Psyllid ID: psy300

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-
Protein Sequence
MEKLAKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENVLNTRVEGESSQGFIPGCRGRTEQVVSSRLETPPLIGSSGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLYLVCFNLPSPLGYLQLNLLQEQQLN
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHccHHHHHcccccccccccEEEEcccccccHHHHHHHHHHcccEEEEEEEEccccccccEEEEEcccHHHHHHHHHHccccccccccccHHHHHHHHHccccHHHHHHHccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccccEEEEEEccccccccccEEEcccccccccHHHHHcccEEEEEEcccccccccccccccccccccccccccccccccccccEEEEEccccccccEEEEEEEEEEEEEEcccccccEEEEEEcccccccccccccccccccccHHHHHHHHHHHcccccccccEEEccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccEEEEEEcccccccccccccccccccEEEEcccccccHHHHHHccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHccccHEEccccccccccEEEEEccccEEcHHHHHHHHccccHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHcccHEEEEEEccccccccccHHHHHEEEEEcccccccccEEEEEEEccEEEccccccccEEEccccEEEEEEEEcccccEcEEEccccccccEEEcEEccEEcEccEEccccccccEEEEccccccccccEEccccEEEcccccEEEEccccccccccEEEEEEEEEEcEEEccEEccEEEEEEcccccHHHcccHHHHHHHcccHHHHHHHHHHHccHHHccccccEcccccHHHHHHHHHHHHHHHHHHHHcccccccccccEccccccEccccccccEEEHHHcEEEEEEEEcccccEcEEEccccccEEEEEEcccccHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MEKLAKKKKVKKEFKKKGKKKierkkpdktkrgrlfiknlpfkiTEEEFKEHFGQYGDIIDAQLlknadgklkgcgfinyANKISAVKAILKSnkkpykgkitEEEFKEHFGQYGDIIDAQLlknadgklkgcgfinyANKISAVKAILKSnkkpykgsenglispfhdiplysnvKDKIFNMVVEiprwtnakmeinlneplnpikqdikkgnlRYVAnvfphhgyiwnygalpqtwenpdetdahtgqkgdgdpidvLEIGERIAKRGEIIQVKALGViglidegqtdWKIIAINvndpnaaklndvadiethfpgylkaTNEWFkiykipdgkpenvlntrvegessqgfipgcrgrtEQVVSsrletppligssgsenglispfhdiplysnvKDKIFNMVVEiprwtnakmEVGNAMEMRLYLVCFNLPSPLGYLQLNLLQEQQLN
Flexible Loop (DISEMBL)
meklakkkkvkkefkkkgkkkierkkpdktkrgrlfiknlpfKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETDAhtgqkgdgdpiDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENVLNTRVEgessqgfipgcrGRTEQVVSSRLETPPLIGSSGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLYLVCFNLPSPLGYLQLNLLQEQQLN
Low Complexity Region (SEG)
MeklakkkkvkkefkkkgkkkierkkpdktkRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENVLNTRVEGESSQGFIPGCRGRTEQVVSSRLETPPLIGSSGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLYLVCFNLPSPLGYlqlnllqeqqln
Disordered region (IsUnstruct)
*********************************RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTW******************IDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDG***********************************************GLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLYLVCFNLPSPLGYLQLNLL******
Disordered Region (DISOPRED)
*********************************RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA***************ITEEEFKEHFGQYGDIIDAQ*************************AILKSNKKPYKGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENVLNTRVEGESSQGFIPGCRGRTEQVV**********GSSGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLYLVCFNLPSPLGYLQLNLLQEQ***
Disordered Region (DISEMBL)
****************************KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENVLNTRVEGESSQGFIPGCRGRTEQVVSSRLETPPLIGSSGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLYLVCFNLPSPLGYLQLNLLQEQQLN
Disordered Region (DISPRO)
MEKLAKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENVLNTRVEGESSQGFIPGCRGRTEQVVSSRLETPPLIGSSGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLYLVCFNLPSPLGYLQLNLLQEQQL*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEKLAKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENVLNTRVEGESSQGFIPGCRGRTEQVVSSRLETPPLIGSSGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLYLVCFNLPSPLGYLQLNLLQEQQLN
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	451	2.2.26 [Sep-21-2011]
O77460	338	Inorganic pyrophosphatase	yes	N/A	0.407	0.544	0.711	6e-78
P13998	287	Inorganic pyrophosphatase	no	N/A	0.390	0.613	0.687	2e-70
P83777	288	Inorganic pyrophosphatase	N/A	N/A	0.390	0.611	0.670	2e-70
Q6FRB7	287	Inorganic pyrophosphatase	yes	N/A	0.390	0.613	0.681	3e-70
Q9D819	289	Inorganic pyrophosphatase	yes	N/A	0.401	0.626	0.644	8e-70
Q6BWA5	287	Inorganic pyrophosphatase	yes	N/A	0.412	0.648	0.618	1e-69
Q757J8	287	Inorganic pyrophosphatase	yes	N/A	0.392	0.616	0.677	2e-69
P00817	287	Inorganic pyrophosphatase	yes	N/A	0.390	0.613	0.681	4e-69
P37980	289	Inorganic pyrophosphatase	no	N/A	0.401	0.626	0.639	7e-69
Q15181	289	Inorganic pyrophosphatase	yes	N/A	0.401	0.626	0.650	9e-69

>sp|O77460|IPYR_DROME Inorganic pyrophosphatase OS=Drosophila melanogaster GN=Nurf-38 PE=1 SV=3

 Score =  291 bits (746), Expect = 6e-78,   Method: Compositional matrix adjust.
 Identities = 131/184 (71%), Positives = 156/184 (84%)

Query: 156 YKGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNL 215
           +K     +ISP HDIPLY+N +  I+NMVVE+PRWTNAKMEI+L  P+NPIKQDIKKG L
Sbjct: 69  FKNKCGNVISPMHDIPLYANEEKTIYNMVVEVPRWTNAKMEISLKTPMNPIKQDIKKGKL 128

Query: 216 RYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQV 275
           R+VAN FPH GYIWNYGALPQTWENPD  +  TG KGD DPIDV+EIG R+AKRG++++V
Sbjct: 129 RFVANCFPHKGYIWNYGALPQTWENPDHIEPSTGCKGDNDPIDVIEIGYRVAKRGDVLKV 188

Query: 276 KALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDG 335
           K LG I LIDEG+TDWKIIAI+VNDP A+K+ND+AD++ +FPG L+AT EWFKIYKIPDG
Sbjct: 189 KVLGTIALIDEGETDWKIIAIDVNDPLASKVNDIADVDQYFPGLLRATVEWFKIYKIPDG 248

Query: 336 KPEN 339
           KPEN
Sbjct: 249 KPEN 252

Component of NURF (nucleosome remodeling factor), a complex which catalyzes ATP-dependent nucleosome sliding and facilitates transcription of chromatin. NURF is required for homeotic gene expression, proper larval blood cell development, normal male X chromosome morphology, ecdysteroid signaling and metamorphosis. Nurf-38 may have adapted to deliver pyrophosphatase to chromatin to assist in replication or transcription by efficient removal of the inhibitory metabolite.
Drosophila melanogaster (taxid: 7227)
EC: 3EC: .EC: 6EC: .EC: 1EC: .EC: 1

>sp|P13998|IPYR_KLULA Inorganic pyrophosphatase OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) GN=IPP1 PE=3 SV=2

 Score =  266 bits (681), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 121/176 (68%), Positives = 144/176 (81%)

Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           IS FHDIPLY++  + IFNMVVEIPRWTNAK+EI   EPLNPI QD KKG LR+V N FP
Sbjct: 27  ISAFHDIPLYADEANGIFNMVVEIPRWTNAKLEITKEEPLNPIIQDTKKGKLRFVRNCFP 86

Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
           HHGYI NYGA PQTWE+P+E+   T   GD DP+DVLEIGE++A  G++ QVK LGV+ L
Sbjct: 87  HHGYIHNYGAFPQTWEDPNESHPETKAVGDNDPLDVLEIGEQVAYTGQVKQVKVLGVMAL 146

Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
           +DEG+TDWK+IAI++NDP A KLND+ D+E H PG L+ATNEWF+IYKIPDGKPEN
Sbjct: 147 LDEGETDWKVIAIDINDPLAPKLNDIEDVEKHLPGLLRATNEWFRIYKIPDGKPEN 202

Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid: 284590)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: 1

>sp|P83777|IPYR_CANAL Inorganic pyrophosphatase OS=Candida albicans (strain SC5314 / ATCC MYA-2876) GN=IPP1 PE=1 SV=2

 Score =  266 bits (681), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 118/176 (67%), Positives = 144/176 (81%)

Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           +SPFHDIPLY+N +  I NM+VE+PRWTNAK+EI+  + LNPI QD KKG LR+V N FP
Sbjct: 28  VSPFHDIPLYANEEKTILNMIVEVPRWTNAKLEISKEQKLNPIIQDTKKGKLRFVRNCFP 87

Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
           HHGYI NYGA PQTWE+P+++   T  KGD DP+DV EIGE++A  GE+ QVK LGV+ L
Sbjct: 88  HHGYIHNYGAFPQTWEDPNQSHPETKAKGDNDPLDVCEIGEKVATVGEVKQVKVLGVMAL 147

Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
           +DEG+TDWK+I I+VNDP A KLND+ D+ETH PG L+ATNEWF+IYKIPDGKPEN
Sbjct: 148 LDEGETDWKVIVIDVNDPLAPKLNDIEDVETHLPGLLRATNEWFRIYKIPDGKPEN 203

Candida albicans (strain SC5314 / ATCC MYA-2876) (taxid: 237561)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: 1

>sp|Q6FRB7|IPYR_CANGA Inorganic pyrophosphatase OS=Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) GN=IPP1 PE=3 SV=1

 Score =  266 bits (679), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 120/176 (68%), Positives = 144/176 (81%)

Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           +SPFHDIPLY++ ++ IFNMVVEIPRWTNAK+EI   E LNPI QD KKG LRYV N FP
Sbjct: 27  VSPFHDIPLYADKEENIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRYVRNCFP 86

Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
           HHGYI NYGA PQTWE+P++T   T   GD DP+DVLEIGE I   G++ QVK LG++ L
Sbjct: 87  HHGYIHNYGAFPQTWEDPNQTHPETKAVGDNDPVDVLEIGETIGYTGQVKQVKVLGIMAL 146

Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
           +DEG+TDWK+IAI++NDP A KLND+ D+E +FPG L+ATNEWF+IYKIPDGKPEN
Sbjct: 147 LDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPEN 202

Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65) (taxid: 284593)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: 1

>sp|Q9D819|IPYR_MOUSE Inorganic pyrophosphatase OS=Mus musculus GN=Ppa1 PE=1 SV=1

 Score =  264 bits (675), Expect = 8e-70,   Method: Compositional matrix adjust.
 Identities = 118/183 (64%), Positives = 151/183 (82%), Gaps = 2/183 (1%)

Query: 157 KGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLR 216
           K  +   ISPFHD+P+Y++ KD +F+MVVE+PRW+NAKMEI   +PLNPIKQD+KKG LR
Sbjct: 22  KNEKGQYISPFHDVPIYAD-KD-VFHMVVEVPRWSNAKMEIATKDPLNPIKQDVKKGKLR 79

Query: 217 YVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVK 276
           YVAN+FP+ GYIWNYGA+PQTWE+P  +D HTG  GD DPIDV EIG ++  RGEII+VK
Sbjct: 80  YVANLFPYKGYIWNYGAIPQTWEDPGHSDKHTGCCGDNDPIDVCEIGSKVCARGEIIRVK 139

Query: 277 ALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGK 336
            LG++ +IDEG+TDWK+IAINV+DP+AA   D++D+E   PGYL+AT +WF+ YK+PDGK
Sbjct: 140 VLGILAMIDEGETDWKVIAINVDDPDAANYKDISDVERLKPGYLEATVDWFRRYKVPDGK 199

Query: 337 PEN 339
           PEN
Sbjct: 200 PEN 202

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: 1

>sp|Q6BWA5|IPYR_DEBHA Inorganic pyrophosphatase OS=Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) GN=IPP1 PE=3 SV=1

 Score =  264 bits (674), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 120/194 (61%), Positives = 149/194 (76%), Gaps = 8/194 (4%)

Query: 146 KAILKSNKKPYKGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNP 205
           +  ++ N KP        +SPFHDIPLY+N +  + NM+VE+PRWTNAK+EI+  E LNP
Sbjct: 17  RVFIEQNGKP--------VSPFHDIPLYANEEKTVLNMIVEVPRWTNAKLEISKEEKLNP 68

Query: 206 IKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGER 265
           I QD KKG LR+V N FPHHGYI NYGA PQTWE+P++    T  KGD DP+DV EIGE+
Sbjct: 69  ILQDTKKGKLRFVRNCFPHHGYIHNYGAFPQTWEDPNQVHPETKAKGDNDPLDVCEIGEQ 128

Query: 266 IAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNE 325
           +   G++ QVK LGV+ L+DEG+TDWKII I+VNDP A+KLND+ D+ETH PG L+ATNE
Sbjct: 129 VGYVGQVKQVKVLGVMALLDEGETDWKIIVIDVNDPLASKLNDIEDVETHLPGLLRATNE 188

Query: 326 WFKIYKIPDGKPEN 339
           WF+IYKIPDGKPEN
Sbjct: 189 WFRIYKIPDGKPEN 202

Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) (taxid: 284592)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: 1

>sp|Q757J8|IPYR_ASHGO Inorganic pyrophosphatase OS=Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) GN=IPP1 PE=3 SV=1

 Score =  263 bits (672), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 120/177 (67%), Positives = 143/177 (80%)

Query: 163 LISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVF 222
           ++SPFHDIPLY++ +++IFNMVVEIPRWTNAK+EI   E +NPI QD KKG LRYV N F
Sbjct: 26  VVSPFHDIPLYADEENQIFNMVVEIPRWTNAKLEITKEEAMNPIIQDTKKGKLRYVRNCF 85

Query: 223 PHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIG 282
           PHHGYI NYGA PQTWE+P+     T   GD DP+DVLEIGE IA  G++ QVK LGV+ 
Sbjct: 86  PHHGYIHNYGAFPQTWEDPNVAHPETKAYGDNDPLDVLEIGETIAYTGQVKQVKVLGVMA 145

Query: 283 LIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
           L+DEG+TDWKII I+V+DP A KLND+ D+E H PG L+ATNEWF+IYKIPDGKPEN
Sbjct: 146 LLDEGETDWKIIVIDVHDPLAPKLNDIEDVEKHLPGLLRATNEWFRIYKIPDGKPEN 202

Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056) (taxid: 284811)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: 1

>sp|P00817|IPYR_YEAST Inorganic pyrophosphatase OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=IPP1 PE=1 SV=4

 Score =  262 bits (670), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 120/176 (68%), Positives = 144/176 (81%)

Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+EI   E LNPI QD KKG LR+V N FP
Sbjct: 27  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFP 86

Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
           HHGYI NYGA PQTWE+P+ +   T   GD DPIDVLEIGE IA  G++ QVKALG++ L
Sbjct: 87  HHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMAL 146

Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
           +DEG+TDWK+IAI++NDP A KLND+ D+E +FPG L+ATNEWF+IYKIPDGKPEN
Sbjct: 147 LDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPEN 202

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: 1

>sp|P37980|IPYR_BOVIN Inorganic pyrophosphatase OS=Bos taurus GN=PPA1 PE=1 SV=2

 Score =  261 bits (668), Expect = 7e-69,   Method: Compositional matrix adjust.
 Identities = 117/183 (63%), Positives = 148/183 (80%), Gaps = 2/183 (1%)

Query: 157 KGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLR 216
           K  +   ISPFHDIP+Y++   ++F+MVVE+PRW+NAKMEI   +PLNPIKQD+KKG LR
Sbjct: 22  KNEKGQYISPFHDIPIYAD--KEVFHMVVEVPRWSNAKMEIATKDPLNPIKQDVKKGKLR 79

Query: 217 YVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVK 276
           YVAN+FP+ GYIWNYGA+PQTWE+P   D HTG  GD DPIDV EIG ++  RGEII+VK
Sbjct: 80  YVANLFPYKGYIWNYGAIPQTWEDPGHNDKHTGCCGDNDPIDVCEIGSKVCARGEIIRVK 139

Query: 277 ALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGK 336
            LG++ +IDEG+TDWK+IAINV DP+AA  ND+ D++   PGYL+AT +WF+ YK+PDGK
Sbjct: 140 VLGILAMIDEGETDWKVIAINVEDPDAANYNDINDVKRLKPGYLEATVDWFRRYKVPDGK 199

Query: 337 PEN 339
           PEN
Sbjct: 200 PEN 202

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: 1

>sp|Q15181|IPYR_HUMAN Inorganic pyrophosphatase OS=Homo sapiens GN=PPA1 PE=1 SV=2

 Score =  261 bits (666), Expect = 9e-69,   Method: Compositional matrix adjust.
 Identities = 119/183 (65%), Positives = 149/183 (81%), Gaps = 2/183 (1%)

Query: 157 KGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLR 216
           K  +   ISPFHDIP+Y++ KD +F+MVVE+PRW+NAKMEI   +PLNPIKQD+KKG LR
Sbjct: 22  KNEKGQYISPFHDIPIYAD-KD-VFHMVVEVPRWSNAKMEIATKDPLNPIKQDVKKGKLR 79

Query: 217 YVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVK 276
           YVAN+FP+ GYIWNYGA+PQTWE+P   D HTG  GD DPIDV EIG ++  RGEII VK
Sbjct: 80  YVANLFPYKGYIWNYGAIPQTWEDPGHNDKHTGCCGDNDPIDVCEIGSKVCARGEIIGVK 139

Query: 277 ALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGK 336
            LG++ +IDEG+TDWK+IAINV+DP+AA  ND+ D++   PGYL+AT +WF+ YK+PDGK
Sbjct: 140 VLGILAMIDEGETDWKVIAINVDDPDAANYNDINDVKRLKPGYLEATVDWFRRYKVPDGK 199

Query: 337 PEN 339
           PEN
Sbjct: 200 PEN 202

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 1

EC: .

EC: 1

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	451
328777671	332	PREDICTED: inorganic pyrophosphatase-lik	0.490	0.665	0.650	7e-79
380015525	332	PREDICTED: LOW QUALITY PROTEIN: inorgani	0.490	0.665	0.654	9e-79
383855060	332	PREDICTED: inorganic pyrophosphatase-lik	0.450	0.611	0.694	1e-78
347969820	395	AGAP003398-PD [Anopheles gambiae str. PE	0.505	0.577	0.621	1e-78
347969818	390	AGAP003398-PB [Anopheles gambiae str. PE	0.505	0.584	0.621	2e-78
156550600	342	PREDICTED: inorganic pyrophosphatase [Na	0.401	0.529	0.756	2e-78
347969826	297	AGAP003398-PF [Anopheles gambiae str. PE	0.421	0.639	0.722	3e-77
347969828	284	AGAP003398-PC [Anopheles gambiae str. PE	0.421	0.669	0.722	4e-77
347969824	292	AGAP003398-PA [Anopheles gambiae str. PE	0.421	0.650	0.722	4e-77
332373982	329	unknown [Dendroctonus ponderosae]	0.509	0.699	0.612	8e-77

>gi|328777671|ref|XP_003249382.1| PREDICTED: inorganic pyrophosphatase-like [Apis mellifera]

 Score =  300 bits (769), Expect = 7e-79,   Method: Compositional matrix adjust.
 Identities = 147/226 (65%), Positives = 173/226 (76%), Gaps = 5/226 (2%)

Query: 129 KLKGCG-FINYANKISAVK----AILKSNKKPYKGSENGLISPFHDIPLYSNVKDKIFNM 183
           K + C  F  YA K+S       A+  ++ + Y  ++ G ISP HDIPLY++  +KI NM
Sbjct: 31  KSRSCSVFKKYAKKMSYTTIERGALNSTDYRIYFRNDVGPISPMHDIPLYADESNKILNM 90

Query: 184 VVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDE 243
           VVEIPRWTNAKMEINL E LNPIKQD+KKG LRYVAN FPHHGYIWNYGALPQTWENP+ 
Sbjct: 91  VVEIPRWTNAKMEINLKETLNPIKQDVKKGKLRYVANCFPHHGYIWNYGALPQTWENPEV 150

Query: 244 TDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNA 303
            D  TG KGD DPIDVLEIG ++AKRGEI++VK LG + LIDEG+TDWKII I+VNDP A
Sbjct: 151 LDEATGCKGDNDPIDVLEIGYKVAKRGEILKVKVLGCVALIDEGETDWKIIVIDVNDPLA 210

Query: 304 AKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENVLNTRVEGES 349
            ++NDV+DIE H+PG +KAT EWFKIYKIPDGKPEN      E +S
Sbjct: 211 EQMNDVSDIEKHYPGLMKATIEWFKIYKIPDGKPENQFAFNGEAKS 256

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380015525|ref|XP_003691751.1| PREDICTED: LOW QUALITY PROTEIN: inorganic pyrophosphatase-like [Apis florea]

 Score =  300 bits (768), Expect = 9e-79,   Method: Compositional matrix adjust.
 Identities = 148/226 (65%), Positives = 173/226 (76%), Gaps = 5/226 (2%)

Query: 129 KLKGCG-FINYANKISAVK----AILKSNKKPYKGSENGLISPFHDIPLYSNVKDKIFNM 183
           K + C  F  YA K+S       A+  ++ + Y  ++ G ISP HDIPLY++  +KI NM
Sbjct: 31  KSRSCSVFEKYAKKMSYTTIERGALNSTDYRIYFRNDVGPISPMHDIPLYADENNKILNM 90

Query: 184 VVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDE 243
           VVEIPRWTNAKMEINL E LNPIKQD+KKG LRYVAN FPHHGYIWNYGALPQTWENP+ 
Sbjct: 91  VVEIPRWTNAKMEINLKEXLNPIKQDVKKGKLRYVANCFPHHGYIWNYGALPQTWENPEV 150

Query: 244 TDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNA 303
            D  TG KGD DPIDVLEIG +IAKRGEI++VK LG + LIDEG+TDWKII I+VNDP A
Sbjct: 151 LDEATGCKGDNDPIDVLEIGYKIAKRGEILKVKVLGCVALIDEGETDWKIIVIDVNDPLA 210

Query: 304 AKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENVLNTRVEGES 349
            ++NDV+DIE H+PG +KAT EWFKIYKIPDGKPEN      E +S
Sbjct: 211 EQMNDVSDIEKHYPGLMKATIEWFKIYKIPDGKPENQFAFNGEAKS 256

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383855060|ref|XP_003703037.1| PREDICTED: inorganic pyrophosphatase-like [Megachile rotundata]

 Score =  300 bits (767), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 141/203 (69%), Positives = 164/203 (80%)

Query: 147 AILKSNKKPYKGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPI 206
           A+  S+ + Y  +E G ISP HDIPLY++  +K+ NMVVEIPRWTNAKMEINL E LNPI
Sbjct: 54  ALNGSDYRVYFRNETGPISPMHDIPLYADEANKVMNMVVEIPRWTNAKMEINLKETLNPI 113

Query: 207 KQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERI 266
           KQD+KKG LRYVAN FPHHGYIWNYGALPQTWENP+  D  TG KGD DPIDVLEIG R+
Sbjct: 114 KQDVKKGKLRYVANCFPHHGYIWNYGALPQTWENPEVLDESTGCKGDNDPIDVLEIGYRV 173

Query: 267 AKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEW 326
           AKRGE+++VK LG + LIDEG+TDWKII I+VNDP A ++NDV+DIE H+PG +KAT EW
Sbjct: 174 AKRGEVLKVKVLGTVALIDEGETDWKIIVIDVNDPLADQMNDVSDIEKHYPGLMKATIEW 233

Query: 327 FKIYKIPDGKPENVLNTRVEGES 349
           FKIYKIPDGKPEN      E +S
Sbjct: 234 FKIYKIPDGKPENQFAFNGEAKS 256

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347969820|ref|XP_003436468.1| AGAP003398-PD [Anopheles gambiae str. PEST] gi|333467607|gb|EGK96619.1| AGAP003398-PD [Anopheles gambiae str. PEST]

 Score =  300 bits (767), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 151/243 (62%), Positives = 179/243 (73%), Gaps = 15/243 (6%)

Query: 112 GQYGDIIDAQLLKNAD----GKLKGCGFINY---ANKISAVKAILKSNKKP-------YK 157
           G    + D++LL +A     G+L G  F +     +K++A K  +     P       Y 
Sbjct: 62  GHLSSVGDSKLLPSASLSRVGQLSGREFSSSNKAKHKMTASKYQIAERGAPNSTDYRVYF 121

Query: 158 GSENG-LISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLR 216
            +ENG  ISP HDIPLY+N +  ++NMVVE+PRWTNAKMEI+L E LNPIKQD+KKG LR
Sbjct: 122 KNENGQSISPLHDIPLYANDERTVYNMVVEVPRWTNAKMEISLGEGLNPIKQDVKKGKLR 181

Query: 217 YVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVK 276
           +VAN FPHHGYIWNYGA PQTWENPD  DA TG KGD DPIDVLEIG RIAKRGE++QVK
Sbjct: 182 FVANCFPHHGYIWNYGAFPQTWENPDHLDADTGCKGDNDPIDVLEIGSRIAKRGEVLQVK 241

Query: 277 ALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGK 336
            LG I LIDEG+TDWKII INVNDP A ++ND+ D+ET FPG L+A+ EWFKIYKIPDGK
Sbjct: 242 ILGTIALIDEGETDWKIITINVNDPLADQVNDIGDVETVFPGLLRASVEWFKIYKIPDGK 301

Query: 337 PEN 339
           PEN
Sbjct: 302 PEN 304

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347969818|ref|XP_003436467.1| AGAP003398-PB [Anopheles gambiae str. PEST] gi|347969822|ref|XP_003436469.1| AGAP003398-PE [Anopheles gambiae str. PEST] gi|333467605|gb|EGK96617.1| AGAP003398-PB [Anopheles gambiae str. PEST] gi|333467608|gb|EGK96620.1| AGAP003398-PE [Anopheles gambiae str. PEST]

 Score =  299 bits (766), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 151/243 (62%), Positives = 179/243 (73%), Gaps = 15/243 (6%)

Query: 112 GQYGDIIDAQLLKNAD----GKLKGCGFINY---ANKISAVKAILKSNKKP-------YK 157
           G    + D++LL +A     G+L G  F +     +K++A K  +     P       Y 
Sbjct: 62  GHLSSVGDSKLLPSASLSRVGQLSGREFSSSNKAKHKMTASKYQIAERGAPNSTDYRVYF 121

Query: 158 GSENG-LISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLR 216
            +ENG  ISP HDIPLY+N +  ++NMVVE+PRWTNAKMEI+L E LNPIKQD+KKG LR
Sbjct: 122 KNENGQSISPLHDIPLYANDERTVYNMVVEVPRWTNAKMEISLGEGLNPIKQDVKKGKLR 181

Query: 217 YVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVK 276
           +VAN FPHHGYIWNYGA PQTWENPD  DA TG KGD DPIDVLEIG RIAKRGE++QVK
Sbjct: 182 FVANCFPHHGYIWNYGAFPQTWENPDHLDADTGCKGDNDPIDVLEIGSRIAKRGEVLQVK 241

Query: 277 ALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGK 336
            LG I LIDEG+TDWKII INVNDP A ++ND+ D+ET FPG L+A+ EWFKIYKIPDGK
Sbjct: 242 ILGTIALIDEGETDWKIITINVNDPLADQVNDIGDVETVFPGLLRASVEWFKIYKIPDGK 301

Query: 337 PEN 339
           PEN
Sbjct: 302 PEN 304

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156550600|ref|XP_001604166.1| PREDICTED: inorganic pyrophosphatase [Nasonia vitripennis]

 Score =  299 bits (766), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 137/181 (75%), Positives = 156/181 (86%)

Query: 159 SENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYV 218
           +EN  ISP HDIPL+++  +K F+MVVE+PRWTNAKMEINL E LNPIKQDIKKGNLR+V
Sbjct: 76  NENSPISPMHDIPLFADEANKTFHMVVEVPRWTNAKMEINLKETLNPIKQDIKKGNLRFV 135

Query: 219 ANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKAL 278
           AN FPHHGYIWNYGALPQTWENPD  D  TG KGD DPIDVLEIG R+AKRGE+++VK L
Sbjct: 136 ANCFPHHGYIWNYGALPQTWENPDVLDEATGFKGDNDPIDVLEIGYRVAKRGEVLKVKVL 195

Query: 279 GVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPE 338
           G + LIDEG+TDWKII I+VNDP A ++NDVADI+ H+PG LKAT EWFKIYKIPDGKPE
Sbjct: 196 GCVALIDEGETDWKIIVIDVNDPLANQMNDVADIDKHYPGLLKATVEWFKIYKIPDGKPE 255

Query: 339 N 339
           N
Sbjct: 256 N 256

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347969826|ref|XP_003436470.1| AGAP003398-PF [Anopheles gambiae str. PEST] gi|333467609|gb|EGK96621.1| AGAP003398-PF [Anopheles gambiae str. PEST]

 Score =  295 bits (755), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 138/191 (72%), Positives = 159/191 (83%), Gaps = 1/191 (0%)

Query: 150 KSNKKPYKGSENG-LISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQ 208
            ++ + Y  +ENG  ISP HDIPLY+N +  ++NMVVE+PRWTNAKMEI+L E LNPIKQ
Sbjct: 16  STDYRVYFKNENGQSISPLHDIPLYANDERTVYNMVVEVPRWTNAKMEISLGEGLNPIKQ 75

Query: 209 DIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAK 268
           D+KKG LR+VAN FPHHGYIWNYGA PQTWENPD  DA TG KGD DPIDVLEIG RIAK
Sbjct: 76  DVKKGKLRFVANCFPHHGYIWNYGAFPQTWENPDHLDADTGCKGDNDPIDVLEIGSRIAK 135

Query: 269 RGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFK 328
           RGE++QVK LG I LIDEG+TDWKII INVNDP A ++ND+ D+ET FPG L+A+ EWFK
Sbjct: 136 RGEVLQVKILGTIALIDEGETDWKIITINVNDPLADQVNDIGDVETVFPGLLRASVEWFK 195

Query: 329 IYKIPDGKPEN 339
           IYKIPDGKPEN
Sbjct: 196 IYKIPDGKPEN 206

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347969828|ref|XP_003436471.1| AGAP003398-PC [Anopheles gambiae str. PEST] gi|333467606|gb|EGK96618.1| AGAP003398-PC [Anopheles gambiae str. PEST]

 Score =  295 bits (755), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 138/191 (72%), Positives = 159/191 (83%), Gaps = 1/191 (0%)

Query: 150 KSNKKPYKGSENG-LISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQ 208
            ++ + Y  +ENG  ISP HDIPLY+N +  ++NMVVE+PRWTNAKMEI+L E LNPIKQ
Sbjct: 16  STDYRVYFKNENGQSISPLHDIPLYANDERTVYNMVVEVPRWTNAKMEISLGEGLNPIKQ 75

Query: 209 DIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAK 268
           D+KKG LR+VAN FPHHGYIWNYGA PQTWENPD  DA TG KGD DPIDVLEIG RIAK
Sbjct: 76  DVKKGKLRFVANCFPHHGYIWNYGAFPQTWENPDHLDADTGCKGDNDPIDVLEIGSRIAK 135

Query: 269 RGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFK 328
           RGE++QVK LG I LIDEG+TDWKII INVNDP A ++ND+ D+ET FPG L+A+ EWFK
Sbjct: 136 RGEVLQVKILGTIALIDEGETDWKIITINVNDPLADQVNDIGDVETVFPGLLRASVEWFK 195

Query: 329 IYKIPDGKPEN 339
           IYKIPDGKPEN
Sbjct: 196 IYKIPDGKPEN 206

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347969824|ref|XP_558852.4| AGAP003398-PA [Anopheles gambiae str. PEST] gi|333467604|gb|EAL40975.4| AGAP003398-PA [Anopheles gambiae str. PEST]

 Score =  295 bits (754), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 138/191 (72%), Positives = 159/191 (83%), Gaps = 1/191 (0%)

Query: 150 KSNKKPYKGSENG-LISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQ 208
            ++ + Y  +ENG  ISP HDIPLY+N +  ++NMVVE+PRWTNAKMEI+L E LNPIKQ
Sbjct: 16  STDYRVYFKNENGQSISPLHDIPLYANDERTVYNMVVEVPRWTNAKMEISLGEGLNPIKQ 75

Query: 209 DIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAK 268
           D+KKG LR+VAN FPHHGYIWNYGA PQTWENPD  DA TG KGD DPIDVLEIG RIAK
Sbjct: 76  DVKKGKLRFVANCFPHHGYIWNYGAFPQTWENPDHLDADTGCKGDNDPIDVLEIGSRIAK 135

Query: 269 RGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFK 328
           RGE++QVK LG I LIDEG+TDWKII INVNDP A ++ND+ D+ET FPG L+A+ EWFK
Sbjct: 136 RGEVLQVKILGTIALIDEGETDWKIITINVNDPLADQVNDIGDVETVFPGLLRASVEWFK 195

Query: 329 IYKIPDGKPEN 339
           IYKIPDGKPEN
Sbjct: 196 IYKIPDGKPEN 206

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332373982|gb|AEE62132.1| unknown [Dendroctonus ponderosae]

 Score =  293 bits (751), Expect = 8e-77,   Method: Compositional matrix adjust.
 Identities = 142/232 (61%), Positives = 170/232 (73%), Gaps = 2/232 (0%)

Query: 119 DAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSENGLISPFHDIPLYSNVKD 178
           D    K     LK C  + Y+  I    +   ++ + Y   ENG +SP HDIPL  +   
Sbjct: 25  DTWSFKGVRRFLKQCRSMPYS--IVERGSQYGTDYRIYINDENGPVSPLHDIPLMLDADK 82

Query: 179 KIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTW 238
           KIFNMVVE+PRWTN KMEI + E LNPIKQD+KKG  R+VAN FPHHGYIWNYGALPQTW
Sbjct: 83  KIFNMVVEVPRWTNTKMEITMKEVLNPIKQDVKKGKPRFVANCFPHHGYIWNYGALPQTW 142

Query: 239 ENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINV 298
           ENP+  D  TG KGD DPIDVLEIG R+AKRGE++QVK LG I LIDEG+TDWK+IAI++
Sbjct: 143 ENPEHLDDGTGCKGDNDPIDVLEIGYRVAKRGEVLQVKVLGTIALIDEGETDWKLIAIDI 202

Query: 299 NDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENVLNTRVEGESS 350
           NDP+A ++NDV+D+E HFPG LKA+ EWFKIYKIPDGKPEN      E +S+
Sbjct: 203 NDPSADQINDVSDVEKHFPGLLKASVEWFKIYKIPDGKPENHFAFNGEAKSA 254

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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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	451
FB|FBgn0016687	338	Nurf-38 "Nucleosome remodeling	0.501	0.668	0.603	4e-74
UNIPROTKB|F1NT28	306	PPA1 "Uncharacterized protein"	0.407	0.601	0.657	3.5e-68
ZFIN|ZDB-GENE-050417-375	291	ppa1b "pyrophosphatase (inorga	0.407	0.632	0.641	9.2e-68
CGD|CAL0006016	288	IPP1 [Candida albicans (taxid:	0.412	0.645	0.645	2.4e-67
UNIPROTKB|P83777	288	IPP1 "Inorganic pyrophosphatas	0.412	0.645	0.645	2.4e-67
RGD|1589773	331	Ppa1 "pyrophosphatase (inorgan	0.401	0.546	0.644	2.4e-67
UNIPROTKB|F1SUE3	289	PPA1 "Uncharacterized protein"	0.401	0.626	0.650	3.1e-67
MGI|MGI:97831	289	Ppa1 "pyrophosphatase (inorgan	0.401	0.626	0.644	3.1e-67
UNIPROTKB|F1PIJ6	284	PPA1 "Uncharacterized protein"	0.410	0.651	0.628	4e-67
UNIPROTKB|Q2KIV7	327	PPA2 "Pyrophosphatase (Inorgan	0.407	0.562	0.641	8.2e-67

FB|FBgn0016687 Nurf-38 "Nucleosome remodeling factor - 38kD" [Drosophila melanogaster (taxid:7227)]

 Score = 748 (268.4 bits), Expect = 4.0e-74, P = 4.0e-74
 Identities = 137/227 (60%), Positives = 170/227 (74%)

Query:   156 YKGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNL 215
             +K     +ISP HDIPLY+N +  I+NMVVE+PRWTNAKMEI+L  P+NPIKQDIKKG L
Sbjct:    69 FKNKCGNVISPMHDIPLYANEEKTIYNMVVEVPRWTNAKMEISLKTPMNPIKQDIKKGKL 128

Query:   216 RYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQV 275
             R+VAN FPH GYIWNYGALPQTWENPD  +  TG KGD DPIDV+EIG R+AKRG++++V
Sbjct:   129 RFVANCFPHKGYIWNYGALPQTWENPDHIEPSTGCKGDNDPIDVIEIGYRVAKRGDVLKV 188

Query:   276 KALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDG 335
             K LG I LIDEG+TDWKIIAI+VNDP A+K+ND+AD++ +FPG L+AT EWFKIYKIPDG
Sbjct:   189 KVLGTIALIDEGETDWKIIAIDVNDPLASKVNDIADVDQYFPGLLRATVEWFKIYKIPDG 248

Query:   336 KPENVLNTRVEGESSQGFIPGCRGRTEQVVSSRLETPPLIGSSGSEN 382
             KPEN      + +++  F       T +   + +   P  GS  + N
Sbjct:   249 KPENQFAFNGDAKNAD-FANTIIAETHKFWQNLVHQSPASGSISTTN 294

GO:0004427 "inorganic diphosphatase activity" evidence=ISS;NAS;IDA

GO:0005737 "cytoplasm" evidence=NAS;IDA

GO:0016589 "NURF complex" evidence=NAS;IDA;TAS;IPI

GO:0005634 "nucleus" evidence=NAS;IDA

GO:0006338 "chromatin remodeling" evidence=IDA

GO:0042766 "nucleosome mobilization" evidence=IDA

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

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0006796 "phosphate-containing compound metabolic process" evidence=IEA

GO:0035076 "ecdysone receptor-mediated signaling pathway" evidence=IGI

GO:0045747 "positive regulation of Notch signaling pathway" evidence=IGI

GO:0035206 "regulation of hemocyte proliferation" evidence=IMP

UNIPROTKB|F1NT28 PPA1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 692 (248.7 bits), Expect = 3.5e-68, P = 3.5e-68
 Identities = 121/184 (65%), Positives = 144/184 (78%)

Query:   156 YKGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNL 215
             +K +    ISPFHDIPLY++    +FNMVVE+PRWTNAKMEI   +PLNPIKQD+KKG L
Sbjct:    37 FKDAAGRYISPFHDIPLYADAGKNVFNMVVEVPRWTNAKMEIATKDPLNPIKQDVKKGKL 96

Query:   216 RYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQV 275
             RYVANVFPH GYIWNYGA+PQTWE+P   D +TG  GD DPIDV EIG ++  RGE+I+V
Sbjct:    97 RYVANVFPHKGYIWNYGAIPQTWEDPGHKDENTGCCGDNDPIDVCEIGSKVCSRGEVIKV 156

Query:   276 KALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDG 335
             K LG + LIDEG+TDWKIIAINV DP A   ND+ D+    PGYL+AT +WF+ YK+PDG
Sbjct:   157 KVLGTLALIDEGETDWKIIAINVEDPEAENYNDINDVRRMKPGYLEATVDWFRRYKVPDG 216

Query:   336 KPEN 339
             KPEN
Sbjct:   217 KPEN 220

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006796 "phosphate-containing compound metabolic process" evidence=IEA

GO:0004427 "inorganic diphosphatase activity" evidence=IEA

ZFIN|ZDB-GENE-050417-375 ppa1b "pyrophosphatase (inorganic) 1b" [Danio rerio (taxid:7955)]

 Score = 688 (247.2 bits), Expect = 9.2e-68, P = 9.2e-68
 Identities = 118/184 (64%), Positives = 148/184 (80%)

Query:   156 YKGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNL 215
             +K S    +SPFHDIP++++    IF+MVVE+PRWTNAKMEI   +PLNPIKQD+KKGNL
Sbjct:    20 FKNSNGKYLSPFHDIPMFADEAQNIFHMVVEVPRWTNAKMEIATKDPLNPIKQDVKKGNL 79

Query:   216 RYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQV 275
             RYVANVFPH GYIWNYGA+PQTWE+P   D  TG  GD DPIDV EIG ++  RG++I+V
Sbjct:    80 RYVANVFPHKGYIWNYGAIPQTWEDPGHKDNDTGCCGDNDPIDVCEIGSKVCSRGDVIKV 139

Query:   276 KALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDG 335
             K LGV+ +IDEG+TDWK+IAINV+DP A  LN+++D+    PGYL+AT +WF+ YK+PDG
Sbjct:   140 KVLGVLAMIDEGETDWKVIAINVDDPEAKDLNNISDVRRLKPGYLEATVDWFRRYKVPDG 199

Query:   336 KPEN 339
             KPEN
Sbjct:   200 KPEN 203

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0006796 "phosphate-containing compound metabolic process" evidence=IEA

GO:0004427 "inorganic diphosphatase activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

CGD|CAL0006016 IPP1 [Candida albicans (taxid:5476)]

 Score = 684 (245.8 bits), Expect = 2.4e-67, P = 2.4e-67
 Identities = 120/186 (64%), Positives = 147/186 (79%)

Query:   154 KPYKGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKG 213
             K Y   +   +SPFHDIPLY+N +  I NM+VE+PRWTNAK+EI+  + LNPI QD KKG
Sbjct:    18 KVYIEKDGKPVSPFHDIPLYANEEKTILNMIVEVPRWTNAKLEISKEQKLNPIIQDTKKG 77

Query:   214 NLRYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEII 273
              LR+V N FPHHGYI NYGA PQTWE+P+++   T  KGD DP+DV EIGE++A  GE+ 
Sbjct:    78 KLRFVRNCFPHHGYIHNYGAFPQTWEDPNQSHPETKAKGDNDPLDVCEIGEKVATVGEVK 137

Query:   274 QVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIP 333
             QVK LGV+ L+DEG+TDWK+I I+VNDP A KLND+ D+ETH PG L+ATNEWF+IYKIP
Sbjct:   138 QVKVLGVMALLDEGETDWKVIVIDVNDPLAPKLNDIEDVETHLPGLLRATNEWFRIYKIP 197

Query:   334 DGKPEN 339
             DGKPEN
Sbjct:   198 DGKPEN 203

GO:0030446 "hyphal cell wall" evidence=IDA

GO:0005634 "nucleus" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0004427 "inorganic diphosphatase activity" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

UNIPROTKB|P83777 IPP1 "Inorganic pyrophosphatase" [Candida albicans SC5314 (taxid:237561)]

 Score = 684 (245.8 bits), Expect = 2.4e-67, P = 2.4e-67
 Identities = 120/186 (64%), Positives = 147/186 (79%)

Query:   154 KPYKGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKG 213
             K Y   +   +SPFHDIPLY+N +  I NM+VE+PRWTNAK+EI+  + LNPI QD KKG
Sbjct:    18 KVYIEKDGKPVSPFHDIPLYANEEKTILNMIVEVPRWTNAKLEISKEQKLNPIIQDTKKG 77

Query:   214 NLRYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEII 273
              LR+V N FPHHGYI NYGA PQTWE+P+++   T  KGD DP+DV EIGE++A  GE+ 
Sbjct:    78 KLRFVRNCFPHHGYIHNYGAFPQTWEDPNQSHPETKAKGDNDPLDVCEIGEKVATVGEVK 137

Query:   274 QVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIP 333
             QVK LGV+ L+DEG+TDWK+I I+VNDP A KLND+ D+ETH PG L+ATNEWF+IYKIP
Sbjct:   138 QVKVLGVMALLDEGETDWKVIVIDVNDPLAPKLNDIEDVETHLPGLLRATNEWFRIYKIP 197

Query:   334 DGKPEN 339
             DGKPEN
Sbjct:   198 DGKPEN 203

GO:0030446 "hyphal cell wall" evidence=IDA

RGD|1589773 Ppa1 "pyrophosphatase (inorganic) 1" [Rattus norvegicus (taxid:10116)]

 Score = 684 (245.8 bits), Expect = 2.4e-67, P = 2.4e-67
 Identities = 118/183 (64%), Positives = 152/183 (83%)

Query:   157 KGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLR 216
             K  +   ISPFHD+P+Y++ KD +F+MVVE+PRW+NAKMEI   +PLNPIKQD+KKG LR
Sbjct:    64 KNEKGQYISPFHDVPIYAD-KD-VFHMVVEVPRWSNAKMEIATKDPLNPIKQDVKKGKLR 121

Query:   217 YVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVK 276
             YVAN+FP+ GYIWNYGA+PQTWE+P  +D HTG  GD DPIDV EIG ++  RGEII+VK
Sbjct:   122 YVANLFPYKGYIWNYGAIPQTWEDPGHSDEHTGCCGDNDPIDVCEIGSKVCARGEIIRVK 181

Query:   277 ALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGK 336
              LG++ +IDEG+TDWK+IAINV+DP+AA  +D++D+E   PGYL+AT +WF+ YK+PDGK
Sbjct:   182 VLGILAMIDEGETDWKVIAINVDDPDAANYHDISDVERLKPGYLEATVDWFRRYKVPDGK 241

Query:   337 PEN 339
             PEN
Sbjct:   242 PEN 244

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0004427 "inorganic diphosphatase activity" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=IEA

GO:0006796 "phosphate-containing compound metabolic process" evidence=IEA

GO:0008152 "metabolic process" evidence=ISO

GO:0016462 "pyrophosphatase activity" evidence=ISO

UNIPROTKB|F1SUE3 PPA1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 683 (245.5 bits), Expect = 3.1e-67, P = 3.1e-67
 Identities = 119/183 (65%), Positives = 151/183 (82%)

Query:   157 KGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLR 216
             K  +   ISPFHDIP+Y++ KD +F+MVVE+PRW+NAKMEI   +PLNPIKQD+KKG LR
Sbjct:    22 KNEKGQYISPFHDIPIYAD-KD-VFHMVVEVPRWSNAKMEIATKDPLNPIKQDVKKGKLR 79

Query:   217 YVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVK 276
             YVAN+FP+ GYIWNYGA+PQTWE+P  +D HTG  GD DPIDV EIG ++  RGEII+VK
Sbjct:    80 YVANLFPYKGYIWNYGAIPQTWEDPGHSDKHTGCCGDNDPIDVCEIGSKVCARGEIIRVK 139

Query:   277 ALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGK 336
              LG++ +IDEG+TDWK+IAINV+DP+AA  ND+ D++   PGYL+AT +WF+ YK+PDGK
Sbjct:   140 VLGILAMIDEGETDWKVIAINVDDPDAANYNDINDVKRLKPGYLEATVDWFRRYKVPDGK 199

Query:   337 PEN 339
             PEN
Sbjct:   200 PEN 202

GO:0004427 "inorganic diphosphatase activity" evidence=IEA

GO:0006796 "phosphate-containing compound metabolic process" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

MGI|MGI:97831 Ppa1 "pyrophosphatase (inorganic) 1" [Mus musculus (taxid:10090)]

 Score = 683 (245.5 bits), Expect = 3.1e-67, P = 3.1e-67
 Identities = 118/183 (64%), Positives = 151/183 (82%)

Query:   157 KGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLR 216
             K  +   ISPFHD+P+Y++ KD +F+MVVE+PRW+NAKMEI   +PLNPIKQD+KKG LR
Sbjct:    22 KNEKGQYISPFHDVPIYAD-KD-VFHMVVEVPRWSNAKMEIATKDPLNPIKQDVKKGKLR 79

Query:   217 YVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVK 276
             YVAN+FP+ GYIWNYGA+PQTWE+P  +D HTG  GD DPIDV EIG ++  RGEII+VK
Sbjct:    80 YVANLFPYKGYIWNYGAIPQTWEDPGHSDKHTGCCGDNDPIDVCEIGSKVCARGEIIRVK 139

Query:   277 ALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGK 336
              LG++ +IDEG+TDWK+IAINV+DP+AA   D++D+E   PGYL+AT +WF+ YK+PDGK
Sbjct:   140 VLGILAMIDEGETDWKVIAINVDDPDAANYKDISDVERLKPGYLEATVDWFRRYKVPDGK 199

Query:   337 PEN 339
             PEN
Sbjct:   200 PEN 202

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0004427 "inorganic diphosphatase activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006796 "phosphate-containing compound metabolic process" evidence=IC

GO:0008152 "metabolic process" evidence=IDA

GO:0016462 "pyrophosphatase activity" evidence=IDA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|F1PIJ6 PPA1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 682 (245.1 bits), Expect = 4.0e-67, P = 4.0e-67
 Identities = 122/194 (62%), Positives = 155/194 (79%)

