS
T ss_pred             cccCC
Confidence            98764

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.3e-18  Score=128.44  Aligned_cols=85  Identities=22%  Similarity=0.394  Sum_probs=80.8

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeE-EEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeE----
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVV-SAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRR----  282 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~-~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~----  282 (299)
                      ..+.++|||+|||+++++++|+++|++||.|. .++++.++.+++++|||||+|.+.++|++|++.||+..+.|+.    
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            45689999999999999999999999999999 9999999889999999999999999999999999999999999    


Q ss_pred             EEEEecCCcc
Q 046966          283 ICVDFSQSVS  292 (299)
Q Consensus       283 l~v~~a~~~~  292 (299)
                      |+|.++++..
T Consensus        86 l~v~~a~~~~   95 (99)
T 2div_A           86 FKLNYATYSG   95 (99)
T ss_dssp             CCEEETTCCS
T ss_pred             EEEeecCCCC
Confidence            9999998764

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D*

Probab=99.77  E-value=1.1e-18  Score=134.63  Aligned_cols=89  Identities=24%  Similarity=0.350  Sum_probs=82.3

Q ss_pred             CCCCCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 046966          204 DADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRI  283 (299)
Q Consensus       204 ~~~~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l  283 (299)
                      ......+.++|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++.||+..++|+.|
T Consensus        15 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   94 (126)
T 3ex7_B           15 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPI   94 (126)
T ss_dssp             CBCCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEE
Confidence            33444568899999999999999999999999999999999998899999999999999999999999999999999999


Q ss_pred             EEEecCCcc
Q 046966          284 CVDFSQSVS  292 (299)
Q Consensus       284 ~v~~a~~~~  292 (299)
                      .|+++.++.
T Consensus        95 ~v~~a~~~~  103 (126)
T 3ex7_B           95 SVDWCFVRG  103 (126)
T ss_dssp             EEEESEESS
T ss_pred             EEEEecCCC
Confidence            999998654

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.77  E-value=1.5e-18  Score=129.71  Aligned_cols=87  Identities=25%  Similarity=0.340  Sum_probs=81.5

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCcee---CCeEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALI---DDRRIC  284 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i---~g~~l~  284 (299)
                      ..+.++|||+|||+++++++|+++|++||.|..++++.++.+++++|||||+|.+.++|.+|++.||+..+   .|+.|.
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            45678999999999999999999999999999999999988999999999999999999999999999988   899999


Q ss_pred             EEecCCcccc
Q 046966          285 VDFSQSVSKI  294 (299)
Q Consensus       285 v~~a~~~~~~  294 (299)
                      |.+++++.+.
T Consensus        90 v~~a~~~~~~   99 (106)
T 2dgp_A           90 VKPADSESRG   99 (106)
T ss_dssp             EEECCCCSCC
T ss_pred             EEECCccccc
Confidence            9999987643

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=2.5e-18  Score=129.99  Aligned_cols=88  Identities=20%  Similarity=0.249  Sum_probs=82.1

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeE--------EEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCcee
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVV--------SAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALI  278 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~--------~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i  278 (299)
                      ...+.++|||+|||+++++++|+++|++||.|.        .++++.++.+++++|||||+|.+.++|++|++.||+..+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            345689999999999999999999999999998        699999988999999999999999999999999999999


Q ss_pred             CCeEEEEEecCCcccc
Q 046966          279 DDRRICVDFSQSVSKI  294 (299)
Q Consensus       279 ~g~~l~v~~a~~~~~~  294 (299)
                      .|+.|+|++++++...
T Consensus        91 ~g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           91 QGSKLKVSLARKKPPM  106 (113)
T ss_dssp             TTEECEEECSSCCCCS
T ss_pred             CCCEEEEEECCCCCCC
Confidence            9999999999987543

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.76  E-value=2.3e-18  Score=124.12  Aligned_cols=83  Identities=22%  Similarity=0.320  Sum_probs=78.1

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCC-eeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGE-SLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~-~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ..++|||+|||+++++++|+++|++||.|..+.++.++.++. ++|||||+|.+.++|++|++.|||..++|+.|+|+++
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            468999999999999999999999999999999999877666 8999999999999999999999999999999999999


Q ss_pred             CCcc
Q 046966          289 QSVS  292 (299)
Q Consensus       289 ~~~~  292 (299)
                      .+.+
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8764

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.76  E-value=5.5e-18  Score=121.96  Aligned_cols=80  Identities=28%  Similarity=0.354  Sum_probs=75.3

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+++++++|+++|++||.|..++++.++.+++++|||||+|.+.++|++|++ +++..++|+.|.|++
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            4568999999999999999999999999999999999998899999999999999999999995 488899999999987


Q ss_pred             c
Q 046966          288 S  288 (299)
Q Consensus       288 a  288 (299)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            6

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.76  E-value=2e-18  Score=131.29  Aligned_cols=84  Identities=25%  Similarity=0.383  Sum_probs=79.5

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .+.++|||+|||+++++++|+++|++||.|..+.++.++ +++++|||||+|.+.++|++|++.|||..++|+.|+|+++
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            457899999999999999999999999999999999997 9999999999999999999999999999999999999999


Q ss_pred             CCccc
Q 046966          289 QSVSK  293 (299)
Q Consensus       289 ~~~~~  293 (299)
                      +++..
T Consensus        84 ~~~~~   88 (116)
T 2fy1_A           84 KKPSF   88 (116)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            87653

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=1.8e-18  Score=128.80  Aligned_cols=86  Identities=22%  Similarity=0.363  Sum_probs=80.7

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhccc-CCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCce-eCCeEEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQ-FGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNAL-IDDRRICV  285 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~-~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~-i~g~~l~v  285 (299)
                      ..+.++|||+|||+++++++|+++|++ ||.|..++++.++ ++.++|||||+|.+.++|.+|++.|++.. ++|+.|.|
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            356799999999999999999999999 9999999999997 99999999999999999999999999999 99999999


Q ss_pred             EecCCcccc
Q 046966          286 DFSQSVSKI  294 (299)
Q Consensus       286 ~~a~~~~~~  294 (299)
                      .++.++...
T Consensus        85 ~~a~~~~~~   93 (104)
T 2dhg_A           85 SVAIPKASR   93 (104)
T ss_dssp             CBCCCCCSC
T ss_pred             EEccCCCcC
Confidence            999876543

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X

Probab=99.76  E-value=5.1e-18  Score=135.83  Aligned_cols=85  Identities=25%  Similarity=0.337  Sum_probs=81.0

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .+.++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|++.||+..|.|+.|+|+++
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            46799999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             CCccc
Q 046966          289 QSVSK  293 (299)
Q Consensus       289 ~~~~~  293 (299)
                      ++...
T Consensus       117 ~~~~~  121 (156)
T 1h2v_Z          117 AGFKE  121 (156)
T ss_dssp             SCCCT
T ss_pred             CCCCC
Confidence            87643

>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=99.76  E-value=1.1e-17  Score=124.36  Aligned_cols=87  Identities=26%  Similarity=0.337  Sum_probs=80.1

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+.+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|+.  +++.++|+.|.|++
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            4567899999999999999999999999999999999998899999999999999999999997  57899999999999


Q ss_pred             cCCcccccc
Q 046966          288 SQSVSKIWK  296 (299)
Q Consensus       288 a~~~~~~~~  296 (299)
                      +.++.....
T Consensus        90 a~~~~~~~~   98 (103)
T 2cqg_A           90 PNSKQSQDS   98 (103)
T ss_dssp             CCTTCCCCC
T ss_pred             cCCCCcCCC
Confidence            998765433

>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=5.1e-18  Score=127.00  Aligned_cols=82  Identities=28%  Similarity=0.408  Sum_probs=78.1

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+.+++++|+++|++||.|..+.++.++ +++++|||||+|.+.++|++|++.||+..++|+.|+|++
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            4568999999999999999999999999999999999997 999999999999999999999999999999999999999


Q ss_pred             cCC
Q 046966          288 SQS  290 (299)
Q Consensus       288 a~~  290 (299)
                      +.+
T Consensus       105 a~s  107 (107)
T 3ulh_A          105 VTS  107 (107)
T ss_dssp             ECC
T ss_pred             eCC
Confidence            864

>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=99.76  E-value=3.8e-18  Score=124.83  Aligned_cols=82  Identities=27%  Similarity=0.354  Sum_probs=77.4

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+.+++++|+++|++||.|..++++.++ +++++|||||+|.+.++|++|++.||+..++|+.|+|++
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 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            3467899999999999999999999999999999999996 499999999999999999999999999999999999999


Q ss_pred             cCC
Q 046966          288 SQS  290 (299)
Q Consensus       288 a~~  290 (299)
                      +++
T Consensus        92 a~~   94 (95)
T 2ywk_A           92 PSS   94 (95)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            875

>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=137.51  Aligned_cols=84  Identities=15%  Similarity=0.215  Sum_probs=78.5

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCC--CeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFG--TVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G--~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ...++|||+|||+++++++|+++|++||  .|.+++++.++.+|+++|||||+|.+.++|++|+..|||..|+|+.|.|.
T Consensus        53 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~  132 (156)
T 3n9u_C           53 NRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVR  132 (156)
T ss_dssp             ---CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEE
Confidence            3568999999999999999999999999  99999999999999999999999999999999999999999999999999


Q ss_pred             ecCCcc
Q 046966          287 FSQSVS  292 (299)
Q Consensus       287 ~a~~~~  292 (299)
                      ++.++.
T Consensus       133 ~a~~~~  138 (156)
T 3n9u_C          133 PATRQN  138 (156)
T ss_dssp             ECCHHH
T ss_pred             EcCCCc
Confidence            998753

>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=99.76  E-value=2.1e-18  Score=133.64  Aligned_cols=87  Identities=32%  Similarity=0.458  Sum_probs=82.1

Q ss_pred             CCCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          206 DVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       206 ~~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      ...++.++|||+|||+++++++|+++|++||.|..++++.++.+++++|||||+|.+.++|++|++.||+..|+|+.|+|
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            34567889999999999999999999999999999999999889999999999999999999999999999999999999


Q ss_pred             EecCCcc
Q 046966          286 DFSQSVS  292 (299)
Q Consensus       286 ~~a~~~~  292 (299)
                      +++++++
T Consensus       121 ~~a~~~~  127 (129)
T 2kxn_B          121 DFSITKR  127 (129)
T ss_dssp             SCCSSSS
T ss_pred             EEecCCC
Confidence            9998764

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=2.9e-18  Score=126.28  Aligned_cols=85  Identities=19%  Similarity=0.281  Sum_probs=79.5

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .+..++|||+|||+.+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..++|+.|+|++
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            45678999999999999999999999999999888888888999999999999999999999999999999999999999


Q ss_pred             cCCcc
Q 046966          288 SQSVS  292 (299)
Q Consensus       288 a~~~~  292 (299)
                      ++.+.
T Consensus        92 a~~~~   96 (98)
T 2cqp_A           92 GSGPS   96 (98)
T ss_dssp             SSCSS
T ss_pred             cCCCC
Confidence            98653

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.76  E-value=6e-18  Score=132.73  Aligned_cols=87  Identities=24%  Similarity=0.344  Sum_probs=82.0

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+++++++|+++|+.||.|.+++++.++.+++++|||||+|.+.++|.+|++.||+..+.|+.|+|.+
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  118 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cCCcccc
Q 046966          288 SQSVSKI  294 (299)
Q Consensus       288 a~~~~~~  294 (299)
                      ++++.+.
T Consensus       119 a~~~~~~  125 (139)
T 1u6f_A          119 AASGHQR  125 (139)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            9987543

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.76  E-value=4.5e-18  Score=122.85  Aligned_cols=80  Identities=23%  Similarity=0.380  Sum_probs=77.3

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      .++|||+|||+++++++|+++|++||.|..++++.++.+++++|||||+|.+.++|++|+ .||+..+.|+.|+|.++++
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            579999999999999999999999999999999999889999999999999999999999 9999999999999999987


Q ss_pred             c
Q 046966          291 V  291 (299)
Q Consensus       291 ~  291 (299)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            5

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.76  E-value=3.4e-18  Score=130.29  Aligned_cols=82  Identities=30%  Similarity=0.519  Sum_probs=77.7

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .++.++|||+|||+++++++|+++|++||.|..++++.++.+++++|||||+|.+.++|++|++.||+..++|+.|+|++
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            35678999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cC
Q 046966          288 SQ  289 (299)
Q Consensus       288 a~  289 (299)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            75

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=5.9e-18  Score=128.62  Aligned_cols=84  Identities=31%  Similarity=0.419  Sum_probs=79.2

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+++++++|+++|++||.|..++++.++.+++++|||||+|.+.++|++|++.|++ .+.|+.|+|++
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            45679999999999999999999999999999999999988999999999999999999999999998 89999999999


Q ss_pred             cCCcc
Q 046966          288 SQSVS  292 (299)
Q Consensus       288 a~~~~  292 (299)
                      +.+..
T Consensus        93 a~~~~   97 (116)
T 2cqd_A           93 AYLGA   97 (116)
T ss_dssp             STTTC
T ss_pred             cccCC
Confidence            97653

>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=99.76  E-value=9.7e-18  Score=124.61  Aligned_cols=85  Identities=22%  Similarity=0.311  Sum_probs=78.1

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+.+++++|+++|++||.|..|+++.++.  .++|||||+|.+.++|++|++.||+..+.|+.|+|.+
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            45679999999999999999999999999999999999853  3689999999999999999999999999999999999


Q ss_pred             cCCcccc
Q 046966          288 SQSVSKI  294 (299)
Q Consensus       288 a~~~~~~  294 (299)
                      ++++...
T Consensus        90 a~~~~~~   96 (103)
T 2cqi_A           90 ATTPSSQ   96 (103)
T ss_dssp             CCCTTCC
T ss_pred             CCCCccc
Confidence            9987543

>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=99.75  E-value=1.6e-17  Score=123.38  Aligned_cols=86  Identities=27%  Similarity=0.432  Sum_probs=78.9

Q ss_pred             CCCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          206 DVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       206 ~~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      ....+.++|||+|||+++++++|+++|++||.|..++++.++.  .++|||||+|.+.++|++|+..||+..++|+.|+|
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            3456689999999999999999999999999999999998853  38999999999999999999999999999999999


Q ss_pred             EecCCccc
Q 046966          286 DFSQSVSK  293 (299)
Q Consensus       286 ~~a~~~~~  293 (299)
                      .+++++..
T Consensus        88 ~~a~~~~~   95 (103)
T 2cq3_A           88 NNATARVM   95 (103)
T ss_dssp             EECCSSCC
T ss_pred             EEcccCCC
Confidence            99998753

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A

Probab=99.75  E-value=2.1e-18  Score=126.23  Aligned_cols=83  Identities=20%  Similarity=0.279  Sum_probs=76.4

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .++.++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..++|+.|+|.+
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            34578999999999999999999999999999888998888999999999999999999999999999999999999999


Q ss_pred             cCC
Q 046966          288 SQS  290 (299)
Q Consensus       288 a~~  290 (299)
                      +.+
T Consensus        92 a~s   94 (95)
T 2ek1_A           92 PSS   94 (95)
T ss_dssp             CC-
T ss_pred             ccC
Confidence            875

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=1e-17  Score=121.56  Aligned_cols=83  Identities=19%  Similarity=0.230  Sum_probs=78.1

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ....++|||+|||+++++++|+++|++| .|..++++.+ .+|+++|||||+|.+.++|++|++ ||+..++|+.|.|.+
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            4567899999999999999999999999 9999999999 799999999999999999999999 999999999999999


Q ss_pred             cCCccc
Q 046966          288 SQSVSK  293 (299)
Q Consensus       288 a~~~~~  293 (299)
                      ++++.+
T Consensus        84 a~~~~~   89 (91)
T 2dgw_A           84 EKSGPS   89 (91)
T ss_dssp             ESSCCC
T ss_pred             CCcCCC
Confidence            998753

>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=99.75  E-value=4.8e-18  Score=124.71  Aligned_cols=83  Identities=18%  Similarity=0.189  Sum_probs=76.7

Q ss_pred             CCCCceEEEEcCCCCCCHHHHH----HhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLH----VIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRI  283 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~----~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l  283 (299)
                      ....++|||+|||+++++++|+    ++|++||.|.+++++.++.+   +|||||+|.+.++|++|++.|||..++|+.|
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            3457899999999999999999    99999999999999988655   8899999999999999999999999999999


Q ss_pred             EEEecCCccc
Q 046966          284 CVDFSQSVSK  293 (299)
Q Consensus       284 ~v~~a~~~~~  293 (299)
                      +|++++++..
T Consensus        83 ~V~~a~~~~~   92 (96)
T 2dgx_A           83 LVSLATGASG   92 (96)
T ss_dssp             EEEECCCSSC
T ss_pred             EEEEcCCCCC
Confidence            9999997653

>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=99.75  E-value=1.1e-18  Score=129.86  Aligned_cols=84  Identities=29%  Similarity=0.402  Sum_probs=80.2

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      +.++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++.|||..++|+.|+|.++.
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            46899999999999999999999999999999999998899999999999999999999999999999999999999999


Q ss_pred             Cccc
Q 046966          290 SVSK  293 (299)
Q Consensus       290 ~~~~  293 (299)
                      ++..
T Consensus        87 ~~~~   90 (104)
T 1p1t_A           87 SEKN   90 (104)
T ss_dssp             CTTH
T ss_pred             Cccc
Confidence            8754

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.75  E-value=5.4e-18  Score=123.29  Aligned_cols=84  Identities=27%  Similarity=0.283  Sum_probs=78.8

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .++.++|||+|||+++++++|+++|++||.|..+.++.+  +++++|||||+|.+.++|++|++.||+..++|+.|+|++
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            356899999999999999999999999999999999874  789999999999999999999999999999999999999


Q ss_pred             cCCccc
Q 046966          288 SQSVSK  293 (299)
Q Consensus       288 a~~~~~  293 (299)
                      +++...
T Consensus        83 a~~~~~   88 (92)
T 2dgv_A           83 DRNASG   88 (92)
T ss_dssp             CSCCSS
T ss_pred             cCCCCC
Confidence            998754

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=9.5e-19  Score=125.41  Aligned_cols=82  Identities=23%  Similarity=0.355  Sum_probs=77.4

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .+.++|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++.|||..+.|+.|+++++
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            46899999999999999999999999999999999999889999999999999999999999999999999999988776


Q ss_pred             CC
Q 046966          289 QS  290 (299)
Q Consensus       289 ~~  290 (299)
                      ++
T Consensus        83 ~s   84 (85)
T 1x4e_A           83 SS   84 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.75  E-value=7.7e-18  Score=136.10  Aligned_cols=85  Identities=26%  Similarity=0.370  Sum_probs=80.0

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+.+++++|+.+|++||.|..|.++.++.+|.++|||||+|.+.++|++|+..|||..|.|+.|.|.+
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            45678999999999999999999999999999999999989999999999999999999999999999999999999999


Q ss_pred             cCCcc
Q 046966          288 SQSVS  292 (299)
Q Consensus       288 a~~~~  292 (299)
                      +.++.
T Consensus       149 a~~~~  153 (165)
T 1rk8_A          149 CFVKG  153 (165)
T ss_dssp             SEECC
T ss_pred             ecCCC
Confidence            98654

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=4.8e-18  Score=126.73  Aligned_cols=86  Identities=27%  Similarity=0.324  Sum_probs=81.0

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|+.. ++..++|+.|.|++
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            45679999999999999999999999999999999999988999999999999999999999988 99999999999999


Q ss_pred             cCCcccc
Q 046966          288 SQSVSKI  294 (299)
Q Consensus       288 a~~~~~~  294 (299)
                      ++++...
T Consensus        92 a~~~~~~   98 (105)
T 2dh8_A           92 CTPRGMQ   98 (105)
T ss_dssp             SCCSSCC
T ss_pred             ccCCCCC
Confidence            9987543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=2.5e-17  Score=124.64  Aligned_cols=84  Identities=30%  Similarity=0.351  Sum_probs=78.8

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ...+.++|||+|||+++++++|+++|++||.|..+.++.++ +++++|||||+|.+.++|++|++.||+..++|+.|.|+
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            34568899999999999999999999999999999999996 69999999999999999999999999999999999999


Q ss_pred             ecCCc
Q 046966          287 FSQSV  291 (299)
Q Consensus       287 ~a~~~  291 (299)
                      +++..
T Consensus        90 ~a~~~   94 (114)
T 2do0_A           90 MDERA   94 (114)
T ss_dssp             ECSCC
T ss_pred             EcccC
Confidence            99754

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.75  E-value=1.4e-18  Score=128.65  Aligned_cols=83  Identities=20%  Similarity=0.363  Sum_probs=76.0

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecC-CCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDY-RTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~-~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ....++|||+|||+++++++|+++|++|| |.+++++.++ .+|+++|||||+|.+.++|.+|+ .|+|..++|+.|+|+
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            45689999999999999999999999999 9999999987 58999999999999999999999 899999999999999


Q ss_pred             ecCCcc
Q 046966          287 FSQSVS  292 (299)
Q Consensus       287 ~a~~~~  292 (299)
                      +++++.
T Consensus        94 ~a~~~~   99 (100)
T 2j76_E           94 VADQAQ   99 (100)
T ss_dssp             ECCCSC
T ss_pred             eccCCC
Confidence            999865

>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=5.5e-18  Score=127.39  Aligned_cols=86  Identities=22%  Similarity=0.299  Sum_probs=77.0

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ...+.++|||+|||+++++++|+++|++||.|..++++.++.+|+++|||||+|.+.++|.+|+..+ +..++|+.|.|.
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            3456789999999999999999999999999999999999889999999999999999999999876 599999999999


Q ss_pred             ecCCccc
Q 046966          287 FSQSVSK  293 (299)
Q Consensus       287 ~a~~~~~  293 (299)
                      ++.++..
T Consensus       100 ~a~~~~~  106 (109)
T 2rs2_A          100 VAFPRRA  106 (109)
T ss_dssp             ECCCCCC
T ss_pred             EccCCCC
Confidence            9998753

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.74  E-value=7.5e-18  Score=123.62  Aligned_cols=82  Identities=21%  Similarity=0.230  Sum_probs=73.1

Q ss_pred             CCCCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCce--eCCeE
Q 046966          205 ADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNAL--IDDRR  282 (299)
Q Consensus       205 ~~~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~--i~g~~  282 (299)
                      ....+|+++|||+|||+.+++++|+++|++||.|.++++++      +||||||+|.+.++|.+|++.|++..  +.|++
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            34456889999999999999999999999999999999875      35899999999999999999999875  78999


Q ss_pred             EEEEecCCcc
Q 046966          283 ICVDFSQSVS  292 (299)
Q Consensus       283 l~v~~a~~~~  292 (299)
                      |.|+||+++.
T Consensus        89 i~V~~S~~k~   98 (100)
T 3r27_A           89 AFVNYSTSQK   98 (100)
T ss_dssp             EEEEECSCSC
T ss_pred             EEEEeccccc
Confidence            9999998764

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.8e-17  Score=125.47  Aligned_cols=83  Identities=27%  Similarity=0.466  Sum_probs=78.0

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCcee--------C
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALI--------D  279 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i--------~  279 (299)
                      ..+.++|||+|||+++++++|+++|++||.|..++++.++ ++.++|||||+|.+.++|++|+..|||..+        .
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            3467899999999999999999999999999999999997 999999999999999999999999999999        6


Q ss_pred             CeEEEEEecCCc
Q 046966          280 DRRICVDFSQSV  291 (299)
Q Consensus       280 g~~l~v~~a~~~  291 (299)
                      +++|.|.|++++
T Consensus       101 ~~~l~v~~a~p~  112 (114)
T 1x5o_A          101 TEPLLCKFSGPS  112 (114)
T ss_dssp             SSCBEEEECCCS
T ss_pred             CCceeEEccCCC
Confidence            888999999975

>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=99.74  E-value=6.9e-18  Score=124.83  Aligned_cols=83  Identities=19%  Similarity=0.254  Sum_probs=74.5

Q ss_pred             CCCCceEEEEcCCC-CCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCc--eeCCeEEE
Q 046966          208 KPPDNVLFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNA--LIDDRRIC  284 (299)
Q Consensus       208 ~~~~~~v~v~nL~~-~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~--~i~g~~l~  284 (299)
                      ..+.++|||+|||+ .+++++|+++|++||.|.++.++++      +|||||+|.+.++|.+|++.|++.  .+.|++|.
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            45789999999999 9999999999999999999999865      479999999999999999998864  59999999


Q ss_pred             EEecCCcccccc
Q 046966          285 VDFSQSVSKIWK  296 (299)
Q Consensus       285 v~~a~~~~~~~~  296 (299)
                      |.+|++.++++.
T Consensus        86 V~~a~~~~~~~~   97 (102)
T 1x4d_A           86 VHLSQKYKRIKS   97 (102)
T ss_dssp             EEEECCCTTSSC
T ss_pred             EEECCCCCCCCC
Confidence            999998766644

>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=99.74  E-value=1.8e-17  Score=124.98  Aligned_cols=84  Identities=20%  Similarity=0.304  Sum_probs=77.7

Q ss_pred             CCCceEEEEcCCCCCCHHHHH---HhcccCCCeEEEEEeecCCCC---CeeeEEEEEecCHHHHHHHHHHhCCceeCCeE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLH---VIFSQFGTVVSAEILRDYRTG---ESLCYAFVEFEKREACEQAYFKMNNALIDDRR  282 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~---~~f~~~G~i~~~~~~~~~~~g---~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~  282 (299)
                      ...++|||+|||+++++++|+   ++|++||.|..+.++.++.++   +++|||||+|.+.++|++|++.||+..++|+.
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            357899999999999999999   999999999999999887644   56699999999999999999999999999999


Q ss_pred             EEEEecCCcc
Q 046966          283 ICVDFSQSVS  292 (299)
Q Consensus       283 l~v~~a~~~~  292 (299)
                      |+|.+++++.
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            9999999875

>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=99.74  E-value=8.2e-18  Score=134.81  Aligned_cols=86  Identities=29%  Similarity=0.351  Sum_probs=81.4

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .+.++|||+|||+++++++|+++|++||.|..++++.++.+|+++|||||+|.+.++|++|++.|||..++|+.|.|.++
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  147 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  147 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45789999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCcccc
Q 046966          289 QSVSKI  294 (299)
Q Consensus       289 ~~~~~~  294 (299)
                      ++....
T Consensus       148 ~~~~~~  153 (158)
T 2kn4_A          148 RYGRPP  153 (158)
T ss_dssp             CCSSCC
T ss_pred             CCCCCC
Confidence            987543

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.74  E-value=1e-18  Score=135.77  Aligned_cols=84  Identities=17%  Similarity=0.352  Sum_probs=79.3

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEE--EEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCc----eeCCeE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVS--AEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNA----LIDDRR  282 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~--~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~----~i~g~~  282 (299)
                      .+.++|||+|||+++++++|+++|++||.|..  |+|++++.+|+++|||||+|.+. +|.+|+..||+.    .++|+.
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            56789999999999999999999999999976  99999988999999999999999 999999999999    999999


Q ss_pred             EEEEecCCccc
Q 046966          283 ICVDFSQSVSK  293 (299)
Q Consensus       283 l~v~~a~~~~~  293 (299)
                      |.|++++++++
T Consensus       100 l~V~~a~~~~~  110 (131)
T 2m2b_A          100 INVEFAKGSKR  110 (131)
T ss_dssp             CCCEECCCSCC
T ss_pred             EEEEECCCCCC
Confidence            99999998643

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=3.8e-18  Score=129.66  Aligned_cols=85  Identities=21%  Similarity=0.261  Sum_probs=79.9

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      +.++|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|+.. ++..++|+.|.|.++.
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEECC
Confidence            358999999999999999999999999999999999988999999999999999999999987 9999999999999999


Q ss_pred             Cccccc
Q 046966          290 SVSKIW  295 (299)
Q Consensus       290 ~~~~~~  295 (299)
                      ++....
T Consensus       105 ~~~~~~  110 (116)
T 1x4b_A          105 AREESG  110 (116)
T ss_dssp             SCCCCC
T ss_pred             CCccCC
Confidence            886543

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=3.9e-18  Score=126.37  Aligned_cols=82  Identities=18%  Similarity=0.277  Sum_probs=73.7

Q ss_pred             CCCCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCC--ceeCCeE
Q 046966          205 ADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNN--ALIDDRR  282 (299)
Q Consensus       205 ~~~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~--~~i~g~~  282 (299)
                      ....++.++|||+|||+++++++|+++|++||.|.+++++++      +|||||+|.+.++|.+|++.|++  ..+.|++
T Consensus        10 ~~~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~   83 (105)
T 1sjq_A           10 HGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQP   83 (105)
T ss_dssp             --CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEE
T ss_pred             cCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEE
Confidence            345677899999999999999999999999999999999865      58999999999999999998864  7899999


Q ss_pred             EEEEecCCcc
Q 046966          283 ICVDFSQSVS  292 (299)
Q Consensus       283 l~v~~a~~~~  292 (299)
                      |+|.+|+++.
T Consensus        84 l~V~~A~~~~   93 (105)
T 1sjq_A           84 IYIQFSNHKE   93 (105)
T ss_dssp             CCBCCCSSSS
T ss_pred             EEEEEcCCCC
Confidence            9999999864

>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=99.74  E-value=2.4e-17  Score=123.77  Aligned_cols=84  Identities=24%  Similarity=0.389  Sum_probs=76.9

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+++++++|+++|++||.|..+.+..+   +.++|||||+|.+.++|++|++.||+..++|+.|+|++
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   95 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   95 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            456789999999999999999999999999999998654   56899999999999999999999999999999999999


Q ss_pred             cCCcccc
Q 046966          288 SQSVSKI  294 (299)
Q Consensus       288 a~~~~~~  294 (299)
                      ++++.+.
T Consensus        96 a~~~~~~  102 (109)
T 1x4a_A           96 PRSGRGT  102 (109)
T ss_dssp             CCCCCCC
T ss_pred             cccCCCC
Confidence            9987644

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.74  E-value=1.5e-17  Score=127.87  Aligned_cols=82  Identities=24%  Similarity=0.383  Sum_probs=78.3

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      .++|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|+ .|||..++|+.|+|.++++
T Consensus        36 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           36 KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCC
Confidence            589999999999999999999999999999999999889999999999999999999999 8999999999999999997


Q ss_pred             ccc
Q 046966          291 VSK  293 (299)
Q Consensus       291 ~~~  293 (299)
                      ...
T Consensus       115 ~~~  117 (124)
T 2jwn_A          115 NMP  117 (124)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            643

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=4.7e-18  Score=126.33  Aligned_cols=80  Identities=11%  Similarity=0.167  Sum_probs=75.6

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ...++|||+|||+++++++|+++|++||.|.+|++++++. ++++|||||+|.+.++|++|+. +++..++|+.|.|.++
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            3468999999999999999999999999999999999976 9999999999999999999998 8999999999999997


Q ss_pred             CC
Q 046966          289 QS  290 (299)
Q Consensus       289 ~~  290 (299)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
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=99.73  E-value=2.3e-17  Score=123.79  Aligned_cols=81  Identities=26%  Similarity=0.302  Sum_probs=74.8

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCC-----eEE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDD-----RRI  283 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g-----~~l  283 (299)
                      ...++|||+|||+++++++|+++|++||.|..+.++.+       |||||+|.+.++|++|++.||+..+.|     +.|
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            45789999999999999999999999999999999876       799999999999999999999999999     999


Q ss_pred             EEEecCCcccccc
Q 046966          284 CVDFSQSVSKIWK  296 (299)
Q Consensus       284 ~v~~a~~~~~~~~  296 (299)
                      +|++++++.+...
T Consensus        86 ~V~~a~~~~~~~~   98 (108)
T 1x4c_A           86 RVKVDGPRSPSYG   98 (108)
T ss_dssp             EEEESSCCSCCCC
T ss_pred             EEEeCCCCCCCCC
Confidence            9999998765433

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=3.9e-17  Score=121.05  Aligned_cols=85  Identities=28%  Similarity=0.408  Sum_probs=77.7

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ...+.++|||+|||+++++++|+++|+.|+   .+.++.++.+++++|||||+|.+.++|++|++.||+..|.|+.|+|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLD   87 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            345689999999999999999999999884   67788888899999999999999999999999999999999999999


Q ss_pred             ecCCcccc
Q 046966          287 FSQSVSKI  294 (299)
Q Consensus       287 ~a~~~~~~  294 (299)
                      +++++...
T Consensus        88 ~a~~~~~~   95 (102)
T 2fc8_A           88 WAKPKGEG   95 (102)
T ss_dssp             ECCCCCSS
T ss_pred             EecCCCCC
Confidence            99987654

>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=5.9e-18  Score=128.20  Aligned_cols=82  Identities=26%  Similarity=0.292  Sum_probs=78.4

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      .++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|+ .||+..++|+.|.|.++++
T Consensus        25 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           25 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEecCC
Confidence            579999999999999999999999999999999999888999999999999999999999 9999999999999999987


Q ss_pred             ccc
Q 046966          291 VSK  293 (299)
Q Consensus       291 ~~~  293 (299)
                      +..
T Consensus       104 ~~~  106 (114)
T 2cq4_A          104 EKN  106 (114)
T ss_dssp             HHH
T ss_pred             Ccc
Confidence            653

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.73  E-value=9.9e-18  Score=125.12  Aligned_cols=84  Identities=21%  Similarity=0.310  Sum_probs=77.0

Q ss_pred             CCCceEEEEcCCCCC------CHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCe-
Q 046966          209 PPDNVLFVCQLNPVT------EDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDR-  281 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~------~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~-  281 (299)
                      ...++|||+|||+.+      ++++|+++|++||.|..+.++  +.+|+++|||||+|.+.++|++|+..|||..++|+ 
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            347899999999999      779999999999999999988  36899999999999999999999999999999998 


Q ss_pred             EEEEEecCCcccc
Q 046966          282 RICVDFSQSVSKI  294 (299)
Q Consensus       282 ~l~v~~a~~~~~~  294 (299)
                      .|+|.++....+.
T Consensus        91 ~l~V~~a~~~~k~  103 (105)
T 2nlw_A           91 TFRVNLFTDFDKY  103 (105)
T ss_dssp             EEEEECSCCCCCC
T ss_pred             eEEEEEcchHhhh
Confidence            9999999876553

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.73  E-value=8.8e-18  Score=129.49  Aligned_cols=84  Identities=15%  Similarity=0.307  Sum_probs=75.5

Q ss_pred             CCCCceEEEEcCCCCCCHHHHH----HhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLH----VIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRI  283 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~----~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l  283 (299)
                      .++.++|||+|||+.+++++|+    ++|++||.|.+|.+.   .+++++|||||+|.+.++|.+|+..|||..+.|+.|
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 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD---LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL  102 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC---CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec---cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEE
Confidence            4567899999999999999876    699999999998774   367899999999999999999999999999999999


Q ss_pred             EEEecCCcccc
Q 046966          284 CVDFSQSVSKI  294 (299)
Q Consensus       284 ~v~~a~~~~~~  294 (299)
                      +|.+|+++...
T Consensus       103 ~V~~a~~~~~~  113 (127)
T 2a3j_A          103 VITFSETPQSQ  113 (127)
T ss_dssp             EEEECCCCCHH
T ss_pred             EEEEccCcchh
Confidence            99999987543

>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=99.73  E-value=1.9e-18  Score=125.20  Aligned_cols=82  Identities=24%  Similarity=0.383  Sum_probs=74.1

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCCc
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSV  291 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~~  291 (299)
                      ++|||+|||+++++++|+++|++||.|.++.++.++.+++++|||||+|.+.+ |.+|+..|||..++|+.|+|++|.+.
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            57999999999999999999999999999999999889999999999999999 99999999999999999999999986


Q ss_pred             ccc
Q 046966          292 SKI  294 (299)
Q Consensus       292 ~~~  294 (299)
                      ...
T Consensus        81 ~~~   83 (90)
T 2ki2_A           81 KSL   83 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            543

>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=3.5e-18  Score=119.42  Aligned_cols=75  Identities=27%  Similarity=0.357  Sum_probs=72.0

Q ss_pred             eEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       213 ~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      +|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++ |++..++|++|.|++|
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            58999999999999999999999999999999998899999999999999999999997 8999999999999875

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.5e-17  Score=124.97  Aligned_cols=84  Identities=26%  Similarity=0.423  Sum_probs=77.6

Q ss_pred             CCCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          206 DVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       206 ~~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      ....+.++|||+|||+++++++|+++|++||.|..++++.++  +.++|||||+|.+.++|++|++.|||..++|+.|+|
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  101 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV  101 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            334568999999999999999999999999999999999884  458999999999999999999999999999999999


Q ss_pred             EecCCc
Q 046966          286 DFSQSV  291 (299)
Q Consensus       286 ~~a~~~  291 (299)
                      ++++++
T Consensus       102 ~~a~~~  107 (109)
T 2err_A          102 NNATAR  107 (109)
T ss_dssp             EECCCS
T ss_pred             EECCCC
Confidence            999875

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.73  E-value=1.7e-17  Score=117.67  Aligned_cols=75  Identities=19%  Similarity=0.265  Sum_probs=70.3

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ....-|||+||++.+++++|+++|.+||+|.++.+..      ++|||||+|.+.++|.+|++.||+..+.|+.|+|++|
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            3467899999999999999999999999999999865      5799999999999999999999999999999999999


Q ss_pred             C
Q 046966          289 Q  289 (299)
Q Consensus       289 ~  289 (299)
                      .
T Consensus        79 ~   79 (89)
T 2wbr_A           79 S   79 (89)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=2.2e-17  Score=126.95  Aligned_cols=84  Identities=27%  Similarity=0.364  Sum_probs=79.7

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+.+++++|+++|++||.|..++++.++ +|+++|||||+|.+.++|++|+..||+..++|+.|+|++
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            4567899999999999999999999999999999999997 999999999999999999999999999999999999999


Q ss_pred             cCCcc
Q 046966          288 SQSVS  292 (299)
Q Consensus       288 a~~~~  292 (299)
                      |.+..
T Consensus       111 a~~~~  115 (124)
T 2kt5_A          111 VASQI  115 (124)
T ss_dssp             ECCTT
T ss_pred             eCCCC
Confidence            98764

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=4e-17  Score=120.80  Aligned_cols=83  Identities=22%  Similarity=0.358  Sum_probs=75.8

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+++++++|+++|++||.|   +++.+ .+++++|||||+|.+.++|++|+..||+..+.|+.|+|++
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            4568999999999999999999999999976   56666 6899999999999999999999999999999999999999


Q ss_pred             cCCcccc
Q 046966          288 SQSVSKI  294 (299)
Q Consensus       288 a~~~~~~  294 (299)
                      ++++.+.
T Consensus        88 a~~~~~~   94 (101)
T 2fc9_A           88 QGPRGSP   94 (101)
T ss_dssp             CSSCCCC
T ss_pred             cCCCCCC
Confidence            9987543

>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=99.73  E-value=4.5e-17  Score=120.42  Aligned_cols=81  Identities=19%  Similarity=0.244  Sum_probs=72.9

Q ss_pred             CCCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHh--CCceeCCeEE
Q 046966          206 DVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM--NNALIDDRRI  283 (299)
Q Consensus       206 ~~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l--~~~~i~g~~l  283 (299)
                      ...++.++|||+|||+.+++++|+++|++||.|..+.++.+      +|||||+|.+.++|.+|++.|  ++..+.|++|
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   83 (101)
T 2cq1_A           10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPI   83 (101)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEE
Confidence            33467899999999999999999999999999999988764      689999999999999999976  4678999999


Q ss_pred             EEEecCCcc
Q 046966          284 CVDFSQSVS  292 (299)
Q Consensus       284 ~v~~a~~~~  292 (299)
                      .|.+++++.
T Consensus        84 ~V~~a~~~~   92 (101)
T 2cq1_A           84 YIQYSNHKE   92 (101)
T ss_dssp             EEEECSCSS
T ss_pred             EEEEcCccc
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=129.10  Aligned_cols=82  Identities=33%  Similarity=0.466  Sum_probs=77.4

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ..++.++|||+|||+.+++++|+++|++||.|..++++.++.+++++|||||+|.+.++|++|++.||+..++|+.|+|+
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34568999999999999999999999999999999999998899999999999999999999999999999999999999


Q ss_pred             ec
Q 046966          287 FS  288 (299)
Q Consensus       287 ~a  288 (299)
                      +|
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            86

>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=99.72  E-value=8e-18  Score=131.22  Aligned_cols=86  Identities=19%  Similarity=0.144  Sum_probs=78.9

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCC---eEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGT---VVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC  284 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~---i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~  284 (299)
                      ....++|||+|||+++++++|+++|++||.   |..|++++++. |+++|||||+|.+.++|++|++ ||+..++||.|.
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~  118 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIE  118 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEE
Confidence            345789999999999999999999999999   88999999976 9999999999999999999998 999999999999


Q ss_pred             EEecCCccccc
Q 046966          285 VDFSQSVSKIW  295 (299)
Q Consensus       285 v~~a~~~~~~~  295 (299)
                      |.++.++...|
T Consensus       119 V~~a~~~e~~~  129 (136)
T 2hgl_A          119 VFKSHRTEMDW  129 (136)
T ss_dssp             EEECCHHHHHH
T ss_pred             EEECChHHHHH
Confidence            99998765444

>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=99.72  E-value=1.2e-17  Score=125.32  Aligned_cols=85  Identities=18%  Similarity=0.250  Sum_probs=79.1

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCC-eEEEEEe-ecCCCCCeeeEEEEEecCHHHHHHHHHHhC--CceeCCeEEE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGT-VVSAEIL-RDYRTGESLCYAFVEFEKREACEQAYFKMN--NALIDDRRIC  284 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~-i~~~~~~-~~~~~g~~~g~afv~f~~~~~a~~al~~l~--~~~i~g~~l~  284 (299)
                      .+.++|||+|||+++++++|+++|++||. |..+.++ .++.++.++|||||+|.+.++|.+|++.|+  +..++|+.|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            45789999999999999999999999998 9999998 788889999999999999999999999996  5899999999


Q ss_pred             EEecCCccc
Q 046966          285 VDFSQSVSK  293 (299)
Q Consensus       285 v~~a~~~~~  293 (299)
                      |.+++++..
T Consensus        86 V~~a~~~~~   94 (109)
T 2dis_A           86 VDWAEPEID   94 (109)
T ss_dssp             EEESCSSCS
T ss_pred             EEEcCCCCC
Confidence            999998754

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.72  E-value=4.5e-18  Score=132.82  Aligned_cols=86  Identities=29%  Similarity=0.351  Sum_probs=81.1

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .+.++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|+..||+..+.|+.|+|+++
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            45789999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCcccc
Q 046966          289 QSVSKI  294 (299)
Q Consensus       289 ~~~~~~  294 (299)
                      ++..+.
T Consensus       125 ~~~~~~  130 (135)
T 2lea_A          125 RYGRPP  130 (135)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            987544

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=3.4e-17  Score=121.51  Aligned_cols=83  Identities=17%  Similarity=0.177  Sum_probs=76.0

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ....++|||+|||+++++++|+++|++||.+ .++|++++ +++++|||||+|.+.++|++|+ .+|+..++||.|.|..
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-DGRVTGEADVEFATHEDAVAAM-AKDKANMQHRYVELFL   88 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHH-TTSSCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHH-HhCCCeECCcEEEEEE
Confidence            4567899999999999999999999999954 99999996 8999999999999999999999 5799999999999999


Q ss_pred             cCCccc
Q 046966          288 SQSVSK  293 (299)
Q Consensus       288 a~~~~~  293 (299)
                      +.+...
T Consensus        89 ~~~~~~   94 (102)
T 1wez_A           89 NSTAGT   94 (102)
T ss_dssp             ECCCCC
T ss_pred             CCCCCC
Confidence            887653