Query:   146 KAILKSNKKPYKGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNP 205
             +A LK+ K  Y       ISPFHD+P+Y++ KD +F+MVVE+PRW+NAKMEI   +PLNP
Sbjct:    13 RAFLKNEKGQY-------ISPFHDVPIYAD-KD-VFHMVVEVPRWSNAKMEIATKDPLNP 63

Query:   206 IKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGER 265
             IKQD+KKG LRYVAN+FP+ GYIWNYGA+PQTWE+P   D HTG  GD DPIDV EIG +
Sbjct:    64 IKQDVKKGKLRYVANLFPYKGYIWNYGAIPQTWEDPGHNDKHTGCCGDNDPIDVCEIGSK 123

Query:   266 IAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNE 325
             +  RGEII+VK LG++ +IDEG+TDWK+IAINV+DP+AA  ND+ D++   PGYL+AT +
Sbjct:   124 VCARGEIIRVKVLGILAMIDEGETDWKVIAINVDDPDAANYNDINDVKRLKPGYLEATVD 183

Query:   326 WFKIYKIPDGKPEN 339
             WF+ YK+PDGKPEN
Sbjct:   184 WFRRYKVPDGKPEN 197

GO:0006796 "phosphate-containing compound metabolic process" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0004427 "inorganic diphosphatase activity" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

UNIPROTKB|Q2KIV7 PPA2 "Pyrophosphatase (Inorganic) 2" [Bos taurus (taxid:9913)]

 Score = 679 (244.1 bits), Expect = 8.2e-67, P = 8.2e-67
 Identities = 118/184 (64%), Positives = 144/184 (78%)

Query:   156 YKGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNL 215
             +K      ISPFHDIPL  + ++ +FNMVVE+PRWTNAKMEI   EPLNPIKQD+K G L
Sbjct:    60 FKNVAGHYISPFHDIPLKVDSEENVFNMVVEVPRWTNAKMEIATKEPLNPIKQDVKDGKL 119

Query:   216 RYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQV 275
             RYVAN+FPH GYIWNYGALPQTWE+P   D  T   GD DPIDV EIG ++  RGE++ V
Sbjct:   120 RYVANIFPHKGYIWNYGALPQTWEDPHRKDKSTDCCGDNDPIDVCEIGSKVLSRGEVVHV 179

Query:   276 KALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDG 335
             K LGV+ LID+G+TDWK+IAINVNDP A+K +D+ D++ + PGYL+AT  WF+ YKIP+G
Sbjct:   180 KILGVLALIDQGETDWKLIAINVNDPEASKFHDIEDVKKYKPGYLEATLNWFRFYKIPEG 239

Query:   336 KPEN 339
             KPEN
Sbjct:   240 KPEN 243

GO:0005739 "mitochondrion" evidence=IEA

GO:0006796 "phosphate-containing compound metabolic process" evidence=IEA

GO:0004427 "inorganic diphosphatase activity" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

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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)
Q6BWA5	IPYR_DEBHA	3, ., 6, ., 1, ., 1	0.6185	0.4124	0.6480	yes	N/A
Q5R8T6	IPYR_PONAB	3, ., 6, ., 1, ., 1	0.6393	0.4013	0.6262	yes	N/A
Q757J8	IPYR_ASHGO	3, ., 6, ., 1, ., 1	0.6779	0.3924	0.6167	yes	N/A
Q54PV8	IPYR_DICDI	3, ., 6, ., 1, ., 1	0.5333	0.3880	0.6272	yes	N/A
P19117	IPYR_SCHPO	3, ., 6, ., 1, ., 1	0.6534	0.3902	0.6089	yes	N/A
Q15181	IPYR_HUMAN	3, ., 6, ., 1, ., 1	0.6502	0.4013	0.6262	yes	N/A
Q6FRB7	IPYR_CANGA	3, ., 6, ., 1, ., 1	0.6818	0.3902	0.6132	yes	N/A
Q9D819	IPYR_MOUSE	3, ., 6, ., 1, ., 1	0.6448	0.4013	0.6262	yes	N/A
Q5B912	IPYR_EMENI	3, ., 6, ., 1, ., 1	0.5817	0.4545	0.7142	yes	N/A
Q8SR69	IPYR_ENCCU	3, ., 6, ., 1, ., 1	0.5591	0.4124	0.6714	yes	N/A
Q9LXC9	IPYR1_ARATH	3, ., 6, ., 1, ., 1	0.5254	0.3747	0.5633	yes	N/A
Q18680	IPYR_CAEEL	3, ., 6, ., 1, ., 1	0.6235	0.3946	0.4373	yes	N/A
O13505	IPYR_PICPA	3, ., 6, ., 1, ., 1	0.5922	0.4478	0.7087	yes	N/A
P00817	IPYR_YEAST	3, ., 6, ., 1, ., 1	0.6818	0.3902	0.6132	yes	N/A
Q6C1T4	IPYR_YARLI	3, ., 6, ., 1, ., 1	0.6534	0.3902	0.6132	yes	N/A
O77460	IPYR_DROME	3, ., 6, ., 1, ., 1	0.7119	0.4079	0.5443	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.6.1.1	0.824
3rd Layer	3.6.1	0.766

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	451
PLN02707	267	PLN02707, PLN02707, Soluble inorganic pyrophosphat	2e-76
cd00412	155	cd00412, pyrophosphatase, Inorganic pyrophosphatas	8e-58
pfam00719	156	pfam00719, Pyrophosphatase, Inorganic pyrophosphat	2e-51
COG0221	171	COG0221, Ppa, Inorganic pyrophosphatase [Energy pr	2e-42
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-18
smart00360	73	smart00360, RRM, RNA recognition motif	4e-18
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-16
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-16
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-15
PLN02373	188	PLN02373, PLN02373, soluble inorganic pyrophosphat	1e-15
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	5e-15
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	4e-14
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-12
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	1e-12
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	1e-12
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	2e-12
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-12
smart00360	73	smart00360, RRM, RNA recognition motif	5e-12
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	5e-12
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	6e-12
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	1e-11
PRK00642	205	PRK00642, PRK00642, inorganic pyrophosphatase; Pro	1e-11
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	2e-11
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	2e-11
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-11
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	3e-11
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-10
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	5e-10
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	5e-10
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	7e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	8e-10
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	9e-10
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	9e-10
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-09
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-09
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	2e-09
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	2e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-09
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	4e-09
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-09
PRK02230	184	PRK02230, PRK02230, inorganic pyrophosphatase; Pro	5e-09
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	7e-09
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	7e-09
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	8e-09
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	1e-08
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	1e-08
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-08
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	1e-08
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	1e-08
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-08
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	3e-08
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	3e-08
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	4e-08
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	4e-08
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	4e-08
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	6e-08
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	7e-08
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	7e-08
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	7e-08
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	7e-08
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	8e-08
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	8e-08
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	8e-08
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	9e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-07
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	1e-07
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	1e-07
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-07
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	1e-07
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-07
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-07
PRK01250	176	PRK01250, PRK01250, inorganic pyrophosphatase; Pro	2e-07
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	3e-07
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	3e-07
PLN02707	267	PLN02707, PLN02707, Soluble inorganic pyrophosphat	4e-07
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	4e-07
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	4e-07
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	4e-07
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	4e-07
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	4e-07
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	5e-07
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	6e-07
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	8e-07
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	8e-07
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	9e-07
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	9e-07
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-06
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	1e-06
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	1e-06
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-06
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-06
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	2e-06
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	2e-06
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	2e-06
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	2e-06
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-06
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	2e-06
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	3e-06
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	3e-06
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	4e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	4e-06
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	4e-06
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	5e-06
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	5e-06
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	6e-06
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	6e-06
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	7e-06
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	7e-06
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	7e-06
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	1e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-05
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	1e-05
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	1e-05
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	1e-05
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	1e-05
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	1e-05
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	1e-05
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	1e-05
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	1e-05
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-05
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	2e-05
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	2e-05
cd12239	82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	2e-05
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	2e-05
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	2e-05
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	2e-05
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	2e-05
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	2e-05
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-05
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	3e-05
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-05
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	3e-05
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	3e-05
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	3e-05
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-05
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	4e-05
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	4e-05
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	4e-05
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	4e-05
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	4e-05
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	5e-05
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	5e-05
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	5e-05
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	5e-05
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	5e-05
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	5e-05
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	5e-05
cd12522	79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	6e-05
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	6e-05
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	6e-05
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	6e-05
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	7e-05
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	8e-05
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	8e-05
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	9e-05
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	9e-05
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-04
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	1e-04
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	1e-04
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	1e-04
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	1e-04
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	1e-04
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-04
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	1e-04
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	1e-04
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	1e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-04
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	2e-04
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	2e-04
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	2e-04
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	2e-04
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	2e-04
COG0221	171	COG0221, Ppa, Inorganic pyrophosphatase [Energy pr	3e-04
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	3e-04
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-04
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	3e-04
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	3e-04
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	3e-04
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	3e-04
cd12340	67	cd12340, RBD_RRM1_NPL3, RNA recognition motif 1 in	3e-04
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	3e-04
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	3e-04
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	3e-04
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	3e-04
cd12262	82	cd12262, RRM2_4_MRN1, RNA recognition motif 2 and	3e-04
cd00412	155	cd00412, pyrophosphatase, Inorganic pyrophosphatas	4e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	4e-04
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	4e-04
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	4e-04
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	4e-04
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	4e-04
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	4e-04
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	4e-04
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	4e-04
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	4e-04
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	4e-04
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	5e-04
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	5e-04
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	5e-04
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	5e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	6e-04
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	6e-04
cd12348	75	cd12348, RRM1_SHARP, RNA recognition motif 1 in SM	6e-04
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	7e-04
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	7e-04
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	7e-04
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	8e-04
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	8e-04
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	8e-04
cd12658	76	cd12658, RRM1_MYEF2, RNA recognition motif 1 in ve	8e-04
cd12262	82	cd12262, RRM2_4_MRN1, RNA recognition motif 2 and	9e-04
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	9e-04
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	0.001
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	0.001
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	0.001
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	0.001
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	0.001
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	0.001
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	0.001
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	0.001
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	0.001
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	0.001
cd12657	76	cd12657, RRM1_hnRNPM, RNA recognition motif 1 in v	0.001
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	0.001
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	0.001
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	0.001
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	0.001
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	0.001
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	0.001
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	0.001
cd12591	80	cd12591, RRM2_p54nrb, RNA recognition motif 2 in v	0.001
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	0.002
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	0.002
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	0.002
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	0.002
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	0.002
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	0.002
cd12317	72	cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition mot	0.002
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	0.002
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	0.002
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	0.002
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	0.002
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	0.002
pfam00719	156	pfam00719, Pyrophosphatase, Inorganic pyrophosphat	0.003
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	0.003
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	0.003
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	0.003
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	0.003
cd12589	80	cd12589, RRM2_PSP1, RNA recognition motif 2 in ver	0.003
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	0.003
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	0.003
cd12281	92	cd12281, RRM1_TatSF1_like, RNA recognition motif 1	0.003
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	0.003
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	0.003
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	0.004
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	0.004
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	0.004
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	0.004
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	0.004
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	0.004
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	0.004
cd12276	71	cd12276, RRM2_MEI2_EAR1_like, RNA recognition moti	0.004

>gnl|CDD|178309 PLN02707, PLN02707, Soluble inorganic pyrophosphatase

 Score =  239 bits (611), Expect = 2e-76
 Identities = 100/180 (55%), Positives = 128/180 (71%), Gaps = 12/180 (6%)

Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           +SP+HDIPL++   D  FN VVEIP+ T+AKME+  +EP  PIKQD KKG LR       
Sbjct: 57  VSPWHDIPLHAG--DGTFNFVVEIPKETSAKMEVATDEPFTPIKQDTKKGKLRDY----- 109

Query: 224 HHGYIWNYGALPQTWENPDETDAHT---GQKGDGDPIDVLEIGERIAKRGEIIQVKALGV 280
            +   WNYG LPQTWE+P  T A+    G  GD DP+DV+EIGER AK GE+++VK LGV
Sbjct: 110 PYNINWNYGLLPQTWEDP--THANPEVEGAFGDNDPVDVVEIGERAAKIGEVLKVKPLGV 167

Query: 281 IGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENV 340
           + +IDEG+ DWK++AI+ +DP A+ +NDV D+E HFPG L A  +WF+ YKIPDGKP N 
Sbjct: 168 LAMIDEGELDWKVVAISADDPKASLVNDVDDVEKHFPGTLTAIRDWFRDYKIPDGKPANK 227

Length = 267

>gnl|CDD|238239 cd00412, pyrophosphatase, Inorganic pyrophosphatase

 Score =  186 bits (476), Expect = 8e-58
 Identities = 65/162 (40%), Positives = 94/162 (58%), Gaps = 26/162 (16%)

Query: 179 KIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTW 238
           ++ N+V+EIP+ +NAK EI+      PIK D      R++ +     GY WNYG +PQT 
Sbjct: 1   EVVNVVIEIPKGSNAKYEIDKET--GPIKVD------RFLYS---SMGYPWNYGFIPQTL 49

Query: 239 ENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINV 298
           E             DGDP+DVL IGE     G +I+V+ LGV+ +IDEG+TDWK+IA+ V
Sbjct: 50  E------------DDGDPLDVLVIGEEPLFPGSVIRVRPLGVLKMIDEGETDWKVIAVPV 97

Query: 299 NDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENV 340
           +DP  + +ND++D+    P  L     +F+ YK  +GK E  
Sbjct: 98  DDPRYSHINDISDVP---PHLLDEIKHFFEHYKDLEGKKEVK 136

These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers. Length = 155

>gnl|CDD|189686 pfam00719, Pyrophosphatase, Inorganic pyrophosphatase

 Score =  170 bits (434), Expect = 2e-51
 Identities = 56/153 (36%), Positives = 84/153 (54%), Gaps = 26/153 (16%)

Query: 182 NMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENP 241
           N+V+EIP+ +  K EI+    L P+ +      + Y +      GY +NYG +PQT E  
Sbjct: 1   NVVIEIPKGSRVKYEIDKESGLLPVDR------VLYTS-----MGYPFNYGFIPQTLE-- 47

Query: 242 DETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDP 301
                     GDGDP+DVL +G      G +++V+ +GV+ +IDEG+TD KIIA+ V+DP
Sbjct: 48  ----------GDGDPLDVLVLGPEPLFPGSVVRVRPIGVLAMIDEGETDDKIIAVPVDDP 97

Query: 302 NAAKLNDVADIETHFPGYLKATNEWFKIYKIPD 334
                +D+ DIE   PG L     +F+ YK  +
Sbjct: 98  RY---DDIKDIEDLPPGLLDEIEHFFEHYKDLE 127

Length = 156

>gnl|CDD|223299 COG0221, Ppa, Inorganic pyrophosphatase [Energy production and conversion]

 Score =  147 bits (374), Expect = 2e-42
 Identities = 50/169 (29%), Positives = 79/169 (46%), Gaps = 25/169 (14%)

Query: 165 SPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPH 224
              H IP   +  D+  N+V+EIP+ +N K E++       + + +K             
Sbjct: 1   MDLHKIPAGPD--DEDINVVIEIPKGSNIKYEVDKETGRLLVDRPLKTP----------- 47

Query: 225 HGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLI 284
            GY  NYG +P T               DGDP+DVL IGE     G +IQ + +GV+ +I
Sbjct: 48  MGYPVNYGFIPNTLS------------DDGDPLDVLVIGEEPLAPGCVIQARPIGVLKMI 95

Query: 285 DEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIP 333
           DEG+ D K+IA+   DP    + D++D+  H    ++   E +K  +  
Sbjct: 96  DEGEKDDKVIAVPKLDPRYEHIKDISDLPEHLLDEIQHFFETYKDLEKG 144

Length = 171

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

 Score = 78.5 bits (194), Expect = 3e-18
 Identities = 24/67 (35%), Positives = 40/67 (59%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
           LF+ NLP   TEE+ +E F ++G+I   +++++ DGK KG  F+ + +   A KA+   N
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 95  KKPYKGK 101
            K   G+
Sbjct: 61  GKELDGR 67

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|214636 smart00360, RRM, RNA recognition motif

 Score = 78.4 bits (194), Expect = 4e-18
 Identities = 24/69 (34%), Positives = 40/69 (57%), Gaps = 1/69 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
            LF+ NLP   TEEE +E F ++G +   +L+++ + GK KG  F+ + ++  A KA+  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 93  SNKKPYKGK 101
            N K   G+
Sbjct: 61  LNGKELDGR 69

Length = 73

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

 Score = 74.2 bits (183), Expect = 1e-16
 Identities = 22/67 (32%), Positives = 39/67 (58%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
           LF+ NLP   TEE+ K+ F ++G I   +++++  G+ KG  F+ + ++  A KA+   N
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 95  KKPYKGK 101
            K   G+
Sbjct: 61  GKELGGR 67

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

 Score = 79.9 bits (197), Expect = 5e-16
 Identities = 43/193 (22%), Positives = 85/193 (44%), Gaps = 49/193 (25%)

Query: 11  KKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADG 70
           K+ +  +  KK ER+     K   L++KNL   + E++ +E F ++G+I  A ++K+  G
Sbjct: 157 KEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSG 216

Query: 71  KLKGCGFINYANKISAVKAILKSN----------KKPYKGK------------------- 101
           + +G  F+N+     A KA+ + N          KK Y G+                   
Sbjct: 217 RSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQ 276

Query: 102 --------------------ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANK 141
                               +T+E+ +E F + G+I  A+++ +  G  +G GF+ ++N 
Sbjct: 277 QERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFSNP 336

Query: 142 ISAVKAILKSNKK 154
             A +A+ + + +
Sbjct: 337 EEANRAVTEMHGR 349

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

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

 Score = 78.7 bits (194), Expect = 1e-15
 Identities = 39/164 (23%), Positives = 77/164 (46%), Gaps = 32/164 (19%)

Query: 33  GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
           G +F+KNL   +  +   + F ++G+I+  ++  + +GK +G GF+++  + SA  AI K
Sbjct: 89  GNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQK 148

Query: 93  SN------KKPYKGK--------------------------ITEEEFKEHFGQYGDIIDA 120
            N      K+ Y G+                          + E++ +E F ++G+I  A
Sbjct: 149 VNGMLLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSA 208

Query: 121 QLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSENGLI 164
            ++K+  G+ +G  F+N+     A KA+ + N K    ++ G  
Sbjct: 209 AVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKK 252

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|178001 PLN02373, PLN02373, soluble inorganic pyrophosphatase

 Score = 74.8 bits (184), Expect = 1e-15
 Identities = 52/174 (29%), Positives = 83/174 (47%), Gaps = 31/174 (17%)

Query: 166 PFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHH 225
           P+HD+ +       IFN VVEI + +  K E++    L      IK   + Y + V+PH 
Sbjct: 11  PWHDLEIGPGAP-AIFNCVVEITKGSKVKYELDKKTGL------IKVDRVLYSSVVYPH- 62

Query: 226 GYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLID 285
               NYG +P+T               D DP+DVL + +     G  ++ +A+G++ +ID
Sbjct: 63  ----NYGFIPRTLCE------------DNDPLDVLVLMQEPVLPGCFLRARAIGLMPMID 106

Query: 286 EGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
           +G+ D KIIA+  +DP      D+ ++  H    L     +F+ YK    K EN
Sbjct: 107 QGEKDDKIIAVCADDPEYRHYTDIKELPPH---RLAEIRRFFEDYK----KNEN 153

Length = 188

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

 Score = 69.6 bits (171), Expect = 5e-15
 Identities = 27/68 (39%), Positives = 40/68 (58%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           RL ++NLPFK TE + K+ F  +G + +  + +  DGK KG  F+ + +K  A KAI   
Sbjct: 1   RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGV 60

Query: 94  NKKPYKGK 101
           N K  KG+
Sbjct: 61  NGKKIKGR 68

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

 Score = 66.8 bits (164), Expect = 4e-14
 Identities = 28/67 (41%), Positives = 45/67 (67%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
           +++KNL   + +E+ KE FG+YG I  A+++K+ +GK KG GF+N+ N  +A KA+ + N
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELN 63

Query: 95  KKPYKGK 101
            K   GK
Sbjct: 64  GKEVNGK 70

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

 Score = 62.7 bits (153), Expect = 1e-12
 Identities = 19/58 (32%), Positives = 33/58 (56%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
             TEE+ +E F ++G+I   +++++ DGK KG  F+ + +   A KA+   N K   G
Sbjct: 9   DTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALNGKELDG 66

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

 Score = 63.0 bits (154), Expect = 1e-12
 Identities = 21/62 (33%), Positives = 39/62 (62%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
          R+ +KNLP  +TE+  +EHF   G++ D ++++  DGK +  GF+ + ++  A +A+   
Sbjct: 2  RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYF 61

Query: 94 NK 95
          NK
Sbjct: 62 NK 63

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|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 = 62.3 bits (152), Expect = 1e-12
 Identities = 25/70 (35%), Positives = 41/70 (58%), Gaps = 1/70 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILK 92
           RLF++NLPF  TEEE +E F  +G+I +  L L     + KG  F+++     AVKA  +
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 93  SNKKPYKGKI 102
            +   ++G++
Sbjct: 61  LDGSIFQGRL 70

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|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 61.9 bits (151), Expect = 2e-12
 Identities = 24/62 (38%), Positives = 34/62 (54%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
          RL +KNLP  I E++ ++ F  +G I D QL    DGK +  GF+ Y  +  A KA+   
Sbjct: 2  RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHF 61

Query: 94 NK 95
          N 
Sbjct: 62 NN 63

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

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

 Score = 61.8 bits (151), Expect = 3e-12
 Identities = 24/57 (42%), Positives = 36/57 (63%), Gaps = 1/57 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAI 90
          +FI+NLPF  TEEE KE F Q+G++  A+++K+      KG  F+ +  K SA K +
Sbjct: 3  VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCL 59

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

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

 Score = 61.1 bits (149), Expect = 5e-12
 Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 1/61 (1%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
             TEEE +E F ++G +   +L+++ + GK KG  F+ + ++  A KA+   N K   G 
Sbjct: 10  DTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGR 69

Query: 160 E 160
            
Sbjct: 70  P 70

Length = 73

>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 = 61.3 bits (149), Expect = 5e-12
 Identities = 25/69 (36%), Positives = 42/69 (60%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           +LF+  LPF +T+EE ++ F ++G +   +L+ N  GK KG  ++ Y N+ SA +A+LK 
Sbjct: 4   KLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKM 63

Query: 94  NKKPYKGKI 102
           +    K K 
Sbjct: 64  DGTEIKEKT 72

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 60.7 bits (148), Expect = 6e-12
 Identities = 18/59 (30%), Positives = 33/59 (55%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
            TEE+ K+ F ++G I   +++++  G+ KG  F+ + ++  A KA+   N K   G E
Sbjct: 10  TTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALNGKELGGRE 68

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

 Score = 59.7 bits (145), Expect = 1e-11
 Identities = 28/72 (38%), Positives = 48/72 (66%), Gaps = 2/72 (2%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
           ++F+  LP  +TEEEFKE+F Q+G ++DAQL+++ D G+ +G GF+ + ++ SAV+ +  
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSE-SAVERVFS 59

Query: 93  SNKKPYKGKITE 104
           +      GK  E
Sbjct: 60  AGMLELGGKQVE 71

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|179080 PRK00642, PRK00642, inorganic pyrophosphatase; Provisional

 Score = 63.1 bits (154), Expect = 1e-11
 Identities = 33/118 (27%), Positives = 55/118 (46%), Gaps = 11/118 (9%)

Query: 231 YGALPQTWENP------DETDAHTGQKGDGDPIDVLEIGERIAKRGEII-QVKALGVIGL 283
           YG +P+T+          E       KGDGDP+D+  + E+    G I+ Q + +G + +
Sbjct: 64  YGFIPRTYCGDLSGKLSGEQSGREDIKGDGDPLDICVLTEKNITHGNILLQARPIGGLRM 123

Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYK-IPDGKPENV 340
           ID G+ D KIIA+  +D    ++ D+++        L     +F  YK  P    + V
Sbjct: 124 IDGGEADDKIIAVLEDDLVYGEIKDISECP---GTLLDRLQHYFLTYKATPGELIKGV 178

Length = 205

>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 = 59.6 bits (145), Expect = 2e-11
 Identities = 27/58 (46%), Positives = 35/58 (60%), Gaps = 1/58 (1%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQ-YGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
          RL +KNLP  +TE E KEHF +  G+I D +LL+  DGK +   FI Y  +  A KA 
Sbjct: 2  RLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAK 59

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

 Score = 65.3 bits (159), Expect = 2e-11
 Identities = 40/187 (21%), Positives = 77/187 (41%), Gaps = 40/187 (21%)

Query: 6   KKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLL 65
             +  +++ ++ G+   E     +     +F+  L  K  E +  E F + G + D Q +
Sbjct: 63  GDRSYRRDDRRSGRNTKEPLTEAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCI 122

Query: 66  KNAD-GKLKGCGFINYANKISAVKAI---------------------------------- 90
           K+ +  + KG  ++ + +  S +KA+                                  
Sbjct: 123 KDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGD 182

Query: 91  LKSNKKPYKG----KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAV 145
           + +  K Y G     ITE+E ++ F  +GDI D QL ++ + G+ KG GFI + +   A 
Sbjct: 183 IPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAK 242

Query: 146 KAILKSN 152
           +A+   N
Sbjct: 243 EALEVMN 249

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|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 = 59.1 bits (144), Expect = 2e-11
 Identities = 21/58 (36%), Positives = 38/58 (65%), Gaps = 1/58 (1%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
          +LF+  LP   TEE+ +  F +YG+I +  ++++ D G+ KGC F+ ++++  A KAI
Sbjct: 1  KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAI 58

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

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

 Score = 58.5 bits (142), Expect = 3e-11
 Identities = 19/62 (30%), Positives = 39/62 (62%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           LF+ NL +   +++ +E F + G+++D ++ ++ DG+ KG G + +A +  A KA+ KS
Sbjct: 1  TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEKS 60

Query: 94 NK 95
           +
Sbjct: 61 GE 62

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

 Score = 56.9 bits (138), Expect = 2e-10
 Identities = 22/67 (32%), Positives = 39/67 (58%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
           L++KNL   I +E  +E F  +G I  A+++ +  G+ KG GF+ +++   A KA+ + N
Sbjct: 4   LYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMN 63

Query: 95  KKPYKGK 101
            +   GK
Sbjct: 64  GRIIGGK 70

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

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

 Score = 55.5 bits (134), Expect = 5e-10
 Identities = 20/71 (28%), Positives = 44/71 (61%), Gaps = 1/71 (1%)

Query: 33  GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAIL 91
           GRLF++NLP+   E++ ++ F ++G++ +  + +    GK KG  ++ + +   AVKA  
Sbjct: 3   GRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYK 62

Query: 92  KSNKKPYKGKI 102
           + + K ++G++
Sbjct: 63  ELDGKVFQGRL 73

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

 Score = 60.3 bits (146), Expect = 5e-10
 Identities = 45/175 (25%), Positives = 72/175 (41%), Gaps = 29/175 (16%)

Query: 32  RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 90
           +  L +  LP  +T+EE +  F   G+I   +L+++   G+  G GF+NY     A KA+
Sbjct: 3   KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAV 62

Query: 91  -----LKSNKKPYK----------------------GKITEEEFKEHFGQYGDIIDAQLL 123
                L+   K  K                        +T+ E +  F  +G II +++L
Sbjct: 63  NSLNGLRLQNKTIKVSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRIL 122

Query: 124 KNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGSENGLISPFHDIPLYSNVK 177
            +   G  KG GFI +  +  A +AI   N     G    +   F + P  SN K
Sbjct: 123 SDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSK 177

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

 Score = 54.9 bits (133), Expect = 7e-10
 Identities = 19/63 (30%), Positives = 39/63 (61%), Gaps = 1/63 (1%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILK 92
          ++F+  LP+  T++  +++F Q+G+I +A ++ +   GK +G GF+ + +K SA +A   
Sbjct: 2  KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 93 SNK 95
           N 
Sbjct: 62 PNP 64

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 54.5 bits (132), Expect = 8e-10
 Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 1/67 (1%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
           L+++NLP  +TEE+ +E F  YG +   +L++N D + +G  F+ +A+   A  A+ K N
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLN 59

Query: 95  KKPYKGK 101
                G+
Sbjct: 60  GLVLDGR 66

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

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

 Score = 54.5 bits (132), Expect = 9e-10
 Identities = 24/57 (42%), Positives = 38/57 (66%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           + +E+ KE FG+YG I  A+++K+ +GK KG GF+N+ N  +A KA+ + N K   G
Sbjct: 13  MDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELNGKEVNG 69

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

 Score = 54.2 bits (131), Expect = 9e-10
 Identities = 30/70 (42%), Positives = 40/70 (57%), Gaps = 5/70 (7%)

Query: 32  RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL 91
           R RLF+ NLP  ITEEEFKE F +YG++ +  L K      KG GFI    + +A KA  
Sbjct: 1   RCRLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE-----KGFGFIRLDTRTNAEKAKA 55

Query: 92  KSNKKPYKGK 101
           + +    KG+
Sbjct: 56  ELDGIMRKGR 65

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

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

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 21/58 (36%), Positives = 31/58 (53%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           K TE + K+ F  +G + +  + +  DGK KG  F+ + +K  A KAI   N K  KG
Sbjct: 10  KCTEADLKKLFSPFGFVWEVTIPRKPDGKKKGFAFVQFTSKADAEKAIKGVNGKKIKG 67

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

 Score = 53.5 bits (129), Expect = 2e-09
 Identities = 20/57 (35%), Positives = 35/57 (61%), Gaps = 1/57 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
          LF+ NL F   E+   E FG+YG+I   +L  + D G+ KG G++ ++++ +A  A+
Sbjct: 1  LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAAL 57

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

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

 Score = 53.6 bits (129), Expect = 2e-09
 Identities = 24/71 (33%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           RL + N+PF+  + + ++ FGQ+G I+D +++ N  G  KG GF+ +AN   A +A  K 
Sbjct: 2   RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGS-KGFGFVTFANSADADRAREKL 60

Query: 94  NKKPYKGKITE 104
           +    +G+  E
Sbjct: 61  HGTVVEGRKIE 71

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

 Score = 53.7 bits (129), Expect = 2e-09
 Identities = 17/57 (29%), Positives = 34/57 (59%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
          +LF+  L  K  E + +  F  +G I +  +L++ +G+ +GC F+ +A++  A+ AI
Sbjct: 3  KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAI 59

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

 Score = 58.7 bits (142), Expect = 3e-09
 Identities = 25/96 (26%), Positives = 56/96 (58%), Gaps = 1/96 (1%)

Query: 6   KKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLL 65
           K+ + + E ++K ++  + +K  K +   L++KNL   +T+E+ +E F + G+I  A+++
Sbjct: 260 KRAEREAELRRKFEELQQERK-MKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVM 318

Query: 66  KNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
            +  G  +G GF+ ++N   A +A+ + + +   GK
Sbjct: 319 LDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGK 354

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

 Score = 52.8 bits (127), Expect = 4e-09
 Identities = 22/49 (44%), Positives = 38/49 (77%), Gaps = 2/49 (4%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAIL 149
           +TEEEFKE+F Q+G ++DAQL+++ D G+ +G GF+ + ++ SAV+ + 
Sbjct: 11  VTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSE-SAVERVF 58

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

 Score = 57.3 bits (137), Expect = 4e-09
 Identities = 28/106 (26%), Positives = 58/106 (54%), Gaps = 1/106 (0%)

Query: 9   KVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA 68
           K  +E   +  +  + ++  K +   LF+ NLP+ +TEE+ +E F ++G +   +L+++ 
Sbjct: 92  KEFEEELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDR 151

Query: 69  D-GKLKGCGFINYANKISAVKAILKSNKKPYKGKITEEEFKEHFGQ 113
           + GK +G  F+ + ++ SA KAI + N K  +G+    +  +   Q
Sbjct: 152 ETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQ 197

Length = 306

>gnl|CDD|179388 PRK02230, PRK02230, inorganic pyrophosphatase; Provisional

 Score = 55.4 bits (134), Expect = 5e-09
 Identities = 43/156 (27%), Positives = 72/156 (46%), Gaps = 32/156 (20%)

Query: 179 KIFNMVVEIPRWTNAKMEINLNEPLNPIKQD-IKKGNLRYVANVFPHHGYIWNYGALPQT 237
           KI  + +EIP+ +N K E   +   N I  D I +G+  Y     P      NYG + + 
Sbjct: 3   KIIEVTIEIPKGSNIKYE--YDRKTNKIVVDRILRGDFVY-----PA-----NYGFIKEA 50

Query: 238 --WENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIA 295
             W              DGD +DVL   ++    G ++  + +G + +ID+G+TD K+IA
Sbjct: 51  LDW--------------DGDELDVLVYSDQKFLPGTVLNARIIGAMKMIDDGETDTKLIA 96

Query: 296 INVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
           ++ +D     +N + D+  H+   L     +F  YK
Sbjct: 97  VHDDDYRLDHINSLKDLPQHW---LDEIEYFFSNYK 129

Length = 184

>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 = 51.9 bits (125), Expect = 7e-09
 Identities = 23/67 (34%), Positives = 43/67 (64%), Gaps = 1/67 (1%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
           +F+ NL + + E+E ++ F + G+I D +L+KN  GK KG  ++ + N+ S  +A LK +
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEA-LKLD 60

Query: 95  KKPYKGK 101
           ++  KG+
Sbjct: 61  RELIKGR 67

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

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

 Score = 52.2 bits (126), Expect = 7e-09
 Identities = 22/77 (28%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKS 93
           LF++NLP+  T+E+ +E F + G I    ++K+    K +G G++ +A +  A +A+ + 
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 94  NKKPYKGKITEEEFKEH 110
            K  + G+    EF + 
Sbjct: 62  KKTKFGGRKIHVEFAKK 78

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

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

 Score = 51.8 bits (125), Expect = 8e-09
 Identities = 23/69 (33%), Positives = 42/69 (60%), Gaps = 1/69 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
            L++ NLP+ +TEE+ K+ FGQ+G++  A+++ + + G+ +G GF+       A  AI K
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 93  SNKKPYKGK 101
            N   + G+
Sbjct: 61  LNGTDFGGR 69

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

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILKS 93
           L + NLP + T+E+F+E    +G +    L+ +      KG GF+ YA+K SA+KA  + 
Sbjct: 2   LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQL 61

Query: 94  NKKPYKGKI 102
           + K   G+ 
Sbjct: 62  DGKQIGGRK 70

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

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 24/62 (38%), Positives = 34/62 (54%), Gaps = 6/62 (9%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLK------GCGFINYANKISAVK 88
          LF+KNL FK TEE  K+HF + G +    + K  D K        G GF+ + +K +A K
Sbjct: 3  LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 89 AI 90
          A+
Sbjct: 63 AL 64

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|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 = 51.1 bits (123), Expect = 1e-08
 Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 5/68 (7%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
           +++ NLP  +TEEE +  F  +G I + ++ K+     KG  F+ +    +A  AI+  N
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD-----KGYAFVRFDTHEAAATAIVAVN 57

Query: 95  KKPYKGKI 102
                G+ 
Sbjct: 58  GTSINGQT 65

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

 Score = 51.2 bits (123), Expect = 1e-08
 Identities = 18/56 (32%), Positives = 35/56 (62%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
          +F+ NL +K+  ++ KE F   G ++ A + ++ +GK +G G + + + I AV+AI
Sbjct: 1  IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAI 56

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

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

 Score = 51.0 bits (123), Expect = 1e-08
 Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 36 FIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSN 94
          F+ NLPF I EEE ++HF   GD+   +++++   G  KG G++ +  K S   A+  + 
Sbjct: 3  FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNG 62

Query: 95 KK 96
           K
Sbjct: 63 IK 64

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

 Score = 50.8 bits (122), Expect = 2e-08
 Identities = 19/57 (33%), Positives = 36/57 (63%), Gaps = 1/57 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
          L +  LP+K TE++ K++F  +G+++  Q+ K+   G+ KG GF+ +A+    VK +
Sbjct: 2  LIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVL 58

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|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 = 50.3 bits (121), Expect = 3e-08
 Identities = 22/67 (32%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 36  FIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSN 94
           F+ N+P+  TEE+  E F + G ++  +L+ + D GK KG GF  + +  +A  AI   N
Sbjct: 2   FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLN 61

Query: 95  KKPYKGK 101
              + G+
Sbjct: 62  GYEFNGR 68

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|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 50.3 bits (121), Expect = 3e-08
 Identities = 21/70 (30%), Positives = 41/70 (58%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
           +F++NLPF +T ++ K+ F + G+++ A +  + DG+ KG G + + +   A +AI   N
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDNDGRSKGFGTVLFESPEDAQRAIEMFN 60

Query: 95  KKPYKGKITE 104
               +G+  E
Sbjct: 61  GYDLEGRELE 70

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

>gnl|CDD|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 50.3 bits (120), Expect = 4e-08
 Identities = 20/57 (35%), Positives = 35/57 (61%), Gaps = 1/57 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 90
          L++ NLP ++TE+E ++ F  YG+I+   LL++ + G  +G  F+ Y  +  A  AI
Sbjct: 3  LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAI 59

This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 79

>gnl|CDD|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 = 50.3 bits (121), Expect = 4e-08
 Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 33  GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAIL 91
            +LF+  L  + TE+E +  F ++G + +  L+K+   G+ +G GF+ + +   A  AI 
Sbjct: 2   NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 92  KSNKKPYKGKI 102
             N K  +G++
Sbjct: 62  DLNGKELEGRV 72

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

 Score = 50.0 bits (120), Expect = 4e-08
 Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 32  RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL 91
             R+F+  +P   TEEE ++ F ++G + D +++ +  G  KG GF+ +  +  A K IL
Sbjct: 2   PNRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEK-IL 60

Query: 92  KSNKKPYKGK 101
                 ++GK
Sbjct: 61  AMGNLNFRGK 70

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

 Score = 49.4 bits (118), Expect = 6e-08
 Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 1/57 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
          LF+ NL F+ TE+E + HFG+ G I   +++   D GK KG  F+++     A  A+
Sbjct: 1  LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 57

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

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

 Score = 49.3 bits (118), Expect = 7e-08
 Identities = 22/74 (29%), Positives = 42/74 (56%), Gaps = 6/74 (8%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILK 92
           +LFI  L ++ T++  K +F Q+G+I D  ++K+    + +G GF+ +A+      A+  
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAM-- 58

Query: 93  SNKKPYK--GKITE 104
            N +P+K  G+  E
Sbjct: 59  -NARPHKVDGREVE 71

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

 Score = 49.2 bits (118), Expect = 7e-08
 Identities = 23/61 (37%), Positives = 38/61 (62%), Gaps = 1/61 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKS 93
          L++ NL F ITE++ +  F  +G+I   QL ++ + G+ KG GFI +A+   A KA+ + 
Sbjct: 1  LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQL 60

Query: 94 N 94
          N
Sbjct: 61 N 61

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

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

 Score = 49.3 bits (118), Expect = 7e-08
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 1/71 (1%)

Query: 33  GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAIL 91
           GRLFI+NL +  TEE+ ++ F +YG + +  L +     K KG  F+ Y     AVKA  
Sbjct: 3   GRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFA 62

Query: 92  KSNKKPYKGKI 102
           + +   ++G++
Sbjct: 63  ELDGTVFQGRL 73

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

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

 Score = 48.8 bits (117), Expect = 7e-08
 Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 8/69 (11%)

Query: 34  RLFIKNLP-FKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
           R+F+ NL   K+++E+ +E F +YG I+   L K       G GF+ + N+  A  A+  
Sbjct: 2   RVFVGNLNTDKVSKEDLEEIFSKYGKILGISLHK-------GYGFVQFDNEEDARAAVAG 54

Query: 93  SNKKPYKGK 101
            N +   G+
Sbjct: 55  ENGREIAGQ 63

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

>gnl|CDD|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 = 49.1 bits (118), Expect = 8e-08
 Identities = 20/66 (30%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK-SNKKPYKG 158
             TEE+ +  F +YG+I +  ++++ D G+ KGC F+ ++++  A KAI     K    G
Sbjct: 10  TATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHGKVTMPG 69

Query: 159 SENGLI 164
           +   L 
Sbjct: 70  ASRPLQ 75

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

 Score = 49.0 bits (117), Expect = 8e-08
 Identities = 18/70 (25%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI-LKSNKKPYKGS 159
           K  E + +  F  +G I +  +L++ +G+ +GC F+ +A++  A+ AI    + +  +G 
Sbjct: 12  KCNENDVRIMFAPFGSIEECTVLRDQNGQSRGCAFVTFASRQCALNAIKAMHHSQTMEGC 71

Query: 160 ENGLISPFHD 169
            + L+  F D
Sbjct: 72  SSPLVVKFAD 81

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|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 = 48.8 bits (117), Expect = 8e-08
 Identities = 19/57 (33%), Positives = 34/57 (59%), Gaps = 1/57 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAI 90
          LFI +LP + T+++  + F  +G++I A++  + +    K  GF++Y N  SA  AI
Sbjct: 1  LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAI 57

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

>gnl|CDD|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 = 49.1 bits (117), Expect = 9e-08
 Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 33  GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAIL 91
           G+LFI  L F   E+  ++ F +YG I +  ++K+ + +  +G GF+ + N   A  A++
Sbjct: 1   GKLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMM 60

Query: 92  KSNKKPYKGK 101
             N K   G+
Sbjct: 61  AMNGKSVDGR 70

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

 Score = 53.3 bits (128), Expect = 1e-07
 Identities = 30/148 (20%), Positives = 66/148 (44%), Gaps = 30/148 (20%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKS 93
           L++ +L   +TE +  + F  +G ++  ++ +++   +  G G++N+ N   A +A+   
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETM 62

Query: 94  NKKPYKGK-----------------------------ITEEEFKEHFGQYGDIIDAQLLK 124
           N K   GK                             +  +   + F ++G+I+  ++  
Sbjct: 63  NFKRLGGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVAT 122

Query: 125 NADGKLKGCGFINYANKISAVKAILKSN 152
           + +GK +G GF+++  + SA  AI K N
Sbjct: 123 DENGKSRGYGFVHFEKEESAKAAIQKVN 150

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

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 16/52 (30%), Positives = 32/52 (61%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK 153
           +TE+  +EHF   G++ D ++++  DGK +  GF+ + ++  A +A+   NK
Sbjct: 12  VTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVKYFNK 63

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|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 18/53 (33%), Positives = 27/53 (50%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK 153
            I E++ ++ F  +G I D QL    DGK +  GF+ Y  +  A KA+   N 
Sbjct: 11  GIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALKHFNN 63

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

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

 Score = 48.4 bits (116), Expect = 1e-07
 Identities = 21/60 (35%), Positives = 38/60 (63%), Gaps = 2/60 (3%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLK-NADGKLKGCGFINYANKISAVKAILKS 93
          LFI  L +  TEE  +E+F +YG+++D  ++K    G+ +G GF+ +A+  S+V  +L +
Sbjct: 1  LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADP-SSVDKVLAA 59

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

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILKS 93
          L++  LP  +T++E +  F  YG II +++L +    L +G GFI +  +I A +AI   
Sbjct: 3  LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 94 NKK 96
          N  
Sbjct: 63 NGT 65

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

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

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 22/70 (31%), Positives = 39/70 (55%), Gaps = 7/70 (10%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
           L+++NLP   TEE+ +E F +YG++   +       K+K   F+++  +  AVKA+ + N
Sbjct: 4   LYVRNLPLSTTEEQLRELFSEYGEVERVK-------KIKDYAFVHFEERDDAVKAMEEMN 56

Query: 95  KKPYKGKITE 104
            K  +G   E
Sbjct: 57  GKELEGSPIE 66

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

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 18/57 (31%), Positives = 33/57 (57%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
          +L ++N+PF+ T++E +E F  +G +   +L K  DG  +G  F+ +  K  A  A+
Sbjct: 2  KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAM 58

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

>gnl|CDD|179262 PRK01250, PRK01250, inorganic pyrophosphatase; Provisional

 Score = 50.3 bits (121), Expect = 2e-07
 Identities = 35/108 (32%), Positives = 51/108 (47%), Gaps = 19/108 (17%)

Query: 227 YIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDE 286
           Y  NYG +P T               DGDP+DVL +       G +I+ + +GV+ + DE
Sbjct: 52  YPCNYGFIPHTLS------------LDGDPVDVLVVTPYPLVPGSVIRCRPVGVLKMEDE 99

Query: 287 GQTDWKIIAINVN--DPNAAKLNDVADIETHFPGYLKATNE-WFKIYK 331
              D KIIA+  +   P    + DV D+    P  LKA  + +F+ YK
Sbjct: 100 SGEDAKIIAVPHDKLSPEYDHIKDVNDL----PELLKAQIKHFFEHYK 143

Length = 176

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

 Score = 47.7 bits (113), Expect = 3e-07
 Identities = 18/58 (31%), Positives = 38/58 (65%), Gaps = 1/58 (1%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAI 90
          +LF+ ++P  ITE+E +  F ++G++++  ++K+   G  +GC F+ Y+ +  A +AI
Sbjct: 1  KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAI 58

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

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

 Score = 47.4 bits (113), Expect = 3e-07
 Identities = 26/77 (33%), Positives = 46/77 (59%), Gaps = 4/77 (5%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLL-KNADGKLKGCGFINYANKISAVKAILKS 93
           LF+ NLP  ITE+E KE F ++G++++ ++  K   G+L   GF+ + +   AV+ IL +
Sbjct: 6   LFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDP-EAVQKILAN 64

Query: 94  NKKPYKG--KITEEEFK 108
               ++G  ++  EE K
Sbjct: 65  KPIYFRGDHRLNVEEKK 81

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

>gnl|CDD|178309 PLN02707, PLN02707, Soluble inorganic pyrophosphatase

 Score = 50.9 bits (122), Expect = 4e-07
 Identities = 21/34 (61%), Positives = 27/34 (79%), Gaps = 2/34 (5%)

Query: 385 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
           +SP+HDIPL++   D  FN VVEIP+ T+AKMEV
Sbjct: 57  VSPWHDIPLHAG--DGTFNFVVEIPKETSAKMEV 88

Length = 267

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

 Score = 47.1 bits (112), Expect = 4e-07
 Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 1/76 (1%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKS 93
           LF++NL F +T+E+  + F     I  A ++ + + G+ +G GF+ +A    A +A+ K 
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 94  NKKPYKGKITEEEFKE 109
             K   G+I   +  E
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|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 48.0 bits (114), Expect = 4e-07
 Identities = 20/62 (32%), Positives = 36/62 (58%), Gaps = 2/62 (3%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKS 93
          LF++NLP+  TEE    HF ++G +  A  + + + G+ KG GF+ + ++ +   A LK+
Sbjct: 4  LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTY-NACLKN 62

Query: 94 NK 95
            
Sbjct: 63 AP 64

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

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

 Score = 46.9 bits (112), Expect = 4e-07
 Identities = 15/66 (22%), Positives = 35/66 (53%), Gaps = 4/66 (6%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL----KGCGFINYANKISAVKAI 90
          ++++NL FK+ E++ +  F ++G++   ++ K  D K      G  F+ + +  SA  A+
Sbjct: 3  IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 91 LKSNKK 96
            +  +
Sbjct: 63 QLNGTE 68

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

 Score = 47.2 bits (112), Expect = 4e-07
 Identities = 21/57 (36%), Positives = 37/57 (64%), Gaps = 1/57 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 90
          L++  LP  +T++E ++ F QYG II +++L++   G  +G GFI +  +I A +AI
Sbjct: 3  LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAI 59

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

>gnl|CDD|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 = 46.9 bits (112), Expect = 4e-07
 Identities = 19/56 (33%), Positives = 33/56 (58%), Gaps = 5/56 (8%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
          +F+  L   +TE+E +  FG +G+I+    +K   GK  GCGF+ + ++ +A  AI
Sbjct: 4  VFVGGLDPAVTEDELRSLFGPFGEIVY---VKIPPGK--GCGFVQFVHRAAAEAAI 54

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

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 46.5 bits (111), Expect = 5e-07
 Identities = 17/68 (25%), Positives = 36/68 (52%), Gaps = 6/68 (8%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS- 93
           L++  L  ++TE++ ++HF Q+G+I    ++       + C F+ +  + +A KA  +  
Sbjct: 4   LYVGGLGERVTEKDLRDHFYQFGEIRSITVVPR-----QQCAFVTFTTREAAEKAAERLF 58

Query: 94  NKKPYKGK 101
           NK    G+
Sbjct: 59  NKLIINGR 66

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

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

 Score = 46.4 bits (111), Expect = 6e-07
 Identities = 18/69 (26%), Positives = 37/69 (53%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           RL + NL + +TEE+ +E FG+ G++   ++  +  G+ +G   + +  +  A +AI + 
Sbjct: 2   RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDRSGRSEGTADVVFEKREDAERAIKQF 61

Query: 94  NKKPYKGKI 102
           N     G+ 
Sbjct: 62  NGVLLDGQP 70

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

 Score = 46.6 bits (110), Expect = 8e-07
 Identities = 24/74 (32%), Positives = 45/74 (60%), Gaps = 6/74 (8%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILK 92
           +LFI  L F+ T+E  + HF Q+G + D  ++++ + K  +G GF+ Y++ +  V A + 
Sbjct: 4   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSS-VEEVDAAM- 61

Query: 93  SNKKPYK--GKITE 104
            N +P+K  G++ E
Sbjct: 62  -NARPHKVDGRVVE 74

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

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

 Score = 46.1 bits (110), Expect = 8e-07
 Identities = 25/73 (34%), Positives = 34/73 (46%), Gaps = 4/73 (5%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKG----CGFINYANKISAVKA 89
           RL+I NL  ++TE    + F +YG I     L +  G LKG      F+ +  K  A KA
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 90  ILKSNKKPYKGKI 102
           +   N K   GK 
Sbjct: 61  LKSLNGKTALGKK 73

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|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 46.2 bits (109), Expect = 9e-07
 Identities = 20/56 (35%), Positives = 35/56 (62%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
          +F+ NL +K+  ++ KE F   G ++ A +L++ DGK +G G + +   I AV+AI
Sbjct: 3  VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAI 58

This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

>gnl|CDD|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins

 Score = 46.3 bits (110), Expect = 9e-07
 Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 10/78 (12%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
           ++I N+   +TEE+ +  F QYG+I     L+      K C F+N+ N  +A+KAI    
Sbjct: 6   VYIGNIDDSLTEEKLRNDFSQYGEIESVNYLRE-----KNCAFVNFTNISNAIKAIDGVK 60

Query: 95  KKPYKGKITEEEFKEHFG 112
             P       ++FK  +G
Sbjct: 61  SHPLF-----KKFKISYG 73

This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

>gnl|CDD|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 = 45.3 bits (108), Expect = 1e-06
 Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 5/58 (8%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
           +TEEE +  F  +G I + ++ K+     KG  F+ +    +A  AI+  N     G 
Sbjct: 12  LTEEELQRTFSPFGAIEEVRVFKD-----KGYAFVRFDTHEAAATAIVAVNGTSINGQ 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|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 = 1e-06
 Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 5/63 (7%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
            +TE+E +  FG +G+I+    +K   GK  GCGF+ + ++ +A  AI +       GS 
Sbjct: 12  AVTEDELRSLFGPFGEIVY---VKIPPGK--GCGFVQFVHRAAAEAAIQQLQGTIIGGSR 66

Query: 161 NGL 163
             L
Sbjct: 67  IRL 69

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

 Score = 46.2 bits (110), Expect = 1e-06
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
           +F+  L   +T+EE  E F ++G I++  L+K A+       FI +  + +A +A+   N
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHT-NAFAFIKFEREQAAARAVESEN 64

Query: 95  KKPYKGKITEEEFKE 109
               K K    ++KE
Sbjct: 65  HSMLKNKTMHVQYKE 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|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 1/47 (2%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAI 148
           TEEE KE F Q+G++  A+++K+      KG  F+ +  K SA K +
Sbjct: 13  TEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCL 59

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

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

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 16/53 (30%), Positives = 31/53 (58%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
           I +E  +E F  +G I  A+++ +  G+ KG GF+ +++   A KA+ + N +
Sbjct: 13  IDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMNGR 65

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|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 45.3 bits (107), Expect = 2e-06
 Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 1/63 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
           +TE+E ++ F  YG+I+   LL++ + G  +G  F+ Y  +  A  AI   N     GS 
Sbjct: 12  LTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSLNGTIPPGST 71

Query: 161 NGL 163
             L
Sbjct: 72  MPL 74

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|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 45.4 bits (107), Expect = 2e-06
 Identities = 23/56 (41%), Positives = 38/56 (67%), Gaps = 1/56 (1%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 89
          ++F++NLPF +T ++ KE F Q G ++ A+ +K  +GK KGCG + + +  SA KA
Sbjct: 1  QIFVRNLPFDLTWQKLKEKFSQCGHVMFAE-IKMENGKSKGCGTVRFDSPESAEKA 55

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

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

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 2/68 (2%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKS 93
           LF+ NLP+  T E+   HF   G     +LL +   GK KGC F+ + +   A+   LK 
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEF-DTAEAMTKALKL 61

Query: 94  NKKPYKGK 101
           +    KG+
Sbjct: 62  HHTLLKGR 69

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

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

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 20/55 (36%), Positives = 31/55 (56%), Gaps = 2/55 (3%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 89
          L+++NLPFKI+ EE  + FG+YG I   Q+      + +G  F+ Y +   A  A
Sbjct: 5  LYVRNLPFKISSEELYDLFGKYGAI--RQIRIGNTKETRGTAFVVYEDIYDAKNA 57

This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

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

 Score = 45.3 bits (108), Expect = 2e-06
 Identities = 20/57 (35%), Positives = 36/57 (63%), Gaps = 1/57 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
          ++I  LP+++TE +    F QYG+I+D  L+++   GK KG  F+ Y ++ S + A+
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAV 68

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

 Score = 45.1 bits (107), Expect = 2e-06
 Identities = 18/57 (31%), Positives = 32/57 (56%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
          +LF+  L  + TE++ +  F  +G I +  +L+  DG  KGC F+ +++   A  AI
Sbjct: 3  KLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAI 59

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

>gnl|CDD|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 44.6 bits (106), Expect = 3e-06
 Identities = 21/49 (42%), Positives = 28/49 (57%), Gaps = 1/49 (2%)

Query: 101 KITEEEFKEHFGQ-YGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
            +TE E KEHF +  G+I D +LL+  DGK +   FI Y  +  A KA 
Sbjct: 11  SLTEAELKEHFSKHGGEITDVKLLRTEDGKSRRIAFIGYKTEEEAQKAK 59

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

 Score = 44.5 bits (106), Expect = 3e-06
 Identities = 17/50 (34%), Positives = 33/50 (66%), Gaps = 2/50 (4%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLK-NADGKLKGCGFINYANKISAVKAILKS 151
           TEE  +E+F +YG+++D  ++K    G+ +G GF+ +A+  S+V  +L +
Sbjct: 11  TEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADP-SSVDKVLAA 59

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

 Score = 43.9 bits (104), Expect = 4e-06
 Identities = 16/49 (32%), Positives = 31/49 (63%), Gaps = 1/49 (2%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
           K TE++ K++F  +G+++  Q+ K+   G+ KG GF+ +A+    VK +
Sbjct: 10  KTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVL 58

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

 Score = 44.2 bits (105), Expect = 4e-06
 Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
          R+++ ++   ++E++ K  F  +G I    L  + + GK KG GFI Y N  SA  AI
Sbjct: 2  RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAI 59

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|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 44.1 bits (104), Expect = 4e-06
 Identities = 23/56 (41%), Positives = 32/56 (57%), Gaps = 3/56 (5%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
          LF+KNLP+ IT +E KE F    D +D +L    DG  KG  +I +  +  A KA+
Sbjct: 6  LFVKNLPYNITVDELKEVF---EDAVDIRLPSGKDGSSKGIAYIEFKTEAEAEKAL 58

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 43.7 bits (104), Expect = 5e-06
 Identities = 17/63 (26%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVKAILKS 93
          + ++ LPF  TEE+ ++ F       D   ++ + DG+  G  ++ +A+   A +A+ K 
Sbjct: 2  VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDDGRPTGEAYVEFASPEDARRALRKH 61

Query: 94 NKK 96
          N K
Sbjct: 62 NNK 64

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 43.9 bits (104), Expect = 5e-06
 Identities = 22/69 (31%), Positives = 42/69 (60%), Gaps = 1/69 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHF-GQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
           R+FI N+P+ +  ++ K+ F  + G++   +L K+ +GK +GCG + + +K S  KA+  
Sbjct: 1   RVFISNIPYDLKWQDLKDLFREKVGEVTYVELFKDEEGKSRGCGVVEFKDKESVQKALET 60

Query: 93  SNKKPYKGK 101
            N+   KG+
Sbjct: 61  MNRYELKGR 69

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 43.9 bits (104), Expect = 6e-06
 Identities = 19/56 (33%), Positives = 33/56 (58%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           T+EE ++ F ++G +   +L+ N  GK KG  ++ Y N+ SA +A+LK +    K 
Sbjct: 15  TKEELEKLFKKHGVVKSVRLVTNRSGKPKGLAYVEYENESSASQAVLKMDGTEIKE 70

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|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 = 43.9 bits (104), Expect = 6e-06
 Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 4/66 (6%)

Query: 25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANK 83
          K  D  K   LF+  +P  + E++ +  F Q+G I +  +LK+   G  KGC F+ Y  +
Sbjct: 1  KDDDAIK---LFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCAR 57

Query: 84 ISAVKA 89
           SA+KA
Sbjct: 58 ESALKA 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|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins

 Score = 43.5 bits (103), Expect = 7e-06
 Identities = 18/69 (26%), Positives = 40/69 (57%), Gaps = 1/69 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
            LF+ NL + + +E  K  F ++G ++ A+++ + + G+ +G G++++ +   A KAI  
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 93  SNKKPYKGK 101
            + K   G+
Sbjct: 61  MDGKELDGR 69

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|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 43.5 bits (103), Expect = 7e-06
 Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 6/70 (8%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK-S 93
           L+I +L  K+TEE+ K  F +YG+I    ++       +GC ++    +  A +A+ K  
Sbjct: 5   LWIGHLSKKVTEEDLKNLFEEYGEIQSIDMIPP-----RGCAYVCMETRQDAHRALQKLR 59

Query: 94  NKKPYKGKIT 103
           N K    KI 
Sbjct: 60  NVKLAGKKIK 69

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

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

 Score = 43.4 bits (103), Expect = 7e-06
 Identities = 17/75 (22%), Positives = 39/75 (52%)

Query: 33  GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
            +L + NL F +++++ KE F ++G +  A +  +  G+  G   + +  +  A+KA+ +
Sbjct: 1   TKLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRSGRSLGTADVVFERRADALKAMKQ 60

Query: 93  SNKKPYKGKITEEEF 107
            N  P  G+  + + 
Sbjct: 61  YNGVPLDGRPMKIQL 75

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

 Score = 43.1 bits (102), Expect = 1e-05
 Identities = 15/53 (28%), Positives = 33/53 (62%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK 153
              +++ +E F + G+++D ++ ++ DG+ KG G + +A +  A KA+ KS +
Sbjct: 10  SAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEKSGE 62

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

 Score = 47.2 bits (112), Expect = 1e-05
 Identities = 25/80 (31%), Positives = 38/80 (47%), Gaps = 1/80 (1%)

Query: 16  KKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKG 74
           K  K    R   D  K   L++  LP  +T+ E +  F  +G II +++L +   G  KG
Sbjct: 73  KTIKVSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKG 132

Query: 75  CGFINYANKISAVKAILKSN 94
            GFI +  +  A +AI   N
Sbjct: 133 VGFIRFDKRDEADRAIKTLN 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|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins

 Score = 42.9 bits (102), Expect = 1e-05
 Identities = 21/62 (33%), Positives = 37/62 (59%)

Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
          G +FIKNL   I  +   + F  +G+I+  ++  + +G  KG GF+++  + +AV+AI K
Sbjct: 3  GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEK 62

Query: 93 SN 94
           N
Sbjct: 63 VN 64

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|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 43.1 bits (101), Expect = 1e-05
 Identities = 17/57 (29%), Positives = 30/57 (52%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
          +LFI  +  K  E + +  F  +G I + ++L+  DG  +GC F+ +  +  A  AI
Sbjct: 3  KLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAI 59

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|240796 cd12350, RRM3_SHARP, RNA recognition motif 3 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 22/58 (37%), Positives = 30/58 (51%), Gaps = 2/58 (3%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
          LFI NL    T  + +E F ++G+IID  + K          FI YA+  S VKA+ K
Sbjct: 5  LFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGN--PAYAFIQYADIASVVKAMRK 60

This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 74

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 42.9 bits (101), Expect = 1e-05
 Identities = 18/68 (26%), Positives = 39/68 (57%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           R+F+  + FK  E + ++ F QYG + + +++ +  G  KG GF+ +  +  A K + ++
Sbjct: 4   RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRAGVSKGYGFVTFETQEDAQKILQEA 63

Query: 94  NKKPYKGK 101
           N+  ++ K
Sbjct: 64  NRLCFRDK 71

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

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 20/66 (30%), Positives = 35/66 (53%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
           L+I NLP  + E++ +     YG +I  ++L+++ G+ +G GF    ++      I K N
Sbjct: 3   LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSKGQSRGVGFARMESREKCEDIISKFN 62

Query: 95  KKPYKG 100
            K  KG
Sbjct: 63  GKYLKG 68

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

 Score = 42.8 bits (100), Expect = 1e-05
 Identities = 24/58 (41%), Positives = 39/58 (67%), Gaps = 1/58 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAIL 91
          +F+ +L  +IT E+ K  F  +G I DA+++K+ A GK KG GF+++ NK+ A  AI+
Sbjct: 4  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 61

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

 Score = 42.9 bits (101), Expect = 1e-05
 Identities = 20/62 (32%), Positives = 36/62 (58%), Gaps = 1/62 (1%)

Query: 34 RLFIKNLPFKITE-EEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
          +L I+NLP+ I +  + K+ FG+YG + +A + +   GKL G  F+    + +A  A+  
Sbjct: 2  KLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLCGFAFVTMKKRKNAEIALEN 61

Query: 93 SN 94
          +N
Sbjct: 62 TN 63

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

 Score = 42.5 bits (101), Expect = 1e-05
 Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 6/71 (8%)

Query: 35  LFIKNLPFKITEEEFKEH----FGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
           L+I NL  KI ++E K      F Q+G ++D    K    K++G  F+ + +  SA  A+
Sbjct: 2   LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASKTL--KMRGQAFVVFKDVESATNAL 59

Query: 91  LKSNKKPYKGK 101
                 P+  K
Sbjct: 60  RALQGFPFYDK 70

This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. . Length = 78

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

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 16/52 (30%), Positives = 32/52 (61%), Gaps = 1/52 (1%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNK 153
           T++  +++F Q+G+I +A ++ +   GK +G GF+ + +K SA +A    N 
Sbjct: 13  TDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDPNP 64

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|241104 cd12660, RRM2_MYEF2, RNA recognition motif 2 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 20/56 (35%), Positives = 33/56 (58%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
          +F+ NL FK+  ++ KE F   G +  A + ++ DGK +G G + +   I AV+AI
Sbjct: 3  IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKDGKSRGMGTVTFEQPIEAVQAI 58

This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

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

 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKS 93
           +F+ NLP    E    + F  +G + + +++++    K KG GF+   N   A  AI   
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 94  NKKPYKGKITEEEFK 108
           N     G++ +  FK
Sbjct: 64  NGYRLGGRVLQVSFK 78

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

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 9/75 (12%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQY-------GDIIDAQLLKNADGKLKGCGFINYANKISA 86
           RL++KNL  ++TEE+    FG++        ++ D +L+   +G++KG  F+ + ++  A
Sbjct: 3   RLYVKNLSKRVTEEDLVYIFGRFVDSSSEEKNMFDIRLMT--EGRMKGQAFVTFPSEEIA 60

Query: 87  VKAILKSNKKPYKGK 101
            KA+   N    KGK
Sbjct: 61  TKALNLVNGYVLKGK 75

This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. . Length = 82

>gnl|CDD|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 42.2 bits (99), Expect = 2e-05
 Identities = 27/70 (38%), Positives = 40/70 (57%), Gaps = 5/70 (7%)

Query: 32  RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL 91
           R RLF+ NLP  ITE+EFK+ F +YG+    ++  N   K KG GFI   ++  A  A  
Sbjct: 1   RCRLFVGNLPADITEDEFKKLFAKYGE--PGEVFIN---KGKGFGFIKLESRALAEIAKA 55

Query: 92  KSNKKPYKGK 101
           + +  P +G+
Sbjct: 56  ELDDTPMRGR 65

This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 71

>gnl|CDD|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 = 42.1 bits (99), Expect = 2e-05
 Identities = 21/68 (30%), Positives = 41/68 (60%), Gaps = 1/68 (1%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKS 93
           +F+ N+P++ TEE+ K+ F + G ++  +L+ + + GK KG GF  Y ++ +A+ A+   
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 94  NKKPYKGK 101
           N     G+
Sbjct: 61  NGYELNGR 68

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

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 19/57 (33%), Positives = 34/57 (59%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
          +LF+  L  + TE+E +E F  YG + D  ++++   + +GC F+ Y++K  A  AI
Sbjct: 1  KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAI 57

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

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

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 90
          +  L +  LP  +T++E +  F   G+I   +L+++   G+  G GF+NY +   A KAI
Sbjct: 1  KTNLIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAI 60

Query: 91 LKSNK 95
             N 
Sbjct: 61 NTLNG 65

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

 Score = 42.4 bits (99), Expect = 2e-05
 Identities = 24/69 (34%), Positives = 40/69 (57%), Gaps = 2/69 (2%)

Query: 31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLL-KNADGKLKGCGFINYANKISAVKA 89
          +   L++  LP  +T++E ++ F QYG II +++L     G  +G GFI +  +I A +A
Sbjct: 1  RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 60

Query: 90 ILKSN-KKP 97
          I   N +KP
Sbjct: 61 IKGLNGQKP 69

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

 Score = 42.0 bits (99), Expect = 2e-05
 Identities = 20/57 (35%), Positives = 34/57 (59%), Gaps = 1/57 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 90
          +F+ +L  +I  E  +  F  +G+I DA+++K+   GK KG GF+++  K  A  AI
Sbjct: 2  IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAI 58

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

 Score = 42.0 bits (99), Expect = 3e-05
 Identities = 15/48 (31%), Positives = 29/48 (60%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
           K+  ++ KE F   G ++ A + ++ +GK +G G + + + I AV+AI
Sbjct: 9   KVGWKKLKEVFKLAGKVVRADIKEDKEGKSRGMGVVQFEHPIEAVQAI 56

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

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

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 19/52 (36%), Positives = 32/52 (61%), Gaps = 1/52 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSN 152
           ITE++ +  F  +G+I   QL ++ + G+ KG GFI +A+   A KA+ + N
Sbjct: 10  ITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 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|240822 cd12376, RRM2_Hu_like, RNA recognition motif 2 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins

 Score = 41.8 bits (98), Expect = 3e-05
 Identities = 22/61 (36%), Positives = 38/61 (62%), Gaps = 2/61 (3%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILK-SNKKPYKGS 159
           +T++E ++ F QYG II +++L++   G  +G GFI +  +I A +AI   + +KP   S
Sbjct: 12  MTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPEGAS 71

Query: 160 E 160
           E
Sbjct: 72  E 72

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

 Score = 41.7 bits (98), Expect = 3e-05
 Identities = 15/46 (32%), Positives = 26/46 (56%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
           TE++ +  F  +G I +  +L+  DG  KGC F+ +++   A  AI
Sbjct: 14  TEDDVRRLFEPFGTIEECTILRGPDGNSKGCAFVKFSSHAEAQAAI 59

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

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

 Score = 42.0 bits (98), Expect = 3e-05
 Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILK 92
           +LFI  L F+ T++  +EHF ++G + D  ++++   K  +G GF+ Y+  +  V A + 
Sbjct: 4   KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSC-VEEVDAAMS 62

Query: 93  SNKKPYKGKITE 104
           +      G++ E
Sbjct: 63  ARPHKVDGRVVE 74

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|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 = 41.1 bits (97), Expect = 4e-05
 Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 103 TEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           TEEE +E F  +G+I +  L L     + KG  F+++     AVKA  + +   ++G
Sbjct: 12  TEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQG 68

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

 Score = 41.5 bits (98), Expect = 4e-05
 Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILKSNKK 154
           T++E +  F  YG II +++L +    L +G GFI +  +I A +AI   N  
Sbjct: 13  TQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKALNGT 65

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

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

 Score = 41.4 bits (98), Expect = 4e-05
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 37  IKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNK 95
           + NL     E++ +E F  +G I    L K+ + G+ +G  F+ +  +  A +AI K N 
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNG 63

Query: 96  KPYKGKITEEEF 107
             Y   I   E+
Sbjct: 64  FGYDNLILSVEW 75

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|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 41.5 bits (97), Expect = 4e-05
 Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           ++F++NLPF  T +  K+ F + G ++ A  +K  +GK KGCG + + +   A +A    
Sbjct: 1   QIFVRNLPFDFTWKMLKDKFNECGHVLYAD-IKMENGKSKGCGVVRFESPEVAERACRMM 59

Query: 94  NKKPYKGK 101
           N     G+
Sbjct: 60  NGYKLNGR 67

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

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

 Score = 41.0 bits (97), Expect = 4e-05
 Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 4/53 (7%)

Query: 49  FKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
             + F  +G++   +LLK       G  F+ ++ + +A KA+   N   + G+
Sbjct: 1   LYKLFSPFGNVEKIKLLKKK----PGFAFVEFSTEEAAEKAVQYLNGVLFGGR 49

(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|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 41.4 bits (97), Expect = 4e-05
 Identities = 26/64 (40%), Positives = 33/64 (51%), Gaps = 1/64 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKS 93
          L + NLP   T EEF+E    YG+I    L+ +   G  KG GF+ Y  K SA KA L+ 
Sbjct: 2  LCVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLEL 61

Query: 94 NKKP 97
            K 
Sbjct: 62 LGKQ 65

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

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

 Score = 41.1 bits (97), Expect = 5e-05
 Identities = 13/53 (24%), Positives = 29/53 (54%), Gaps = 4/53 (7%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA 86
          ++F+  L   +TEE+ +++F Q+G++ D  + K      +   F+ +A+   A
Sbjct: 2  KVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP----FRAFAFVTFADPEVA 50

This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 71

>gnl|CDD|241032 cd12588, RRM1_p54nrb, RNA recognition motif 1 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 41.0 bits (96), Expect = 5e-05
 Identities = 26/70 (37%), Positives = 37/70 (52%), Gaps = 5/70 (7%)

Query: 32  RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL 91
           R RLF+ NLP  ITEEE ++ F +YG     ++  + D   KG GFI    +  A  A  
Sbjct: 1   RSRLFVGNLPPDITEEEMRKLFEKYGKA--GEIFIHKD---KGFGFIRLETRTLAEIAKA 55

Query: 92  KSNKKPYKGK 101
           + +  P +GK
Sbjct: 56  ELDNMPLRGK 65

This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

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

 Score = 41.3 bits (96), Expect = 5e-05
 Identities = 23/60 (38%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAI 90
          +  L +  LP  +T+EEFK  FG  G+I   +L+++   G+  G GF+NY +   A KAI
Sbjct: 3  KTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAI 62

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

 Score = 41.2 bits (96), Expect = 5e-05
 Identities = 19/72 (26%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILK 92
           +LFI  L F+ TEE  + ++ Q+G + D  ++++ A  + +G GF+ ++  ++ V A + 
Sbjct: 4   KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSC-MNEVDAAMA 62

Query: 93  SNKKPYKGKITE 104
           +      G++ E
Sbjct: 63  ARPHTIDGRVVE 74

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

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

 Score = 41.0 bits (96), Expect = 5e-05
 Identities = 15/49 (30%), Positives = 33/49 (67%), Gaps = 1/49 (2%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYAN 82
          +FI  L ++ T++  +E+FGQ+G++ D  ++++ A G+ +G GF+ +  
Sbjct: 1  MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKK 49

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|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 41.2 bits (97), Expect = 5e-05
 Identities = 17/69 (24%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILKS 93
           L++  L       + K+ F +YG ++ A+++ NA      C GF+  A+   A K I   
Sbjct: 2   LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 94  NKKPYKGKI 102
           ++    G++
Sbjct: 62  HRTELHGRV 70

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

 Score = 41.2 bits (96), Expect = 5e-05
 Identities = 23/57 (40%), Positives = 37/57 (64%), Gaps = 1/57 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 90
          +F+ +L  +IT ++ K  F  +G I DA+++K+ A GK KG GF+++ NK  A  AI
Sbjct: 4  VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 60

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|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins

 Score = 40.9 bits (96), Expect = 6e-05
 Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 5/54 (9%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY 156
           TEE+ +  F QYG+I     L+      K C F+N+ N  +A+KAI      P 
Sbjct: 16  TEEKLRNDFSQYGEIESVNYLRE-----KNCAFVNFTNISNAIKAIDGVKSHPL 64

This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 79

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

 Score = 41.5 bits (98), Expect = 6e-05
 Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 5/70 (7%)

Query: 27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKIS 85
          P  T    LF+  L  + TEE  +E F +YGDI   +L+++   G  KG  F+ Y ++  
Sbjct: 2  PYLT----LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERD 57

Query: 86 AVKAILKSNK 95
          A++A   ++K
Sbjct: 58 ALRAYRDAHK 67

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

 Score = 41.3 bits (96), Expect = 6e-05
 Identities = 24/70 (34%), Positives = 39/70 (55%), Gaps = 3/70 (4%)

Query: 31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLL-KNADGKLKGCGFINYANKISAVKA 89
          +   L++  LP  +T++E ++ F QYG II +++L     G  +G GFI +  +I A +A
Sbjct: 4  RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 63

Query: 90 I--LKSNKKP 97
          I  L   K P
Sbjct: 64 IKGLNGQKPP 73

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

 Score = 41.0 bits (96), Expect = 6e-05
 Identities = 14/50 (28%), Positives = 32/50 (64%), Gaps = 1/50 (2%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYAN 82
          +LF+  L ++ T+E  + +F QYG+++D  ++K+    + +G GF+ + +
Sbjct: 1  KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKD 50

This subfamily corresponds to the RRM1 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated form is predominantly nuclear and the nonacetylated form is in cytoplasm. It also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. . Length = 82

>gnl|CDD|241030 cd12586, RRM1_PSP1, RNA recognition motif 1 in vertebrate paraspeckle protein 1 (PSP1)

 Score = 40.7 bits (95), Expect = 7e-05
 Identities = 23/55 (41%), Positives = 34/55 (61%), Gaps = 5/55 (9%)

Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA 86
          R RLF+ NLP  ITEE+FK+ F +YG+   +++  N D   +G GFI   ++  A
Sbjct: 1  RCRLFVGNLPTDITEEDFKKLFEKYGE--PSEVFINRD---RGFGFIRLESRTLA 50

This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 71

>gnl|CDD|241014 cd12570, RRM5_MRD1, RNA recognition motif 5 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 40.6 bits (95), Expect = 8e-05
 Identities = 15/58 (25%), Positives = 32/58 (55%)

Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
           ++ +KNLPF+ T+++ +  F  YG +   ++ K  D   +G  F+ ++    A+ A+
Sbjct: 1  TKILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSARGFAFVEFSTAKEALNAM 58

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

>gnl|CDD|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins

 Score = 40.5 bits (95), Expect = 8e-05
 Identities = 16/64 (25%), Positives = 33/64 (51%), Gaps = 5/64 (7%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
          ++I NLP   +EEE +E   ++G I   +++K      K   F+++ +  +A+K +    
Sbjct: 6  VYIGNLPESYSEEELREDLEKFGPIDQIKIVKE-----KNIAFVHFLSIANAIKVVTTLP 60

Query: 95 KKPY 98
           +P 
Sbjct: 61 CEPD 64

This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 78

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

 Score = 40.2 bits (95), Expect = 9e-05
 Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 1/59 (1%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
            +TEE+ +E F  YG +   +L++N D + +G  F+ +A+   A  A+ K N     G 
Sbjct: 9   SVTEEDLREFFSPYGKVEGVRLVRNKD-RPRGFAFVEFASPEDAEAALKKLNGLVLDGR 66

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

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

 Score = 40.8 bits (95), Expect = 9e-05
 Identities = 23/65 (35%), Positives = 40/65 (61%), Gaps = 2/65 (3%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKS 93
          L++  LP  ++++E ++ F QYG II +++L +   G  +G GFI +  +I A +AI   
Sbjct: 4  LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGL 63

Query: 94 N-KKP 97
          N +KP
Sbjct: 64 NGQKP 68

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

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 15/48 (31%), Positives = 29/48 (60%), Gaps = 1/48 (2%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
             E+   E FG+YG+I   +L  + D G+ KG G++ ++++ +A  A+
Sbjct: 10  ADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAAL 57

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

>gnl|CDD|240844 cd12398, RRM_CSTF2_RNA15_like, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           TEE+  E F + G ++  +L+ + D GK KG GF  + +  +A  AI   N   + G
Sbjct: 11  TEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGYEFNG 67

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

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 16/58 (27%), Positives = 33/58 (56%), Gaps = 4/58 (6%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYK 157
           + T++  K +F Q+G+I D  ++K+    + +G GF+ +A+      A+   N +P+K
Sbjct: 10  ETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAM---NARPHK 64

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 7/58 (12%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
           TEE+ +E F +YG++   +       K+K   F+++  +  AVKA+ + N K  +GS 
Sbjct: 14  TEEQLRELFSEYGEVERVK-------KIKDYAFVHFEERDDAVKAMEEMNGKELEGSP 64

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

 Score = 40.3 bits (94), Expect = 1e-04
 Identities = 15/48 (31%), Positives = 31/48 (64%), Gaps = 1/48 (2%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAI 148
           ITE+E +  F ++G++++  ++K+   G  +GC F+ Y+ +  A +AI
Sbjct: 11  ITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAI 58

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

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

 Score = 39.4 bits (93), Expect = 1e-04
 Identities = 12/52 (23%), Positives = 24/52 (46%), Gaps = 4/52 (7%)

Query: 107 FKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
             + F  +G++   +LLK       G  F+ ++ + +A KA+   N   + G
Sbjct: 1   LYKLFSPFGNVEKIKLLKKK----PGFAFVEFSTEEAAEKAVQYLNGVLFGG 48

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

 Score = 40.4 bits (95), Expect = 1e-04
 Identities = 19/56 (33%), Positives = 32/56 (57%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
          LF+ NL  ++TEE   E F Q G +   ++ K+ +GK K   F+ + +++S   AI
Sbjct: 4  LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAI 59

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

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

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 90
          L +  LP  +T+EE +  F   G I   +++++   G+  G GF++Y ++  A KAI
Sbjct: 3  LIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAI 59

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

 Score = 40.1 bits (94), Expect = 1e-04
 Identities = 19/58 (32%), Positives = 34/58 (58%), Gaps = 2/58 (3%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
          RLF+  +P   TEE+ +E F ++GDI    ++K+ + G+ KG G++ +     A  A+
Sbjct: 3  RLFVV-IPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 59

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|240684 cd12238, RRM1_RBM40_like, RNA recognition motif 1 in RNA-binding protein 40 (RBM40) and similar proteins

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 13/59 (22%), Positives = 33/59 (55%), Gaps = 2/59 (3%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
           L +++LP +++E++ ++    +G     +++    GKLK   F  + N+ +A +A+ +
Sbjct: 1  TLLVRHLPPELSEDDKEDLLKHFG-ASSVRVMSR-RGKLKNTAFATFDNEQAASQALSR 57

This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. . Length = 73

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

 Score = 43.5 bits (102), Expect = 1e-04
 Identities = 28/111 (25%), Positives = 52/111 (46%), Gaps = 16/111 (14%)

Query: 6   KKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLL 65
           + K++K  + + G + I        K   L++ NLP  IT+++    FG+YG I+   +L
Sbjct: 175 RNKRLKVSYARPGGESI--------KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNIL 226

Query: 66  KNA-DGKLKGCGFINYANKISAVKAILKSNK-------KPYKGKITEEEFK 108
           ++   G  +G  F+ +  +  A +AI   N        +P   ++ EE  K
Sbjct: 227 RDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRLAEEHGK 277

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

 Score = 43.7 bits (103), Expect = 1e-04
 Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 1/70 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILK 92
           R++I NLP  + E++ KE    +GD+    L+K+ A G  KG  F  Y +      AI  
Sbjct: 297 RIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAA 356

Query: 93  SNKKPYKGKI 102
            N K      
Sbjct: 357 LNGKDTGDNK 366

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

>gnl|CDD|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 13/54 (24%), Positives = 29/54 (53%), Gaps = 5/54 (9%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
           ++TE++ ++HF Q+G+I    ++       + C F+ +  + +A KA  +   K
Sbjct: 12  RVTEKDLRDHFYQFGEIRSITVVPR-----QQCAFVTFTTREAAEKAAERLFNK 60

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

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

 Score = 40.1 bits (93), Expect = 2e-04
 Identities = 22/60 (36%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAI 90
          +  L +  LP  +T+EEF+  FG  G+I   +L+++   G+  G GF+NY +   A KAI
Sbjct: 2  KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

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

 Score = 39.8 bits (93), Expect = 2e-04
 Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 1/53 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISA 86
          ++I +LP    E+E K++F Q+G + + ++ ++   G  K  GFI + N   A
Sbjct: 2  IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVA 54

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|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 12/58 (20%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 36 FIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           +  +   ++E++ KE F   G++   +L  +     +   F+ +A+  SA+ A+  S
Sbjct: 4  HVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFA-FVEFADAESALSALNLS 60

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

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

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 17/60 (28%), Positives = 36/60 (60%), Gaps = 1/60 (1%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
          +LF+  L   +TEE+ +E+F QYG++   +++ + + GK +G  F+ + +     K +L+
Sbjct: 1  KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

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

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 14/58 (24%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAI 90
          +LF+  L  K ++   + HF +YG + +  ++ + + K     GFI +++   A +A+
Sbjct: 4  KLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61

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|223299 COG0221, Ppa, Inorganic pyrophosphatase [Energy production and conversion]

 Score = 41.1 bits (97), Expect = 3e-04
 Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 2/33 (6%)

Query: 386 SPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
              H IP   +  D+  N+V+EIP+ +N K EV
Sbjct: 1   MDLHKIPAGPD--DEDINVVIEIPKGSNIKYEV 31

Length = 171

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

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 23/57 (40%), Positives = 31/57 (54%), Gaps = 5/57 (8%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           ITEEEFKE F +YG++ +  L K      KG GFI    + +A KA  + +    KG
Sbjct: 13  ITEEEFKELFSKYGEVSEVFLNKE-----KGFGFIRLDTRTNAEKAKAELDGIMRKG 64

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

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

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 1/59 (1%)

Query: 100 GKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
              TEEE ++ F ++G + D +++ +  G  KG GF+ +  +  A K IL      ++G
Sbjct: 12  PDTTEEELRDFFSRFGSVKDVKIITDRAGVSKGYGFVTFETQEDAEK-ILAMGNLNFRG 69

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|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 = 38.8 bits (91), Expect = 3e-04
 Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAI 148
           T+++  + F  +G++I A++  + +    K  GF++Y N  SA  AI
Sbjct: 11  TDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAI 57

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

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

 Score = 39.3 bits (91), Expect = 3e-04
 Identities = 22/50 (44%), Positives = 34/50 (68%), Gaps = 1/50 (2%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAIL 149
           +IT E+ K  F  +G I DA+++K+ A GK KG GF+++ NK+ A  AI+
Sbjct: 12  EITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 61

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

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 18/48 (37%), Positives = 28/48 (58%), Gaps = 1/48 (2%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 148
           I  E  +  F  +G+I DA+++K+   GK KG GF+++  K  A  AI
Sbjct: 11  IDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAI 58

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

 Score = 40.8 bits (95), Expect = 3e-04
 Identities = 19/69 (27%), Positives = 42/69 (60%), Gaps = 1/69 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
           +LFI  L +   +   ++ F  +GD++DA+++ + + G+ +G GF+N+ ++ +A  AI +
Sbjct: 36  KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95

Query: 93  SNKKPYKGK 101
            + K   G+
Sbjct: 96  MDGKELNGR 104

Length = 144

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

 Score = 39.0 bits (91), Expect = 3e-04
 Identities = 14/67 (20%), Positives = 30/67 (44%), Gaps = 7/67 (10%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           RL+++  P   +E   +E F  YG + + +++ N         F+ + +  SA++A    
Sbjct: 1   RLYVRPFPPDTSESAIREIFSPYGAVKEVKMISNF-------AFVEFESLESAIRAKDSV 53

Query: 94  NKKPYKG 100
           + K    
Sbjct: 54  HGKVLNN 60

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

 Score = 38.7 bits (90), Expect = 3e-04
 Identities = 20/57 (35%), Positives = 35/57 (61%), Gaps = 7/57 (12%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
          +LF+ NLP + TE+E +  F QYG +++  ++KN        GF++  +K +A +AI
Sbjct: 2  KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKNY-------GFVHMDDKTAADEAI 51

This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. . Length = 67

>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating protein-binding protein 2 (G3BP2) and similar proteins

 Score = 39.2 bits (91), Expect = 3e-04
 Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 2/70 (2%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILK 92
           +LF+ NLP  I E E KE F  +G++++ ++  K   GKL   GF+ + +    V+ IL 
Sbjct: 7   QLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDS-EPVQRILG 65

Query: 93  SNKKPYKGKI 102
           +    ++G++
Sbjct: 66  AKPIMFRGEV 75

This subgroup corresponds to the RRM of G3BP2, also termed GAP SH3 domain-binding protein 2, a cytoplasmic protein that interacts with both IkappaBalpha and IkappaBalpha/NF-kappaB complexes, indicating that G3BP2 may play a role in the control of nucleocytoplasmic distribution of IkappaBalpha and cytoplasmic anchoring of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing five PXXP motifs, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). It binds to the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity, through its N-terminal NTF2-like domain. The acidic domain is sufficient for the interaction of G3BP2 with the IkappaBalpha cytoplasmic retention sequence. Furthermore, G3BP2 might influence stability or translational efficiency of particular mRNAs by binding to RNA-containing structures within the cytoplasm through its RNA-binding domain. Length = 83

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

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 16/51 (31%), Positives = 33/51 (64%), Gaps = 1/51 (1%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANK 83
          +LF+ NLP+ +  +E KE+F Q+G +    +  + + G  KG GF++++++
Sbjct: 1  KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSR 51

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

 Score = 38.7 bits (91), Expect = 3e-04
 Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 5/55 (9%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 89
          LF++NLP + T+E  +  F Q+    + +L+       +G  F+ +  +  A  A
Sbjct: 5  LFLQNLPEETTKEMLEMLFNQFPGFKEVRLVPR-----RGIAFVEFETEEQATVA 54

This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding. . Length = 72

>gnl|CDD|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding protein MRN1 and similar proteins

 Score = 39.1 bits (91), Expect = 3e-04
 Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 6/67 (8%)

Query: 33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
          G +        + E+E ++   +YG+I   ++L+      K C FIN+ N  +A+ A+  
Sbjct: 8  GNVSDVGDERNLPEKELRKECEKYGEIESIRILRE-----KACAFINFMNIPNAIAALQT 62

Query: 93 SN-KKPY 98
           N KKPY
Sbjct: 63 LNGKKPY 69

This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 82

>gnl|CDD|238239 cd00412, pyrophosphatase, Inorganic pyrophosphatase

 Score = 40.2 bits (95), Expect = 4e-04
 Identities = 9/19 (47%), Positives = 16/19 (84%)

Query: 400 KIFNMVVEIPRWTNAKMEV 418
           ++ N+V+EIP+ +NAK E+
Sbjct: 1   EVVNVVIEIPKGSNAKYEI 19

These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers. Length = 155

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

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 7/58 (12%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           K+++E+ +E F +YG I+   L K       G GF+ + N+  A  A+   N +   G
Sbjct: 12  KVSKEDLEEIFSKYGKILGISLHK-------GYGFVQFDNEEDARAAVAGENGREIAG 62

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

>gnl|CDD|241078 cd12634, RRM2_CELF1_2, RNA recognition motif 2 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 38.9 bits (90), Expect = 4e-04
 Identities = 14/48 (29%), Positives = 25/48 (52%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
           K  E + +  F  +G I + ++L+  DG  +GC F+ +  +  A  AI
Sbjct: 12  KCNENDIRVMFSPFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAI 59

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

 Score = 38.7 bits (90), Expect = 4e-04
 Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK-KPYKGSEN 161
           TE+E +E F  YG + D  ++++   + +GC F+ Y++K  A  AI   N     +G + 
Sbjct: 12  TEKEVEEVFSPYGRVEDIYMMRDEMKQSRGCAFVKYSSKEMAQAAIKALNGVYTMRGCDQ 71

Query: 162 GLISPFHD 169
            LI  F D
Sbjct: 72  PLIVRFAD 79

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

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

 Score = 38.8 bits (91), Expect = 4e-04
 Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADG-KLKGCGFINYANKISAVKAILKS 93
          +++ NLPF +T  +  + F +YG ++   ++K+ +  K KG  FI + ++  A K +   
Sbjct: 4  VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 94 NKK 96
          N K
Sbjct: 64 NNK 66

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|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 38.4 bits (89), Expect = 4e-04
 Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 7/73 (9%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
           LF++NL   +TEE  ++ FGQ+G +   +       KLK   FI++  +  AVKA+ + N
Sbjct: 4   LFVRNLANTVTEEILEKAFGQFGKLERVK-------KLKDYAFIHFDERDGAVKAMEEMN 56

Query: 95  KKPYKGKITEEEF 107
            K  +G+  E  F
Sbjct: 57  GKELEGENIEIVF 69

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

 Score = 38.8 bits (90), Expect = 4e-04
 Identities = 21/61 (34%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILKS 93
          LFI +LP + T+ +  + F  +G++I A++  +    L  C GF++Y N  SA  AI   
Sbjct: 7  LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAM 66

Query: 94 N 94
          N
Sbjct: 67 N 67

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

 Score = 38.9 bits (90), Expect = 4e-04
 Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 1/60 (1%)

Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAI 90
          +  L +  LP  +T+EE K  FG  G+I   +L+++   G+  G GF+NY +   A KAI
Sbjct: 4  KTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 63

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|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins

 Score = 38.8 bits (90), Expect = 4e-04
 Identities = 22/69 (31%), Positives = 41/69 (59%), Gaps = 3/69 (4%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           +LF+ NLP  + + E KE F QYG++++ ++  N+ GKL   GF+ + +    V+ IL +
Sbjct: 5   QLFVGNLPHDVDKSELKEFFQQYGNVVELRI--NSGGKLPNFGFVVFDDS-EPVQKILSN 61

Query: 94  NKKPYKGKI 102
               ++G +
Sbjct: 62  RPIMFRGDV 70

This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript. Length = 80

>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 5/57 (8%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
          RLFI   P    +   ++ F ++G +ID  L+       K  G+  YA++ SA +AI
Sbjct: 1  RLFIVCNPSPPPDYILEDVFCRFGGLIDVYLVPG-----KNYGYAKYADRESAERAI 52

This subfamily corresponds to the RRM4 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 = 68

>gnl|CDD|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

 Score = 38.3 bits (89), Expect = 4e-04
 Identities = 21/51 (41%), Positives = 32/51 (62%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKIS 85
          LF+ NL  K+TEE   E F Q G +I  ++ K+ DGK K   F+N+ +++S
Sbjct: 4  LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVS 54

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

 Score = 38.4 bits (90), Expect = 5e-04
 Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 1/57 (1%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           TEE+ K+ FGQ+G++  A+++ + + G+ +G GF+       A  AI K N   + G
Sbjct: 12  TEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKLNGTDFGG 68

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

 Score = 38.0 bits (89), Expect = 5e-04
 Identities = 15/53 (28%), Positives = 32/53 (60%), Gaps = 1/53 (1%)

Query: 99  KGKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 150
           K  +TEE+ +E+F QYG++   +++ + + GK +G  F+ + +     K +L+
Sbjct: 8   KEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

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

 Score = 38.4 bits (90), Expect = 5e-04
 Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAI 90
          L++  L  ++ E+     F  +GDI D Q+ L     K +G  F+ +     A  AI
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAI 57

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

 Score = 38.1 bits (89), Expect = 5e-04
 Identities = 22/72 (30%), Positives = 42/72 (58%), Gaps = 2/72 (2%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILK 92
           ++F+  L  + TEE+ +E+FG++G+I++ +L +     K +G  FI + ++   VK IL+
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSE-EPVKKILE 59

Query: 93  SNKKPYKGKITE 104
           +      GK  E
Sbjct: 60  TQFHVIGGKKVE 71

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

 Score = 37.8 bits (88), Expect = 6e-04
 Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 1/48 (2%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
            TE+E + HFG+ G I   +++   D GK KG  F+++     A  A+
Sbjct: 10  TTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL 57

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

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

 Score = 38.1 bits (89), Expect = 6e-04
 Identities = 21/63 (33%), Positives = 37/63 (58%), Gaps = 3/63 (4%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLL-KNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
           ITE+E KE F ++G++++ ++  K   G+L   GF+ + +   AV+ IL  NK  Y   +
Sbjct: 15  ITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDP-EAVQKILA-NKPIYFRGD 72

Query: 161 NGL 163
           + L
Sbjct: 73  HRL 75

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

>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 38.2 bits (89), Expect = 6e-04
 Identities = 17/55 (30%), Positives = 28/55 (50%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 89
          L++ NLP  + EE   EHF +YG +   ++L           F+++ +  SA KA
Sbjct: 2  LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVAAFVDFVDIKSAQKA 56

This subfamily corresponds to the RRM1 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. . Length = 75

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

 Score = 37.6 bits (88), Expect = 7e-04
 Identities = 20/58 (34%), Positives = 36/58 (62%), Gaps = 1/58 (1%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            + E+E ++ F + G+I D +L+KN  GK KG  ++ + N+ S  +A LK +++  KG
Sbjct: 10  SVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEA-LKLDRELIKG 66

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

 Score = 37.6 bits (88), Expect = 7e-04
 Identities = 12/62 (19%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 36 FIKNLPFKITEEEFKEHFGQYGDIIDAQLLK-NADGKLKGCGFINYANKISAVKAILKSN 94
          F+  L  K+ E +  E F + G + D ++++     + KG  ++ + ++ S   A+  + 
Sbjct: 3  FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGLTG 62

Query: 95 KK 96
          ++
Sbjct: 63 QR 64

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|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 38.2 bits (88), Expect = 7e-04
 Identities = 14/43 (32%), Positives = 26/43 (60%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGF 77
          L+I NLP  + E+E +     +G +I  ++L+++ G  +G GF
Sbjct: 3  LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGF 45

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|241103 cd12659, RRM2_hnRNPM, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 37.7 bits (87), Expect = 8e-04
 Identities = 17/48 (35%), Positives = 29/48 (60%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
           K+  ++ KE F   G ++ A +L++ DGK +G G + +   I AV+AI
Sbjct: 11  KVGWKKLKEVFSMAGMVVRADILEDKDGKSRGIGTVTFEQPIEAVQAI 58

This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

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

 Score = 37.8 bits (88), Expect = 8e-04
 Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNK 153
           +T++E +  F   G+I   +L+++   G+  G GF+NY +   A KAI   N 
Sbjct: 13  MTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNG 65

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

 Score = 38.1 bits (88), Expect = 8e-04
 Identities = 21/65 (32%), Positives = 38/65 (58%), Gaps = 2/65 (3%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQ-LLKNADGKLKGCGFINYANKISAVKAILKS 93
          L+I  LP  +T+++ ++ F ++G II+++ L+  A G  +G  FI +  +  A +AI   
Sbjct: 3  LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 94 N-KKP 97
          N  KP
Sbjct: 63 NGHKP 67

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|241102 cd12658, RRM1_MYEF2, RNA recognition motif 1 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 37.7 bits (87), Expect = 8e-04
 Identities = 20/69 (28%), Positives = 39/69 (56%), Gaps = 1/69 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHF-GQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
           R+FI N+P+ +  +  K+    + G++   +L K+A+GK +GCG + + ++    KA+  
Sbjct: 1   RVFISNIPYDMKWQAIKDLMREKVGEVTYVELFKDAEGKSRGCGVVEFKDEEFVKKALEV 60

Query: 93  SNKKPYKGK 101
            NK    G+
Sbjct: 61  MNKYDLNGR 69

This subgroup corresponds to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding protein MRN1 and similar proteins

 Score = 38.0 bits (88), Expect = 9e-04
 Identities = 19/56 (33%), Positives = 32/56 (57%), Gaps = 6/56 (10%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN-KKPY 156
           + E+E ++   +YG+I   ++L+      K C FIN+ N  +A+ A+   N KKPY
Sbjct: 19  LPEKELRKECEKYGEIESIRILRE-----KACAFINFMNIPNAIAALQTLNGKKPY 69

This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 82

>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 38.2 bits (88), Expect = 9e-04
 Identities = 15/43 (34%), Positives = 27/43 (62%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGF 77
          L+I NLP  + E+E +     +G +I  ++L++A+G  +G GF
Sbjct: 4  LYISNLPVSMDEQELENMLKPFGHVISTRILRDANGVSRGVGF 46

This subgroup corresponds to the RRM2 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 88

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

 Score = 37.4 bits (87), Expect = 0.001
 Identities = 13/57 (22%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 103 TEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            E++ ++ F ++G++ +  + +    GK KG  ++ + +   AVKA  + + K ++G
Sbjct: 15  KEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKELDGKVFQG 71