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=5.9e-18  Score=118.82  Aligned_cols=76  Identities=25%  Similarity=0.353  Sum_probs=73.1

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.++ ..++|+.|.|++|
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            579999999999999999999999999999999998899999999999999999999999999 9999999999987

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.72  E-value=1.2e-17  Score=127.29  Aligned_cols=82  Identities=21%  Similarity=0.151  Sum_probs=76.6

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCC---eEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGT---VVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~---i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      ...++|||+|||+++++++|+++|++||.   |..++++.++. |+++|||||+|.+.++|++|++ ||+..++|+.|.|
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            45789999999999999999999999999   89999999965 9999999999999999999998 9999999999999


Q ss_pred             EecCCcc
Q 046966          286 DFSQSVS  292 (299)
Q Consensus       286 ~~a~~~~  292 (299)
                      .++....
T Consensus        93 ~~a~~~~   99 (118)
T 2db1_A           93 FKSHRTE   99 (118)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9987654

>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=1.5e-17  Score=125.97  Aligned_cols=84  Identities=13%  Similarity=0.173  Sum_probs=78.1

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCe-EEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTV-VSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i-~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      ...+.++|||+|||+++++++|+++|++||.| ..++++.++ +++++|||||+|.+.++|++|++. |+..|+|+.|.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v   88 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFV   88 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEE
Confidence            34567899999999999999999999999999 889999997 999999999999999999999977 999999999999


Q ss_pred             EecCCcc
Q 046966          286 DFSQSVS  292 (299)
Q Consensus       286 ~~a~~~~  292 (299)
                      .++.++.
T Consensus        89 ~~a~~~~   95 (114)
T 2cpy_A           89 HVVTLED   95 (114)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9998754

>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=99.71  E-value=3e-17  Score=124.60  Aligned_cols=80  Identities=19%  Similarity=0.291  Sum_probs=73.2

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCC--ceeCCeEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNN--ALIDDRRIC  284 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~--~~i~g~~l~  284 (299)
                      ..++.++|||+|||+++++++|+++|++||.|.+++++.+      +|||||+|.+.++|.+|++.|++  ..+.|++|.
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~  100 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY  100 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEE
Confidence            3467899999999999999999999999999999999875      68999999999999999998874  689999999


Q ss_pred             EEecCCcc
Q 046966          285 VDFSQSVS  292 (299)
Q Consensus       285 v~~a~~~~  292 (299)
                      |.+|+++.
T Consensus       101 V~~a~~k~  108 (119)
T 2ad9_A          101 IQFSNHKE  108 (119)
T ss_dssp             EEECSSSS
T ss_pred             EEEccCCC
Confidence            99999865

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.71  E-value=2.9e-17  Score=123.24  Aligned_cols=80  Identities=26%  Similarity=0.424  Sum_probs=73.1

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+++++++|+++|++||.|..+.++        +|||||+|.+.++|++|++.|||..++|+.|.|.+
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            4567999999999999999999999999999999986        68999999999999999999999999999999999


Q ss_pred             cCCccccc
Q 046966          288 SQSVSKIW  295 (299)
Q Consensus       288 a~~~~~~~  295 (299)
                      ++++.+.|
T Consensus       100 a~~~~~r~  107 (108)
T 2jvo_A          100 SKLPAKRY  107 (108)
T ss_dssp             CSCCC---
T ss_pred             ecCCCCCC
Confidence            99887654

>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=99.71  E-value=4e-17  Score=120.38  Aligned_cols=84  Identities=21%  Similarity=0.392  Sum_probs=76.8

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ..++.++|||+|||+.+++++|+++|++||.|..+.+..+      +|||||+|.+.++|++|++.||+..++|+.|+|+
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 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVR   84 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEE
Confidence            3456789999999999999999999999999999998754      6899999999999999999999999999999999


Q ss_pred             ecCCcccccc
Q 046966          287 FSQSVSKIWK  296 (299)
Q Consensus       287 ~a~~~~~~~~  296 (299)
                      +++++...+.
T Consensus        85 ~a~~~~~~~~   94 (99)
T 2cpj_A           85 FACHSASLTS   94 (99)
T ss_dssp             ESSCCSCCCC
T ss_pred             EcCCCCCCCC
Confidence            9998876554

>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=99.71  E-value=5.1e-17  Score=121.01  Aligned_cols=83  Identities=25%  Similarity=0.235  Sum_probs=76.9

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEE-EEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVS-AEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~-~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ....++|||+|||+++++++|+++|++||.|.. +.++.+ .+|+++|||||+|.+.++|++|+.. ++..++||.|.|.
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 7999999999999999999999987 9999999999999


Q ss_pred             ecCCcc
Q 046966          287 FSQSVS  292 (299)
Q Consensus       287 ~a~~~~  292 (299)
                      .+.+..
T Consensus        90 ~~~~~~   95 (104)
T 1wg5_A           90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            988654

>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=99.70  E-value=8.6e-18  Score=127.42  Aligned_cols=87  Identities=23%  Similarity=0.372  Sum_probs=74.9

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .++.++|||+|||+++++++|+++|++||.|..+.+..+..+++++|||||+|.+.++|++|++.||+..++|+.|+|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~  101 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF  101 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            35679999999999999999999999999984332222223788999999999999999999999999999999999999


Q ss_pred             cCCcccc
Q 046966          288 SQSVSKI  294 (299)
Q Consensus       288 a~~~~~~  294 (299)
                      ++++...
T Consensus       102 a~~~~~~  108 (115)
T 2cpx_A          102 GKNKKQR  108 (115)
T ss_dssp             CCCCSCC
T ss_pred             ccCCCCC
Confidence            9987543

>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=99.70  E-value=9.2e-17  Score=118.06  Aligned_cols=79  Identities=20%  Similarity=0.360  Sum_probs=72.1

Q ss_pred             CCCCCceEEEEcCCC-CCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          207 VKPPDNVLFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~-~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      ..++.++|||+|||+ ++++++|+++|++||.|..+++.        +|||||+|.+.++|.+|++.|||..++|+.|+|
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   89 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL   89 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345789999999998 99999999999999999999883        689999999999999999999999999999999


Q ss_pred             EecCCccc
Q 046966          286 DFSQSVSK  293 (299)
Q Consensus       286 ~~a~~~~~  293 (299)
                      ++++++.|
T Consensus        90 ~~a~~~~r   97 (97)
T 2xnq_A           90 EVSSSNAR   97 (97)
T ss_dssp             EECCCCC-
T ss_pred             EecCCCCC
Confidence            99988653

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=3.4e-17  Score=120.32  Aligned_cols=83  Identities=16%  Similarity=0.211  Sum_probs=74.2

Q ss_pred             CCCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          206 DVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       206 ~~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      ...+..++|||+|||+++++++|+++|++||.|. +.++.+    +++|||||+|.+.++|++|++.|||..++|+.|+|
T Consensus        14 ~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   88 (97)
T 2e5j_A           14 EGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRV   88 (97)
T ss_dssp             SSSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            3345678999999999999999999999999996 666654    57899999999999999999999999999999999


Q ss_pred             EecCCccc
Q 046966          286 DFSQSVSK  293 (299)
Q Consensus       286 ~~a~~~~~  293 (299)
                      ++++++++
T Consensus        89 ~~a~~~~~   96 (97)
T 2e5j_A           89 ALARQQRD   96 (97)
T ss_dssp             EECCCCCC
T ss_pred             EEcCCCCC
Confidence            99998753

>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=99.70  E-value=1.5e-17  Score=122.13  Aligned_cols=84  Identities=23%  Similarity=0.421  Sum_probs=76.8

Q ss_pred             CCCCceEEEEcCCCCCCHHHHH----HhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLH----VIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRI  283 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~----~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l  283 (299)
                      .++.++|||+|||+++++++|+    ++|++||.|..+.+..   ++.++|||||+|.+.++|.+|++.|||..++|+.|
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            4568999999999999999999    9999999999998863   57788999999999999999999999999999999


Q ss_pred             EEEecCCcccc
Q 046966          284 CVDFSQSVSKI  294 (299)
Q Consensus       284 ~v~~a~~~~~~  294 (299)
                      +|.+++++...
T Consensus        82 ~v~~a~~~~~~   92 (97)
T 1nu4_A           82 RIQYAKTDSDI   92 (97)
T ss_dssp             EEEECSSCCTH
T ss_pred             EEEEccCCCcc
Confidence            99999987654

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=7.5e-17  Score=116.77  Aligned_cols=79  Identities=25%  Similarity=0.426  Sum_probs=73.3

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+++++++|+++|++||.|..+.++        +|||||+|.+.++|++|++.||+..++|+.|+|++
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            3567999999999999999999999999999999986        47999999999999999999999999999999999


Q ss_pred             cCCcccc
Q 046966          288 SQSVSKI  294 (299)
Q Consensus       288 a~~~~~~  294 (299)
                      ++++.+.
T Consensus        77 a~~~~~~   83 (90)
T 2dnq_A           77 SKNKSKA   83 (90)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            9987643

>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=99.70  E-value=6e-17  Score=120.47  Aligned_cols=80  Identities=20%  Similarity=0.237  Sum_probs=71.9

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCc--eeCCeEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNA--LIDDRRIC  284 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~--~i~g~~l~  284 (299)
                      ..++.++|||+|||+.+++++|+++|++||.|..+.++.+      +|||||+|.+.++|.+|++.|++.  .+.|++|.
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            3467899999999999999999999999999999988753      689999999999999999988754  59999999


Q ss_pred             EEecCCcc
Q 046966          285 VDFSQSVS  292 (299)
Q Consensus       285 v~~a~~~~  292 (299)
                      |.+++++.
T Consensus        85 V~~a~~~~   92 (104)
T 1wex_A           85 FNYSTSKR   92 (104)
T ss_dssp             EEECSSSS
T ss_pred             EEEccCcc
Confidence            99999764

>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=99.70  E-value=6.1e-17  Score=118.92  Aligned_cols=81  Identities=28%  Similarity=0.470  Sum_probs=74.2

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC--CeEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID--DRRIC  284 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~--g~~l~  284 (299)
                      ..++.++|||+|||+++++++|+++|++||.|..+.+..+      +|||||+|.+.++|++|++.||+..+.  |+.|+
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~   86 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR   86 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEE
Confidence            3456799999999999999999999999999999988653      689999999999999999999999999  99999


Q ss_pred             EEecCCccc
Q 046966          285 VDFSQSVSK  293 (299)
Q Consensus       285 v~~a~~~~~  293 (299)
                      |++++++..
T Consensus        87 V~~a~~~~~   95 (97)
T 1why_A           87 VDFAKSGPS   95 (97)
T ss_dssp             EEECCCCCC
T ss_pred             EEECCCCCC
Confidence            999998753

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.70  E-value=3.6e-17  Score=122.98  Aligned_cols=81  Identities=14%  Similarity=0.050  Sum_probs=72.4

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCC-CeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFG-TVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G-~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      .+..++|||+|||+++++++|+++|++|| .|..+.+..    ..++|||||+|.+.++|++|++.|||..++|+.|+|.
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            34578999999999999999999999999 899988753    2478999999999999999999999999999999999


Q ss_pred             ecCCcc
Q 046966          287 FSQSVS  292 (299)
Q Consensus       287 ~a~~~~  292 (299)
                      +++...
T Consensus       101 ~a~~~p  106 (111)
T 2jvr_A          101 RDDNPP  106 (111)
T ss_dssp             ESCC--
T ss_pred             ECCCCC
Confidence            998654

>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=1.6e-17  Score=127.84  Aligned_cols=84  Identities=15%  Similarity=0.173  Sum_probs=76.8

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ....++|||+|||+++++++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|++|+. ||+..|+|+.|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~  100 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP  100 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEE
Confidence            3457899999999999999999999999999886666666799999999999999999999998 999999999999999


Q ss_pred             cCCcc
Q 046966          288 SQSVS  292 (299)
Q Consensus       288 a~~~~  292 (299)
                      +.++.
T Consensus       101 a~~~~  105 (124)
T 1wel_A          101 ITKKG  105 (124)
T ss_dssp             ECHHH
T ss_pred             CCHHH
Confidence            98754

>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=99.70  E-value=7.6e-17  Score=121.05  Aligned_cols=81  Identities=17%  Similarity=0.378  Sum_probs=75.2

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      +..++|||+|||+.+++++|+.+|++||.|..++++.+      +|||||+|.+.++|.+|+..|++..++|+.|+|.++
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            35789999999999999999999999999999999875      689999999999999999999999999999999999


Q ss_pred             CCccccc
Q 046966          289 QSVSKIW  295 (299)
Q Consensus       289 ~~~~~~~  295 (299)
                      +++...+
T Consensus        97 ~~~~~~~  103 (109)
T 1x4g_A           97 KESPDMT  103 (109)
T ss_dssp             CCCCSSC
T ss_pred             CCCCCCC
Confidence            9876543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.70  E-value=4e-18  Score=126.25  Aligned_cols=84  Identities=23%  Similarity=0.280  Sum_probs=76.9

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+++++++|+++|++||.|.. .++.++.+++++|||||+|.+.++|++|++ ||+..+.|+.|+|.+
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            346789999999999999999999999999887 666776788999999999999999999998 999999999999999


Q ss_pred             cCCccc
Q 046966          288 SQSVSK  293 (299)
Q Consensus       288 a~~~~~  293 (299)
                      ++++..
T Consensus        92 a~~~~~   97 (101)
T 1fj7_A           92 PKGRDG   97 (101)
T ss_dssp             CSCCCC
T ss_pred             cCCCCC
Confidence            998754

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=2.4e-16  Score=116.21  Aligned_cols=81  Identities=28%  Similarity=0.402  Sum_probs=73.4

Q ss_pred             CCCCCCceEEEEcCCCCCCHHHHHHhcccC--CCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 046966          206 DVKPPDNVLFVCQLNPVTEDEDLHVIFSQF--GTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRI  283 (299)
Q Consensus       206 ~~~~~~~~v~v~nL~~~~~e~~L~~~f~~~--G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l  283 (299)
                      ....+.++|||+|||+.+++++|+++|++|  |.|..+.+.        +|||||+|.+.++|++|+..||+..++|+.|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (99)
T 2cpd_A           10 DTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPI   81 (99)
T ss_dssp             SCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEE
T ss_pred             cccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            344568999999999999999999999999  999988764        5699999999999999999999999999999


Q ss_pred             EEEecCCcccc
Q 046966          284 CVDFSQSVSKI  294 (299)
Q Consensus       284 ~v~~a~~~~~~  294 (299)
                      +|.+++++.+.
T Consensus        82 ~v~~a~~~~~~   92 (99)
T 2cpd_A           82 EVTLAKPVDKD   92 (99)
T ss_dssp             EEECCCCCCCC
T ss_pred             EEEECCCCCCC
Confidence            99999987653

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.53  E-value=1.4e-18  Score=132.15  Aligned_cols=86  Identities=21%  Similarity=0.259  Sum_probs=81.0

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEE--------EEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCC
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVS--------AEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDD  280 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~--------~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g  280 (299)
                      .+.++|||+|||+.+++++|+++|++||.|..        ++++.++.+++++|||||+|.+.++|++|+..||+..+.|
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            45789999999999999999999999999998        8999998899999999999999999999999999999999


Q ss_pred             eEEEEEecCCcccc
Q 046966          281 RRICVDFSQSVSKI  294 (299)
Q Consensus       281 ~~l~v~~a~~~~~~  294 (299)
                      +.|+|++++++...
T Consensus        85 ~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           85 NPIKVSFATRRADF   98 (116)
Confidence            99999999987644

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.9e-16  Score=115.13  Aligned_cols=79  Identities=25%  Similarity=0.486  Sum_probs=73.1

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+++++++|+++|++||.|..+.+++        +||||+|.+.++|++|++.||+..+.|+.|+|++
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 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQL   78 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            45679999999999999999999999999999999864        3999999999999999999999999999999999


Q ss_pred             cCCcccc
Q 046966          288 SQSVSKI  294 (299)
Q Consensus       288 a~~~~~~  294 (299)
                      ++++.+.
T Consensus        79 a~~~~~~   85 (92)
T 2dgt_A           79 STSRLRT   85 (92)
T ss_dssp             SSCCCSC
T ss_pred             ccCCCCC
Confidence            9987654

>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=99.69  E-value=3.1e-17  Score=139.38  Aligned_cols=82  Identities=16%  Similarity=0.215  Sum_probs=77.5

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCC--CeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFG--TVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G--~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..++|||+||++++++++|+++|++||  .|.+|+|++++.+++++|||||+|.+.++|++||+.||++.|+|+.|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            467899999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             cCCc
Q 046966          288 SQSV  291 (299)
Q Consensus       288 a~~~  291 (299)
                      +++.
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            8764

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.69  E-value=5.8e-17  Score=118.76  Aligned_cols=81  Identities=17%  Similarity=0.258  Sum_probs=73.8

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+.+++++|+++|++||.|..+     ..++.++|||||+|.+.++|++|+..|++..++|+.|.|++
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            3457899999999999999999999999987665     25789999999999999999999999999999999999999


Q ss_pred             cCCccc
Q 046966          288 SQSVSK  293 (299)
Q Consensus       288 a~~~~~  293 (299)
                      ++++.+
T Consensus        88 a~~~~~   93 (96)
T 1fjc_A           88 TGEKGG   93 (96)
T ss_dssp             CSSSCC
T ss_pred             cCCCCC
Confidence            998764

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=4.7e-17  Score=122.04  Aligned_cols=79  Identities=20%  Similarity=0.214  Sum_probs=73.5

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ..++|||+|||+++++++|+++|++| .|..+.|+.++ .|+++|||||+|.+.++|++|+ .||+..++||.|.|..+.
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT-TCCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC-CCCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECC
Confidence            35799999999999999999999999 89999999996 4999999999999999999999 689999999999999887


Q ss_pred             Cc
Q 046966          290 SV  291 (299)
Q Consensus       290 ~~  291 (299)
                      ++
T Consensus        92 ~~   93 (109)
T 2dnn_A           92 ER   93 (109)
T ss_dssp             HH
T ss_pred             cc
Confidence            64

>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=99.69  E-value=1.2e-17  Score=125.01  Aligned_cols=83  Identities=16%  Similarity=0.073  Sum_probs=77.4

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCC---eEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGT---VVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC  284 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~---i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~  284 (299)
                      ....++|||+|||+++++++|+++|+.||.   |..++++.++. |+++|||||+|.+.++|++|+. ||+..++|+.|.
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   89999999976 9999999999999999999998 999999999999


Q ss_pred             EEecCCcc
Q 046966          285 VDFSQSVS  292 (299)
Q Consensus       285 v~~a~~~~  292 (299)
                      |.++.++.
T Consensus        86 V~~a~~~~   93 (107)
T 2lmi_A           86 VYEINNED   93 (107)
T ss_dssp             CEECCHHH
T ss_pred             EEECCHHH
Confidence            99998764

>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=99.69  E-value=1.7e-16  Score=113.49  Aligned_cols=76  Identities=28%  Similarity=0.455  Sum_probs=70.8

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHh-CCceeCCeEEEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM-NNALIDDRRICVD  286 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l-~~~~i~g~~l~v~  286 (299)
                      .++.++|||+|||+.+++++|+++|++||.|..+.++.+      +|||||+|.+.++|.+|++.| ++..++|+.|+|+
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~   82 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVK   82 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEE
Confidence            456789999999999999999999999999999998864      689999999999999999988 9999999999999


Q ss_pred             ecC
Q 046966          287 FSQ  289 (299)
Q Consensus       287 ~a~  289 (299)
                      +++
T Consensus        83 ~ak   85 (85)
T 2ytc_A           83 WGR   85 (85)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            985

>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=99.69  E-value=1.9e-16  Score=117.58  Aligned_cols=78  Identities=29%  Similarity=0.444  Sum_probs=72.0

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+++++++|+++|++||.|..+.++        +|||||+|.+.++|++|++.||+..+.|+.|.|.+
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            3467899999999999999999999999999999886        35999999999999999999999999999999999


Q ss_pred             cCCccc
Q 046966          288 SQSVSK  293 (299)
Q Consensus       288 a~~~~~  293 (299)
                      ++++.+
T Consensus        80 a~~~~~   85 (103)
T 2dgu_A           80 AKPPDQ   85 (103)
T ss_dssp             CCCCCC
T ss_pred             cCCCcc
Confidence            997654

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.69  E-value=1.9e-16  Score=133.19  Aligned_cols=85  Identities=31%  Similarity=0.415  Sum_probs=78.8

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+++++++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|++|++.+++..+.|+.|++.+
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~   91 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW   91 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccc
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCcc
Q 046966          288 SQSVS  292 (299)
Q Consensus       288 a~~~~  292 (299)
                      +....
T Consensus        92 ~~~~~   96 (213)
T 4f02_A           92 SQRDP   96 (213)
T ss_dssp             CCCCT
T ss_pred             ccccc
Confidence            87653

>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=99.68  E-value=8.2e-17  Score=122.00  Aligned_cols=82  Identities=16%  Similarity=0.247  Sum_probs=75.7

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .++.++|||+|||+.+++++|+++|++||.|..+.++.+   +.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
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            346789999999999999999999999999999999875   45589999999999999999999999999999999999


Q ss_pred             cCCcc
Q 046966          288 SQSVS  292 (299)
Q Consensus       288 a~~~~  292 (299)
                      +.++.
T Consensus        82 a~~~~   86 (115)
T 3lqv_A           82 YNANR   86 (115)
T ss_dssp             CCHHH
T ss_pred             ecCCh
Confidence            99754

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=2e-16  Score=114.55  Aligned_cols=79  Identities=24%  Similarity=0.430  Sum_probs=72.9

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+++++++|+++|++||.|..+.+++        +||||+|.+.++|++|++.||+..++|+.|+|.+
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 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVEL   77 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            45688999999999999999999999999999999864        3999999999999999999999999999999999


Q ss_pred             cCCcccc
Q 046966          288 SQSVSKI  294 (299)
Q Consensus       288 a~~~~~~  294 (299)
                      +++..+.
T Consensus        78 a~~~~~~   84 (90)
T 2dnp_A           78 STKGQKK   84 (90)
T ss_dssp             SCCCCCC
T ss_pred             CCCCCCC
Confidence            9987543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.68  E-value=2.3e-17  Score=117.08  Aligned_cols=73  Identities=23%  Similarity=0.353  Sum_probs=67.7

Q ss_pred             CceEEEEcCCCCC------CHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCe-EE
Q 046966          211 DNVLFVCQLNPVT------EDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDR-RI  283 (299)
Q Consensus       211 ~~~v~v~nL~~~~------~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~-~l  283 (299)
                      +++|||+|||+.+      ++++|+++|++||.|.++.++  +.+|+++|||||+|.+.++|++|++.|||..++|+ +|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            3789999999999      679999999999999999987  35899999999999999999999999999999999 88


Q ss_pred             EE
Q 046966          284 CV  285 (299)
Q Consensus       284 ~v  285 (299)
                      +|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            76

>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=99.68  E-value=5.3e-17  Score=121.85  Aligned_cols=81  Identities=20%  Similarity=0.272  Sum_probs=72.3

Q ss_pred             CCCCceEEEEcCCCC-CCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCC--ceeCCeEEE
Q 046966          208 KPPDNVLFVCQLNPV-TEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNN--ALIDDRRIC  284 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~-~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~--~~i~g~~l~  284 (299)
                      .++.++|||+|||++ +++++|+++|++||.|.++.+++      ++|||||+|.+.++|.+|++.|++  ..+.|++|+
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            456899999999998 99999999999999999999864      368999999999999999998864  569999999


Q ss_pred             EEecCCcccc
Q 046966          285 VDFSQSVSKI  294 (299)
Q Consensus       285 v~~a~~~~~~  294 (299)
                      |.+|+.+++.
T Consensus        96 V~~a~~~~~~  105 (112)
T 1x4f_A           96 VDLSEKYKKL  105 (112)
T ss_dssp             EEEECSCSSS
T ss_pred             EEECcccccc
Confidence            9999987654

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.68  E-value=7.7e-17  Score=119.26  Aligned_cols=76  Identities=12%  Similarity=0.290  Sum_probs=71.2

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ..++|||+|||+++++++|+++|++||.|.++++.      +++|||||+|.+.++|.+|+..|||..++|+.|+|.+++
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            46899999999999999999999999999999887      356899999999999999999999999999999999998


Q ss_pred             Cc
Q 046966          290 SV  291 (299)
Q Consensus       290 ~~  291 (299)
                      ++
T Consensus       100 ~~  101 (101)
T 2la4_A          100 ER  101 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            74

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.68  E-value=4.8e-17  Score=120.36  Aligned_cols=77  Identities=26%  Similarity=0.411  Sum_probs=72.5

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCCc
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSV  291 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~~  291 (299)
                      ++|||+|||+++++++|+++|++||.|..+.++.+     ++|||||+|.+.++|++|++.||+..++|+.|+|++++++
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            57999999999999999999999999999999876     6789999999999999999999999999999999999986


Q ss_pred             cc
Q 046966          292 SK  293 (299)
Q Consensus       292 ~~  293 (299)
                      .+
T Consensus        76 ~~   77 (101)
T 2hvz_A           76 PR   77 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.67  E-value=1.4e-16  Score=120.58  Aligned_cols=80  Identities=13%  Similarity=0.163  Sum_probs=72.8

Q ss_pred             ceEEEEcC----CCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecC----HHH----HHHHHH--HhCCce
Q 046966          212 NVLFVCQL----NPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEK----REA----CEQAYF--KMNNAL  277 (299)
Q Consensus       212 ~~v~v~nL----~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~----~~~----a~~al~--~l~~~~  277 (299)
                      ..|||+||    |+.+++.+|+.+|++||+|.++.++.|+.||+++|||||+|.+    .++    |.+|+.  .|+|..
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    888888  789999


Q ss_pred             eCCeEEEEEecCCc
Q 046966          278 IDDRRICVDFSQSV  291 (299)
Q Consensus       278 i~g~~l~v~~a~~~  291 (299)
                      |+|+.|+|.+.+..
T Consensus        83 I~Gr~irV~ln~~g   96 (136)
T 2j8a_A           83 IMGFKFEVILNKHS   96 (136)
T ss_dssp             ETTEEEEEEECCTT
T ss_pred             ecCcEEEEEECccc
Confidence            99999999997754

>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=99.67  E-value=3.8e-17  Score=128.78  Aligned_cols=85  Identities=22%  Similarity=0.379  Sum_probs=73.9

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEE--E---eecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAE--I---LRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRR  282 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~--~---~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~  282 (299)
                      ..+.++|||+|||+.+++++|+.+|++||.|..+.  +   +....+++++|||||+|.+.++|.+|+..|||..+.|+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            45789999999999999999999999999987641  1   111247889999999999999999999999999999999


Q ss_pred             EEEEecCCcc
Q 046966          283 ICVDFSQSVS  292 (299)
Q Consensus       283 l~v~~a~~~~  292 (299)
                      |.|.+|++..
T Consensus       122 l~V~~a~~~~  131 (143)
T 3egn_A          122 MVVQFARSAR  131 (143)
T ss_dssp             CEEEECCCSC
T ss_pred             EEEEECCCCC
Confidence            9999998753

>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=99.67  E-value=2e-16  Score=118.91  Aligned_cols=77  Identities=21%  Similarity=0.446  Sum_probs=71.4

Q ss_pred             CCCCceEEEEcCCCC-CCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          208 KPPDNVLFVCQLNPV-TEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~-~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ....++|||+|||+. +++++|+++|++||.|..+.+        ++|||||+|.+.++|++|++.|++..++|+.|+|.
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            345689999999999 999999999999999999988        56899999999999999999999999999999999


Q ss_pred             ecCCcc
Q 046966          287 FSQSVS  292 (299)
Q Consensus       287 ~a~~~~  292 (299)
                      ++++++
T Consensus        96 ~a~~~~  101 (110)
T 1wf1_A           96 MAGEPK  101 (110)
T ss_dssp             ESCCCC
T ss_pred             ECCCCC
Confidence            998554

>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=5.7e-17  Score=120.19  Aligned_cols=82  Identities=18%  Similarity=0.327  Sum_probs=76.1

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .+.++|||+|||+++++++|+++|++||.|..++++.++ +|+++|||||+|.+.++|++|+.  ++..++|+.|.|.++
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            346899999999999999999999999999999999997 99999999999999999999997  999999999999998


Q ss_pred             CCccc
Q 046966          289 QSVSK  293 (299)
Q Consensus       289 ~~~~~  293 (299)
                      .++..
T Consensus        84 ~~~~~   88 (102)
T 2xs2_A           84 IRKQN   88 (102)
T ss_dssp             EECC-
T ss_pred             CcCcc
Confidence            86643

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.67  E-value=1.8e-17  Score=115.68  Aligned_cols=75  Identities=24%  Similarity=0.387  Sum_probs=71.4

Q ss_pred             eEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       213 ~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      +|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++. ++..++|+.|.|++|
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            589999999999999999999999999999999988999999999999999999999975 899999999999875

>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=99.67  E-value=1.5e-16  Score=126.40  Aligned_cols=80  Identities=24%  Similarity=0.366  Sum_probs=75.1

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+++++++|+++|++||.|.+++++.+     ++|||||+|.+.++|.+|+..|||..++|++|+|++
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            456799999999999999999999999999999999876     579999999999999999999999999999999999


Q ss_pred             cCCcc
Q 046966          288 SQSVS  292 (299)
Q Consensus       288 a~~~~  292 (299)
                      +++++
T Consensus       145 a~~~~  149 (150)
T 2i2y_A          145 SNGEK  149 (150)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            99875

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.67  E-value=1e-16  Score=117.51  Aligned_cols=79  Identities=23%  Similarity=0.424  Sum_probs=71.3

Q ss_pred             CCCCceEEEEcCCC-CCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          208 KPPDNVLFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       208 ~~~~~~v~v~nL~~-~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      .++.++|||+|||+ .+++++|+++|++||.|..+.+.        +|||||+|.+.++|++|++.||+..+.|+.|+|.
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            45689999999999 99999999999999999999883        6799999999999999999999999999999999


Q ss_pred             ecCCcccc
Q 046966          287 FSQSVSKI  294 (299)
Q Consensus       287 ~a~~~~~~  294 (299)
                      +++++.+.
T Consensus        79 ~a~~~~~~   86 (96)
T 2kvi_A           79 VSSSNARP   86 (96)
T ss_dssp             EEECCCC-
T ss_pred             EcCcCCCC
Confidence            99876543

>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=99.67  E-value=1.4e-16  Score=116.07  Aligned_cols=79  Identities=20%  Similarity=0.306  Sum_probs=70.6

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCC-eEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCC-ceeCCeEEEEE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGT-VVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNN-ALIDDRRICVD  286 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~-i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~-~~i~g~~l~v~  286 (299)
                      .+.++|||+|||+++++++|+++|++||. |..+.+       .++|||||+|.+.++|++|++.||+ ..++|+.|+|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~-------~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVL-------LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEE-------EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEE-------cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            45789999999999999999999999999 555554       2468999999999999999999999 99999999999


Q ss_pred             ecCCcccc
Q 046966          287 FSQSVSKI  294 (299)
Q Consensus       287 ~a~~~~~~  294 (299)
                      +++++...
T Consensus        79 ~a~~~~~~   86 (93)
T 2cqh_A           79 YSVSKKLR   86 (93)
T ss_dssp             ECCCCCCC
T ss_pred             EccCcccc
Confidence            99987543

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.67  E-value=7.1e-16  Score=123.80  Aligned_cols=83  Identities=27%  Similarity=0.448  Sum_probs=79.3

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      +.++|||+|||+++++++|+++|++||.|.++.++.++.+|+++|||||+|.+.++|.+|++.|++..+.|+.|.|.++.
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            36899999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             Ccc
Q 046966          290 SVS  292 (299)
Q Consensus       290 ~~~  292 (299)
                      +..
T Consensus        81 ~~~   83 (167)
T 1fxl_A           81 PSS   83 (167)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            764

>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=9.4e-16  Score=122.97  Aligned_cols=82  Identities=27%  Similarity=0.450  Sum_probs=78.4

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|||..++|++|+|.||
T Consensus        85 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  164 (166)
T 3md3_A           85 DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWA  164 (166)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEec
Confidence            45789999999999999999999999999999999999889999999999999999999999999999999999999998


Q ss_pred             CC
Q 046966          289 QS  290 (299)
Q Consensus       289 ~~  290 (299)
                      +.
T Consensus       165 ~~  166 (166)
T 3md3_A          165 AK  166 (166)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.66  E-value=4e-16  Score=114.25  Aligned_cols=80  Identities=21%  Similarity=0.269  Sum_probs=72.9

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEE-EeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAE-ILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~-~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ....++|||+|||+++++++|+++|++||.|..++ ++.++.++.    |||+|.+.++|.+|+..|||..++|+.|+|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~----afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   87 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV----VNVTYSSKDQARQALDKLNGFQLENFTLKVA   87 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEE----EEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCE----EEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            34578999999999999999999999999999994 887765443    9999999999999999999999999999999


Q ss_pred             ecCCc
Q 046966          287 FSQSV  291 (299)
Q Consensus       287 ~a~~~  291 (299)
                      ++.++
T Consensus        88 ~a~~~   92 (96)
T 2e44_A           88 YIPDE   92 (96)
T ss_dssp             ECCCC
T ss_pred             EcCcc
Confidence            99986

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.66  E-value=4.6e-16  Score=125.20  Aligned_cols=83  Identities=28%  Similarity=0.496  Sum_probs=79.5

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      +.++|||+|||+++++++|+++|++||.|.++.++.++.+|.++|||||+|.+.++|++|++.|++..+.|+.|.|.++.
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            57899999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             Ccc
Q 046966          290 SVS  292 (299)
Q Consensus       290 ~~~  292 (299)
                      +..
T Consensus        82 ~~~   84 (168)
T 1b7f_A           82 PGG   84 (168)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            754

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.66  E-value=3e-16  Score=128.07  Aligned_cols=85  Identities=27%  Similarity=0.362  Sum_probs=80.1

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.++.++ ++.++|||||+|.+.++|++|++.||+..++|+.|+|.+
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            4567999999999999999999999999999999999997 999999999999999999999999999999999999999


Q ss_pred             cCCccc
Q 046966          288 SQSVSK  293 (299)
Q Consensus       288 a~~~~~  293 (299)
                      |.+...
T Consensus       164 a~~~~~  169 (177)
T 2f3j_A          164 VASQID  169 (177)
T ss_dssp             ESSGGG
T ss_pred             ecCCCC
Confidence            987643

>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=99.65  E-value=5.7e-16  Score=143.50  Aligned_cols=84  Identities=27%  Similarity=0.465  Sum_probs=80.1

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .+.++|||+|||+.+++++|..+|++||.|..|.|+.++.++.++|||||+|.+.++|.+||..|||..|+|+.|.|.++
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            45689999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCcc
Q 046966          289 QSVS  292 (299)
Q Consensus       289 ~~~~  292 (299)
                      .++.
T Consensus       180 ~~~~  183 (437)
T 3pgw_S          180 RGRT  183 (437)
T ss_pred             CCCC
Confidence            9753

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=1.3e-15  Score=111.83  Aligned_cols=80  Identities=23%  Similarity=0.335  Sum_probs=72.2

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ...+.++|||+||  ++++++|+++|++||.|..+.+.      +++|||||+|.+.++|++|+..||+..++|+.|+|.
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~   82 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVN   82 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            3456789999996  89999999999999999999884      467899999999999999999999999999999999


Q ss_pred             ecCCcccc
Q 046966          287 FSQSVSKI  294 (299)
Q Consensus       287 ~a~~~~~~  294 (299)
                      +++++...
T Consensus        83 ~a~~~~~~   90 (97)
T 1x5p_A           83 IARKQPML   90 (97)
T ss_dssp             CCSSCCCC
T ss_pred             ECCCCCCC
Confidence            99987543

>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=99.64  E-value=7.6e-16  Score=111.25  Aligned_cols=78  Identities=19%  Similarity=0.297  Sum_probs=63.3

Q ss_pred             CCCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCce--eCCeEE
Q 046966          206 DVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNAL--IDDRRI  283 (299)
Q Consensus       206 ~~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~--i~g~~l  283 (299)
                      ...++.++|||+|||+++++++|+++|++||.|.+++++++     ++|||||+|.+.++|++    |++..  +.|+.|
T Consensus         6 ~~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v   76 (89)
T 3d2w_A            6 HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISV   76 (89)
T ss_dssp             -----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEE
Confidence            34567899999999999999999999999999999999874     78999999999999884    45554  559999


Q ss_pred             EEEecCCcc
Q 046966          284 CVDFSQSVS  292 (299)
Q Consensus       284 ~v~~a~~~~  292 (299)
                      .|.++.++.
T Consensus        77 ~v~~a~~k~   85 (89)
T 3d2w_A           77 HISNAEPKH   85 (89)
T ss_dssp             EEEECC---
T ss_pred             EEEEcCCCC
Confidence            999999875

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.64  E-value=1.3e-15  Score=125.94  Aligned_cols=86  Identities=23%  Similarity=0.391  Sum_probs=81.6

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|++.|||..++|+.|.|++
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            35679999999999999999999999999999999999988999999999999999999999999999999999999999


Q ss_pred             cCCccc
Q 046966          288 SQSVSK  293 (299)
Q Consensus       288 a~~~~~  293 (299)
                      ++++.+
T Consensus       191 a~~~~~  196 (198)
T 2yh0_A          191 ASVGAK  196 (198)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            998754

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=1.1e-15  Score=111.50  Aligned_cols=77  Identities=22%  Similarity=0.260  Sum_probs=70.2

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ..++|||+|||+++++++|+++|++||.|..|  +.++.+++   ||||+|.+.++|++|+. ||+..++|+.|.|+++.
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            46799999999999999999999999999987  56656665   99999999999999999 99999999999999988


Q ss_pred             Ccc
Q 046966          290 SVS  292 (299)
Q Consensus       290 ~~~  292 (299)
                      ++.
T Consensus        81 ~~~   83 (94)
T 2e5g_A           81 QKE   83 (94)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            664

>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=1.7e-16  Score=121.45  Aligned_cols=82  Identities=20%  Similarity=0.174  Sum_probs=74.6

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCe----EEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTV----VSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC  284 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i----~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~  284 (299)
                      ...++|||+|||+++++++|+++|++||.|    ..|.|+.+ .+|+++|||||+|.+.++|++|++. |+..++||.|.
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 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            347899999999999999999999999975    68999998 5899999999999999999999976 99999999999


Q ss_pred             EEecCCcc
Q 046966          285 VDFSQSVS  292 (299)
Q Consensus       285 v~~a~~~~  292 (299)
                      |..+.++.
T Consensus        99 V~~a~~~e  106 (123)
T 2dha_A           99 LFRSTAAE  106 (123)
T ss_dssp             CEEECHHH
T ss_pred             EEECCHHH
Confidence            99887543

>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=99.63  E-value=6.2e-16  Score=117.23  Aligned_cols=77  Identities=27%  Similarity=0.331  Sum_probs=67.7

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeE-----EE
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRR-----IC  284 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~-----l~  284 (299)
                      ..++|||+|||+++++++|+++|++||.|..+.++.+       |||||+|.+.++|++|++.||+..|+|+.     |+
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            4689999999999999999999999999999999765       89999999999999999999999999998     88


Q ss_pred             EEecCCccc
Q 046966          285 VDFSQSVSK  293 (299)
Q Consensus       285 v~~a~~~~~  293 (299)
                      |..+.++..
T Consensus        88 v~~~~~~~~   96 (115)
T 3beg_B           88 VKVDGPRSP   96 (115)
T ss_dssp             EEECC----
T ss_pred             eccCCCCCC
Confidence            888876543

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.63  E-value=2.7e-16  Score=120.73  Aligned_cols=81  Identities=26%  Similarity=0.236  Sum_probs=73.2

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeE--EEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVV--SAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~--~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      ....++|||+|||+++++++|+++|++| .|.  .|+|+.++. |+++|||||+|.+.++|++|++. ++..|+||.|.|
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-GKITGEAFVQFASQELAEKALGK-HKERIGHRYIEV  115 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEE
Confidence            3457899999999999999999999999 566  899999975 99999999999999999999975 789999999999


Q ss_pred             EecCCc
Q 046966          286 DFSQSV  291 (299)
Q Consensus       286 ~~a~~~  291 (299)
                      ..+.++
T Consensus       116 ~~a~~~  121 (126)
T 2hgm_A          116 FKSSQE  121 (126)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            988654

>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=99.63  E-value=2.6e-16  Score=118.54  Aligned_cols=76  Identities=16%  Similarity=0.226  Sum_probs=70.4

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ..++|||+|||+.+++++|+++|++||.|..+.++.      ++|||||+|.+.++|++|++.|||..+.|+.|.|.|+.
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            468999999999999999999999999999998763      56899999999999999999999999999999999987


Q ss_pred             Cc
Q 046966          290 SV  291 (299)
Q Consensus       290 ~~  291 (299)
                      ..
T Consensus        83 ~~   84 (111)
T 1whx_A           83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            53

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.63  E-value=1.8e-15  Score=122.22  Aligned_cols=80  Identities=24%  Similarity=0.417  Sum_probs=76.9

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ..++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|++.|||..++|++|.|++|.
T Consensus        93 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A           93 GAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             TTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            37899999999999999999999999999999999998899999999999999999999999999999999999999973

>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=99.63  E-value=1e-15  Score=110.24  Aligned_cols=76  Identities=12%  Similarity=0.169  Sum_probs=70.6

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ..++|||+|||+.+++++|+++|++| .|..+++.      +++|||||+|.+.++|++|++.|||..++|++|+|+++.
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            46899999999999999999999999 99999884      578999999999999999999999999999999999997


Q ss_pred             Ccc
Q 046966          290 SVS  292 (299)
Q Consensus       290 ~~~  292 (299)
                      ...
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            654

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.63  E-value=2.1e-15  Score=126.46  Aligned_cols=84  Identities=26%  Similarity=0.415  Sum_probs=80.3

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      +.++|||+|||+.+++++|+++|++||.|..++++.++.+|+++|||||+|.+.++|.+|++.|||..++|+.|.|.++.
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            46899999999999999999999999999999999998899999999999999999999999999999999999999999


Q ss_pred             Cccc
Q 046966          290 SVSK  293 (299)
Q Consensus       290 ~~~~  293 (299)
                      ++..
T Consensus       204 ~~~~  207 (216)
T 2qfj_A          204 TPPM  207 (216)
T ss_dssp             SCSS
T ss_pred             CCCC
Confidence            8753

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=9.6e-16  Score=109.72  Aligned_cols=76  Identities=26%  Similarity=0.429  Sum_probs=67.5

Q ss_pred             CCCce-EEEEcCCCCCCHHH----HHHhcccC-CCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeE
Q 046966          209 PPDNV-LFVCQLNPVTEDED----LHVIFSQF-GTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRR  282 (299)
Q Consensus       209 ~~~~~-v~v~nL~~~~~e~~----L~~~f~~~-G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~  282 (299)
                      +|..+ |||+|||+.+++++    |+++|++| |.|.++       ++   |+|||.|.+.++|.+|++.|+|..+.||+
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            34555 99999999999987    55899999 599887       34   99999999999999999999999999999


Q ss_pred             EEEEecCCcccc
Q 046966          283 ICVDFSQSVSKI  294 (299)
Q Consensus       283 l~v~~a~~~~~~  294 (299)
                      |+|++|+.++..
T Consensus        76 i~v~~A~~~sd~   87 (96)
T 2diu_A           76 IIVSFTPKNREL   87 (96)
T ss_dssp             CEEESSCCSCCC
T ss_pred             EEEEecCCCcce
Confidence            999999987654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.62  E-value=3.7e-15  Score=113.90  Aligned_cols=78  Identities=19%  Similarity=0.179  Sum_probs=69.1