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

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILKSNKKPYKG 158
           T+E+F+E    +G +    L+ +      KG GF+ YA+K SA+KA  + + K   G
Sbjct: 12  TDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLDGKQIGG 68

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

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 3/59 (5%)

Query: 97  PYKGKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKK 154
           P+   I EEE ++HF   GD+   +++++   G  KG G++ +  K S   A+  +  K
Sbjct: 8   PFD--IEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNGIK 64

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|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 = 37.5 bits (87), Expect = 0.001
 Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILKSNKKPYKG 158
            E+  ++ F +YG I +  ++K+ + +  +G GF+ + N   A  A++  N K   G
Sbjct: 13  NEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDG 69

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

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
            +T+EE  E F ++G I++  L+K A+       FI +  + +A +A+   N    K  
Sbjct: 14  DVTKEELNERFSRHGKILEVNLIKRANHT-NAFAFIKFEREQAAARAVESENHSMLKNK 71

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 19/48 (39%), Positives = 26/48 (54%), Gaps = 1/48 (2%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
           ++E++ K  F  +G I    L  + + GK KG GFI Y N  SA  AI
Sbjct: 12  LSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAI 59

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

 Score = 37.1 bits (87), Expect = 0.001
 Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYK 157
             E++ +E F  +G I    L K+ + G+ +G  F+ +  +  A +AI K N   Y 
Sbjct: 11  ADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGFGYD 67

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

 Score = 37.8 bits (87), Expect = 0.001
 Identities = 21/49 (42%), Positives = 32/49 (65%), Gaps = 1/49 (2%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 148
           +IT ++ K  F  +G I DA+++K+ A GK KG GF+++ NK  A  AI
Sbjct: 12  EITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI 60

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

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 1/47 (2%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
           TEE+ +E F ++GDI    ++K+ + G+ KG G++ +     A  A+
Sbjct: 13  TEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 59

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 15/43 (34%), Positives = 26/43 (60%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGF 77
          L+I NLP  + E+E +     +G +I  ++L++A G  +G GF
Sbjct: 3  LYISNLPLSMDEQELESMLKPFGQVISTRILRDASGTSRGVGF 45

This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

>gnl|CDD|241101 cd12657, RRM1_hnRNPM, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 37.7 bits (87), Expect = 0.001
 Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQ-YGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
           R FI N+PF +  +  K+   +  G++   +LL +A+GK +GC  + +  + S  KA+  
Sbjct: 1   RAFISNIPFDVKWQSLKDLVKEKVGEVTYVELLMDAEGKSRGCAVVEFKMEESMKKAVEV 60

Query: 93  SNKKPYKGK 101
            NK    G+
Sbjct: 61  LNKHVLNGR 69

This subgroup corresponds to the RRM1 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 76

>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 = 37.2 bits (87), Expect = 0.001
 Identities = 14/50 (28%), Positives = 28/50 (56%), Gaps = 1/50 (2%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANK 83
          ++I +LP    E E +++F Q+G +   +L ++   GK KG  F+ + + 
Sbjct: 2  VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESP 51

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

 Score = 37.6 bits (88), Expect = 0.001
 Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 5/65 (7%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD---GKLKGCGFINYANKISAVKAIL 91
          +F+  +  +  EE+  + F ++G+I +  L  N D   G +KG   I Y  K  A  AI 
Sbjct: 9  IFVTGVHEEAQEEDVHDKFAEFGEIKNLHL--NLDRRTGFVKGYALIEYETKKEAQAAIE 66

Query: 92 KSNKK 96
            N K
Sbjct: 67 GLNGK 71

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

 Score = 37.6 bits (87), Expect = 0.001
 Identities = 20/59 (33%), Positives = 34/59 (57%), Gaps = 1/59 (1%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAIL 91
          +LF+  L   + E +  EHF Q+G +  A+++ +   GK +G GF+ + N  SA KA +
Sbjct: 1  KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAV 59

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 1/65 (1%)

Query: 44  ITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGKI 102
            TE + +E F +YG I   Q++ +   G+ +G GF+ + +   A +A  + N     G+ 
Sbjct: 11  TTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNGMEIDGRR 70

Query: 103 TEEEF 107
              ++
Sbjct: 71  IRVDY 75

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|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 17/58 (29%), Positives = 34/58 (58%), Gaps = 2/58 (3%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA--DGKLKGCGFINYANKISAVKA 89
          ++ ++N+PF+ T +E +E F  +G++   +L K     G  +G GF+++  K  A +A
Sbjct: 2  KILVRNIPFEATVKELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFITKQDAKRA 59

This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 17/72 (23%), Positives = 40/72 (55%), Gaps = 2/72 (2%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILK 92
           ++F+  LP  +TE + +++F Q+G + +  ++ + + K  +G GFI + ++  +V  ++ 
Sbjct: 4   KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESE-DSVDQVVN 62

Query: 93  SNKKPYKGKITE 104
            +     GK  E
Sbjct: 63  EHFHDINGKKVE 74

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

 Score = 37.1 bits (87), Expect = 0.001
 Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 1/68 (1%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKS 93
           L++ +L   +TE    E F   G ++  ++ ++    +  G  ++N+ N   A +A+   
Sbjct: 2   LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 94  NKKPYKGK 101
           N    KGK
Sbjct: 62  NFDVIKGK 69

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

>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 19/56 (33%), Positives = 32/56 (57%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
          L +KNLP  ++ E  +E F  +G +  A ++ +  G+  G G + +A K SA KA+
Sbjct: 2  LTVKNLPQFVSNELLEEAFSMFGQVERAVVIVDDRGRPTGKGIVEFAGKPSARKAL 57

This subgroup corresponds to the RRM2 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. It binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. p54nrb forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner. It also forms a heterodimer with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

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

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 16/47 (34%), Positives = 29/47 (61%), Gaps = 1/47 (2%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 147
           +  + + ++ FGQ+G I+D +++ N  G  KG GF+ +AN   A +A
Sbjct: 11  RFRDPDLRQMFGQFGPILDVEIIFNERGS-KGFGFVTFANSADADRA 56

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

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 15/58 (25%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            T+E+ +E F + G I    ++K+    K +G G++ +A +  A +A+ +  K  + G
Sbjct: 11  TTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEKKKTKFGG 68

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

 Score = 37.0 bits (85), Expect = 0.002
 Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 2/61 (3%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLL-KNADGKLKGCGFINYANKISAVKAILKSN-KKPYKGS 159
           +T++E ++ F QYG II +++L     G  +G GFI +  +I A +AI   N +KP   +
Sbjct: 14  MTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGAA 73

Query: 160 E 160
           E
Sbjct: 74  E 74

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

 Score = 36.6 bits (84), Expect = 0.002
 Identities = 20/48 (41%), Positives = 30/48 (62%), Gaps = 1/48 (2%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAI 148
           +T+EEFK  FG  G+I   +L+++   G+  G GF+NY +   A KAI
Sbjct: 15  MTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAI 62

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

 Score = 36.8 bits (86), Expect = 0.002
 Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 1/52 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSN 152
            TE + +E F +YG I   Q++ +   G+ +G GF+ + +   A +A  + N
Sbjct: 11  TTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLN 62

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|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 8/61 (13%)

Query: 34 RLFI---KNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKA 89
          RLFI   K+    +TE++ +E F  +G+I D  ++K+   K  KG  ++ +A   SA +A
Sbjct: 5  RLFIVCGKS----VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARA 60

Query: 90 I 90
          +
Sbjct: 61 M 61

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|240763 cd12317, RRM4_RBM19_RRM3_MRD1, RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 36.4 bits (85), Expect = 0.002
 Identities = 12/25 (48%), Positives = 18/25 (72%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDI 59
          + +KNLPF  TEEE +E F ++G +
Sbjct: 3  ILVKNLPFGTTEEELRELFEKFGSL 27

This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 72

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

 Score = 37.2 bits (87), Expect = 0.002
 Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 1/52 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKIS 85
          LF+  L +  TE + +  F +YG I   +L+++   GK +G  FI + ++  
Sbjct: 4  LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERD 55

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

 Score = 36.9 bits (86), Expect = 0.002
 Identities = 18/70 (25%), Positives = 39/70 (55%), Gaps = 4/70 (5%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLL--KNADGKLKG--CGFINYANKISAVKAI 90
           L++ NL  K+TEE   + FG++G +   +++  +  + + +   CGF+ + N+  A +A+
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 91  LKSNKKPYKG 100
            + + K   G
Sbjct: 64  DELDGKDVMG 73

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

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 17/68 (25%), Positives = 38/68 (55%), Gaps = 2/68 (2%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILKS 93
           +FI  L ++ T E  +E+F ++G+I +  ++++   K  +G GF+ +++  ++V  +L  
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDP-ASVDKVLAQ 59

Query: 94  NKKPYKGK 101
                 GK
Sbjct: 60  GPHELDGK 67

This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 75

>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 36.6 bits (85), Expect = 0.002
 Identities = 18/55 (32%), Positives = 28/55 (50%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 89
          LF+ NL   ITEEE +  F +YG + D  + +   G+     F+ + N   A +A
Sbjct: 5  LFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNAYAFVKFLNLDMAHRA 59

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

 Score = 37.0 bits (85), Expect = 0.002
 Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILKS 93
          LFI +LP +  +++  + F  +G+++ A++  +    L  C GF++Y N +SA  AI   
Sbjct: 10 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69

Query: 94 N 94
          N
Sbjct: 70 N 70

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|189686 pfam00719, Pyrophosphatase, Inorganic pyrophosphatase

 Score = 37.8 bits (89), Expect = 0.003
 Identities = 7/16 (43%), Positives = 12/16 (75%)

Query: 403 NMVVEIPRWTNAKMEV 418
           N+V+EIP+ +  K E+
Sbjct: 1   NVVIEIPKGSRVKYEI 16

Length = 156

>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 = 36.0 bits (83), Expect = 0.003
 Identities = 12/39 (30%), Positives = 27/39 (69%), Gaps = 1/39 (2%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYAN 140
           T++  +E+FGQ+G++ D  ++++ A G+ +G GF+ +  
Sbjct: 11  TDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKK 49

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

 Score = 36.3 bits (83), Expect = 0.003
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLL-KNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
           +T++E ++ F QYG II +++L     G  +G GFI +  +I A +AI   N +   G+ 
Sbjct: 17  MTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPPGAT 76

Query: 161 NGLISPFHDIP 171
             +   F + P
Sbjct: 77  EPITVKFANNP 87

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

 Score = 36.4 bits (84), Expect = 0.003
 Identities = 19/52 (36%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 99  KGKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAIL 149
           KG + E +  EHF Q+G +  A+++ +   GK +G GF+ + N  SA KA +
Sbjct: 8   KGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAV 59

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|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 = 36.4 bits (84), Expect = 0.003
 Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKS 93
          LFI +LP +  + E  + F  +G++I A++ +  A  + K  GF+++ N  SA  AI   
Sbjct: 7  LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAM 66

Query: 94 N 94
          N
Sbjct: 67 N 67

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|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)

 Score = 36.6 bits (84), Expect = 0.003
 Identities = 18/56 (32%), Positives = 33/56 (58%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
          L +KNL   ++ E  ++ F Q+G +  A ++ +  G+  G GF+ +A K +A KA+
Sbjct: 2  LTVKNLSPVVSNELLEQAFSQFGPVERAVVIVDDRGRPTGKGFVEFAAKPAARKAL 57

This subgroup corresponds to the RRM2 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

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

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 8/75 (10%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDI-IDA-------QLLKNADGKLKGCGFINYANKISA 86
           ++I  LP  +TE+   E FG  G I  D        ++  + + + KG   + Y +  +A
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETEPKGEATVTYDDPSAA 60

Query: 87  VKAILKSNKKPYKGK 101
             AI   N   ++G 
Sbjct: 61  QAAIEWFNGYEFRGN 75

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

>gnl|CDD|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 36.0 bits (84), Expect = 0.003
 Identities = 18/67 (26%), Positives = 36/67 (53%), Gaps = 1/67 (1%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
           +++K  P   T ++ +E F ++G + + ++ ++ D K KG  F+ +  +  A K  L+  
Sbjct: 2   VYVKGFPKDATLDDIQEFFEKFGKVNNIRMRRDLDKKFKGSVFVEFKTEEDA-KKFLEKE 60

Query: 95  KKPYKGK 101
           K  YK K
Sbjct: 61  KLKYKEK 67

This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 72

>gnl|CDD|240727 cd12281, RRM1_TatSF1_like, RNA recognition motif 1 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 36.4 bits (85), Expect = 0.003
 Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 8/55 (14%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIID--------AQLLKNADGKLKGCGFINYA 81
          +++  LP  IT EEF E F + G I +         +L ++ +G LKG     Y 
Sbjct: 4  VYVSGLPLDITVEEFVEVFSKCGIIKEDPETGKPKIKLYRDENGNLKGDALCCYL 58

This subfamily corresponds to the RRM1 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well. . Length = 92

>gnl|CDD|240978 cd12534, RRM_SARFH, RNA recognition motif in Drosophila melanogaster RNA-binding protein cabeza and similar proteins

 Score = 36.2 bits (84), Expect = 0.003
 Identities = 25/75 (33%), Positives = 35/75 (46%), Gaps = 9/75 (12%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDI-IDAQLLK--------NADGKLKGCGFINYANKIS 85
           +F+ NLP   TE++  EHFG  G I ID +  K           G+ KG   + Y +  +
Sbjct: 1   VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 86  AVKAILKSNKKPYKG 100
           A  AI   N K + G
Sbjct: 61  ASAAIEWFNNKDFMG 75

This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

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

 Score = 36.2 bits (83), Expect = 0.003
 Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 1/60 (1%)

Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 90
          R  L +  LP  +T++E +  F   G++  A+L+++   G   G GF+NY N   A +AI
Sbjct: 1  RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAI 60

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

 Score = 36.0 bits (84), Expect = 0.004
 Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 6/54 (11%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLK------GCGFINYANKISAVKAI 148
           K TEE  K+HF + G +    + K  D K        G GF+ + +K +A KA+
Sbjct: 11  KTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKAL 64

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

 Score = 36.0 bits (84), Expect = 0.004
 Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           + TE+E +  F ++G + +  L+K+   G+ +G GF+ + +   A  AI   N K  +G
Sbjct: 12  RTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDLNGKELEG 70

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

 Score = 36.1 bits (84), Expect = 0.004
 Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 4/58 (6%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKG----CGFINYANKISAVKAILKSNKK 154
           ++TE    + F +YG I     L +  G LKG      F+ +  K  A KA+   N K
Sbjct: 10  RLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNGK 67

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

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 21/61 (34%), Positives = 37/61 (60%), Gaps = 2/61 (3%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSN-KKPYKGS 159
           ++++E ++ F QYG II +++L +   G  +G GFI +  +I A +AI   N +KP   +
Sbjct: 13  MSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGLNGQKPLGAA 72

Query: 160 E 160
           E
Sbjct: 73  E 73

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

 Score = 35.8 bits (83), Expect = 0.004
 Identities = 15/48 (31%), Positives = 28/48 (58%), Gaps = 1/48 (2%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 148
           +T+EE +  F   G I   +++++   G+  G GF++Y ++  A KAI
Sbjct: 12  MTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAI 59

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|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 36.1 bits (83), Expect = 0.004
 Identities = 18/60 (30%), Positives = 32/60 (53%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
          +F+  +P  + E+E    F   G I + +L+ + DGK +G  F+ Y  K  A +A+ + N
Sbjct: 4  VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFDGKNRGYAFVMYTQKHEAKRAVRELN 63

This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 35.7 bits (82), Expect = 0.004
 Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKA 89
          L I NLP   T+++F+E    +G++    L+ +   G  KG GF+ Y  K SA +A
Sbjct: 2  LCIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARA 57

This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in Mei2-like proteins and terminal EAR1-like proteins

 Score = 35.7 bits (83), Expect = 0.004
 Identities = 16/69 (23%), Positives = 34/69 (49%), Gaps = 4/69 (5%)

Query: 33  GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
           G L + NL   I+++E +  F Q+G++ D   ++    +     F+ + +  +A  A+  
Sbjct: 2   GTLLVFNLDSPISDQELRSLFSQFGEVKD---IRETPLR-PSQKFVEFYDIRAAEAALDA 57

Query: 93  SNKKPYKGK 101
            N +P+ G 
Sbjct: 58  LNGRPFLGG 66

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	451
KOG1626|consensus	279		100.0
PLN02707	267	Soluble inorganic pyrophosphatase	100.0
PRK00642	205	inorganic pyrophosphatase; Provisional	100.0
PLN02373	188	soluble inorganic pyrophosphatase	100.0
PRK01250	176	inorganic pyrophosphatase; Provisional	100.0
PRK02230	184	inorganic pyrophosphatase; Provisional	100.0
cd00412	155	pyrophosphatase Inorganic pyrophosphatase. These e	100.0
PF00719	156	Pyrophosphatase: Inorganic pyrophosphatase; InterP	100.0
COG0221	171	Ppa Inorganic pyrophosphatase [Energy production a	100.0
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.9
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.88
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.87
KOG0144|consensus	510		99.87
KOG0148|consensus	321		99.85
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.84
KOG0145|consensus	360		99.83
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.83
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.82
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.82
KOG0117|consensus	506		99.81
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.76
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.76
KOG0145|consensus	360		99.75
KOG0124|consensus	544		99.73
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.71
KOG0131|consensus	203		99.7
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.7
KOG0123|consensus	369		99.7
KOG0123|consensus	369		99.69
KOG0127|consensus	678		99.69
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.68
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.66
KOG0127|consensus	678		99.64
KOG0109|consensus	346		99.62
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.55
KOG0146|consensus	371		99.54
KOG1626|consensus	279		99.52
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.49
KOG0144|consensus	510		99.49
KOG0110|consensus	725		99.48
KOG0148|consensus	321		99.47
KOG4205|consensus	311		99.46
KOG0147|consensus	549		99.45
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.44
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.43
PLN02707	267	Soluble inorganic pyrophosphatase	99.42
KOG0105|consensus	241		99.42
KOG0147|consensus	549		99.33
KOG1548|consensus	382		99.31
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.28
KOG0149|consensus	247		99.28
KOG4212|consensus	608		99.24
KOG0126|consensus	219		99.19
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.18
KOG0122|consensus	270		99.17
KOG4206|consensus	221		99.12
smart00362	72	RRM_2 RNA recognition motif.	99.11
KOG0125|consensus	376		99.1
PRK00642	205	inorganic pyrophosphatase; Provisional	99.09
PLN03120	260	nucleic acid binding protein; Provisional	99.09
KOG0106|consensus	216		99.09
KOG0107|consensus	195		99.06
KOG0113|consensus	335		99.06
KOG0124|consensus	544		99.05
KOG4207|consensus	256		99.02
PLN03213	759	repressor of silencing 3; Provisional	99.02
PLN02373	188	soluble inorganic pyrophosphatase	99.02
KOG4211|consensus	510		99.01
KOG0114|consensus	124		99.01
smart00360	71	RRM RNA recognition motif.	99.01
PLN03121	243	nucleic acid binding protein; Provisional	99.0
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.0
KOG0121|consensus	153		98.98
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.96
KOG1457|consensus	284		98.92
KOG0120|consensus	500		98.92
KOG0108|consensus	435		98.86
KOG0111|consensus	298		98.8
KOG1456|consensus	494		98.8
KOG4454|consensus	267		98.77
KOG0110|consensus	725		98.77
KOG0130|consensus	170		98.73
smart00361	70	RRM_1 RNA recognition motif.	98.73
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	98.7
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	98.68
KOG4208|consensus	214		98.66
KOG0149|consensus	247		98.66
KOG0122|consensus	270		98.57
smart00361	70	RRM_1 RNA recognition motif.	98.55
KOG0117|consensus	506		98.53
KOG0146|consensus	371		98.49
KOG0128|consensus	881		98.43
KOG0129|consensus	520		98.43
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.42
KOG0415|consensus	479		98.41
KOG0131|consensus	203		98.4
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	98.39
KOG1190|consensus	492		98.36
KOG0132|consensus	894		98.33
smart00360	71	RRM RNA recognition motif.	98.33
KOG4205|consensus	311		98.29
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.29
KOG0109|consensus	346		98.25
KOG4207|consensus	256		98.22
KOG0125|consensus	376		98.22
PRK01250	176	inorganic pyrophosphatase; Provisional	98.21
KOG1365|consensus	508		98.18
smart00362	72	RRM_2 RNA recognition motif.	98.17
KOG0226|consensus	290		98.14
PLN03120	260	nucleic acid binding protein; Provisional	98.13
KOG4661|consensus	940		98.11
KOG0533|consensus	243		98.11
KOG4211|consensus	510		98.07
KOG0153|consensus	377		98.06
KOG0107|consensus	195		98.02
KOG0113|consensus	335		98.0
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	97.99
PLN03121	243	nucleic acid binding protein; Provisional	97.97
PLN03213	759	repressor of silencing 3; Provisional	97.97
KOG1190|consensus	492		97.96
KOG4208|consensus	214		97.96
KOG0120|consensus	500		97.95
KOG0151|consensus	877		97.92
KOG0226|consensus	290		97.89
KOG0126|consensus	219		97.84
KOG0116|consensus	419		97.84
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.84
KOG4210|consensus	285		97.83
KOG4212|consensus	608		97.82
COG0724	306	RNA-binding proteins (RRM domain) [General functio	97.8
KOG0121|consensus	153		97.8
COG0221	171	Ppa Inorganic pyrophosphatase [Energy production a	97.76
KOG4660|consensus	549		97.71
KOG0111|consensus	298		97.69
KOG0130|consensus	170		97.66
KOG0112|consensus	975		97.63
KOG4209|consensus	231		97.6
KOG0108|consensus	435		97.56
KOG1456|consensus	494		97.55
KOG0415|consensus	479		97.31
KOG0114|consensus	124		97.23
KOG0132|consensus	894		97.05
cd00412	155	pyrophosphatase Inorganic pyrophosphatase. These e	97.01
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.98
KOG2193|consensus	584		96.97
KOG4206|consensus	221		96.96
KOG0105|consensus	241		96.94
KOG1457|consensus	284		96.92
KOG0153|consensus	377		96.84
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.66
KOG4661|consensus	940		96.65
KOG1365|consensus	508		96.41
KOG3152|consensus	278		96.19
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	96.18
KOG1995|consensus	351		96.12
KOG4676|consensus	479		96.1
KOG2314|consensus	698		96.07
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	95.88
KOG1548|consensus	382		95.85
KOG4210|consensus	285		95.79
KOG0106|consensus	216		95.44
KOG0533|consensus	243		95.33
KOG4849|consensus	498		95.25
KOG0129|consensus	520		95.18
KOG0115|consensus	275		95.16
KOG2314|consensus	698		95.07
KOG1855|consensus	484		95.05
KOG0116|consensus	419		94.85
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	94.82
KOG4454|consensus	267		94.7
KOG4307|consensus	944		94.57
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	94.25
KOG4307|consensus	944		94.25
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	94.06
KOG4209|consensus	231		93.86
KOG0128|consensus	881		93.82
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	93.7
KOG2068|consensus	327		93.61
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	93.57
KOG4660|consensus	549		93.36
KOG0151|consensus	877		93.36
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	93.09
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	92.51
KOG2202|consensus	260		92.33
KOG0115|consensus	275		91.83
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	90.18
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	89.92
KOG1996|consensus	378		88.34
KOG1996|consensus	378		87.6
KOG2202|consensus	260		86.8
KOG0112|consensus	975		86.67
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	84.49
KOG0804|consensus	493		81.04
COG5175	480	MOT2 Transcriptional repressor [Transcription]	80.34

>KOG1626|consensus

Probab=100.00  E-value=1.1e-70  Score=512.76  Aligned_cols=223  Identities=55%  Similarity=0.908  Sum_probs=215.4

Q ss_pred             HHHHhcCCCcccCCCCCc-ccccccCCccccccccccceeeccCCCCccccccccCCCCCCCcccccCCeeeeecccCCC
Q psy300          146 KAILKSNKKPYKGSENGL-ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPH  224 (451)
Q Consensus       146 ~Ai~~ln~riy~~~~~G~-iSp~hdiPl~v~~~p~~vn~vvEIPrgS~~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~  224 (451)
                      .+.+++++++|+...+|+ +|+|||+|+... ....++|++|||||+++|||+++++.+|||+||.++|++||++++||+
T Consensus         9 g~~~s~~~rvy~~~~~~~~iS~fhdipl~a~-~~~~~nmvvEiPrwtnak~EIs~k~~~~pikqD~KkGklR~v~n~fp~   87 (279)
T KOG1626|consen    9 GKKYSLDYRVYFPKLNGRIISPFHDIPLAAH-PWHDLNMVVEIPRWTNAKMEISKKEPFNPIKQDKKKGKLRFVRNLFPY   87 (279)
T ss_pred             cccCCccceeeecCCCCccccccccCccccC-ccccEeecccccceeeeEEEEeccCCCCcceeeccCCceEEEEecccc
Confidence            456789999999999997 999999999986 468899999999999999999999999999999999999999999999


Q ss_pred             CCCccccCCCCccCCCCCCCCcCCCCCCCCCcceEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecCCcccc
Q psy300          225 HGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAA  304 (451)
Q Consensus       225 ~~yp~nYG~iP~T~~~p~~~~~~~~~~~D~DPlD~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~d~~~~  304 (451)
                      .+||||||||||||+||++.++.|++.|||||||||+||+.+..+|++++||+||+|+|||+||+|||||||.++||+++
T Consensus        88 ~gYiwNYGalPqTwedP~~~~~~t~~~gDnDPiDV~eIg~~~~~~G~vl~vKvLG~malIDeGE~DwKiIAIdvnDP~A~  167 (279)
T KOG1626|consen   88 KGYIWNYGALPQTWEDPNHVDPETKAKGDNDPIDVLEIGQEPVLPGCVLQVKVLGLMALIDEGETDWKIIAIDVNDPLAS  167 (279)
T ss_pred             cccccccccCcccccCCCcccccccccCCCCcceeeEecccccccccEEEEEeeeeeecccCCCccceEEEEECCCcchh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCcccccccCcchHHHHHHHhhhccCCCCCcccccCCCcchhh---hhhhHHHHHHHHHHhhcccc
Q psy300          305 KLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENVLNTRVEGES---SQGFIPGCRGRTEQVVSSRL  369 (451)
Q Consensus       305 ~i~~~~d~~~~~p~~~~~i~~~F~~yk~~~gk~~~~~~~~~~~~~---~~~~i~~~~~~~~~~i~~~~  369 (451)
                      .+|+|+||++++||+|++|++|||.||.||||+.|.|+|+|++..   |.++|++||+.|+.+|.+.+
T Consensus       168 ~~ndi~DV~~~~Pg~L~~tr~wFr~YKiPdGKpeN~faf~~~f~n~~~A~~iIk~t~d~w~~li~~~~  235 (279)
T KOG1626|consen  168 EYNDIEDVEKLFPGLLEATRRWFRDYKIPDGKPENKFAFVGDFLNKKFALDIIKETHDLWAALIKGKL  235 (279)
T ss_pred             hhccHHHHHHhCcchHHHHHHHHHHcCCCCCCCccchhhcccccChHHHHHHHHHHHHHHHHHHhccc
Confidence            999999999999999999999999999999999999999998875   58999999999999999876

>PLN02707 Soluble inorganic pyrophosphatase

Probab=100.00  E-value=5.4e-67  Score=502.59  Aligned_cols=217  Identities=47%  Similarity=0.836  Sum_probs=204.1

Q ss_pred             HHHHhcCCCcccCCCCCc-ccccccCCccccccccccceeeccCCCCccccccccCCCCCCCcccccCCeeeeecccCCC
Q psy300          146 KAILKSNKKPYKGSENGL-ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPH  224 (451)
Q Consensus       146 ~Ai~~ln~riy~~~~~G~-iSp~hdiPl~v~~~p~~vn~vvEIPrgS~~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~  224 (451)
                      .+..++++|+||...+|. +|+|||+|++  ..+..+|++||||+||++|||+++++++|||+||.++|++|+    ||+
T Consensus        38 G~~~t~~~r~~~~~~~g~~~spwHdIpl~--~~~~~vn~VVEIPrgs~~KyEidk~~~~npi~qD~~~g~lr~----yP~  111 (267)
T PLN02707         38 GEAETLDYRVFFSDGSGKKVSPWHDIPLH--AGDGTFNFVVEIPKETSAKMEVATDEPFTPIKQDTKKGKLRD----YPY  111 (267)
T ss_pred             cCCCCcceEEEEECCCCCccCchhcCCCC--CCCCEEEEEEEECCCCceeEEECccCCCCCEEEeeecCceEE----CCC
Confidence            456788999999998898 9999999998  357899999999999999999999999999999999999996    677


Q ss_pred             CCCccccCCCCccCCCCCCCCcCCC-CCCCCCcceEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecCCccc
Q psy300          225 HGYIWNYGALPQTWENPDETDAHTG-QKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNA  303 (451)
Q Consensus       225 ~~yp~nYG~iP~T~~~p~~~~~~~~-~~~D~DPlD~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~d~~~  303 (451)
                       +||||||||||||+||++.++.++ ++|||||||||||++.++.||+|++|||||+|+|+|+||+|||||||+++||+|
T Consensus       112 -~~~~NYGfIPqTwedp~~~~~~~~~l~gDgDPLDVlvi~~~~~~pG~Vv~vR~IGvL~miDeGE~D~KIIaV~~~Dp~~  190 (267)
T PLN02707        112 -NINWNYGLLPQTWEDPTHANPEVEGAFGDNDPVDVVEIGERAAKIGEVLKVKPLGVLAMIDEGELDWKVVAISADDPKA  190 (267)
T ss_pred             -cCccccccccccccCcccccccccccCCCCCccEEEEecCCCcCCccEEEEEEeEEEEEEeCCCCCCEEEEEECCCCcc
Confidence             999999999999999999998876 999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCcccccccCcchHHHHHHHhhhccCCCCCcccccC----CCcchhhhhhhHHHHHHHHHHhhccccC
Q psy300          304 AKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENVLN----TRVEGESSQGFIPGCRGRTEQVVSSRLE  370 (451)
Q Consensus       304 ~~i~~~~d~~~~~p~~~~~i~~~F~~yk~~~gk~~~~~~----~~~~~~~~~~~i~~~~~~~~~~i~~~~~  370 (451)
                      ++|+|++||++++||++++|+|||++||.++||++|+|+    |.|+ +.|+++|++||++|+++++++..
T Consensus       191 ~~i~di~Dv~~~~pg~l~~I~~fF~~YK~~eGK~~n~~~~~~~~~~~-~~A~~vI~e~~~~y~~l~~~~~~  260 (267)
T PLN02707        191 SLVNDVDDVEKHFPGTLTAIRDWFRDYKIPDGKPANKFGLDNKPMDK-DYALKVIEETNEAWAKLVKRSIP  260 (267)
T ss_pred             cccCChhHhhhhhhhHHHHHHHHHHHhcCCCCCceeeccccCCcCCH-HHHHHHHHHHHHHHHHHhccCCC
Confidence            999999999999999999999999999999999999986    5654 56799999999999999998763

>PRK00642 inorganic pyrophosphatase; Provisional

Probab=100.00  E-value=4.8e-56  Score=414.39  Aligned_cols=185  Identities=23%  Similarity=0.346  Sum_probs=169.7

Q ss_pred             ccccccCCccccccccccceeeccCCCCccccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccCCCCCC
Q psy300          164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDE  243 (451)
Q Consensus       164 iSp~hdiPl~v~~~p~~vn~vvEIPrgS~~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~~~p~~  243 (451)
                      +|+||++|++.+ .+..+++++|||+||++|||+++           ++|.+++++.++.++.||||||||||||+||++
T Consensus         9 ~spwhdi~~~~~-~~~~vn~VIEIP~gs~~KyE~dk-----------~~g~~~ldr~l~~~~~yP~nYGfIPqT~~dp~~   76 (205)
T PRK00642          9 AHPWHGLSLGPD-APESVCCYIEITPFDTVKYELDK-----------ATGYLKVDRPQKFSNFCPALYGFIPRTYCGDLS   76 (205)
T ss_pred             cCccccCCCCCC-CCCEEEEEEEECCCCCeeEEEec-----------CCCceEEeeecccCCcCCcccCcCcccccCccc
Confidence            799999999753 47889999999999999999986           568888999999999999999999999999987


Q ss_pred             CCcC------CCCCCCCCcceEEEeccccCCCccE-EEEEEeeeeeeecCCCccceEEEEecCCccccCCCCcccccccC
Q psy300          244 TDAH------TGQKGDGDPIDVLEIGERIAKRGEI-IQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHF  316 (451)
Q Consensus       244 ~~~~------~~~~~D~DPlD~~~~~~~~~~~G~v-~~vr~lG~l~~~d~~e~D~Kii~v~~~d~~~~~i~~~~d~~~~~  316 (451)
                      .+..      ++++|||||||||||++.++.||++ ++|||||+|+|+|+||+|||||||+++||+|++|++++||++  
T Consensus        77 ~~~~~~~~~~~~~~gDgDPLDvlvl~~~~~~~G~v~i~~R~iG~l~miD~ge~D~KIiaV~~~Dp~~~~i~dl~Dl~~--  154 (205)
T PRK00642         77 GKLSGEQSGREDIKGDGDPLDICVLTEKNITHGNILLQARPIGGLRMIDGGEADDKIIAVLEDDLVYGEIKDISECPG--  154 (205)
T ss_pred             ccccccccccccCCCCCCceEEEEecCCCcCCCceEEEEEEeEEEEEecCCCccceEEEEECCCCccccCCChHHCCH--
Confidence            7643      5788999999999999999999996 799999999999999999999999999999999999999986  


Q ss_pred             cchHHHHHHHhhhccCCCCCc---ccccCCCcchhhhhhhHHHHHHHHHHh
Q psy300          317 PGYLKATNEWFKIYKIPDGKP---ENVLNTRVEGESSQGFIPGCRGRTEQV  364 (451)
Q Consensus       317 p~~~~~i~~~F~~yk~~~gk~---~~~~~~~~~~~~~~~~i~~~~~~~~~~  364 (451)
                       +++++|+|||++||.++||+   +.+.+|.|. ++|+++|++||++|+++
T Consensus       155 -~~l~~I~~fF~~YK~legk~~k~~~~~g~~~~-~~A~~vI~~~~~~y~~~  203 (205)
T PRK00642        155 -TLLDRLQHYFLTYKATPGELIKGVEIVGIYGK-EEAQKVIQLAHEDYANK  203 (205)
T ss_pred             -HHHHHHHHHHHHHcCcccCCCCeEEECCCcCH-HHHHHHHHHHHHHHHHh
Confidence             59999999999999999755   678899974 77899999999999984

>PLN02373 soluble inorganic pyrophosphatase

Probab=100.00  E-value=3e-54  Score=396.34  Aligned_cols=176  Identities=27%  Similarity=0.427  Sum_probs=162.7

Q ss_pred             ccccccCCccccccccccceeeccCCCCccccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccCCCCCC
Q psy300          164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDE  243 (451)
Q Consensus       164 iSp~hdiPl~v~~~p~~vn~vvEIPrgS~~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~~~p~~  243 (451)
                      +|+||++|++.. .+..+++++|||+||++|||++++           +|.++.++.++.++.||||||||||||     
T Consensus         9 ~~~whdi~~~~~-~~~~v~vVIEIP~gs~~KyE~dk~-----------~g~i~~Dr~l~~~~~yP~nYGfIP~T~-----   71 (188)
T PLN02373          9 AHPWHDLEIGPG-APAIFNCVVEITKGSKVKYELDKK-----------TGLIKVDRVLYSSVVYPHNYGFIPRTL-----   71 (188)
T ss_pred             CCccccCCCCCC-CCCEEEEEEEECCCCCeeEEEccC-----------CCCEEEeeecccCCcCCcccccccccc-----
Confidence            789999999754 578899999999999999999874           455556667778899999999999999     


Q ss_pred             CCcCCCCCCCCCcceEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecCCccccCCCCcccccccCcchHHHH
Q psy300          244 TDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKAT  323 (451)
Q Consensus       244 ~~~~~~~~~D~DPlD~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~d~~~~~i~~~~d~~~~~p~~~~~i  323 (451)
                             +|||||||+|||++.++.||++++|||||+|+|+|+||+|||||||+++||+|++|++++||++   +++++|
T Consensus        72 -------~~DgDPLDvlvl~~~~~~~G~vi~~R~iG~l~m~D~ge~D~KiIaV~~~dp~~~~i~dl~Dl~~---~~l~~I  141 (188)
T PLN02373         72 -------CEDNDPLDVLVLMQEPVLPGCFLRARAIGLMPMIDQGEKDDKIIAVCADDPEYRHYTDIKELPP---HRLAEI  141 (188)
T ss_pred             -------cCCCCccEEEEecCCCCCCceEEEEEEEEEEEEeeCCCCCCeEEEEECCCcccccCCChHHCCH---HHHHHH
Confidence                   7999999999999999999999999999999999999999999999999999999999999975   599999


Q ss_pred             HHHhhhccCCCCCcccccCCCcchhhhhhhHHHHHHHHHHhhcc
Q psy300          324 NEWFKIYKIPDGKPENVLNTRVEGESSQGFIPGCRGRTEQVVSS  367 (451)
Q Consensus       324 ~~~F~~yk~~~gk~~~~~~~~~~~~~~~~~i~~~~~~~~~~i~~  367 (451)
                      +|||++||.++||++++.+|.|. ++|+++|++||++|++++..
T Consensus       142 ~~fF~~YK~legK~v~v~g~~~~-~~A~~~I~~~~~~y~~~~~~  184 (188)
T PLN02373        142 RRFFEDYKKNENKEVAVNDFLPA-EAAIEAIQYSMDLYAEYIVE  184 (188)
T ss_pred             HHHHHHhcccCCCeEEeCCccCH-HHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999995 78899999999999987654

>PRK01250 inorganic pyrophosphatase; Provisional

Probab=100.00  E-value=1.6e-52  Score=382.02  Aligned_cols=170  Identities=28%  Similarity=0.389  Sum_probs=158.9

Q ss_pred             ccccCCccccccccccceeeccCCCCc-cccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccCCCCCCC
Q psy300          166 PFHDIPLYSNVKDKIFNMVVEIPRWTN-AKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDET  244 (451)
Q Consensus       166 p~hdiPl~v~~~p~~vn~vvEIPrgS~-~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~~~p~~~  244 (451)
                      .||++|.+. ..+..+++++|||+||+ +|||+++           ++|.++++|.++.++.||||||||||||      
T Consensus         2 ~~~~l~~~~-~~~~~v~vvvEIPkgs~~~KyE~d~-----------~~g~~~~dR~l~~~~~yP~nYGfIP~T~------   63 (176)
T PRK01250          2 SLNKIPAGK-DLPEDINVIIEIPANSDPIKYEVDK-----------ESGALFVDRFLYTAMFYPCNYGFIPHTL------   63 (176)
T ss_pred             ChhhCCCCC-CCCCEEEEEEEeCCCCCceeEEEec-----------CCCCEEEeeccCCCCcCCcCcccCCCcc------
Confidence            478888854 56899999999999999 8999986           5788899999999999999999999999      


Q ss_pred             CcCCCCCCCCCcceEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecC--CccccCCCCcccccccCcchHHH
Q psy300          245 DAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVN--DPNAAKLNDVADIETHFPGYLKA  322 (451)
Q Consensus       245 ~~~~~~~~D~DPlD~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~--d~~~~~i~~~~d~~~~~p~~~~~  322 (451)
                            +|||||||+|||++.++.||++++|||||+|+|+|+||+|||||||+++  ||++++|++++||++   +++++
T Consensus        64 ------~~DgDPLDvlvl~~~~~~~G~vv~~r~iG~l~m~D~ge~D~KiiaV~~~~~dp~~~~i~dl~dl~~---~~l~e  134 (176)
T PRK01250         64 ------SLDGDPVDVLVVTPYPLVPGSVIRCRPVGVLKMEDESGEDAKIIAVPHDKLSPEYDHIKDVNDLPE---LLKAQ  134 (176)
T ss_pred             ------cCCCCceEEEEecCCCCCCceEEEEEEEEEEEeecCCCCCCeEEEEECCCCCccccccCChHHCCH---HHHHH
Confidence                  6999999999999999999999999999999999999999999999998  799999999999986   49999


Q ss_pred             HHHHhhhccCCC-CCcccccCCCcchhhhhhhHHHHHHHHHH
Q psy300          323 TNEWFKIYKIPD-GKPENVLNTRVEGESSQGFIPGCRGRTEQ  363 (451)
Q Consensus       323 i~~~F~~yk~~~-gk~~~~~~~~~~~~~~~~~i~~~~~~~~~  363 (451)
                      |+|||++||.++ ||++++.+|.|+ ++|+++|++||++|++
T Consensus       135 I~~fF~~YK~le~gk~~~v~g~~~~-~~A~~~I~~~~~~y~~  175 (176)
T PRK01250        135 IKHFFEHYKDLEKGKWVKVEGWGGA-EEAKAEIVEAIERAKK  175 (176)
T ss_pred             HHHHHHHhcCCCCCCCEEecCccCH-HHHHHHHHHHHHHHhc
Confidence            999999999997 999999999985 7889999999999975

>PRK02230 inorganic pyrophosphatase; Provisional

Probab=100.00  E-value=1.9e-50  Score=369.07  Aligned_cols=159  Identities=26%  Similarity=0.375  Sum_probs=151.3

Q ss_pred             cccceeeccCCCCccccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccCCCCCCCCcCCCCCCCCCcce
Q psy300          179 KIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPID  258 (451)
Q Consensus       179 ~~vn~vvEIPrgS~~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~~~p~~~~~~~~~~~D~DPlD  258 (451)
                      ..++++||||+||++|||+++           ++|.+++++.+++++.||+|||||||||            +|||||||
T Consensus         3 ~~vnvvIEIP~gs~~KyE~d~-----------~~g~i~~DR~l~~~~~YP~NYGfIP~Tl------------~~DGDPLD   59 (184)
T PRK02230          3 KIIEVTIEIPKGSNIKYEYDR-----------KTNKIVVDRILRGDFVYPANYGFIKEAL------------DWDGDELD   59 (184)
T ss_pred             cEEEEEEEECCCCCeeEEEec-----------CCCCEEEEeecCCCCCCCcCcccCCCcc------------CCCCCceE
Confidence            458999999999999999975           6899999999999999999999999999            69999999


Q ss_pred             EEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecCCccccCCCCcccccccCcchHHHHHHHhhhccCCCCCcc
Q psy300          259 VLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPE  338 (451)
Q Consensus       259 ~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~d~~~~~i~~~~d~~~~~p~~~~~i~~~F~~yk~~~gk~~  338 (451)
                      ||||++.++.||++++|||||+|+|+|+||.|||||||+.+||.+++|++++||+++   ++++|+|||++||.++||++
T Consensus        60 vlvl~~~~~~pG~vi~~r~IGvl~m~D~ge~D~KIIaV~~~dp~~~~i~di~Dlp~~---~l~~I~~fF~~YK~legk~~  136 (184)
T PRK02230         60 VLVYSDQKFLPGTVLNARIIGAMKMIDDGETDTKLIAVHDDDYRLDHINSLKDLPQH---WLDEIEYFFSNYKNWKRKGI  136 (184)
T ss_pred             EEEECCCCCCCccEEEEEEEEEEEeccCCCcCcEEEEEECCCCChhhcCChHHCCHH---HHHHHHHHHHHhcCCCCCCe
Confidence            999999999999999999999999999999999999999999999999999999976   89999999999999999987


Q ss_pred             c-ccCCCcchhhhhhhHHHHHHHHHHh
Q psy300          339 N-VLNTRVEGESSQGFIPGCRGRTEQV  364 (451)
Q Consensus       339 ~-~~~~~~~~~~~~~~i~~~~~~~~~~  364 (451)
                      + +.||.|+ .+|.++|++|+++|+++
T Consensus       137 ~~v~g~~~~-~~A~~~I~~~~~~y~~~  162 (184)
T PRK02230        137 TKVKGFEDE-KWALKEYKECVELMKKY  162 (184)
T ss_pred             EEeCCccCH-HHHHHHHHHHHHHHHHc
Confidence            5 8999985 78899999999999986

>cd00412 pyrophosphatase Inorganic pyrophosphatase

Probab=100.00  E-value=1.3e-48  Score=349.76  Aligned_cols=153  Identities=40%  Similarity=0.716  Sum_probs=141.4

Q ss_pred             ccceeeccCCCCccccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccCCCCCCCCcCCCCCCCCCcceE
Q psy300          180 IFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDV  259 (451)
Q Consensus       180 ~vn~vvEIPrgS~~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~~~p~~~~~~~~~~~D~DPlD~  259 (451)
                      .+++++|||+||++|||++++           +|.++.+|.++.++.||+|||||||||            ++||||||+
T Consensus         2 ~v~vvIEIP~gs~~KyE~d~~-----------~g~i~~DR~l~~~~~yP~nYGfiP~T~------------~~DgDPlDv   58 (155)
T cd00412           2 VVNVVIEIPKGSNAKYEIDKE-----------TGPIKVDRFLYSSMGYPWNYGFIPQTL------------EDDGDPLDV   58 (155)
T ss_pred             EEEEEEEECCCCceeEEEccC-----------CCceeeccccccCCcCcccccccCCcc------------cCCCCceEE
Confidence            478999999999999999874           455566677777899999999999999            589999999


Q ss_pred             EEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecCCccccCCCCcccccccCcchHHHHHHHhhhccCCCC-Ccc
Q psy300          260 LEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDG-KPE  338 (451)
Q Consensus       260 ~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~d~~~~~i~~~~d~~~~~p~~~~~i~~~F~~yk~~~g-k~~  338 (451)
                      |||++.++.||++++||+||+|+|+|+||+|||||||+.+||+|++|++++||++   +++++|+|||++||.++| |++
T Consensus        59 lvl~~~~~~~G~~~~~r~iG~l~m~D~ge~D~KiiaV~~~dp~~~~i~~l~Dl~~---~~l~~I~~fF~~YK~le~~k~~  135 (155)
T cd00412          59 LVIGEEPLFPGSVIRVRPLGVLKMIDEGETDWKVIAVPVDDPRYSHINDISDVPP---HLLDEIKHFFEHYKDLEGKKEV  135 (155)
T ss_pred             EEEcCCCCCCeeEEEEEEEEEEEeccCCCccceEEEeeCCCcccccCCChHHCCH---HHHHHHHHHHHHhcccCCCCce
Confidence            9999999999999999999999999999999999999999999999999999985   599999999999999997 789


Q ss_pred             cccCCCcchhhhhhhHHHHHH
Q psy300          339 NVLNTRVEGESSQGFIPGCRG  359 (451)
Q Consensus       339 ~~~~~~~~~~~~~~~i~~~~~  359 (451)
                      .+.+|.|+ ++|+++|++||+
T Consensus       136 ~~~g~~~~-~~A~~~I~~~~~  155 (155)
T cd00412         136 KVAGWKDK-EEALKIIKESIE  155 (155)
T ss_pred             EECcCcCH-HHHHHHHHHHhC
Confidence            99999985 788999999984

These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers.

>PF00719 Pyrophosphatase: Inorganic pyrophosphatase; InterPro: IPR008162 Inorganic pyrophosphatase (3

Probab=100.00  E-value=1.6e-48  Score=351.19  Aligned_cols=155  Identities=34%  Similarity=0.559  Sum_probs=137.2

Q ss_pred             ceeeccCCCCccccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccCCCCCCCCcCCCCCCCCCcceEEE
Q psy300          182 NMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLE  261 (451)
Q Consensus       182 n~vvEIPrgS~~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~~~p~~~~~~~~~~~D~DPlD~~~  261 (451)
                      |+++|||+||++|||++++           +|.++.++.++.++.||+|||||||||            +||||||||||
T Consensus         1 n~viEIP~gs~~KyE~d~~-----------~~~~~idr~~~~~~~yP~NYGfIP~T~------------~~DGDPLDvlv   57 (156)
T PF00719_consen    1 NVVIEIPKGSRAKYEYDKE-----------TGLNPIDRPLYSSMPYPFNYGFIPQTL------------GGDGDPLDVLV   57 (156)
T ss_dssp             EEEEEE-TTSSEEEEEETT-----------TTEEEEEEE-SSSBS-SSEEEEETTEE------------BTTSSCEEEEE
T ss_pred             CEEEEECCCCCeeEEECCC-----------CCCccceeccccCcCCcccccccccee------------cCCCCeeeEEE
Confidence            6899999999999999874           555566666777899999999999999            59999999999


Q ss_pred             eccccCCCccEEEEEEeeeeeeecCCCccceEEEEecCCccccCCCCcccccccCcchHHHHHHHhhhccCC-CCCcccc
Q psy300          262 IGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIP-DGKPENV  340 (451)
Q Consensus       262 ~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~d~~~~~i~~~~d~~~~~p~~~~~i~~~F~~yk~~-~gk~~~~  340 (451)
                      |++.++.||++++||+||+|+|+|+||+|||||||+.+||++++|++++|++   |+++++|++||++||.+ +||.+..
T Consensus        58 l~~~~~~~G~v~~~r~iG~l~m~D~ge~D~KiiaV~~~dp~~~~i~dl~dl~---~~~~~~i~~fF~~YK~l~~~k~~~~  134 (156)
T PF00719_consen   58 LGSEPLPPGSVVRVRVIGVLKMIDDGERDDKIIAVPVDDPRYDDIKDLEDLP---PHLLDEIEHFFRNYKDLEENKWVEV  134 (156)
T ss_dssp             ESSS---TTEEEEEEEEEEEEEEETTEEEEEEEEEETTCGGGTTHHSGGGSS---HHHHHHHHHHHHHTTTTSTTEEEEE
T ss_pred             EecccccceeEEEEeceEEEEEeeCCCCceEEEEeccCCcccCCcCcHHHhC---hhHHHHHHHHHHHhcCcCCCCeEEe
Confidence            9999999999999999999999999999999999999999999888888886   55999999999999999 8999999


Q ss_pred             cCCCcchhhhhhhHHHHHHHHHH
Q psy300          341 LNTRVEGESSQGFIPGCRGRTEQ  363 (451)
Q Consensus       341 ~~~~~~~~~~~~~i~~~~~~~~~  363 (451)
                      .+|.++ +.|+++|++||++|++
T Consensus       135 ~~~~~~-~~A~~~i~~~~~~y~~  156 (156)
T PF00719_consen  135 GGWEDA-EEALKVIKEAHERYKK  156 (156)
T ss_dssp             EEEEEH-HHHHHHHHHHHHHHHH
T ss_pred             CCCcCH-HHHHHHHHHHHHHhhC
Confidence            999985 7889999999999986

6.1.1 from EC) (PPase) [, ] is the enzyme responsible for the hydrolysis of pyrophosphate (PPi) which is formed principally as the product of the many biosynthetic reactions that utilise ATP. All known PPases require the presence of divalent metal cations, with magnesium conferring the highest activity. Among other residues, a lysine has been postulated to be part of or close to the active site. PPases have been sequenced from bacteria such as Escherichia coli (homohexamer), Bacillus PS3 (Thermophilic bacterium PS-3) and Thermus thermophilus, from the archaebacteria Thermoplasma acidophilum, from fungi (homodimer), from a plant, and from bovine retina. In yeast, a mitochondrial isoform of PPase has been characterised which seems to be involved in energy production and whose activity is stimulated by uncouplers of ATP synthesis. The sequences of PPases share some regions of similarities, among which is a region that contains three conserved aspartates that are involved in the binding of cations.; GO: 0000287 magnesium ion binding, 0004427 inorganic diphosphatase activity, 0006796 phosphate-containing compound metabolic process, 0005737 cytoplasm; PDB: 2UXS_A 1WCF_A 1SXV_A 3I4Q_A 2PRD_A 2IHP_B 1PYP_A 2IK7_A 2IK4_A 1E9G_A ....

>COG0221 Ppa Inorganic pyrophosphatase [Energy production and conversion]

Probab=100.00  E-value=1.6e-46  Score=340.41  Aligned_cols=170  Identities=34%  Similarity=0.508  Sum_probs=159.5

Q ss_pred             cccccCCccccccccccceeeccCCCCccccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccCCCCCCC
Q psy300          165 SPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDET  244 (451)
Q Consensus       165 Sp~hdiPl~v~~~p~~vn~vvEIPrgS~~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~~~p~~~  244 (451)
                      +.||++|...+.  ..+++++|||++|+.|||+++           ++|.+..++.++.+++||+||||||+||      
T Consensus         1 ~~~~~~~~~~~~--~~i~vviEIP~~s~~KyE~dk-----------~~~~~~vdR~l~~~~~YP~NYGfiP~Tl------   61 (171)
T COG0221           1 MDLHKIPAGPDD--EDINVVIEIPKGSNIKYEVDK-----------ETGRLLVDRPLKTPMGYPVNYGFIPNTL------   61 (171)
T ss_pred             CCccccCCCCCc--ceEEEEEeccCCCccceEEee-----------ecCceeeeecCCCCCcCCccccccCCcc------
Confidence            368999998755  599999999999999999976           6788888899998999999999999999      


Q ss_pred             CcCCCCCCCCCcceEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecCCccccCCCCcccccccCcchHHHHH
Q psy300          245 DAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATN  324 (451)
Q Consensus       245 ~~~~~~~~D~DPlD~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~d~~~~~i~~~~d~~~~~p~~~~~i~  324 (451)
                            .+|||||||||++..++.||++++||+||+|+|+|+||.|||||||+..||++++|++++|++++   ++++|+
T Consensus        62 ------~~DGDPlDvlVi~~~p~~pG~vi~~r~iG~l~m~D~~e~D~Kviav~~~dp~~~~i~di~d~~~~---~~~~i~  132 (171)
T COG0221          62 ------SDDGDPLDVLVIGEEPLAPGCVIQARPIGVLKMIDEGEKDDKVIAVPKLDPRYEHIKDISDLPEH---LLDEIQ  132 (171)
T ss_pred             ------cCCCCceEEEEEcCcCCCceeEEEEEEEEEEEEeeCCCcceEEEEecCCCcchhhccchhHHHHH---HHHHHH
Confidence                  57999999999999999999999999999999999999999999999999999999999999998   899999


Q ss_pred             HHhhhccCCCC-CcccccCCCcchhhhhhhHHHHHHHHHH
Q psy300          325 EWFKIYKIPDG-KPENVLNTRVEGESSQGFIPGCRGRTEQ  363 (451)
Q Consensus       325 ~~F~~yk~~~g-k~~~~~~~~~~~~~~~~~i~~~~~~~~~  363 (451)
                      |||.+||.++. |++.+.||.|. ++|+++|++|+++|++
T Consensus       133 ~ffe~yK~le~~k~~~~~gw~~~-~~A~~~i~~~~~~~k~  171 (171)
T COG0221         133 HFFETYKDLEKGKWVKVEGWEDA-EEAKKEIKEAIERYKE  171 (171)
T ss_pred             HHHHHHHhcCCCcEEEeccccCH-HHHHHHHHHHHHHhhC
Confidence            99999999995 99999999995 7889999999999974

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.90  E-value=7.3e-23  Score=207.77  Aligned_cols=130  Identities=22%  Similarity=0.453  Sum_probs=120.3

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC-----
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG-----  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G-----  100 (451)
                      ......++|||+|||.++++++|+++|+.||+|.+|+|++|. +++++|||||+|.++++|.+|+..|++..+.+     
T Consensus       102 ~~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V  181 (346)
T TIGR01659       102 DTNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKV  181 (346)
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeee
Confidence            345578999999999999999999999999999999999997 99999999999999999999999999876654     


Q ss_pred             ----------------------CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 ----------------------KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ----------------------~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                                            .+|+++|+++|++||.|..+.++++ .+++++|||||+|.+.++|.+|+..+|+..+
T Consensus       182 ~~a~p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~  260 (346)
T TIGR01659       182 SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIP  260 (346)
T ss_pred             ecccccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCcc
Confidence                                  3799999999999999999999988 4889999999999999999999999998754

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=99.88  E-value=4.5e-22  Score=212.70  Aligned_cols=131  Identities=26%  Similarity=0.452  Sum_probs=119.4

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC----
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG----  100 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G----  100 (451)
                      .......++|||+|||+++++++|+++|++||+|.+|++++|+ +|+++|||||+|.+.++|.+|+..+||..+.|    
T Consensus       101 ~~a~~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~Ik  180 (612)
T TIGR01645       101 QQALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIK  180 (612)
T ss_pred             hhhhcCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceee
Confidence            3345577899999999999999999999999999999999997 99999999999999999999999998876544    


Q ss_pred             ----------------------------------CCcHHHHHHHhcccCcceeeEEeeCC-CCCccceEEEEecchHHHH
Q psy300          101 ----------------------------------KITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAV  145 (451)
Q Consensus       101 ----------------------------------~~tee~L~~~F~~fG~V~~v~v~~d~-~g~srG~gFV~F~s~e~A~  145 (451)
                                                        .+++++|+++|+.||.|.++++++++ +++++|||||+|.+.++|.
T Consensus       181 V~rp~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~  260 (612)
T TIGR01645       181 VGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQS  260 (612)
T ss_pred             ecccccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHH
Confidence                                              25899999999999999999999984 6789999999999999999


Q ss_pred             HHHHhcCCCcc
Q psy300          146 KAILKSNKKPY  156 (451)
Q Consensus       146 ~Ai~~ln~riy  156 (451)
                      +|+..+|+..+
T Consensus       261 kAI~amNg~el  271 (612)
T TIGR01645       261 EAIASMNLFDL  271 (612)
T ss_pred             HHHHHhCCCee
Confidence            99999998754

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.87  E-value=8.7e-22  Score=200.19  Aligned_cols=126  Identities=29%  Similarity=0.519  Sum_probs=117.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC---------
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG---------  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G---------  100 (451)
                      +.++|||+|||.++++++|+++|++||+|.+|++++++ +|+++|||||+|.+.++|.+|+..+||..+.|         
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            47899999999999999999999999999999999997 89999999999999999999999999887765         


Q ss_pred             ------------------CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 ------------------KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ------------------~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                                        .+++++|+++|++||.|..+.++.+ .++.++|||||+|.+.++|..|+..+|+..+
T Consensus        82 ~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~  156 (352)
T TIGR01661        82 PSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTP  156 (352)
T ss_pred             ccccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCcc
Confidence                              3699999999999999999999887 4678999999999999999999999998765

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

>KOG0144|consensus

Probab=99.87  E-value=4.3e-22  Score=198.53  Aligned_cols=127  Identities=31%  Similarity=0.627  Sum_probs=117.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCc-----------
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKK-----------   96 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~-----------   96 (451)
                      +...-++|||-+|..++|.||+++|++||.|.+|.|++|+ |+.++|||||.|.+.++|.+|+.++++.           
T Consensus        31 d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvq  110 (510)
T KOG0144|consen   31 DGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQ  110 (510)
T ss_pred             CchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCccee
Confidence            3566799999999999999999999999999999999999 9999999999999999999999887542           


Q ss_pred             ----------------cCCC----CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCc
Q psy300           97 ----------------PYKG----KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP  155 (451)
Q Consensus        97 ----------------~f~G----~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~ri  155 (451)
                                      .|.|    ++||.+++++|++||.|++|.+++|+.+.|||||||.|++.+.|..||.++|+..
T Consensus       111 vk~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~  189 (510)
T KOG0144|consen  111 VKYADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQ  189 (510)
T ss_pred             ecccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccce
Confidence                            2333    4799999999999999999999999999999999999999999999999999864

>KOG0148|consensus

Probab=99.85  E-value=4.6e-21  Score=181.51  Aligned_cols=125  Identities=29%  Similarity=0.582  Sum_probs=114.4

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC----
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG----  100 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G----  100 (451)
                      +...+..-.+||+.|+..++.++|++.|.+||+|.+++++||. |++|||||||.|.+.++|++||..|||.=+.+    
T Consensus        56 k~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IR  135 (321)
T KOG0148|consen   56 KPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIR  135 (321)
T ss_pred             CCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceee
Confidence            3444457799999999999999999999999999999999998 99999999999999999999999999854332    


Q ss_pred             ---------------------------------------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecch
Q psy300          101 ---------------------------------------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANK  141 (451)
Q Consensus       101 ---------------------------------------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~  141 (451)
                                                             -+|+++|++.|++||.|.++++.++     +||+||.|++.
T Consensus       136 TNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~-----qGYaFVrF~tk  210 (321)
T KOG0148|consen  136 TNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD-----QGYAFVRFETK  210 (321)
T ss_pred             ccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc-----cceEEEEecch
Confidence                                                   1799999999999999999999998     89999999999


Q ss_pred             HHHHHHHHhcCCCc
Q psy300          142 ISAVKAILKSNKKP  155 (451)
Q Consensus       142 e~A~~Ai~~ln~ri  155 (451)
                      |+|.+||..+|+.-
T Consensus       211 EaAahAIv~mNnte  224 (321)
T KOG0148|consen  211 EAAAHAIVQMNNTE  224 (321)
T ss_pred             hhHHHHHHHhcCce
Confidence            99999999999764

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

Probab=99.84  E-value=1.5e-20  Score=203.22  Aligned_cols=124  Identities=23%  Similarity=0.509  Sum_probs=116.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC-----------
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG-----------  100 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G-----------  100 (451)
                      .+|||+|||.++|+++|+++|++||+|.+|++.+|. |++++|||||+|.+.++|.+|+..+|+..+.|           
T Consensus         1 ~sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~   80 (562)
T TIGR01628         1 ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRD   80 (562)
T ss_pred             CeEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccccc
Confidence            379999999999999999999999999999999998 89999999999999999999999998875544           


Q ss_pred             ------------------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 ------------------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ------------------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                                        ++++++|+++|++||.|.+|.++.+.+|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        81 ~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~~lng~~~  154 (562)
T TIGR01628        81 PSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLL  154 (562)
T ss_pred             ccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHHHhcccEe
Confidence                              37999999999999999999999998999999999999999999999999998765

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

>KOG0145|consensus

Probab=99.83  E-value=2.6e-20  Score=175.43  Aligned_cols=127  Identities=30%  Similarity=0.564  Sum_probs=116.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC-------
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG-------  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G-------  100 (451)
                      ...+++|.|..||.++|+++++.+|+..|+|++|+++||+ +|.|.|||||.|.++++|++|+..+||-.+.-       
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            3467899999999999999999999999999999999999 99999999999999999999999999854322       


Q ss_pred             --------------------CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCc
Q psy300          101 --------------------KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKP  155 (451)
Q Consensus       101 --------------------~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~ri  155 (451)
                                          .+|..+|+++|++||.|..-+++.| -+|.+||.|||.|..+++|..||..+||..
T Consensus       118 ARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~  193 (360)
T KOG0145|consen  118 ARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQK  193 (360)
T ss_pred             ccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCC
Confidence                                4799999999999999888888776 579999999999999999999999999865

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.83  E-value=9e-20  Score=185.39  Aligned_cols=127  Identities=28%  Similarity=0.513  Sum_probs=116.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC--------
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG--------  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G--------  100 (451)
                      ...++|||+|||.++++++|+++|++||.|..++++.+. ++.++|||||+|.+.++|.+|+..|||..+.|        
T Consensus        87 ~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~  166 (352)
T TIGR01661        87 IKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVK  166 (352)
T ss_pred             cccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEE
Confidence            356799999999999999999999999999999999887 88999999999999999999999888654322        


Q ss_pred             --------------------------------------------------------------------------------
Q psy300          101 --------------------------------------------------------------------------------  100 (451)
Q Consensus       101 --------------------------------------------------------------------------------  100 (451)
                                                                                                      
T Consensus       167 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  246 (352)
T TIGR01661       167 FANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASP  246 (352)
T ss_pred             ECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCC
Confidence                                                                                            


Q ss_pred             ---------------------------------CCcHHHHHHHhcccCcceeeEEeeCC-CCCccceEEEEecchHHHHH
Q psy300          101 ---------------------------------KITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVK  146 (451)
Q Consensus       101 ---------------------------------~~tee~L~~~F~~fG~V~~v~v~~d~-~g~srG~gFV~F~s~e~A~~  146 (451)
                                                       .+++++|+++|++||.|.++++++|+ +|.++|||||+|.+.++|.+
T Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~  326 (352)
T TIGR01661       247 PATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAM  326 (352)
T ss_pred             ccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHH
Confidence                                             25899999999999999999999985 89999999999999999999


Q ss_pred             HHHhcCCCcc
Q psy300          147 AILKSNKKPY  156 (451)
Q Consensus       147 Ai~~ln~riy  156 (451)
                      |+.+|||+.+
T Consensus       327 Ai~~lnG~~~  336 (352)
T TIGR01661       327 AILSLNGYTL  336 (352)
T ss_pred             HHHHhCCCEE
Confidence            9999999775

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

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

Probab=99.82  E-value=1.1e-19  Score=191.45  Aligned_cols=126  Identities=29%  Similarity=0.498  Sum_probs=114.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC--------
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG--------  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G--------  100 (451)
                      ...++|||+|||.++++++|+++|++||.|.+|+++.+. +|+++|||||+|.+.++|.+|+. ++|..+.|        
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            457799999999999999999999999999999999997 89999999999999999999996 66554433        


Q ss_pred             -------------------------------CCcHHHHHHHhcccCcceeeEEeeCC-CCCccceEEEEecchHHHHHHH
Q psy300          101 -------------------------------KITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAI  148 (451)
Q Consensus       101 -------------------------------~~tee~L~~~F~~fG~V~~v~v~~d~-~g~srG~gFV~F~s~e~A~~Ai  148 (451)
                                                     .+++++|+++|++||.|..+.++.+. +|+++|||||+|.+.++|.+|+
T Consensus       166 ~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~  245 (457)
T TIGR01622       166 QAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEAL  245 (457)
T ss_pred             chhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHH
Confidence                                           37899999999999999999999884 5689999999999999999999


Q ss_pred             HhcCCCcc
Q psy300          149 LKSNKKPY  156 (451)
Q Consensus       149 ~~ln~riy  156 (451)
                      ..+|+..+
T Consensus       246 ~~l~g~~i  253 (457)
T TIGR01622       246 EVMNGFEL  253 (457)
T ss_pred             HhcCCcEE
Confidence            99998554

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=99.82  E-value=1.4e-19  Score=195.57  Aligned_cols=128  Identities=28%  Similarity=0.567  Sum_probs=119.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCC----C----
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK----G----  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~----G----  100 (451)
                      ....++|||+|||.++++++|+++|++||.|.++.++++.+|+++|||||.|.+.++|.+|++.++|+.+.    |    
T Consensus       175 ~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~  254 (562)
T TIGR01628       175 LKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLY  254 (562)
T ss_pred             ccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeE
Confidence            34567899999999999999999999999999999999999999999999999999999999999888776    3    


Q ss_pred             -----------------------------------------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEec
Q psy300          101 -----------------------------------------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYA  139 (451)
Q Consensus       101 -----------------------------------------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~  139 (451)
                                                               .+|+++|+++|++||.|.+++++.+.+|.++|||||+|.
T Consensus       255 v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~~g~~~g~gfV~f~  334 (562)
T TIGR01628       255 VGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKGVSRGFGFVCFS  334 (562)
T ss_pred             eecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECCCCCcCCeEEEEeC
Confidence                                                     279999999999999999999999988999999999999


Q ss_pred             chHHHHHHHHhcCCCcc
Q psy300          140 NKISAVKAILKSNKKPY  156 (451)
Q Consensus       140 s~e~A~~Ai~~ln~riy  156 (451)
                      +.++|.+|+..+|++.+
T Consensus       335 ~~~~A~~A~~~~~g~~~  351 (562)
T TIGR01628       335 NPEEANRAVTEMHGRML  351 (562)
T ss_pred             CHHHHHHHHHHhcCCee
Confidence            99999999999998765

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

>KOG0117|consensus

Probab=99.81  E-value=2e-19  Score=180.28  Aligned_cols=126  Identities=25%  Similarity=0.480  Sum_probs=114.0

Q ss_pred             cCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccC----
Q psy300           24 RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPY----   98 (451)
Q Consensus        24 ~~~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f----   98 (451)
                      .........+.||||.||.++.|++|..+|++.|+|.+++||+|+ +|.+||||||.|.+.+.|++|++.+|+..+    
T Consensus        75 weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK  154 (506)
T KOG0117|consen   75 WEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGK  154 (506)
T ss_pred             ccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCC
Confidence            344445678999999999999999999999999999999999997 999999999999999999999999887532    


Q ss_pred             --------------CC----------------------------------------------------------------
Q psy300           99 --------------KG----------------------------------------------------------------  100 (451)
Q Consensus        99 --------------~G----------------------------------------------------------------  100 (451)
                                    .|                                                                
T Consensus       155 ~igvc~Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~k  234 (506)
T KOG0117|consen  155 LLGVCVSVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIK  234 (506)
T ss_pred             EeEEEEeeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCcee
Confidence                          22                                                                


Q ss_pred             -----------------------------------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHH
Q psy300          101 -----------------------------------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAV  145 (451)
Q Consensus       101 -----------------------------------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~  145 (451)
                                                         ++|++.|+++|++||.|+.|+.++|       ||||+|.++++|.
T Consensus       235 lwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-------YaFVHf~eR~dav  307 (506)
T KOG0117|consen  235 LWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-------YAFVHFAEREDAV  307 (506)
T ss_pred             ecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc-------eeEEeecchHHHH
Confidence                                               2799999999999999999999876       9999999999999


Q ss_pred             HHHHhcCCCcc
Q psy300          146 KAILKSNKKPY  156 (451)
Q Consensus       146 ~Ai~~ln~riy  156 (451)
                      +|+..+|++..
T Consensus       308 kAm~~~ngkel  318 (506)
T KOG0117|consen  308 KAMKETNGKEL  318 (506)
T ss_pred             HHHHHhcCcee
Confidence            99999999875

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

Probab=99.76  E-value=5.5e-18  Score=180.76  Aligned_cols=126  Identities=29%  Similarity=0.458  Sum_probs=112.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC--------
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK--------  101 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~--------  101 (451)
                      ..++|||+|||..+++++|+++|++||.|..+.++.+. +|.++|||||+|.+.++|..|+..|||..+.|+        
T Consensus       294 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~  373 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRAC  373 (509)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECc
Confidence            45799999999999999999999999999999999987 899999999999999999999999998766541        


Q ss_pred             --------------------------------------------C-------------cHHHHHHHhcccCcceeeEEee
Q psy300          102 --------------------------------------------I-------------TEEEFKEHFGQYGDIIDAQLLK  124 (451)
Q Consensus       102 --------------------------------------------~-------------tee~L~~~F~~fG~V~~v~v~~  124 (451)
                                                                  +             ..++|+++|++||.|..|.|++
T Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~  453 (509)
T TIGR01642       374 VGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPR  453 (509)
T ss_pred             cCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeec
Confidence                                                        0             1257899999999999999987


Q ss_pred             C----CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          125 N----ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       125 d----~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      +    .++.+.|++||+|.+.++|.+|+..|||+.|
T Consensus       454 ~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~  489 (509)
T TIGR01642       454 PNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKF  489 (509)
T ss_pred             cCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEE
Confidence            5    2345679999999999999999999999987

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

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.76  E-value=9.4e-18  Score=179.30  Aligned_cols=122  Identities=23%  Similarity=0.414  Sum_probs=107.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCC-C---------
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK-G---------  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~-G---------  100 (451)
                      ..++|||+|||.++++++|+++|++||.|.+++|++|.+|+|+|||||+|.+.++|++|+..||+..+. |         
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~  136 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISV  136 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccccc
Confidence            468999999999999999999999999999999999999999999999999999999999999876543 1         


Q ss_pred             ------------CCcHHHHHHHhcccCc-ceeeEEeeC--CCCCccceEEEEecchHHHHHHHHhcC
Q psy300          101 ------------KITEEEFKEHFGQYGD-IIDAQLLKN--ADGKLKGCGFINYANKISAVKAILKSN  152 (451)
Q Consensus       101 ------------~~tee~L~~~F~~fG~-V~~v~v~~d--~~g~srG~gFV~F~s~e~A~~Ai~~ln  152 (451)
                                  .+++++|.+.|++++. +.++.+...  ..++++|||||+|.++++|..|+..++
T Consensus       137 ~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~  203 (578)
T TIGR01648       137 DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLM  203 (578)
T ss_pred             cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhh
Confidence                        3689999999999875 555555432  456789999999999999999998874

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.

>KOG0145|consensus

Probab=99.75  E-value=3.6e-18  Score=160.96  Aligned_cols=131  Identities=28%  Similarity=0.516  Sum_probs=118.2

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC---
Q psy300           25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG---  100 (451)
Q Consensus        25 ~~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G---  100 (451)
                      .+.+.-...+|||.+||+.+|.++|..+|++||.|...+++.|. +|.|||.|||.|....+|+.|+..+||..-.|   
T Consensus       120 PSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~te  199 (360)
T KOG0145|consen  120 PSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTE  199 (360)
T ss_pred             CChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCC
Confidence            34456678899999999999999999999999999999999988 99999999999999999999999999854322   


Q ss_pred             --------------------------------------------------------------------------------
Q psy300          101 --------------------------------------------------------------------------------  100 (451)
Q Consensus       101 --------------------------------------------------------------------------------  100 (451)
                                                                                                      
T Consensus       200 pItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~  279 (360)
T KOG0145|consen  200 PITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGW  279 (360)
T ss_pred             CeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCee
Confidence                                                                                            


Q ss_pred             ---------CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCc
Q psy300          101 ---------KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKP  155 (451)
Q Consensus       101 ---------~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~ri  155 (451)
                               ..+|.-|-++|.+||.|..+++++| .+++++|||||++++.++|..||..+||.-
T Consensus       280 ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~  344 (360)
T KOG0145|consen  280 CIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYR  344 (360)
T ss_pred             EEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCcc
Confidence                     2588899999999999999999999 458999999999999999999999999753

>KOG0124|consensus

Probab=99.73  E-value=5.6e-18  Score=166.00  Aligned_cols=128  Identities=27%  Similarity=0.492  Sum_probs=118.2

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC----
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG----  100 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G----  100 (451)
                      ...-.-+|+||||.+++.+.|+.|+..|..||+|.+|.+..|+ |++++|||||+|+-++.|+.|++.|||..+.|    
T Consensus       107 qqALaiMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiK  186 (544)
T KOG0124|consen  107 QQALAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIK  186 (544)
T ss_pred             HHHHHHhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCcccc
Confidence            3345568999999999999999999999999999999999999 99999999999999999999999999988877    


Q ss_pred             ----------------------------------CCcHHHHHHHhcccCcceeeEEeeCCCC-CccceEEEEecchHHHH
Q psy300          101 ----------------------------------KITEEEFKEHFGQYGDIIDAQLLKNADG-KLKGCGFINYANKISAV  145 (451)
Q Consensus       101 ----------------------------------~~tee~L~~~F~~fG~V~~v~v~~d~~g-~srG~gFV~F~s~e~A~  145 (451)
                                                        .++++||+..|+.||.|.+|.+.+++++ ..+||||++|.+..+..
T Consensus       187 VgrPsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~  266 (544)
T KOG0124|consen  187 VGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQS  266 (544)
T ss_pred             ccCCCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchH
Confidence                                              2699999999999999999999998654 57999999999999999


Q ss_pred             HHHHhcCC
Q psy300          146 KAILKSNK  153 (451)
Q Consensus       146 ~Ai~~ln~  153 (451)
                      .|+..||-
T Consensus       267 eAiasMNl  274 (544)
T KOG0124|consen  267 EAIASMNL  274 (544)
T ss_pred             HHhhhcch
Confidence            99999983

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

Probab=99.71  E-value=7.1e-17  Score=171.55  Aligned_cols=119  Identities=17%  Similarity=0.240  Sum_probs=103.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhc--CCccCCC--------
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS--NKKPYKG--------  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~l--ng~~f~G--------  100 (451)
                      +++.|||+|||.++++++|+++|++||.|.++.++++     +|||||+|.+.++|.+|+..+  ++..+.|        
T Consensus         1 ps~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~-----k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s   75 (481)
T TIGR01649         1 PSPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG-----KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYS   75 (481)
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC-----CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEec
Confidence            3679999999999999999999999999999999853     789999999999999999853  3221111        


Q ss_pred             -------------------------------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHH
Q psy300          101 -------------------------------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL  149 (451)
Q Consensus       101 -------------------------------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~  149 (451)
                                                     .+|+++|+++|+.||.|.++.++++..   +|+|||+|.+.++|.+|+.
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~---~~~afVef~~~~~A~~A~~  152 (481)
T TIGR01649        76 TSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNN---VFQALVEFESVNSAQHAKA  152 (481)
T ss_pred             CCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCC---ceEEEEEECCHHHHHHHHH
Confidence                                           379999999999999999999987632   4799999999999999999


Q ss_pred             hcCCCccc
Q psy300          150 KSNKKPYK  157 (451)
Q Consensus       150 ~ln~riy~  157 (451)
                      .||++.+.
T Consensus       153 ~Lng~~i~  160 (481)
T TIGR01649       153 ALNGADIY  160 (481)
T ss_pred             HhcCCccc
Confidence            99998764

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).

>KOG0131|consensus

Probab=99.70  E-value=3.7e-17  Score=147.26  Aligned_cols=128  Identities=28%  Similarity=0.443  Sum_probs=113.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC------
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG------  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G------  100 (451)
                      +.....+|||+||+..++++.|.++|-+.|+|.++++.+|+ +...+||||++|.++++|.-|++-||...+.|      
T Consensus         5 ~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~   84 (203)
T KOG0131|consen    5 ERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVN   84 (203)
T ss_pred             ccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEE
Confidence            34577899999999999999999999999999999999998 88899999999999999999998877543333      


Q ss_pred             ----------------------CCcHHHHHHHhcccCcce-eeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCc
Q psy300          101 ----------------------KITEEEFKEHFGQYGDII-DAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKP  155 (451)
Q Consensus       101 ----------------------~~tee~L~~~F~~fG~V~-~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~ri  155 (451)
                                            .+++..|.+.|+.||.+. ...++++ .+|.++|||||.|.+.+++.+|+..+|+..
T Consensus        85 kas~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~  163 (203)
T KOG0131|consen   85 KASAHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQY  163 (203)
T ss_pred             ecccccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccch
Confidence                                  379999999999999954 4677887 468899999999999999999999999875

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

Probab=99.70  E-value=1.2e-16  Score=170.44  Aligned_cols=122  Identities=25%  Similarity=0.401  Sum_probs=102.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccC------------CCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCc
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQY------------GDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK   96 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~------------G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~   96 (451)
                      ....++|||||||.++++++|.++|+++            +.|..+.+     +.++|||||+|.+.++|..||. |+|.
T Consensus       172 ~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~-----~~~kg~afVeF~~~e~A~~Al~-l~g~  245 (509)
T TIGR01642       172 TRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI-----NKEKNFAFLEFRTVEEATFAMA-LDSI  245 (509)
T ss_pred             CccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE-----CCCCCEEEEEeCCHHHHhhhhc-CCCe
Confidence            4456899999999999999999999975            23444444     3568999999999999999994 6554


Q ss_pred             cCC----------------------------------------------------C----CCcHHHHHHHhcccCcceee
Q psy300           97 PYK----------------------------------------------------G----KITEEEFKEHFGQYGDIIDA  120 (451)
Q Consensus        97 ~f~----------------------------------------------------G----~~tee~L~~~F~~fG~V~~v  120 (451)
                      .|.                                                    |    .+++++|+++|+.||.|..+
T Consensus       246 ~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~  325 (509)
T TIGR01642       246 IYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAF  325 (509)
T ss_pred             EeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEE
Confidence            322                                                    2    36999999999999999999


Q ss_pred             EEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          121 QLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       121 ~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .++++ .+|.++|||||+|.+.++|..|+..+|+..+
T Consensus       326 ~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~  362 (509)
T TIGR01642       326 NLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDT  362 (509)
T ss_pred             EEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEE
Confidence            99988 5789999999999999999999999988654

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

>KOG0123|consensus

Probab=99.70  E-value=1.1e-16  Score=163.61  Aligned_cols=117  Identities=24%  Similarity=0.451  Sum_probs=110.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC------------
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG------------  100 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G------------  100 (451)
                      ..||||   +++|+..|.++|+++|+|.++++.+|. + |.|||||.|.++++|.+|+.++|...+.|            
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t-slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~   76 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T-SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP   76 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C-ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC
Confidence            478999   999999999999999999999999998 6 99999999999999999999999988887            


Q ss_pred             ----------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 ----------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ----------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                                .++...|.++|+.||.|.+|++..+..| ++|| ||+|++.++|.+|+..+|+.+.
T Consensus        77 ~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll  140 (369)
T KOG0123|consen   77 SLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-SKGY-FVQFESEESAKKAIEKLNGMLL  140 (369)
T ss_pred             ceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-ceee-EEEeCCHHHHHHHHHHhcCccc
Confidence                      3799999999999999999999999888 8999 9999999999999999998775

>KOG0123|consensus

Probab=99.69  E-value=1.5e-16  Score=162.71  Aligned_cols=120  Identities=35%  Similarity=0.605  Sum_probs=113.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC--------------
Q psy300           35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG--------------  100 (451)
Q Consensus        35 lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G--------------  100 (451)
                      +||.||+++++..+|.++|+.||+|++|++.++..| ++|| ||+|.+++.|.+|+..+||..+.|              
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er  156 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEER  156 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhh
Confidence            999999999999999999999999999999999988 9999 999999999999999999987765              


Q ss_pred             ---------------------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 ---------------------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ---------------------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                                           .++++.|.++|+.+|.|.++.++.+..|+++|||||.|.++++|..|+..+++..+
T Consensus       157 ~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~av~~l~~~~~  233 (369)
T KOG0123|consen  157 EAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKAVETLNGKIF  233 (369)
T ss_pred             cccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHHHHhccCCcC
Confidence                                 25778999999999999999999999999999999999999999999999998775

>KOG0127|consensus

Probab=99.69  E-value=1.2e-16  Score=163.61  Aligned_cols=125  Identities=27%  Similarity=0.539  Sum_probs=116.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC-----------
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG-----------  100 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G-----------  100 (451)
                      .||||++||++++.++|.++|+.+|+|.++.++.+. ++.+||||||.|.-.+++++|+...+++.|.|           
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R   85 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKR   85 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceeccccccccc
Confidence            799999999999999999999999999999999998 78999999999999999999999988877766           


Q ss_pred             ------------------------------------------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEe
Q psy300          101 ------------------------------------------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINY  138 (451)
Q Consensus       101 ------------------------------------------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F  138 (451)
                                                                .+...+|+.+|+.||.|.++.|++...|+-+|||||+|
T Consensus        86 ~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~f  165 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQF  165 (678)
T ss_pred             ccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEE
Confidence                                                      15678999999999999999999988888889999999


Q ss_pred             cchHHHHHHHHhcCCCccc
Q psy300          139 ANKISAVKAILKSNKKPYK  157 (451)
Q Consensus       139 ~s~e~A~~Ai~~ln~riy~  157 (451)
                      ....+|..|+..+|+..+.
T Consensus       166 k~~~dA~~Al~~~N~~~i~  184 (678)
T KOG0127|consen  166 KEKKDAEKALEFFNGNKID  184 (678)
T ss_pred             eeHHHHHHHHHhccCceec
Confidence            9999999999999987763

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

Probab=99.68  E-value=2.8e-16  Score=165.57  Aligned_cols=123  Identities=27%  Similarity=0.481  Sum_probs=109.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC--------
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK--------  101 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~--------  101 (451)
                      ..++|||+|||.++++++|+++|++||.|.+|.++++. +|.++|||||+|.+.++|.+|+..|||..+.|+        
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            36899999999999999999999999999999999988 789999999999999999999999887544320        


Q ss_pred             --------------------------------------------------------------------------------
Q psy300          102 --------------------------------------------------------------------------------  101 (451)
Q Consensus       102 --------------------------------------------------------------------------------  101 (451)
                                                                                                      
T Consensus       265 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  344 (457)
T TIGR01622       265 DSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGAL  344 (457)
T ss_pred             CCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhcccccccccccccccccccccc
Confidence                                                                                            


Q ss_pred             --------C-------------------------------cHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchH
Q psy300          102 --------I-------------------------------TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKI  142 (451)
Q Consensus       102 --------~-------------------------------tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e  142 (451)
                              +                               -.++|++.|++||.|..+.+...   .+.|++||+|.+.+
T Consensus       345 ~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~---~~~G~~fV~F~~~e  421 (457)
T TIGR01622       345 AIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTK---NSAGKIYLKFSSVD  421 (457)
T ss_pred             ccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCC---CCceeEEEEECCHH
Confidence                    0                               03689999999999999999743   35799999999999


Q ss_pred             HHHHHHHhcCCCcc
Q psy300          143 SAVKAILKSNKKPY  156 (451)
Q Consensus       143 ~A~~Ai~~ln~riy  156 (451)
                      +|.+|+.+|||+.|
T Consensus       422 ~A~~A~~~lnGr~f  435 (457)
T TIGR01622       422 AALAAFQALNGRYF  435 (457)
T ss_pred             HHHHHHHHhcCccc
Confidence            99999999999988

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

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

Probab=99.66  E-value=8e-16  Score=163.52  Aligned_cols=122  Identities=21%  Similarity=0.341  Sum_probs=106.4

Q ss_pred             CCCceEEEcCCCC-CCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC--------
Q psy300           30 TKRGRLFIKNLPF-KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG--------  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~-~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G--------  100 (451)
                      .+.++|||+|||. .+++++|+++|+.||.|.+|+++++    .+|||||+|.+.++|.+|+..|||..+.|        
T Consensus       273 ~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~----~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s  348 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKN----KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPS  348 (481)
T ss_pred             CCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeC----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            3668999999997 6999999999999999999999886    36999999999999999999887753322        


Q ss_pred             --------------------------------------------------------CCcHHHHHHHhcccCc--ceeeEE
Q psy300          101 --------------------------------------------------------KITEEEFKEHFGQYGD--IIDAQL  122 (451)
Q Consensus       101 --------------------------------------------------------~~tee~L~~~F~~fG~--V~~v~v  122 (451)
                                                                              ++++++|+++|+.||.  +..+++
T Consensus       349 ~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~  428 (481)
T TIGR01649       349 KQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKF  428 (481)
T ss_pred             ccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEE
Confidence                                                                    2589999999999998  888888


Q ss_pred             eeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          123 LKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       123 ~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ....++ ++|+|||+|++.++|..|+..+|++.+
T Consensus       429 ~~~~~~-~~~~gfVeF~~~e~A~~Al~~ln~~~l  461 (481)
T TIGR01649       429 FPKDNE-RSKMGLLEWESVEDAVEALIALNHHQL  461 (481)
T ss_pred             ecCCCC-cceeEEEEcCCHHHHHHHHHHhcCCcc
Confidence            765444 589999999999999999999998765

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

>KOG0127|consensus

Probab=99.64  E-value=1.6e-15  Score=155.42  Aligned_cols=122  Identities=34%  Similarity=0.625  Sum_probs=112.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC----------
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG----------  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G----------  100 (451)
                      +..+|.|+|||+.+.+.+|..+|+.||.|.+|.|++...|+-.|||||+|.+..+|..|+..+|+..+.|          
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~  195 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVD  195 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecc
Confidence            3789999999999999999999999999999999988877777999999999999999999999876655          


Q ss_pred             --------------------------------------------------------------------------------
Q psy300          101 --------------------------------------------------------------------------------  100 (451)
Q Consensus       101 --------------------------------------------------------------------------------  100 (451)
                                                                                                      
T Consensus       196 Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~  275 (678)
T KOG0127|consen  196 KDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKE  275 (678)
T ss_pred             cccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccCc
Confidence                                                                                            


Q ss_pred             ---------------------------CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcC
Q psy300          101 ---------------------------KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSN  152 (451)
Q Consensus       101 ---------------------------~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln  152 (451)
                                                 .+|+++|.++|++||.|.++.++.+ .+++|+|.|||.|.+..+|+.||..-.
T Consensus       276 ~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~As  355 (678)
T KOG0127|consen  276 SDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAAS  355 (678)
T ss_pred             ccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcC
Confidence                                       1699999999999999999999998 689999999999999999999998863

>KOG0109|consensus

Probab=99.62  E-value=2.3e-15  Score=144.33  Aligned_cols=113  Identities=31%  Similarity=0.622  Sum_probs=103.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC------------
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG------------  100 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G------------  100 (451)
                      .+|||||||..+++.+|+.+|++||+|.+|.|+++       ||||..++...|..|+..|+|-.+.|            
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN-------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksKs   75 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN-------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSKS   75 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc-------cceEEeecccccHHHHhhcccceecceEEEEEeccccC
Confidence            47999999999999999999999999999999965       99999999999999999888766655            


Q ss_pred             -------------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcccCC
Q psy300          101 -------------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS  159 (451)
Q Consensus       101 -------------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~~~  159 (451)
                                   +++.++|+..|++||.|.+|.+++|       |+||+|...++|..|+..||++.|-+.
T Consensus        76 k~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd-------y~fvh~d~~eda~~air~l~~~~~~gk  140 (346)
T KOG0109|consen   76 KASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD-------YAFVHFDRAEDAVEAIRGLDNTEFQGK  140 (346)
T ss_pred             CCccccccCCCCccccCHHHhhhhcccCCceeeeeecc-------eeEEEEeeccchHHHHhcccccccccc
Confidence                         3688999999999999999999965       999999999999999999999988443

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.55  E-value=3.5e-14  Score=152.04  Aligned_cols=120  Identities=25%  Similarity=0.439  Sum_probs=99.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCC-eEEEEEeECC--CCCceeEEEEEEccHHHHHHHHHhcCC-c---------
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGD-IIDAQLLKNA--DGKLKGCGFINYANKISAVKAILKSNK-K---------   96 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~-I~~i~l~~d~--tg~skG~aFV~F~~~~~A~~Al~~lng-~---------   96 (451)
                      ...++|||+|||.++++++|.+.|++++. +.++.+....  .++++|||||+|.+.++|..|+..++. .         
T Consensus       136 ~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~  215 (578)
T TIGR01648       136 VDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIA  215 (578)
T ss_pred             ccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEE
Confidence            35789999999999999999999999975 5555444332  578899999999999999999987642 1         


Q ss_pred             --------------------cCCC----CCcHHHHHHHhccc--CcceeeEEeeCCCCCccceEEEEecchHHHHHHHHh
Q psy300           97 --------------------PYKG----KITEEEFKEHFGQY--GDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK  150 (451)
Q Consensus        97 --------------------~f~G----~~tee~L~~~F~~f--G~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~  150 (451)
                                          +|.+    .+++++|+++|++|  |.|+++.++       ++||||+|++.++|.+|+..
T Consensus       216 VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~-------rgfAFVeF~s~e~A~kAi~~  288 (578)
T TIGR01648       216 VDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI-------RDYAFVHFEDREDAVKAMDE  288 (578)
T ss_pred             EEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee-------cCeEEEEeCCHHHHHHHHHH
Confidence                                1112    37999999999999  999998876       46999999999999999999


Q ss_pred             cCCCcc
Q psy300          151 SNKKPY  156 (451)
Q Consensus       151 ln~riy  156 (451)
                      +|++.+
T Consensus       289 lnG~~i  294 (578)
T TIGR01648       289 LNGKEL  294 (578)
T ss_pred             hCCCEE
Confidence            998876

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.

>KOG0146|consensus

Probab=99.54  E-value=2.8e-14  Score=135.36  Aligned_cols=68  Identities=25%  Similarity=0.523  Sum_probs=63.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCc
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK   96 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~   96 (451)
                      ....++||||-|.+.-+|+|++.+|..||.|.+|.+++.++|.||||+||.|.+..+|+.||..++|.
T Consensus        16 g~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgS   83 (371)
T KOG0146|consen   16 GGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGS   83 (371)
T ss_pred             CccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhccc
Confidence            34678999999999999999999999999999999999999999999999999999999999988764

>KOG1626|consensus

Probab=99.52  E-value=4.1e-15  Score=140.25  Aligned_cols=46  Identities=52%  Similarity=0.814  Sum_probs=42.3

Q ss_pred             CCCccCCccCCCccccCCCCEEEEEEeecCCCccceeeeccccceEE
Q psy300          381 ENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLY  427 (451)
Q Consensus       381 ~~~~~s~~hd~~l~~~~~~~~~~~~~e~p~~~~~k~e~~~~~~~~~~  427 (451)
                      .|++|||||||||+++ ...+|||||||||||||||||+|++++|=|
T Consensus        24 ~~~~iS~fhdipl~a~-~~~~~nmvvEiPrwtnak~EIs~k~~~~pi   69 (279)
T KOG1626|consen   24 NGRIISPFHDIPLAAH-PWHDLNMVVEIPRWTNAKMEISKKEPFNPI   69 (279)
T ss_pred             CCccccccccCccccC-ccccEeecccccceeeeEEEEeccCCCCcc
Confidence            3469999999999998 469999999999999999999999999966

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

Probab=99.49  E-value=2.5e-13  Score=145.90  Aligned_cols=67  Identities=30%  Similarity=0.491  Sum_probs=62.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCcc
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKP   97 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~   97 (451)
                      ..++|||+|||.++++++|+++|+.||.|.++++.+++ +|+++|||||+|.+.++|.+|+..||+..
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~e  270 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFD  270 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCe
Confidence            45799999999999999999999999999999999998 78999999999999999999999887653

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.

>KOG0144|consensus

Probab=99.49  E-value=4.1e-14  Score=141.87  Aligned_cols=67  Identities=34%  Similarity=0.614  Sum_probs=63.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCc
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK   96 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~   96 (451)
                      ...++||||-|++.++|.+++++|++||.|++|.|+||..|.|||||||.|.+.+.|..|++.|||+
T Consensus       122 ~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~  188 (510)
T KOG0144|consen  122 VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGT  188 (510)
T ss_pred             ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccc
Confidence            4578999999999999999999999999999999999999999999999999999999999998874

>KOG0110|consensus

Probab=99.48  E-value=8.2e-14  Score=147.12  Aligned_cols=125  Identities=26%  Similarity=0.462  Sum_probs=110.2

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCC----ceeEEEEEEccHHHHHHHHHhcCCccCCCC------
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGK----LKGCGFINYANKISAVKAILKSNKKPYKGK------  101 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~----skG~aFV~F~~~~~A~~Al~~lng~~f~G~------  101 (451)
                      .++|||.||+++++.++|..+|...|.|.++.|..-+++.    |.|||||+|.++++|++|++.|+|+.+.|.      
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            4459999999999999999999999999999887655442    569999999999999999999999888771      


Q ss_pred             ------------------------------CcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHh
Q psy300          102 ------------------------------ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILK  150 (451)
Q Consensus       102 ------------------------------~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~  150 (451)
                                                    .+-.+++++|..||.+.++++++. ..+.++|||||.|-++.+|.+|+..
T Consensus       595 S~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~a  674 (725)
T KOG0110|consen  595 SENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDA  674 (725)
T ss_pred             ccCccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHh
Confidence                                          477999999999999999999986 4566799999999999999999999


Q ss_pred             cCCCcc
Q psy300          151 SNKKPY  156 (451)
Q Consensus       151 ln~riy  156 (451)
                      +...-+
T Consensus       675 l~STHl  680 (725)
T KOG0110|consen  675 LGSTHL  680 (725)
T ss_pred             hcccce
Confidence            865444

>KOG0148|consensus

Probab=99.47  E-value=1.7e-13  Score=130.39  Aligned_cols=122  Identities=25%  Similarity=0.414  Sum_probs=92.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC----CCcH
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG----KITE  104 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G----~~te  104 (451)
                      ....++|||+||+.++||+-|..+|++.|+|.+++++.+.-+...  ++.. .+  . .+-...-+-..|.|    .++.
T Consensus         3 ~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~e~~v~w--a~~p-~n--Q-sk~t~~~hfhvfvgdls~eI~~   76 (321)
T KOG0148|consen    3 SDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFDELKVNW--ATAP-GN--Q-SKPTSNQHFHVFVGDLSPEIDN   76 (321)
T ss_pred             CCCCceEEeeccChhhHHHHHHHHHHhccccccceeehhhhcccc--ccCc-cc--C-CCCccccceeEEehhcchhcch
Confidence            346789999999999999999999999999999999987311100  0000 00  0 00000001123333    4788


Q ss_pred             HHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          105 EEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       105 e~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|++.|.+||+|.+++|++| .+++|+|||||.|-..++|..||..|||...
T Consensus        77 e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWl  129 (321)
T KOG0148|consen   77 EKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWL  129 (321)
T ss_pred             HHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeee
Confidence            999999999999999999999 6899999999999999999999999999763

>KOG4205|consensus

Probab=99.46  E-value=7.8e-14  Score=138.72  Aligned_cols=120  Identities=29%  Similarity=0.630  Sum_probs=105.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHh----cCC----------
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILK----SNK----------   95 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~----lng----------   95 (451)
                      +.+++||++|+.+++++.|++.|++||+|.+|.+++|+ +++++||+||+|.+++.+.+++..    +.|          
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~   84 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVS   84 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccC
Confidence            77899999999999999999999999999999999999 999999999999998888887754    222          


Q ss_pred             --------------ccCCC----CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHh
Q psy300           96 --------------KPYKG----KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILK  150 (451)
Q Consensus        96 --------------~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~  150 (451)
                                    ++|.|    .+++++++++|++||.|..+.++.| .+.+++|||||.|.+++++.++...
T Consensus        85 r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~  158 (311)
T KOG4205|consen   85 REDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQ  158 (311)
T ss_pred             cccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceeccc
Confidence                          23344    4799999999999999999999887 5678999999999999998887654

>KOG0147|consensus

Probab=99.45  E-value=7.6e-14  Score=143.89  Aligned_cols=125  Identities=26%  Similarity=0.456  Sum_probs=112.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC-------
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG-------  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G-------  100 (451)
                      ....+++|+-.|+...+.-+|.+||+.+|.|..|+++.|+ +++++|.|||+|.+.+.+..|+. |.|..+.|       
T Consensus       176 ERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv~vq~  254 (549)
T KOG0147|consen  176 ERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPVIVQL  254 (549)
T ss_pred             HHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCceeEecc
Confidence            3356899999999999999999999999999999999998 99999999999999999888873 45443333       


Q ss_pred             ----------------------------------CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHH
Q psy300          101 ----------------------------------KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAV  145 (451)
Q Consensus       101 ----------------------------------~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~  145 (451)
                                                        ++++++|+.+|+.||.|+.+.+++| ++|+++||||++|.+.++|.
T Consensus       255 sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar  334 (549)
T KOG0147|consen  255 SEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDAR  334 (549)
T ss_pred             cHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHH
Confidence                                              4899999999999999999999998 49999999999999999999


Q ss_pred             HHHHhcCCC
Q psy300          146 KAILKSNKK  154 (451)
Q Consensus       146 ~Ai~~ln~r  154 (451)
                      +|+..+|+.
T Consensus       335 ~a~e~lngf  343 (549)
T KOG0147|consen  335 KALEQLNGF  343 (549)
T ss_pred             HHHHHhccc
Confidence            999999983

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

Probab=99.44  E-value=4.5e-13  Score=120.03  Aligned_cols=72  Identities=26%  Similarity=0.622  Sum_probs=67.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....++|||+|||.++++++|+++|++||.|.+++++.+. +++++|||||+|.+.++|++|++.+|+..+.|
T Consensus        31 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~G  103 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNG  103 (144)
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            3457799999999999999999999999999999999998 99999999999999999999999999987665

>PF00076 RRM_1: RNA recognition motif

Probab=99.43  E-value=4.4e-13  Score=103.54  Aligned_cols=66  Identities=36%  Similarity=0.683  Sum_probs=63.3

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        35 lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      |||+|||.++++++|+++|++||.|..+.+..+.++.++|+|||+|.+.++|.+|++.++|..+.|
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~   66 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKING   66 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECc
Confidence            799999999999999999999999999999998889999999999999999999999999988776

(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 ....