Q ss_pred             CCCce--EEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeE-EEEEecCHHHHHHHHHHhCCceeCC--eEE
Q 046966          209 PPDNV--LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCY-AFVEFEKREACEQAYFKMNNALIDD--RRI  283 (299)
Q Consensus       209 ~~~~~--v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~-afv~f~~~~~a~~al~~l~~~~i~g--~~l  283 (299)
                      ++.+.  |||+||++.+++++|+++|++||.|.++.+...      .|| |||+|.+.++|.+|++.|||..|.|  +.|
T Consensus        21 ~ps~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l   94 (124)
T 2e5i_A           21 GGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTL   94 (124)
T ss_dssp             CCCSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEE
T ss_pred             CCCcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEE
Confidence            44444  679999999999999999999999999998652      276 9999999999999999999999987  699


Q ss_pred             EEEecCCcc
Q 046966          284 CVDFSQSVS  292 (299)
Q Consensus       284 ~v~~a~~~~  292 (299)
                      +|.+|+++.
T Consensus        95 ~V~~Ak~~~  103 (124)
T 2e5i_A           95 KIEYARPTR  103 (124)
T ss_dssp             EEECCSCSC
T ss_pred             EEEEecCCc
Confidence            999999874

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.62  E-value=2.7e-15  Score=115.19  Aligned_cols=76  Identities=24%  Similarity=0.330  Sum_probs=69.5

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeE-EEEEecCHHHHHHHHHHhCCceeCC--eEEEEEec
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCY-AFVEFEKREACEQAYFKMNNALIDD--RRICVDFS  288 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~-afv~f~~~~~a~~al~~l~~~~i~g--~~l~v~~a  288 (299)
                      -.|||+||++.+++++|+++|++||.|.++.+..+     .+|| |||+|.+.++|++|++.|||..|.|  +.|+|+|+
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            46789999999999999999999999999988764     2577 9999999999999999999999988  99999999


Q ss_pred             CCcc
Q 046966          289 QSVS  292 (299)
Q Consensus       289 ~~~~  292 (299)
                      ++.+
T Consensus       104 k~~~  107 (130)
T 3zzy_A          104 KLTS  107 (130)
T ss_dssp             SCSS
T ss_pred             CCCc
Confidence            9864

>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=99.62  E-value=2.3e-15  Score=124.27  Aligned_cols=85  Identities=21%  Similarity=0.369  Sum_probs=76.0

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .+.++|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|+.. ++..++|+.|.|.++
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a  180 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKA  180 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEEC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEec
Confidence            3468999999999999999999999999999999999988999999999999999999999976 899999999999999


Q ss_pred             CCcccc
Q 046966          289 QSVSKI  294 (299)
Q Consensus       289 ~~~~~~  294 (299)
                      .++...
T Consensus       181 ~~k~~~  186 (196)
T 1l3k_A          181 LSKQEM  186 (196)
T ss_dssp             C-----
T ss_pred             CChhHh
Confidence            987654

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.62  E-value=1.8e-15  Score=127.13  Aligned_cols=80  Identities=34%  Similarity=0.513  Sum_probs=75.3

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      ..+|||+|||+.+++++|+++|++||.|..++++.+.  +.++|||||+|.+.++|.+|++.|||..|+|++|.|.++++
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            4689999999999999999999999999999999984  45899999999999999999999999999999999999998


Q ss_pred             cc
Q 046966          291 VS  292 (299)
Q Consensus       291 ~~  292 (299)
                      +.
T Consensus       181 ~~  182 (213)
T 4f02_A          181 RK  182 (213)
T ss_dssp             HH
T ss_pred             Cc
Confidence            64

>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=99.62  E-value=2.2e-15  Score=124.43  Aligned_cols=84  Identities=26%  Similarity=0.313  Sum_probs=77.6

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+++++++|+++|++||.|.++.++.++.+|.++|||||+|.+.++|.+|++. ++..+.|+.|.|.+
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            34578999999999999999999999999999999999998999999999999999999999976 99999999999999


Q ss_pred             cCCcc
Q 046966          288 SQSVS  292 (299)
Q Consensus       288 a~~~~  292 (299)
                      +.+..
T Consensus        89 ~~~~~   93 (196)
T 1l3k_A           89 AVSRE   93 (196)
T ss_dssp             CCC--
T ss_pred             ccCcc
Confidence            88653

>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=99.62  E-value=1.1e-16  Score=125.22  Aligned_cols=82  Identities=20%  Similarity=0.182  Sum_probs=74.7

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ....++|||+|||+++++++|+++|++|| +..|+|+.++. ++++|||||+|.+.++|++|+ .+|+..++||.|.|..
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~  119 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFL  119 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEE
Confidence            34578999999999999999999999999 66999999964 999999999999999999999 7899999999999999


Q ss_pred             cCCcc
Q 046966          288 SQSVS  292 (299)
Q Consensus       288 a~~~~  292 (299)
                      +.+..
T Consensus       120 a~~~~  124 (139)
T 2hgn_A          120 NSTTG  124 (139)
T ss_dssp             CCCSC
T ss_pred             CCCCC
Confidence            88754

>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=8.1e-16  Score=123.73  Aligned_cols=80  Identities=24%  Similarity=0.452  Sum_probs=76.7

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      .++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|++ +++..++|++|.|.+|.|
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            5689999999999999999999999999999999998899999999999999999999997 899999999999999998


Q ss_pred             c
Q 046966          291 V  291 (299)
Q Consensus       291 ~  291 (299)
                      +
T Consensus       166 k  166 (167)
T 2cjk_A          166 R  166 (167)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.61  E-value=1.1e-15  Score=114.76  Aligned_cols=77  Identities=18%  Similarity=0.301  Sum_probs=69.7

Q ss_pred             CCCceEEE--EcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCcee-----CCe
Q 046966          209 PPDNVLFV--CQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALI-----DDR  281 (299)
Q Consensus       209 ~~~~~v~v--~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i-----~g~  281 (299)
                      .+..+|||  +||++++++++|+++|++||.|..+.++.      .+|||||+|.+.++|++|++.|||..+     .|+
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~   96 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            46788999  77999999999999999999999987753      268999999999999999999999998     689


Q ss_pred             EEEEEecCCc
Q 046966          282 RICVDFSQSV  291 (299)
Q Consensus       282 ~l~v~~a~~~  291 (299)
                      +|.|.|++..
T Consensus        97 ~l~v~~a~~~  106 (114)
T 2cq2_A           97 TLYLNFVEKV  106 (114)
T ss_dssp             ECEEEEESCC
T ss_pred             EEEEEecccC
Confidence            9999999854

>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=99.60  E-value=2.9e-15  Score=119.35  Aligned_cols=78  Identities=23%  Similarity=0.297  Sum_probs=70.7

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEec
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDD--RRICVDFS  288 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g--~~l~v~~a  288 (299)
                      -.+|||+||++.+++++|+++|++||.|.++.+...    .++|||||+|.+.++|++|++.|||..|.|  +.|+|+|+
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~A  121 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            346899999999999999999999999999998654    257899999999999999999999999965  99999999


Q ss_pred             CCcc
Q 046966          289 QSVS  292 (299)
Q Consensus       289 ~~~~  292 (299)
                      +++.
T Consensus       122 k~~~  125 (164)
T 1sjr_A          122 KLTS  125 (164)
T ss_dssp             SSSS
T ss_pred             cCCc
Confidence            9864

>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=8.5e-15  Score=117.74  Aligned_cols=80  Identities=33%  Similarity=0.559  Sum_probs=76.0

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDD--RRICVD  286 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g--~~l~v~  286 (299)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|++.|||..+.|  ++|+|+
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            346899999999999999999999999999999999998899999999999999999999999999999987  999999


Q ss_pred             ec
Q 046966          287 FS  288 (299)
Q Consensus       287 ~a  288 (299)
                      +|
T Consensus       167 ~A  168 (168)
T 1b7f_A          167 LA  168 (168)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.59  E-value=8.5e-15  Score=108.95  Aligned_cols=83  Identities=17%  Similarity=0.215  Sum_probs=73.9

Q ss_pred             CCCceEEEEcCCC-----CCCHHHHHHhcccCCCeEEEEEeecCCC-CCeeeEEEEEecCHHHHHHHHHHhCCceeCCeE
Q 046966          209 PPDNVLFVCQLNP-----VTEDEDLHVIFSQFGTVVSAEILRDYRT-GESLCYAFVEFEKREACEQAYFKMNNALIDDRR  282 (299)
Q Consensus       209 ~~~~~v~v~nL~~-----~~~e~~L~~~f~~~G~i~~~~~~~~~~~-g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~  282 (299)
                      .++++|+|.||..     +-.+++|++.|++||.|.++.++.++.+ +.++|||||+|.+.++|.+|++.|||..++||.
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            4688999999963     2368999999999999999999998654 688999999999999999999999999999999


Q ss_pred             EEEEecCCc
Q 046966          283 ICVDFSQSV  291 (299)
Q Consensus       283 l~v~~a~~~  291 (299)
                      |.|.++.+.
T Consensus        86 i~v~~a~~~   94 (105)
T 2pe8_A           86 VKACFYNLD   94 (105)
T ss_dssp             CEEEECCHH
T ss_pred             EEEEEcCHH
Confidence            999999863

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.59  E-value=6.2e-15  Score=118.14  Aligned_cols=80  Identities=21%  Similarity=0.397  Sum_probs=74.7

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCCc
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSV  291 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~~  291 (299)
                      ++|||+|||+++++++|+++|++||.|.+++++.++ +++++|||||+|.+.++|.+|++.|++..+.|+.|.|.++.+.
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            589999999999999999999999999999999985 5789999999999999999999999999999999999999765


Q ss_pred             c
Q 046966          292 S  292 (299)
Q Consensus       292 ~  292 (299)
                      .
T Consensus        80 ~   80 (166)
T 3md3_A           80 Q   80 (166)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=2.5e-15  Score=113.67  Aligned_cols=78  Identities=18%  Similarity=0.240  Sum_probs=68.0

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCC---CCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRT---GESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~---g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      ...++|||+|||+++++++|+++|++||.|. +.++.++.+   |+++|||||+|.+.++|++|++.|+  .++|+.+.+
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            4578999999999999999999999999999 888887766   7999999999999999999999884  366777666


Q ss_pred             EecC
Q 046966          286 DFSQ  289 (299)
Q Consensus       286 ~~a~  289 (299)
                      ..+.
T Consensus        83 ~~~~   86 (114)
T 2dnl_A           83 VSSP   86 (114)
T ss_dssp             ECCS
T ss_pred             ccCC
Confidence            6554

>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=99.58  E-value=4.8e-15  Score=123.82  Aligned_cols=78  Identities=21%  Similarity=0.309  Sum_probs=72.3

Q ss_pred             CCCceEEEEcCC-CCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          209 PPDNVLFVCQLN-PVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       209 ~~~~~v~v~nL~-~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      +++++|||+||| +.+++++|+++|++||.|.+|+++.+     .+|||||+|.+.++|++|++.|||..+.|+.|+|.+
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            457899999999 89999999999999999999999875     368999999999999999999999999999999999


Q ss_pred             cCCc
Q 046966          288 SQSV  291 (299)
Q Consensus       288 a~~~  291 (299)
                      ++..
T Consensus        77 s~~~   80 (205)
T 3tyt_A           77 SKQP   80 (205)
T ss_dssp             CSCS
T ss_pred             ccCC
Confidence            8743

>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=99.57  E-value=2.3e-15  Score=108.35  Aligned_cols=79  Identities=18%  Similarity=0.294  Sum_probs=67.5

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .+.++|||+|||+++++++|+++|++||.|..++++.+     ++|||||+|.+.++|+++..  ....+.|+.|.|.++
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            35799999999999999999999999999999998764     68999999999999986532  134568999999999


Q ss_pred             CCcccc
Q 046966          289 QSVSKI  294 (299)
Q Consensus       289 ~~~~~~  294 (299)
                      .++...
T Consensus        76 ~~~~~~   81 (88)
T 1wf0_A           76 EPKHNS   81 (88)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            987643

>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=1.4e-14  Score=116.20  Aligned_cols=79  Identities=32%  Similarity=0.487  Sum_probs=74.4

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeE--EEEEe
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRR--ICVDF  287 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~--l~v~~  287 (299)
                      +.++|||+|||+.+++++|+++|++||.|..++++.++.+|.++|||||+|.+.++|.+|++.|||..+.|+.  |.|+|
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            3678999999999999999999999999999999999889999999999999999999999999999999975  88887


Q ss_pred             c
Q 046966          288 S  288 (299)
Q Consensus       288 a  288 (299)
                      |
T Consensus       167 A  167 (167)
T 1fxl_A          167 A  167 (167)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.56  E-value=8.3e-15  Score=122.76  Aligned_cols=83  Identities=24%  Similarity=0.346  Sum_probs=75.7

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      +.++|||+|||+++++++|+++|++||.|.+++++.++.+++++|||||+|.+.++|.+|++.|++..++|+.|.|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            36899999999999999999999999999999999998899999999999999999999999999999999999999987


Q ss_pred             Ccc
Q 046966          290 SVS  292 (299)
Q Consensus       290 ~~~  292 (299)
                      +..
T Consensus       107 ~~~  109 (216)
T 2qfj_A          107 NIG  109 (216)
T ss_dssp             CCG
T ss_pred             Ccc
Confidence            654

>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=99.56  E-value=7.9e-15  Score=105.16  Aligned_cols=72  Identities=19%  Similarity=0.335  Sum_probs=66.3

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccC----C-------CeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCce
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQF----G-------TVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNAL  277 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~----G-------~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~  277 (299)
                      .+.++|||+|||+++++++|+++|++|    |       .|.++++..+      +|||||+|.+.++|++|+ .||+..
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            357899999999999999999999999    8       8999988654      689999999999999999 999999


Q ss_pred             eCCeEEEEEe
Q 046966          278 IDDRRICVDF  287 (299)
Q Consensus       278 i~g~~l~v~~  287 (299)
                      ++|+.|+|+.
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

>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=99.56  E-value=1.4e-14  Score=117.24  Aligned_cols=79  Identities=30%  Similarity=0.468  Sum_probs=73.6

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC---CeEEEEE
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID---DRRICVD  286 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~---g~~l~v~  286 (299)
                      +.++|||+|||+.+++++|+++|++||.|.++.++.++ +|.++|||||+|.+.++|.+|++.|||..+.   +++|.|+
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            46789999999999999999999999999999999985 6999999999999999999999999998776   4999999


Q ss_pred             ecC
Q 046966          287 FSQ  289 (299)
Q Consensus       287 ~a~  289 (299)
                      ||.
T Consensus       173 ~ad  175 (175)
T 3nmr_A          173 FAD  175 (175)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            984

>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=99.56  E-value=1.6e-14  Score=116.78  Aligned_cols=83  Identities=27%  Similarity=0.342  Sum_probs=75.8

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCC--CeeeEEEEEecCHHHHHHHHHHhCCceeC---CeEEE
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTG--ESLCYAFVEFEKREACEQAYFKMNNALID---DRRIC  284 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g--~~~g~afv~f~~~~~a~~al~~l~~~~i~---g~~l~  284 (299)
                      ..++|||+|||+++++++|+++|++||.|.+++++.++.++  +++|||||+|.+.++|++|++.|++..+.   ++.+.
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            46899999999999999999999999999999999998776  89999999999999999999999998876   67888


Q ss_pred             EEecCCcc
Q 046966          285 VDFSQSVS  292 (299)
Q Consensus       285 v~~a~~~~  292 (299)
                      +.++.+..
T Consensus        82 ~~~~~~~~   89 (175)
T 3nmr_A           82 MKPADSEK   89 (175)
T ss_dssp             EEECGGGC
T ss_pred             Eccccccc
Confidence            88877553

>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=99.55  E-value=1.8e-14  Score=116.82  Aligned_cols=78  Identities=18%  Similarity=0.284  Sum_probs=72.3

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      +.++|||+|||+.+++++|+++|++||.|..+     ..++.++|||||+|.+.++|.+|+..|||..++|+.|.|++++
T Consensus        98 ~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~  172 (175)
T 1fje_B           98 AARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG  172 (175)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEECS
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEecC
Confidence            46899999999999999999999999987765     3688999999999999999999999999999999999999998


Q ss_pred             Ccc
Q 046966          290 SVS  292 (299)
Q Consensus       290 ~~~  292 (299)
                      +++
T Consensus       173 ~k~  175 (175)
T 1fje_B          173 EKG  175 (175)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            863

>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=99.54  E-value=3.8e-14  Score=117.20  Aligned_cols=79  Identities=11%  Similarity=0.167  Sum_probs=72.7

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      .++|||+|||+++++++|+++|++||.|..++++++. ++.++|||||+|.+.++|++|+..+ +..++|+.|.|.+++.
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhHH
Confidence            5799999999999999999999999999999999985 6999999999999999999999765 4599999999999775


Q ss_pred             c
Q 046966          291 V  291 (299)
Q Consensus       291 ~  291 (299)
                      -
T Consensus       187 y  187 (193)
T 2voo_A          187 Y  187 (193)
T ss_dssp             C
T ss_pred             H
Confidence            3

>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=99.54  E-value=9.7e-15  Score=117.34  Aligned_cols=81  Identities=25%  Similarity=0.403  Sum_probs=75.4

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      +.++|||+|||+++++++|+++|++||.|.++++++++.+|.++|||||+|.+.++|.+|++.  +..++|+.|.|.++.
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 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            468999999999999999999999999999999999988999999999999999999999974  678999999999988


Q ss_pred             Ccc
Q 046966          290 SVS  292 (299)
Q Consensus       290 ~~~  292 (299)
                      ++.
T Consensus        80 ~~~   82 (167)
T 2cjk_A           80 PRD   82 (167)
T ss_dssp             CHH
T ss_pred             chh
Confidence            653

>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=4.7e-14  Score=123.30  Aligned_cols=82  Identities=23%  Similarity=0.417  Sum_probs=75.7

Q ss_pred             CCCCceEEEEcCCCCCCHHHHH----HhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLH----VIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRI  283 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~----~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l  283 (299)
                      ..+.++|||+|||+++++++|+    ++|++||.|.+|++++   +++++|||||+|.+.++|.+|++.|||..+.|+.|
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            4568999999999999999976    8999999999998875   68899999999999999999999999999999999


Q ss_pred             EEEecCCcc
Q 046966          284 CVDFSQSVS  292 (299)
Q Consensus       284 ~v~~a~~~~  292 (299)
                      +|.++++..
T Consensus        83 ~v~~a~~~~   91 (282)
T 3pgw_A           83 RIQYAKTDS   91 (282)
T ss_pred             EEEEeccCc
Confidence            999998654

>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=99.52  E-value=4e-14  Score=124.39  Aligned_cols=83  Identities=23%  Similarity=0.432  Sum_probs=76.5

Q ss_pred             CCCCceEEEEcCCCC-CCHHHHHHhcccCCCeEEEEEeecCC-CCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          208 KPPDNVLFVCQLNPV-TEDEDLHVIFSQFGTVVSAEILRDYR-TGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~-~~e~~L~~~f~~~G~i~~~~~~~~~~-~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      ..+.++|||+|||+. +++++|+++|++||.|..++++.+.. ||.++|||||+|.+.++|.+|+ .|||..++|+.|.|
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            345789999999999 99999999999999999999999865 5999999999999999999999 99999999999999


Q ss_pred             EecCCc
Q 046966          286 DFSQSV  291 (299)
Q Consensus       286 ~~a~~~  291 (299)
                      .+++++
T Consensus       286 ~~a~~k  291 (292)
T 2ghp_A          286 SLADKK  291 (292)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            999986

>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=9.8e-14  Score=121.39  Aligned_cols=83  Identities=22%  Similarity=0.405  Sum_probs=79.2

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      +.++|||+|||+.+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+..|+|..++|+.|.|.++.
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~  173 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD  173 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            35799999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             Ccc
Q 046966          290 SVS  292 (299)
Q Consensus       290 ~~~  292 (299)
                      +..
T Consensus       174 ~~~  176 (284)
T 3smz_A          174 AGQ  176 (284)
T ss_dssp             GGG
T ss_pred             CCC
Confidence            764

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.50  E-value=2.7e-14  Score=121.08  Aligned_cols=79  Identities=18%  Similarity=0.321  Sum_probs=70.4

Q ss_pred             CCCceEEEEcCCCCC---------CHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCcee-
Q 046966          209 PPDNVLFVCQLNPVT---------EDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALI-  278 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~---------~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i-  278 (299)
                      ...++|||+||+..+         ++++|+.+|++||.|.+|+++.      ++|||||+|.+.++|+.|++.|+|..| 
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            457899999999998         6999999999999999999975      468999999999999999999999999 


Q ss_pred             -----------CCeEEEEEecCCccc
Q 046966          279 -----------DDRRICVDFSQSVSK  293 (299)
Q Consensus       279 -----------~g~~l~v~~a~~~~~  293 (299)
                                 .|+.|.|+||++...
T Consensus       206 ~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          206 LPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CTTSTTGGGGGGSCCCEEEECC----
T ss_pred             ccccccccccCCCCEEEEEEccCCCC
Confidence                       899999999997643

>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=99.50  E-value=1.4e-13  Score=103.68  Aligned_cols=84  Identities=18%  Similarity=0.210  Sum_probs=71.8

Q ss_pred             CCCCCceEEEEcCCCCCC-----------HHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCC
Q 046966          207 VKPPDNVLFVCQLNPVTE-----------DEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNN  275 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~-----------e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~  275 (299)
                      .+.+.++|+|.||.....           +++|+++|++||.|.++.+ .++   .++|||||+|.+.++|++|+..|||
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng   86 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDG   86 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCC
Confidence            345689999999944332           5799999999999999965 553   3789999999999999999999999


Q ss_pred             ceeCCeEEEEEecCCcccc
Q 046966          276 ALIDDRRICVDFSQSVSKI  294 (299)
Q Consensus       276 ~~i~g~~l~v~~a~~~~~~  294 (299)
                      ..++|+.|.|.++.++.+.
T Consensus        87 ~~~~gr~l~v~~a~~~~~~  105 (112)
T 2dit_A           87 RWFGGRQITAQAWDGTTDY  105 (112)
T ss_dssp             CEETTEECEEEECCSCCCS
T ss_pred             CEECCcEEEEEEeCCCCCc
Confidence            9999999999999987544

>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=9e-14  Score=121.61  Aligned_cols=84  Identities=18%  Similarity=0.205  Sum_probs=78.7

Q ss_pred             CCCceEEEEcCCCCC-CHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          209 PPDNVLFVCQLNPVT-EDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~-~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .+.++|||+|||+.+ ++++|+++|++||.|..+.++.++ +|.++|||||+|.+.++|.+|+..|||..++|+.|.|.+
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            457899999999995 999999999999999999999985 899999999999999999999999999999999999999


Q ss_pred             cCCccc
Q 046966          288 SQSVSK  293 (299)
Q Consensus       288 a~~~~~  293 (299)
                      +.++..
T Consensus       261 a~~~~~  266 (284)
T 3smz_A          261 CAPGPP  266 (284)
T ss_dssp             CCSSSC
T ss_pred             ecCCCc
Confidence            998753

>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=99.49  E-value=5.6e-14  Score=119.29  Aligned_cols=81  Identities=22%  Similarity=0.347  Sum_probs=74.8

Q ss_pred             CCCCCCceEEEEcCCC-CCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 046966          206 DVKPPDNVLFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC  284 (299)
Q Consensus       206 ~~~~~~~~v~v~nL~~-~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~  284 (299)
                      ...++.++|||+|||+ .+++++|+++|++||.|.+++++.++     +|||||+|.+.++|++|++.|++..+.|+.|.
T Consensus        29 ~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~  103 (229)
T 2adc_A           29 LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIR  103 (229)
T ss_dssp             GGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            3346789999999999 99999999999999999999998874     78999999999999999999999999999999


Q ss_pred             EEecCCc
Q 046966          285 VDFSQSV  291 (299)
Q Consensus       285 v~~a~~~  291 (299)
                      |.++++.
T Consensus       104 v~~a~~~  110 (229)
T 2adc_A          104 ITLSKHQ  110 (229)
T ss_dssp             EECCSCC
T ss_pred             EEEecCc
Confidence            9999865

>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=99.45  E-value=2.3e-14  Score=116.20  Aligned_cols=84  Identities=23%  Similarity=0.297  Sum_probs=73.2

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ...+.++|||+|||+++++++|+++|.+||.+.. .++.+..++.++|||||+|.+.++|.+|+ .|++..+.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~   86 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLE   86 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEe
Confidence            3456899999999999999999999999987765 33444467889999999999999999999 599999999999999


Q ss_pred             ecCCcc
Q 046966          287 FSQSVS  292 (299)
Q Consensus       287 ~a~~~~  292 (299)
                      ++.++.
T Consensus        87 ~~~~~~   92 (175)
T 1fje_B           87 KPKGRD   92 (175)
T ss_dssp             CCCCSS
T ss_pred             cCCCcc
Confidence            998653

>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=99.45  E-value=3.3e-13  Score=117.86  Aligned_cols=77  Identities=23%  Similarity=0.406  Sum_probs=71.7

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC-CeEEEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID-DRRICVD  286 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~-g~~l~v~  286 (299)
                      .++.++|||+|||..+++++|+++|++||.|.+++++.++     +|||||+|.+.++|.+|++.|||..+. |+.|+|+
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            4567899999999999999999999999999999998653     589999999999999999999999999 9999999


Q ss_pred             ecC
Q 046966          287 FSQ  289 (299)
Q Consensus       287 ~a~  289 (299)
                      |++
T Consensus       279 ~ak  281 (282)
T 3pgw_A          279 FAK  281 (282)
T ss_pred             Eec
Confidence            986

>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=99.45  E-value=2.5e-13  Score=117.52  Aligned_cols=83  Identities=22%  Similarity=0.364  Sum_probs=75.0

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+++++++|+++|++||.|..+.+.++      +|||||+|.+.++|.+|+..|+|..+.|+.|.|.+
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 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            356789999999999999999999999999999988543      68999999999999999999999999999999999


Q ss_pred             cCCcccccc
Q 046966          288 SQSVSKIWK  296 (299)
Q Consensus       288 a~~~~~~~~  296 (299)
                      +.+...++.
T Consensus        93 a~~~~~l~v  101 (261)
T 3sde_A           93 ATHGAALTV  101 (261)
T ss_dssp             CCCSSEEEE
T ss_pred             cccCCcccc
Confidence            988665543

>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=99.45  E-value=2.7e-13  Score=100.76  Aligned_cols=83  Identities=23%  Similarity=0.276  Sum_probs=71.9

Q ss_pred             CCCceEEEEcC--CCCCC--------HHHHHHhcccCCCeEEEEEeecCCC--CCeeeEEEEEecCHHHHHHHHHHhCCc
Q 046966          209 PPDNVLFVCQL--NPVTE--------DEDLHVIFSQFGTVVSAEILRDYRT--GESLCYAFVEFEKREACEQAYFKMNNA  276 (299)
Q Consensus       209 ~~~~~v~v~nL--~~~~~--------e~~L~~~f~~~G~i~~~~~~~~~~~--g~~~g~afv~f~~~~~a~~al~~l~~~  276 (299)
                      .|++.|.+.|+  |....        +++|++.|++||.|.++.|++++.+  +.++|++||+|.+.++|.+|++.|||.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            46788999998  33333        3689999999999999999988654  467899999999999999999999999


Q ss_pred             eeCCeEEEEEecCCc
Q 046966          277 LIDDRRICVDFSQSV  291 (299)
Q Consensus       277 ~i~g~~l~v~~a~~~  291 (299)
                      .++||.|+|.++...
T Consensus        83 ~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           83 KFANRVVVTKYCDPD   97 (105)
T ss_dssp             EETTEECEEEEECHH
T ss_pred             EeCCCEEEEEEeCHH
Confidence            999999999998754

>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=99.45  E-value=1.5e-13  Score=114.76  Aligned_cols=79  Identities=14%  Similarity=0.252  Sum_probs=70.1

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCe--EEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCe----
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTV--VSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDR----  281 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i--~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~----  281 (299)
                      .++.++|||+|||+.+++++|+++|++||.|  .+++++.++  +..+|||||+|.+.++|.+|+..|||+.+.|+    
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            3567899999999999999999999999999  899988774  55679999999999999999999999999887    


Q ss_pred             EEEEEec
Q 046966          282 RICVDFS  288 (299)
Q Consensus       282 ~l~v~~a  288 (299)
                      ++.|++|
T Consensus       198 p~~vk~~  204 (205)
T 3tyt_A          198 PYTLKLC  204 (205)
T ss_dssp             CEECEEE
T ss_pred             ceEEEec
Confidence            5776664

>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=99.44  E-value=2.9e-13  Score=118.88  Aligned_cols=81  Identities=12%  Similarity=0.249  Sum_probs=71.4

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..+.++|||+|||+++++++|+++|++||.|..|+++.++.+  ++|||||+|.+.++|.+|++ +++..++|+.|.|.+
T Consensus        38 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~~  114 (292)
T 2ghp_A           38 NRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSH  114 (292)
T ss_dssp             ----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC--CcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEEE
Confidence            346899999999999999999999999999999999998533  57999999999999999994 899999999999999


Q ss_pred             cCCc
Q 046966          288 SQSV  291 (299)
Q Consensus       288 a~~~  291 (299)
                      +.+.
T Consensus       115 ~~~~  118 (292)
T 2ghp_A          115 LTEC  118 (292)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            8654

>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=99.44  E-value=6.4e-14  Score=104.03  Aligned_cols=72  Identities=18%  Similarity=0.374  Sum_probs=63.7

Q ss_pred             EEcCCCCCCHHHHHHhc------------ccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 046966          216 VCQLNPVTEDEDLHVIF------------SQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRI  283 (299)
Q Consensus       216 v~nL~~~~~e~~L~~~f------------~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l  283 (299)
                      +.+|++.+++++|++.|            ++||.|.++.+++++ +++++|||||+|.+.++|.+|+..|||..++||.|
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            45677777777776666            999999999999885 58899999999999999999999999999999999


Q ss_pred             EEEec
Q 046966          284 CVDFS  288 (299)
Q Consensus       284 ~v~~a  288 (299)
                      +|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>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=99.43  E-value=4.4e-13  Score=113.76  Aligned_cols=79  Identities=27%  Similarity=0.452  Sum_probs=72.7

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCC-CeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC-CeEEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFG-TVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID-DRRICV  285 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G-~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~-g~~l~v  285 (299)
                      .++.++|||+|||+.+++++|+++|++|| .|..++++.+     .+|||||+|.+.++|.+|+..|||..++ |+.|+|
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            45689999999999999999999999999 9999998653     3689999999999999999999999999 999999


Q ss_pred             EecCCc
Q 046966          286 DFSQSV  291 (299)
Q Consensus       286 ~~a~~~  291 (299)
                      .|++++
T Consensus       223 ~~a~~~  228 (229)
T 2adc_A          223 SFSKST  228 (229)
T ss_dssp             EECSSC
T ss_pred             EEecCC
Confidence            999874

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.42  E-value=3e-13  Score=111.92  Aligned_cols=79  Identities=27%  Similarity=0.452  Sum_probs=72.9

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCC-CeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC-CeEEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFG-TVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID-DRRICV  285 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G-~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~-g~~l~v  285 (299)
                      .++.++|||+|||..+++++|+++|++|| .|..++++.+     .+|+|||+|.+.++|.+|+..|||..++ |+.|+|
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            45689999999999999999999999999 9999998654     2689999999999999999999999999 999999


Q ss_pred             EecCCc
Q 046966          286 DFSQSV  291 (299)
Q Consensus       286 ~~a~~~  291 (299)
                      .|++++
T Consensus       192 ~~a~~~  197 (198)
T 1qm9_A          192 SFSKST  197 (198)
T ss_dssp             EEECCC
T ss_pred             Eeeccc
Confidence            999874

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.42  E-value=1.4e-13  Score=113.88  Aligned_cols=76  Identities=24%  Similarity=0.397  Sum_probs=71.6

Q ss_pred             CceEEEEcCCC-CCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          211 DNVLFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       211 ~~~v~v~nL~~-~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      +++|||+|||+ .+++++|+++|++||.|..++++.++     +|||||+|.+.++|.+|+..|||..+.|+.|.|.+++
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            68999999999 99999999999999999999998773     6899999999999999999999999999999999998


Q ss_pred             Cc
Q 046966          290 SV  291 (299)
Q Consensus       290 ~~  291 (299)
                      +.
T Consensus        78 ~~   79 (198)
T 1qm9_A           78 HQ   79 (198)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=7.2e-13  Score=100.44  Aligned_cols=81  Identities=16%  Similarity=0.263  Sum_probs=71.5

Q ss_pred             CCceEEEEcCCC--CC---CHHHHHHhcccCCCeEEEEEeecCC----CCCeeeEEEEEecCHHHHHHHHHHhCCceeCC
Q 046966          210 PDNVLFVCQLNP--VT---EDEDLHVIFSQFGTVVSAEILRDYR----TGESLCYAFVEFEKREACEQAYFKMNNALIDD  280 (299)
Q Consensus       210 ~~~~v~v~nL~~--~~---~e~~L~~~f~~~G~i~~~~~~~~~~----~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g  280 (299)
                      ++++|++.|+-.  ++   -+++|++.|++||.|.++.|+.++.    ++.++|++||+|.+.++|.+|++.|||..++|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            688999999832  22   2589999999999999999998854    46789999999999999999999999999999


Q ss_pred             eEEEEEecCC
Q 046966          281 RRICVDFSQS  290 (299)
Q Consensus       281 ~~l~v~~a~~  290 (299)
                      |.|.|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999875

>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=99.40  E-value=1.3e-12  Score=113.09  Aligned_cols=82  Identities=29%  Similarity=0.400  Sum_probs=74.6

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhC-CceeC---CeEEEE
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMN-NALID---DRRICV  285 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~-~~~i~---g~~l~v  285 (299)
                      +..+|||+|||+.+++++|+++|++||.|..+.++.+ .+|+++|||||+|.+.++|.+|+..|| +..+.   +++|.|
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v  173 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIV  173 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEE
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEE
Confidence            3679999999999999999999999999999999999 689999999999999999999999995 44554   999999


Q ss_pred             EecCCcc
Q 046966          286 DFSQSVS  292 (299)
Q Consensus       286 ~~a~~~~  292 (299)
                      .++.+..
T Consensus       174 ~~~~~~~  180 (261)
T 3sde_A          174 EPMEQFD  180 (261)
T ss_dssp             EECCCEE
T ss_pred             eeccccC
Confidence            9988653

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.32  E-value=2.6e-12  Score=105.93  Aligned_cols=75  Identities=17%  Similarity=0.318  Sum_probs=66.2

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccC----C-------CeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCcee
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQF----G-------TVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALI  278 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~----G-------~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i  278 (299)
                      ..++|||+|||+++++++|+++|++|    |       .|..+.+      ++++|||||+|.+.++|++|+ .|||..+
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            46899999999999999999999999    5       5555554      445799999999999999999 8999999


Q ss_pred             CCeEEEEEecCCc
Q 046966          279 DDRRICVDFSQSV  291 (299)
Q Consensus       279 ~g~~l~v~~a~~~  291 (299)
                      .|+.|.|.++.+.
T Consensus        76 ~g~~i~v~~~~~~   88 (198)
T 2yh0_A           76 QGQSLKIRRPHDY   88 (198)
T ss_dssp             TTEEEEEECCCCC
T ss_pred             cCceEEEeCCCCC
Confidence            9999999998764

>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=99.32  E-value=3.1e-12  Score=103.10  Aligned_cols=75  Identities=17%  Similarity=0.315  Sum_probs=67.2

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccC----C-------CeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCcee
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQF----G-------TVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALI  278 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~----G-------~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i  278 (299)
                      +.++|||+|||+++++++|+++|++|    |       .|..+.+.      +++|||||+|.+.++|++|+ .|++..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            46899999999999999999999999    6       66776654      34789999999999999999 8999999


Q ss_pred             CCeEEEEEecCCc
Q 046966          279 DDRRICVDFSQSV  291 (299)
Q Consensus       279 ~g~~l~v~~a~~~  291 (299)
                      .|+.|.|.++.+.
T Consensus        76 ~g~~i~v~~~~~~   88 (172)
T 2g4b_A           76 QGQSLKIRRPHDY   88 (172)
T ss_dssp             TTEECEEECCSSC
T ss_pred             cCceeeecCCccc
Confidence            9999999998764

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.30  E-value=1.8e-11  Score=89.85  Aligned_cols=66  Identities=17%  Similarity=0.199  Sum_probs=58.3

Q ss_pred             CCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCCccc
Q 046966          221 PVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVSK  293 (299)
Q Consensus       221 ~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~~~~  293 (299)
                      ..+++++|+++|++||.|..+.++     ++++|||||+|.+.++|++|++.+++  +.|++|+|.|++++.+
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCC
Confidence            468999999999999999999987     36789999999999999999987554  6799999999987653

>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=99.26  E-value=1.1e-11  Score=110.48  Aligned_cols=76  Identities=17%  Similarity=0.308  Sum_probs=66.1

Q ss_pred             CCCCceEEEEc--CCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC---Ce-
Q 046966          208 KPPDNVLFVCQ--LNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID---DR-  281 (299)
Q Consensus       208 ~~~~~~v~v~n--L~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~---g~-  281 (299)
                      .++..+|||+|  |++.+++++|+++|++||.|.++.+..      +||||||+|.+.++|++|++.|||..+.   |+ 
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            46788999999  688999999999999999999887643      4699999999999999999999999873   45 


Q ss_pred             -EEEEEecC
Q 046966          282 -RICVDFSQ  289 (299)
Q Consensus       282 -~l~v~~a~  289 (299)
                       .|.+.|+.
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             57788875

>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=99.22  E-value=4.6e-11  Score=89.87  Aligned_cols=78  Identities=9%  Similarity=0.087  Sum_probs=65.9

Q ss_pred             CCCceEEEEcCCCCC----------CHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCcee
Q 046966          209 PPDNVLFVCQLNPVT----------EDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALI  278 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~----------~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i  278 (299)
                      .+++.|.+.|+=..-          -+++|++.|++||.|.++.+.++.    ++|++||+|.+.++|.+|++.|||..+
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            457788899873211          135789999999999999987652    489999999999999999999999999


Q ss_pred             CCeEEEEEecCC
Q 046966          279 DDRRICVDFSQS  290 (299)
Q Consensus       279 ~g~~l~v~~a~~  290 (299)
                      +||.|.|.++..
T Consensus        81 ~GR~i~v~~~~~   92 (114)
T 3s6e_A           81 AGKMITAAYVPL   92 (114)
T ss_dssp             TTEECEEEEECH
T ss_pred             CCEEEEEEEEcH
Confidence            999999999864

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.18  E-value=1.1e-10  Score=82.76  Aligned_cols=74  Identities=18%  Similarity=0.284  Sum_probs=64.8

Q ss_pred             CCCCceEEEEcCCC----CCCH----HHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC
Q 046966          208 KPPDNVLFVCQLNP----VTED----EDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID  279 (299)
Q Consensus       208 ~~~~~~v~v~nL~~----~~~e----~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~  279 (299)
                      .||..+|+|...+.    ++..    .+|...|.+||.|..++++.++        +||+|.+.++|.+|++ |||..++
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~   74 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELL   74 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEET
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeC
Confidence            47889999988772    3434    6789999999999999998873        8999999999999997 9999999


Q ss_pred             CeEEEEEecCC
Q 046966          280 DRRICVDFSQS  290 (299)
Q Consensus       280 g~~l~v~~a~~  290 (299)
                      ||.|+|+++++
T Consensus        75 Gr~LkV~lkt~   85 (91)
T 2dnr_A           75 NRTITIALKSP   85 (91)
T ss_dssp             TEEEEEEECCC
T ss_pred             CeEEEEEeCCC
Confidence            99999999886

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.03  E-value=1.1e-09  Score=82.63  Aligned_cols=78  Identities=17%  Similarity=0.209  Sum_probs=68.9

Q ss_pred             CCCCCceEEEEcCCCC-CCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecC-HHHHHHHHHHhC--CceeCCeE
Q 046966          207 VKPPDNVLFVCQLNPV-TEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEK-REACEQAYFKMN--NALIDDRR  282 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~-~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~-~~~a~~al~~l~--~~~i~g~~  282 (299)
                      .-++++.|||+||++. +++++|+++|++||.|..|.+..+..      .|||.|.+ ..+|..|++.|+  +..|.|..
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~   87 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKE   87 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSS
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcE
Confidence            3467999999999999 99999999999999999999987743      49999999 899999999995  67889999


Q ss_pred             EEEEecCC
Q 046966          283 ICVDFSQS  290 (299)
Q Consensus       283 l~v~~a~~  290 (299)
                      +.++....
T Consensus        88 ~~~evL~G   95 (121)
T 1owx_A           88 VTWEVLEG   95 (121)
T ss_dssp             EEEEECCH
T ss_pred             EEEEECCC
Confidence            98887654

>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=98.98  E-value=6.7e-10  Score=79.08  Aligned_cols=74  Identities=18%  Similarity=0.254  Sum_probs=64.1

Q ss_pred             CCCCceEEEEcCCCC-----CCH----HHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCcee
Q 046966          208 KPPDNVLFVCQLNPV-----TED----EDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALI  278 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~-----~~e----~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i  278 (299)
                      .||..+|+|..++..     +..    .+|.+.|.+||.|..++++.++        +||+|.+.++|.+|++ |+|..+
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v   82 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKV   82 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEE
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeee
Confidence            578999999988742     333    5688999999999999998883        9999999999999998 999999


Q ss_pred             CCeEEEEEecCC
Q 046966          279 DDRRICVDFSQS  290 (299)
Q Consensus       279 ~g~~l~v~~a~~  290 (299)
                      +||.|+|++..|
T Consensus        83 ~Gr~L~V~~k~~   94 (95)
T 1ufw_A           83 KGRAVKISGPSS   94 (95)
T ss_dssp             TTEEEEEECCCC
T ss_pred             CCeEEEEeccCC
Confidence            999999998654

>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=98.81  E-value=1e-08  Score=86.21  Aligned_cols=67  Identities=18%  Similarity=0.295  Sum_probs=60.2

Q ss_pred             CHHHHHHhcccCCCeEEEEEeecC----CCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          224 EDEDLHVIFSQFGTVVSAEILRDY----RTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       224 ~e~~L~~~f~~~G~i~~~~~~~~~----~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      .+++|++.|++||.|.++.++.+.    .++.++|++||+|.+.++|.+|++.|||..++||.|.+.++..
T Consensus       142 ~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          142 LEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             HHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            346899999999999999998553    3458999999999999999999999999999999999999864

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.23  E-value=7.1e-06  Score=59.57  Aligned_cols=75  Identities=8%  Similarity=0.123  Sum_probs=66.8

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccC-----CCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQF-----GTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRI  283 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~-----G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l  283 (299)
                      ...+++-+-|||..++...++.+..++     |.+.++.+..|-      +-|+|+|.+...|-+|.-.|+|.+|.||.|
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            347889999999999999999999999     999999887763      479999999999999998999999999999


Q ss_pred             EEEecC
Q 046966          284 CVDFSQ  289 (299)
Q Consensus       284 ~v~~a~  289 (299)
                      ++.-..
T Consensus        93 r~gTv~   98 (117)
T 2l9w_A           93 RSGTIN   98 (117)
T ss_dssp             EEECHH
T ss_pred             EecCHH
Confidence            987543

>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=97.25  E-value=0.00082  Score=48.50  Aligned_cols=76  Identities=11%  Similarity=0.280  Sum_probs=61.7