>PLN02707 Soluble inorganic pyrophosphatase

Probab=99.42  E-value=1.5e-13  Score=133.14  Aligned_cols=48  Identities=44%  Similarity=0.608  Sum_probs=42.2

Q ss_pred             CCCCccCCccCCCccccCCCCEEEEEEeecCCCccceeeeccccceEEEE
Q psy300          380 SENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLYLV  429 (451)
Q Consensus       380 ~~~~~~s~~hd~~l~~~~~~~~~~~~~e~p~~~~~k~e~~~~~~~~~~~~  429 (451)
                      .+|+++||||||||+.  ..+++||||||||||++||||+|++++|..-+
T Consensus        52 ~~g~~~spwHdIpl~~--~~~~vn~VVEIPrgs~~KyEidk~~~~npi~q   99 (267)
T PLN02707         52 GSGKKVSPWHDIPLHA--GDGTFNFVVEIPKETSAKMEVATDEPFTPIKQ   99 (267)
T ss_pred             CCCCccCchhcCCCCC--CCCEEEEEEEECCCCceeEEECccCCCCCEEE
Confidence            4588899999999983  35999999999999999999999999886544

>KOG0105|consensus

Probab=99.42  E-value=1.1e-12  Score=118.78  Aligned_cols=119  Identities=24%  Similarity=0.439  Sum_probs=103.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC---------
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG---------  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G---------  100 (451)
                      ...++|||+|||.++.+.+|.++|.+||.|.+|.|...  -...+||||+|+++.+|+.|+..-+|-.|.|         
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r--~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfpr   81 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR--PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPR   81 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC--CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEecc
Confidence            46789999999999999999999999999999988432  2236799999999999999998877655543         


Q ss_pred             --------------------------------------------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEE
Q psy300          101 --------------------------------------------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFI  136 (451)
Q Consensus       101 --------------------------------------------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV  136 (451)
                                                                  +.++++|++++.+-|.|....+.+|      |++.|
T Consensus        82 ggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD------g~GvV  155 (241)
T KOG0105|consen   82 GGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD------GVGVV  155 (241)
T ss_pred             CCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc------cceee
Confidence                                                        2589999999999999999999997      57899


Q ss_pred             EecchHHHHHHHHhcCCCcc
Q psy300          137 NYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       137 ~F~s~e~A~~Ai~~ln~riy  156 (451)
                      +|...++.+-|+.+++...+
T Consensus       156 ~~~r~eDMkYAvr~ld~~~~  175 (241)
T KOG0105|consen  156 EYLRKEDMKYAVRKLDDQKF  175 (241)
T ss_pred             eeeehhhHHHHHHhhccccc
Confidence            99999999999999987655

>KOG0147|consensus

Probab=99.33  E-value=3.2e-12  Score=132.03  Aligned_cols=122  Identities=30%  Similarity=0.478  Sum_probs=108.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC--------
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK--------  101 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~--------  101 (451)
                      ++.+||||||-.++++++|+.+|+.||.|..|.+.+|. ||.++||||++|.+.++|.+|+..|||..+-|+        
T Consensus       277 p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~  356 (549)
T KOG0147|consen  277 PMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVT  356 (549)
T ss_pred             chhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEee
Confidence            45559999999999999999999999999999999998 999999999999999999999999998554330        


Q ss_pred             --------------------------------------------------------------------------------
Q psy300          102 --------------------------------------------------------------------------------  101 (451)
Q Consensus       102 --------------------------------------------------------------------------------  101 (451)
                                                                                                      
T Consensus       357 ~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~  436 (549)
T KOG0147|consen  357 ERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADAS  436 (549)
T ss_pred             eecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCccccc
Confidence                                                                                            


Q ss_pred             ----------------------------CcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCC
Q psy300          102 ----------------------------ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK  153 (451)
Q Consensus       102 ----------------------------~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~  153 (451)
                                                  --.+++.+.+.+||.|..+-|.++    |-|+.||.|.+.+.|..|+.++||
T Consensus       437 p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~n----s~g~VYvrc~s~~~A~~a~~alhg  512 (549)
T KOG0147|consen  437 PAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKN----SAGCVYVRCPSAEAAGTAVKALHG  512 (549)
T ss_pred             cccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccC----CCceEEEecCcHHHHHHHHHHHhh
Confidence                                        023778888899999999888765    249999999999999999999999


Q ss_pred             Ccc
Q psy300          154 KPY  156 (451)
Q Consensus       154 riy  156 (451)
                      ++|
T Consensus       513 rWF  515 (549)
T KOG0147|consen  513 RWF  515 (549)
T ss_pred             hhh
Confidence            998

>KOG1548|consensus

Probab=99.31  E-value=1.4e-11  Score=120.90  Aligned_cols=126  Identities=22%  Similarity=0.395  Sum_probs=110.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEE--------EEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIID--------AQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK   99 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~--------i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~   99 (451)
                      ....++.|||.|||.++|.+++.++|+++|-|..        |+|-++..|.-+|=|.+.|...+++..|+..|++..|.
T Consensus       130 ~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~r  209 (382)
T KOG1548|consen  130 EPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELR  209 (382)
T ss_pred             ccccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCccccc
Confidence            3455778999999999999999999999998854        78888889999999999999999999999999887776


Q ss_pred             CC----------------------------------------------------------------------------Cc
Q psy300          100 GK----------------------------------------------------------------------------IT  103 (451)
Q Consensus       100 G~----------------------------------------------------------------------------~t  103 (451)
                      |.                                                                            --
T Consensus       210 g~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dl  289 (382)
T KOG1548|consen  210 GKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDL  289 (382)
T ss_pred             CcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHH
Confidence            60                                                                            13


Q ss_pred             HHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          104 EEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       104 ee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .++|++-+++||.|.++.|...   .+.|.+-|.|.+.++|..|+..|+||.|
T Consensus       290 kedl~eec~K~G~v~~vvv~d~---hPdGvvtV~f~n~eeA~~ciq~m~GR~f  339 (382)
T KOG1548|consen  290 KEDLTEECEKFGQVRKVVVYDR---HPDGVVTVSFRNNEEADQCIQTMDGRWF  339 (382)
T ss_pred             HHHHHHHHHHhCCcceEEEecc---CCCceeEEEeCChHHHHHHHHHhcCeee
Confidence            5788888999999999999753   4578899999999999999999999998

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.28  E-value=1.5e-11  Score=95.69  Aligned_cols=67  Identities=31%  Similarity=0.641  Sum_probs=61.2

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        35 lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      |||+|||.++++++|+++|+.||.|..+++..++.|.++|+|||+|.++++|.+|+..+++..+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~   67 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGR   67 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCE
Confidence            7999999999999999999999999999999987889999999999999999999999988887763

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 ....

>KOG0149|consensus

Probab=99.28  E-value=6.4e-12  Score=117.90  Aligned_cols=75  Identities=24%  Similarity=0.546  Sum_probs=65.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCCCcH
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGKITE  104 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~~te  104 (451)
                      +..-++||||||+..+..+.|+++|++||+|++..++.|+ +|+|||||||+|.+.++|.+|++..| -++.||.+.
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~-piIdGR~aN   84 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPN-PIIDGRKAN   84 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCC-Ccccccccc
Confidence            3356799999999999999999999999999999999999 99999999999999999999987654 345554443

>KOG4212|consensus

Probab=99.24  E-value=7.8e-11  Score=118.57  Aligned_cols=123  Identities=25%  Similarity=0.509  Sum_probs=111.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhc-cCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC----------
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFG-QYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG----------  100 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~-~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G----------  100 (451)
                      .+.+||.|+|+++...+|+++|. +.|+|..|.|+.|.+|++||+|.|+|.+++.+++|++.||...+.|          
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d  123 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHD  123 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCc
Confidence            45699999999999999999997 7899999999999999999999999999999999999887644332          


Q ss_pred             --------------------------------------------------------------------------------
Q psy300          101 --------------------------------------------------------------------------------  100 (451)
Q Consensus       101 --------------------------------------------------------------------------------  100 (451)
                                                                                                      
T Consensus       124 ~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~F  203 (608)
T KOG4212|consen  124 EQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSASF  203 (608)
T ss_pred             hhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchhhh
Confidence                                                                                            


Q ss_pred             ----------------------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCC
Q psy300          101 ----------------------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK  154 (451)
Q Consensus       101 ----------------------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~r  154 (451)
                                            .+..+.|++.|.--|.|+.+.+-.|+.|.++||+.++|+.+-+|..||..++..
T Consensus       204 lr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~~  279 (608)
T KOG4212|consen  204 LRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDRQ  279 (608)
T ss_pred             hhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhccC
Confidence                                  157799999999999999999999989999999999999999999999999853

>KOG0126|consensus

Probab=99.19  E-value=3.2e-12  Score=115.45  Aligned_cols=101  Identities=28%  Similarity=0.493  Sum_probs=80.9

Q ss_pred             ChhhhhhhhhhhhhhhcCccccccC---CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEE
Q psy300            1 MEKLAKKKKVKKEFKKKGKKKIERK---KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCG   76 (451)
Q Consensus         1 ~e~~~~kk~~~~~~~~~~~~~~~~~---~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~a   76 (451)
                      |+-+.+-|+..+-+.++-+......   -..-..+.-|||||||++.||.||.-+|++||+|..|.|+||. ||+|+|||
T Consensus         1 mnplt~vk~i~~lne~Elq~g~~~~~SWH~~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFa   80 (219)
T KOG0126|consen    1 MNPLTNVKNIQKLNERELQLGIADKKSWHQEYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFA   80 (219)
T ss_pred             CchhHHHHHHHHhhHHhhccccccccchhhhcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceE
Confidence            3444444555454444444333321   1234578899999999999999999999999999999999998 99999999


Q ss_pred             EEEEccHHHHHHHHHhcCCccCCCC
Q psy300           77 FINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        77 FV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      |+.|++..+...|+..+||..+.|+
T Consensus        81 FLcYEDQRSTILAVDN~NGiki~gR  105 (219)
T KOG0126|consen   81 FLCYEDQRSTILAVDNLNGIKILGR  105 (219)
T ss_pred             EEEecCccceEEEEeccCCceecce
Confidence            9999999999999999999988885

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.18  E-value=6.7e-11  Score=120.52  Aligned_cols=71  Identities=30%  Similarity=0.607  Sum_probs=66.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...++|||+|||.++++++|+++|++||.|.+++++++. +++++|||||+|.+.++|++|++.||+..+.|
T Consensus       191 ~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g  262 (346)
T TIGR01659       191 IKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEG  262 (346)
T ss_pred             cccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            356789999999999999999999999999999999998 99999999999999999999999999987765

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

Probab=99.17  E-value=7.4e-11  Score=111.22  Aligned_cols=70  Identities=24%  Similarity=0.457  Sum_probs=65.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPY   98 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f   98 (451)
                      ...+++|-|.|||.++++.+|.++|.+||.|..+.|.+|+ ||.+||||||.|.+.++|.+|+..|||.-|
T Consensus       186 R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gy  256 (270)
T KOG0122|consen  186 RDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGY  256 (270)
T ss_pred             CCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCccc
Confidence            3378899999999999999999999999999999999998 999999999999999999999999998643

>KOG4206|consensus

Probab=99.12  E-value=6.2e-10  Score=104.24  Aligned_cols=118  Identities=25%  Similarity=0.439  Sum_probs=102.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHH----HhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC-----
Q psy300           30 TKRGRLFIKNLPFKITEEEFKE----HFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG-----  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~----~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G-----  100 (451)
                      .++.||||.||+..+..++|++    +|++||.|..|...  ++.+.||-|||.|.+.+.|..|+.+|+|..|.|     
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~--kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mri   84 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAF--KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRI   84 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEec--CCCCccCceEEEecChhHHHHHHHHhcCCcccCchhhe
Confidence            3555999999999999999988    99999999988875  378899999999999999999999999987766     


Q ss_pred             ------------------------------------------------------------------------CCcHHHHH
Q psy300          101 ------------------------------------------------------------------------KITEEEFK  108 (451)
Q Consensus       101 ------------------------------------------------------------------------~~tee~L~  108 (451)
                                                                                              .++.+.|.
T Consensus        85 qyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~  164 (221)
T KOG4206|consen   85 QYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLS  164 (221)
T ss_pred             ecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHH
Confidence                                                                                    13568889


Q ss_pred             HHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCC
Q psy300          109 EHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK  153 (451)
Q Consensus       109 ~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~  153 (451)
                      .+|++|.....++++...    .+.|||+|.+...|..|...+.+
T Consensus       165 ~lf~qf~g~keir~i~~~----~~iAfve~~~d~~a~~a~~~lq~  205 (221)
T KOG4206|consen  165 DLFEQFPGFKEIRLIPPR----SGIAFVEFLSDRQASAAQQALQG  205 (221)
T ss_pred             HHHhhCcccceeEeccCC----CceeEEecchhhhhHHHhhhhcc
Confidence            999999999999998753    67899999999888888888754

>smart00362 RRM_2 RNA recognition motif

Probab=99.11  E-value=2.9e-10  Score=86.62  Aligned_cols=66  Identities=38%  Similarity=0.621  Sum_probs=61.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        34 ~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      +|||+|||..++.++|+++|++||++.++.+.++. +.++|+|||+|.+.++|.+|+..+++..+.|
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~-~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~   66 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT-GKSKGFAFVEFESEEDAEKAIEALNGTKLGG   66 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC-CCCCceEEEEeCCHHHHHHHHHHhCCcEECC
Confidence            58999999999999999999999999999998876 7789999999999999999999999877765

>KOG0125|consensus

Probab=99.10  E-value=1.3e-10  Score=113.53  Aligned_cols=75  Identities=25%  Similarity=0.563  Sum_probs=67.8

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ++.....++|+|+|||+...+-||+.+|.+||+|++|.|+.+..| |||||||+|++.++|++|.++|+|..+.||
T Consensus        90 s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERG-SKGFGFVTmen~~dadRARa~LHgt~VEGR  164 (376)
T KOG0125|consen   90 SSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERG-SKGFGFVTMENPADADRARAELHGTVVEGR  164 (376)
T ss_pred             CCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCC-CCccceEEecChhhHHHHHHHhhcceeece
Confidence            334456689999999999999999999999999999999987544 799999999999999999999999999885

>PRK00642 inorganic pyrophosphatase; Provisional

Probab=99.09  E-value=1.3e-10  Score=109.32  Aligned_cols=44  Identities=18%  Similarity=0.246  Sum_probs=38.8

Q ss_pred             CCccCCccCCCccccCCCCEEEEEEeecCCCccceeeeccccceE
Q psy300          382 NGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRL  426 (451)
Q Consensus       382 ~~~~s~~hd~~l~~~~~~~~~~~~~e~p~~~~~k~e~~~~~~~~~  426 (451)
                      +-.+|||||||+..+. .+++||||||||||++|||+.+++....
T Consensus         6 ~~~~spwhdi~~~~~~-~~~vn~VIEIP~gs~~KyE~dk~~g~~~   49 (205)
T PRK00642          6 LSRAHPWHGLSLGPDA-PESVCCYIEITPFDTVKYELDKATGYLK   49 (205)
T ss_pred             ccccCccccCCCCCCC-CCEEEEEEEECCCCCeeEEEecCCCceE
Confidence            4568999999998765 5899999999999999999999987664

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.09  E-value=3.2e-10  Score=109.55  Aligned_cols=68  Identities=19%  Similarity=0.301  Sum_probs=62.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ..++|||+|||+++++++|+++|+.||.|.+|.|+++.  .++|||||+|.++++|..|+. |+|..+.|+
T Consensus         3 ~~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~--~~~GfAFVtF~d~eaAe~All-LnG~~l~gr   70 (260)
T PLN03120          3 QVRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN--ERSQIAYVTFKDPQGAETALL-LSGATIVDQ   70 (260)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC--CCCCEEEEEeCcHHHHHHHHH-hcCCeeCCc
Confidence            35799999999999999999999999999999998875  357999999999999999995 999988884

>KOG0106|consensus

Probab=99.09  E-value=8.8e-11  Score=110.67  Aligned_cols=113  Identities=25%  Similarity=0.521  Sum_probs=98.9

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC-----------
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG-----------  100 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G-----------  100 (451)
                      +.++|||+||+.+.+.+|..+|..||.+.++.+.       .||+||.|.+..+|..|+..+|++.|.|           
T Consensus         1 m~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk-------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    1 MPRVYIGRLPYRARERDVERFFKGYGKIPDADMK-------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CCceeecccCCccchhHHHHHHhhccccccceee-------cccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            3579999999999999999999999999999885       4799999999999999999998887653           


Q ss_pred             ------------------------------------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHH
Q psy300          101 ------------------------------------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA  144 (451)
Q Consensus       101 ------------------------------------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A  144 (451)
                                                          ++.+++|.++|.++|.+.+...       .++++||+|++.++|
T Consensus        74 ~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~-------~~~~~~v~Fs~~~da  146 (216)
T KOG0106|consen   74 RRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA-------RRNFAFVEFSEQEDA  146 (216)
T ss_pred             ccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh-------hccccceeehhhhhh
Confidence                                                1477999999999999965555       267999999999999


Q ss_pred             HHHHHhcCCCcccC
Q psy300          145 VKAILKSNKKPYKG  158 (451)
Q Consensus       145 ~~Ai~~ln~riy~~  158 (451)
                      .+|+..+++...+.
T Consensus       147 ~ra~~~l~~~~~~~  160 (216)
T KOG0106|consen  147 KRALEKLDGKKLNG  160 (216)
T ss_pred             hhcchhccchhhcC
Confidence            99999999876643

>KOG0107|consensus

Probab=99.06  E-value=2.4e-10  Score=102.96  Aligned_cols=67  Identities=21%  Similarity=0.399  Sum_probs=62.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .-.++||||||+.++++.+|...|..||++.++.+-+.    ..|||||+|+++.+|..|+..|+|+.+.|
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn----PPGfAFVEFed~RDA~DAvr~LDG~~~cG   74 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN----PPGFAFVEFEDPRDAEDAVRYLDGKDICG   74 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec----CCCceEEeccCcccHHHHHhhcCCccccC
Confidence            45889999999999999999999999999999998764    57899999999999999999999998876

>KOG0113|consensus

Probab=99.06  E-value=3.2e-10  Score=109.61  Aligned_cols=71  Identities=25%  Similarity=0.495  Sum_probs=67.1

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .+-+||||+-|+++++|..|+..|+.||+|..|+|++|. ||+|+|||||+|+.+.+...|....+|..+.|
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idg  170 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDG  170 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecC
Confidence            467899999999999999999999999999999999998 99999999999999999999999988887766

>KOG0124|consensus

Probab=99.05  E-value=1.2e-09  Score=107.98  Aligned_cols=66  Identities=30%  Similarity=0.528  Sum_probs=60.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSN   94 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~ln   94 (451)
                      ...-.+|||..+-++.+++||+.+|+.||+|.+|++-+++ ++.++||||++|.+..+...|+..||
T Consensus       207 Ak~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMN  273 (544)
T KOG0124|consen  207 AKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMN  273 (544)
T ss_pred             HHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcc
Confidence            3456899999999999999999999999999999999998 56689999999999999999988776

>KOG4207|consensus

Probab=99.02  E-value=2.6e-10  Score=105.16  Aligned_cols=87  Identities=21%  Similarity=0.456  Sum_probs=79.5

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCCCcHH
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGKITEE  105 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~~tee  105 (451)
                      ++-..+.+|-|-||.+.++.++|+.+|++||.|-+|.|.+|. |+.++|||||.|....+|+.|+++|+|.++.|    -
T Consensus         8 Pdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldg----R   83 (256)
T KOG4207|consen    8 PDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDG----R   83 (256)
T ss_pred             CCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeecc----c
Confidence            455688999999999999999999999999999999999999 99999999999999999999999999999998    3


Q ss_pred             HHHHHhcccCcc
Q psy300          106 EFKEHFGQYGDI  117 (451)
Q Consensus       106 ~L~~~F~~fG~V  117 (451)
                      +|+-.|.+||.-
T Consensus        84 elrVq~arygr~   95 (256)
T KOG4207|consen   84 ELRVQMARYGRP   95 (256)
T ss_pred             eeeehhhhcCCC
Confidence            555557888875

>PLN03213 repressor of silencing 3; Provisional

Probab=99.02  E-value=6.9e-10  Score=113.27  Aligned_cols=69  Identities=17%  Similarity=0.320  Sum_probs=63.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccH--HHHHHHHHhcCCccCCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANK--ISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~--~~A~~Al~~lng~~f~G~  101 (451)
                      ....+||||||++++++++|+.+|+.||.|.++.|++. +|  ||||||+|.+.  .++.+|+..|||..+.|+
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE-TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR   78 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT-KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGG   78 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc-cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCc
Confidence            35579999999999999999999999999999999954 67  99999999987  689999999999999983

>PLN02373 soluble inorganic pyrophosphatase

Probab=99.02  E-value=3.5e-10  Score=104.79  Aligned_cols=54  Identities=30%  Similarity=0.365  Sum_probs=43.6

Q ss_pred             CccCCccCCCccccCCCCEEEEEEeecCCCccceeeeccccceEEEEEeeCCCCchh
Q psy300          383 GLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLYLVCFNLPSPLGY  439 (451)
Q Consensus       383 ~~~s~~hd~~l~~~~~~~~~~~~~e~p~~~~~k~e~~~~~~~~~~~~~~~~~~~~~~  439 (451)
                      -.+|||||||+.++. .+++||||||||||++|+|+.+++.+  ..+-.-|++++.|
T Consensus         7 ~~~~~whdi~~~~~~-~~~v~vVIEIP~gs~~KyE~dk~~g~--i~~Dr~l~~~~~y   60 (188)
T PLN02373          7 VAAHPWHDLEIGPGA-PAIFNCVVEITKGSKVKYELDKKTGL--IKVDRVLYSSVVY   60 (188)
T ss_pred             ccCCccccCCCCCCC-CCEEEEEEEECCCCCeeEEEccCCCC--EEEeeecccCCcC
Confidence            458999999998764 68999999999999999999999753  4445556666555

>KOG4211|consensus

Probab=99.01  E-value=2.5e-09  Score=109.67  Aligned_cols=122  Identities=22%  Similarity=0.401  Sum_probs=97.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcC---Ccc----------
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN---KKP----------   97 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~ln---g~~----------   97 (451)
                      ...-|-+++||.++|+++|.+||+..+ |.++.+.+. +|+..|-|||+|.+++++++|+++-.   +.-          
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~-~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~~~   86 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRR-NGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAGGA   86 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEEecc-CCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccCCc
Confidence            334566789999999999999999984 777666553 79999999999999999999997511   100          


Q ss_pred             ---------------------CCC---CCcHHHHHHHhcccCccee-eEEeeCCCCCccceEEEEecchHHHHHHHHhcC
Q psy300           98 ---------------------YKG---KITEEEFKEHFGQYGDIID-AQLLKNADGKLKGCGFINYANKISAVKAILKSN  152 (451)
Q Consensus        98 ---------------------f~G---~~tee~L~~~F~~fG~V~~-v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln  152 (451)
                                           +.|   .+|+++|.++|+---.|.. +.++.+..+++.|-|||+|++.+.|+.|+....
T Consensus        87 e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~rhr  166 (510)
T KOG4211|consen   87 EADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGRHR  166 (510)
T ss_pred             cccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHHHH
Confidence                                 011   4899999999998766666 445667889999999999999999999998765


Q ss_pred             CC
Q psy300          153 KK  154 (451)
Q Consensus       153 ~r  154 (451)
                      .+
T Consensus       167 e~  168 (510)
T KOG4211|consen  167 EN  168 (510)
T ss_pred             Hh
Confidence            43

>KOG0114|consensus

Probab=99.01  E-value=1.5e-09  Score=89.99  Aligned_cols=71  Identities=31%  Similarity=0.484  Sum_probs=63.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      +..-++-|||+|||+++|.+++.++|.+||.|..|++=.  +...+|-|||.|++..+|.+|+..|+|..+.+
T Consensus        14 ppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~--~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~   84 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGN--TKETRGTAFVVYEDIFDAKKACDHLSGYNVDN   84 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecC--ccCcCceEEEEehHhhhHHHHHHHhcccccCC
Confidence            344678999999999999999999999999999999833  44568999999999999999999999988776

>smart00360 RRM RNA recognition motif

Probab=99.01  E-value=1.2e-09  Score=82.71  Aligned_cols=64  Identities=36%  Similarity=0.631  Sum_probs=59.6

Q ss_pred             EcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           37 IKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        37 VgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      |+|||..+++++|+++|++||.|.++.+..++ ++.++|+|||+|.+.++|.+|+..+++..+.|
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~   65 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDG   65 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCC
Confidence            58999999999999999999999999999887 78999999999999999999999999877765

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.00  E-value=1.2e-09  Score=104.27  Aligned_cols=68  Identities=15%  Similarity=0.268  Sum_probs=61.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ...+|||+||++.+|+++|+++|+.||+|.+|+|+++  ++++|+|||+|.++++|..|+ .|+|..+.+.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D--~et~gfAfVtF~d~~aaetAl-lLnGa~l~d~   71 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS--GEYACTAYVTFKDAYALETAV-LLSGATIVDQ   71 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC--CCcceEEEEEECCHHHHHHHH-hcCCCeeCCc
Confidence            4579999999999999999999999999999999987  556789999999999999998 6999888773

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.00  E-value=1.2e-09  Score=104.16  Aligned_cols=70  Identities=34%  Similarity=0.685  Sum_probs=67.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .++|||+|||.++++++|.++|.+||.|..+.+..++ +|+++|||||.|.+.++|..|+..+++..|.|+
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~  185 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGR  185 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCc
Confidence            5999999999999999999999999999999999997 999999999999999999999999999888874

>KOG0121|consensus

Probab=98.98  E-value=5.2e-10  Score=95.95  Aligned_cols=95  Identities=22%  Similarity=0.277  Sum_probs=77.6

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCCCc
Q psy300           25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGKIT  103 (451)
Q Consensus        25 ~~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~~t  103 (451)
                      .......+++||||||+.-++|++|.++|++.|+|..|.+=.|+ +..+-|||||+|.+.++|..|+.-++|..+..++-
T Consensus        29 ~~~a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~i  108 (153)
T KOG0121|consen   29 QLEALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPI  108 (153)
T ss_pred             HHHHHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccce
Confidence            33455688999999999999999999999999999999887787 77889999999999999999999999988877544


Q ss_pred             HHHHHHHhc---ccCccee
Q psy300          104 EEEFKEHFG---QYGDIID  119 (451)
Q Consensus       104 ee~L~~~F~---~fG~V~~  119 (451)
                      .-++-.=|.   +||.-.+
T Consensus       109 r~D~D~GF~eGRQyGRG~s  127 (153)
T KOG0121|consen  109 RIDWDAGFVEGRQYGRGKS  127 (153)
T ss_pred             eeeccccchhhhhhcCCCC
Confidence            444444342   4555433

>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=98.96  E-value=3.5e-09  Score=80.96  Aligned_cols=67  Identities=33%  Similarity=0.625  Sum_probs=62.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        34 ~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      +|+|+|||..+++++|+++|+.+|.|..+.+..++.+.++|+|||+|.+.++|..|+..+++..+.|
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~   67 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGG   67 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            5899999999999999999999999999999988766889999999999999999999999887665

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).

>KOG1457|consensus

Probab=98.92  E-value=1.2e-08  Score=95.36  Aligned_cols=125  Identities=18%  Similarity=0.236  Sum_probs=101.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeEC-C-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC-------
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-A-DGKLKGCGFINYANKISAVKAILKSNKKPYKG-------  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d-~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G-------  100 (451)
                      ..-++|||.+||.++...+|..+|..|-.-+.+.+... + ....+-+||+.|.+...|..|+..|||..|.-       
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            35799999999999999999999999977666655432 2 23456899999999999999999999876531       


Q ss_pred             --------------------------------------------------------------------------------
Q psy300          101 --------------------------------------------------------------------------------  100 (451)
Q Consensus       101 --------------------------------------------------------------------------------  100 (451)
                                                                                                      
T Consensus       112 iElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~~P  191 (284)
T KOG1457|consen  112 IELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSKAP  191 (284)
T ss_pred             eeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhcCC
Confidence                                                                                            


Q ss_pred             -----------------------------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhc
Q psy300          101 -----------------------------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS  151 (451)
Q Consensus       101 -----------------------------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~l  151 (451)
                                                   +++|++|+.+|+.|......++.. +.|  ...||+.|+..+.|..|+..+
T Consensus       192 ~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~-~~g--~~vaf~~~~~~~~at~am~~l  268 (284)
T KOG1457|consen  192 SANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA-RGG--MPVAFADFEEIEQATDAMNHL  268 (284)
T ss_pred             cccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec-CCC--cceEeecHHHHHHHHHHHHHh
Confidence                                         279999999999998877777643 344  347999999999999999999


Q ss_pred             CCCccc
Q psy300          152 NKKPYK  157 (451)
Q Consensus       152 n~riy~  157 (451)
                      .|.+.-
T Consensus       269 qg~~~s  274 (284)
T KOG1457|consen  269 QGNLLS  274 (284)
T ss_pred             hcceec
Confidence            886643

>KOG0120|consensus

Probab=98.92  E-value=2.2e-09  Score=112.27  Aligned_cols=126  Identities=21%  Similarity=0.428  Sum_probs=109.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC--------
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK--------  101 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~--------  101 (451)
                      ...++||++||...++.++.++...||++....++.+. +|.++||||.+|.++.....|++.+||+.+.++        
T Consensus       288 ~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~  367 (500)
T KOG0120|consen  288 SPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAI  367 (500)
T ss_pred             ccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhh
Confidence            45789999999999999999999999999999999988 899999999999999999999999888654430        


Q ss_pred             ----------------------------------------Cc-------------HHHHHHHhcccCcceeeEEeeC-CC
Q psy300          102 ----------------------------------------IT-------------EEEFKEHFGQYGDIIDAQLLKN-AD  127 (451)
Q Consensus       102 ----------------------------------------~t-------------ee~L~~~F~~fG~V~~v~v~~d-~~  127 (451)
                                                              +|             -++++.-+.+||.|.+|.++++ ..
T Consensus       368 ~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~  447 (500)
T KOG0120|consen  368 VGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPD  447 (500)
T ss_pred             ccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCC
Confidence                                                    11             2566677889999999999886 32


Q ss_pred             C---CccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          128 G---KLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       128 g---~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      +   ...|..||+|.+.++|++|..+|+|+.|
T Consensus       448 ~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF  479 (500)
T KOG0120|consen  448 ENPVPGTGKVFVEFADTEDSQRAMEELTGRKF  479 (500)
T ss_pred             CCcCCCcccEEEEecChHHHHHHHHHccCcee
Confidence            2   2468899999999999999999999998

>KOG0108|consensus

Probab=98.86  E-value=4.9e-09  Score=108.93  Aligned_cols=69  Identities=28%  Similarity=0.572  Sum_probs=67.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      +.+||||+|+++++++|.++|+..|.|.+++++.|+ ||+++||||++|.+.++|..|++.|||..+.|+
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr   88 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGR   88 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCc
Confidence            899999999999999999999999999999999998 999999999999999999999999999999884

>KOG0111|consensus

Probab=98.80  E-value=2.5e-09  Score=99.43  Aligned_cols=73  Identities=26%  Similarity=0.415  Sum_probs=67.9

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .....++||||+|..++++.-|...|-+||.|..|.++.|. ++++||||||+|...++|..|+..||+..+.|
T Consensus         6 ~a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~G   79 (298)
T KOG0111|consen    6 MANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFG   79 (298)
T ss_pred             ccccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcc
Confidence            34567899999999999999999999999999999999997 99999999999999999999999999986665

>KOG1456|consensus

Probab=98.80  E-value=8.8e-08  Score=95.28  Aligned_cols=118  Identities=13%  Similarity=0.208  Sum_probs=97.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhc-CCccCCC------
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS-NKKPYKG------  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~l-ng~~f~G------  100 (451)
                      ..+.+--|.|++|-..++|.+|.+..+.||+|..+..+..     +..+.|+|++.+.|+.|+..- ...++.+      
T Consensus        27 k~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~-----~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~  101 (494)
T KOG1456|consen   27 KPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPH-----KRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALF  101 (494)
T ss_pred             CCCCCceEEEeccccccchhHHHHHHhcCCceEEEEeccc-----cceeeeeeccccchhhheehhccCcccccCchhhc
Confidence            4456678999999999999999999999999998887643     557999999999999887421 1111111      


Q ss_pred             -------------------------------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHH
Q psy300          101 -------------------------------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL  149 (451)
Q Consensus       101 -------------------------------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~  149 (451)
                                                     .+|-+-|..++...|.|..+.|++. +   .-.|.|+|++.+.|++|..
T Consensus       102 NyStsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk-n---gVQAmVEFdsv~~AqrAk~  177 (494)
T KOG1456|consen  102 NYSTSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK-N---GVQAMVEFDSVEVAQRAKA  177 (494)
T ss_pred             ccchhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec-c---ceeeEEeechhHHHHHHHh
Confidence                                           2799999999999999999999885 3   3479999999999999999


Q ss_pred             hcCCC
Q psy300          150 KSNKK  154 (451)
Q Consensus       150 ~ln~r  154 (451)
                      +|||-
T Consensus       178 alNGA  182 (494)
T KOG1456|consen  178 ALNGA  182 (494)
T ss_pred             hcccc
Confidence            99874

>KOG4454|consensus

Probab=98.77  E-value=2.6e-09  Score=99.36  Aligned_cols=120  Identities=23%  Similarity=0.309  Sum_probs=105.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC---------
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG---------  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G---------  100 (451)
                      ...++|||+|+...++++-|.++|-+.|+|..+.|..+++++.+ ||||.|.++-.+.-|++.+||..+.+         
T Consensus         7 e~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~   85 (267)
T KOG4454|consen    7 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRC   85 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccchhhccccc
Confidence            35689999999999999999999999999999999988888888 99999999999999999999865543         


Q ss_pred             ---------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHh
Q psy300          101 ---------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK  150 (451)
Q Consensus       101 ---------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~  150 (451)
                               +++++.+...|+.-|.+..+++.++..|+++.++|+.+...-+.-.+...
T Consensus        86 G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~  144 (267)
T KOG4454|consen   86 GNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDL  144 (267)
T ss_pred             CCCcchhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhh
Confidence                     47999999999999999999999988899999999998766555555443

>KOG0110|consensus

Probab=98.77  E-value=3e-08  Score=105.60  Aligned_cols=124  Identities=25%  Similarity=0.386  Sum_probs=102.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC-------
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG-------  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G-------  100 (451)
                      .....+-++|+|||..+..++|..+|..||+|..+-+.  +.|.   -++|.|.++.+|.+|...+..+.|..       
T Consensus       381 ~~rs~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp--~~G~---~aiv~fl~p~eAr~Afrklaysr~k~~plyle~  455 (725)
T KOG0110|consen  381 AERSDTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLP--PGGT---GAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEW  455 (725)
T ss_pred             hhhhcceeeeccCccccccHHHHHHhhcccccceeecC--cccc---eeeeeecCccchHHHHHHhchhhhccCcccccc
Confidence            45567899999999999999999999999999988443  3333   28999999999999998765432211       


Q ss_pred             ----------------------------------------------------------------------CCcHHHHHHH
Q psy300          101 ----------------------------------------------------------------------KITEEEFKEH  110 (451)
Q Consensus       101 ----------------------------------------------------------------------~~tee~L~~~  110 (451)
                                                                                            .+|.++|..+
T Consensus       456 aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~  535 (725)
T KOG0110|consen  456 APEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLEDL  535 (725)
T ss_pred             ChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHHH
Confidence                                                                                  1588999999


Q ss_pred             hcccCcceeeEEeeCCCC----CccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          111 FGQYGDIIDAQLLKNADG----KLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       111 F~~fG~V~~v~v~~d~~g----~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      |...|.|.++.|.+.+.+    .|.|||||+|.+.++|++|+..|+|...
T Consensus       536 F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvl  585 (725)
T KOG0110|consen  536 FSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVL  585 (725)
T ss_pred             HHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCcee
Confidence            999999999999765433    3669999999999999999999997764

>KOG0130|consensus

Probab=98.73  E-value=1.7e-08  Score=87.46  Aligned_cols=71  Identities=25%  Similarity=0.402  Sum_probs=65.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...--|||.++-..+++++|.+.|..||+|..+.|-.|+ ||..+|||+|+|++.++|++|+..+||..+.|
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~  141 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLG  141 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhC
Confidence            345679999999999999999999999999999998887 99999999999999999999999999976655

>smart00361 RRM_1 RNA recognition motif

Probab=98.73  E-value=3e-08  Score=77.69  Aligned_cols=56  Identities=20%  Similarity=0.506  Sum_probs=50.0

Q ss_pred             HHHHHHHhc----cCCCeEEEE-EeECC-C--CCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           46 EEEFKEHFG----QYGDIIDAQ-LLKNA-D--GKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        46 e~~L~~~F~----~~G~I~~i~-l~~d~-t--g~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      +++|+++|+    +||.|.++. ++.++ +  ++++|||||.|.+.++|.+|+..|||+.+.|+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr   65 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGR   65 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            578889998    999999995 66665 5  89999999999999999999999999988874

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

Probab=98.70  E-value=2.4e-08  Score=89.51  Aligned_cols=63  Identities=25%  Similarity=0.610  Sum_probs=55.1

Q ss_pred             CCccCCC----CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           94 NKKPYKG----KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        94 ng~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ..++|.+    .+++++|+++|++||.|.++.++.+ .+++++|||||+|.+.++|..|+..+|+..+
T Consensus        34 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i  101 (144)
T PLN03134         34 STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKEL  101 (144)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEE
Confidence            3445555    4799999999999999999999988 5789999999999999999999999987653

>PF00076 RRM_1: RNA recognition motif

Probab=98.68  E-value=3.7e-08  Score=75.68  Aligned_cols=57  Identities=33%  Similarity=0.605  Sum_probs=53.0

Q ss_pred             CCCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          100 GKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       100 G~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ..+|+++|+++|++||.|..+.+..+.++.++|+|||+|.+.++|.+|+..+++..+
T Consensus         8 ~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~   64 (70)
T PF00076_consen    8 PDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKI   64 (70)
T ss_dssp             TTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             CcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEE
Confidence            368999999999999999999999987889999999999999999999999998665

(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 ....

>KOG4208|consensus

Probab=98.66  E-value=5.1e-08  Score=90.24  Aligned_cols=76  Identities=24%  Similarity=0.426  Sum_probs=68.1

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHHHhccC-CCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQY-GDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        25 ~~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~-G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..+......-+||+.+|..+.+.++..+|.+| |.+..+++.|++ ||.|+|||||+|++++.|.-|-+.||+.+|.|
T Consensus        42 ~~p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e  119 (214)
T KOG4208|consen   42 EKPEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLME  119 (214)
T ss_pred             cCCccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhh
Confidence            34455677899999999999999999999999 678888888887 99999999999999999999999999987766

>KOG0149|consensus

Probab=98.66  E-value=2.5e-08  Score=93.96  Aligned_cols=60  Identities=27%  Similarity=0.563  Sum_probs=54.3

Q ss_pred             ccCCC----CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCc
Q psy300           96 KPYKG----KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKP  155 (451)
Q Consensus        96 ~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~ri  155 (451)
                      |+|.|    .+..+.|+++|++||+|+++.|+.| .+|+|+|||||+|.+.++|.+|....|-.+
T Consensus        14 KifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piI   78 (247)
T KOG0149|consen   14 KIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPII   78 (247)
T ss_pred             EEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcc
Confidence            56777    4788999999999999999999998 589999999999999999999999887655

>KOG0122|consensus

Probab=98.57  E-value=9.5e-08  Score=90.47  Aligned_cols=56  Identities=27%  Similarity=0.514  Sum_probs=52.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++++|+++|.+||.|..+-+.+| .+|.++|||||+|.++++|++||..|||.=|
T Consensus       200 d~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gy  256 (270)
T KOG0122|consen  200 DMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGY  256 (270)
T ss_pred             ccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCccc
Confidence            4799999999999999999999998 6899999999999999999999999998543

>smart00361 RRM_1 RNA recognition motif

Probab=98.55  E-value=1.2e-07  Score=74.21  Aligned_cols=53  Identities=19%  Similarity=0.475  Sum_probs=46.4

Q ss_pred             HHHHHHHhc----ccCcceeeE-EeeC-CC--CCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          104 EEEFKEHFG----QYGDIIDAQ-LLKN-AD--GKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       104 ee~L~~~F~----~fG~V~~v~-v~~d-~~--g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      +++|+++|+    +||.|.++. ++.+ .+  +.++|||||+|.+.++|.+|+..+|++.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~   62 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYF   62 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            578888888    999999995 5544 34  88999999999999999999999999876

>KOG0117|consensus

Probab=98.53  E-value=1e-07  Score=96.89  Aligned_cols=63  Identities=30%  Similarity=0.523  Sum_probs=59.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...-|||+||+.++|++.|+++|++||.|..|+.++|       ||||.|.+.++|.+||+.+||+.+.|
T Consensus       258 ~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD-------YaFVHf~eR~davkAm~~~ngkeldG  320 (506)
T KOG0117|consen  258 KVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD-------YAFVHFAEREDAVKAMKETNGKELDG  320 (506)
T ss_pred             heeeeeeeccchhhhHHHHHHHHHhccceEEeecccc-------eeEEeecchHHHHHHHHHhcCceecC
Confidence            4568999999999999999999999999999998876       99999999999999999999998877

>KOG0146|consensus

Probab=98.49  E-value=2e-07  Score=89.20  Aligned_cols=73  Identities=26%  Similarity=0.414  Sum_probs=67.9

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPY   98 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f   98 (451)
                      ....++.|+|||-.||.+..+.+|..+|-.||-|.+.++..|+ |..||.||||.|.++.+|+.||..|||..+
T Consensus       279 qreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQI  352 (371)
T KOG0146|consen  279 QREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQI  352 (371)
T ss_pred             hhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhh
Confidence            3356688999999999999999999999999999999999998 999999999999999999999999999644

>KOG0128|consensus

Probab=98.43  E-value=2.1e-08  Score=108.60  Aligned_cols=126  Identities=21%  Similarity=0.357  Sum_probs=108.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeEC-CCCCceeEEEEEEccHHHHHHHHHhcCCccCC-------C--
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYK-------G--  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d-~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~-------G--  100 (451)
                      .-.++||+||+..+.+.+|...|+.+|.+..+++..- ..++-||+||+.|..++++.+|+....+..+.       |  
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK~~v~i~g~p  745 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGKISVAISGPP  745 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhhhhhhheeCCC
Confidence            4478999999999999999999999999888877632 37888999999999999999998754433221       1  


Q ss_pred             -CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 -KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 -~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                       +.|.+.|+.+++.+|.+.+.+++..+.|+++|-+||.|.+..++.++..+.+...+
T Consensus       746 f~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~  802 (881)
T KOG0128|consen  746 FQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGK  802 (881)
T ss_pred             CCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhh
Confidence             35999999999999999999999999999999999999999999999988876543

>KOG0129|consensus

Probab=98.43  E-value=1.3e-06  Score=90.48  Aligned_cols=121  Identities=23%  Similarity=0.425  Sum_probs=96.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC--CC--Ccee---EEEEEEccHHHHHHHHHhcC--------
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA--DG--KLKG---CGFINYANKISAVKAILKSN--------   94 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~--tg--~skG---~aFV~F~~~~~A~~Al~~ln--------   94 (451)
                      .-.++||||+||.+++|+.|...|..||.+. +...+..  .+  -++|   |+|+.|+++.++..-+.+..        
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~yf  335 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGNYYF  335 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccceEE
Confidence            3568999999999999999999999999964 4444221  11  2356   99999999988876554311        


Q ss_pred             -----------------------------------CccCCC----CCcHHHHHHHhc-ccCcceeeEEeeC-CCCCccce
Q psy300           95 -----------------------------------KKPYKG----KITEEEFKEHFG-QYGDIIDAQLLKN-ADGKLKGC  133 (451)
Q Consensus        95 -----------------------------------g~~f~G----~~tee~L~~~F~-~fG~V~~v~v~~d-~~g~srG~  133 (451)
                                                         .++|.|    -++-++|..+|+ -||.|.++.|-.| +-+-++|-
T Consensus       336 ~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGa  415 (520)
T KOG0129|consen  336 KVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGA  415 (520)
T ss_pred             EEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCc
Confidence                                               123333    379999999999 6999999999998 56779999


Q ss_pred             EEEEecchHHHHHHHHhc
Q psy300          134 GFINYANKISAVKAILKS  151 (451)
Q Consensus       134 gFV~F~s~e~A~~Ai~~l  151 (451)
                      |-|+|++..+-.+||.+.
T Consensus       416 GRVtFsnqqsYi~AIsar  433 (520)
T KOG0129|consen  416 GRVTFSNQQAYIKAISAR  433 (520)
T ss_pred             ceeeecccHHHHHHHhhh
Confidence            999999999999999775

>PF13893 RRM_5: RNA recognition motif

Probab=98.42  E-value=4.7e-07  Score=67.42  Aligned_cols=49  Identities=24%  Similarity=0.579  Sum_probs=42.9

Q ss_pred             HHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           49 FKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        49 L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      |.++|++||+|.++.+..+.    +++|||+|.+.++|.+|++.+||..|.|+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~   49 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK----RGFAFVEFASVEDAQKAIEQLNGRQFNGR   49 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS----TTEEEEEESSHHHHHHHHHHHTTSEETTE
T ss_pred             ChHHhCCcccEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            67899999999999997652    58999999999999999999999988763

(a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....

>KOG0415|consensus

Probab=98.41  E-value=3.1e-07  Score=90.92  Aligned_cols=72  Identities=24%  Similarity=0.418  Sum_probs=66.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .++.+-|||..|.+-++.++|.-+|+.||.|.+|.+++|. ||.|..||||+|.+.+++++|.-+|++.++..
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDD  308 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDD  308 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeecc
Confidence            4567899999999999999999999999999999999998 99999999999999999999999998876654

>KOG0131|consensus

Probab=98.40  E-value=2.9e-07  Score=83.71  Aligned_cols=72  Identities=28%  Similarity=0.444  Sum_probs=64.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEE-EEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i-~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..-..++||+||.+.+++..|.+.|+.||.+.+. ++++++ ||.++||||+.|.+.+.+.+|+..+||..+..
T Consensus        93 l~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~n  166 (203)
T KOG0131|consen   93 LDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCN  166 (203)
T ss_pred             ccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcC
Confidence            3345899999999999999999999999997764 788888 89999999999999999999999999987664

>PF14259 RRM_6: RNA recognition motif (a

Probab=98.39  E-value=6.9e-07  Score=69.21  Aligned_cols=56  Identities=29%  Similarity=0.574  Sum_probs=49.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++++|+++|+.||.|..+.+..++.+.++|+|||+|.+.++|.+|+...++..+
T Consensus         9 ~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~   64 (70)
T PF14259_consen    9 STTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEI   64 (70)
T ss_dssp             T--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             CCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEE
Confidence            58999999999999999999999986789999999999999999999999876554

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 ....

>KOG1190|consensus

Probab=98.36  E-value=3.5e-06  Score=84.98  Aligned_cols=161  Identities=20%  Similarity=0.300  Sum_probs=118.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeE-EEEEEccHHHHHHHHHhcCCccCC-C--------
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILKSNKKPYK-G--------  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~-aFV~F~~~~~A~~Al~~lng~~f~-G--------  100 (451)
                      .--+++|+|+-+.++-+-|..+|++||.|..|.-..    ++-|| |.|+|.+...|+.|...|+|..+. |        
T Consensus       149 ~vLr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~----Knn~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~  224 (492)
T KOG1190|consen  149 PVLRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFT----KNNGFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDF  224 (492)
T ss_pred             eeEEEEeccceeeeEHHHHHHHHhhcceeEEEEEEe----cccchhhhhhccchhhHHHHHHhccCCcccCceeEEEeeh
Confidence            334788999999999999999999999998874432    23455 899999999999998887775321 1        


Q ss_pred             --------------------------------------------------------------------------------
Q psy300          101 --------------------------------------------------------------------------------  100 (451)
Q Consensus       101 --------------------------------------------------------------------------------  100 (451)
                                                                                                      
T Consensus       225 Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsn  304 (492)
T KOG1190|consen  225 SKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSN  304 (492)
T ss_pred             hhcccceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEec
Confidence                                                                                            


Q ss_pred             ----CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcccCCCCCcccccccCCccccc
Q psy300          101 ----KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSENGLISPFHDIPLYSNV  176 (451)
Q Consensus       101 ----~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~~~~~G~iSp~hdiPl~v~~  176 (451)
                          .+|.+.|-.+|..||.|..++++.++    +--|.|+|.+...|+-|+..++|.+           |++.++.+..
T Consensus       305 ln~~~VT~d~LftlFgvYGdVqRVkil~nk----kd~ALIQmsd~~qAqLA~~hL~g~~-----------l~gk~lrvt~  369 (492)
T KOG1190|consen  305 LNEEAVTPDVLFTLFGVYGDVQRVKILYNK----KDNALIQMSDGQQAQLAMEHLEGHK-----------LYGKKLRVTL  369 (492)
T ss_pred             CchhccchhHHHHHHhhhcceEEEEeeecC----CcceeeeecchhHHHHHHHHhhcce-----------ecCceEEEee
Confidence                16899999999999999999999863    3469999999999999999998865           4555554422


Q ss_pred             cccccceeeccCCCCccccccccCCCCCCCcccccCC
Q psy300          177 KDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKG  213 (451)
Q Consensus       177 ~p~~vn~vvEIPrgS~~K~E~~k~~~~npI~qD~~~g  213 (451)
                         ..+--+.+|+.....-.+.++....|+.+=.+.|
T Consensus       370 ---SKH~~vqlp~egq~d~glT~dy~~spLhrfkkpg  403 (492)
T KOG1190|consen  370 ---SKHTNVQLPREGQEDQGLTKDYGNSPLHRFKKPG  403 (492)
T ss_pred             ---ccCccccCCCCCCccccccccCCCCchhhccCcc
Confidence               1233455666555444444554445555433334

>KOG0132|consensus

Probab=98.33  E-value=6.5e-07  Score=96.30  Aligned_cols=65  Identities=25%  Similarity=0.488  Sum_probs=59.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      -++|||||+|+.++++.||.++|+.||+|.+|.++.     ++|||||.+....+|.+|+++|++..+.+
T Consensus       420 ~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~-----~R~cAfI~M~~RqdA~kalqkl~n~kv~~  484 (894)
T KOG0132|consen  420 CSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP-----PRGCAFIKMVRRQDAEKALQKLSNVKVAD  484 (894)
T ss_pred             eeeeeeeccccchhhHHHHHHHHHhcccceeEeecc-----CCceeEEEEeehhHHHHHHHHHhcccccc
Confidence            468999999999999999999999999999999975     49999999999999999999998655544

>smart00360 RRM RNA recognition motif

Probab=98.33  E-value=1.6e-06  Score=65.35  Aligned_cols=57  Identities=33%  Similarity=0.578  Sum_probs=50.6

Q ss_pred             CCCcHHHHHHHhcccCcceeeEEeeCC-CCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          100 GKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       100 G~~tee~L~~~F~~fG~V~~v~v~~d~-~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ..+++++|+++|++||.|..+.+..++ ++.++|+|||+|.+.++|..|+..+++..+
T Consensus         6 ~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~   63 (71)
T smart00360        6 PDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKEL   63 (71)
T ss_pred             cccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCee
Confidence            357999999999999999999998874 588999999999999999999999986543

>KOG4205|consensus

Probab=98.29  E-value=1e-06  Score=88.13  Aligned_cols=153  Identities=22%  Similarity=0.325  Sum_probs=101.6

Q ss_pred             CCccCCC----CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcccCCCCCc-cccc
Q psy300           94 NKKPYKG----KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYKGSENGL-ISPF  167 (451)
Q Consensus        94 ng~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~~~~~G~-iSp~  167 (451)
                      .+++|.|    .++++.|++.|.+||.|.+|.+++| .+++++||+||+|.+.+....++....+.+     +|+ +.+.
T Consensus         6 ~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~-----dgr~ve~k   80 (311)
T KOG4205|consen    6 SGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKL-----DGRSVEPK   80 (311)
T ss_pred             CcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeeccccccc-----CCccccce
Confidence            3567777    4799999999999999999999998 468999999999999999999998877765     555 5555


Q ss_pred             ccCCcccccccc-----ccceeeccCCCCccc-----cccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCcc
Q psy300          168 HDIPLYSNVKDK-----IFNMVVEIPRWTNAK-----MEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQT  237 (451)
Q Consensus       168 hdiPl~v~~~p~-----~vn~vvEIPrgS~~K-----~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T  237 (451)
                      ..+|-.......     ...++--+|.+...+     +|.-.....+.++.|..+.+.|             .+||+  |
T Consensus        81 ~av~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~r-------------gFgfv--~  145 (311)
T KOG4205|consen   81 RAVSREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPR-------------GFGFV--T  145 (311)
T ss_pred             eccCcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccc-------------cceee--E
Confidence            555543221111     122333455443211     1211112222344444433332             33443  4


Q ss_pred             CCCCCCCCcCCCCCCCCCcceEEEeccccCCCccEEEEEEee
Q psy300          238 WENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALG  279 (451)
Q Consensus       238 ~~~p~~~~~~~~~~~D~DPlD~~~~~~~~~~~G~v~~vr~lG  279 (451)
                      +             .+.|-+|.+.....+...|..++||--.
T Consensus       146 ~-------------~~e~sVdkv~~~~f~~~~gk~vevkrA~  174 (311)
T KOG4205|consen  146 F-------------DSEDSVDKVTLQKFHDFNGKKVEVKRAI  174 (311)
T ss_pred             e-------------ccccccceecccceeeecCceeeEeecc
Confidence            4             5778899999999998999999998733

>PF13893 RRM_5: RNA recognition motif

Probab=98.29  E-value=1.3e-06  Score=65.09  Aligned_cols=46  Identities=24%  Similarity=0.544  Sum_probs=40.9

Q ss_pred             HHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          107 FKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       107 L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      |.++|++||.|..+.+..+.    +++|||+|.+.++|..|+..+|++.+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~----~~~a~V~f~~~~~A~~a~~~l~~~~~   46 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK----RGFAFVEFASVEDAQKAIEQLNGRQF   46 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS----TTEEEEEESSHHHHHHHHHHHTTSEE
T ss_pred             ChHHhCCcccEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCEE
Confidence            68899999999999998763    68999999999999999999998875

(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 ....

>KOG0109|consensus

Probab=98.25  E-value=1.1e-06  Score=85.29  Aligned_cols=77  Identities=22%  Similarity=0.472  Sum_probs=67.7

Q ss_pred             cCccccccCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCc
Q psy300           17 KGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK   96 (451)
Q Consensus        17 ~~~~~~~~~~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~   96 (451)
                      ......+.++.....+++++|+||.+..+.++|+..|.+||+|.+|.++++       |+||.|.-.++|..|+..|++.
T Consensus        63 g~nInVeaSksKsk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd-------y~fvh~d~~eda~~air~l~~~  135 (346)
T KOG0109|consen   63 GVNINVEASKSKSKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD-------YAFVHFDRAEDAVEAIRGLDNT  135 (346)
T ss_pred             ceEEEEEeccccCCCccccccCCCCccccCHHHhhhhcccCCceeeeeecc-------eeEEEEeeccchHHHHhccccc
Confidence            333444555555668899999999999999999999999999999999854       9999999999999999999999


Q ss_pred             cCCC
Q psy300           97 PYKG  100 (451)
Q Consensus        97 ~f~G  100 (451)
                      .|.|
T Consensus       136 ~~~g  139 (346)
T KOG0109|consen  136 EFQG  139 (346)
T ss_pred             cccc
Confidence            9988

>KOG4207|consensus

Probab=98.22  E-value=1.1e-06  Score=81.38  Aligned_cols=61  Identities=18%  Similarity=0.388  Sum_probs=55.3

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcccCCCC
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYKGSEN  161 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~~~~~  161 (451)
                      +++.++|+.+|++||.|-+|-|++| -+..++|||||.|....+|+.|+..|+|++..+...
T Consensus        24 RTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRel   85 (256)
T KOG4207|consen   24 RTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGREL   85 (256)
T ss_pred             cCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeecccee
Confidence            5799999999999999999999999 478899999999999999999999999998754443

>KOG0125|consensus

Probab=98.22  E-value=1.1e-06  Score=86.53  Aligned_cols=55  Identities=22%  Similarity=0.490  Sum_probs=50.3

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      +..+.||+..|++||.|.+|+|+.++.| |||||||+|++.++|.+|..+++|.+.
T Consensus       107 rFRdpDL~aMF~kfG~VldVEIIfNERG-SKGFGFVTmen~~dadRARa~LHgt~V  161 (376)
T KOG0125|consen  107 RFRDPDLRAMFEKFGKVLDVEIIFNERG-SKGFGFVTMENPADADRARAELHGTVV  161 (376)
T ss_pred             cccCccHHHHHHhhCceeeEEEEeccCC-CCccceEEecChhhHHHHHHHhhccee
Confidence            4688999999999999999999987655 799999999999999999999998764

>PRK01250 inorganic pyrophosphatase; Provisional

Probab=98.21  E-value=1.5e-06  Score=80.07  Aligned_cols=50  Identities=24%  Similarity=0.304  Sum_probs=37.6

Q ss_pred             CccCCCccccCCCCEEEEEEeecCCCc-cceeeeccccceEEEEEeeCCCCchh
Q psy300          387 PFHDIPLYSNVKDKIFNMVVEIPRWTN-AKMEVGNAMEMRLYLVCFNLPSPLGY  439 (451)
Q Consensus       387 ~~hd~~l~~~~~~~~~~~~~e~p~~~~-~k~e~~~~~~~~~~~~~~~~~~~~~~  439 (451)
                      .||++|...+ ..+.+||||||||||+ +|+|+.++..  +..+---|+++++|
T Consensus         2 ~~~~l~~~~~-~~~~v~vvvEIPkgs~~~KyE~d~~~g--~~~~dR~l~~~~~y   52 (176)
T PRK01250          2 SLNKIPAGKD-LPEDINVIIEIPANSDPIKYEVDKESG--ALFVDRFLYTAMFY   52 (176)
T ss_pred             ChhhCCCCCC-CCCEEEEEEEeCCCCCceeEEEecCCC--CEEEeeccCCCCcC
Confidence            5899999643 4699999999999999 9999999965  23333345555544

>KOG1365|consensus

Probab=98.18  E-value=3.8e-06  Score=84.13  Aligned_cols=123  Identities=26%  Similarity=0.370  Sum_probs=96.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccC----CCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhc--------------
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFGQY----GDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS--------------   93 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~~~----G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~l--------------   93 (451)
                      .--|-.++||++.++.++.++|.+-    |....+-+++.++|+..|-|||.|..+++|+.|+.+-              
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElFRS  240 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELFRS  240 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence            3455667999999999999999732    3455677777779999999999999999999998641              


Q ss_pred             ---------CCcc---CCC-------------------------------CCcHHHHHHHhcccCc-cee--eEEeeCCC
Q psy300           94 ---------NKKP---YKG-------------------------------KITEEEFKEHFGQYGD-IID--AQLLKNAD  127 (451)
Q Consensus        94 ---------ng~~---f~G-------------------------------~~tee~L~~~F~~fG~-V~~--v~v~~d~~  127 (451)
                               |+..   +.+                               ..+.++|.++|..|-. |..  +.++.+.+
T Consensus       241 TaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~q  320 (508)
T KOG1365|consen  241 TAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQ  320 (508)
T ss_pred             hHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCC
Confidence                     1110   100                               2588999999988866 443  67777889


Q ss_pred             CCccceEEEEecchHHHHHHHHhcCCC
Q psy300          128 GKLKGCGFINYANKISAVKAILKSNKK  154 (451)
Q Consensus       128 g~srG~gFV~F~s~e~A~~Ai~~ln~r  154 (451)
                      |++.|-|||+|.+.++|..|..+-+.+
T Consensus       321 GrPSGeAFIqm~nae~a~aaaqk~hk~  347 (508)
T KOG1365|consen  321 GRPSGEAFIQMRNAERARAAAQKCHKK  347 (508)
T ss_pred             CCcChhhhhhhhhhHHHHHHHHHHHHh
Confidence            999999999999999999998876544

>smart00362 RRM_2 RNA recognition motif

Probab=98.17  E-value=4.7e-06  Score=62.96  Aligned_cols=55  Identities=35%  Similarity=0.564  Sum_probs=49.5

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.+..+.+..+. +.++|+|||+|.+.++|..|+..+++..+
T Consensus        10 ~~~~~~l~~~~~~~g~v~~~~~~~~~-~~~~~~~~v~f~~~~~a~~a~~~~~~~~~   64 (72)
T smart00362       10 DVTEEDLKELFSKFGPIESVKIPKDT-GKSKGFAFVEFESEEDAEKAIEALNGTKL   64 (72)
T ss_pred             cCCHHHHHHHHHhcCCEEEEEEecCC-CCCCceEEEEeCCHHHHHHHHHHhCCcEE
Confidence            57899999999999999999998876 77899999999999999999999886543

>KOG0226|consensus

Probab=98.14  E-value=3.3e-06  Score=80.54  Aligned_cols=71  Identities=21%  Similarity=0.424  Sum_probs=65.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....+||.|.|..+++.+.|.+.|.+|-.-...++++|. ||+++||+||.|.+++++.+|+.+|+|+...-
T Consensus       188 ~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgs  259 (290)
T KOG0226|consen  188 EDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGS  259 (290)
T ss_pred             cccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhccccccc
Confidence            356899999999999999999999999888888999998 99999999999999999999999999986654

>PLN03120 nucleic acid binding protein; Provisional

Probab=98.13  E-value=4.2e-06  Score=81.23  Aligned_cols=53  Identities=23%  Similarity=0.345  Sum_probs=47.6

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|+.||.|.++.+++++.  ++|||||+|.++++|..|+. +++..+
T Consensus        15 ~tTE~dLrefFS~~G~I~~V~I~~d~~--~~GfAFVtF~d~eaAe~All-LnG~~l   67 (260)
T PLN03120         15 KATERDIKEFFSFSGDIEYVEMQSENE--RSQIAYVTFKDPQGAETALL-LSGATI   67 (260)
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEeecCC--CCCEEEEEeCcHHHHHHHHH-hcCCee
Confidence            589999999999999999999998753  57999999999999999995 888765

>KOG4661|consensus

Probab=98.11  E-value=4.4e-06  Score=87.15  Aligned_cols=71  Identities=23%  Similarity=0.437  Sum_probs=64.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .-.++|||.+|+..+.-.+|+++|++||.|+-.+++++. +--.+.|+||++.+.++|.+||..|+.+.++|
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHG  474 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHG  474 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcc
Confidence            346899999999999999999999999999999999986 55568999999999999999999988887777

>KOG0533|consensus

Probab=98.11  E-value=6.8e-06  Score=79.37  Aligned_cols=73  Identities=21%  Similarity=0.465  Sum_probs=67.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ....++|+|.|||+.++++||.++|..||.+..+-+-.+++|+|.|.|-|.|...++|.+|++.+++..+.|+
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~  152 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGR  152 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCc
Confidence            3345789999999999999999999999999989998899999999999999999999999999999877774

>KOG4211|consensus

Probab=98.07  E-value=1.7e-05  Score=81.89  Aligned_cols=120  Identities=25%  Similarity=0.393  Sum_probs=95.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEE-EEEeECCCCCceeEEEEEEccHHHHHHHHHhcCC--------------
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIID-AQLLKNADGKLKGCGFINYANKISAVKAILKSNK--------------   95 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~-i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng--------------   95 (451)
                      ....|-+++||+.++++||.+||+..-.+.. +.++.+..+++.|-|||+|++.+.|++|+..-..              
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIEvF~Ss~  181 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIALGRHRENIGHRYIEVFRSSR  181 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHHHHHHHHhhccceEEeehhHH
Confidence            5568889999999999999999998865555 5677777889999999999999999999864100              


Q ss_pred             -----cc------------------------CC-----------------C-----------------------------
Q psy300           96 -----KP------------------------YK-----------------G-----------------------------  100 (451)
Q Consensus        96 -----~~------------------------f~-----------------G-----------------------------  100 (451)
                           ..                        +.                 |                             
T Consensus       182 ~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~g~~~~~~~~d~~~~gs~~~~~~~~~~~  261 (510)
T KOG4211|consen  182 AEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYYGFSRYPSLQDYGNFGSYGGGRDPNYPV  261 (510)
T ss_pred             HHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCccccccCccccccccccccccccccccCC
Confidence                 00                        00                 0                             


Q ss_pred             ------------------------------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHh
Q psy300          101 ------------------------------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK  150 (451)
Q Consensus       101 ------------------------------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~  150 (451)
                                                    ..++.++..+|+..-.+ .+.+-..++|+..|-|+|+|.+.++|..|+.+
T Consensus       262 ~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl~p~-~v~i~ig~dGr~TGEAdveF~t~edav~Amsk  340 (510)
T KOG4211|consen  262 SSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPLNPY-RVHIEIGPDGRATGEADVEFATGEDAVGAMGK  340 (510)
T ss_pred             CCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCCCce-eEEEEeCCCCccCCcceeecccchhhHhhhcc
Confidence                                          15889999999876443 67776778999999999999999999999866


Q ss_pred             c
Q psy300          151 S  151 (451)
Q Consensus       151 l  151 (451)
                      -
T Consensus       341 d  341 (510)
T KOG4211|consen  341 D  341 (510)
T ss_pred             C
Confidence            3

>KOG0153|consensus

Probab=98.06  E-value=6.7e-06  Score=81.56  Aligned_cols=65  Identities=34%  Similarity=0.620  Sum_probs=56.9

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK   95 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng   95 (451)
                      .+.+..-.+|||++|-..+++.+|+++|.+||+|.+++++..     +|+|||+|.+..+|+.|..+.-.
T Consensus       222 pPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~-----~~CAFv~ftTR~aAE~Aae~~~n  286 (377)
T KOG0153|consen  222 PPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR-----KGCAFVTFTTREAAEKAAEKSFN  286 (377)
T ss_pred             CCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc-----cccceeeehhhHHHHHHHHhhcc
Confidence            444556789999999889999999999999999999999865     67999999999999999876443

>KOG0107|consensus

Probab=98.02  E-value=6.2e-06  Score=74.79  Aligned_cols=62  Identities=26%  Similarity=0.457  Sum_probs=54.4

Q ss_pred             cCCccCCC----CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcccC
Q psy300           93 SNKKPYKG----KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  158 (451)
Q Consensus        93 lng~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~~  158 (451)
                      ++-++|+|    ++++.+|...|..||.+.++.|.+.    +.|||||+|+++.+|..|+..||++.+.+
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn----PPGfAFVEFed~RDA~DAvr~LDG~~~cG   74 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN----PPGFAFVEFEDPRDAEDAVRYLDGKDICG   74 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec----CCCceEEeccCcccHHHHHhhcCCccccC
Confidence            45577777    4799999999999999999999885    48999999999999999999999987643

>KOG0113|consensus

Probab=98.00  E-value=8.3e-06  Score=79.45  Aligned_cols=55  Identities=25%  Similarity=0.491  Sum_probs=51.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKP  155 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~ri  155 (451)
                      .++|..|+..|+.||.|+.+.+++| .+|+|+|||||+|+..-+...|-...+|.+
T Consensus       112 dT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~  167 (335)
T KOG0113|consen  112 DTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIK  167 (335)
T ss_pred             cccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCce
Confidence            4799999999999999999999999 799999999999999999999998887654

>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=97.99  E-value=1.8e-05  Score=60.00  Aligned_cols=56  Identities=29%  Similarity=0.570  Sum_probs=50.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|+.||.|..+.+..++.+.++|+|||+|.+.++|..|+..+++..+
T Consensus        10 ~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~   65 (74)
T cd00590          10 DVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKEL   65 (74)
T ss_pred             ccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeE
Confidence            47899999999999999999999887667899999999999999999999987653

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).

>PLN03121 nucleic acid binding protein; Provisional

Probab=97.97  E-value=1.3e-05  Score=76.83  Aligned_cols=53  Identities=15%  Similarity=0.367  Sum_probs=46.4

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|+.||.|.++.++++  +.++|||||+|.++++|..|+ .|+|..+
T Consensus        16 ~tTE~dLrefFS~~G~I~~V~I~~D--~et~gfAfVtF~d~~aaetAl-lLnGa~l   68 (243)
T PLN03121         16 KATEKDVYDFFSHCGAIEHVEIIRS--GEYACTAYVTFKDAYALETAV-LLSGATI   68 (243)
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEecC--CCcceEEEEEECCHHHHHHHH-hcCCCee
Confidence            6899999999999999999999987  355789999999999999998 6766543

>PLN03213 repressor of silencing 3; Provisional

Probab=97.97  E-value=9.4e-06  Score=83.61  Aligned_cols=62  Identities=16%  Similarity=0.367  Sum_probs=53.1

Q ss_pred             ccCCC----CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecch--HHHHHHHHhcCCCcccCCC
Q psy300           96 KPYKG----KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANK--ISAVKAILKSNKKPYKGSE  160 (451)
Q Consensus        96 ~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~--e~A~~Ai~~ln~riy~~~~  160 (451)
                      ++|.|    .+++++|+..|..||.|.++.|++. +|  ||||||+|.+.  .++.+||..||+..|.+..
T Consensus        12 RIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE-TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~   79 (759)
T PLN03213         12 RLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT-KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGR   79 (759)
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc-cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCce
Confidence            45666    4899999999999999999999964 56  99999999987  6899999999998775443

>KOG1190|consensus

Probab=97.96  E-value=4.5e-05  Score=77.18  Aligned_cols=115  Identities=22%  Similarity=0.307  Sum_probs=94.7

Q ss_pred             CceEEEcCCC-CCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC----------
Q psy300           32 RGRLFIKNLP-FKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG----------  100 (451)
Q Consensus        32 ~~~lfVgnLp-~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G----------  100 (451)
                      +..|-|.||- ..+|.+-|..+|+-||.|..|+++.++    +--|.|+|.+..+|+.|+..|+|..+.|          
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH  372 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKH  372 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC----CcceeeeecchhHHHHHHHHhhcceecCceEEEeeccC
Confidence            6788999995 679999999999999999999999863    2459999999999999999988865544          


Q ss_pred             ----------------------------------------------------CCcHHHHHHHhcccCcceeeEEeeCCCC
Q psy300          101 ----------------------------------------------------KITEEEFKEHFGQYGDIIDAQLLKNADG  128 (451)
Q Consensus       101 ----------------------------------------------------~~tee~L~~~F~~fG~V~~v~v~~d~~g  128 (451)
                                                                          +++|++++..|..-|.....-..-.   
T Consensus       373 ~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~---  449 (492)
T KOG1190|consen  373 TNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQ---  449 (492)
T ss_pred             ccccCCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecC---
Confidence                                                                2699999999999887544433221   


Q ss_pred             CccceEEEEecchHHHHHHHHhcCC
Q psy300          129 KLKGCGFINYANKISAVKAILKSNK  153 (451)
Q Consensus       129 ~srG~gFV~F~s~e~A~~Ai~~ln~  153 (451)
                      +.+-++.+.+++.|+|..|+..++.
T Consensus       450 kd~kmal~q~~sveeA~~ali~~hn  474 (492)
T KOG1190|consen  450 KDRKMALPQLESVEEAIQALIDLHN  474 (492)
T ss_pred             CCcceeecccCChhHhhhhcccccc
Confidence            2266899999999999999988754

>KOG4208|consensus

Probab=97.96  E-value=8.5e-06  Score=75.73  Aligned_cols=62  Identities=23%  Similarity=0.262  Sum_probs=53.5

Q ss_pred             CcHHHHHHHhccc-CcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcccCCCCCc
Q psy300          102 ITEEEFKEHFGQY-GDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYKGSENGL  163 (451)
Q Consensus       102 ~tee~L~~~F~~f-G~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~~~~~G~  163 (451)
                      +.+.++..+|.+| |.|..+++.++ ++|.|+|||||+|++.+.|.-|.++||..++++.--.+
T Consensus        61 ~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c  124 (214)
T KOG4208|consen   61 FFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLEC  124 (214)
T ss_pred             hhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeee
Confidence            4678888888887 77888888787 79999999999999999999999999998887655444

>KOG0120|consensus

Probab=97.95  E-value=1.5e-05  Score=83.92  Aligned_cols=121  Identities=27%  Similarity=0.452  Sum_probs=99.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccC-----------CC-eEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCc
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQY-----------GD-IIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK   96 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~-----------G~-I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~   96 (451)
                      ..+..++||+++|..++++.+-.+|..-           |+ +..+.+-.     .+.++|++|.+.+.|..|+.. ++.
T Consensus       172 t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~-----~~nfa~ie~~s~~~at~~~~~-~~~  245 (500)
T KOG0120|consen  172 TRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNL-----EKNFAFIEFRSISEATEAMAL-DGI  245 (500)
T ss_pred             hhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecc-----cccceeEEecCCCchhhhhcc-cch
Confidence            3456899999999999999999999754           33 56666543     378999999999999988742 222


Q ss_pred             cCCC--------------------------------------------------CCcHHHHHHHhcccCcceeeEEeeC-
Q psy300           97 PYKG--------------------------------------------------KITEEEFKEHFGQYGDIIDAQLLKN-  125 (451)
Q Consensus        97 ~f~G--------------------------------------------------~~tee~L~~~F~~fG~V~~v~v~~d-  125 (451)
                      .|.|                                                  .+++.++.++.+.||.+....++.+ 
T Consensus       246 ~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~  325 (500)
T KOG0120|consen  246 IFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDS  325 (500)
T ss_pred             hhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeeccc
Confidence            2221                                                  4799999999999999999999998 


Q ss_pred             CCCCccceEEEEecchHHHHHHHHhcCCCc
Q psy300          126 ADGKLKGCGFINYANKISAVKAILKSNKKP  155 (451)
Q Consensus       126 ~~g~srG~gFV~F~s~e~A~~Ai~~ln~ri  155 (451)
                      .+|.++||||.+|.+......|+..+||.+
T Consensus       326 ~~g~skg~af~ey~dpsvtd~A~agLnGm~  355 (500)
T KOG0120|consen  326 ATGNSKGFAFCEYCDPSVTDQAIAGLNGMQ  355 (500)
T ss_pred             ccccccceeeeeeeCCcchhhhhcccchhh
Confidence            568999999999999999999999998865

>KOG0151|consensus

Probab=97.92  E-value=1.4e-05  Score=85.51  Aligned_cols=72  Identities=18%  Similarity=0.408  Sum_probs=64.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC----CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA----DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~----tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .+..++|||+||++.++++.|...|..||+|.+++++..+    ..+.+-||||.|.+..+|++|+..|+|.++.+
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~  246 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVME  246 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeee
Confidence            5567899999999999999999999999999999998765    34567899999999999999999999987764

>KOG0226|consensus

Probab=97.89  E-value=6e-06  Score=78.84  Aligned_cols=142  Identities=19%  Similarity=0.347  Sum_probs=105.5

Q ss_pred             CCceEEEcCCCCCCCHHH-H--HHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCC------------
Q psy300           31 KRGRLFIKNLPFKITEEE-F--KEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK------------   95 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~-L--~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng------------   95 (451)
                      ..-..+++++-.++..+- |  ...|+.+-.....+++++.-+.-++++|+.|.....-.++-..-++            
T Consensus        95 ~vf~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~  174 (290)
T KOG0226|consen   95 AVFRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAA  174 (290)
T ss_pred             ccccccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeecc
Confidence            345667777766666655 3  6678888778888888887777889999999876655544322221            


Q ss_pred             -----------------ccCCC----CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCC
Q psy300           96 -----------------KPYKG----KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNK  153 (451)
Q Consensus        96 -----------------~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~  153 (451)
                                       ++|+|    .++++.|...|.+|-.....++++| ++|+++|||||.|.+..++.+|+.+||+
T Consensus       175 gtswedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~g  254 (290)
T KOG0226|consen  175 GTSWEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNG  254 (290)
T ss_pred             ccccCCcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcc
Confidence                             23444    3789999999999999999999998 7999999999999999999999999999


Q ss_pred             CcccCCCCCc-ccccccCCc
Q psy300          154 KPYKGSENGL-ISPFHDIPL  172 (451)
Q Consensus       154 riy~~~~~G~-iSp~hdiPl  172 (451)
                      +..-..+..- .|.|....+
T Consensus       255 kyVgsrpiklRkS~wkeRn~  274 (290)
T KOG0226|consen  255 KYVGSRPIKLRKSEWKERNL  274 (290)
T ss_pred             cccccchhHhhhhhHHhhhh
Confidence            8543333222 555655333

>KOG0126|consensus

Probab=97.84  E-value=1.6e-06  Score=78.87  Aligned_cols=56  Identities=32%  Similarity=0.558  Sum_probs=52.0

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+||.+|...|++||.|..+.+++| .+|+|+||||+.|++..+..-|+..+||...
T Consensus        46 ~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki  102 (219)
T KOG0126|consen   46 ELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKI  102 (219)
T ss_pred             cccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCcee
Confidence            4799999999999999999999998 7899999999999999999999999988654

>KOG0116|consensus

Probab=97.84  E-value=2.3e-05  Score=81.44  Aligned_cols=63  Identities=32%  Similarity=0.483  Sum_probs=54.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhc
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKS   93 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~l   93 (451)
                      ...+|||+|||.+++.++|.++|++||+|....|.... .+++.+||||+|.+.+.++.|+.+-
T Consensus       287 ~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As  350 (419)
T KOG0116|consen  287 DGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS  350 (419)
T ss_pred             cccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC
Confidence            34569999999999999999999999999999886543 5555599999999999999999864

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=97.84  E-value=8.2e-05  Score=62.07  Aligned_cols=69  Identities=22%  Similarity=0.270  Sum_probs=59.6

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccC--CCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFGQY--GDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~~~--G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .+||-++|+|...|.++|.+++...  |...-+.++.|. ++.+.|||||.|.+++.|.+-.+.++|+.+..
T Consensus         1 RTTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~   72 (97)
T PF04059_consen    1 RTTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPN   72 (97)
T ss_pred             CeeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCcccc
Confidence            4799999999999999998888643  556667888887 88899999999999999999999999987753

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4210|consensus

Probab=97.83  E-value=1.5e-05  Score=79.37  Aligned_cols=121  Identities=24%  Similarity=0.326  Sum_probs=102.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCC---------
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYK---------   99 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~---------   99 (451)
                      ...++.|++++..++.+.+...++..+|......+.... ...++|++++.|...+.+..|+.........         
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            357899999999999999999999999988888776654 7889999999999999999998753221110         


Q ss_pred             -------------------------C----CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHH
Q psy300          100 -------------------------G----KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAIL  149 (451)
Q Consensus       100 -------------------------G----~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~  149 (451)
                                               +    .+++++|+.+|..+|.|..++++.+ +++.++|||||.|.....+..++.
T Consensus       166 ~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~  245 (285)
T KOG4210|consen  166 TRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALN  245 (285)
T ss_pred             ccccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhh
Confidence                                     0    3799999999999999999999886 688999999999999999999987


Q ss_pred             h
Q psy300          150 K  150 (451)
Q Consensus       150 ~  150 (451)
                      .
T Consensus       246 ~  246 (285)
T KOG4210|consen  246 D  246 (285)
T ss_pred             c
Confidence            5

>KOG4212|consensus

Probab=97.82  E-value=2.5e-05  Score=79.48  Aligned_cols=69  Identities=26%  Similarity=0.506  Sum_probs=62.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .++.++|||+|||.+.|++.|++-|..||.|..+.++-  .|+++|  .|.|.++++|++|+..|+|..+.|+
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime--~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr  601 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME--NGKSKG--VVRFFSPEDAERACALMNGSRLDGR  601 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhhc--cCCccc--eEEecCHHHHHHHHHHhccCcccCc
Confidence            45678999999999999999999999999999998843  588887  8999999999999999999988874

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=97.80  E-value=3.6e-05  Score=73.18  Aligned_cols=62  Identities=31%  Similarity=0.584  Sum_probs=56.0

Q ss_pred             CccCCC----CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           95 KKPYKG----KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        95 g~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ..+|.|    .+++++|+++|.+||.+..+.+..+ .++.++|||||+|.+.++|..|+..+++..+
T Consensus       116 ~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~  182 (306)
T COG0724         116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKEL  182 (306)
T ss_pred             ceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeE
Confidence            556666    4899999999999999999999998 4899999999999999999999999997665

>KOG0121|consensus

Probab=97.80  E-value=4.3e-05  Score=66.08  Aligned_cols=73  Identities=25%  Similarity=0.278  Sum_probs=59.1

Q ss_pred             cHHHHHHHHHhcCCccCCCC----CcHHHHHHHhcccCcceeeEEeeCC-CCCccceEEEEecchHHHHHHHHhcCCCc
Q psy300           82 NKISAVKAILKSNKKPYKGK----ITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKP  155 (451)
Q Consensus        82 ~~~~A~~Al~~lng~~f~G~----~tee~L~~~F~~fG~V~~v~v~~d~-~g~srG~gFV~F~s~e~A~~Ai~~ln~ri  155 (451)
                      +.++...|+... ..+|.|+    ++|++|.++|+++|.|..+.+--|+ +..+.||+||+|.+.++|..|+.-+++..
T Consensus        25 t~~e~~~a~r~S-~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~Alryisgtr  102 (153)
T KOG0121|consen   25 TDEEQLEALRKS-CTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTR  102 (153)
T ss_pred             chHHHHHHHhhc-ceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCc
Confidence            555666676543 3567775    7999999999999999998886664 45689999999999999999999887653

>COG0221 Ppa Inorganic pyrophosphatase [Energy production and conversion]

Probab=97.76  E-value=2.5e-05  Score=71.64  Aligned_cols=51  Identities=33%  Similarity=0.457  Sum_probs=41.4

Q ss_pred             CCccCCCccccCCCCEEEEEEeecCCCccceeeeccccceEEEEEeeCCCCchhh
Q psy300          386 SPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLYLVCFNLPSPLGYL  440 (451)
Q Consensus       386 s~~hd~~l~~~~~~~~~~~~~e~p~~~~~k~e~~~~~~~~~~~~~~~~~~~~~~~  440 (451)
                      |+||+||+.++.  ..+|||+|||+||+.|.|+.++......  ---|.++++|.
T Consensus         1 ~~~~~~~~~~~~--~~i~vviEIP~~s~~KyE~dk~~~~~~v--dR~l~~~~~YP   51 (171)
T COG0221           1 MDLHKIPAGPDD--EDINVVIEIPKGSNIKYEVDKETGRLLV--DRPLKTPMGYP   51 (171)
T ss_pred             CCccccCCCCCc--ceEEEEEeccCCCccceEEeeecCceee--eecCCCCCcCC
Confidence            689999999887  4999999999999999999999877653  33455555553

>KOG4660|consensus

Probab=97.71  E-value=3.1e-05  Score=81.18  Aligned_cols=71  Identities=23%  Similarity=0.447  Sum_probs=61.1

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .+.....++|+|-|||..+++++|+.+|+.||+|..++..    -..+|..||+|.+..+|++|++++++..+.|
T Consensus        69 ~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t----~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~  139 (549)
T KOG4660|consen   69 SEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRET----PNKRGIVFVEFYDVRDAERALKALNRREIAG  139 (549)
T ss_pred             CcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcc----cccCceEEEEEeehHhHHHHHHHHHHHHhhh
Confidence            3345678999999999999999999999999999997653    3457899999999999999999998866544

>KOG0111|consensus

Probab=97.69  E-value=1.9e-05  Score=73.93  Aligned_cols=64  Identities=30%  Similarity=0.494  Sum_probs=55.5

Q ss_pred             CccCCC----CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcccC
Q psy300           95 KKPYKG----KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYKG  158 (451)
Q Consensus        95 g~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~~  158 (451)
                      +.+|.|    .+++.-|...|-+||.|..+.++.| .+++.||||||+|...|+|.+||..||..-.++
T Consensus        11 rtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~G   79 (298)
T KOG0111|consen   11 RTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFG   79 (298)
T ss_pred             eeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcc
Confidence            345666    4788889999999999999999998 788999999999999999999999999765543

>KOG0130|consensus

Probab=97.66  E-value=5.1e-05  Score=66.15  Aligned_cols=57  Identities=28%  Similarity=0.438  Sum_probs=51.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCccc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYK  157 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~  157 (451)
                      ..+++++.+.|..||.|..+.+-.| ++|-.+|||.|+|++.++|+.|+..+|+.-.+
T Consensus        83 EatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll  140 (170)
T KOG0130|consen   83 EATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELL  140 (170)
T ss_pred             chhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhh
Confidence            4699999999999999999999766 78999999999999999999999999976543

>KOG0112|consensus

Probab=97.63  E-value=3.8e-05  Score=84.24  Aligned_cols=124  Identities=19%  Similarity=0.253  Sum_probs=103.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCC--------
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK--------   99 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~--------   99 (451)
                      +...+++||+|||+..+++.+|+..|..+|.|.+|.+-+-.-+.-.-|+||.|.+...+-.|...+.+..+.        
T Consensus       368 D~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~gl  447 (975)
T KOG0112|consen  368 DFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGL  447 (975)
T ss_pred             chhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCcccccc
Confidence            456789999999999999999999999999999999866544444568999999999988888776654332        


Q ss_pred             C-----------------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          100 G-----------------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       100 G-----------------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      |                 .+....|...|..||.|..+.+-..     .-|+||.|++...|+.|...+-+..+
T Consensus       448 G~~kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg-----q~yayi~yes~~~aq~a~~~~rgap~  516 (975)
T KOG0112|consen  448 GQPKSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG-----QPYAYIQYESPPAAQAATHDMRGAPL  516 (975)
T ss_pred             cccccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC-----CcceeeecccCccchhhHHHHhcCcC
Confidence            1                 2577899999999999998877543     45999999999999999999987764

>KOG4209|consensus

Probab=97.60  E-value=8.2e-05  Score=71.82  Aligned_cols=75  Identities=17%  Similarity=0.307  Sum_probs=68.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCCCc
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGKIT  103 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~~t  103 (451)
                      .......+||+|+.+.++.+++...|+.+|.|..+.+..|. +|.++||+||+|.+.+.+..|+. |++..+.|..+
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i  172 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAI  172 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccc
Confidence            45567899999999999999999999999999999999998 77899999999999999999999 99998887443

>KOG0108|consensus

Probab=97.56  E-value=0.0001  Score=77.12  Aligned_cols=62  Identities=26%  Similarity=0.468  Sum_probs=56.5

Q ss_pred             CccCCC----CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           95 KKPYKG----KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        95 g~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ..+|.|    .+++++|.++|+..|.|.+++++.| ++|+++||||++|.+.+.|..|+..+|+..+
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~   85 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEF   85 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCccc
Confidence            455666    4799999999999999999999998 6899999999999999999999999998776

>KOG1456|consensus

Probab=97.55  E-value=0.001  Score=66.82  Aligned_cols=123  Identities=18%  Similarity=0.324  Sum_probs=100.0

Q ss_pred             CCCCCceEEEcCCCCC-CCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC------
Q psy300           28 DKTKRGRLFIKNLPFK-ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG------  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~-vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G------  100 (451)
                      ...+.+-+.|-+|... +.-+.|.++|=.||.|..|++++.+    .|-|.|++.+....++|+..||+..+.|      
T Consensus       283 g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~  358 (494)
T KOG1456|consen  283 GGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVC  358 (494)
T ss_pred             CCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc----cceeEEEcCcHHHHHHHHHHhccCccccceEEEe
Confidence            3456788899999865 5567899999999999999999864    4579999999999999999998765433      


Q ss_pred             ----------------------------------------------------------CCcHHHHHHHhcccCc-ceeeE
Q psy300          101 ----------------------------------------------------------KITEEEFKEHFGQYGD-IIDAQ  121 (451)
Q Consensus       101 ----------------------------------------------------------~~tee~L~~~F~~fG~-V~~v~  121 (451)
                                                                                .+||++|..+|...+. -.+++
T Consensus       359 ~SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~svk  438 (494)
T KOG1456|consen  359 VSKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSVK  438 (494)
T ss_pred             eccccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcceEE
Confidence                                                                      2699999999987665 56777


Q ss_pred             EeeCCCCCccceEEEEecchHHHHHHHHhcCCCc
Q psy300          122 LLKNADGKLKGCGFINYANKISAVKAILKSNKKP  155 (451)
Q Consensus       122 v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~ri  155 (451)
                      +...++.+| --|.++|++.++|..|+..+|+..
T Consensus       439 vFp~kserS-ssGllEfe~~s~Aveal~~~NH~p  471 (494)
T KOG1456|consen  439 VFPLKSERS-SSGLLEFENKSDAVEALMKLNHYP  471 (494)
T ss_pred             eeccccccc-ccceeeeehHHHHHHHHHHhcccc
Confidence            766555543 347999999999999999999854

>KOG0415|consensus

Probab=97.31  E-value=0.00017  Score=71.87  Aligned_cols=54  Identities=24%  Similarity=0.490  Sum_probs=50.5

Q ss_pred             CcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCc
Q psy300          102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKP  155 (451)
Q Consensus       102 ~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~ri  155 (451)
                      +|+++|.-+|+.||.|.+|.|++| ++|.|-.||||+|++.+++.+|.-+|+..+
T Consensus       251 TtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvL  305 (479)
T KOG0415|consen  251 TTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVL  305 (479)
T ss_pred             ccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhccee
Confidence            689999999999999999999998 789999999999999999999999987644

>KOG0114|consensus

Probab=97.23  E-value=0.00058  Score=57.11  Aligned_cols=53  Identities=30%  Similarity=0.456  Sum_probs=46.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP  155 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~ri  155 (451)
                      ++|.++..++|.+||.|..+++-..+  ..+|-|||.|++..+|.+|+..++|.-
T Consensus        29 ~ITseemydlFGkyg~IrQIRiG~~k--~TrGTAFVVYedi~dAk~A~dhlsg~n   81 (124)
T KOG0114|consen   29 KITSEEMYDLFGKYGTIRQIRIGNTK--ETRGTAFVVYEDIFDAKKACDHLSGYN   81 (124)
T ss_pred             cccHHHHHHHhhcccceEEEEecCcc--CcCceEEEEehHhhhHHHHHHHhcccc
Confidence            58999999999999999999996543  348999999999999999999998753

>KOG0132|consensus

Probab=97.05  E-value=0.00051  Score=74.57  Aligned_cols=53  Identities=28%  Similarity=0.604  Sum_probs=47.2

Q ss_pred             CccCCC----CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcC
Q psy300           95 KKPYKG----KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN  152 (451)
Q Consensus        95 g~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln  152 (451)
                      .++|.|    ++++.+|.++|+.||.|.++.+...     +|||||.+.++.+|.+|+.+|+
T Consensus       422 rTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~-----R~cAfI~M~~RqdA~kalqkl~  478 (894)
T KOG0132|consen  422 RTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP-----RGCAFIKMVRRQDAEKALQKLS  478 (894)
T ss_pred             eeeeeccccchhhHHHHHHHHHhcccceeEeeccC-----CceeEEEEeehhHHHHHHHHHh
Confidence            345555    5799999999999999999999765     8999999999999999999987

>cd00412 pyrophosphatase Inorganic pyrophosphatase

Probab=97.01  E-value=0.00049  Score=62.32  Aligned_cols=24  Identities=38%  Similarity=0.654  Sum_probs=21.8

Q ss_pred             CEEEEEEeecCCCccceeeecccc
Q psy300          400 KIFNMVVEIPRWTNAKMEVGNAME  423 (451)
Q Consensus       400 ~~~~~~~e~p~~~~~k~e~~~~~~  423 (451)
                      .++||||||||||++|+|+.+++.
T Consensus         1 ~~v~vvIEIP~gs~~KyE~d~~~g   24 (155)
T cd00412           1 EVVNVVIEIPKGSNAKYEIDKETG   24 (155)
T ss_pred             CEEEEEEEECCCCceeEEEccCCC
Confidence            369999999999999999999874

These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.98  E-value=0.0014  Score=65.03  Aligned_cols=103  Identities=23%  Similarity=0.408  Sum_probs=71.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHH------HHHhccCCCeEEEEEeECC-CCCc-ee-E-EEEEEccHHHHHHHHHhcCCcc
Q psy300           28 DKTKRGRLFIKNLPFKITEEEF------KEHFGQYGDIIDAQLLKNA-DGKL-KG-C-GFINYANKISAVKAILKSNKKP   97 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L------~~~F~~~G~I~~i~l~~d~-tg~s-kG-~-aFV~F~~~~~A~~Al~~lng~~   97 (451)
                      +-....-+||-+||+.+-.++.      .++|.+||.|..|.+-+.. +-.+ .+ + .||.|.+.++|.+|+.+.+|..
T Consensus       110 RVvQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~  189 (480)
T COG5175         110 RVVQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSL  189 (480)
T ss_pred             eeeecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccc
Confidence            3445678899999998877763      6799999999988875542 1111 22 3 3999999999999999999999


Q ss_pred             CCCCCcHHHHHHHhcccCcceeeEE-eeCCCCCccceEEEE
Q psy300           98 YKGKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFIN  137 (451)
Q Consensus        98 f~G~~tee~L~~~F~~fG~V~~v~v-~~d~~g~srG~gFV~  137 (451)
                      +.|++-       =..||...+|.. +++..-.+..|.|+.
T Consensus       190 ~DGr~l-------katYGTTKYCtsYLRn~~CpNp~CMyLH  223 (480)
T COG5175         190 LDGRVL-------KATYGTTKYCTSYLRNAVCPNPDCMYLH  223 (480)
T ss_pred             ccCceE-------eeecCchHHHHHHHcCCCCCCCCeeeec
Confidence            998532       134777777665 333322334455554

>KOG2193|consensus

Probab=96.97  E-value=0.0003  Score=71.56  Aligned_cols=118  Identities=22%  Similarity=0.303  Sum_probs=90.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCcc-CCC----------
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP-YKG----------  100 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~-f~G----------  100 (451)
                      ++.+|++||.+.++.++|..+|...-.-.+-.++.     ..||+||.+.+...|.+|++.++|+. +.|          
T Consensus         1 mnklyignL~p~~~psdl~svfg~ak~~~~g~fl~-----k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    1 MNKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV-----KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CCcccccccCCCCChHHHHHHhccccCCCCcceee-----ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            35799999999999999999998552211222221     26899999999999999999988864 333          


Q ss_pred             ---------------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 ---------------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ---------------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                                     ...++-|..+..+||.++.|..+...+.  ....-|+|.+.+.+..|+.+++|-++
T Consensus        76 kkqrsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~e--tavvnvty~~~~~~~~ai~kl~g~Q~  144 (584)
T KOG2193|consen   76 KKQRSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSE--TAVVNVTYSAQQQHRQAIHKLNGPQL  144 (584)
T ss_pred             HHHHhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchH--HHHHHHHHHHHHHHHHHHHhhcchHh
Confidence                           1467888889999999999998653221  23345889999999999999998664

>KOG4206|consensus

Probab=96.96  E-value=0.0015  Score=61.82  Aligned_cols=57  Identities=28%  Similarity=0.532  Sum_probs=47.5