Q ss_pred             CCceEEEEcCCCCC-CH----HHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 046966          210 PDNVLFVCQLNPVT-ED----EDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC  284 (299)
Q Consensus       210 ~~~~v~v~nL~~~~-~e----~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~  284 (299)
                      -+.+|+|.||+.++ ..    +.++++|..|+.+......+.-  .    -..|.|.+.++|.+|-..||+..++|+.|+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF--R----Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r   77 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF--K----RVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT--T----EEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc--e----EEEEEeCChHHHHHHHHHhccceecCceeE
Confidence            36789999998865 22    4678999999988776655431  1    246899999999999999999999999999


Q ss_pred             EEecCCc
Q 046966          285 VDFSQSV  291 (299)
Q Consensus       285 v~~a~~~  291 (299)
                      |-++.+.
T Consensus        78 ~YFgq~~   84 (104)
T 1wey_A           78 LYFAQTL   84 (104)
T ss_dssp             EECCCCS
T ss_pred             EEecCCC
Confidence            9998854

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.97  E-value=0.0051  Score=44.19  Aligned_cols=73  Identities=19%  Similarity=0.248  Sum_probs=58.5

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhccc-----CCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQ-----FGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC  284 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~-----~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~  284 (299)
                      ...+|.|.|||+.+.++.|.-+|++     -|.|..+....        +-|+|+|.+...|++.++. ..+.|.+..|.
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~Ls   77 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQLS   77 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBCE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEEE
Confidence            4689999999999999999999976     25677776532        4789999999999999853 47889999998


Q ss_pred             EEecCCc
Q 046966          285 VDFSQSV  291 (299)
Q Consensus       285 v~~a~~~  291 (299)
                      |.-.-++
T Consensus        78 V~P~~~~   84 (104)
T 2dhx_A           78 LRPAPPR   84 (104)
T ss_dssp             EEECCCC
T ss_pred             EEcCCCC
Confidence            8755443

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=96.91  E-value=0.005  Score=43.73  Aligned_cols=56  Identities=29%  Similarity=0.383  Sum_probs=47.3

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMN  274 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~  274 (299)
                      ..+.+++ ++|..+...||..+|+.||. ..|+++-|.       .|||.|.+++.|..|+..+.
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            3556666 99999999999999999995 457787773       79999999999999998763

>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=96.90  E-value=0.0017  Score=46.27  Aligned_cols=55  Identities=29%  Similarity=0.376  Sum_probs=47.3

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMN  274 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~  274 (299)
                      .+.+++ ++|..+...||..+|+.|| -..|+++-|.       .|||.|.+++.|..|+..+.
T Consensus         6 ~HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            6 DHVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             CeEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            456777 9999999999999999999 4567887773       79999999999999998764

>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=96.75  E-value=0.013  Score=41.40  Aligned_cols=68  Identities=12%  Similarity=0.119  Sum_probs=53.9

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCC--eeeEEEEEecCHHHHHHHHHHhCCceeC
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGE--SLCYAFVEFEKREACEQAYFKMNNALID  279 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~--~~g~afv~f~~~~~a~~al~~l~~~~i~  279 (299)
                      ++|.|.+||+.++++++.+.++....+..........+.+  .-+-|||.|.+.+++..-.+.++|+.+.
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            4788999999999999999999888766555444332222  2356899999999999999999999865

>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=95.77  E-value=0.039  Score=40.80  Aligned_cols=72  Identities=11%  Similarity=0.204  Sum_probs=55.6

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCC-eEEEEEec
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDD-RRICVDFS  288 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g-~~l~v~~a  288 (299)
                      ..+-|.|.+.|+.. -..+...|++||.|.+.....      ...+-.|.|.++.+|++||. .||..++| -.|-|...
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL~-kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC------CCCeEEEEeCCHHHHHHHHH-hCCeEecCCEEEEEEEC
Confidence            46778888998875 466778899999999876521      22478899999999999995 49999984 66667664


Q ss_pred             C
Q 046966          289 Q  289 (299)
Q Consensus       289 ~  289 (299)
                      .
T Consensus        95 ~   95 (119)
T 1wwh_A           95 I   95 (119)
T ss_dssp             C
T ss_pred             C
Confidence            3

>3kop_A Uncharacterized protein; protein with A cyclophilin-like fold, structural genomics, J center for structural genomics, JCSG; 1.90A {Arthrobacter SP}

Probab=95.33  E-value=0.14  Score=40.28  Aligned_cols=105  Identities=17%  Similarity=0.131  Sum_probs=60.4

Q ss_pred             eEEEEecCCCChHHHHHHHHhhh--C----CCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCCCCC
Q 046966           11 DIVIDLFVDKCPRTTNNFLQHCK--N----KYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKHDK   84 (299)
Q Consensus        11 ~i~ieL~~~~~P~~~~nF~~l~~--~----~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~   84 (299)
                      .++.+|..+.||+||+.|+++.=  +    ..|-|-.++-..|.|-.                  .....|+.+..+  .
T Consensus        34 ~~~A~Lldd~APkTcaA~~~~LP~~~~viHarwSGeeVy~~lp~f~~------------------~~~g~EN~T~~P--~   93 (188)
T 3kop_A           34 TCKALLLDDVAPRTSKAVWDALPQSSQVFHGKYARNEIYNLVPAFAP------------------KEPGAENTTVTP--I   93 (188)
T ss_dssp             EEEEEECTTTSHHHHHHHHHHCCEEEECEECSSSSSEEEEEEECCSS------------------SCCCSCSEESSC--C
T ss_pred             EEEEEEccccChHHHHHHHHhCCCCcceEEEEEecceEEEECCcccc------------------cCCCcCCCCCCC--C
Confidence            47899999999999999999761  1    12444444433333110                  113445344333  4


Q ss_pred             ceEEEEEcC-----C-------C------CCCcceEEEEecCCCCCCCCC-----ceEEEEeecCHHHHHHHHh
Q 046966           85 VGTVGMASA-----G-------R------DLNASQFYITLRDNLHYLDEK-----HTIFGEVAEGLETLTRINQ  135 (299)
Q Consensus        85 ~G~l~~~~~-----~-------~------~~~~s~FfI~~~~~~~~ld~~-----~~vfG~V~~G~~vl~~i~~  135 (299)
                      +|-|++...     |       +      .....++.|-.+.+.-.+.++     -.+|++|++|+|-+.++.+
T Consensus        94 pGDIl~f~f~p~~lG~~~yGy~~~~~~~~~~~~~dl~ifYG~~~~l~~~~~GwlpGN~F~TIveGle~la~~c~  167 (188)
T 3kop_A           94 PGDVCYFTFTSNDLKTPSHGYEADSGTDEVQTIVDLAVFYGRNNLLLNGDTGWVPGNVFATIVEGLDEMAAACQ  167 (188)
T ss_dssp             TTEEEEEEEEHHHHSSGGGCC--------CCEEEEEEEECSSSCCCEETTTEECCEEEEEEEEESHHHHHHHHH
T ss_pred             CCcEEEEecCCcccCCccccccccccccCCCcceEEEEEecccccccccccceecCcEEEEEecCHHHHHHHHH
Confidence            677777411     1       0      111246777777532212222     2699999999998877754

>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=95.23  E-value=0.023  Score=44.10  Aligned_cols=35  Identities=9%  Similarity=0.012  Sum_probs=28.8

Q ss_pred             EEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCc
Q 046966          240 SAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNA  276 (299)
Q Consensus       240 ~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~  276 (299)
                      .++++.+.  .+++|||||+|.+.++|++|++.+++.
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhccc
Confidence            35666763  468999999999999999999888754

>2nnz_A Hypothetical protein; beta-barrel, structural genomics, ontario centre for structu proteomics, OCSP, unknown function; NMR {Archaeoglobus fulgidus}

Probab=94.77  E-value=0.071  Score=41.41  Aligned_cols=102  Identities=14%  Similarity=0.258  Sum_probs=63.4

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhh--hC--CCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCccccc-c
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHC--KN--KYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVD-E   75 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~--~~--~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~-e   75 (299)
                      |.|.|.-.-..++++|+.+.||+||+.|+++.  +.  ..|.+-.++.+ |-.                      +.. |
T Consensus        30 ~~I~i~~~~~~~~a~L~D~~aP~Ta~~f~~~LPl~~~~~~~g~E~y~~l-p~~----------------------l~~~e   86 (153)
T 2nnz_A           30 MRLRIRFESAECEVELYEEWAPETVRAIADALPIKSTANRWGDEIYFTT-QVA----------------------VEKEE   86 (153)
T ss_dssp             CCEEEEETTEEEEECCCTTSCHHHHHHHHHTCSEEEEEEEETTEEEECC-SCC----------------------CCCSS
T ss_pred             eEEEEEECCEEEEEEEcCCCCHHHHHHHHHhCCcEEEHHhhCCcEEEEC-CCC----------------------CCCCC
Confidence            56777777788999999999999999999976  11  12322222211 100                      011 2


Q ss_pred             cccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCC------CCceEEEEeecCHHHHHHH
Q 046966           76 IRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLD------EKHTIFGEVAEGLETLTRI  133 (299)
Q Consensus        76 ~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld------~~~~vfG~V~~G~~vl~~i  133 (299)
                       +.. .....|-|++...+     ..+.|-.++. +...      ..-.+||+|++|++.|..+
T Consensus        87 -n~~-~~~~~GDI~Yy~pg-----~~LaIFYg~~-p~s~~e~~~as~~~~lG~I~~gle~L~~~  142 (153)
T 2nnz_A           87 -NSK-DVVELGDVAYWIPG-----KAICLFFGKT-PISDDKIRPASAVNVIGRIVNSMEGLKGV  142 (153)
T ss_dssp             -CCB-CCCCTTEEEEETTT-----TEEEEESSCC-TTCTTSCCCCSSEEEEEECCSCCCCGGGC
T ss_pred             -CCc-ccCCCCeEEEeCCC-----CEEEEEECCc-cccccccccccccEEEEEEccCHHHHhhC
Confidence             111 12357888886543     2488888763 2221      2357999999998888776

>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=94.32  E-value=0.027  Score=43.38  Aligned_cols=42  Identities=12%  Similarity=0.030  Sum_probs=38.2

Q ss_pred             CCCeeeEEEEEecCHHHHHHHHHHh-CCceeCCeEEEEEecCCc
Q 046966          249 TGESLCYAFVEFEKREACEQAYFKM-NNALIDDRRICVDFSQSV  291 (299)
Q Consensus       249 ~g~~~g~afv~f~~~~~a~~al~~l-~~~~i~g~~l~v~~a~~~  291 (299)
                      ....+|+++++|.+.++|++|++.| ||..++| .+.++++.++
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~   51 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKT   51 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTE
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCc
Confidence            4567899999999999999999999 9999999 9999998764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=94.17  E-value=0.082  Score=37.57  Aligned_cols=78  Identities=13%  Similarity=0.148  Sum_probs=53.2

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCC--CeeeEEEEEecCHHHHHHHHHHhCCceeCC-----eEE
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTG--ESLCYAFVEFEKREACEQAYFKMNNALIDD-----RRI  283 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g--~~~g~afv~f~~~~~a~~al~~l~~~~i~g-----~~l  283 (299)
                      .-+|.|..||+.+||+++.+.++..-.+..........+.  ..-.-|||.|.+.++...-.+.++|+.+.+     .+.
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            5679999999999999998888765443221111111111  112458999999999999999999987643     234


Q ss_pred             EEEec
Q 046966          284 CVDFS  288 (299)
Q Consensus       284 ~v~~a  288 (299)
                      .|++|
T Consensus        89 ~VE~A   93 (97)
T 2l08_A           89 VVEFA   93 (97)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            45555

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=93.49  E-value=0.047  Score=50.26  Aligned_cols=55  Identities=20%  Similarity=0.296  Sum_probs=40.8

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHH
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF  271 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~  271 (299)
                      .+.|+|. .|..+++.+|.++|++||.|.++..-.+  .|   -||.|+|.+.+++..++.
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~--~g---~~~~vef~~~~~~~~~~~  107 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYES--FG---LYAVVEFCQKESIGSLQN  107 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECS--SS---EEEEEECC---CCHHHHS
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEcc--CC---eEEEEEeCCHHHHHHHHh
Confidence            4789997 7999999999999999999999876554  23   599999999999887764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=93.41  E-value=0.077  Score=39.84  Aligned_cols=78  Identities=15%  Similarity=0.261  Sum_probs=53.2

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEE-EEEeec--------CCCC-----CeeeEEEEEecCHHHHHHHHHHhCCc
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVS-AEILRD--------YRTG-----ESLCYAFVEFEKREACEQAYFKMNNA  276 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~-~~~~~~--------~~~g-----~~~g~afv~f~~~~~a~~al~~l~~~  276 (299)
                      ...|.|-+.|++.. ..+.+.|++||.|.+ ......        +.+.     .....-.|.|.+..+|.+||. .||.
T Consensus         7 e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~-~NG~   84 (132)
T 3p3d_A            7 ELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALL-ENGA   84 (132)
T ss_dssp             -CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHT-TTTC
T ss_pred             ceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHH-hCCe
Confidence            45677778877655 446678999999875 211110        0000     123566899999999999995 4999


Q ss_pred             eeCCeEEEEEecCC
Q 046966          277 LIDDRRICVDFSQS  290 (299)
Q Consensus       277 ~i~g~~l~v~~a~~  290 (299)
                      .++|..|-|...++
T Consensus        85 ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           85 VFNGVLLGVIPYTK   98 (132)
T ss_dssp             EETTEECEEEECCH
T ss_pred             EeCcEEEEEEECCH
Confidence            99999887877653

>1zx8_A Hypothetical protein TM1367; structural genomics, joint center for structural genomics, J protein structure initiative, PSI; HET: 1PE; 1.90A {Thermotoga maritima} SCOP: b.62.1.3 PDB: 2ka0_A

Probab=86.41  E-value=2.9  Score=31.54  Aligned_cols=101  Identities=21%  Similarity=0.222  Sum_probs=61.3

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhh----hCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCccccccc
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHC----KNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEI   76 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~----~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~   76 (299)
                      |.|.+-.....+.++|+..  |.|++.|++..    +-..|. ..++--.|-.. .                    .+| 
T Consensus        13 ~~~~~~~~~~~v~a~L~Dn--p~Ta~~~~~~LPl~~~~~~~g-~E~y~~~p~~l-~--------------------~~e-   67 (136)
T 1zx8_A           13 MRVELLFESGKCVIDLNEE--YEVVKLLKEKIPFESVVNTWG-EEIYFSTPVNV-Q--------------------KME-   67 (136)
T ss_dssp             EEEEEECSSCEEEEEEETT--SHHHHHHHHHCSEEEECEESS-SEEEEECSCCC-C--------------------CCS-
T ss_pred             eEEEEeeCCcEEEEEEcCC--HHHHHHHHHHCCcEEEHHHhC-CcEEEECCccC-C--------------------CCC-
Confidence            5566777778899999744  88999999987    222353 33332222210 0                    001 


Q ss_pred             ccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCC------CCceEEEEeecCHHHHHHH
Q 046966           77 RADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLD------EKHTIFGEVAEGLETLTRI  133 (299)
Q Consensus        77 ~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld------~~~~vfG~V~~G~~vl~~i  133 (299)
                      +.... ...|-|+.-..+     ..|.|-.++. +...      ...++||+|.+|++.+..+
T Consensus        68 ~~~~~-~~~GDIaYw~pg-----g~LaIFyg~~-p~s~~e~~~a~~v~~lGrI~~~l~~l~~v  123 (136)
T 1zx8_A           68 NPREV-VEIGDVGYWPPG-----KALCLFFGKT-PMSDDKIQPASAVNVIGKIVEGLEDLKKI  123 (136)
T ss_dssp             SEESS-BCTTEEEEEGGG-----TEEEEESSCC-TTCSSSBCCSSCEEEEEEEEECGGGGGGC
T ss_pred             CCCcc-CCCCcEEEeCCC-----CEEEEEeCCC-ccccCccccCcCcEEEEEEccCHHHHhhC
Confidence            11111 256888876553     3588888873 3222      2368999999998877766

---

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	299
d1xwna1	166	b.62.1.1 (A:1-166) Peptidyl-prolyl cis-trans isome	9e-44
d1zkca1	178	b.62.1.1 (A:280-457) Peptidyl-prolyl cis-trans iso	1e-40
d2ok3a1	159	b.62.1.1 (A:1-159) Cyclophilin-like protein PPIL3B	1e-38
d2b71a1	169	b.62.1.1 (A:23-191) Cyclophilin-like protein PY006	9e-33
d1w74a_	171	b.62.1.1 (A:) Peptidyl-prolyl cis-trans isomerase	7e-32
d2cfea1	162	b.62.1.1 (A:1-162) Cyclophilin-like allergen Mal s	2e-31
d2a2na1	164	b.62.1.1 (A:483-646) Peptidylprolyl isomerase doma	8e-31
d2fu0a1	155	b.62.1.1 (A:5-159) Putative cyclophilin PFE0505w {	1e-30
d1qnga_	170	b.62.1.1 (A:) Cyclophilin (eukaryotic) {Plasmodium	1e-30
d1a33a_	174	b.62.1.1 (A:) Cyclophilin (eukaryotic) {Nematode (	9e-29
d1h0pa_	182	b.62.1.1 (A:) Cyclophilin (eukaryotic) {Caenorhabd	1e-28
d2rmca_	182	b.62.1.1 (A:) Cyclophilin (eukaryotic) {Mouse (Mus	1e-28
d2c3ba1	171	b.62.1.1 (A:1-171) Cyclophilin (eukaryotic) {Asper	6e-28
d1ihga2	195	b.62.1.1 (A:2-196) Cyclophilin 40 isomerase domain	3e-27
d1xo7a_	166	b.62.1.1 (A:) Cyclophilin (eukaryotic) {Trypanosom	4e-27
d1lopa_	164	b.62.1.1 (A:) Peptidyl-prolyl cis-trans isomerase	6e-27
d2igva1	172	b.62.1.1 (A:1-172) Cyclophilin (eukaryotic) {Caeno	2e-26
d2z6wa1	164	b.62.1.1 (A:2-165) Mitochondrial peptidyl-prolyl c	5e-26
d1qoia_	173	b.62.1.1 (A:) Cyclophilin (eukaryotic) {Human (Hom	1e-23
d2r99a1	161	b.62.1.1 (A:139-299) Mitochondrial peptidyl-prolyl	4e-23
d1v9ta_	166	b.62.1.1 (A:) Peptidyl-prolyl cis-trans isomerase	2e-22
d1z81a1	186	b.62.1.1 (A:25-210) Cyclophilin (eukaryotic) {Plas	1e-21
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	5e-17
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	6e-16
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-15
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-14
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-14
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-14
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-14
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-14
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	3e-14
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-14
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-14
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	5e-14
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-13
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	5e-13
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	6e-13
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	6e-13
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	7e-13
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	9e-13
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-12
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	1e-12
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-12
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-12
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-12
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-12
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	4e-12
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	5e-12
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	7e-12
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	8e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	9e-12
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-11
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 3e-11
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	3e-11
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-11
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	4e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	4e-11
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-11
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-11
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	5e-11
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	6e-11
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	7e-11
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-10
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-10
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	3e-10
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-10
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-08
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	7e-10
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-09
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	1e-09
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	2e-09
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-09
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-09
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	4e-09
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	4e-09
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	5e-09
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	6e-09
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	8e-09
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-08
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-08
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-08
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-08
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	8e-08
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-08
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	1e-07
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-07
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-07
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	2e-07
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-07
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	3e-07
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	7e-07
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	8e-07
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	2e-06
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-06
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	9e-06
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	9e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	3e-05
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	4e-05
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	4e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	0.001
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	0.003

>d1xwna1 b.62.1.1 (A:1-166) Peptidyl-prolyl cis-trans isomerase-like 1, PPIL1 {Human (Homo sapiens) [TaxId: 9606]} Length = 166

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidyl-prolyl cis-trans isomerase-like 1, PPIL1
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  145 bits (366), Expect = 9e-44
 Identities = 67/153 (43%), Positives = 92/153 (60%), Gaps = 2/153 (1%)

Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTG 62
           V +ETS+G IV++L+    P+T  NF +  +  YYNG  FH I KDF+ Q GDPTGTG G
Sbjct: 14  VYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGRG 73

Query: 63  GRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGE 122
           G S+Y  + F DE+  DLK    G + MA+AG D N SQF++TL      LD KHTIFG 
Sbjct: 74  GASIY-GKQFEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPTQW-LDGKHTIFGR 131

Query: 123 VAEGLETLTRINQAVVDEENRPPQQIIIKQTYV 155
           V +G+  + R+     + ++RP   + I + Y 
Sbjct: 132 VCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYP 164

>d1zkca1 b.62.1.1 (A:280-457) Peptidyl-prolyl cis-trans isomerase-like 2, Cyclophilin-60, PPI domain {Human (Homo sapiens) [TaxId: 9606]} Length = 178

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidyl-prolyl cis-trans isomerase-like 2, Cyclophilin-60, PPI domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  137 bits (346), Expect = 1e-40
 Identities = 71/177 (40%), Positives = 102/177 (57%), Gaps = 3/177 (1%)

Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTG 62
           V + T+ GD+ ++L  D  P+T  NF++ CK  YY+G +FH   ++F+ Q GDPTGTGTG
Sbjct: 3   VRLHTNKGDLNLELHCDLTPKTCENFIRLCKKHYYDGTIFHRSIRNFVIQGGDPTGTGTG 62

Query: 63  GRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGE 122
           G S +  + F DE R +L H   G + MA++G + N SQF+IT R   + LD+KHTIFG 
Sbjct: 63  GESYW-GKPFKDEFRPNLSHTGRGILSMANSGPNSNRSQFFITFRSCAY-LDKKHTIFGR 120

Query: 123 VAEGLETLTRINQAVVDEEN-RPPQQIIIKQTYVLYPPELADDSIPEGEPKDELEPP 178
           V  G + LT +     D +  RP ++I I  T V   P    D+    E K +L+  
Sbjct: 121 VVGGFDVLTAMENVESDPKTDRPKEEIRIDATTVFVDPYEEADAQIAQERKTQLKVA 177

>d2ok3a1 b.62.1.1 (A:1-159) Cyclophilin-like protein PPIL3B {Human (Homo sapiens) [TaxId: 9606]} Length = 159

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin-like protein PPIL3B
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  131 bits (331), Expect = 1e-38
 Identities = 72/160 (45%), Positives = 100/160 (62%), Gaps = 3/160 (1%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTG 60
           MSV + T +GDI I++F ++ P+T  NFL  C + YYNGC+FH   K F+ QTGDPTGTG
Sbjct: 1   MSVTLHTDVGDIKIEVFCERTPKTCENFLALCASNYYNGCIFHRNIKGFMVQTGDPTGTG 60

Query: 61  TGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIF 120
            GG S++  + F DE    LKH+  G V MA+ G + N SQF+IT      +LD K+T+F
Sbjct: 61  RGGNSIW-GKKFEDEYSEYLKHNVRGVVSMANNGPNTNGSQFFITYGKQ-PHLDMKYTVF 118

Query: 121 GEVAEGLETLTRINQAVVDEEN-RPPQQIIIKQTYVLYPP 159
           G+V +GLETL  + +  V+E+  RP   + IK   +   P
Sbjct: 119 GKVIDGLETLDELEKLPVNEKTYRPLNDVHIKDITIHANP 158

>d2b71a1 b.62.1.1 (A:23-191) Cyclophilin-like protein PY00693 {Plasmodium yoelii [TaxId: 5861]} Length = 169

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin-like protein PY00693
species: Plasmodium yoelii [TaxId: 5861]

 Score =  116 bits (292), Expect = 9e-33
 Identities = 58/151 (38%), Positives = 88/151 (58%), Gaps = 2/151 (1%)

Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTG 62
           + I T+LGD  ++L+    P+T  NF   C+  +Y+  +FH +  +F+ Q GDPTGTG G
Sbjct: 19  ITIYTNLGDFEVELYWYHSPKTCLNFYTLCEMGFYDNTIFHRVIPNFVIQGGDPTGTGKG 78

Query: 63  GRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGE 122
           G+S+Y + F  DEI  +LKH   G + M++ G + N+SQF+ITL    H LD KHTIF  
Sbjct: 79  GKSIYGEYFE-DEINKELKHTGAGILSMSNNGPNTNSSQFFITLAPLPH-LDGKHTIFAR 136

Query: 123 VAEGLETLTRINQAVVDEENRPPQQIIIKQT 153
           V++ +  +  I        N+P   + I +T
Sbjct: 137 VSKNMTCIENIASVQTTATNKPIFDLKILRT 167

>d1w74a_ b.62.1.1 (A:) Peptidyl-prolyl cis-trans isomerase A, PpiA {Mycobacterium tuberculosis [TaxId: 1773]} Length = 171

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidyl-prolyl cis-trans isomerase A, PpiA
species: Mycobacterium tuberculosis [TaxId: 1773]

 Score =  114 bits (286), Expect = 7e-32
 Identities = 57/172 (33%), Positives = 87/172 (50%), Gaps = 22/172 (12%)

Query: 1   MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNK---------------YYNGCLFHNI 45
            +  + T+ GDI I LF +  P+T  NF+   +                 +Y+G +FH +
Sbjct: 4   ATATLHTNRGDIKIALFGNHAPKTVANFVGLAQGTKDYSTQNASGGPSGPFYDGAVFHRV 63

Query: 46  HKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYIT 105
            + F+ Q GDPTGTG GG        F DE   +L+ DK   + MA+AG   N SQF+IT
Sbjct: 64  IQGFMIQGGDPTGTGRGG----PGYKFADEFHPELQFDKPYLLAMANAGPGTNGSQFFIT 119

Query: 106 LRDNLHYLDEKHTIFGEV--AEGLETLTRINQAVVDEENRPPQQIIIKQTYV 155
           +     +L+ +HTIFGEV  AE    +  I++   D  +RP   ++I+   +
Sbjct: 120 VGKT-PHLNRRHTIFGEVIDAESQRVVEAISKTATDGNDRPTDPVVIESITI 170

>d2cfea1 b.62.1.1 (A:1-162) Cyclophilin-like allergen Mal s 6 {Malassezia sympodialis [TaxId: 76777]} Length = 162

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin-like allergen Mal s 6
species: Malassezia sympodialis [TaxId: 76777]

 Score =  113 bits (283), Expect = 2e-31
 Identities = 55/148 (37%), Positives = 71/148 (47%), Gaps = 6/148 (4%)

Query: 7   TSLGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQTGDPTGTGTGG 63
             LG I   LF D  P+T  NF   C   K   Y G  FH +  DF+ Q GD T     G
Sbjct: 13  APLGTIKFKLFDDVVPKTAANFRALCTGEKGFGYAGSHFHRVIPDFMLQGGDFTAGNGTG 72

Query: 64  RSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEV 123
                   F DE    LKH+K G + MA+AG + N SQF+IT      +LD KH +FGEV
Sbjct: 73  GKSIYGAKFADENF-QLKHNKPGLLSMANAGPNTNGSQFFITTVVT-SWLDGKHVVFGEV 130

Query: 124 AEGLETLTRINQAVVDEENRPPQQIIIK 151
            +G+  +  I +A      +P  +I I 
Sbjct: 131 IDGMNVVKAI-EAEGSGSGKPRSRIEIA 157

>d2a2na1 b.62.1.1 (A:483-646) Peptidylprolyl isomerase domain and WD repeat-containing protein 1, PPWD1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 164

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidylprolyl isomerase domain and WD repeat-containing protein 1, PPWD1, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  111 bits (278), Expect = 8e-31
 Identities = 70/155 (45%), Positives = 97/155 (62%), Gaps = 3/155 (1%)

Query: 2   SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGT 61
           S +I TS+GDI   LF  +CP+T  NF  H +N YYNG  FH I K F+ QTGDPTGTG 
Sbjct: 11  SAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNGYYNGHTFHRIIKGFMIQTGDPTGTGM 70

Query: 62  GGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFG 121
           GG S++   F  DE  + L+HD+  T+ MA+AG + N SQF+IT+     +LD KHT+FG
Sbjct: 71  GGESIWGGEFE-DEFHSTLRHDRPYTLSMANAGSNTNGSQFFITVVPT-PWLDNKHTVFG 128

Query: 122 EVAEGLETLTRINQAVVDEEN-RPPQQIIIKQTYV 155
            V +G+E + RI+   V+ +  +P + + I    V
Sbjct: 129 RVTKGMEVVQRISNVKVNPKTDKPYEDVSIINITV 163

>d2fu0a1 b.62.1.1 (A:5-159) Putative cyclophilin PFE0505w {Plasmodium falciparum [TaxId: 5833]} Length = 155

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Putative cyclophilin PFE0505w
species: Plasmodium falciparum [TaxId: 5833]

 Score =  110 bits (276), Expect = 1e-30
 Identities = 64/154 (41%), Positives = 90/154 (58%), Gaps = 2/154 (1%)

Query: 2   SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGT 61
           S +I T++GDI I LF  +C +T  NF  H  N YYN C+FH + K F+ QTGDP+G GT
Sbjct: 3   SAIIYTTMGDIHISLFYKECKKTVQNFSVHSINGYYNNCIFHRVIKHFMVQTGDPSGDGT 62

Query: 62  GGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFG 121
           GG S++    F DE    L H K   V MA+ G + N SQF+IT      +LD KHT+FG
Sbjct: 63  GGESIW-GNEFEDEFFDHLNHSKPFMVSMANCGPNTNGSQFFITTVPC-PWLDFKHTVFG 120

Query: 122 EVAEGLETLTRINQAVVDEENRPPQQIIIKQTYV 155
           +V +G + +  I +   D+ ++P + I I    +
Sbjct: 121 KVTQGSKIVLDIEKVRTDKRDKPLEDIKILNIKI 154

>d1qnga_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Plasmodium falciparum [TaxId: 5833]} Length = 170

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Plasmodium falciparum [TaxId: 5833]

 Score =  111 bits (277), Expect = 1e-30
 Identities = 53/154 (34%), Positives = 82/154 (53%), Gaps = 14/154 (9%)

Query: 7   TSLGDIVIDLFVDKCPRTTNNFLQHC---------KNKYYNGCLFHNIHKDFIAQTGDP- 56
           ++ G I+ +LF D  PRT  NF   C         KN +Y   +FH I   F+ Q GD  
Sbjct: 15  SNAGRIIFELFSDITPRTCENFRALCTGEKIGSRGKNLHYKNSIFHRIIPQFMCQGGDIT 74

Query: 57  TGTGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEK 116
            G G+GG S+Y   F   +   ++KHD+ G + MA+AG + N+SQF+ITL     +LD K
Sbjct: 75  NGNGSGGESIYGRSF--TDENFNMKHDQPGLLSMANAGPNTNSSQFFITLVPC-PWLDGK 131

Query: 117 HTIFGEVAEGLETLTRINQAVVDEENRPPQQIII 150
           H +FG+V EG+  +  + +    +     + ++I
Sbjct: 132 HVVFGKVIEGMNVVREM-EKEGAKSGYVKRSVVI 164

>d1a33a_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Nematode (Brugia malayi) [TaxId: 6279]} Length = 174

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Nematode (Brugia malayi) [TaxId: 6279]

 Score =  106 bits (265), Expect = 9e-29
 Identities = 58/156 (37%), Positives = 82/156 (52%), Gaps = 15/156 (9%)

Query: 7   TSLGDIVIDLFVDKCPRTTNNFLQHC-----------KNKYYNGCLFHNIHKDFIAQTGD 55
              G IV++L+ D  PRT NNFL  C           K  +Y G  FH + K+F+ Q GD
Sbjct: 15  NLAGRIVMELYNDIAPRTCNNFLMLCTGMAGTGKISGKPLHYKGSTFHRVIKNFMIQGGD 74

Query: 56  PT-GTGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLD 114
            T G GTGG S+Y      D+    +KHD+   V MA+ G + N SQF+IT      +L+
Sbjct: 75  FTKGDGTGGESIY--GGMFDDEEFVMKHDEPFVVSMANKGPNTNGSQFFITTTPA-PHLN 131

Query: 115 EKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIII 150
             H +FG+V  G E +T+I     + +NRP   ++I
Sbjct: 132 NIHVVFGKVVSGQEVVTKIEYLKTNSKNRPLADVVI 167

>d1h0pa_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Caenorhabditis elegans, isoform 5 [TaxId: 6239]} Length = 182

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Caenorhabditis elegans, isoform 5 [TaxId: 6239]

 Score =  106 bits (265), Expect = 1e-28
 Identities = 60/167 (35%), Positives = 91/167 (54%), Gaps = 10/167 (5%)

Query: 7   TSLGDIVIDLFVDKCPRTTNNFLQHCK---NKYYNGCLFHNIHKDFIAQTGDPT-GTGTG 62
             +G IVI LF    P+T  NF++  K    + Y G  FH +  DF+ Q GD T G GTG
Sbjct: 18  KPIGRIVIGLFGKTVPKTATNFIELAKKPKGEGYPGSKFHRVIADFMIQGGDFTRGDGTG 77

Query: 63  GRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGE 122
           GRS+Y ++F   +    LKH   G + MA+AG D N SQF+IT      +LD +H +FG+
Sbjct: 78  GRSIYGEKF--ADENFKLKHYGAGWLSMANAGADTNGSQFFITTVKT-PWLDGRHVVFGK 134

Query: 123 VAEGLETLTRINQAVVDEENRPPQQIIIKQTYVL---YPPELADDSI 166
           + EG++ + +I Q      +RP Q +II  +  +    P  +  +++
Sbjct: 135 ILEGMDVVRKIEQTEKLPGDRPKQDVIIAASGHIAVDTPFSVEREAV 181

>d2rmca_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Mouse (Mus musculus), variant C [TaxId: 10090]} Length = 182

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Mouse (Mus musculus), variant C [TaxId: 10090]

 Score =  106 bits (264), Expect = 1e-28
 Identities = 59/166 (35%), Positives = 83/166 (50%), Gaps = 7/166 (4%)

Query: 7   TSLGDIVIDLFVDKCPRTTNNFLQHCKNK---YYNGCLFHNIHKDFIAQTGDPT-GTGTG 62
             +G IVI LF +  P+T  NF+     +    Y G +FH + KDF+ Q GD T   GTG
Sbjct: 19  KDVGRIVIGLFGNVVPKTVENFVALATGEKGYGYKGSIFHRVIKDFMIQGGDFTARDGTG 78

Query: 63  GRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGE 122
           G S+Y + F   +    LKH  +G V MA+AG D N SQF+ITL      LD KH +FG+
Sbjct: 79  GMSIYGETF--PDENFKLKHYGIGWVSMANAGPDTNGSQFFITLTKPTW-LDGKHVVFGK 135

Query: 123 VAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPPELADDSIPE 168
           V +G+  +  I     D  +RP     I  +  +         +P+
Sbjct: 136 VLDGMTVVHSIELQATDGHDRPLTDCTIVNSGKIDVKTPFVVEVPD 181

>d2c3ba1 b.62.1.1 (A:1-171) Cyclophilin (eukaryotic) {Aspergillus fumigatus [TaxId: 5085]} Length = 171

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Aspergillus fumigatus [TaxId: 5085]

 Score =  104 bits (259), Expect = 6e-28
 Identities = 58/153 (37%), Positives = 77/153 (50%), Gaps = 10/153 (6%)

Query: 5   IETSLGDIVIDLFVDKCPRTTNNFLQHCKNK---YYNGCLFHNIHKDFIAQTGDP-TGTG 60
            ET +G IV +LF    P+T  NF + CK      Y    FH I  +F+ Q GD   G G
Sbjct: 16  AETKVGRIVFNLFDKDVPKTAKNFRELCKRPAGEGYRESTFHRIIPNFMIQGGDFTRGNG 75

Query: 61  TGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIF 120
           TGGRS+Y D+F   +     KHDK G + MA+AG + N SQF+IT      +LD KH +F
Sbjct: 76  TGGRSIYGDKF--ADENFSRKHDKKGILSMANAGPNTNGSQFFITTAVT-SWLDGKHVVF 132

Query: 121 GEVAE--GLETLTRINQAVVDEEN-RPPQQIII 150
           GEVA+      +  I        + R   +  I
Sbjct: 133 GEVADEKSYSVVKEIEALGSSSGSVRSNTRPKI 165

>d1ihga2 b.62.1.1 (A:2-196) Cyclophilin 40 isomerase domain {Cow (Bos taurus) [TaxId: 9913]} Length = 195

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin 40 isomerase domain
species: Cow (Bos taurus) [TaxId: 9913]

 Score =  102 bits (256), Expect = 3e-27
 Identities = 59/178 (33%), Positives = 83/178 (46%), Gaps = 19/178 (10%)

Query: 7   TSLGDIVIDLFVDKCPRTTNNFLQHC-----------KNKYYNGCLFHNIHKDFIAQTGD 55
             +G IV++LF D  P+T  NF   C           K  ++ GC FH I K F+ Q GD
Sbjct: 26  ERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGD 85

Query: 56  PTGTGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDE 115
            +     G        F DE     KHDK G + MA+AG + N SQF+IT      +LD 
Sbjct: 86  FSNQNGTGGESIYGEKFEDENF-HYKHDKEGLLSMANAGSNTNGSQFFITTVPT-PHLDG 143

Query: 116 KHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLYPPELADDSIPEGEPKD 173
           KH +FG+V +G+     + + V  +  +P +  +I +   L   E  D  I    PKD
Sbjct: 144 KHVVFGQVIKGMGVAKIL-ENVEVKGEKPAKLCVIAECGEL--KEGDDWGI---FPKD 195

>d1xo7a_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Trypanosoma cruzi [TaxId: 5693]} Length = 166

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Trypanosoma cruzi [TaxId: 5693]

 Score =  101 bits (253), Expect = 4e-27
 Identities = 51/154 (33%), Positives = 82/154 (53%), Gaps = 8/154 (5%)

Query: 7   TSLGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQTGDPT-GTGTG 62
             +G +VI LF +  P+T  NF Q         Y G +FH + ++F+ Q GD T   GTG
Sbjct: 17  EPVGRVVIGLFGNDVPKTVENFKQLASGENGFGYKGSIFHRVIRNFMIQGGDFTNFDGTG 76

Query: 63  GRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGE 122
           G+S+Y  RF  + ++       VG V MA+AG + N SQF++T      +LD +H +FG+
Sbjct: 77  GKSIYGTRFDDENLK---IKHFVGAVSMANAGPNSNGSQFFVTTAPT-PWLDGRHVVFGK 132

Query: 123 VAEGLETLTRINQAVVDEENRPPQQIIIKQTYVL 156
           V EG++ + ++        ++P + + I    VL
Sbjct: 133 VVEGMDVVKKVENTKTGLNDKPKKAVKINDCGVL 166

>d1lopa_ b.62.1.1 (A:) Peptidyl-prolyl cis-trans isomerase A, PpiA {Escherichia coli [TaxId: 562]} Length = 164

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidyl-prolyl cis-trans isomerase A, PpiA
species: Escherichia coli [TaxId: 562]

 Score =  101 bits (252), Expect = 6e-27
 Identities = 40/165 (24%), Positives = 67/165 (40%), Gaps = 14/165 (8%)

Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTG 62
           V   T+ GDIVI  F DK P T  NFL +C+  +YN  +FH +   F+ Q G        
Sbjct: 2   VTFHTNHGDIVIKTFDDKAPETVKNFLDYCREGFYNNTIFHRVINGFMIQGGGFEPGMKQ 61

Query: 63  GRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHY-------LDE 115
             +        +E    LK+ +       +       +QF+I + DN             
Sbjct: 62  KATKE---PIKNEANNGLKNTRGTLAMARTQAPHSATAQFFINVVDNDFLNFSGESLQGW 118

Query: 116 KHTIFGEVAEGLETLTRINQAVVDE----ENRPPQQIIIKQTYVL 156
            + +F EV +G++ + +I           ++ P + +II+   V 
Sbjct: 119 GYCVFAEVVDGMDEVDKIKGVATGRSGMHQDVPKEDVIIESVTVS 163

>d2igva1 b.62.1.1 (A:1-172) Cyclophilin (eukaryotic) {Caenorhabditis elegans, isoform 3 [TaxId: 6239]} Length = 172

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Caenorhabditis elegans, isoform 3 [TaxId: 6239]

 Score = 99.9 bits (248), Expect = 2e-26
 Identities = 46/154 (29%), Positives = 70/154 (45%), Gaps = 13/154 (8%)

Query: 7   TSLGDIVIDLFVDKCPRTTNNFLQHC----------KNKYYNGCLFHNIHKDFIAQTGDP 56
            + G IV++L+ D  P+T  NF   C          K  ++ G  FH I  +F+ Q GD 
Sbjct: 15  KASGRIVMELYDDVVPKTAGNFRALCTGENGIGKSGKPLHFKGSKFHRIIPNFMIQGGDF 74

Query: 57  TGTGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEK 116
           T     G        F DE     KH   G + MA+AG + N SQF++         D K
Sbjct: 75  TRGNGTGGESIYGEKFPDENF-KEKHTGPGVLSMANAGPNTNGSQFFLCTVKTEWL-DGK 132

Query: 117 HTIFGEVAEGLETLTRINQAVVDEENRPPQQIII 150
           H +FG V EGL+ +  + ++   +  +P +  +I
Sbjct: 133 HVVFGRVVEGLDVVKAV-ESNGSQSGKPVKDCMI 165

>d2z6wa1 b.62.1.1 (A:2-165) Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F {Human (Homo sapiens) [TaxId: 9606]} Length = 164

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 98.8 bits (245), Expect = 5e-26
 Identities = 53/148 (35%), Positives = 78/148 (52%), Gaps = 8/148 (5%)

Query: 7   TSLGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQTGD-PTGTGTG 62
             LG +V++L  D  P+T  NF   C   K   Y G  FH +   F+ Q GD     GTG
Sbjct: 14  KPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTG 73

Query: 63  GRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGE 122
           G+S+Y  RF   +    LKH   G + MA+AG + N SQF+I       +LD KH +FG 
Sbjct: 74  GKSIYGSRF--PDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKT-DWLDGKHVVFGH 130

Query: 123 VAEGLETLTRINQAVVDEENRPPQQIII 150
           V EG++ + +I ++   +  R  ++I+I
Sbjct: 131 VIEGMDVVKKI-ESFGSKSGRTSKKIVI 157

>d1qoia_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Human (Homo sapiens), U4/U6 snRNP-specific cyclophilin snucyp-20 [TaxId: 9606]} Length = 173

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Human (Homo sapiens), U4/U6 snRNP-specific cyclophilin snucyp-20 [TaxId: 9606]

 Score = 92.6 bits (229), Expect = 1e-23
 Identities = 46/152 (30%), Positives = 67/152 (44%), Gaps = 10/152 (6%)

Query: 7   TSLGDIVIDLFVDKCPRTTNNFLQHC--------KNKYYNGCLFHNIHKDFIAQTGDPTG 58
             +G + I+LF D  P+T  NF Q C            Y G  FH + KDF+ Q GD   
Sbjct: 18  QEVGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRVIKDFMIQGGDFV- 76

Query: 59  TGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHT 118
            G G       R    +    L+H   G + MA++G   N  QF+IT        D KH 
Sbjct: 77  NGDGTGVASIYRGPFADENFKLRHSAPGLLSMANSGPSTNGCQFFITCSKCDWL-DGKHV 135

Query: 119 IFGEVAEGLETLTRINQAVVDEENRPPQQIII 150
           +FG++ +GL  + +I        N+P   ++I
Sbjct: 136 VFGKIIDGLLVMRKIENVPTGPNNKPKLPVVI 167

>d2r99a1 b.62.1.1 (A:139-299) Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F {Human (Homo sapiens) [TaxId: 9606]} Length = 161

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 91.1 bits (225), Expect = 4e-23
 Identities = 56/148 (37%), Positives = 79/148 (53%), Gaps = 8/148 (5%)

Query: 7   TSLGDIVIDLFVDKCPRTTNNFLQHC---KNKYYNGCLFHNIHKDFIAQTGDPT-GTGTG 62
              G I + L  D  P T  NF   C   K   + G  FH I   F+ Q GD T   GTG
Sbjct: 13  KPAGRIQMLLRSDVVPMTAENFRCLCTHEKGFGFKGSSFHRIIPQFMCQGGDFTNHNGTG 72

Query: 63  GRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGE 122
           G+S+Y  +F   +    LKH   G + MA++G + N SQF++T      +LD KH +FGE
Sbjct: 73  GKSIYGKKFD--DENFILKHTGPGLLSMANSGPNTNGSQFFLTCDKT-DWLDGKHVVFGE 129

Query: 123 VAEGLETLTRINQAVVDEENRPPQQIII 150
           V EGL+ L +I +A   ++ +P Q++II
Sbjct: 130 VTEGLDVLRQI-EAQGSKDGKPKQKVII 156

>d1v9ta_ b.62.1.1 (A:) Peptidyl-prolyl cis-trans isomerase A, PpiA {Escherichia coli [TaxId: 562]} Length = 166

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidyl-prolyl cis-trans isomerase A, PpiA
species: Escherichia coli [TaxId: 562]

 Score = 89.2 bits (220), Expect = 2e-22
 Identities = 40/162 (24%), Positives = 74/162 (45%), Gaps = 11/162 (6%)

Query: 3   VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTG 62
           VL+ TS G+I ++L   K P +  NF+ +  + +YN   FH +   F+ Q G  T     
Sbjct: 7   VLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQ 66

Query: 63  GRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRD----NLHYLDEKHT 118
            +         +E    L++ +       +A +D   SQF+I + D    +    D  + 
Sbjct: 67  KKPNP---PIKNEADNGLRNTRGTIAMARTADKDSATSQFFINVADNAFLDHGQRDFGYA 123

Query: 119 IFGEVAEGLETLTRINQAVVDE----ENRPPQQIIIKQTYVL 156
           +FG+V +G++   +I+Q    +    +N P + ++I    VL
Sbjct: 124 VFGKVVKGMDVADKISQVPTHDVGPYQNVPSKPVVILSATVL 165

>d1z81a1 b.62.1.1 (A:25-210) Cyclophilin (eukaryotic) {Plasmodium yoelii [TaxId: 5861]} Length = 186

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Plasmodium yoelii [TaxId: 5861]

 Score = 87.6 bits (216), Expect = 1e-21
 Identities = 51/156 (32%), Positives = 80/156 (51%), Gaps = 15/156 (9%)

Query: 7   TSLGDIVIDLFVDKCPRTTNNFLQHCKNKY--------YNGCLFHNIHKDFIAQTGDP-T 57
             LG    +LF +  P+T+ NF Q C  +Y        Y   +FH + K+F+ Q GD   
Sbjct: 28  NFLGKFKFELFQNIVPKTSENFRQFCTGEYKVNNLPVGYKNTIFHRVIKEFMIQGGDFIN 87

Query: 58  GTGTGGRSVYEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKH 117
             G+G  S+Y ++F  D+   D+KHDK G + MA++G + N  QF+IT      +LD K+
Sbjct: 88  HNGSGSLSIYGEKF--DDENFDIKHDKEGLLSMANSGPNTNGCQFFITT-KKCEWLDGKN 144

Query: 118 TIFGEVAEG--LETLTRI-NQAVVDEENRPPQQIII 150
            +FG + +   L  L +I N +V     +P   I +
Sbjct: 145 VVFGRIIDNDSLLLLKKIENVSVTPYIYKPKIPINV 180

>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 = 72.3 bits (177), Expect = 5e-17
 Identities = 25/76 (32%), Positives = 41/76 (53%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L+P   +  L+  FS  G ++S  + RD  T  SL YA+V F++    E+A   M
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 274 NNALIDDRRICVDFSQ 289
           N  +I  + + + +SQ
Sbjct: 63  NFDVIKGKPVRIMWSQ 78

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 69.6 bits (170), Expect = 6e-16
 Identities = 15/89 (16%), Positives = 41/89 (46%), Gaps = 2/89 (2%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYR-TGESLCYAFVEFEKREAC 266
           K   + + V  +       ++  +FS FG + +  + +    TG    + FV+F  ++  
Sbjct: 5   KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 64

Query: 267 EQAYFKMNN-ALIDDRRICVDFSQSVSKI 294
           ++A+  + +   +  RR+ ++++ S   +
Sbjct: 65  KKAFNALCHSTHLYGRRLVLEWADSEVTV 93

>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 = 67.2 bits (164), Expect = 6e-15
 Identities = 17/92 (18%), Positives = 39/92 (42%), Gaps = 9/92 (9%)

Query: 200 GDIPDADVKPPDNVLFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFV 258
           G     D +  ++ +F+  LN  V +  D+  IFS++G +V   + + +        AFV
Sbjct: 4   GSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGF--------AFV 55

Query: 259 EFEKREACEQAYFKMNNALIDDRRICVDFSQS 290
           ++        A    +  +I  + + ++ +  
Sbjct: 56  QYVNERNARAAVAGEDGRMIAGQVLDINLAAE 87

>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 = 65.5 bits (159), Expect = 2e-14
 Identities = 27/81 (33%), Positives = 39/81 (48%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
               VL+V  L    +D+ LH  F  FG +   +I  DY T +   +AFVEFE  E    
Sbjct: 3   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 62

Query: 269 AYFKMNNALIDDRRICVDFSQ 289
           A   MN + +  R I V+ ++
Sbjct: 63  AIDNMNESELFGRTIRVNLAK 83

>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 = 65.4 bits (159), Expect = 2e-14
 Identities = 24/91 (26%), Positives = 44/91 (48%), Gaps = 1/91 (1%)

Query: 203 PDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEK 262
           P ++ +  D  ++V  L+    +  L  +F Q G VV+  + +D  TG+   Y FVEF  
Sbjct: 2   PISE-RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 60

Query: 263 REACEQAYFKMNNALIDDRRICVDFSQSVSK 293
            E  + A   M+   +  + I V+ + + +K
Sbjct: 61  EEDADYAIKIMDMIKLYGKPIRVNKASAHNK 91

>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 = 65.4 bits (159), Expect = 2e-14
 Identities = 21/80 (26%), Positives = 37/80 (46%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L+  T +E ++ +FS+ G +    +  D     +  + FVE+  R   E A   +
Sbjct: 10  LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 69

Query: 274 NNALIDDRRICVDFSQSVSK 293
           N   +DDR I  D+     +
Sbjct: 70  NGTRLDDRIIRTDWDAGFKE 89

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 65.1 bits (158), Expect = 2e-14
 Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 3/83 (3%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEIL---RDYRTGESLCYAFVEFEKREACEQAY 270
           LF+  LN  T +E L  +FS+ G + S  I           S+ + FVE++K E  ++A 
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 271 FKMNNALIDDRRICVDFSQSVSK 293
            ++    +D  ++ V  S+  +K
Sbjct: 61  KQLQGHTVDGHKLEVRISERATK 83

>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 = 65.0 bits (158), Expect = 2e-14
 Identities = 23/79 (29%), Positives = 42/79 (53%)

Query: 211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
           +  L V  L     D +L+ +F   G + +  I+RDY+TG S  YAFV+F      ++A 
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 271 FKMNNALIDDRRICVDFSQ 289
             +N   + ++R+ V +++
Sbjct: 62  KVLNGITVRNKRLKVSYAR 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 = 64.6 bits (157), Expect = 3e-14
 Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L V  L+    D D+  +F++FGT+  A +    R+G SL  A V FE++    +A  + 
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHY-DRSGRSLGTADVHFERKADALKAMKQY 61

Query: 274 NNALIDDRRICVDFSQS 290
           N   +D R + +    S
Sbjct: 62  NGVPLDGRPMNIQLVTS 78

>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 = 65.0 bits (158), Expect = 3e-14
 Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L+V  L     D+ L  IF ++G++V   ILRD  TG     AFV + KRE  ++A   +
Sbjct: 9   LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 68

Query: 274 NNALID--DRRICVDF 287
           NN + +   + + V  
Sbjct: 69  NNVIPEGGSQPLSVRL 84

>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 = 65.4 bits (159), Expect = 3e-14
 Identities = 15/82 (18%), Positives = 36/82 (43%), Gaps = 3/82 (3%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
             + +L++  L      E+++ IF ++G +      R   T E+   A+V +E     + 
Sbjct: 5   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIFDAKN 61

Query: 269 AYFKMNNALIDDRRICVDFSQS 290
           A   ++   + +R + V +  +
Sbjct: 62  ACDHLSGFNVCNRYLVVLYYNA 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.3 bits (156), Expect = 5e-14
 Identities = 25/77 (32%), Positives = 41/77 (53%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
            P+  L V  L+  T + DL  +FS++G +    I+ D ++  S  +AFV FE  +  ++
Sbjct: 7   DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 66

Query: 269 AYFKMNNALIDDRRICV 285
           A  + N   +D RRI V
Sbjct: 67  AKERANGMELDGRRIRV 83

>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 = 62.0 bits (150), Expect = 4e-13
 Identities = 20/80 (25%), Positives = 39/80 (48%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LF+  L     D+ +  + + FG + +  +++D  TG S  YAF E+      +QA   +
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 274 NNALIDDRRICVDFSQSVSK 293
           N   + D+++ V  +   +K
Sbjct: 64  NGMQLGDKKLLVQRASVGAK 83

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.6 bits (149), Expect = 5e-13
 Identities = 23/90 (25%), Positives = 35/90 (38%), Gaps = 6/90 (6%)

Query: 204 DADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKR 263
           D D      +L+V  L   T +E +   F+              R  +   YAFV F  R
Sbjct: 1   DEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPG------AVERVKKIRDYAFVHFSNR 54

Query: 264 EACEQAYFKMNNALIDDRRICVDFSQSVSK 293
           E   +A   +N  ++D   I V  ++ V K
Sbjct: 55  EDAVEAMKALNGKVLDGSPIEVTLAKPVDK 84

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.6 bits (149), Expect = 6e-13
 Identities = 22/91 (24%), Positives = 35/91 (38%), Gaps = 4/91 (4%)

Query: 203 PDADVKPPD---NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVE 259
           P  ++ P +     +F  QL       DL   FS  G V    I+ D  +  S   A+VE
Sbjct: 7   PVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVE 66

Query: 260 FEKREACEQAYFKMNNALIDDRRICVDFSQS 290
           F + ++       +    +    I V  SQ+
Sbjct: 67  FCEIQSVP-LAIGLTGQRLLGVPIIVQASQA 96

>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 = 61.2 bits (148), Expect = 6e-13
 Identities = 15/80 (18%), Positives = 31/80 (38%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
           KP   ++ V  +      +++   F  +  +  +  L+    G     A V FE R+   
Sbjct: 6   KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEAT 65

Query: 268 QAYFKMNNALIDDRRICVDF 287
            A   +N+  I  R++ +  
Sbjct: 66  AAVIDLNDRPIGSRKVKLVL 85

>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 = 60.8 bits (147), Expect = 7e-13
 Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 3/85 (3%)

Query: 208 KPPDNV--LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREA 265
           K P+ +  LF+  L+  T DE L   F Q+GT+    ++RD  T  S  + FV +   E 
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 266 CEQAYFKMNNALIDDRRICVDFSQS 290
            + A        +D R +    + S
Sbjct: 61  VDAAM-NARPHKVDGRVVEPKRAVS 84

>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 = 61.3 bits (148), Expect = 9e-13
 Identities = 27/82 (32%), Positives = 41/82 (50%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
           P    LF+  L     D+DL  +F  FG VVSA++  D +T  S C+ FV ++   + + 
Sbjct: 16  PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQA 75

Query: 269 AYFKMNNALIDDRRICVDFSQS 290
           A   MN   I  +R+ V   +S
Sbjct: 76  AIQSMNGFQIGMKRLKVQLKRS 97

>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 = 60.0 bits (145), Expect = 1e-12
 Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 1/74 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +F+  L+  T  E L   F QFG V    ++RD  T  S  + FV F  +   ++     
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV-LAQ 61

Query: 274 NNALIDDRRICVDF 287
           +   +D + I    
Sbjct: 62  SRHELDSKTIDPKV 75

>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 = 60.1 bits (145), Expect = 1e-12
 Identities = 26/86 (30%), Positives = 42/86 (48%), Gaps = 4/86 (4%)

Query: 205 ADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKRE 264
           A ++  D  L+V  L      ++L  +FSQ+G ++++ IL D  TG S    F+ F+KR 
Sbjct: 2   ASIR--DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRI 59

Query: 265 ACEQAYFKMNNALID--DRRICVDFS 288
             E+A   +N          I V F+
Sbjct: 60  EAEEAIKGLNGQKPSGATEPITVKFA 85

>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 = 60.4 bits (146), Expect = 1e-12
 Identities = 14/82 (17%), Positives = 31/82 (37%), Gaps = 6/82 (7%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
           P +  ++   +     D+ +   FS FG ++   +  +        Y+FV F   E+   
Sbjct: 16  PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAH 69

Query: 269 AYFKMNNALIDDRRICVDFSQS 290
           A   +N   I+   +   + + 
Sbjct: 70  AIVSVNGTTIEGHVVKCYWGKE 91

>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 = 60.1 bits (145), Expect = 2e-12
 Identities = 21/76 (27%), Positives = 37/76 (48%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L V  L      E+   +F   G + S +++RD  TG+SL Y FV +   +  E+A   +
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 274 NNALIDDRRICVDFSQ 289
           N   +  + I V +++
Sbjct: 65  NGLRLQTKTIKVSYAR 80

>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 = 59.7 bits (144), Expect = 2e-12
 Identities = 20/82 (24%), Positives = 41/82 (50%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
              +  + V  L+  T + DL  +F  FG++    + +D  TG+S  +AF+ F +RE   
Sbjct: 5   ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 64

Query: 268 QAYFKMNNALIDDRRICVDFSQ 289
           +A   ++    D   + V++++
Sbjct: 65  RAIAGVSGFGYDHLILNVEWAK 86

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.2 bits (145), Expect = 2e-12
 Identities = 19/95 (20%), Positives = 33/95 (34%), Gaps = 8/95 (8%)

Query: 204 DADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEIL--------RDYRTGESLCY 255
           D D    ++ ++V  LN     +DL   F Q G V   +           D  TG+    
Sbjct: 1   DPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD 60

Query: 256 AFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS 290
           A V +E     + A    +       ++ V  ++ 
Sbjct: 61  ATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 95

>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 = 59.3 bits (143), Expect = 3e-12
 Identities = 28/83 (33%), Positives = 47/83 (56%), Gaps = 2/83 (2%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
           K     +F+  L+   +++ L+  FS FG ++S +++ D     S  Y FV FE +EA E
Sbjct: 5   KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAE 62

Query: 268 QAYFKMNNALIDDRRICVDFSQS 290
           +A  KMN  L++DR++ V   +S
Sbjct: 63  RAIEKMNGMLLNDRKVFVGRFKS 85

>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 = 59.3 bits (143), Expect = 4e-12
 Identities = 17/89 (19%), Positives = 39/89 (43%), Gaps = 1/89 (1%)

Query: 210 PDNVLFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
           P++ +++  LN  + +DE    + + F        +   R+ +    AFV F++  +   
Sbjct: 2   PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATN 61

Query: 269 AYFKMNNALIDDRRICVDFSQSVSKIWKK 297
           A   M      D+ + + ++++ S I  K
Sbjct: 62  ALRSMQGFPFYDKPMRIQYAKTDSDIIAK 90

>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 = 58.9 bits (142), Expect = 5e-12
 Identities = 21/91 (23%), Positives = 38/91 (41%), Gaps = 3/91 (3%)

Query: 200 GDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVE 259
           G +        D  ++V  L P    +D+  +F ++G +   ++           +AFVE
Sbjct: 3   GGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGP---PFAFVE 59

Query: 260 FEKREACEQAYFKMNNALIDDRRICVDFSQS 290
           FE     E A +  +    D  R+ V+F +S
Sbjct: 60  FEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS 90

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.4 bits (141), Expect = 7e-12
 Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L V  L   T ++DL   FS FG V+  ++ +D +TG S  + FV F + E   +   + 
Sbjct: 11  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR 70

Query: 274 NNALIDDRRICVDFSQS 290
           +  +ID R        S
Sbjct: 71  H--MIDGRWCDCKLPNS 85

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.2 bits (140), Expect = 8e-12
 Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 1/78 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAE-ILRDYRTGESLCYAFVEFEKREACEQAYFK 272
           +F+  L+P  +++ L+  FS FG ++    I+RD  TG S  YAF+ F   +A + A   
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 273 MNNALIDDRRICVDFSQS 290
           MN   + +R I V ++  
Sbjct: 61  MNGQYLCNRPITVSYAFK 78

>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 = 58.2 bits (140), Expect = 9e-12
 Identities = 22/87 (25%), Positives = 43/87 (49%), Gaps = 2/87 (2%)

Query: 204 DADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKR 263
           +++ K     L V  +     D DL  +F QFG ++  EI+ +     S  + FV FE  
Sbjct: 4   NSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENS 61

Query: 264 EACEQAYFKMNNALIDDRRICVDFSQS 290
              ++A  K++  +++ R+I V+ + +
Sbjct: 62  ADADRAREKLHGTVVEGRKIEVNNATA 88

>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 = 57.3 bits (138), Expect = 1e-11
 Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +F+  L+  T  +DL   FS+FG VV   +  D  TG S  + FV F++ E+ ++     
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKV-MDQ 60

Query: 274 NNALIDDRRICV 285
               ++ + I  
Sbjct: 61  KEHKLNGKVIDP 72

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.0 bits (137), Expect = 3e-11
 Identities = 12/75 (16%), Positives = 30/75 (40%), Gaps = 1/75 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           + + +      +E    +  ++G V    +  +      +   +V+F + E  E+A   +
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDL 88

Query: 274 NNALIDDRRICVDFS 288
           NN   + + I  + S
Sbjct: 89  NNRWFNGQPIHAELS 103

>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 = 57.1 bits (137), Expect = 3e-11
 Identities = 8/90 (8%), Positives = 27/90 (30%), Gaps = 11/90 (12%)

Query: 209 PPDNVLFVCQLNP-----VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKR 263
              + L  C  N               +F  +    + +  + ++         + F   
Sbjct: 3   SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK------RVRINFSNP 56

Query: 264 EACEQAYFKMNNALIDDRRICVDFSQSVSK 293
            +   A  +++      + + + F+Q++  
Sbjct: 57  LSAADARLRLHKTEFLGKEMKLYFAQTLHI 86

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 56.7 bits (136), Expect = 3e-11
 Identities = 22/79 (27%), Positives = 39/79 (49%)

Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
            +LFV  ++   +++++   F  +G + +  +  D RTG S  YA VE+E  +    A  
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 272 KMNNALIDDRRICVDFSQS 290
            +N A I  + I VD+   
Sbjct: 68  ALNGAEIMGQTIQVDWCFV 86

>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 = 56.7 bits (136), Expect = 4e-11
 Identities = 24/97 (24%), Positives = 43/97 (44%), Gaps = 3/97 (3%)

Query: 197 ECIGDIP---DADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESL 253
           E I  IP     +   P+ VL++  L+P   + DL  +F++F       I     TG   
Sbjct: 1   EEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMR 60

Query: 254 CYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS 290
             AF+ F  +E   QA   +N   +  + + ++F ++
Sbjct: 61  GQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKN 97

>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 = 56.6 bits (136), Expect = 4e-11
 Identities = 22/82 (26%), Positives = 36/82 (43%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
                LFV  L+  + +EDL  +FS +G +       D  T +   +AFV F   E   +
Sbjct: 6   SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVK 65

Query: 269 AYFKMNNALIDDRRICVDFSQS 290
           AY +++  +   R + V  S  
Sbjct: 66  AYAEVDGQVFQGRMLHVLPSTI 87

>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 = 55.7 bits (134), Expect = 5e-11
 Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L+P T +E +   F  FG V S E+  D +T +   + F+ F++ E  ++   + 
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI-MEK 60

Query: 274 NNALIDDRRICV 285
               +   +  +
Sbjct: 61  KYHNVGLSKCEI 72

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.2 bits (135), Expect = 5e-11
 Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 2/82 (2%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
                L+V  L+    +  +  +FSQ G   S +++ ++    +  Y FVEF +      
Sbjct: 6   GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAA 63

Query: 269 AYFKMNNALIDDRRICVDFSQS 290
           A   MN   I  + + V+++ +
Sbjct: 64  ALAAMNGRKILGKEVKVNWATT 85

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.7 bits (134), Expect = 5e-11
 Identities = 18/83 (21%), Positives = 38/83 (45%), Gaps = 6/83 (7%)

Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
           + LFV  L P   +E++  +F ++G      I +D        + F+  E R   E A  
Sbjct: 9   SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAKV 62

Query: 272 KMNNALIDDRRICVDFSQSVSKI 294
           +++N  +  +++ V F+   + +
Sbjct: 63  ELDNMPLRGKQLRVRFACHSASL 85

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 56.2 bits (135), Expect = 6e-11
 Identities = 15/92 (16%), Positives = 34/92 (36%), Gaps = 5/92 (5%)

Query: 199 IGDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFV 258
           + D   +        L    L+    +++L  +F     +         + G+S   A++
Sbjct: 4   LEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYI 58

Query: 259 EFEKREACEQAYFKMNNALIDDRRICVDFSQS 290
           EF+     E+   +   A ID R + + ++  
Sbjct: 59  EFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE 90

>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 = 55.1 bits (132), Expect = 7e-11
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L+  T  ED+   F QFG V  A ++ D  T     + FV FE  +  E+   ++
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EI 60

Query: 274 NNALIDDRRICVDF 287
           +   I+++ +    
Sbjct: 61  HFHEINNKMVECKK 74

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.3 bits (133), Expect = 1e-10
 Identities = 14/68 (20%), Positives = 23/68 (33%), Gaps = 4/68 (5%)

Query: 226 EDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV 285
           EDL V  S+FG +    +   +  G     A V F   E  +     ++      R+I  
Sbjct: 34  EDLRVECSKFGQIRKLLLFDRHPDG----VASVSFRDPEEADYCIQTLDGRWFGGRQITA 89

Query: 286 DFSQSVSK 293
                 + 
Sbjct: 90  QAWDGTTD 97

>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 = 54.4 bits (130), Expect = 1e-10
 Identities = 12/79 (15%), Positives = 27/79 (34%)

Query: 211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
           +  L++    P     ++  +      V  +  L   R   S  +A+++   +E      
Sbjct: 1   ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 60

Query: 271 FKMNNALIDDRRICVDFSQ 289
            K+N   I+   +    S 
Sbjct: 61  EKLNGLKIEGYTLVTKVSN 79

>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 = 54.7 bits (131), Expect = 2e-10
 Identities = 18/77 (23%), Positives = 32/77 (41%), Gaps = 1/77 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LF+  L+  T +E L   + Q+G +    ++RD  +  S  + FV F      + A    
Sbjct: 23  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA-MAA 81

Query: 274 NNALIDDRRICVDFSQS 290
               ID R +    + +
Sbjct: 82  RPHSIDGRVVEPKRAVA 98

>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 = 54.3 bits (130), Expect = 3e-10
 Identities = 14/81 (17%), Positives = 26/81 (32%), Gaps = 1/81 (1%)

Query: 210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQA 269
           P    F+  L     +E +   F                      + + EFE  ++   A
Sbjct: 14  PPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSA 73

Query: 270 YFKMNNALIDDRRICVDFSQS 290
              +N   + ++RI VD +  
Sbjct: 74  -LSLNEESLGNKRIRVDVADQ 93

>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 = 55.8 bits (133), Expect = 4e-10
 Identities = 18/82 (21%), Positives = 35/82 (42%), Gaps = 1/82 (1%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
                +FV  +   TE+  L   F Q+G +   EI+ D  +G+   +AFV F+  ++ ++
Sbjct: 95  LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK 154

Query: 269 AYFKMNNALIDDRRICVDFSQS 290
                    ++     V  + S
Sbjct: 155 I-VIQKYHTVNGHNCEVRKALS 175

>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 = 51.9 bits (123), Expect = 1e-08
 Identities = 21/94 (22%), Positives = 36/94 (38%), Gaps = 2/94 (2%)

Query: 208 KPPDNV--LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREA 265
           K P+ +  LF+  L+  T DE L   F Q+GT+    ++RD  T  S  + FV +   E 
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 266 CEQAYFKMNNALIDDRRICVDFSQSVSKIWKKSY 299
            + A     + +                    ++
Sbjct: 61  VDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAH 94

>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 = 52.4 bits (125), Expect = 7e-10
 Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 1/75 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  +   TE+  L   F Q+G +   EI+ D  +G+   +AFV F+  ++ ++     
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQ 63

Query: 274 NNALIDDRRICVDFS 288
               ++     V  +
Sbjct: 64  KYHTVNGHNCEVRKA 78

>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 = 52.8 bits (126), Expect = 1e-09
 Identities = 28/80 (35%), Positives = 40/80 (50%), Gaps = 1/80 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  L   T D  L   F  FG +  A ++ D +TG+S  Y FV    R A E+A  K 
Sbjct: 13  IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC-KD 71

Query: 274 NNALIDDRRICVDFSQSVSK 293
            N +ID R+  V+ +   +K
Sbjct: 72  PNPIIDGRKANVNLAYLGAK 91

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.1 bits (124), Expect = 1e-09
 Identities = 22/86 (25%), Positives = 37/86 (43%), Gaps = 5/86 (5%)

Query: 206 DVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREA 265
           ++ PP   L +  + P   +EDL V+FS  G VV           +    A ++    E 
Sbjct: 5   NIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVK----GFKFFQKDRKMALIQMGSVEE 60

Query: 266 CEQAYFKMNNALIDD-RRICVDFSQS 290
             QA   ++N  + +   + V FS+S
Sbjct: 61  AVQALIDLHNHDLGENHHLRVSFSKS 86

>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 = 51.7 bits (123), Expect = 2e-09
 Identities = 25/80 (31%), Positives = 41/80 (51%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           LFV  L+  T ++ L  +FS++G +    +++D  T  S  + FV FE  +  + A   M
Sbjct: 8   LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 67

Query: 274 NNALIDDRRICVDFSQSVSK 293
           N   +D R+I VD +   S 
Sbjct: 68  NGKSVDGRQIRVDQAGKSSD 87

>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 = 50.8 bits (121), Expect = 3e-09
 Identities = 16/80 (20%), Positives = 34/80 (42%), Gaps = 7/80 (8%)

Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
           N L++  L+P    +DL  +F      +        +      YAFV++  +    +A  
Sbjct: 2   NKLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIE 55

Query: 272 KMNNAL-IDDRRICVDFSQS 290
            ++  + +  + + VD+S S
Sbjct: 56  TLSGKVELHGKIMEVDYSVS 75

>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 = 51.2 bits (122), Expect = 3e-09
 Identities = 15/80 (18%), Positives = 33/80 (41%), Gaps = 4/80 (5%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSA--EILRDYRTGESLCYAFVEFEKREACEQAYF 271
           LF+  +  + + E++    ++    V             ++  +AFVE+E   A   A  
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 272 KMNNA--LIDDRRICVDFSQ 289
           K+      +   +I VD+++
Sbjct: 64  KLMPGRIQLWGHQIAVDWAE 83

>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 = 50.8 bits (121), Expect = 4e-09
 Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 8/84 (9%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
            P   L+V  L P T    L   F +FG++ + + ++         +A++++E  +A + 
Sbjct: 15  NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD------SFAYIQYESLDAAQA 68

Query: 269 AYFKMNNALID--DRRICVDFSQS 290
           A  KM    +   DRR+ VDF++S
Sbjct: 69  ACAKMRGFPLGGPDRRLRVDFAKS 92

>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 = 51.8 bits (123), Expect = 4e-09
 Identities = 26/110 (23%), Positives = 52/110 (47%), Gaps = 3/110 (2%)

Query: 187 KEAHSRAVALECIGDIPDADVKPPDNV---LFVCQLNPVTEDEDLHVIFSQFGTVVSAEI 243
           + A  + +  +    IP   + P  +V   L V  +    ++  L  +F ++G + S +I
Sbjct: 15  QTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKI 74

Query: 244 LRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVSK 293
           + D  T +S  Y FV+F+   + +QA   +N   I ++R+ V  + S  +
Sbjct: 75  VCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQ 124

>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 = 50.4 bits (120), Expect = 5e-09
 Identities = 15/77 (19%), Positives = 33/77 (42%), Gaps = 7/77 (9%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV +      +++L   FSQ+G V+   I + +R      +AFV F   +  +      
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQIAQSL--CG 60

Query: 274 NNALIDDRRICVDFSQS 290
            + +I    + +  ++ 
Sbjct: 61  EDLIIKGISVHISNAEP 77

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (121), Expect = 6e-09
 Identities = 18/80 (22%), Positives = 33/80 (41%), Gaps = 6/80 (7%)

Query: 212 NVLFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
           +VL V  LNP     + L ++F  +G V   +IL + +       A V+       + A 
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK-----ENALVQMADGNQAQLAM 57

Query: 271 FKMNNALIDDRRICVDFSQS 290
             +N   +  + I +  S+ 
Sbjct: 58  SHLNGHKLHGKPIRITLSKH 77

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.6 bits (118), Expect = 8e-09
 Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 8/78 (10%)

Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
           N L+V     +T    L   FS FG +       D         AFV +EK E+ +QA  
Sbjct: 6   NTLYVYGE-DMTP-TLLRGAFSPFGNI------IDLSMDPPRNCAFVTYEKMESADQAVA 57

Query: 272 KMNNALIDDRRICVDFSQ 289
           ++N   ++  ++ V+ ++
Sbjct: 58  ELNGTQVESVQLKVNIAR 75

>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 = 49.7 bits (118), Expect = 1e-08
 Identities = 10/77 (12%), Positives = 26/77 (33%), Gaps = 6/77 (7%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILR-----DYRTGESLCYAFVEFEKREACEQ 268
           L+V  +     +E +   F+    +              +  +   +AF+EF   +   Q
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 269 AYFKMNNALIDDRRICV 285
           A    +  +   + + +
Sbjct: 64  AMA-FDGIIFQGQSLKI 79

>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 = 49.0 bits (116), Expect = 2e-08
 Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 6/78 (7%)

Query: 212 NVLFVCQLNPVTEDEDLHVIF---SQFGTVVSAEILRDYRTGESLC---YAFVEFEKREA 265
           N++FV  L+    D ++        +FG +    I        S      A+V + + E 
Sbjct: 9   NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 266 CEQAYFKMNNALIDDRRI 283
             +A   +NN ++D R +
Sbjct: 69  ALRAIQCVNNVVVDGRTL 86

>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 = 48.5 bits (115), Expect = 2e-08
 Identities = 18/88 (20%), Positives = 30/88 (34%), Gaps = 9/88 (10%)

Query: 210 PDNVLFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
              V+ +            L  +   FG + +  IL           AF+E    E  + 
Sbjct: 7   TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQA 60

Query: 269 A--YFKMNNALIDDRRICVDFSQSVSKI 294
           A  Y+    AL+  + + V  SQ   +I
Sbjct: 61  AVDYYTTTPALVFGKPVRVHLSQKYKRI 88

>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 = 49.0 bits (116), Expect = 2e-08
 Identities = 16/84 (19%), Positives = 31/84 (36%), Gaps = 8/84 (9%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
               V+ V  L     + DL     +FGT+    ++           A VEFE  ++ ++
Sbjct: 13  SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK------RQALVEFENIDSAKE 66

Query: 269 A--YFKMNNALIDDRRICVDFSQS 290
              +       I  ++   ++S S
Sbjct: 67  CVTFAADVPVYIAGQQAFFNYSTS 90

>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 = 47.7 bits (113), Expect = 8e-08
 Identities = 17/79 (21%), Positives = 31/79 (39%), Gaps = 6/79 (7%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           + V  L      + LH IFS+FGTV+                A +++    + + A   +
Sbjct: 10  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQF----QALLQYADPVSAQHAKLSL 65

Query: 274 NNALI--DDRRICVDFSQS 290
           +   I      + +DFS+ 
Sbjct: 66  DGQNIYNACCTLRIDFSKL 84

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.1 bits (111), Expect = 9e-08
 Identities = 20/82 (24%), Positives = 30/82 (36%), Gaps = 1/82 (1%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
              D  + +  L      E++   FS    V +   L     G S   AFV+F  +E  E
Sbjct: 12  TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAE 71

Query: 268 QAYFKMNNALIDDRRICVDFSQ 289
           +A    +   I  R I +  S 
Sbjct: 72  KALK-KHKERIGHRYIEIFKSS 92

>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 = 46.8 bits (110), Expect = 1e-07
 Identities = 11/86 (12%), Positives = 28/86 (32%), Gaps = 1/86 (1%)

Query: 204 DADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKR 263
           + DV        +  +       D+           +A  +     G+ L  A V+F+  
Sbjct: 1   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 60

Query: 264 EACEQAYFKMNNALIDDRRICVDFSQ 289
           +   ++  +++   ++ R   V    
Sbjct: 61  DDARKSE-RLHRKKLNGREAFVHVVT 85

>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 = 46.3 bits (109), Expect = 1e-07
 Identities = 9/80 (11%), Positives = 24/80 (30%), Gaps = 7/80 (8%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           + V  L   +  +++H +   +         +      +   AFV     E  + A    
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYDL-------KYCYVDRNKRTAFVTLLNGEQAQNAIQMF 60

Query: 274 NNALIDDRRICVDFSQSVSK 293
           +      + + V    + + 
Sbjct: 61  HQYSFRGKDLIVQLQPTDAL 80

>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 = 45.9 bits (108), Expect = 1e-07
 Identities = 18/70 (25%), Positives = 35/70 (50%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L++  L P T D+DL  +   +G +VS + + D  T +   Y FV+F+   A ++A   +
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 274 NNALIDDRRI 283
             + +  +  
Sbjct: 61  KASGVQAQMA 70

>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 = 46.3 bits (109), Expect = 2e-07
 Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 6/83 (7%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +F+  L+  +E+E L  +  QFG +    ++    T  S   AF +F  +EA ++     
Sbjct: 11  VFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAA 70

Query: 274 NNAL------IDDRRICVDFSQS 290
           +         +D R++ VD + +
Sbjct: 71  SLEAEGGGLKLDGRQLKVDLAVT 93

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.3 bits (109), Expect = 2e-07
 Identities = 15/82 (18%), Positives = 28/82 (34%), Gaps = 7/82 (8%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
           +  D  + V  L P    +DL     + G V        Y   +      VE+ ++E  E
Sbjct: 12  RRSDFRVLVSGLPPSGSWQDLKDHMREAGDV-------CYADVQKDGMGMVEYLRKEDME 64

Query: 268 QAYFKMNNALIDDRRICVDFSQ 289
            A  K+++           + +
Sbjct: 65  YALRKLDDTKFRSHEGETSYIR 86

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 45.5 bits (107), Expect = 2e-07
 Identities = 19/78 (24%), Positives = 39/78 (50%), Gaps = 3/78 (3%)

Query: 214 LFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYR-TGESLCYAFVEFEKREACEQAYF 271
           + +  L+  + ++  L   F  FG++    I    +    + C AF+ FE +++ E+A  
Sbjct: 7   IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL- 65

Query: 272 KMNNALIDDRRICVDFSQ 289
           +MN +L+ +R I V  + 
Sbjct: 66  QMNRSLLGNREISVSLAD 83

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.9 bits (108), Expect = 3e-07
 Identities = 24/77 (31%), Positives = 37/77 (48%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +FV  +     +E L  IFS+ G VVS  ++ D  TG+   Y F E++ +E    A   +
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70

Query: 274 NNALIDDRRICVDFSQS 290
           N      R + VD + S
Sbjct: 71  NGREFSGRALRVDNAAS 87

>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 = 44.7 bits (105), Expect = 7e-07
 Identities = 17/92 (18%), Positives = 32/92 (34%), Gaps = 10/92 (10%)

Query: 207 VKPPDNVLFVC--QLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKRE 264
           V      L V    L        L  +  + G V +  +  +        Y+F  +   E
Sbjct: 14  VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTE 67

Query: 265 ACEQAYFKMNNA-LIDDRRICVDFSQS-VSKI 294
             ++AY  +N   ++DD    +    + V K+
Sbjct: 68  ESKRAYVTLNGKEVVDDLGQKITLYLNFVEKV 99

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 44.1 bits (103), Expect = 8e-07
 Identities = 18/82 (21%), Positives = 33/82 (40%), Gaps = 6/82 (7%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
           PP+ +LF+  L   T +  L ++F+QF       ++ +         AFVEF        
Sbjct: 6   PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRH-----DIAFVEFTTELQSNA 60

Query: 269 AYFKMNNALIDD-RRICVDFSQ 289
           A   +    I     + + F++
Sbjct: 61  AKEALQGFKITPTHAMKITFAK 82

>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 = 43.3 bits (101), Expect = 2e-06
 Identities = 15/84 (17%), Positives = 30/84 (35%), Gaps = 8/84 (9%)

Query: 209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQ 268
            P  VL + +L     + ++  +   FG V       +    +    AF+E    EA   
Sbjct: 6   APSRVLHIRKLPGEVTETEVIALGLPFGKV------TNILMLKGKNQAFLELATEEAAIT 59

Query: 269 A--YFKMNNALIDDRRICVDFSQS 290
              Y+      + ++ I + +S  
Sbjct: 60  MVNYYSAVTPHLRNQPIYIQYSNH 83

>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 = 43.4 bits (102), Expect = 2e-06
 Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 2/66 (3%)

Query: 226 EDLHVIFSQFGTVVSAEILRDYRTGE--SLCYAFVEFEKREACEQAYFKMNNALIDDRRI 283
           ED+    S++G V S EI R     E       FVEF     C++A   +      +R +
Sbjct: 29  EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 88

Query: 284 CVDFSQ 289
              +  
Sbjct: 89  VTKYCD 94

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.7 bits (97), Expect = 8e-06
 Identities = 14/91 (15%), Positives = 28/91 (30%), Gaps = 3/91 (3%)

Query: 200 GDIPDADVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVE 259
           G    +      + + +  L     + D++  FS    +           G     A VE
Sbjct: 4   GSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIE--IGPDGRVTGEADVE 61

Query: 260 FEKREACEQAYFKMNNALIDDRRICVDFSQS 290
           F   E    A    + A +  R + +  + +
Sbjct: 62  FATHEDAVAA-MAKDKANMQHRYVELFLNST 91

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.3 bits (96), Expect = 9e-06
 Identities = 9/75 (12%), Positives = 25/75 (33%), Gaps = 2/75 (2%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           +++         +D+       G V++   +R           FV F+  E+ ++   + 
Sbjct: 9   VYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIESAKKFV-ET 66

Query: 274 NNALIDDRRICVDFS 288
                 +  + + F 
Sbjct: 67  PGQKYKETDLLILFK 81

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.9 bits (97), Expect = 9e-06
 Identities = 13/83 (15%), Positives = 29/83 (34%), Gaps = 6/83 (7%)

Query: 208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACE 267
                V+    L   T   ++   FS+FG++            E    A VEF +     
Sbjct: 7   GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRV------LLPEGGITAIVEFLEPLEAR 60

Query: 268 QAYFKMNNALIDDRRICVDFSQS 290
           +A+  +  +      + ++++  
Sbjct: 61  KAFRHLAYSKFHHVPLYLEWAPI 83

>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 = 40.2 bits (93), Expect = 3e-05
 Identities = 14/76 (18%), Positives = 26/76 (34%), Gaps = 1/76 (1%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           L++  L    ++++L  +   F   V +  +    +G S    F   E  E CE      
Sbjct: 21  LYISNLPLSMDEQELENMLKPF-GQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHF 79

Query: 274 NNALIDDRRICVDFSQ 289
           N   I         ++
Sbjct: 80  NGKFIKTPPGVSAPTE 95

>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 = 39.1 bits (90), Expect = 4e-05
 Identities = 11/81 (13%), Positives = 29/81 (35%), Gaps = 7/81 (8%)

Query: 214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM 273
           + +  L     ++++H + S +         +     +    AFV     E  E A    
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYEL-------KYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 274 NNALIDDRRICVDFSQSVSKI 294
           + + + +R + V    + + +
Sbjct: 54  HQSRLRERELSVQLQPTDALL 74

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.1 bits (90), Expect = 4e-05
 Identities = 16/78 (20%), Positives = 25/78 (32%), Gaps = 7/78 (8%)

Query: 212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF 271
           N + V  L P    +DL     + G V        Y          VEF ++E    A  
Sbjct: 1   NRVVVSGLPPSGSWQDLKDHMREAGDV-------CYADVYRDGTGVVEFVRKEDMTYAVR 53

Query: 272 KMNNALIDDRRICVDFSQ 289
           K++N           + +
Sbjct: 54  KLDNTKFRSHEGETAYIR 71

>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 = 35.3 bits (81), Expect = 0.001
 Identities = 7/74 (9%), Positives = 24/74 (32%), Gaps = 8/74 (10%)

Query: 211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAY 270
           D  + V      +    L   F+Q+G ++   +           +  + ++ +    +A 
Sbjct: 4   DTWVTVFGFPQASASYILLQ-FAQYGNILKHVMSNT------GNWMHIRYQSKLQARKA- 55

Query: 271 FKMNNALIDDRRIC 284
              +  +  +  + 
Sbjct: 56  LSKDGRIFGESIMI 69

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.4 bits (78), Expect = 0.003
 Identities = 21/92 (22%), Positives = 36/92 (39%), Gaps = 5/92 (5%)

Query: 206 DVKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREA 265
           + K    + F   L+  T  EDLH++FS  G +   + +R  + G  L       EK + 
Sbjct: 6   EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILF-----KEKAKE 60

Query: 266 CEQAYFKMNNALIDDRRICVDFSQSVSKIWKK 297
                   NN  +  R   V +     ++ K+
Sbjct: 61  ALGKAKDANNGNLQLRNKEVTWEVLEGEVEKE 92

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	299
d2ok3a1	159	Cyclophilin-like protein PPIL3B {Human (Homo sapie	100.0
d2fu0a1	155	Putative cyclophilin PFE0505w {Plasmodium falcipar	100.0
d1zkca1	178	Peptidyl-prolyl cis-trans isomerase-like 2, Cyclop	100.0
d1xwna1	166	Peptidyl-prolyl cis-trans isomerase-like 1, PPIL1	100.0
d2b71a1	169	Cyclophilin-like protein PY00693 {Plasmodium yoeli	100.0
d1w74a_	171	Peptidyl-prolyl cis-trans isomerase A, PpiA {Mycob	100.0
d2a2na1	164	Peptidylprolyl isomerase domain and WD repeat-cont	100.0
d2r99a1	161	Mitochondrial peptidyl-prolyl cis-trans isomerase,	100.0
d1v9ta_	166	Peptidyl-prolyl cis-trans isomerase A, PpiA {Esche	100.0
d1xo7a_	166	Cyclophilin (eukaryotic) {Trypanosoma cruzi [TaxId	100.0
d2rmca_	182	Cyclophilin (eukaryotic) {Mouse (Mus musculus), va	100.0
d2igva1	172	Cyclophilin (eukaryotic) {Caenorhabditis elegans,	100.0
d1h0pa_	182	Cyclophilin (eukaryotic) {Caenorhabditis elegans,	100.0
d2cfea1	162	Cyclophilin-like allergen Mal s 6 {Malassezia symp	100.0
d1lopa_	164	Peptidyl-prolyl cis-trans isomerase A, PpiA {Esche	100.0
d1qnga_	170	Cyclophilin (eukaryotic) {Plasmodium falciparum [T	100.0
d1qoia_	173	Cyclophilin (eukaryotic) {Human (Homo sapiens), U4	100.0
d2z6wa1	164	Mitochondrial peptidyl-prolyl cis-trans isomerase,	100.0
d1a33a_	174	Cyclophilin (eukaryotic) {Nematode (Brugia malayi)	100.0
d1ihga2	195	Cyclophilin 40 isomerase domain {Cow (Bos taurus)	100.0
d1z81a1	186	Cyclophilin (eukaryotic) {Plasmodium yoelii [TaxId	100.0
d2c3ba1	171	Cyclophilin (eukaryotic) {Aspergillus fumigatus [T	100.0
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.85
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.85
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.85
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.85
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.85
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.85
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.84
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.84
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.83
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.83
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.83
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.82
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.82
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.82
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.82
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.81
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.81
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.81
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.81
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.8
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.8
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.8
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.8
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.8
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.8
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.8
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.79
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.79
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.78
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.78
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.78
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.78
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.78
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.77
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.77
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.76
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.76
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.76
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.76
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.75
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.75
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.74
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.74
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.74
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.73
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.73
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.73
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.73
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.73
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.73
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.72
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.72
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.71
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.71
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.7
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.7
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.69
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.69
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.68
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.68
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.68
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.68
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.67
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.67
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.67
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.67
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.67
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.66
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.66
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.64
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.63
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.62
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.62
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.62
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.61
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.56
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.51
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	99.51
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.4
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.4
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.37
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.37
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.32
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.27
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.36
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.32
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.65
d1zx8a1	124	Hypothetical protein TM1367 {Thermotoga maritima [	92.36
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	91.48

>d2ok3a1 b.62.1.1 (A:1-159) Cyclophilin-like protein PPIL3B {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin-like protein PPIL3B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.9e-46  Score=300.49  Aligned_cols=155  Identities=46%  Similarity=0.791  Sum_probs=144.0

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCC
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADL   80 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~   80 (299)
                      |||+|+|++|+|+||||++.||+||+||++||++++|+|+.|||+++++++|+||....+.++...++.. ++.|....+
T Consensus         1 msV~~~T~~G~i~ieL~~~~aP~tv~nF~~L~~~g~Y~~~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~-~~~e~~~~~   79 (159)
T d2ok3a1           1 MSVTLHTDVGDIKIEVFCERTPKTCENFLALCASNYYNGCIFHRNIKGFMVQTGDPTGTGRGGNSIWGKK-FEDEYSEYL   79 (159)
T ss_dssp             CEEEEEETTEEEEEEECTTTCHHHHHHHHHHHHTTTTTTCBCCEEETTTEEEECCTTSSSSCCCCTTSSC-BCCCCCTTC
T ss_pred             CEEEEEeCCeEEEEEEcCCCChHHHHHHHHHHhhhcccceeEecccCCeEEEeCCccccCCCCcccCCCc-cccccccCC
Confidence            9999999999999999999999999999999999999999999999999999999887766666666554 466767889


Q ss_pred             CCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCC-CCCCceeEEEEEEEEEC
Q 046966           81 KHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDE-ENRPPQQIIIKQTYVLY  157 (299)
Q Consensus        81 ~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~-~~~p~~~v~I~~~~v~~  157 (299)
                      +|+.+|+|+|++.++++++|||||++++ .++||++|+|||+|++||++|++|++.++++ +++|..+|+|++|+|+.
T Consensus        80 ~~~~~G~lsma~~~~~s~~sqFfIt~~~-~p~ld~~~tvFG~V~~G~~vl~~I~~~~~~~~~~~P~~~i~I~~v~i~~  156 (159)
T d2ok3a1          80 KHNVRGVVSMANNGPNTNGSQFFITYGK-QPHLDMKYTVFGKVIDGLETLDELEKLPVNEKTYRPLNDVHIKDITIHA  156 (159)
T ss_dssp             CSCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTCCBCTTTCCBSSCCBEEEEEEEC
T ss_pred             CCCCCeEEEEeeCCCCCcCcceEeeecc-CcccccceEEEEecccchHHHHHHHcCcCCCCCCCcCCCcEEEEEEEEe
Confidence            9999999999999999999999999998 6999999999999999999999999999876 57899999999999997

>d2fu0a1 b.62.1.1 (A:5-159) Putative cyclophilin PFE0505w {Plasmodium falciparum [TaxId: 5833]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Putative cyclophilin PFE0505w
species: Plasmodium falciparum [TaxId: 5833]

Probab=100.00  E-value=1.5e-44  Score=288.56  Aligned_cols=152  Identities=42%  Similarity=0.739  Sum_probs=144.0

Q ss_pred             EEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCC
Q 046966            2 SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLK   81 (299)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~   81 (299)
                      +|+|+|++|+|+||||.+.||+||+||++||++++|+|+.|||+++++++|+||+...+.++.+.++.. ++++....+.
T Consensus         3 ~~~i~T~~G~i~ieL~~~~aP~tv~nF~~l~~~g~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~-~~~~~~~~~~   81 (155)
T d2fu0a1           3 SAIIYTTMGDIHISLFYKECKKTVQNFSVHSINGYYNNCIFHRVIKHFMVQTGDPSGDGTGGESIWGNE-FEDEFFDHLN   81 (155)
T ss_dssp             EEEEEETTEEEEEEECTTTCHHHHHHHHHHHHTTTTTTCBCCEEETTTEEEECCTTSSSSCCCCTTSSC-BCCCCBTTBC
T ss_pred             eEEEEEcccEEEEEEcCCCChHHHHHHhhHhhCCccccceeeeeeecceeeccCCCCCCcCCcccCCCc-cccccccccc
Confidence            789999999999999999999999999999999999999999999999999999998888888877665 5777788899


Q ss_pred             CCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEE
Q 046966           82 HDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYV  155 (299)
Q Consensus        82 ~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v  155 (299)
                      |.++|+++|++.++++++|||||++++ .++||++|+|||+|++||+||++|++.+++.+++|+.+|+|.+|.|
T Consensus        82 ~~~~~~~~~~~~~~~s~~sqFfI~~~~-~~~ld~~~tvFG~Vi~G~~vv~~I~~~~t~~~~~P~~~i~I~~v~i  154 (155)
T d2fu0a1          82 HSKPFMVSMANCGPNTNGSQFFITTVP-CPWLDFKHTVFGKVTQGSKIVLDIEKVRTDKRDKPLEDIKILNIKI  154 (155)
T ss_dssp             SSSSSEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTSCBSSCCBEEEEEE
T ss_pred             cCCccEEEecccCCCCCCccceecccC-ccccccceEEEEEEeccHHHHHHHHhCCCCCCCCcCCCcEEEEEEE
Confidence            999999999999999999999999998 6999999999999999999999999999999999999999999976

>d1zkca1 b.62.1.1 (A:280-457) Peptidyl-prolyl cis-trans isomerase-like 2, Cyclophilin-60, PPI domain {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidyl-prolyl cis-trans isomerase-like 2, Cyclophilin-60, PPI domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.7e-43  Score=288.19  Aligned_cols=153  Identities=44%  Similarity=0.798  Sum_probs=143.5

Q ss_pred             EEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCCC
Q 046966            3 VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKH   82 (299)
Q Consensus         3 v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~~   82 (299)
                      |.|+|++|+|+||||.+.||+||+||++||+.++|+|+.|||+++++++|+|+....+.++.+.++.. +.+|....++|
T Consensus         3 v~l~T~~G~i~IeL~~~~aP~tv~nF~~L~~~~~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~-~~~E~~~~l~~   81 (178)
T d1zkca1           3 VRLHTNKGDLNLELHCDLTPKTCENFIRLCKKHYYDGTIFHRSIRNFVIQGGDPTGTGTGGESYWGKP-FKDEFRPNLSH   81 (178)
T ss_dssp             EEEEETTEEEEEEECTTTSHHHHHHHHHHHHTTTTTTEEEEEEETTTEEEECCTTSSSSCCCBTTBSC-BCCCCCTTCCS
T ss_pred             EEEEeCCEEEEEEEcCCCChHHHHHHHHHHhcCCcCceEeeeccceeEEecCCccCCCCCCcccCCCC-cCCccccccCC
Confidence            88999999999999999999999999999999999999999999999999999988888887766655 67787788999


Q ss_pred             CCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccC-CCCCCceeEEEEEEEEEC
Q 046966           83 DKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVD-EENRPPQQIIIKQTYVLY  157 (299)
Q Consensus        83 ~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~-~~~~p~~~v~I~~~~v~~  157 (299)
                      +.+|+|+|++.++++++|||||++++ .++||++|+|||+|++||++|++|++.+++ .+++|..+|+|.+|.|+.
T Consensus        82 ~~~G~lsma~~~~~s~~sqF~It~~~-~~~ld~~~~vFG~Vv~G~dvl~~I~~~~t~~~~~~P~~~v~I~~~~Il~  156 (178)
T d1zkca1          82 TGRGILSMANSGPNSNRSQFFITFRS-CAYLDKKHTIFGRVVGGFDVLTAMENVESDPKTDRPKEEIRIDATTVFV  156 (178)
T ss_dssp             CSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHHSCBCTTTCCBSSCCEEEEEEEEE
T ss_pred             CCCeEEEEeecCCCCccceeeccccC-CcccCCcceEEEEeeCcHHHHHHHHcCCCCCCCCccCCCeEEEEEEEEc
Confidence            99999999999999999999999998 699999999999999999999999999987 468999999999999986

>d1xwna1 b.62.1.1 (A:1-166) Peptidyl-prolyl cis-trans isomerase-like 1, PPIL1 {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidyl-prolyl cis-trans isomerase-like 1, PPIL1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.9e-43  Score=283.81  Aligned_cols=152  Identities=44%  Similarity=0.798  Sum_probs=142.5

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCC
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADL   80 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~   80 (299)
                      ..|.|+|++|+|+||||.+.||+||+||++||+.++|+|+.|||+++++++|+||+...+.++...++.. +++|.+..+
T Consensus        12 p~v~~~T~~G~i~ieL~~~~aP~tv~nF~~L~~~g~Y~g~~f~rv~~~~~iq~Gd~~~~~~~~~~~~~~~-~~~e~~~~~   90 (166)
T d1xwna1          12 PNVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGRGGASIYGKQ-FEDELHPDL   90 (166)
T ss_dssp             CEEEEEESSCEEEEEECTTTCHHHHHHHHHHHHHTSSTTCCEEEEETTTEEEECCSTTTTSSCCCSSCSC-CCCCCCTTC
T ss_pred             CEEEEEECceeEEEEEcCCCChHHHHHHHHHHhcCCcCceeeeEEcccEEEEeCCCCCCCCCCccCCCCc-cccccCCCC
Confidence            3699999999999999999999999999999999999999999999999999999988888877776655 677878889


Q ss_pred             CCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEE
Q 046966           81 KHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTY  154 (299)
Q Consensus        81 ~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~  154 (299)
                      .|+.+|+|+|++.++++++|||||++++ .++||++|+|||+|++||+||++|++.+++.+++|..+|+|.+..
T Consensus        91 ~~~~~G~lsm~~~~~~s~~sqFfI~~~~-~~~ld~~~tvFG~Vi~G~dvl~~I~~~~t~~~~~P~~~I~I~~a~  163 (166)
T d1xwna1          91 KFTGAGILAMANAGPDTNGSQFFVTLAP-TQWLDGKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAY  163 (166)
T ss_dssp             CSCSSSEEEEEEEETTEEEEEEEEECSC-CSTTTTTSEEEEECSSCHHHHHHHHHSCBCSSSCBSSCCCEEEEE
T ss_pred             CCCCCeEEEecccCCCCCCcceEEeecC-hhhccccceEEEEEechHHHHHHHHhCCCCCCCCCCCCeEEEEee
Confidence            9999999999999999999999999998 699999999999999999999999999999999999999998864

>d2b71a1 b.62.1.1 (A:23-191) Cyclophilin-like protein PY00693 {Plasmodium yoelii [TaxId: 5861]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin-like protein PY00693
species: Plasmodium yoelii [TaxId: 5861]

Probab=100.00  E-value=5.2e-43  Score=283.08  Aligned_cols=151  Identities=38%  Similarity=0.689  Sum_probs=141.1

Q ss_pred             EEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCC
Q 046966            2 SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLK   81 (299)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~   81 (299)
                      .|+|+|++|+|+||||++.||++|+||++||+.++|+|+.|||+++++++|||+..+.+.++.++.... +++|....++
T Consensus        18 ~V~l~T~~G~i~IeL~~d~aP~tv~nF~~L~~~g~Y~~~~f~rv~~~~~iq~g~~~~~~~~~~~~~~~~-~~~e~~~~l~   96 (169)
T d2b71a1          18 YITIYTNLGDFEVELYWYHSPKTCLNFYTLCEMGFYDNTIFHRVIPNFVIQGGDPTGTGKGGKSIYGEY-FEDEINKELK   96 (169)
T ss_dssp             EEEEEETTEEEEEEECTTTSHHHHHHHHHHHHTTTTTTEEEEEEETTTEEEEEETTSSSSCCCBTTBSC-BCCCCCTTCC
T ss_pred             EEEEEeCceeEEEEEeCCCCcHHHHHHHHHhhCCccceeeeccccceeeEeccccccccCCCccccccc-cccccccccC
Confidence            489999999999999999999999999999999999999999999999999999988777776665544 5777778899


Q ss_pred             CCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEE
Q 046966           82 HDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTY  154 (299)
Q Consensus        82 ~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~  154 (299)
                      |.++|+|+|++.+|++++|||||++++ .++||++|+|||+|++||+||++|++.+++++++|..+|.|.+++
T Consensus        97 h~~~g~ls~~~~~p~s~~sqFfIt~~~-~~~ld~~~tvFG~Vv~G~dvl~~I~~~~~~~~~~P~~~i~I~~~~  168 (169)
T d2b71a1          97 HTGAGILSMSNNGPNTNSSQFFITLAP-LPHLDGKHTIFARVSKNMTCIENIASVQTTATNKPIFDLKILRTS  168 (169)
T ss_dssp             CCSTTEEEECCSSTTCBSSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTCCBSSCCEEEEEE
T ss_pred             CCCcEEEEhhhCCCCCCCCEEEEecCC-cchhhhhcceeeEEeccHHHHHHHHhCCCCCCCCCCCCeEEEEcc
Confidence            999999999999999999999999998 699999999999999999999999999999999999999999875

>d1w74a_ b.62.1.1 (A:) Peptidyl-prolyl cis-trans isomerase A, PpiA {Mycobacterium tuberculosis [TaxId: 1773]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidyl-prolyl cis-trans isomerase A, PpiA
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=100.00  E-value=1.2e-41  Score=275.96  Aligned_cols=149  Identities=37%  Similarity=0.681  Sum_probs=136.9

Q ss_pred             EEEEEEcceeEEEEecCCCChHHHHHHHHhhhCC---------------CcCCceeeEeecCcEEEecCCCCCCCCCCCC
Q 046966            2 SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNK---------------YYNGCLFHNIHKDFIAQTGDPTGTGTGGRSV   66 (299)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~---------------~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~   66 (299)
                      +|+|+|+.|+|+||||++.||+||+||++||+++               +|+++.|||+++++++|||++...+.++...
T Consensus         5 ~~ti~T~~G~I~ieL~~d~aP~tv~nF~~L~~~~~~~~~~~~~~~~~~~~Y~g~~~~rv~~~~~iq~g~~~~~~~~~~~~   84 (171)
T d1w74a_           5 TATLHTNRGDIKIALFGNHAPKTVANFVGLAQGTKDYSTQNASGGPSGPFYDGAVFHRVIQGFMIQGGDPTGTGRGGPGY   84 (171)
T ss_dssp             EEEEEETTEEEEEEECTTTSHHHHHHHHHHHHTCSCCSSCCTTBSSSSCSSTTEEEEEEETTTEEEECCTTSSSSCCSSC
T ss_pred             EEEEEECCEEEEEEEcCCCChHHHHHHHHHHhcCCccccccccccccCceECCeecccccCCceeEcccccCCCCCCccc
Confidence            7999999999999999999999999999999977               7999999999999999999988766554331


Q ss_pred             CCCcccccccccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeec--CHHHHHHHHhcccCCCCCC
Q 046966           67 YEDRFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAE--GLETLTRINQAVVDEENRP  144 (299)
Q Consensus        67 ~~~~~~~~e~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~--G~~vl~~i~~~~~~~~~~p  144 (299)
                          .+.+|..+.++|+++|+|+|++.++++++|||||++++ .++||++|+|||+|++  ||+||++|++.+++.+++|
T Consensus        85 ----~~~~e~~~~~~~~~~g~v~~~~~~~~s~~sqFfIt~~~-~p~ld~~~tVFG~Vv~geGmdvl~~I~~~~~~~~~~P  159 (171)
T d1w74a_          85 ----KFADEFHPELQFDKPYLLAMANAGPGTNGSQFFITVGK-TPHLNRRHTIFGEVIDAESQRVVEAISKTATDGNDRP  159 (171)
T ss_dssp             ----CBCCCCCTTCCSCSSSEEEECCSSTTCBSSCEEEESSC-CGGGTTTSCEEEEECSHHHHHHHHHHHTSCBCTTSCB
T ss_pred             ----ccccccCCCcCCCCCEEEEEEecCCCCCCcceEeeccC-CCccccccEEEEEEeccccHHHHHHHHcCCcCCCCcc
Confidence                24666678899999999999999999999999999998 6999999999999995  9999999999999999999


Q ss_pred             ceeEEEEEEEE
Q 046966          145 PQQIIIKQTYV  155 (299)
Q Consensus       145 ~~~v~I~~~~v  155 (299)
                      ..+|+|+++.|
T Consensus       160 ~~~i~I~~v~i  170 (171)
T d1w74a_         160 TDPVVIESITI  170 (171)
T ss_dssp             SSCCEEEEEEE
T ss_pred             CCCcEEEEEEE
Confidence            99999999987

>d2a2na1 b.62.1.1 (A:483-646) Peptidylprolyl isomerase domain and WD repeat-containing protein 1, PPWD1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidylprolyl isomerase domain and WD repeat-containing protein 1, PPWD1, C-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=3.6e-41  Score=271.46  Aligned_cols=153  Identities=46%  Similarity=0.793  Sum_probs=138.9

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCC
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADL   80 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~   80 (299)
                      .+|+|+|++|+|+||||.+.||+||+||++||+.++|+|+.|||+++++++|+|++.....++....... +.++....+
T Consensus        10 ~~a~~~T~~G~i~ieL~~~~aP~tv~nF~~l~~~g~Y~g~~f~rv~~~~~iq~G~~~~~~~~~~~~~~~~-~~~~~~~~~   88 (164)
T d2a2na1          10 DSAIIHTSMGDIHTKLFPVECPKTVENFCVHSRNGYYNGHTFHRIIKGFMIQTGDPTGTGMGGESIWGGE-FEDEFHSTL   88 (164)
T ss_dssp             SEEEEEETTEEEEEEECTTTCHHHHHHHHHHHHTTTTTTCBCCEEETTTEEEECCTTSSSSCCCCTTSSC-BCCCCCTTC
T ss_pred             CEEEEEeceeEEEEEEcCCCChHHHHHHHHHHhCCCcccceeeEEeeeeeEeecccccccCCCceeeecc-ccccccccc
Confidence            3799999999999999999999999999999999999999999999999999999876655544433333 566668889


Q ss_pred             CCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCC-CCCCceeEEEEEEEE
Q 046966           81 KHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDE-ENRPPQQIIIKQTYV  155 (299)
Q Consensus        81 ~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~-~~~p~~~v~I~~~~v  155 (299)
                      +|+.+|+|+|++.++++++|||||++++ .++||++|+|||+|++||+||++|++.+++. +++|..+|+|.++.|
T Consensus        89 ~~~~~~~l~~~~~~~~s~~sqFfI~~~~-~~~ld~~~tVFG~V~~G~dvv~~I~~~~~~~~~~~P~~~V~I~~v~i  163 (164)
T d2a2na1          89 RHDRPYTLSMANAGSNTNGSQFFITVVP-TPWLDNKHTVFGRVTKGMEVVQRISNVKVNPKTDKPYEDVSIINITV  163 (164)
T ss_dssp             CSCSSSEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTTCCBSSCCBEEEEEE
T ss_pred             ccCccceeehhhcCCCCCcccceecccC-ccccccceeEEEEecChHHHHHHHHcCCcCCCCCCcCCCcEEEEEEE
Confidence            9999999999999999999999999998 6999999999999999999999999999985 589999999999987

>d2r99a1 b.62.1.1 (A:139-299) Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.6e-40  Score=264.97  Aligned_cols=150  Identities=38%  Similarity=0.622  Sum_probs=130.0

Q ss_pred             EEEE-EEcceeEEEEecCCCChHHHHHHHHhhh---CCCcCCceeeEeecCcEEEecCCCCC-CCCCCCCCCCccccccc
Q 046966            2 SVLI-ETSLGDIVIDLFVDKCPRTTNNFLQHCK---NKYYNGCLFHNIHKDFIAQTGDPTGT-GTGGRSVYEDRFFVDEI   76 (299)
Q Consensus         2 ~v~~-~T~~G~i~ieL~~~~~P~~~~nF~~l~~---~~~y~~~~f~ri~~~~~iq~G~~~~~-~~~~~~~~~~~~~~~e~   76 (299)
                      .|.| .++.|+|+||||.++||+||+||++||+   +++|+|+.|||++|++++|+|+.... +.++.+.++.. +.++ 
T Consensus         7 di~i~~~~~G~i~ieL~~~~aP~tv~nF~~L~~~~~~~~Y~g~~f~Rv~~~~~iq~G~~~~~~~~~~~~~~~~~-~~~~-   84 (161)
T d2r99a1           7 DIKIGNKPAGRIQMLLRSDVVPMTAENFRCLCTHEKGFGFKGSSFHRIIPQFMCQGGDFTNHNGTGGKSIYGKK-FDDE-   84 (161)
T ss_dssp             EEEETTEEEEEEEEEECTTTCHHHHHHHHHHHHTTTSCCSTTCBEEEEETTTEEEECCTTTSSSSCCCBTTBSC-BCCC-
T ss_pred             EEEECCEeceEEEEEEcCCCCcHHHHHHHHhhhhccccccCCcEEEEEEEeeeEEeeeccCCCCCCCccccCcc-cccc-
Confidence            3444 3678999999999999999999999995   47899999999999999999998764 45555555543 3444 


Q ss_pred             ccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEE
Q 046966           77 RADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYV  155 (299)
Q Consensus        77 ~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v  155 (299)
                      ....+|+.+|+|+|++.++++++|||||++.+ .++||++|+|||+|++||+||++|+.. .+.+++|..+|+|++|+.
T Consensus        85 ~~~~~~~~~G~ls~~~~~~~s~~sqFfI~~~~-~~~Ldg~~tvFG~Vv~G~dvl~~I~~~-~~~~~~P~~~i~I~~CGe  161 (161)
T d2r99a1          85 NFILKHTGPGLLSMANSGPNTNGSQFFLTCDK-TDWLDGKHVVFGEVTEGLDVLRQIEAQ-GSKDGKPKQKVIIADCGE  161 (161)
T ss_dssp             CCCSCCCSSSEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTT-CCTTCCCSSCEEEEEEEE
T ss_pred             ccccccccceeeeecccCCCCcCcceEeccCC-ccccCCcceEEEEEeehHHHHHHHHcc-CCCCCcCCCCEEEEeCCC
Confidence            67788889999999999999999999999998 699999999999999999999999654 557899999999999984

>d1v9ta_ b.62.1.1 (A:) Peptidyl-prolyl cis-trans isomerase A, PpiA {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidyl-prolyl cis-trans isomerase A, PpiA
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=2.2e-40  Score=267.08  Aligned_cols=150  Identities=30%  Similarity=0.496  Sum_probs=130.0

Q ss_pred             EEEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCC
Q 046966            2 SVLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLK   81 (299)
Q Consensus         2 ~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~   81 (299)
                      .|+|+|+.|+|+||||.++||+||+||++||+.++|+|+.|||+++++++|+|+.......+  .++ ..+++|....++
T Consensus         6 ~V~l~T~~G~i~ieL~~~~aP~tv~nF~~L~~~~~Y~g~~fhRv~~~~~iq~G~~~~~~~~~--~~~-~~~~~e~~~~~~   82 (166)
T d1v9ta_           6 HVLLTTSAGNIELELDKQKAPVSVQNFVDYVNSGFYNNTTFHRVIPGFMIQGGGFTEQMQQK--KPN-PPIKNEADNGLR   82 (166)
T ss_dssp             EEEEEETTEEEEEEECTTTCHHHHHHHHHHHHTTTTTTCBEEEEETTTEEEESSBCTTCCBC--CCC-CCBCCCGGGSCC
T ss_pred             EEEEEECCeeEEEEEeCCCChHHHHHHHHHhhCCccccceeeEEEEEeecccCCcCCccccc--CCC-CCcccccccccc
Confidence            58999999999999999999999999999999999999999999999999999976542222  222 236778677777


Q ss_pred             CCCceEEEEEc-CCCCCCcceEEEEecCCCCCCCC-----CceEEEEeecCHHHHHHHHhcccCCC----CCCceeEEEE
Q 046966           82 HDKVGTVGMAS-AGRDLNASQFYITLRDNLHYLDE-----KHTIFGEVAEGLETLTRINQAVVDEE----NRPPQQIIIK  151 (299)
Q Consensus        82 ~~~~G~l~~~~-~~~~~~~s~FfI~~~~~~~~ld~-----~~~vfG~V~~G~~vl~~i~~~~~~~~----~~p~~~v~I~  151 (299)
                      | .+|.|+|++ .++++++|||||++.+ .++||+     +|+|||+|++||++|++|+++++++.    ++|..+|+|.
T Consensus        83 ~-~rg~v~~~~~~~~~s~~sqFfI~~~~-~~~ld~~~~~~~~tvfG~VveG~dvl~~I~~~~~~~~~~~~~~P~~~v~I~  160 (166)
T d1v9ta_          83 N-TRGTIAMARTADKDSATSQFFINVAD-NAFLDHGQRDFGYAVFGKVVKGMDVADKISQVPTHDVGPYQNVPSKPVVIL  160 (166)
T ss_dssp             C-CTTEEEECCCSSTTCBCSCEEEESSC-CGGGSCCSSCCCCCEEEEEEECHHHHHHHHTSCEEEETTEEEEESSCCBEE
T ss_pred             c-cCCEEEEEeeecCCCcccccccccCC-ccccccccccCCEEEeeEEeccHHHHHHHHhCcccCCCCCCCccCCCeEEE
Confidence            6 789999988 5689999999999998 577876     48999999999999999999988764    4899999999


Q ss_pred             EEEEE
Q 046966          152 QTYVL  156 (299)
Q Consensus       152 ~~~v~  156 (299)
                      +|+|+
T Consensus       161 ~~~vl  165 (166)
T d1v9ta_         161 SATVL  165 (166)
T ss_dssp             EEEEC
T ss_pred             EEEEc
Confidence            99986

>d1xo7a_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Trypanosoma cruzi [TaxId: 5693]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Trypanosoma cruzi [TaxId: 5693]

Probab=100.00  E-value=3.1e-40  Score=266.15  Aligned_cols=146  Identities=36%  Similarity=0.655  Sum_probs=129.4

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhCCC---cCCceeeEeecCcEEEecCCCC-CCCCCCCCCCCcccccccccCCCC
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKNKY---YNGCLFHNIHKDFIAQTGDPTG-TGTGGRSVYEDRFFVDEIRADLKH   82 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~---y~~~~f~ri~~~~~iq~G~~~~-~~~~~~~~~~~~~~~~e~~~~~~~   82 (299)
                      ++.|+|+||||.+.||++|+||++||++++   |+|+.|||+++++++|+|+... ++.++...++. .++++ . ...|
T Consensus        17 ~~~G~i~ieL~~~~aP~t~~nF~~l~~~~~~~~Y~g~~f~rv~~~~~iq~G~~~~~~~~~~~~~~~~-~~~~~-~-~~~~   93 (166)
T d1xo7a_          17 EPVGRVVIGLFGNDVPKTVENFKQLASGENGFGYKGSIFHRVIRNFMIQGGDFTNFDGTGGKSIYGT-RFDDE-N-LKIK   93 (166)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTTTSCCSTTCBEEEEETTTEEEECCTTTSSSSCCCBTTBS-CBCCC-C-CCSC
T ss_pred             EECcEEEEEECCCCChHHHHHHHHhhcccccccccCcEEEEEcCCCEEEeCCCCCCCCCCCCCCCCc-ccccc-c-cccc
Confidence            789999999999999999999999999988   9999999999999999999664 35555554433 33444 2 3445


Q ss_pred             CCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEE
Q 046966           83 DKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVL  156 (299)
Q Consensus        83 ~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~  156 (299)
                      +.+|+|+|++.++++++|||||++++ .++||++|+|||+|++||++|++|++.+++.+++|..+|.|++|+++
T Consensus        94 ~~~G~l~~a~~g~~s~~sqFfIt~~~-~~~ld~~~~vfG~Vi~G~~vl~~I~~~~~~~~~~P~~~i~I~~cgvl  166 (166)
T d1xo7a_          94 HFVGAVSMANAGPNSNGSQFFVTTAP-TPWLDGRHVVFGKVVEGMDVVKKVENTKTGLNDKPKKAVKINDCGVL  166 (166)
T ss_dssp             CCTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCGGGCBSSCEEEEEEEEC
T ss_pred             ccccceeecccCCCCCCCeeEEccCC-ccccCccceeeeEEeeHHHHHHHHHcCCCCCCCCCCCCEEEEeeEeC
Confidence            58899999999999999999999998 69999999999999999999999999999999999999999999985

>d2rmca_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Mouse (Mus musculus), variant C [TaxId: 10090]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Mouse (Mus musculus), variant C [TaxId: 10090]

Probab=100.00  E-value=5.9e-40  Score=268.21  Aligned_cols=148  Identities=41%  Similarity=0.675  Sum_probs=134.0

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhCC---CcCCceeeEeecCcEEEecCCCC-CCCCCCCCCCCcccccccccCCCC
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKNK---YYNGCLFHNIHKDFIAQTGDPTG-TGTGGRSVYEDRFFVDEIRADLKH   82 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~~---~y~~~~f~ri~~~~~iq~G~~~~-~~~~~~~~~~~~~~~~e~~~~~~~   82 (299)
                      |+.|+|+||||.+.||++|+||++||+++   +|+|+.|||+++++++|+|+... ++.++.++++.. ++++ .....|
T Consensus        19 ~~~G~ivieL~~d~aP~tv~nF~~l~~~~k~~~Y~g~~f~rv~~~~~iq~G~~~~~~~~~~~~~~~~~-~~~~-~~~~~~   96 (182)
T d2rmca_          19 KDVGRIVIGLFGNVVPKTVENFVALATGEKGYGYKGSIFHRVIKDFMIQGGDFTARDGTGGMSIYGET-FPDE-NFKLKH   96 (182)
T ss_dssp             EEEEEEEEEECTTTSHHHHHHHHHHHHTTTSCSSTTCBEEEEETTTEEEECCCSSSSSSCCCBTTBSC-BCCC-CCCSCC
T ss_pred             EECcEEEEEEcCCCCcHHHHHHHHhhhcCCCccccCceeeeeecCceEEcCCCCCCCCCCCCCCcCCc-cccc-cccccc
Confidence            88999999999999999999999999765   69999999999999999999764 356666666544 4555 466778


Q ss_pred             CCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEEC
Q 046966           83 DKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY  157 (299)
Q Consensus        83 ~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~~  157 (299)
                      +.+|+|+|++.++++++|||||++.+ .++||++|+|||+|++||+||++|++.+++.+++|..+|+|.+|++++
T Consensus        97 ~~~G~lsma~~~~~s~~sqFfI~~~~-~~~ld~~~~vFG~Vi~G~dvl~~I~~~~~~~~~~P~~~v~I~~~g~l~  170 (182)
T d2rmca_          97 YGIGWVSMANAGPDTNGSQFFITLTK-PTWLDGKHVVFGKVLDGMTVVHSIELQATDGHDRPLTDCTIVNSGKID  170 (182)
T ss_dssp             CSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTSCBSSCEEEEEEEEEE
T ss_pred             CCCccEehhhcCCCccCccccccccC-CchhcccceEEEEEechHHHHHHHHhCCcCCCCcCCCCeEEEEeeEEe
Confidence            89999999999999999999999998 699999999999999999999999999999999999999999999996

>d2igva1 b.62.1.1 (A:1-172) Cyclophilin (eukaryotic) {Caenorhabditis elegans, isoform 3 [TaxId: 6239]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Caenorhabditis elegans, isoform 3 [TaxId: 6239]

Probab=100.00  E-value=6.4e-40  Score=265.69  Aligned_cols=147  Identities=35%  Similarity=0.631  Sum_probs=130.9

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhC----------CCcCCceeeEeecCcEEEecCCCC-CCCCCCCCCCCcccccc
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKN----------KYYNGCLFHNIHKDFIAQTGDPTG-TGTGGRSVYEDRFFVDE   75 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~----------~~y~~~~f~ri~~~~~iq~G~~~~-~~~~~~~~~~~~~~~~e   75 (299)
                      |+.|+|+||||.+.||+||+||++||++          ++|+++.|||+++++++|+|+... ++.++..+++.. +++|
T Consensus        15 ~~~G~i~ieL~~~~aP~tv~nF~~L~~~~~~~~~~~k~~~y~~~~f~rv~~~~~i~~G~~~~~~~~~~~~~~~~~-~~~e   93 (172)
T d2igva1          15 KASGRIVMELYDDVVPKTAGNFRALCTGENGIGKSGKPLHFKGSKFHRIIPNFMIQGGDFTRGNGTGGESIYGEK-FPDE   93 (172)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTTTCBCTTSSBSCCTTCBCCEEETTTEEEECCTTTSSSSCCCBTTBSC-BCCC
T ss_pred             EeccEEEEEEcCCCCcHHHHHHHHHHhccccccccCcccccCCcceeEEEecceEEcCCccCCCCCCCcccCCCc-cCcc
Confidence            6789999999999999999999999965          589999999999999999999654 466666666655 5777


Q ss_pred             cccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEE
Q 046966           76 IRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYV  155 (299)
Q Consensus        76 ~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v  155 (299)
                       .....|+.+|+|+|++.++++++|||||++.+ .++||++|+|||+|++||+||++|+..++ .+++|+.+|.|++|++
T Consensus        94 -~~~~~~~~~G~lsma~~~~~~~~sqFfIt~~~-~~~ld~~~~vFG~Vv~Gmdvl~~I~~~~~-~~g~P~~~i~I~~cG~  170 (172)
T d2igva1          94 -NFKEKHTGPGVLSMANAGPNTNGSQFFLCTVK-TEWLDGKHVVFGRVVEGLDVVKAVESNGS-QSGKPVKDCMIADCGQ  170 (172)
T ss_dssp             -CCCSCCCSTTEEEECCSSTTCBSSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTTCC-TTSCCSSCEEEEEEEE
T ss_pred             -ccccccCCCcEEEEeecCCCCcCceeEeeecC-CcccCCceeEEEEEeccHHHHHHHHcCCC-CCCCCCCCeEEEeccc
Confidence             45667789999999999999999999999998 79999999999999999999999987654 6899999999999999


Q ss_pred             EC
Q 046966          156 LY  157 (299)
Q Consensus       156 ~~  157 (299)
                      ++
T Consensus       171 l~  172 (172)
T d2igva1         171 LK  172 (172)
T ss_dssp             EC
T ss_pred             cC
Confidence            85

>d1h0pa_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Caenorhabditis elegans, isoform 5 [TaxId: 6239]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Caenorhabditis elegans, isoform 5 [TaxId: 6239]

Probab=100.00  E-value=3.1e-40  Score=269.97  Aligned_cols=149  Identities=40%  Similarity=0.681  Sum_probs=134.7

Q ss_pred             EEcceeEEEEecCCCChHHHHHHHHhhhCC---CcCCceeeEeecCcEEEecCCCC-CCCCCCCCCCCcccccccccCCC
Q 046966            6 ETSLGDIVIDLFVDKCPRTTNNFLQHCKNK---YYNGCLFHNIHKDFIAQTGDPTG-TGTGGRSVYEDRFFVDEIRADLK   81 (299)
Q Consensus         6 ~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~---~y~~~~f~ri~~~~~iq~G~~~~-~~~~~~~~~~~~~~~~e~~~~~~   81 (299)
                      .|+.|+|+||||.+.||+||+||++||+++   +|+++.|||+++++++|+|+... ++.++.+.++.. +.++ .....
T Consensus        17 ~~~~G~i~IeL~~d~aP~tv~nF~~l~~~g~~~~y~g~~f~rv~~~~~iq~G~~~~~~~~g~~~~~~~~-~~~~-~~~~~   94 (182)
T d1h0pa_          17 GKPIGRIVIGLFGKTVPKTATNFIELAKKPKGEGYPGSKFHRVIADFMIQGGDFTRGDGTGGRSIYGEK-FADE-NFKLK   94 (182)
T ss_dssp             TEEEEEEEEEECTTTSHHHHHHHHHHHHSCTTTSSTTCBCCEEETTTEEEECCTTTSSSSCCCBTTBSC-BCCC-CCCSC
T ss_pred             CEECeEEEEEECCCCChHHHHHHHHHHHhcccCCcCCceEEEEEecceEEcCCCCCCCCCCCCCCCCCc-cCcc-ccccc
Confidence            388999999999999999999999999765   89999999999999999999764 466666666654 4555 45677


Q ss_pred             CCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEEC
Q 046966           82 HDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY  157 (299)
Q Consensus        82 ~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~~  157 (299)
                      |+.+|+++|++.++++++|||||++.+ .++||++|+|||+|++||++|++|++.+++.+++|..+|+|++|+++.
T Consensus        95 ~~~~G~~~~a~~g~~s~~sqFfIt~~~-~~~ldg~ytvFG~Vi~G~dvl~~I~~~~~~~~~~P~~~v~I~~cG~l~  169 (182)
T d1h0pa_          95 HYGAGWLSMANAGADTNGSQFFITTVK-TPWLDGRHVVFGKILEGMDVVRKIEQTEKLPGDRPKQDVIIAASGHIA  169 (182)
T ss_dssp             CCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCEETTTEESSCEEEEEEEEEE
T ss_pred             ccCCceeeecccCCCCcCccccccccc-cccccccceeEEEEeehHHHHHHHHhcCCCCCCCCCCCEEEEECCeEe
Confidence            889999999999999999999999998 699999999999999999999999999999999999999999999987

>d2cfea1 b.62.1.1 (A:1-162) Cyclophilin-like allergen Mal s 6 {Malassezia sympodialis [TaxId: 76777]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin-like allergen Mal s 6
species: Malassezia sympodialis [TaxId: 76777]

Probab=100.00  E-value=7.3e-40  Score=262.70  Aligned_cols=145  Identities=41%  Similarity=0.686  Sum_probs=129.8

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhCCC---cCCceeeEeecCcEEEecCCCC-CCCCCCCCCCCcccccccccCCCC
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKNKY---YNGCLFHNIHKDFIAQTGDPTG-TGTGGRSVYEDRFFVDEIRADLKH   82 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~---y~~~~f~ri~~~~~iq~G~~~~-~~~~~~~~~~~~~~~~e~~~~~~~   82 (299)
                      |++|+|+||||.++||+||+||++||++++   |+|+.|||++|++++|+|++.. ++.++.+.+... +.+| ...++|
T Consensus        13 ~~~G~i~ieL~~~~aP~tv~nF~~L~~~~~~~~Y~g~~f~rv~~~~~iq~G~~~~~~~~~~~~~~~~~-~~~e-~~~~~h   90 (162)
T d2cfea1          13 APLGTIKFKLFDDVVPKTAANFRALCTGEKGFGYAGSHFHRVIPDFMLQGGDFTAGNGTGGKSIYGAK-FADE-NFQLKH   90 (162)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTTTSCCSTTCBCCEEETTTEEEECCTTTSSSSCCCBTTBSC-BCCC-CCCSCC
T ss_pred             EEeeEEEEEEcCCCChHHHHHHHHHHhhccCCccCCCEEEEEEecceEecCCCCCCCCCCCcccCCCc-cccc-cCCCCC
Confidence            558999999999999999999999999986   9999999999999999999764 355566665555 4666 567889


Q ss_pred             CCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEE
Q 046966           83 DKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYV  155 (299)
Q Consensus        83 ~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v  155 (299)
                      +.+|+|+|++.++++++|||||++.+ .++||++|+|||+|++||+||++|+. ..+++++|..+|+|.+|+|
T Consensus        91 ~~~G~vsm~~~~~~s~~sqF~I~~~~-~~~ld~~~~vFG~Vi~G~dvl~~I~~-~~~~~~~P~~~i~I~~cgv  161 (162)
T d2cfea1          91 NKPGLLSMANAGPNTNGSQFFITTVV-TSWLDGKHVVFGEVIDGMNVVKAIEA-EGSGSGKPRSRIEIAKCGV  161 (162)
T ss_dssp             CSTTEEEECCSSTTCBSSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHT-TCCTTSCCSSCEEEEEEEE
T ss_pred             CCceEEEEeecCCCCCCcceEEeecC-CccccccceEEEEEEehHHHHHHHhc-CCCCCCCCCCCeEEEeeEc
Confidence            99999999999999999999999998 69999999999999999999999965 4567899999999999998

>d1lopa_ b.62.1.1 (A:) Peptidyl-prolyl cis-trans isomerase A, PpiA {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Peptidyl-prolyl cis-trans isomerase A, PpiA
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=3e-40  Score=265.72  Aligned_cols=151  Identities=29%  Similarity=0.483  Sum_probs=130.1

Q ss_pred             EEEEEcceeEEEEecCCCChHHHHHHHHhhhCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCcccccccccCCCC
Q 046966            3 VLIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEIRADLKH   82 (299)
Q Consensus         3 v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~~~~~~~   82 (299)
                      |+|+|+.|+|+||||.+.||+||+||++||+.++|+|+.|||+++++++|+|+.......+  .++. .+++|....++|
T Consensus         2 V~l~T~~G~i~ieL~~~~aP~t~~nF~~l~~~g~Y~g~~fhrv~~~~~iq~G~~~~~~~~~--~~~~-~~~~e~~~~~~h   78 (164)
T d1lopa_           2 VTFHTNHGDIVIKTFDDKAPETVKNFLDYCREGFYNNTIFHRVINGFMIQGGGFEPGMKQK--ATKE-PIKNEANNGLKN   78 (164)
T ss_dssp             EEEEETTEEEEEEECTTTSHHHHHHHHHHHHTTTTTTEECCEEETTTEEEESSEETTTEEC--CCCC-CBCCCCCSSCCC
T ss_pred             EEEEeCCeEEEEEEcCCCCHHHHHHHHHHHHccCcCCceeeEEcCCceeeeeccccCCcCC--ccCC-Cccccccccccc
Confidence            8999999999999999999999999999999999999999999999999999875442222  1222 356776677777


Q ss_pred             CCceEEEEEcC-CCCCCcceEEEEecCC-------CCCCCCCceEEEEeecCHHHHHHHHhcccCCCC----CCceeEEE
Q 046966           83 DKVGTVGMASA-GRDLNASQFYITLRDN-------LHYLDEKHTIFGEVAEGLETLTRINQAVVDEEN----RPPQQIII  150 (299)
Q Consensus        83 ~~~G~l~~~~~-~~~~~~s~FfI~~~~~-------~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~----~p~~~v~I  150 (299)
                       .+|.|+|++. ++++++|||||++.+.       .+++|++|+|||+|++||+||++|++.++++.+    +|+.+|+|
T Consensus        79 -~~g~l~~~~~~~~~~~~sqFfi~~~~~~~~~~~~~~~~~~~ytvFG~Vv~G~dvl~~I~~~~t~~~~~~~~~P~~~v~I  157 (164)
T d1lopa_          79 -TRGTLAMARTQAPHSATAQFFINVVDNDFLNFSGESLQGWGYCVFAEVVDGMDEVDKIKGVATGRSGMHQDVPKEDVII  157 (164)
T ss_dssp             -CTTEEEECCCSSTTCBCSCEEEESSCCGGGSCCSSSTTTSCCCEEEEEEECHHHHHHHHTSCEEEETTEEEEESSCCEE
T ss_pred             -eeeEEEEeccCCCCCccceeeeeccccccccccCCCcCCCceeecCEEeccHHHHHHHHhCCcCCCCCcCCCcCCCeEE
Confidence             6789999874 6899999999999863       378999999999999999999999999987654    89999999


Q ss_pred             EEEEEEC
Q 046966          151 KQTYVLY  157 (299)
Q Consensus       151 ~~~~v~~  157 (299)
                      +++.|.+
T Consensus       158 ~~v~I~e  164 (164)
T d1lopa_         158 ESVTVSE  164 (164)
T ss_dssp             EEEEECC
T ss_pred             EEEEEeC
Confidence            9999854

>d1qnga_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Plasmodium falciparum [TaxId: 5833]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Plasmodium falciparum [TaxId: 5833]

Probab=100.00  E-value=5.4e-40  Score=265.74  Aligned_cols=152  Identities=36%  Similarity=0.665  Sum_probs=132.3

Q ss_pred             CEEEEE-EcceeEEEEecCCCChHHHHHHHHhhhC---------CCcCCceeeEeecCcEEEecCCCCC-CCCCCCCCCC
Q 046966            1 MSVLIE-TSLGDIVIDLFVDKCPRTTNNFLQHCKN---------KYYNGCLFHNIHKDFIAQTGDPTGT-GTGGRSVYED   69 (299)
Q Consensus         1 ~~v~~~-T~~G~i~ieL~~~~~P~~~~nF~~l~~~---------~~y~~~~f~ri~~~~~iq~G~~~~~-~~~~~~~~~~   69 (299)
                      |.|.|. |+.|+|+||||++.||+||+||++||++         ++|+|+.|||+++++++|+|+.... +.++...++.
T Consensus         8 ~Di~i~~t~~G~ivIeL~~~~aP~tv~nF~~l~~~~~~~~~~~~~~y~g~~~~rv~~~~~iq~g~~~~~~~~~~~~~~~~   87 (170)
T d1qnga_           8 FDISIDNSNAGRIIFELFSDITPRTCENFRALCTGEKIGSRGKNLHYKNSIFHRIIPQFMCQGGDITNGNGSGGESIYGR   87 (170)
T ss_dssp             EEEEESSSEEEEEEEEECTTTCHHHHHHHHHHHHTCEECTTSSEECCTTCBCCEEETTTEEEECCTTTSSSSCCCBTTBS
T ss_pred             EEEEECCEEccEEEEEECCCCChHHHHHHHhhhccccccccCccCccCcccceEEEeCceEEecCccCCCCCCCcccCCC
Confidence            345554 8999999999999999999999999974         5799999999999999999997644 5555555554


Q ss_pred             cccccccccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEE
Q 046966           70 RFFVDEIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQII  149 (299)
Q Consensus        70 ~~~~~e~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~  149 (299)
                      . +.++ .+.+.|+.+|+|+|++.++++++|||||++.+ .++||++|+|||+|++||+||++|++.++ .+++|..+|+
T Consensus        88 ~-~~~~-~~~~~~~~~G~lsma~~~~~s~~sqFfIt~~~-~~~Ld~~~~vFG~Vv~Gmdvl~~I~~~~~-~~g~P~~~i~  163 (170)
T d1qnga_          88 S-FTDE-NFNMKHDQPGLLSMANAGPNTNSSQFFITLVP-CPWLDGKHVVFGKVIEGMNVVREMEKEGA-KSGYVKRSVV  163 (170)
T ss_dssp             C-BCCC-CCCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTTCC-TTCCCSSCEE
T ss_pred             c-cccc-cccccCCCCeEEEEeecCCCCccccceeccCC-cccccccccEEeEEeccHHHHHHHHhcCC-CCcCCccCEE
Confidence            4 4555 56788889999999999999999999999998 69999999999999999999999988766 4789999999


Q ss_pred             EEEEEEE
Q 046966          150 IKQTYVL  156 (299)
Q Consensus       150 I~~~~v~  156 (299)
                      |++|+++
T Consensus       164 I~~CG~l  170 (170)
T d1qnga_         164 ITDCGEL  170 (170)
T ss_dssp             EEEEEEC
T ss_pred             EEeeEcC
Confidence            9999975

>d1qoia_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Human (Homo sapiens), U4/U6 snRNP-specific cyclophilin snucyp-20 [TaxId: 9606]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Human (Homo sapiens), U4/U6 snRNP-specific cyclophilin snucyp-20 [TaxId: 9606]

Probab=100.00  E-value=1.3e-39  Score=264.49  Aligned_cols=147  Identities=36%  Similarity=0.688  Sum_probs=129.1

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhCCC--------cCCceeeEeecCcEEEecCCCCC-CCCCCCCCCCcccccccc
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKNKY--------YNGCLFHNIHKDFIAQTGDPTGT-GTGGRSVYEDRFFVDEIR   77 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~--------y~~~~f~ri~~~~~iq~G~~~~~-~~~~~~~~~~~~~~~e~~   77 (299)
                      +++|+|+||||.+.||+||+||++||+.++        |+++.|||+++++++|+|+.... +......+... +.++ .
T Consensus        18 ~~~G~i~ieL~~~~aP~tv~nF~~L~~~~~~~~~~~~~y~~~~f~rv~~~~~~q~G~~~~~~~~~~~~~~~~~-~~~~-~   95 (173)
T d1qoia_          18 QEVGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRVIKDFMIQGGDFVNGDGTGVASIYRGP-FADE-N   95 (173)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHSCCEETTEECSSTTCBCCEEETTTEEEECCTTTSSSCCCCCTTSSC-BCCC-C
T ss_pred             EeCeEEEEEEcCCCCcHHHHHHHHhhcccccccCCCCCcCCcccceeccceeeccCCcccCCcceeecccCCc-cccc-c
Confidence            458999999999999999999999999998        99999999999999999997643 33333333333 4445 3


Q ss_pred             cCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEE
Q 046966           78 ADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVL  156 (299)
Q Consensus        78 ~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~  156 (299)
                      ....|+.+|+|+|++.++++++|||||++++ .++||++|+|||+|++||+||++|++.+++++++|..+|+|++||.+
T Consensus        96 ~~~~~~~~G~l~ma~~~~~s~~sqFfI~~~~-~~~ldg~~tvFG~Vi~G~dvl~~I~~~~t~~~~~P~~~i~I~~cGel  173 (173)
T d1qoia_          96 FKLRHSAPGLLSMANSGPSTNGCQFFITCSK-CDWLDGKHVVFGKIIDGLLVMRKIENVPTGPNNKPKLPVVISQCGEM  173 (173)
T ss_dssp             CCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCGGGCBSSCEEEEEEEEC
T ss_pred             cccccCCCcEEEeeecCCCCCCceeeeeccC-CccCCcceeEEEEEechHHHHHHHHhCCcCCCCcCCCCEEEEcccCC
Confidence            4566779999999999999999999999998 79999999999999999999999999999999999999999999864

>d2z6wa1 b.62.1.1 (A:2-165) Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.4e-39  Score=260.33  Aligned_cols=147  Identities=38%  Similarity=0.666  Sum_probs=130.0

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhCC---CcCCceeeEeecCcEEEecCCCCC-CCCCCCCCCCcccccccccCCCC
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKNK---YYNGCLFHNIHKDFIAQTGDPTGT-GTGGRSVYEDRFFVDEIRADLKH   82 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~~---~y~~~~f~ri~~~~~iq~G~~~~~-~~~~~~~~~~~~~~~e~~~~~~~   82 (299)
                      ++.|+|+||||.+.||+||+||++||+++   +|+|+.|||+++++++|+|+.... +.++...++.. ++++ ...+.|
T Consensus        14 ~~~G~i~ieL~~~~aP~tv~nF~~l~~~~~~~~Y~g~~f~rv~~~~~iq~g~~~~~~~~~~~~~~~~~-~~~~-~~~~~~   91 (164)
T d2z6wa1          14 KPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSR-FPDE-NFTLKH   91 (164)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTTTSCCSTTCBEEEEETTTEEEECCTTTSSSSCCCBTTBSC-BCCC-CCCSCC
T ss_pred             EeceEEEEEECCCcCcHHHHHHHHHHhcCCCcccCCcEEEEecccceEecCCccCCCCCCCccccCCc-CCcc-cccccc
Confidence            44799999999999999999999999776   799999999999999999997754 56666666554 3555 456777


Q ss_pred             CCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEEEEC
Q 046966           83 DKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTYVLY  157 (299)
Q Consensus        83 ~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~v~~  157 (299)
                      +.+|+|+|++.++++++|||||++.+ .++||++|+|||+|++||+||++|++.++ .+++|..+|+|++|+++.
T Consensus        92 ~~~G~lsma~~~~~s~~sqFfi~~~~-~~~ldg~ytVFG~Vv~G~dvl~~I~~~~~-~~~~P~~~i~I~~cG~l~  164 (164)
T d2z6wa1          92 VGPGVLSMANAGPNTNGSQFFICTIK-TDWLDGKHVVFGHVIEGMDVVKKIESFGS-KSGRTSKKIVITDCGQLS  164 (164)
T ss_dssp             CSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHHTCC-TTSCCSSCEEEEEEEECC
T ss_pred             CCccEEEEecCCCCCCCcceeccccC-CCcccccceEEEEecccHHHHHHHHhCCC-CCCCCCCCEEEEeCeecC
Confidence            79999999999999999999999998 69999999999999999999999988876 578999999999999863

>d1a33a_ b.62.1.1 (A:) Cyclophilin (eukaryotic) {Nematode (Brugia malayi) [TaxId: 6279]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Nematode (Brugia malayi) [TaxId: 6279]

Probab=100.00  E-value=8.1e-39  Score=259.96  Aligned_cols=147  Identities=39%  Similarity=0.616  Sum_probs=131.0

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhC-----------CCcCCceeeEeecCcEEEecCCCCC-CCCCCCCCCCccccc
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKN-----------KYYNGCLFHNIHKDFIAQTGDPTGT-GTGGRSVYEDRFFVD   74 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~-----------~~y~~~~f~ri~~~~~iq~G~~~~~-~~~~~~~~~~~~~~~   74 (299)
                      ++.|+|+||||.+.||+||+||++||++           ++|+++.|||+++++++|+|+.... +.++.+.+...  .+
T Consensus        15 ~~~G~I~ieL~~d~aP~tv~nF~~l~~~~~~~~~~~~k~~~Y~~~~f~Rv~~~~~iq~g~~~~~~~~~~~~~~~~~--~~   92 (174)
T d1a33a_          15 NLAGRIVMELYNDIAPRTCNNFLMLCTGMAGTGKISGKPLHYKGSTFHRVIKNFMIQGGDFTKGDGTGGESIYGGM--FD   92 (174)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHCTTCBCTTTCSBCCCTTCBEEEEETTTEEEECCTTTSSSSCCCCTTSSC--BC
T ss_pred             EeceEEEEEECCCCChHHHHHHHHHHhcccCCCcccCccceeCCceeeEEEeCCEEeeCCCCCCCCCCCCCccCcc--cc
Confidence            3469999999999999999999999965           5799999999999999999997643 55555555433  33


Q ss_pred             ccccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEE
Q 046966           75 EIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTY  154 (299)
Q Consensus        75 e~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~  154 (299)
                      +.....+|+.+|+|+|++.++++++|||||++++ .++||++|+|||+|++||+||++|++.+++.+++|..+|+|.+|+
T Consensus        93 ~~~~~~~~~~~g~l~~~~~~~~s~~sqFfI~~~~-~p~ld~~~~vFG~VveG~dvl~~I~~~~t~~~~~P~~~i~I~~cG  171 (174)
T d1a33a_          93 DEEFVMKHDEPFVVSMANKGPNTNGSQFFITTTP-APHLNNIHVVFGKVVSGQEVVTKIEYLKTNSKNRPLADVVILNCG  171 (174)
T ss_dssp             CCCSCSCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCBCTTSCBSSCEEEEEEE
T ss_pred             ccccccccCcceeeeeeccCCCCCCcccccccCC-cccccccceeEEEEechHHHHHHHHhCCcCCCCCCCCCEEEEeeE
Confidence            3367788999999999999999999999999998 799999999999999999999999999999999999999999999


Q ss_pred             EE
Q 046966          155 VL  156 (299)
Q Consensus       155 v~  156 (299)
                      ++
T Consensus       172 el  173 (174)
T d1a33a_         172 EL  173 (174)
T ss_dssp             EC
T ss_pred             EE
Confidence            86

>d1ihga2 b.62.1.1 (A:2-196) Cyclophilin 40 isomerase domain {Cow (Bos taurus) [TaxId: 9913]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin 40 isomerase domain
species: Cow (Bos taurus) [TaxId: 9913]

Probab=100.00  E-value=7.4e-39  Score=264.33  Aligned_cols=147  Identities=39%  Similarity=0.687  Sum_probs=130.4

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhCC-----------CcCCceeeEeecCcEEEecCCCCC-CCCCCCCCCCccccc
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKNK-----------YYNGCLFHNIHKDFIAQTGDPTGT-GTGGRSVYEDRFFVD   74 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~~-----------~y~~~~f~ri~~~~~iq~G~~~~~-~~~~~~~~~~~~~~~   74 (299)
                      ++.|+|+||||.+.||+||+||++||+++           +|+|+.|||+++++++|+|+.... +.++...++.. +.+
T Consensus        26 ~~~G~I~IeL~~d~aP~tv~nF~~L~~~~~~~~~~~~~~~~y~g~~f~rv~~~~~i~~G~~~~~~~~~~~~~~~~~-~~~  104 (195)
T d1ihga2          26 ERVGRIVLELFADIVPKTAENFRALCTGEKGIGPTTGKPLHFKGCPFHRIIKKFMIQGGDFSNQNGTGGESIYGEK-FED  104 (195)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHCTTCBCTTTSSBSCCTTCBEEEEETTTEEEECCTTTSSSSCCCBTTBSC-BCC
T ss_pred             EeeeEEEEEECCCCChHHHHHHHHHhccccccccccCCccccCCceeeEEEcCceeecCCccCCCCCCCccCCCCc-ccc
Confidence            56899999999999999999999999853           699999999999999999997654 55555555544 456


Q ss_pred             ccccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecCHHHHHHHHhcccCCCCCCceeEEEEEEE
Q 046966           75 EIRADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEGLETLTRINQAVVDEENRPPQQIIIKQTY  154 (299)
Q Consensus        75 e~~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G~~vl~~i~~~~~~~~~~p~~~v~I~~~~  154 (299)
                      + ...+.|+.+|+|+|++.++++++|||||+|++ .++||++|+|||+|++||+||++|++.++ .+++|..+|+|++|+
T Consensus       105 ~-~~~~~h~~~G~lsm~~~~~~s~~SqFfItl~~-~~~LDg~ytVFG~Vv~Gmdvl~~I~~~~t-~~~~P~~~i~I~~cG  181 (195)
T d1ihga2         105 E-NFHYKHDKEGLLSMANAGSNTNGSQFFITTVP-TPHLDGKHVVFGQVIKGMGVAKILENVEV-KGEKPAKLCVIAECG  181 (195)
T ss_dssp             C-CCCBCCCSTTEEEECCSSTTCBCSCEEEESSC-CGGGTTTSCEEEEEEECHHHHHHHHTSCE-ETTEESSCEEEEEEE
T ss_pred             c-ccCcccCcceEEeeeecCCCCCCceeEeeccC-CcccCCcceEEEEEecCHHHHHHHHcCCC-CCCCcCCCeEEEECc
Confidence            6 55678889999999999999999999999998 69999999999999999999999998887 478999999999999


Q ss_pred             EEC
Q 046966          155 VLY  157 (299)
Q Consensus       155 v~~  157 (299)
                      +++
T Consensus       182 ~l~  184 (195)
T d1ihga2         182 ELK  184 (195)
T ss_dssp             EEC
T ss_pred             ccC
Confidence            998

>d1z81a1 b.62.1.1 (A:25-210) Cyclophilin (eukaryotic) {Plasmodium yoelii [TaxId: 5861]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Plasmodium yoelii [TaxId: 5861]

Probab=100.00  E-value=1.5e-38  Score=260.72  Aligned_cols=147  Identities=35%  Similarity=0.656  Sum_probs=130.0

Q ss_pred             EcceeEEEEecCCCChHHHHHHHHhhhCCC--------cCCceeeEeecCcEEEecCCCCC-CCCCCCCCCCcccccccc
Q 046966            7 TSLGDIVIDLFVDKCPRTTNNFLQHCKNKY--------YNGCLFHNIHKDFIAQTGDPTGT-GTGGRSVYEDRFFVDEIR   77 (299)
Q Consensus         7 T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~--------y~~~~f~ri~~~~~iq~G~~~~~-~~~~~~~~~~~~~~~e~~   77 (299)
                      ++.|+|+||||.+.||+||+||++||++++        |+|+.|||+++++++|+|+.... +......++.. +.++ .
T Consensus        28 ~~~G~I~ieL~~d~aP~tv~nF~~L~~~~~~~~~~~~~Y~g~~f~rv~~~~~i~~G~~~~~~~~~~~~~~~~~-~~~~-~  105 (186)
T d1z81a1          28 NFLGKFKFELFQNIVPKTSENFRQFCTGEYKVNNLPVGYKNTIFHRVIKEFMIQGGDFINHNGSGSLSIYGEK-FDDE-N  105 (186)
T ss_dssp             EEEEEEEEEECTTTCHHHHHHHHHHHHTCCBSSSSBCSSTTEECCEEETTTEEEECCTTTSSSCCCCBTTBSC-CCCC-C
T ss_pred             EeceEEEEEEcCCCChHHHHHHHHHHhcccccCCcccccCCCeeeeeecceeeecCCccccCCcccccccCCc-cccc-c
Confidence            456999999999999999999999999998        99999999999999999997654 44444444433 4555 6


Q ss_pred             cCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeecC--HHHHHHHHhcccCC-CCCCceeEEEEEEE
Q 046966           78 ADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAEG--LETLTRINQAVVDE-ENRPPQQIIIKQTY  154 (299)
Q Consensus        78 ~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~G--~~vl~~i~~~~~~~-~~~p~~~v~I~~~~  154 (299)
                      ..++|+.+|+++|++.++++++|||||++++ .++||++|+|||+|++|  |++|++|+..++++ .++|..+|+|++|+
T Consensus       106 ~~~~~~~~G~~~~~~~g~~~~~sqFfIt~~~-~p~Ldg~~tVFG~Vv~G~~mdvv~kI~~~~~~~~~~~P~~~i~I~~CG  184 (186)
T d1z81a1         106 FDIKHDKEGLLSMANSGPNTNGCQFFITTKK-CEWLDGKNVVFGRIIDNDSLLLLKKIENVSVTPYIYKPKIPINVVECG  184 (186)
T ss_dssp             CCSCCCSTTEEEECCSSSSCCCSCEEEESSC-CGGGBTTBCEEEEECSHHHHHHHHHHHHSCBCTTTCCBSSCEEEEEEE
T ss_pred             cccccCCCccchhhhcCCCccccceeeeccc-ccccCCCccEEEEEEeCccHHHHHHHhccCCCCCCCccCCCEEEEeCC
Confidence            6788899999999999999999999999998 69999999999999998  99999999998875 68999999999999


Q ss_pred             EE
Q 046966          155 VL  156 (299)
Q Consensus       155 v~  156 (299)
                      ++
T Consensus       185 el  186 (186)
T d1z81a1         185 EL  186 (186)
T ss_dssp             EC
T ss_pred             cC
Confidence            74

>d2c3ba1 b.62.1.1 (A:1-171) Cyclophilin (eukaryotic) {Aspergillus fumigatus [TaxId: 5085]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: Cyclophilin (peptidylprolyl isomerase)
domain: Cyclophilin (eukaryotic)
species: Aspergillus fumigatus [TaxId: 5085]

Probab=100.00  E-value=4.5e-39  Score=260.34  Aligned_cols=150  Identities=41%  Similarity=0.627  Sum_probs=110.5

Q ss_pred             EEEEcceeEEEEecCCCChHHHHHHHHhhhCCC---cCCceeeEeecCcEEEecCCCC-CCCCCCCCCCCcccccccccC
Q 046966            4 LIETSLGDIVIDLFVDKCPRTTNNFLQHCKNKY---YNGCLFHNIHKDFIAQTGDPTG-TGTGGRSVYEDRFFVDEIRAD   79 (299)
Q Consensus         4 ~~~T~~G~i~ieL~~~~~P~~~~nF~~l~~~~~---y~~~~f~ri~~~~~iq~G~~~~-~~~~~~~~~~~~~~~~e~~~~   79 (299)
                      ..+|++|+|+||||.+.||+||+||++||+.++   |+++.|||++|++++|+|+... ++.++...++.. +.++ ...
T Consensus        15 ~~~T~~G~i~IeL~~~~aP~tv~nF~~l~~~~~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~-~~~~-~~~   92 (171)
T d2c3ba1          15 TAETKVGRIVFNLFDKDVPKTAKNFRELCKRPAGEGYRESTFHRIIPNFMIQGGDFTRGNGTGGRSIYGDK-FADE-NFS   92 (171)
T ss_dssp             CSCCEEEEEEEEECTTTSHHHHHHHHHHHHSCTTTSSTTCBCCEEETTTEEEECC------------------------C
T ss_pred             cccceeeEEEEEEcCCCChHHHHHHHHHhhhcccccccCceeeEEEEEEeeEcCCccCCCCCCCCcCCCCc-cccc-ccc
Confidence            346899999999999999999999999999887   9999999999999999999654 355554444433 3444 566


Q ss_pred             CCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCCCCceEEEEeec--CHHHHHHHHhcccCC-CCCCceeEEEEEEEEE
Q 046966           80 LKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLDEKHTIFGEVAE--GLETLTRINQAVVDE-ENRPPQQIIIKQTYVL  156 (299)
Q Consensus        80 ~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld~~~~vfG~V~~--G~~vl~~i~~~~~~~-~~~p~~~v~I~~~~v~  156 (299)
                      +.|+.+|+|+|++.++++++|||||++++ .++||++|+|||+|++  ||+||++|++.+++. ...|..+|+|.+|+++
T Consensus        93 ~~~~~~G~lsma~~~~~s~~sqFfI~~~~-~~~ldg~~tvFG~Vie~~G~dvl~~I~~~~t~~g~~~p~~~v~I~~cGel  171 (171)
T d2c3ba1          93 RKHDKKGILSMANAGPNTNGSQFFITTAV-TSWLDGKHVVFGEVADEKSYSVVKEIEALGSSSGSVRSNTRPKIVNCGEL  171 (171)
T ss_dssp             HHHHHTCEEEEC---------CEEEECSC-CTTCCSCCEEEEEECSHHHHHHHHHHHTTCCTTSCCCSSSCCEEEEEEEC
T ss_pred             ccCCCCceEEeeecCCCCCCcceeeccCC-ccccCCCceEEEEEEeccCHHHHHHHHcCCCCCCCcCCCCCEEEEeCccC
Confidence            77889999999999999999999999998 6999999999999995  999999999888866 3478999999999974

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=2.1e-21  Score=142.47  Aligned_cols=87  Identities=31%  Similarity=0.486  Sum_probs=82.5

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ..+++++|||+|||+++++++|+++|++||.+.++.++.++.+|.++|||||+|.+.++|++|++.|||..++|+.|+|+
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            34567899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCCccc
Q 046966          287 FSQSVSK  293 (299)
Q Consensus       287 ~a~~~~~  293 (299)
                      +++++..
T Consensus        94 ~a~~k~~  100 (102)
T d2cpza1          94 LKRSKND  100 (102)
T ss_dssp             CCCCSCC
T ss_pred             EeCCCCC
Confidence            9998764

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.85  E-value=1.8e-21  Score=137.24  Aligned_cols=80  Identities=29%  Similarity=0.525  Sum_probs=77.8

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      +++|||+|||+++++++|+++|++||.|.++++++++.+|+++|||||+|.+.++|++|++.|||..++|+.|+|++|+|
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            57899999999999999999999999999999999989999999999999999999999999999999999999999987

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=1.7e-21  Score=140.61  Aligned_cols=86  Identities=27%  Similarity=0.355  Sum_probs=81.7

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .++.++|||+|||+++++++|+++|++||.|.++++++++.+|.++|||||+|.+.++|++|++.|||..++|+.|+|++
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             cCCccc
Q 046966          288 SQSVSK  293 (299)
Q Consensus       288 a~~~~~  293 (299)
                      |+++++
T Consensus        86 A~~~~~   91 (93)
T d1x5ua1          86 ASAHNK   91 (93)
T ss_dssp             TTTTSC
T ss_pred             cCCCCC
Confidence            998764

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=5.4e-21  Score=137.08  Aligned_cols=84  Identities=24%  Similarity=0.412  Sum_probs=80.3

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .+.++|||+|||+++++++|+++|++||.|.++.++.++.+|.++|||||+|.+.++|.+|++.|||..++|+.|+|++|
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            35689999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             CCcc
Q 046966          289 QSVS  292 (299)
Q Consensus       289 ~~~~  292 (299)
                      +|+.
T Consensus        86 kp~~   89 (90)
T d2cq0a1          86 KPST   89 (90)
T ss_dssp             SCCC
T ss_pred             eCCC
Confidence            9864

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.85  E-value=4.6e-21  Score=136.83  Aligned_cols=83  Identities=27%  Similarity=0.377  Sum_probs=79.0

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .++++|||+|||+++++++|+++|++||.|.++++++++.+|+++|||||+|.+.++|++|+..|||..++|+.|+|+||
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a   84 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC   84 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            35789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCc
Q 046966          289 QSV  291 (299)
Q Consensus       289 ~~~  291 (299)
                      .++
T Consensus        85 ~~k   87 (88)
T d1rk8a_          85 FVK   87 (88)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            875

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=5.7e-21  Score=137.75  Aligned_cols=85  Identities=25%  Similarity=0.337  Sum_probs=80.7

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .++++|||+|||+++++++|+++|++||.|.++.++.++.++.++|||||+|.+.++|+.|++.|||..++|+.|+|+|+
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            35789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCccc
Q 046966          289 QSVSK  293 (299)
Q Consensus       289 ~~~~~  293 (299)
                      .+...
T Consensus        85 ~~~~~   89 (93)
T d1h2vz_          85 AGFKE   89 (93)
T ss_dssp             SCCCT
T ss_pred             CCCCC
Confidence            87543

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=9.2e-21  Score=133.50  Aligned_cols=80  Identities=26%  Similarity=0.458  Sum_probs=77.4

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      .++|||+|||+++++++|+++|++||.|.+++++++..++.++|||||+|.+.++|++|++.|||..++|++|+|.+|+|
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            46799999999999999999999999999999999988999999999999999999999999999999999999999987

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=2.7e-21  Score=138.35  Aligned_cols=83  Identities=33%  Similarity=0.479  Sum_probs=79.7

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ..++|||+|||+++++++|+++|++||.|.++.++.++.+|+++|||||+|.+.++|++|++.||+..++|+.|+|++|+
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Ccc
Q 046966          290 SVS  292 (299)
Q Consensus       290 ~~~  292 (299)
                      |++
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            864

>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=1.3e-20  Score=132.08  Aligned_cols=77  Identities=32%  Similarity=0.464  Sum_probs=75.2

Q ss_pred             eEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       213 ~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      .|||+|||+.+++++|+++|++||.|.+++|++++.+|+++|||||+|.+.++|.+|++.|||..++|++|+|.+|+
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            69999999999999999999999999999999999999999999999999999999999999999999999999985

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.8e-20  Score=132.28  Aligned_cols=78  Identities=32%  Similarity=0.472  Sum_probs=74.7

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      +++.++|||+|||+++++++|+++|++||.|.++++++++.+++++|||||+|.+.++|++|++.||+..++|++|+|
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            456789999999999999999999999999999999999999999999999999999999999999999999999987

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=6.1e-21  Score=135.23  Aligned_cols=82  Identities=24%  Similarity=0.415  Sum_probs=78.8

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCCc
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSV  291 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~~  291 (299)
                      ++|||+|||+++++++|+++|++||.|.++++++++.+|.++|||||+|.+.++|.+|++.||+..++|++|.|++|.+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999976


Q ss_pred             cc
Q 046966          292 SK  293 (299)
Q Consensus       292 ~~  293 (299)
                      .+
T Consensus        82 ~~   83 (85)
T d2u2fa_          82 AK   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.83  E-value=1.5e-20  Score=137.15  Aligned_cols=86  Identities=26%  Similarity=0.325  Sum_probs=81.2

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ...++|||+|||+++++++|+++|++||.|.+++++.++.+++++|||||+|.+.++|++|++.||+..++|+.|+|.++
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             CCcccc
Q 046966          289 QSVSKI  294 (299)
Q Consensus       289 ~~~~~~  294 (299)
                      +++...
T Consensus        86 ~~~~~~   91 (99)
T d1whwa_          86 TIKKEA   91 (99)
T ss_dssp             CCCSTT
T ss_pred             CCCCcc
Confidence            987543

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=7.8e-20  Score=130.71  Aligned_cols=82  Identities=28%  Similarity=0.395  Sum_probs=76.6

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ...++|||+|||+++++++|+++|++||.|.++++++|+.+|+++|||||+|.+.++|++|++.  .+.++|+.|.|++|
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 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeC
Confidence            3568899999999999999999999999999999999999999999999999999999999974  45899999999999


Q ss_pred             CCcc
Q 046966          289 QSVS  292 (299)
Q Consensus       289 ~~~~  292 (299)
                      .++.
T Consensus        84 ~~k~   87 (90)
T d2cqga1          84 NSKQ   87 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            9864

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.82  E-value=1.6e-20  Score=131.89  Aligned_cols=81  Identities=15%  Similarity=0.283  Sum_probs=70.8

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      .++|||+|||+++++++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|++|++.|||..++|++|+|++|+|
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            47999999999999999999999999999888888878899999999999999999999999999999999999999988


Q ss_pred             c
Q 046966          291 V  291 (299)
Q Consensus       291 ~  291 (299)
                      .
T Consensus        81 ~   81 (81)
T d2ghpa1          81 L   81 (81)
T ss_dssp             C
T ss_pred             c
Confidence            3

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.82  E-value=3.4e-20  Score=143.81  Aligned_cols=84  Identities=25%  Similarity=0.371  Sum_probs=79.9

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ..++|||+|||+++++++|+++|++||.|.+++++.++.+++++|||||+|.+.++|.+|++.|||..|+|+.|+|++|+
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            45789999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             Cccc
Q 046966          290 SVSK  293 (299)
Q Consensus       290 ~~~~  293 (299)
                      ++.+
T Consensus       121 ~~~~  124 (139)
T d1u6fa1         121 SGHQ  124 (139)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.82  E-value=6.7e-20  Score=129.86  Aligned_cols=79  Identities=33%  Similarity=0.577  Sum_probs=75.3

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEe
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDD--RRICVDF  287 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g--~~l~v~~  287 (299)
                      .+++|||+|||+++++++|+++|++||.|.++++++++.+|+++|||||+|.+.++|.+|++.||+..+.|  ++|+|+|
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            46789999999999999999999999999999999999999999999999999999999999999999876  8899998


Q ss_pred             c
Q 046966          288 S  288 (299)
Q Consensus       288 a  288 (299)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=6.8e-20  Score=129.43  Aligned_cols=79  Identities=28%  Similarity=0.345  Sum_probs=75.2

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      .++|||+|||+++++++|+++|++||.|..+++++++.+|+++|||||+|.+.++|++|++ ++++.|+|+.|+|+.|.+
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            5789999999999999999999999999999999999999999999999999999999996 599999999999998864

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=5.5e-20  Score=130.27  Aligned_cols=78  Identities=32%  Similarity=0.499  Sum_probs=74.3

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCC--eEEEEEec
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDD--RRICVDFS  288 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g--~~l~v~~a  288 (299)
                      +++|||+|||+.+++++|+++|++||.|.++++++++.+|+++|||||+|.+.++|++|++.|||..+.|  ++|.|+||
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            6789999999999999999999999999999999998899999999999999999999999999999997  55999886

>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=99.81  E-value=3.9e-20  Score=133.57  Aligned_cols=85  Identities=16%  Similarity=0.409  Sum_probs=78.7

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecC-CCCCeeeEEEEEecCHHHHHHHHHHh-CCceeCCeEEEEE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDY-RTGESLCYAFVEFEKREACEQAYFKM-NNALIDDRRICVD  286 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~-~~g~~~g~afv~f~~~~~a~~al~~l-~~~~i~g~~l~v~  286 (299)
                      .+..+|||+|||+++++++|+++|++||.|.+++|++++ .+|+++|||||+|.+.++|.+|++.| |+..+.|++|.|+
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            457889999999999999999999999999999998875 47999999999999999999999998 8999999999999


Q ss_pred             ecCCccc
Q 046966          287 FSQSVSK  293 (299)
Q Consensus       287 ~a~~~~~  293 (299)
                      ||++..+
T Consensus        86 ~A~~~~~   92 (94)
T d2cpha1          86 WADSEVT   92 (94)
T ss_dssp             ECCCCCC
T ss_pred             EcCCCCC
Confidence            9998653

>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=99.81  E-value=1.1e-20  Score=131.24  Aligned_cols=76  Identities=25%  Similarity=0.352  Sum_probs=73.1

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      |+|||+|||+++++++|+++|++||.|.++++++++.+|+++|||||+|.+.++|++|++ ++++.++|+.|.|+.|
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            689999999999999999999999999999999999999999999999999999999996 6999999999999876

>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=99.81  E-value=5.9e-20  Score=127.94  Aligned_cols=77  Identities=30%  Similarity=0.442  Sum_probs=74.1

Q ss_pred             eEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       213 ~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      +|||+|||+++++++|+++|++||.|.++++..++ +++++|||||+|.+.++|++|++.|||..++|++|+|+++.+
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            69999999999999999999999999999999984 899999999999999999999999999999999999999875

>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=99.80  E-value=1.6e-19  Score=129.23  Aligned_cols=82  Identities=23%  Similarity=0.331  Sum_probs=75.9

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .+.++|||+|||+++++++|+++|++||.|.+++++.++.++  +|||||+|.+.++|.+|++.|||..+.|+.|+|.+|
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            346799999999999999999999999999999999886544  789999999999999999999999999999999999


Q ss_pred             CCcc
Q 046966          289 QSVS  292 (299)
Q Consensus       289 ~~~~  292 (299)
                      +++.
T Consensus        84 ~~~~   87 (90)
T d2cqia1          84 TTPS   87 (90)
T ss_dssp             CCTT
T ss_pred             CCCC
Confidence            9764

>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=99.80  E-value=1.4e-19  Score=132.93  Aligned_cols=81  Identities=32%  Similarity=0.427  Sum_probs=76.0

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ..++|||+|||+.+++++|+++|++||.|.+++++.++.+|+++|||||+|.+.++|++|++.+|+ .++|+.|+|+++.
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            356799999999999999999999999999999999999999999999999999999999998876 7999999999988


Q ss_pred             Cc
Q 046966          290 SV  291 (299)
Q Consensus       290 ~~  291 (299)
                      +.
T Consensus        88 ~~   89 (103)
T d2cqda1          88 LG   89 (103)
T ss_dssp             TT
T ss_pred             CC
Confidence            64

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=4.7e-20  Score=135.76  Aligned_cols=83  Identities=29%  Similarity=0.405  Sum_probs=79.1

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      .++|||+|||+++++++|+++|++||.|.++++++++.+|+++|||||+|.+.++|++|++.||+..++|+.|+|++|.+
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            46899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             ccc
Q 046966          291 VSK  293 (299)
Q Consensus       291 ~~~  293 (299)
                      ...
T Consensus        88 ~~~   90 (104)
T d1p1ta_          88 EKN   90 (104)
T ss_dssp             TTH
T ss_pred             CCC
Confidence            643

>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=99.80  E-value=3.4e-19  Score=128.31  Aligned_cols=83  Identities=27%  Similarity=0.424  Sum_probs=76.9

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ....++|||+|||+.+++++|+++|++||.|.+++++.++  +.++|||||+|.+.++|.+|++.||+..++|+.|+|++
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 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   85 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            4457889999999999999999999999999999999885  33689999999999999999999999999999999999


Q ss_pred             cCCcc
Q 046966          288 SQSVS  292 (299)
Q Consensus       288 a~~~~  292 (299)
                      |+++.
T Consensus        86 A~~r~   90 (93)
T d2cq3a1          86 ATARV   90 (93)
T ss_dssp             CCSSC
T ss_pred             cCcCC
Confidence            99875

>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=99.80  E-value=1.3e-19  Score=128.44  Aligned_cols=79  Identities=28%  Similarity=0.475  Sum_probs=73.6

Q ss_pred             EEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCC---CeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTG---ESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       214 v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g---~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      |||+|||+++++++|+++|++||.|.++.+++++.++   .++|||||+|.+.++|++|++.|||..++|+.|+|++|++
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            7999999999999999999999999999999886655   5799999999999999999999999999999999999976


Q ss_pred             cc
Q 046966          291 VS  292 (299)
Q Consensus       291 ~~  292 (299)
                      ..
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=5.3e-20  Score=131.86  Aligned_cols=84  Identities=30%  Similarity=0.481  Sum_probs=79.6

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ...+|||+|||+++++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|++|+..|||..++|++|+|++|.
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            46789999999999999999999999999999999988899999999999999999999999999999999999999998


Q ss_pred             Cccc
Q 046966          290 SVSK  293 (299)
Q Consensus       290 ~~~~  293 (299)
                      ++..
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>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=99.80  E-value=5.1e-20  Score=129.91  Aligned_cols=79  Identities=32%  Similarity=0.540  Sum_probs=74.8

Q ss_pred             EEEEcCCCCCCHHHHHHhcccCCCeEE-EEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCCcc
Q 046966          214 LFVCQLNPVTEDEDLHVIFSQFGTVVS-AEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVS  292 (299)
Q Consensus       214 v~v~nL~~~~~e~~L~~~f~~~G~i~~-~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~~~  292 (299)
                      |||+|||+++++++|+++|++||.|.+ +++++++.+|+++|||||+|.+.++|++|++.|+|..++|++|+|++|.++.
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            799999999999999999999999875 4788898999999999999999999999999999999999999999999865

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=4.7e-20  Score=134.78  Aligned_cols=81  Identities=26%  Similarity=0.275  Sum_probs=76.8

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      .++|||+|||+++++++|+++|+.||.|.++++++++.+|+++|||||+|.+.++|++|++ |||..++|+.|.|+++.+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999999999999999999999999999999999999995 999999999999999986


Q ss_pred             cc
Q 046966          291 VS  292 (299)
Q Consensus       291 ~~  292 (299)
                      ++
T Consensus        97 ~~   98 (101)
T d2cq4a1          97 EK   98 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            54

>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=99.79  E-value=1.3e-19  Score=132.79  Aligned_cols=82  Identities=22%  Similarity=0.293  Sum_probs=77.5

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      .++|||+|||+++++++|+++|++||.|..+.|++++.++.++|||||+|.+.++|++|++ ++++.|+|+.|.|++|.+
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCSS
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECcc
Confidence            3689999999999999999999999999999999999999999999999999999999995 799999999999999998


Q ss_pred             ccc
Q 046966          291 VSK  293 (299)
Q Consensus       291 ~~~  293 (299)
                      +.+
T Consensus        99 ke~  101 (103)
T d1x4ba1          99 REE  101 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            764

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.2e-19  Score=125.40  Aligned_cols=75  Identities=27%  Similarity=0.356  Sum_probs=71.3

Q ss_pred             eEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       213 ~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      +|||+|||+++++++|+++|++||.|.++.+++++.+++++|||||+|.+.++|++|++ +++..|+|+.|.|+.|
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            58999999999999999999999999999999999999999999999999999999996 7999999999998654

>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=99.78  E-value=4.2e-19  Score=129.14  Aligned_cols=85  Identities=22%  Similarity=0.346  Sum_probs=78.8

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhC------CceeCCeE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMN------NALIDDRR  282 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~------~~~i~g~~  282 (299)
                      ..+++|||+|||+++++++|+++|++||.+..+.++.++.+++++|||||+|.+.++|.+|++.||      |..+.|+.
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            357899999999999999999999999999999999998899999999999999999999999886      67799999


Q ss_pred             EEEEecCCccc
Q 046966          283 ICVDFSQSVSK  293 (299)
Q Consensus       283 l~v~~a~~~~~  293 (299)
                      |+|++|.++.+
T Consensus        86 l~v~~a~~k~~   96 (98)
T d1x4ha1          86 LKVDLAVTRDE   96 (98)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEECCCCCc
Confidence            99999998653

>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=99.78  E-value=2.1e-19  Score=128.40  Aligned_cols=80  Identities=34%  Similarity=0.513  Sum_probs=74.9

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      ..+|||+|||+++++++|+++|++||.|.+++++.++  +.++|||||+|.+.++|++|++.|||..++|+.|.|.++++
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            4579999999999999999999999999999999885  44789999999999999999999999999999999999998


Q ss_pred             cc
Q 046966          291 VS  292 (299)
Q Consensus       291 ~~  292 (299)
                      ++
T Consensus        86 ~~   87 (89)
T d1cvja2          86 RK   87 (89)
T ss_dssp             TT
T ss_pred             CC
Confidence            65

>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=7.3e-19  Score=122.65  Aligned_cols=77  Identities=22%  Similarity=0.394  Sum_probs=73.3

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      -++|||+|||+++++++|+++|++||.+..+.+..++.+++++|||||+|.+.+++++|++ |+++.|+|+.|.|+.|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            3689999999999999999999999999999999999999999999999999999999995 7999999999999876

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=4.3e-19  Score=129.81  Aligned_cols=85  Identities=21%  Similarity=0.258  Sum_probs=78.0

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeE--------EEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVV--------SAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID  279 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~--------~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~  279 (299)
                      .....+|||+|||+.+++++|+++|++||.|.        .+.+..++.+|+++|||||+|.+.++|.+|++.|||..++
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            34578999999999999999999999999874        5667788889999999999999999999999999999999


Q ss_pred             CeEEEEEecCCcc
Q 046966          280 DRRICVDFSQSVS  292 (299)
Q Consensus       280 g~~l~v~~a~~~~  292 (299)
                      |+.|+|++|+++.
T Consensus        85 gr~i~V~~a~~~~   97 (101)
T d2cpea1          85 GSKLKVSLARKKP   97 (101)
T ss_dssp             TEECEEECSSCCC
T ss_pred             CEEEEEEEcCCCC
Confidence            9999999999864

>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=99.78  E-value=3.5e-19  Score=126.29  Aligned_cols=81  Identities=23%  Similarity=0.402  Sum_probs=71.1

Q ss_pred             CCceEEEEcCCCCCC-HHHHHHhcccCCCeEEEEEeec-CCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          210 PDNVLFVCQLNPVTE-DEDLHVIFSQFGTVVSAEILRD-YRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~-e~~L~~~f~~~G~i~~~~~~~~-~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..++|||+|||++++ +++|+++|++||.|.+++++.+ ..+++++|||||+|.+.++|++|++ ||+..++|+.|+|++
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            368999999999976 5569999999999999998764 5688999999999999999999995 999999999999999


Q ss_pred             cCCc
Q 046966          288 SQSV  291 (299)
Q Consensus       288 a~~~  291 (299)
                      |+++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            9875

>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=8.1e-20  Score=134.04  Aligned_cols=86  Identities=23%  Similarity=0.386  Sum_probs=80.5

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ..|+++|||+|||.++++++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|++|++.|||..+.|++|+|+|
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   94 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF   94 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            35678999999999999999999999999999988888878899999999999999999999999999999999999999


Q ss_pred             cCCccc
Q 046966          288 SQSVSK  293 (299)
Q Consensus       288 a~~~~~  293 (299)
                      |+++..
T Consensus        95 ak~k~~  100 (102)
T d2cpxa1          95 GKNKKQ  100 (102)
T ss_dssp             CCCCSC
T ss_pred             CCCccc
Confidence            998753

>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=1.3e-19  Score=124.96  Aligned_cols=75  Identities=23%  Similarity=0.367  Sum_probs=71.0

Q ss_pred             eEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       213 ~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      +|||+|||+++++++|+++|++||.|..++|+.++.+++++|||||+|.+.++|++|++ ++++.++|+.|.|+.|
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 4778899999999875

>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=99.76  E-value=2.2e-18  Score=124.54  Aligned_cols=83  Identities=24%  Similarity=0.400  Sum_probs=75.1

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ...++++|||+|||+++++++|+++|++||.|..+.+..+   +.++|||||+|.+.++|+.|++.||++.+.|++|+|+
T Consensus        10 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~   86 (95)
T d1x4aa1          10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   86 (95)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3456789999999999999999999999999999887544   4578999999999999999999999999999999999


Q ss_pred             ecCCcc
Q 046966          287 FSQSVS  292 (299)
Q Consensus       287 ~a~~~~  292 (299)
                      +|++.+
T Consensus        87 ~a~~~r   92 (95)
T d1x4aa1          87 FPRSGR   92 (95)
T ss_dssp             CCCCCC
T ss_pred             eccCCC
Confidence            998753

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.76  E-value=1e-19  Score=130.45  Aligned_cols=82  Identities=22%  Similarity=0.292  Sum_probs=75.4

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ....++|||+|||+++++++|+++|++||.|..+.++.+ .+|+++|||||+|.+.++|++|++ ||+..++|+.|+|++
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            445779999999999999999999999999998888765 689999999999999999999995 999999999999999


Q ss_pred             cCCc
Q 046966          288 SQSV  291 (299)
Q Consensus       288 a~~~  291 (299)
                      |+++
T Consensus        88 ak~k   91 (91)
T d1fjeb1          88 PKGR   91 (91)
T ss_dssp             CCCS
T ss_pred             cCCC
Confidence            9874

>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=99.76  E-value=1.4e-18  Score=127.05  Aligned_cols=82  Identities=24%  Similarity=0.418  Sum_probs=76.3

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ..+++|||+|||+++++++|+++|++||.|..+.+..+ .++.++|||||+|.+.++|.+|++.|||..|.|+++.|..+
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            34689999999999999999999999999999999888 58899999999999999999999999999999999999887


Q ss_pred             CCc
Q 046966          289 QSV  291 (299)
Q Consensus       289 ~~~  291 (299)
                      +|-
T Consensus        95 ~Pl   97 (101)
T d1x5oa1          95 EPL   97 (101)
T ss_dssp             SCB
T ss_pred             CCc
Confidence            764

>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=99.76  E-value=1.7e-18  Score=129.50  Aligned_cols=80  Identities=16%  Similarity=0.244  Sum_probs=74.0

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      +.+++|||+|||+.+++++|+++|++||.|.+|++..+   +.++|||||+|.+.++|..|++.|||+.|.|+.|.|.++
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45789999999999999999999999999999998754   567899999999999999999999999999999999998


Q ss_pred             CCc
Q 046966          289 QSV  291 (299)
Q Consensus       289 ~~~  291 (299)
                      .+.
T Consensus        82 ~~~   84 (114)
T d2f9da1          82 NAN   84 (114)
T ss_dssp             CHH
T ss_pred             CCC
Confidence            764

>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=99.75  E-value=6.2e-19  Score=121.75  Aligned_cols=75  Identities=27%  Similarity=0.357  Sum_probs=71.9

Q ss_pred             eEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       213 ~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      +|||+|||+++++++|+++|++||.+..+.++.++.++.++|||||+|.+.++|++|++ ||++.++|++|+|+.|
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            58999999999999999999999999999999998899999999999999999999996 8999999999999876

>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=99.75  E-value=1.8e-18  Score=125.04  Aligned_cols=78  Identities=18%  Similarity=0.395  Sum_probs=72.8

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      +..++|||+|||..+++++|+++|++||.|.+++++.+      +|||||+|.+.++|.+|+..|||..++|+.|+|.|+
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            34678999999999999999999999999999999865      589999999999999999999999999999999999


Q ss_pred             CCcc
Q 046966          289 QSVS  292 (299)
Q Consensus       289 ~~~~  292 (299)
                      +++.
T Consensus        90 k~~p   93 (96)
T d1x4ga1          90 KESP   93 (96)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8764

>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=99.74  E-value=3.9e-18  Score=120.85  Aligned_cols=79  Identities=25%  Similarity=0.352  Sum_probs=71.6

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ...++|||+|||+++++++|+++|++||.+..+.+.      +++|||||+|.+.++|.+|+..|||..++|+.|+|+||
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~a   79 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA   79 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            346789999999999999999999999998877653      35789999999999999999999999999999999999


Q ss_pred             CCccc
Q 046966          289 QSVSK  293 (299)
Q Consensus       289 ~~~~~  293 (299)
                      +|+.+
T Consensus        80 kP~~~   84 (86)
T d2cpda1          80 KPVDK   84 (86)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98764

>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=99.74  E-value=9e-18  Score=123.32  Aligned_cols=83  Identities=18%  Similarity=0.344  Sum_probs=74.0

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecC-CCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDY-RTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~-~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .+.++|||+|||+++++++|+++|++|| +..+.++.+. .+++++|||||+|.+.++|++|+ .||+..|+|+.|+|++
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            3568999999999999999999999999 7777777654 57889999999999999998777 5999999999999999


Q ss_pred             cCCccc
Q 046966          288 SQSVSK  293 (299)
Q Consensus       288 a~~~~~  293 (299)
                      |.++..
T Consensus        91 a~~~~~   96 (104)
T d1wi8a_          91 ADQAQD   96 (104)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            998754

>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=99.74  E-value=5.6e-18  Score=122.55  Aligned_cols=80  Identities=18%  Similarity=0.277  Sum_probs=72.9

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .+.++|||+|||+++++++|+++|++||.|..++     .+++++|||||+|.+.++|++|++.||+..++|++|+|.|+
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a   88 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            4578999999999999999999999999876553     36889999999999999999999999999999999999999


Q ss_pred             CCccc
Q 046966          289 QSVSK  293 (299)
Q Consensus       289 ~~~~~  293 (299)
                      .++..
T Consensus        89 ~~k~~   93 (96)
T d1fjca_          89 GEKGG   93 (96)
T ss_dssp             SSSCC
T ss_pred             CCCCC
Confidence            98753

>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=99.73  E-value=5.8e-18  Score=119.10  Aligned_cols=77  Identities=23%  Similarity=0.404  Sum_probs=70.8

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC-CeEEEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID-DRRICVD  286 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~-g~~l~v~  286 (299)
                      .+|+++|||+|||+++++++|+++|++||.|..++++.+     .+|||||+|.+.++|.+|++.|||..+. |++|+|.
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            467899999999999999999999999999999999765     3689999999999999999999999885 7999999


Q ss_pred             ecC
Q 046966          287 FSQ  289 (299)
Q Consensus       287 ~a~  289 (299)
                      ||+
T Consensus        80 ~ak   82 (83)
T d2b0ga1          80 FAK   82 (83)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            986

>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=99.73  E-value=1e-17  Score=118.30  Aligned_cols=77  Identities=12%  Similarity=0.168  Sum_probs=72.3

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      .++|||+|||+++++++|+++|+.||.|..+++..+ .+++++|||||+|.+.++|++|++ +++..+.|+.|.|.++.
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 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEEC-TTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeee-ccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            578999999999999999999999999999999887 589999999999999999999995 69999999999999854

>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=99.73  E-value=1.3e-17  Score=120.94  Aligned_cols=78  Identities=19%  Similarity=0.413  Sum_probs=70.0

Q ss_pred             CCCCCceEEEEcCC-CCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          207 VKPPDNVLFVCQLN-PVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       207 ~~~~~~~v~v~nL~-~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      .....++|||+||| ..+++++|+++|++||.|.++++        ++|||||+|.+.++|++|++.|||+.+.|+.|+|
T Consensus        11 ~~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V   82 (98)
T d1wf2a_          11 PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDI   82 (98)
T ss_dssp             CSSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEE
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34456789999997 56888999999999999999988        4689999999999999999999999999999999


Q ss_pred             EecCCcc
Q 046966          286 DFSQSVS  292 (299)
Q Consensus       286 ~~a~~~~  292 (299)
                      +++++++
T Consensus        83 ~~a~~~~   89 (98)
T d1wf2a_          83 NLAAEPK   89 (98)
T ss_dssp             EETTSCC
T ss_pred             EECCCCC
Confidence            9998653

>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=99.73  E-value=5.1e-18  Score=120.25  Aligned_cols=81  Identities=19%  Similarity=0.290  Sum_probs=72.0

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .+..++|||+|||+++++++|+++|+.||.+....++....+++++|+|||+|.+.++|++|++.||+..++||+|+|.+
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            45577899999999999999999999999987643334446899999999999999999999999999999999999987


Q ss_pred             c
Q 046966          288 S  288 (299)
Q Consensus       288 a  288 (299)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            5

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=7.2e-18  Score=120.16  Aligned_cols=76  Identities=24%  Similarity=0.354  Sum_probs=69.8

Q ss_pred             CceEEEEcCCCCCCHHHH---HHhcccCCCeEEEEEeecCCCCCe---eeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 046966          211 DNVLFVCQLNPVTEDEDL---HVIFSQFGTVVSAEILRDYRTGES---LCYAFVEFEKREACEQAYFKMNNALIDDRRIC  284 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L---~~~f~~~G~i~~~~~~~~~~~g~~---~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~  284 (299)
                      ..+|||+|||+.+++++|   +++|++||.|.++.+++++.++.+   +|||||+|.+.++|.+|++.|||..++|+.|+
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            568999999999999999   778999999999999998766554   49999999999999999999999999999999


Q ss_pred             EE
Q 046966          285 VD  286 (299)
Q Consensus       285 v~  286 (299)
                      |+
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            85

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=7.2e-18  Score=120.00  Aligned_cols=80  Identities=28%  Similarity=0.437  Sum_probs=71.7

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCcee-CCeEEEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALI-DDRRICVD  286 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i-~g~~l~v~  286 (299)
                      .||.++|||+|||+++++++|+++|++||.+..+.+...    +++|||||+|.+.++|.+|+..|||..+ +|+.|+|+
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 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS   82 (88)
T ss_dssp             CCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEE
Confidence            467889999999999999999999999999988776543    4578999999999999999999999998 48999999


Q ss_pred             ecCCc
Q 046966          287 FSQSV  291 (299)
Q Consensus       287 ~a~~~  291 (299)
                      |++++
T Consensus        83 ~sk~~   87 (88)
T d2adca2          83 FSKST   87 (88)
T ss_dssp             ECSSC
T ss_pred             eCCCC
Confidence            99864

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=2.7e-18  Score=117.50  Aligned_cols=71  Identities=25%  Similarity=0.440  Sum_probs=68.3

Q ss_pred             EEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEE
Q 046966          214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRIC  284 (299)
Q Consensus       214 v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~  284 (299)
                      |||+|||+++++++|+++|++||.|..+++..++.++.++|||||+|.+.++|++|++.|||..++|+.|+
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            79999999999999999999999999999999989999999999999999999999999999999998763

>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=99.72  E-value=5.7e-18  Score=122.54  Aligned_cols=83  Identities=18%  Similarity=0.258  Sum_probs=74.4

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCC-eEEEEEeecC-CCCCeeeEEEEEecCHHHHHHHHHHhCC--ceeCCeEEEEE
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGT-VVSAEILRDY-RTGESLCYAFVEFEKREACEQAYFKMNN--ALIDDRRICVD  286 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~-i~~~~~~~~~-~~g~~~g~afv~f~~~~~a~~al~~l~~--~~i~g~~l~v~  286 (299)
                      +|+|||+|||.++++++|+++|++||. |..+.++.++ .+++++|||||+|.+.++|.+|++.|++  ..++|+.|+|+
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            478999999999999999999999996 8899998875 4689999999999999999999999865  45679999999


Q ss_pred             ecCCccc
Q 046966          287 FSQSVSK  293 (299)
Q Consensus       287 ~a~~~~~  293 (299)
                      ||+|+..
T Consensus        81 ~A~p~~~   87 (96)
T d2disa1          81 WAEPEID   87 (96)
T ss_dssp             ESCSSCS
T ss_pred             EcCCCCC
Confidence            9998654

>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=99.71  E-value=1.7e-17  Score=117.43  Aligned_cols=77  Identities=23%  Similarity=0.443  Sum_probs=71.8

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ..++|||+|||+++++++|+++|++||.|.++++..+      +|||||+|.+.++|.+|++.|||..++|+.|+|++|.
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            3578999999999999999999999999999998765      4799999999999999999999999999999999998


Q ss_pred             Ccc
Q 046966          290 SVS  292 (299)
Q Consensus       290 ~~~  292 (299)
                      +..
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            765

>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=6.2e-18  Score=121.09  Aligned_cols=82  Identities=23%  Similarity=0.427  Sum_probs=73.6

Q ss_pred             CCceEEEEcCCCCCCHHHHHH----hcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEE
Q 046966          210 PDNVLFVCQLNPVTEDEDLHV----IFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICV  285 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~----~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v  285 (299)
                      |+++|||+|||+.+++++|++    +|++||.|.++++..   +++++|||||+|.+.++|.+|++.|||..++|+.|.|
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            578999999999999998864    589999999988753   5678999999999999999999999999999999999


Q ss_pred             EecCCcccc
Q 046966          286 DFSQSVSKI  294 (299)
Q Consensus       286 ~~a~~~~~~  294 (299)
                      ++|++++..
T Consensus        79 ~~ak~~~~~   87 (91)
T d1nu4a_          79 QYAKTDSDI   87 (91)
T ss_dssp             EECSSCCTH
T ss_pred             EEeCCCchh
Confidence            999987644

>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=99.70  E-value=6.2e-18  Score=118.06  Aligned_cols=76  Identities=22%  Similarity=0.379  Sum_probs=68.2

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCc-eeCCeEEEEEecCC
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNA-LIDDRRICVDFSQS  290 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~-~i~g~~l~v~~a~~  290 (299)
                      .+|||+|||+++++++|+++|++||.+..+.+..      ++|||||+|.+.++|.+|++.|||. .++|++|+|++|.|
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            4799999999999999999999999987665543      4689999999999999999999996 69999999999998


Q ss_pred             ccc
Q 046966          291 VSK  293 (299)
Q Consensus       291 ~~~  293 (299)
                      +++
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            754

>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=99.70  E-value=2.9e-17  Score=120.06  Aligned_cols=84  Identities=17%  Similarity=0.170  Sum_probs=74.7

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ..+.+++|||+|||+++++++|+++|..||. ..+.++.+ .++..+|||||+|.+.++|++|++ ||+..|+||.|+|.
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~-~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~   87 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIG-PDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEES-SSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEe-cCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            3456789999999999999999999999984 57778887 478999999999999999999985 89999999999999


Q ss_pred             ecCCccc
Q 046966          287 FSQSVSK  293 (299)
Q Consensus       287 ~a~~~~~  293 (299)
                      ++.+...
T Consensus        88 ~s~~~~~   94 (102)
T d1weza_          88 LNSTAGT   94 (102)
T ss_dssp             EECCCCC
T ss_pred             EcCCCCC
Confidence            9887653

>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=99.69  E-value=7.5e-17  Score=110.94  Aligned_cols=74  Identities=14%  Similarity=0.302  Sum_probs=67.6

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .+|||+|||+++++++|+++|++||.|..+++..++..  .++||||+|.+.++|++|+ .|+++.|+|++|.|..+
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            47999999999999999999999999999999988543  4579999999999999999 58999999999999865

>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=99.69  E-value=3.7e-17  Score=113.75  Aligned_cols=75  Identities=24%  Similarity=0.367  Sum_probs=68.9

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ..+++|||+|++  +++++|+++|++||.|.++++.++      +|||||+|.+.++|.+|+..|||..++|+.|+|+|+
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            457899999986  899999999999999999988654      479999999999999999999999999999999999


Q ss_pred             CCc
Q 046966          289 QSV  291 (299)
Q Consensus       289 ~~~  291 (299)
                      +++
T Consensus        75 ~~~   77 (79)
T d2bz2a1          75 RKQ   77 (79)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            875

>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=99.68  E-value=9.6e-17  Score=117.69  Aligned_cols=84  Identities=24%  Similarity=0.186  Sum_probs=75.6

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .....+|||+|||+++++++|+++|..+|.+....++.+..+++++|||||+|.+.++|++|++ +|+..|+||.|.|..
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            3456689999999999999999999999999876666766789999999999999999999995 899999999999999


Q ss_pred             cCCcc
Q 046966          288 SQSVS  292 (299)
Q Consensus       288 a~~~~  292 (299)
                      +++..
T Consensus        91 ~~~~~   95 (104)
T d1wg5a_          91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            98764

>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=99.68  E-value=3.2e-17  Score=116.49  Aligned_cols=78  Identities=12%  Similarity=0.172  Sum_probs=68.0

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ...+|||+|||+++++++|+++|++||. ..+.+      ++++|||||+|.+.++|++|++.||++.++|++|+|++++
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            4678999999999999999999999992 22322      4567899999999999999999999999999999999998


Q ss_pred             Ccccc
Q 046966          290 SVSKI  294 (299)
Q Consensus       290 ~~~~~  294 (299)
                      ++...
T Consensus        77 ~~~~~   81 (88)
T d1wg1a_          77 TDALL   81 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76544

>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=99.68  E-value=1.5e-17  Score=118.07  Aligned_cols=73  Identities=25%  Similarity=0.285  Sum_probs=67.1

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCCc
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSV  291 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~~  291 (299)
                      .+|||+|||+++++++|+++|++||.|..+++..+       |||||+|.+.++|++|+..|||..+.|+.|+|.+++++
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            36999999999999999999999999999998654       79999999999999999999999999999988877644

>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=99.68  E-value=2.8e-17  Score=122.07  Aligned_cols=76  Identities=17%  Similarity=0.240  Sum_probs=70.0

Q ss_pred             CCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          210 PDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       210 ~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      ..++|||+|||+.+++++|+++|++||.|..|.|.      .++|||||+|.+.++|.+|++.|||..+.|+.|.|+|+.
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            46799999999999999999999999999998873      356899999999999999999999999999999999987


Q ss_pred             Cc
Q 046966          290 SV  291 (299)
Q Consensus       290 ~~  291 (299)
                      ..
T Consensus        83 ~~   84 (111)
T d1whxa_          83 IG   84 (111)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.67  E-value=3e-17  Score=116.67  Aligned_cols=78  Identities=18%  Similarity=0.290  Sum_probs=69.9

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ...++|||+|||+++++++|+++|++||.|..+++.     ..++|||||+|.+.++|++|+.  +++.|+|+.|.|++|
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            357899999999999999999999999999998764     3467899999999999999984  788999999999999


Q ss_pred             CCccc
Q 046966          289 QSVSK  293 (299)
Q Consensus       289 ~~~~~  293 (299)
                      +++..
T Consensus        76 ~~k~~   80 (88)
T d1wf0a_          76 EPKHN   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98754

>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=5.7e-17  Score=120.00  Aligned_cols=76  Identities=24%  Similarity=0.397  Sum_probs=70.3

Q ss_pred             CceEEEEcCCC-CCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecC
Q 046966          211 DNVLFVCQLNP-VTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQ  289 (299)
Q Consensus       211 ~~~v~v~nL~~-~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~  289 (299)
                      +++|||+|||+ .+++++|+++|++||.|..+.+++++     +|||||+|.+.++|.+|++.|||..|.|+.|+|++++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            57999999965 59999999999999999999998873     6899999999999999999999999999999999997


Q ss_pred             Cc
Q 046966          290 SV  291 (299)
Q Consensus       290 ~~  291 (299)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.67  E-value=3.4e-16  Score=111.15  Aligned_cols=79  Identities=19%  Similarity=0.275  Sum_probs=71.1

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHh--CCceeCCeEEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM--NNALIDDRRICV  285 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l--~~~~i~g~~l~v  285 (299)
                      .+|+++|||+|||+.+++++|+++|++||.|.++++..+      +|||||+|.+.++|++|++.|  ++..+.|++|+|
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            568899999999999999999999999999999988754      379999999999999999865  577899999999


Q ss_pred             EecCCcc
Q 046966          286 DFSQSVS  292 (299)
Q Consensus       286 ~~a~~~~  292 (299)
                      .|++.+.
T Consensus        79 ~~sk~~~   85 (88)
T d2cq1a1          79 QYSNHKE   85 (88)
T ss_dssp             EECSCSS
T ss_pred             EECCCCC
Confidence            9998653

>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=99.67  E-value=1.4e-16  Score=115.24  Aligned_cols=79  Identities=28%  Similarity=0.469  Sum_probs=71.8

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCC--eEEEE
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDD--RRICV  285 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g--~~l~v  285 (299)
                      .+|.++|||+|||+++++++|+++|++||.|..+++.++      ++||||+|.+.++|.+|++.||+..+.|  ++|+|
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            356799999999999999999999999999999988654      5799999999999999999999999986  58999


Q ss_pred             EecCCcc
Q 046966          286 DFSQSVS  292 (299)
Q Consensus       286 ~~a~~~~  292 (299)
                      +||++.+
T Consensus        88 ~~ak~~~   94 (97)
T d1whya_          88 DFAKSGP   94 (97)
T ss_dssp             EECCCCC
T ss_pred             EeCCCCC
Confidence            9999764

>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=99.67  E-value=1.6e-16  Score=109.25  Aligned_cols=72  Identities=15%  Similarity=0.268  Sum_probs=64.4

Q ss_pred             EEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCCcc
Q 046966          214 LFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQSVS  292 (299)
Q Consensus       214 v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~~~  292 (299)
                      |||+|||+++++++|+++|++|| +..+.+      ++++|||||+|.+.++|++|++.|||..+.|++|+|+++.+..
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            79999999999999999999999 444433      4567899999999999999999999999999999999997654

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=6.7e-17  Score=118.35  Aligned_cols=83  Identities=11%  Similarity=0.113  Sum_probs=72.8

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .....+|||+|||+++++++|+++|..||.+..+.++....+|+++|||||+|.+.++|++|++ ||+..|+||.|.|..
T Consensus         5 ~~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~   83 (103)
T d2cpya1           5 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHV   83 (103)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEE
T ss_pred             CCCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEE
Confidence            3456789999999999999999999999998765444444789999999999999999999995 899999999999998


Q ss_pred             cCCc
Q 046966          288 SQSV  291 (299)
Q Consensus       288 a~~~  291 (299)
                      +...
T Consensus        84 ~~~~   87 (103)
T d2cpya1          84 VTLE   87 (103)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            7643

>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=99.66  E-value=1.3e-16  Score=115.55  Aligned_cols=77  Identities=19%  Similarity=0.237  Sum_probs=70.8

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ...++|||+|||+.+++++|+++|++||.|..+.+..       +|||||+|.+.++|++|++.||+..+.|+.|+|.++
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~   85 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEE
Confidence            3567899999999999999999999999999998854       379999999999999999999999999999999998


Q ss_pred             CCcc
Q 046966          289 QSVS  292 (299)
Q Consensus       289 ~~~~  292 (299)
                      +++.
T Consensus        86 ~~~~   89 (98)
T d1wg4a_          86 RVYP   89 (98)
T ss_dssp             EEEC
T ss_pred             ecCC
Confidence            8654

>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=99.64  E-value=1.8e-16  Score=117.00  Aligned_cols=80  Identities=24%  Similarity=0.301  Sum_probs=72.2

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCcee--CCeEEEEE
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALI--DDRRICVD  286 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i--~g~~l~v~  286 (299)
                      .+..+|||+|||+.+++++|+++|++||.|.++.+..++    ++|||||+|.+.++|++|+..|||..|  .+++|+|.
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            345679999999999999999999999999999998763    579999999999999999999999998  48899999


Q ss_pred             ecCCcc
Q 046966          287 FSQSVS  292 (299)
Q Consensus       287 ~a~~~~  292 (299)
                      +++++.
T Consensus        81 ~s~~~~   86 (108)
T d2adba1          81 FSKLTS   86 (108)
T ss_dssp             ECSSCS
T ss_pred             ecCCcc
Confidence            998753

>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=1.7e-16  Score=117.91  Aligned_cols=83  Identities=16%  Similarity=0.173  Sum_probs=73.9

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEe
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      ....++|||+|||+++++++|+++|+.||.+..+.++.+..+|.++|||||+|.+.++|++|++ ||+..|+||.|.|..
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~   93 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHP   93 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEE
Confidence            3457799999999999999999999999998765555555799999999999999999999995 899999999999998


Q ss_pred             cCCc
Q 046966          288 SQSV  291 (299)
Q Consensus       288 a~~~  291 (299)
                      +...
T Consensus        94 ~~~~   97 (112)
T d1wela1          94 ITKK   97 (112)
T ss_dssp             ECHH
T ss_pred             cChH
Confidence            8654

>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=99.62  E-value=9.9e-16  Score=108.79  Aligned_cols=81  Identities=21%  Similarity=0.269  Sum_probs=71.4

Q ss_pred             CCCCceEEEEcCCCC-CCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHh--CCceeCCeEEE
Q 046966          208 KPPDNVLFVCQLNPV-TEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM--NNALIDDRRIC  284 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~-~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l--~~~~i~g~~l~  284 (299)
                      ..++++|||+|||.. +++++|.++|++||.|.++.++.+      +++|||+|.+.++|..|++.|  ++..+.|++|+
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            456889999999986 789999999999999999998765      358999999999999999865  67789999999


Q ss_pred             EEecCCcccc
Q 046966          285 VDFSQSVSKI  294 (299)
Q Consensus       285 v~~a~~~~~~  294 (299)
                      |+||++.+++
T Consensus        79 V~~s~~~~~l   88 (89)
T d1x4da1          79 VHLSQKYKRI   88 (89)
T ss_dssp             EEEECCCTTS
T ss_pred             EEECCCcccc
Confidence            9999876543

>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=99.62  E-value=7.1e-16  Score=111.84  Aligned_cols=80  Identities=20%  Similarity=0.260  Sum_probs=70.9

Q ss_pred             CCCceEEEEcCCCC-CCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHH--HhCCceeCCeEEEE
Q 046966          209 PPDNVLFVCQLNPV-TEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYF--KMNNALIDDRRICV  285 (299)
Q Consensus       209 ~~~~~v~v~nL~~~-~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~--~l~~~~i~g~~l~v  285 (299)
                      .++++|||+|||.+ +++++|.++|++||.|.++.++.+      +|+|||+|.+.++|.+|++  .+++..++|+.|+|
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            45789999999985 899999999999999999998754      4799999999999999997  57888999999999


Q ss_pred             EecCCcccc
Q 046966          286 DFSQSVSKI  294 (299)
Q Consensus       286 ~~a~~~~~~  294 (299)
                      .+|+.++++
T Consensus        90 ~~s~~~~~l   98 (99)
T d1x4fa1          90 DLSEKYKKL   98 (99)
T ss_dssp             EEECSCSSS
T ss_pred             EEcCCcccC
Confidence            999876543

>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=99.62  E-value=1.6e-15  Score=110.97  Aligned_cols=80  Identities=20%  Similarity=0.216  Sum_probs=71.0

Q ss_pred             CCCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHh--CCceeCCeEEE
Q 046966          207 VKPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKM--NNALIDDRRIC  284 (299)
Q Consensus       207 ~~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l--~~~~i~g~~l~  284 (299)
                      ..++..+|||+|||+.+++++|..+|++||.|..+++.++      +|+|||+|.+.++|++|+..|  ++..+.|++|+
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~   84 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAF   84 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEE
Confidence            3467889999999999999999999999999999988654      579999999999999999877  55678899999


Q ss_pred             EEecCCcc
Q 046966          285 VDFSQSVS  292 (299)
Q Consensus       285 v~~a~~~~  292 (299)
                      |+|++.++
T Consensus        85 v~~s~~~~   92 (104)
T d1wexa_          85 FNYSTSKR   92 (104)
T ss_dssp             EEECSSSS
T ss_pred             EEEcCCCc
Confidence            99998653

>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=99.61  E-value=2e-15  Score=121.69  Aligned_cols=85  Identities=21%  Similarity=0.359  Sum_probs=79.0

Q ss_pred             CCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          209 PPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      ...++|||+|||+.+++++|+++|+.||.|..+.++.++.++.++|||||+|.+.++|.+|++ +++..++|+.|+|.+|
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            346789999999999999999999999999999999998899999999999999999999996 7899999999999999


Q ss_pred             CCcccc
Q 046966          289 QSVSKI  294 (299)
Q Consensus       289 ~~~~~~  294 (299)
                      .++.++
T Consensus       174 ~~k~e~  179 (183)
T d1u1qa_         174 LSKQEM  179 (183)
T ss_dssp             CCHHHH
T ss_pred             CCcccc
Confidence            987643

>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=99.56  E-value=2.4e-15  Score=109.84  Aligned_cols=79  Identities=11%  Similarity=0.249  Sum_probs=69.7

Q ss_pred             CCCceEEEEcCCCCC-CH----HHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEE
Q 046966          209 PPDNVLFVCQLNPVT-ED----EDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRI  283 (299)
Q Consensus       209 ~~~~~v~v~nL~~~~-~e----~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l  283 (299)
                      ....+|||+||+.++ ++    ++|+++|++||.|.++++++      +++||||+|.+.++|.+|++.|||..++|+.|
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            457899999999986 33    46899999999999998864      45799999999999999999999999999999


Q ss_pred             EEEecCCccc
Q 046966          284 CVDFSQSVSK  293 (299)
Q Consensus       284 ~v~~a~~~~~  293 (299)
                      +|.|+++...
T Consensus        77 ~v~~a~~~~~   86 (104)
T d1weya_          77 KLYFAQTLHI   86 (104)
T ss_dssp             EEECCCCSSC
T ss_pred             EEeecccCCC
Confidence            9999987653

>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=99.51  E-value=8.5e-17  Score=114.82  Aligned_cols=77  Identities=13%  Similarity=0.192  Sum_probs=67.0

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEe-----ecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEE
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEIL-----RDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVD  286 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~-----~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~  286 (299)
                      ++|||+|||+++++++|+++|++||.+..+.+.     .+..+++++|||||+|.+.++|++|+ .|||..+.|+.|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhCCcEECCEEEEEC
Confidence            689999999999999999999999987655442     34467788999999999999999998 499999999999997


Q ss_pred             ecC
Q 046966          287 FSQ  289 (299)
Q Consensus       287 ~a~  289 (299)
                      .++
T Consensus        81 r~k   83 (90)
T d1u2fa_          81 RPH   83 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            544

>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=99.51  E-value=1.6e-15  Score=110.85  Aligned_cols=75  Identities=16%  Similarity=0.236  Sum_probs=70.1

Q ss_pred             eEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEec
Q 046966          213 VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFS  288 (299)
Q Consensus       213 ~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a  288 (299)
                      .++|.+++.++++++|+++|++||.|.+++|+++ .+++++|+|||+|.+.++|.+|++.|||..++||+|.|+++
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            4677888888999999999999999999999877 68999999999999999999999999999999999999985

>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=1e-12  Score=105.44  Aligned_cols=81  Identities=27%  Similarity=0.330  Sum_probs=73.8

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      .++|||+|||+.+++++|+++|++||.|.++.++++..++.++|||||+|.+.++|.+|+.. ++..++++.+.+....+
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhhhh
Confidence            37899999999999999999999999999999999999999999999999999999999965 67778999988887765


Q ss_pred             cc
Q 046966          291 VS  292 (299)
Q Consensus       291 ~~  292 (299)
                      ..
T Consensus        85 ~~   86 (183)
T d1u1qa_          85 RE   86 (183)
T ss_dssp             TT
T ss_pred             cc
Confidence            54

>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=2.8e-13  Score=98.14  Aligned_cols=65  Identities=18%  Similarity=0.287  Sum_probs=58.3

Q ss_pred             CCCceEEEEc--CCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeC
Q 046966          209 PPDNVLFVCQ--LNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALID  279 (299)
Q Consensus       209 ~~~~~v~v~n--L~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~  279 (299)
                      .|..++||.|  ||.++++++|+++|++||.|..+.++.+      ++||||+|.+.++|.+|+..|||+.+.
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            4678899955  9999999999999999999999987654      479999999999999999999999873

>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=99.37  E-value=7.1e-13  Score=95.59  Aligned_cols=81  Identities=19%  Similarity=0.238  Sum_probs=69.6

Q ss_pred             CCCceEEEEcC--CCCCC---------HHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCce
Q 046966          209 PPDNVLFVCQL--NPVTE---------DEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNAL  277 (299)
Q Consensus       209 ~~~~~v~v~nL--~~~~~---------e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~  277 (299)
                      ...++|+|.||  |.++.         +++|++.|++||.|..+.+..+    ..+|++||.|.+.++|.+|+..|||..
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            45789999999  54321         3678999999999999988654    356899999999999999999999999


Q ss_pred             eCCeEEEEEecCCccc
Q 046966          278 IDDRRICVDFSQSVSK  293 (299)
Q Consensus       278 i~g~~l~v~~a~~~~~  293 (299)
                      ++||+|+|.++.++.+
T Consensus        82 ~~gr~i~v~~~~g~~~   97 (99)
T d2dita1          82 FGGRQITAQAWDGTTD   97 (99)
T ss_dssp             ETTEECEEEECCSCCC
T ss_pred             ECCEEEEEEEeCCcCC
Confidence            9999999999988764

>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=99.37  E-value=6.2e-13  Score=98.36  Aligned_cols=75  Identities=21%  Similarity=0.263  Sum_probs=64.0

Q ss_pred             CCc-eEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCH-HHHHHHHHHhCCceeCCeEEEEEe
Q 046966          210 PDN-VLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKR-EACEQAYFKMNNALIDDRRICVDF  287 (299)
Q Consensus       210 ~~~-~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~-~~a~~al~~l~~~~i~g~~l~v~~  287 (299)
                      .++ .+||||||+.+++++|+++|++||.|.+|.++.+      +|||||.|.+. ++|..|+..|++..+.++.+.|.+
T Consensus         9 ~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~   82 (113)
T d1owxa_           9 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTW   82 (113)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEE
T ss_pred             CCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEE
Confidence            345 4599999999999999999999999999999754      68999999985 789999999999988877766666


Q ss_pred             cCC
Q 046966          288 SQS  290 (299)
Q Consensus       288 a~~  290 (299)
                      +..
T Consensus        83 ~~~   85 (113)
T d1owxa_          83 EVL   85 (113)
T ss_dssp             EEC
T ss_pred             eec
Confidence            543

>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=1.6e-12  Score=89.92  Aligned_cols=74  Identities=12%  Similarity=0.209  Sum_probs=62.7

Q ss_pred             CceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeE-EEEEecC
Q 046966          211 DNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRR-ICVDFSQ  289 (299)
Q Consensus       211 ~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~-l~v~~a~  289 (299)
                      .+.|+|+++|++.+++.| +.|++||.|.++++.      +.+|||||+|.+.++|++|++ +||..++|+. |.|..+.
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeCC
Confidence            567999999999987666 579999999998764      346899999999999999995 8999999985 5688877


Q ss_pred             Ccc
Q 046966          290 SVS  292 (299)
Q Consensus       290 ~~~  292 (299)
                      .+.
T Consensus        76 ~k~   78 (81)
T d1wwha1          76 DKN   78 (81)
T ss_dssp             CHH
T ss_pred             Chh
Confidence            654

>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=99.27  E-value=2.8e-12  Score=93.27  Aligned_cols=83  Identities=23%  Similarity=0.276  Sum_probs=70.3

Q ss_pred             CCCceEEEEcC--CCCCC--------HHHHHHhcccCCCeEEEEEeecCCCC--CeeeEEEEEecCHHHHHHHHHHhCCc
Q 046966          209 PPDNVLFVCQL--NPVTE--------DEDLHVIFSQFGTVVSAEILRDYRTG--ESLCYAFVEFEKREACEQAYFKMNNA  276 (299)
Q Consensus       209 ~~~~~v~v~nL--~~~~~--------e~~L~~~f~~~G~i~~~~~~~~~~~g--~~~g~afv~f~~~~~a~~al~~l~~~  276 (299)
                      +|++.|.+.|+  +....        .++|++.|++||.|.++.|++++.+.  ...|++||+|.+.++|.+|++.|||.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            46888999999  44432        35789999999999999998865443  35689999999999999999999999


Q ss_pred             eeCCeEEEEEecCCc
Q 046966          277 LIDDRRICVDFSQSV  291 (299)
Q Consensus       277 ~i~g~~l~v~~a~~~  291 (299)
                      .++||.|.|.++.+.
T Consensus        82 ~f~gR~v~v~f~~~~   96 (104)
T d1o0pa_          82 KFANRVVVTKYCDPD   96 (104)
T ss_dssp             CSSSSCCEEEEECHH
T ss_pred             EECCeEEEEEEcCHH
Confidence            999999999998753

>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=97.36  E-value=0.00027  Score=47.62  Aligned_cols=74  Identities=18%  Similarity=0.302  Sum_probs=58.8

Q ss_pred             CCCCceEEEEcCCCCC------CH---HHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCcee
Q 046966          208 KPPDNVLFVCQLNPVT------ED---EDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALI  278 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~------~e---~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i  278 (299)
                      .|+..+|.|.-..+..      .+   .+|.+.|..||+|.-+|++.+        --+|+|.+-++|.+|+ .++|..+
T Consensus        12 GPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al-~l~g~~v   82 (95)
T d1ufwa_          12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVL-DVDGMKV   82 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHH-HGGGSEE
T ss_pred             CCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHh-ccCCeEE
Confidence            4678888886554332      22   357778899999998888776        5799999999999999 5799999


Q ss_pred             CCeEEEEEecCC
Q 046966          279 DDRRICVDFSQS  290 (299)
Q Consensus       279 ~g~~l~v~~a~~  290 (299)
                      .|+.|.|....|
T Consensus        83 ~G~~l~It~~~~   94 (95)
T d1ufwa_          83 KGRAVKISGPSS   94 (95)
T ss_dssp             TTEEEEEECCCC
T ss_pred             cceEEEEecCCC
Confidence            999999986543

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.32  E-value=0.00065  Score=43.39  Aligned_cols=62  Identities=21%  Similarity=0.239  Sum_probs=51.1

Q ss_pred             HHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhCCceeCCeEEEEEecCC
Q 046966          226 EDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMNNALIDDRRICVDFSQS  290 (299)
Q Consensus       226 ~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~~~~i~g~~l~v~~a~~  290 (299)
                      +.|...|.+++.|.++.+.... .+.  -.|-|...+.++|.-|+..|+...|++++|.|.++..
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~-dg~--~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT-DYQ--LKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-STT--CCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEecc-CCc--EEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            3455778899999999886542 232  2678999999999999999999999999999999763

>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=96.65  E-value=0.0057  Score=41.45  Aligned_cols=68  Identities=12%  Similarity=0.119  Sum_probs=55.0

Q ss_pred             ceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCC--eeeEEEEEecCHHHHHHHHHHhCCceeC
Q 046966          212 NVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGE--SLCYAFVEFEKREACEQAYFKMNNALID  279 (299)
Q Consensus       212 ~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~--~~g~afv~f~~~~~a~~al~~l~~~~i~  279 (299)
                      ++|.|.+||+..+|+++.+.++..|.+..........+.+  .-.-|+|.|.+.++...-.+.++|+.+.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            5788999999999999999999988887665554433322  2356899999999999999999999864

>d1zx8a1 b.62.1.3 (A:1-124) Hypothetical protein TM1367 {Thermotoga maritima [TaxId: 2336]}

class: All beta proteins
fold: Cyclophilin-like
superfamily: Cyclophilin-like
family: TM1367-like
domain: Hypothetical protein TM1367
species: Thermotoga maritima [TaxId: 2336]

Probab=92.36  E-value=0.35  Score=34.25  Aligned_cols=102  Identities=19%  Similarity=0.239  Sum_probs=64.2

Q ss_pred             CEEEEEEcceeEEEEecCCCChHHHHHHHHhh----hCCCcCCceeeEeecCcEEEecCCCCCCCCCCCCCCCccccccc
Q 046966            1 MSVLIETSLGDIVIDLFVDKCPRTTNNFLQHC----KNKYYNGCLFHNIHKDFIAQTGDPTGTGTGGRSVYEDRFFVDEI   76 (299)
Q Consensus         1 ~~v~~~T~~G~i~ieL~~~~~P~~~~nF~~l~----~~~~y~~~~f~ri~~~~~iq~G~~~~~~~~~~~~~~~~~~~~e~   76 (299)
                      |-+.|....+.++++|.  ..|.|++.|.+..    +-..|-+-.++.. |-                     . +..|.
T Consensus         1 mki~l~f~~~~~~~~l~--~s~~ta~~i~~~LPl~~~~~~wG~Eiyf~~-p~---------------------~-l~~e~   55 (124)
T d1zx8a1           1 MRVELLFESGKCVIDLN--EEYEVVKLLKEKIPFESVVNTWGEEIYFST-PV---------------------N-VQKME   55 (124)
T ss_dssp             EEEEEECSSCEEEEEEE--TTSHHHHHHHHHCSEEEECEESSSEEEEEC-SC---------------------C-CCCCS
T ss_pred             CeEEEEeCCeEEEEEeC--CCHHHHHHHHHhCCeEEEHHHccceEEEeC-Cc---------------------C-CCccc
Confidence            67889999999999999  3678999999875    1223422222221 10                     0 11110


Q ss_pred             ccCCCCCCceEEEEEcCCCCCCcceEEEEecCCCCCCC------CCceEEEEeecCHHHHHHHH
Q 046966           77 RADLKHDKVGTVGMASAGRDLNASQFYITLRDNLHYLD------EKHTIFGEVAEGLETLTRIN  134 (299)
Q Consensus        77 ~~~~~~~~~G~l~~~~~~~~~~~s~FfI~~~~~~~~ld------~~~~vfG~V~~G~~vl~~i~  134 (299)
                      ...-. ...|-|++-..+     ..+.|-.++ .++-+      ....++|++.++++.|..+.
T Consensus        56 ~~~~~-~~~GDiaYw~pg-----~~iaifyg~-tp~S~~~irlas~~n~iGki~~~~~~l~~i~  112 (124)
T d1zx8a1          56 NPREV-VEIGDVGYWPPG-----KALCLFFGK-TPMSDDKIQPASAVNVIGKIVEGLEDLKKIK  112 (124)
T ss_dssp             SEESS-BCTTEEEEEGGG-----TEEEEESSC-CTTCSSSBCCSSCEEEEEEEEECGGGGGGCC
T ss_pred             Ccccc-cccccEEEECCC-----CEEEEEECC-ccCCCCcccccCcceEeEEecCCHHHHhcCC
Confidence            11111 256888887654     358888887 45443      34679999999998887773

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.48  E-value=0.47  Score=31.87  Aligned_cols=59  Identities=24%  Similarity=0.348  Sum_probs=46.8

Q ss_pred             CCCCceEEEEcCCCCCCHHHHHHhcccCCCeEEEEEeecCCCCCeeeEEEEEecCHHHHHHHHHHhC
Q 046966          208 KPPDNVLFVCQLNPVTEDEDLHVIFSQFGTVVSAEILRDYRTGESLCYAFVEFEKREACEQAYFKMN  274 (299)
Q Consensus       208 ~~~~~~v~v~nL~~~~~e~~L~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~al~~l~  274 (299)
                      .+...-||.-..|..+...+|.++|+.||.|. +.++-+  |     -|||...+.+.++.+++.+.
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIdd--T-----Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDD--T-----SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEET--T-----EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecC--c-----eEEEEecCHHHHHHHHHHhc
Confidence            34445588889999999999999999999864 445544  2     68999999999998886644