Q ss_pred             CcHHHHHH----HhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcccCCC
Q psy300          102 ITEEEFKE----HFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE  160 (451)
Q Consensus       102 ~tee~L~~----~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~~~~  160 (451)
                      +..++|+.    +|++||.|..+...+  +.+.||.|||.|.+.+.|..|+..++|..|++.+
T Consensus        21 I~~~elkrsL~~LFsqfG~ildI~a~k--t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~   81 (221)
T KOG4206|consen   21 IKKDELKRSLYLLFSQFGKILDISAFK--TPKMRGQAFVVFKETEAASAALRALQGFPFYGKP   81 (221)
T ss_pred             ccHHHHHHHHHHHHHhhCCeEEEEecC--CCCccCceEEEecChhHHHHHHHHhcCCcccCch
Confidence            45555555    999999999888875  4577999999999999999999999998776543

>KOG0105|consensus

Probab=96.94  E-value=0.00094  Score=61.32  Aligned_cols=55  Identities=25%  Similarity=0.434  Sum_probs=47.1

Q ss_pred             CCCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          100 GKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       100 G~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      +.+.+.+++++|.+||.|..+.+-..+  .+.+||||+|+++.+|..||...++.-|
T Consensus        16 ~diRekeieDlFyKyg~i~~ieLK~r~--g~ppfafVeFEd~RDAeDAiygRdGYdy   70 (241)
T KOG0105|consen   16 GDIREKEIEDLFYKYGRIREIELKNRP--GPPPFAFVEFEDPRDAEDAIYGRDGYDY   70 (241)
T ss_pred             cchhhccHHHHHhhhcceEEEEeccCC--CCCCeeEEEecCccchhhhhhccccccc
Confidence            357899999999999999999885432  2367999999999999999999988665

>KOG1457|consensus

Probab=96.92  E-value=0.0008  Score=63.45  Aligned_cols=69  Identities=20%  Similarity=0.276  Sum_probs=56.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK   99 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~   99 (451)
                      ..+..++|||.||..+++|++|+.+|+.|-....+++ +.+.|  ...||++|++.+.|..|+..++|..+.
T Consensus       206 ~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~-~~~~g--~~vaf~~~~~~~~at~am~~lqg~~~s  274 (284)
T KOG1457|consen  206 GARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKI-RARGG--MPVAFADFEEIEQATDAMNHLQGNLLS  274 (284)
T ss_pred             cchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEE-ecCCC--cceEeecHHHHHHHHHHHHHhhcceec
Confidence            3446789999999999999999999999977655555 33344  357999999999999999999887653

>KOG0153|consensus

Probab=96.84  E-value=0.0011  Score=66.19  Aligned_cols=51  Identities=35%  Similarity=0.658  Sum_probs=45.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++.+|+++|.+||.|+++.++..     +++|||+|+++++|..|..++-.++.
T Consensus       239 ~v~e~dIrdhFyqyGeirsi~~~~~-----~~CAFv~ftTR~aAE~Aae~~~n~lv  289 (377)
T KOG0153|consen  239 EVLEQDIRDHFYQYGEIRSIRILPR-----KGCAFVTFTTREAAEKAAEKSFNKLV  289 (377)
T ss_pred             chhHHHHHHHHhhcCCeeeEEeecc-----cccceeeehhhHHHHHHHHhhcceee
Confidence            5899999999999999999999876     67999999999999999988755443

>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=96.66  E-value=0.0034  Score=53.23  Aligned_cols=57  Identities=23%  Similarity=0.359  Sum_probs=37.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcC
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN   94 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~ln   94 (451)
                      +-|.+.+++..++.++|++.|++||.|..|.+.+.     -..|+|.|.+++.|++|+..+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G-----~~~g~VRf~~~~~A~~a~~~~~   58 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG-----DTEGYVRFKTPEAAQKALEKLK   58 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT------SEEEEEESS---HHHHHHHHH
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC-----CCEEEEEECCcchHHHHHHHHH
Confidence            45888999999999999999999999999888643     3368999999999999998654

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG4661|consensus

Probab=96.65  E-value=0.0018  Score=68.14  Aligned_cols=54  Identities=20%  Similarity=0.440  Sum_probs=46.7

Q ss_pred             CcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCc
Q psy300          102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKP  155 (451)
Q Consensus       102 ~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~ri  155 (451)
                      +.-.+|+.+|++||.|.-++|+.+ ++--.+.||||++.+.++|.+||..|+..-
T Consensus       417 TRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTE  471 (940)
T KOG4661|consen  417 TRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTE  471 (940)
T ss_pred             hhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhh
Confidence            456899999999999999999987 444468899999999999999999987543

>KOG1365|consensus

Probab=96.41  E-value=0.02  Score=58.03  Aligned_cols=120  Identities=19%  Similarity=0.326  Sum_probs=86.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeE-CCCCCceeEEEEEEccHHHHHHHHHhcC----Cc----------
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLK-NADGKLKGCGFINYANKISAVKAILKSN----KK----------   96 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~-d~tg~skG~aFV~F~~~~~A~~Al~~ln----g~----------   96 (451)
                      +.-+-.++||...++.++-.+|...--..-.+.+. +..|+.-|.+.|.|.+++.-..|++.-.    +.          
T Consensus        60 ~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryievYka~ge  139 (508)
T KOG1365|consen   60 NVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYIEVYKATGE  139 (508)
T ss_pred             ceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHhhhhhccCCceeeeccCch
Confidence            34455679999999999999997542111112222 2267777899999999988888876411    10          


Q ss_pred             cC---C----------------------C---CCcHHHHHHHhcc----cCcceeeEEeeCCCCCccceEEEEecchHHH
Q psy300           97 PY---K----------------------G---KITEEEFKEHFGQ----YGDIIDAQLLKNADGKLKGCGFINYANKISA  144 (451)
Q Consensus        97 ~f---~----------------------G---~~tee~L~~~F~~----fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A  144 (451)
                      .|   .                      |   .+++.++.++|.+    -|.++.+-+++..+|+..|-|||.|..+++|
T Consensus       140 ~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~a  219 (508)
T KOG1365|consen  140 EFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEEDA  219 (508)
T ss_pred             hheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHHH
Confidence            00   0                      0   3799999999953    2346677777778999999999999999999


Q ss_pred             HHHHHhc
Q psy300          145 VKAILKS  151 (451)
Q Consensus       145 ~~Ai~~l  151 (451)
                      +.|+.+.
T Consensus       220 q~aL~kh  226 (508)
T KOG1365|consen  220 QFALRKH  226 (508)
T ss_pred             HHHHHHH
Confidence            9999774

>KOG3152|consensus

Probab=96.19  E-value=0.0069  Score=58.33  Aligned_cols=70  Identities=23%  Similarity=0.390  Sum_probs=60.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-C--------CCceeE----EEEEEccHHHHHHHHHhcCCcc
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-D--------GKLKGC----GFINYANKISAVKAILKSNKKP   97 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-t--------g~skG~----aFV~F~~~~~A~~Al~~lng~~   97 (451)
                      .+.-||+++||+.+...-|+++|++||.|-.|.|-... +        |.++++    |.|+|.+...|.++...||+..
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            67899999999999999999999999999999886653 3        333332    6789999999999999999998


Q ss_pred             CCC
Q psy300           98 YKG  100 (451)
Q Consensus        98 f~G  100 (451)
                      +.|
T Consensus       153 Igg  155 (278)
T KOG3152|consen  153 IGG  155 (278)
T ss_pred             cCC
Confidence            887

>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=96.18  E-value=0.013  Score=47.38  Aligned_cols=59  Identities=17%  Similarity=0.325  Sum_probs=41.3

Q ss_pred             ceEEEcCCCCCCCHHHH----HHHhccCC-CeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           33 GRLFIKNLPFKITEEEF----KEHFGQYG-DIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L----~~~F~~~G-~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      +.|||.|||.+.+...+    +.++..+| .|.++.         .+.|+|.|.+++.|.+|...|+|....|
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~---------~~tAilrF~~~~~A~RA~KRmegEdVfG   66 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS---------GGTAILRFPNQEFAERAQKRMEGEDVFG   66 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE-----------TT-EEEEESSHHHHHHHHHHHTT--SSS
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe---------CCEEEEEeCCHHHHHHHHHhhccccccc
Confidence            57999999999888765    56677776 466552         4679999999999999999999875555

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG1995|consensus

Probab=96.12  E-value=0.0092  Score=60.05  Aligned_cols=82  Identities=23%  Similarity=0.318  Sum_probs=69.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEE--------EEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIID--------AQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPY   98 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~--------i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f   98 (451)
                      ......++||-+||..+++++|.++|.++|.|..        |.+-+++ |+.+||-|.|.|.+...|+.|+.-++++.|
T Consensus        62 ~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf  141 (351)
T KOG1995|consen   62 DKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDF  141 (351)
T ss_pred             cccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccc
Confidence            3556789999999999999999999999998843        5556666 999999999999999999999999999999


Q ss_pred             CCCCcHHHHHH
Q psy300           99 KGKITEEEFKE  109 (451)
Q Consensus        99 ~G~~tee~L~~  109 (451)
                      .|++...-+.+
T Consensus       142 ~gn~ikvs~a~  152 (351)
T KOG1995|consen  142 CGNTIKVSLAE  152 (351)
T ss_pred             cCCCchhhhhh
Confidence            99654443333

>KOG4676|consensus

Probab=96.10  E-value=0.0044  Score=62.83  Aligned_cols=115  Identities=16%  Similarity=0.230  Sum_probs=84.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC----CCCceeEEEEEEccHHHHHHHHHhcCCccCCC--------
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA----DGKLKGCGFINYANKISAVKAILKSNKKPYKG--------  100 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~----tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G--------  100 (451)
                      .-|-|.||.++++.++++.+|.-.|.|.+++|+...    -......|||.|.+...+..|- .|.+.+|.+        
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQ-hLtntvfvdraliv~p~   86 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQ-HLTNTVFVDRALIVRPY   86 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHh-hhccceeeeeeEEEEec
Confidence            478899999999999999999999999999997643    1244678999999988776653 333332221        


Q ss_pred             ---------------------------------------------------------------------------CCcHH
Q psy300          101 ---------------------------------------------------------------------------KITEE  105 (451)
Q Consensus       101 ---------------------------------------------------------------------------~~tee  105 (451)
                                                                                                 .+...
T Consensus        87 ~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~  166 (479)
T KOG4676|consen   87 GDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAILP  166 (479)
T ss_pred             CCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcch
Confidence                                                                                       14567


Q ss_pred             HHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhc
Q psy300          106 EFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS  151 (451)
Q Consensus       106 ~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~l  151 (451)
                      ++-+.|+.+|.|.+..+....   ..-++-+.|....+...|+...
T Consensus       167 e~~e~f~r~Gev~ya~~ask~---~s~~c~~sf~~qts~~halr~~  209 (479)
T KOG4676|consen  167 ESGESFERKGEVSYAHTASKS---RSSSCSHSFRKQTSSKHALRSH  209 (479)
T ss_pred             hhhhhhhhcchhhhhhhhccC---CCcchhhhHhhhhhHHHHHHhc
Confidence            888999999999988775432   2334558888877777776554

>KOG2314|consensus

Probab=96.07  E-value=0.0072  Score=63.86  Aligned_cols=71  Identities=21%  Similarity=0.267  Sum_probs=58.9

Q ss_pred             CCCceEEEcCCCCCCC--H----HHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKIT--E----EEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vt--e----~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .-.+.|+|.|+|.-=.  -    .-|.++|+++|++....++.+..|.++||.|++|.+..+|+.|++.+||+.+.-
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldk  132 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDK  132 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecc
Confidence            3467899999985321  1    236789999999999999888866699999999999999999999999987754

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=95.88  E-value=0.016  Score=42.92  Aligned_cols=52  Identities=25%  Similarity=0.503  Sum_probs=41.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHH
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI   90 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al   90 (451)
                      +.|-|.|.+.+.. +.+...|.+||+|.++.+.     ...-..+|.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~-----~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVP-----ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcC-----CCCcEEEEEECCHHHHHhhC
Confidence            4577888887755 4556699999999998875     23458999999999999985

>KOG1548|consensus

Probab=95.85  E-value=0.03  Score=56.17  Aligned_cols=71  Identities=15%  Similarity=0.333  Sum_probs=56.7

Q ss_pred             CCCCCceEEEcCC--CC--CCC-------HHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCc
Q psy300           28 DKTKRGRLFIKNL--PF--KIT-------EEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK   96 (451)
Q Consensus        28 ~~~~~~~lfVgnL--p~--~vt-------e~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~   96 (451)
                      ..+..++|.++|+  |.  ..+       .++|++-.++||+|.+|.+.-   ..+.|.+-|.|.+.++|..|++.|+|+
T Consensus       261 k~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d---~hPdGvvtV~f~n~eeA~~ciq~m~GR  337 (382)
T KOG1548|consen  261 KARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYD---RHPDGVVTVSFRNNEEADQCIQTMDGR  337 (382)
T ss_pred             cccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEec---cCCCceeEEEeCChHHHHHHHHHhcCe
Confidence            4456789999998  22  233       245667789999999998853   456789999999999999999999999


Q ss_pred             cCCCC
Q psy300           97 PYKGK  101 (451)
Q Consensus        97 ~f~G~  101 (451)
                      .|.|+
T Consensus       338 ~fdgR  342 (382)
T KOG1548|consen  338 WFDGR  342 (382)
T ss_pred             eecce
Confidence            99884

>KOG4210|consensus

Probab=95.79  E-value=0.0072  Score=60.29  Aligned_cols=64  Identities=25%  Similarity=0.501  Sum_probs=57.4

Q ss_pred             CCCCceEE-EcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHh
Q psy300           29 KTKRGRLF-IKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILK   92 (451)
Q Consensus        29 ~~~~~~lf-VgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~   92 (451)
                      .....++| |++|+.++++++|+..|..+|.|..+++..++ ++.++|||++.|.+...+..++..
T Consensus       181 ~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~  246 (285)
T KOG4210|consen  181 SGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND  246 (285)
T ss_pred             cCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc
Confidence            33455666 99999999999999999999999999998887 999999999999999999888875

>KOG0106|consensus

Probab=95.44  E-value=0.011  Score=56.37  Aligned_cols=66  Identities=21%  Similarity=0.473  Sum_probs=57.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ....+.+.|.+++..+.+.+|.+.|.++|.+.+...       ..+++||+|...++|.+|+..++++.+.|.
T Consensus        96 ~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~-------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~  161 (216)
T KOG0106|consen   96 SRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA-------RRNFAFVEFSEQEDAKRALEKLDGKKLNGR  161 (216)
T ss_pred             ccccceeeeccchhhhhHHHHhhhhcccCCCchhhh-------hccccceeehhhhhhhhcchhccchhhcCc
Confidence            456789999999999999999999999999855444       367899999999999999999999877663

>KOG0533|consensus

Probab=95.33  E-value=0.023  Score=55.22  Aligned_cols=53  Identities=19%  Similarity=0.397  Sum_probs=50.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCC
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK  153 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~  153 (451)
                      .+++++|+++|..||.+..+-+..++.|.|.|.|=|.|...++|.+|+..+++
T Consensus        94 ~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~g  146 (243)
T KOG0533|consen   94 GVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNG  146 (243)
T ss_pred             CcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcC
Confidence            57999999999999999999999999999999999999999999999999988

>KOG4849|consensus

Probab=95.25  E-value=0.013  Score=58.55  Aligned_cols=69  Identities=16%  Similarity=0.290  Sum_probs=61.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCC--eEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFGQYGD--IIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~~~G~--I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .-.+|||||-.-+|++||.+.....|-  +.++++.-++ +|.|||||+|...+...+++-++.|-.+.++|
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHG  151 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHG  151 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecC
Confidence            457899999999999999999988874  7788888777 89999999999999999999999999888888

>KOG0129|consensus

Probab=95.18  E-value=0.05  Score=57.24  Aligned_cols=67  Identities=22%  Similarity=0.353  Sum_probs=60.4

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhc-cCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHh
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFG-QYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILK   92 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~-~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~   92 (451)
                      ...-.+.+|||||+||.-++-++|-.+|+ -||.|..+-|=+|+ -+.++|-|=|.|.+..+-.+||.+
T Consensus       364 sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  364 NQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            33455789999999999999999999999 89999999998885 788999999999999999999875

>KOG0115|consensus

Probab=95.16  E-value=0.025  Score=54.67  Aligned_cols=71  Identities=23%  Similarity=0.357  Sum_probs=62.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .....|||.||+.-++.+.+..-|+.||+|....+..|..+++.|-++|.|...-.|.+|....+-.-|.+
T Consensus        29 a~~a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~   99 (275)
T KOG0115|consen   29 AMHAELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFGG   99 (275)
T ss_pred             eccceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCcccc
Confidence            34489999999999999999999999999999888888888889999999999999999998876555554

>KOG2314|consensus

Probab=95.07  E-value=0.026  Score=59.75  Aligned_cols=54  Identities=26%  Similarity=0.368  Sum_probs=48.7

Q ss_pred             HHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcccC
Q psy300          105 EEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  158 (451)
Q Consensus       105 e~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~~  158 (451)
                      .-|..+|+++|.+....++.++.|.++||.|++|.+..+|+.|+.++||+.+..
T Consensus        79 ~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldk  132 (698)
T KOG2314|consen   79 KVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDK  132 (698)
T ss_pred             HHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecc
Confidence            567889999999999999988878899999999999999999999999987543

>KOG1855|consensus

Probab=95.05  E-value=0.024  Score=58.21  Aligned_cols=70  Identities=24%  Similarity=0.359  Sum_probs=58.0

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeEC---C---CCC--------ceeEEEEEEccHHHHHHHH
Q psy300           25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN---A---DGK--------LKGCGFINYANKISAVKAI   90 (451)
Q Consensus        25 ~~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d---~---tg~--------skG~aFV~F~~~~~A~~Al   90 (451)
                      ......+.++|.+-|||.+-.-+.|.++|+.+|.|.+|++..-   +   .+.        .+-+|+|+|...+.|.+|.
T Consensus       224 ~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~  303 (484)
T KOG1855|consen  224 FDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAR  303 (484)
T ss_pred             ccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHH
Confidence            3444457899999999999999999999999999999999765   2   222        2567899999999999998


Q ss_pred             HhcC
Q psy300           91 LKSN   94 (451)
Q Consensus        91 ~~ln   94 (451)
                      +.++
T Consensus       304 e~~~  307 (484)
T KOG1855|consen  304 ELLN  307 (484)
T ss_pred             Hhhc
Confidence            8774

>KOG0116|consensus

Probab=94.85  E-value=0.032  Score=58.34  Aligned_cols=51  Identities=29%  Similarity=0.453  Sum_probs=44.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEee-CCCCCccceEEEEecchHHHHHHHHhc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLK-NADGKLKGCGFINYANKISAVKAILKS  151 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~-d~~g~srG~gFV~F~s~e~A~~Ai~~l  151 (451)
                      +++..+|+++|+.||.|+...|.. ...+++..||||+|.+.++++.|+.+.
T Consensus       299 da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~As  350 (419)
T KOG0116|consen  299 DATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEAS  350 (419)
T ss_pred             CCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcC
Confidence            579999999999999999999965 345555699999999999999999886

>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=94.82  E-value=0.037  Score=46.89  Aligned_cols=47  Identities=23%  Similarity=0.461  Sum_probs=31.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcC
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN  152 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln  152 (451)
                      .++.++|++.|++||.|.+|.+.+.     -.-|||.|.+.++|+.|+..+.
T Consensus        12 ~~~re~iK~~f~~~g~V~yVD~~~G-----~~~g~VRf~~~~~A~~a~~~~~   58 (105)
T PF08777_consen   12 PTSREDIKEAFSQFGEVAYVDFSRG-----DTEGYVRFKTPEAAQKALEKLK   58 (105)
T ss_dssp             S--HHHHHHHT-SS--EEEEE--TT------SEEEEEESS---HHHHHHHHH
T ss_pred             CcCHHHHHHHHHhcCCcceEEecCC-----CCEEEEEECCcchHHHHHHHHH
Confidence            5788999999999999999999875     2358999999999999998874

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG4454|consensus

Probab=94.70  E-value=0.059  Score=51.03  Aligned_cols=59  Identities=22%  Similarity=0.241  Sum_probs=52.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcccCCC
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE  160 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~~~~  160 (451)
                      .++++-|.++|-+-|.|..+.|+.++.+..+ ||||.|.++.+..-|++.+||--.+..+
T Consensus        20 ~v~eelL~ElfiqaGPV~kv~ip~~~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e   78 (267)
T KOG4454|consen   20 GVSEELLSELFIQAGPVYKVGIPSGQDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDE   78 (267)
T ss_pred             hhhHHHHHHHhhccCceEEEeCCCCccCCCc-eeeeecccccchhhhhhhcccchhccch
Confidence            5899999999999999999999998888877 9999999999999999999986655444

>KOG4307|consensus

Probab=94.57  E-value=0.083  Score=57.36  Aligned_cols=72  Identities=21%  Similarity=0.339  Sum_probs=61.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeE-EEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDII-DAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK   99 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~-~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~   99 (451)
                      .....+-|-+.|+|++++-+||.+||..|-.+- +|.+.++..|...|-|-|.|++.++|.+|...++++.+.
T Consensus       863 ~~pGp~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~  935 (944)
T KOG4307|consen  863 KSPGPRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIR  935 (944)
T ss_pred             CCCCCeEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCccc
Confidence            444556788999999999999999999997653 567777779999999999999999999999998886543

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=94.25  E-value=0.19  Score=40.73  Aligned_cols=54  Identities=13%  Similarity=0.286  Sum_probs=40.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcC
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN   94 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~ln   94 (451)
                      .-.||+ +|..+...||..+|+.||.|. |..+.|      .-|||...+.+.|..|+..+.
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~d------TSAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWIND------TSAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCCCCEE-EEEECT------TEEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcC------CcEEEEeecHHHHHHHHHHhc
Confidence            445565 999999999999999999974 655544      359999999999999887765

; 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.

>KOG4307|consensus

Probab=94.25  E-value=0.036  Score=60.03  Aligned_cols=120  Identities=13%  Similarity=0.149  Sum_probs=89.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCC----ccC-------
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNK----KPY-------   98 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng----~~f-------   98 (451)
                      ..+.+-+++.+.+.+..+++++|... .|.+..|..+. .+...|.++|.|....++++|+..-+-    ..|       
T Consensus       310 d~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~rn~~~~~~R~~q~~P~g~  388 (944)
T KOG4307|consen  310 DKYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTRNPSDDVNRPFQTGPPGN  388 (944)
T ss_pred             hhheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhcCchhhhhcceeecCCCc
Confidence            34566677999999999999999744 35666666665 333478899999999999999864210    000       


Q ss_pred             ------------C---------C---------------------------------CCcHHHHHHHhcccCccee-eEEe
Q psy300           99 ------------K---------G---------------------------------KITEEEFKEHFGQYGDIID-AQLL  123 (451)
Q Consensus        99 ------------~---------G---------------------------------~~tee~L~~~F~~fG~V~~-v~v~  123 (451)
                                  .         |                                 .+++.++.+.|+.--.|++ +.+.
T Consensus       389 ~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt  468 (944)
T KOG4307|consen  389 LGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELT  468 (944)
T ss_pred             cccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEec
Confidence                        0         0                                 2688899999988767777 5666


Q ss_pred             eCCCCCccceEEEEecchHHHHHHHHhc
Q psy300          124 KNADGKLKGCGFINYANKISAVKAILKS  151 (451)
Q Consensus       124 ~d~~g~srG~gFV~F~s~e~A~~Ai~~l  151 (451)
                      +.++++.++.|||.|..++++..|..-.
T Consensus       469 ~~P~~~~~~~afv~F~~~~a~~~a~~~~  496 (944)
T KOG4307|consen  469 RLPTDLLRPAAFVAFIHPTAPLTASSVK  496 (944)
T ss_pred             cCCcccccchhhheeccccccchhhhcc
Confidence            6688899999999999988888776544

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=94.06  E-value=0.07  Score=39.44  Aligned_cols=40  Identities=30%  Similarity=0.590  Sum_probs=33.5

Q ss_pred             HHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHH
Q psy300          104 EEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI  148 (451)
Q Consensus       104 ee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai  148 (451)
                      .+.+..+|..||.|....+...     ..+.||.|.++.+|.+|+
T Consensus        14 ~~~vl~~F~~fGeI~~~~~~~~-----~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen   14 AEEVLEHFASFGEIVDIYVPES-----TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             HHHHHHHHHhcCCEEEEEcCCC-----CcEEEEEECCHHHHHhhC
Confidence            3667789999999999888632     568999999999999985

>KOG4209|consensus

Probab=93.86  E-value=0.061  Score=52.03  Aligned_cols=54  Identities=19%  Similarity=0.296  Sum_probs=47.0

Q ss_pred             CcHHHHHHHhcccCcceeeEEeeCC-CCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          102 ITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       102 ~tee~L~~~F~~fG~V~~v~v~~d~-~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      +|.+++..+|+.||.+..+.++.|. .+.++||+||+|.+.+.+..|+. +|+..+
T Consensus       113 ~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i  167 (231)
T KOG4209|consen  113 VTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEI  167 (231)
T ss_pred             cccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccc
Confidence            4556699999999999999999885 45799999999999999999998 887654

>KOG0128|consensus

Probab=93.82  E-value=0.022  Score=62.93  Aligned_cols=74  Identities=20%  Similarity=0.268  Sum_probs=64.4

Q ss_pred             CCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccC
Q psy300           25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY   98 (451)
Q Consensus        25 ~~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f   98 (451)
                      .+.-.-.+..|+|+|.|+.-|.+.++.+++.+|.+.+.+++..+.|+++|-++|.|.++.++.+++..+.+..+
T Consensus       729 ~d~~~~gK~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~  802 (881)
T KOG0128|consen  729 RDSCFFGKISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGK  802 (881)
T ss_pred             hhhhhhhhhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchhhhh
Confidence            33344457899999999999999999999999999999999888999999999999999999999876655433

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=93.70  E-value=0.27  Score=41.12  Aligned_cols=56  Identities=20%  Similarity=0.199  Sum_probs=44.9

Q ss_pred             CCcHHHHHHHhcc--cCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQ--YGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~--fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      +.|.+.|.+++..  .|...-+-++.| .++.+.|||||.|.++++|.+-....+|+.+
T Consensus        12 ~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w   70 (97)
T PF04059_consen   12 KYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKW   70 (97)
T ss_pred             CCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCcc
Confidence            4677888888764  455666666777 6777899999999999999999999988765

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG2068|consensus

Probab=93.61  E-value=0.043  Score=55.01  Aligned_cols=73  Identities=22%  Similarity=0.377  Sum_probs=56.9

Q ss_pred             CCCceEEEcCCCCCCCHHHH---HHHhccCCCeEEEEEeECCC--CCce--eEEEEEEccHHHHHHHHHhcCCccCCCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEF---KEHFGQYGDIIDAQLLKNAD--GKLK--GCGFINYANKISAVKAILKSNKKPYKGKI  102 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L---~~~F~~~G~I~~i~l~~d~t--g~sk--G~aFV~F~~~~~A~~Al~~lng~~f~G~~  102 (451)
                      ..+.-+||-+|+.++..+.+   .+.|.+||.|..+...++.+  ..+-  .-++|.|...++|..||...+|.++.|+.
T Consensus        75 Vqknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~  154 (327)
T KOG2068|consen   75 VQKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRA  154 (327)
T ss_pred             hhhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhh
Confidence            45578899999988766665   45899999999998877652  1111  12799999999999999999998888754

>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=93.57  E-value=0.14  Score=43.05  Aligned_cols=69  Identities=20%  Similarity=0.340  Sum_probs=45.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEE-EeEC-------CCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQ-LLKN-------ADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~-l~~d-------~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ..+-|-|=+.|+. ....+.+.|++||.|.+.. +.++       +.......-.|.|.++.+|.+||+ -||.++.|.
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~-~NG~i~~g~   81 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQ-KNGTIFSGS   81 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHT-TTTEEETTC
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHH-hCCeEEcCc
Confidence            3456778889888 5677889999999998774 1111       111224578999999999999997 577777663

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.

>KOG4660|consensus

Probab=93.36  E-value=0.048  Score=57.78  Aligned_cols=59  Identities=20%  Similarity=0.396  Sum_probs=49.6

Q ss_pred             CCCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcccCCCCC
Q psy300          100 GKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSENG  162 (451)
Q Consensus       100 G~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~~~~~G  162 (451)
                      ..+++++|..+|+.||+|..++.-..    .+|..||+|.+..+|++|+.+++++-+.+..-+
T Consensus        85 ~~Vsn~~L~~~f~~yGeir~ir~t~~----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   85 RSVSNDTLLRIFGAYGEIREIRETPN----KRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             CcCCHHHHHHHHHhhcchhhhhcccc----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            36899999999999999999665443    378999999999999999999998877655444

>KOG0151|consensus

Probab=93.36  E-value=0.13  Score=56.16  Aligned_cols=74  Identities=22%  Similarity=0.473  Sum_probs=57.4

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCC----CCCccceEEEEecchHHHHHHHHhcCCCcccCCCC----CcccccccCCc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNA----DGKLKGCGFINYANKISAVKAILKSNKKPYKGSEN----GLISPFHDIPL  172 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~----~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~~~~~----G~iSp~hdiPl  172 (451)
                      +++++.|...|..||+|.+++++.-+    ..+.+.||||.|-++.+|.+|+..+++.++....-    |+..++..+|+
T Consensus       185 sv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~gWgk~V~ip~~p~  264 (877)
T KOG0151|consen  185 SVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLGWGKAVPIPNIPI  264 (877)
T ss_pred             cccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeeccccccccCCccc
Confidence            47999999999999999999998642    23457899999999999999999999988654332    22344555555


Q ss_pred             cc
Q psy300          173 YS  174 (451)
Q Consensus       173 ~v  174 (451)
                      +.
T Consensus       265 ~i  266 (877)
T KOG0151|consen  265 YI  266 (877)
T ss_pred             cC
Confidence            43

>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=93.09  E-value=0.85  Score=39.01  Aligned_cols=68  Identities=12%  Similarity=0.168  Sum_probs=49.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCC-eEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGD-IIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK   99 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~-I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~   99 (451)
                      ....+.+...|..++-++|..+.+.+-. |.+++++++.+ .++=.+.+.|.+.++|..-...+||+.|.
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~-pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT-PNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC-CceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            3334444445555666677766666644 77889988743 25556899999999999999999999886

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=92.51  E-value=0.38  Score=42.80  Aligned_cols=65  Identities=15%  Similarity=0.276  Sum_probs=51.2

Q ss_pred             CCCCCCCCceEEEcCCCCCCCH----HHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCC
Q psy300           25 KKPDKTKRGRLFIKNLPFKITE----EEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK   95 (451)
Q Consensus        25 ~~~~~~~~~~lfVgnLp~~vte----~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng   95 (451)
                      +.....++++|.|+=|..++..    ..+....+.||+|.++.+.    |  +-.|.|.|.+..+|.+|+.++..
T Consensus        79 k~~kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c----G--rqsavVvF~d~~SAC~Av~Af~s  147 (166)
T PF15023_consen   79 KNTKEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC----G--RQSAVVVFKDITSACKAVSAFQS  147 (166)
T ss_pred             ccCCCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec----C--CceEEEEehhhHHHHHHHHhhcC
Confidence            3455778999999987777654    3455667899999999884    3  44699999999999999998764

>KOG2202|consensus

Probab=92.33  E-value=0.072  Score=51.55  Aligned_cols=56  Identities=21%  Similarity=0.393  Sum_probs=46.1

Q ss_pred             HHHHHHhc-ccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcccCCC
Q psy300          105 EEFKEHFG-QYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE  160 (451)
Q Consensus       105 e~L~~~F~-~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~~~~  160 (451)
                      +++...|+ +||.|+.+.|..+..-.-+|=+||.|...++|.+|+..+|++.|-+.+
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~p  139 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRP  139 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCc
Confidence            55555555 899999998887755566888999999999999999999999984433

>KOG0115|consensus

Probab=91.83  E-value=0.39  Score=46.63  Aligned_cols=63  Identities=22%  Similarity=0.361  Sum_probs=56.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcccCCCCCc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSENGL  163 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~~~~~G~  163 (451)
                      .++.+.|.+.|+.||.|+...+..|..+++.+-++|.|...-.|.+|........++....+.
T Consensus        42 ~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~  104 (275)
T KOG0115|consen   42 GASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGR  104 (275)
T ss_pred             hhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCccccCCCCC
Confidence            478899999999999999999988888899999999999999999999999888877766665

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=90.18  E-value=0.4  Score=44.45  Aligned_cols=71  Identities=20%  Similarity=0.179  Sum_probs=46.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhcc-CCCe---EEEEEeECC--CCC-ceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQ-YGDI---IDAQLLKNA--DGK-LKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~-~G~I---~~i~l~~d~--tg~-skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....+|-|++||+++|++++.+.++. ++.-   ..+.-....  .+. .-.-|||.|.+.+++..-...++|..|..
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D   82 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVD   82 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEEC
Confidence            35669999999999999999887776 6665   344322222  222 23459999999999888888899887764

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.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=89.92  E-value=1.4  Score=33.76  Aligned_cols=55  Identities=11%  Similarity=0.292  Sum_probs=43.7

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccC---CCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhc
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFGQY---GDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS   93 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~~~---G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~l   93 (451)
                      ...|+|+|+ .+++.++|+.+|..|   .....|..+-|      .-|=|.|.+.+.|.+|+.+|
T Consensus         5 peavhirGv-d~lsT~dI~~y~~~y~~~~~~~~IEWIdD------tScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGV-DELSTDDIKAYFSEYFDEEGPFRIEWIDD------TSCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcC-CCCCHHHHHHHHHHhcccCCCceEEEecC------CcEEEEECCHHHHHHHHHcC
Confidence            357999998 458899999999999   12457777766      23779999999999999764

>KOG1996|consensus

Probab=88.34  E-value=0.88  Score=45.00  Aligned_cols=55  Identities=22%  Similarity=0.320  Sum_probs=44.1

Q ss_pred             cHHHHHHHhcccCcceeeEEeeCCCC--CccceEEEEecchHHHHHHHHhcCCCccc
Q psy300          103 TEEEFKEHFGQYGDIIDAQLLKNADG--KLKGCGFINYANKISAVKAILKSNKKPYK  157 (451)
Q Consensus       103 tee~L~~~F~~fG~V~~v~v~~d~~g--~srG~gFV~F~s~e~A~~Ai~~ln~riy~  157 (451)
                      -++++++.+++||.|..|.|.-.++.  .-----||+|+..++|.+|+-.+|||.|.
T Consensus       299 lede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFG  355 (378)
T KOG1996|consen  299 LEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFG  355 (378)
T ss_pred             HHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceec
Confidence            45788889999999999998765321  11235799999999999999999999873

>KOG1996|consensus

Probab=87.60  E-value=1.2  Score=44.09  Aligned_cols=56  Identities=21%  Similarity=0.404  Sum_probs=45.0

Q ss_pred             HHHHHHhccCCCeEEEEEeECCCC-Ccee-EEEEEEccHHHHHHHHHhcCCccCCCCC
Q psy300           47 EEFKEHFGQYGDIIDAQLLKNADG-KLKG-CGFINYANKISAVKAILKSNKKPYKGKI  102 (451)
Q Consensus        47 ~~L~~~F~~~G~I~~i~l~~d~tg-~skG-~aFV~F~~~~~A~~Al~~lng~~f~G~~  102 (451)
                      +++.+-+++||.|..|.+.-.++- ...- --||+|...++|.+|+-.|||..|.|++
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~  358 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRV  358 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceeccee
Confidence            467888999999999988766521 1122 3699999999999999999999999964

>KOG2202|consensus

Probab=86.80  E-value=0.27  Score=47.72  Aligned_cols=55  Identities=22%  Similarity=0.421  Sum_probs=44.4

Q ss_pred             HHHHHHhc-cCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           47 EEFKEHFG-QYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        47 ~~L~~~F~-~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      +++...|+ +||+|.++.+-.+-.-.-+|=++|.|...++|++|++.||+.-|.|+
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~  138 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGR  138 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCC
Confidence            34444555 99999999776554445578899999999999999999999999884

>KOG0112|consensus

Probab=86.67  E-value=0.76  Score=51.57  Aligned_cols=68  Identities=19%  Similarity=0.197  Sum_probs=59.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .....+.+|+++|..-.....|...|..||.|..|.+-.     ...|++|+|.+...|+.|+..|.|..|.|
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h-----gq~yayi~yes~~~aq~a~~~~rgap~G~  518 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH-----GQPYAYIQYESPPAAQAATHDMRGAPLGG  518 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc-----CCcceeeecccCccchhhHHHHhcCcCCC
Confidence            345678999999999999999999999999999887742     25699999999999999999999988876

>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=84.49  E-value=1.8  Score=36.43  Aligned_cols=53  Identities=25%  Similarity=0.396  Sum_probs=36.0

Q ss_pred             cHHHHHHHhcccCcceeeE-EeeC-------CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          103 TEEEFKEHFGQYGDIIDAQ-LLKN-------ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       103 tee~L~~~F~~fG~V~~v~-v~~d-------~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .-..+.++|++||.|.+.. +.++       +......+..|+|.++.+|.+|+.. ||+++
T Consensus        18 ~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~   78 (100)
T PF05172_consen   18 ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIF   78 (100)
T ss_dssp             GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEE
T ss_pred             HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEE
Confidence            4467889999999987764 1111       1112256899999999999999954 56654

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.

>KOG0804|consensus

Probab=81.04  E-value=5.2  Score=41.94  Aligned_cols=69  Identities=14%  Similarity=0.196  Sum_probs=58.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCC-CeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYG-DIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G-~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      +.+.|+|=.+|.-++-.||..|...+- .|.+++++||... ++=...+.|.+.++|..-...+||+.|..
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~p-nrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMP-NRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCC-ceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            378999999999999999999998775 4899999996422 23347999999999999999999998873

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=80.34  E-value=2.3  Score=42.85  Aligned_cols=49  Identities=27%  Similarity=0.367  Sum_probs=37.0

Q ss_pred             HHHhcccCcceeeEEeeCC-CCCc-cc--eEEEEecchHHHHHHHHhcCCCcc
Q psy300          108 KEHFGQYGDIIDAQLLKNA-DGKL-KG--CGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       108 ~~~F~~fG~V~~v~v~~d~-~g~s-rG--~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .++|.+||.|..+.+-+.. +..+ .+  -.||+|.+.++|.+||...+|.+.
T Consensus       138 ~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~  190 (480)
T COG5175         138 HEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLL  190 (480)
T ss_pred             hhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccc
Confidence            5789999999998886542 1111 12  249999999999999999888764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	451
1huj_A	281	Refined Structure Of Yeast Inorganic Pyrophosphatas		4e-70
1huj_A	281	Refined Structure Of Yeast Inorganic Pyrophosphatas		5e-09
1wgi_A	286	Structure Of Inorganic Pyrophosphatase Length = 286		5e-70
1wgi_A	286	Structure Of Inorganic Pyrophosphatase Length = 286		5e-09
1m38_A	287	Structure Of Inorganic Pyrophosphatase Length = 287		5e-70
1m38_A	287	Structure Of Inorganic Pyrophosphatase Length = 287		5e-09
1huk_A	281	Refined Structure Of Yeast Inorganic Pyrophosphatas		5e-70
1huk_A	281	Refined Structure Of Yeast Inorganic Pyrophosphatas		5e-09
8prk_A	287	The R78k And D117e Active Site Variants Of Saccharo		1e-69
8prk_A	287	The R78k And D117e Active Site Variants Of Saccharo		5e-09
2ik1_A	286	Yeast Inorganic Pyrophosphatase Variant Y93f With M		1e-69
2ik1_A	286	Yeast Inorganic Pyrophosphatase Variant Y93f With M		5e-09
2ik0_A	286	Yeast Inorganic Pyrophosphatase Variant E48d With M		1e-69
2ik0_A	286	Yeast Inorganic Pyrophosphatase Variant E48d With M		1e-08
117e_A	286	The R78k And D117e Active Site Variants Of Saccharo		2e-69
117e_A	286	The R78k And D117e Active Site Variants Of Saccharo		5e-09
2ik6_A	286	Yeast Inorganic Pyrophosphatase Variant D120e With		2e-69
2ik6_A	286	Yeast Inorganic Pyrophosphatase Variant D120e With		5e-09
2ik9_A	286	Yeast Inorganic Pyrophosphatase Variant D152e With		2e-69
2ik9_A	286	Yeast Inorganic Pyrophosphatase Variant D152e With		5e-09
2ik2_A	286	Yeast Inorganic Pyrophosphatase Variant D115e With		2e-69
2ik2_A	286	Yeast Inorganic Pyrophosphatase Variant D115e With		5e-09
2ik7_A	286	Yeast Inorganic Pyrophosphatase Variant D120n With		2e-69
2ik7_A	286	Yeast Inorganic Pyrophosphatase Variant D120n With		5e-09
1ypp_A	286	Acid Anhydride Hydrolase Length = 286		2e-69
1ypp_A	286	Acid Anhydride Hydrolase Length = 286		5e-09
1pyp_A	285	X-Ray Diffraction Study Of Inorganic Pyrophosphatas		4e-66
1pyp_A	285	X-Ray Diffraction Study Of Inorganic Pyrophosphatas		1e-09
1ude_A	195	Crystal Structure Of The Inorganic Pyrophosphatase		2e-12
3i98_A	178	X-Ray Crystallographic Structure Of Inorganic Pyrop		4e-12
3q46_A	178	Magnesium Activated Inorganic Pyrophosphatase From		2e-11
3r6e_A	178	The Structure Of Thermococcus Thioreducens' Inorgan		8e-11
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		9e-11
1twl_A	186	Inorganic Pyrophosphatase From Pyrococcus Furiosus		2e-10
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		6e-10
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		6e-09
3d63_A	196	Crystal Structure Of Inorganic Pyrophosphatase From		1e-08
1qez_A	173	Sulfolobus Acidocaldarius Inorganic Pyrophosphatase		2e-08
3lo0_A	193	Crystal Structure Of Inorganic Pyrophosphatase From		6e-08
2bqx_A	173	Inorganic Pyrophosphatase From The Pathogenic Bacte		8e-08
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		8e-08
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		1e-07
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		1e-07
1ygz_A	173	Crystal Structure Of Inorganic Pyrophosphatase From		2e-07
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		7e-07
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		7e-07
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		3e-06
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		3e-06
2do4_A	100	Solution Structure Of The Rna Binding Domain Of Squ		3e-06
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		3e-06
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		3e-06
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		3e-06
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-06
3d53_A	173	2.2 A Crystal Structure Of Inorganic Pyrophosphatas		7e-06
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		1e-05
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		1e-05
3ld3_A	199	Crystal Structure Of Inorganic Phosphatase From Ana		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
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		3e-05
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		6e-05
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		6e-04
2uxs_A	169	2.7a Crystal Structure Of Inorganic Pyrophosphatase		6e-05
1sxv_A	172	1.3a Crystal Structure Of Rv3628, Mycobacterium Tub		6e-05
1wcf_A	171	1.54 A Crystal Structure Of Rv3628, Mycobacterium T		7e-05
2do0_A	114	Solution Structure Of The Rna Binding Domain Of Het		8e-05
2cpj_A	99	Solution Structure Of The N-Terminal Rna Recognitio		1e-04
4ecp_A	167	X-Ray Crystal Structure Of Inorganic Pyrophosphate		1e-04
3sw5_A	180	Crystal Structure Of Inorganic Pyrophosphatase From		2e-04
1sxl_A	97	Resonance Assignments And Solution Structure Of The		2e-04
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		2e-04
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		3e-04
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		3e-04
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		5e-04
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		6e-04
2dgp_A	106	Solution Structure Of The N-Terminal Rna Binding Do		8e-04

>pdb|1HUJ|A Chain A, Refined Structure Of Yeast Inorganic Pyrophosphatase And Its K61r Mutant Length = 281

Iteration: 1
 Score =  261 bits (668), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 120/176 (68%), Positives = 144/176 (81%)
Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+EI   E LNPI QD KKG LR+V N FP
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITREETLNPIIQDTKKGKLRFVRNCFP 85
Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
           HHGYI NYGA PQTWE+P+ +   T   GD DPIDVLEIGE IA  G++ QVKALG++ L
Sbjct: 86  HHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMAL 145
Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
           +DEG+TDWK+IAI++NDP A KLND+ D+E +FPG L+ATNEWF+IYKIPDGKPEN
Sbjct: 146 LDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPEN 201

>pdb|1HUJ|A Chain A, Refined Structure Of Yeast Inorganic Pyrophosphatase And Its K61r Mutant Length = 281

Iteration: 1
 Score = 58.9 bits (141), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 24/34 (70%), Positives = 31/34 (91%)
Query: 385 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+E+
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEI 59

>pdb|1WGI|A Chain A, Structure Of Inorganic Pyrophosphatase Length = 286

Iteration: 1
 Score =  261 bits (668), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 120/176 (68%), Positives = 144/176 (81%)
Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+EI   E LNPI QD KKG LR+V N FP
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFP 85
Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
           HHGYI NYGA PQTWE+P+ +   T   GD DPIDVLEIGE IA  G++ QVKALG++ L
Sbjct: 86  HHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMAL 145
Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
           +DEG+TDWK+IAI++NDP A KLND+ D+E +FPG L+ATNEWF+IYKIPDGKPEN
Sbjct: 146 LDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPEN 201

>pdb|1WGI|A Chain A, Structure Of Inorganic Pyrophosphatase Length = 286

Iteration: 1
 Score = 58.9 bits (141), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 24/34 (70%), Positives = 31/34 (91%)
Query: 385 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+E+
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEI 59

>pdb|1M38|A Chain A, Structure Of Inorganic Pyrophosphatase Length = 287

Iteration: 1
 Score =  261 bits (667), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 120/176 (68%), Positives = 144/176 (81%)
Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+EI   E LNPI QD KKG LR+V N FP
Sbjct: 27  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFP 86
Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
           HHGYI NYGA PQTWE+P+ +   T   GD DPIDVLEIGE IA  G++ QVKALG++ L
Sbjct: 87  HHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMAL 146
Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
           +DEG+TDWK+IAI++NDP A KLND+ D+E +FPG L+ATNEWF+IYKIPDGKPEN
Sbjct: 147 LDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPEN 202

>pdb|1M38|A Chain A, Structure Of Inorganic Pyrophosphatase Length = 287

Iteration: 1
 Score = 58.9 bits (141), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 24/34 (70%), Positives = 31/34 (91%)
Query: 385 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+E+
Sbjct: 27  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEI 60

>pdb|1HUK|A Chain A, Refined Structure Of Yeast Inorganic Pyrophosphatase And Its K61r Mutant Length = 281

Iteration: 1
 Score =  261 bits (667), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 120/176 (68%), Positives = 144/176 (81%)
Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+EI   E LNPI QD KKG LR+V N FP
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFP 85
Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
           HHGYI NYGA PQTWE+P+ +   T   GD DPIDVLEIGE IA  G++ QVKALG++ L
Sbjct: 86  HHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMAL 145
Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
           +DEG+TDWK+IAI++NDP A KLND+ D+E +FPG L+ATNEWF+IYKIPDGKPEN
Sbjct: 146 LDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPEN 201

>pdb|1HUK|A Chain A, Refined Structure Of Yeast Inorganic Pyrophosphatase And Its K61r Mutant Length = 281

Iteration: 1
 Score = 58.9 bits (141), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 24/34 (70%), Positives = 31/34 (91%)
Query: 385 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+E+
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEI 59

>pdb|8PRK|A Chain A, The R78k And D117e Active Site Variants Of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies And Mechanistic Implications Length = 287

Iteration: 1
 Score =  260 bits (664), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 119/176 (67%), Positives = 144/176 (81%)
Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+EI   E LNPI QD KKG L++V N FP
Sbjct: 27  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLKFVRNCFP 86
Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
           HHGYI NYGA PQTWE+P+ +   T   GD DPIDVLEIGE IA  G++ QVKALG++ L
Sbjct: 87  HHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMAL 146
Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
           +DEG+TDWK+IAI++NDP A KLND+ D+E +FPG L+ATNEWF+IYKIPDGKPEN
Sbjct: 147 LDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPEN 202

>pdb|8PRK|A Chain A, The R78k And D117e Active Site Variants Of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies And Mechanistic Implications Length = 287

Iteration: 1
 Score = 58.9 bits (141), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 24/34 (70%), Positives = 31/34 (91%)
Query: 385 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+E+
Sbjct: 27  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEI 60

>pdb|2IK1|A Chain A, Yeast Inorganic Pyrophosphatase Variant Y93f With Magnesium And Phosphate Length = 286

Iteration: 1
 Score =  260 bits (664), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 119/176 (67%), Positives = 144/176 (81%)
Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+EI   E LNPI QD KKG LR+V N FP
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFP 85
Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
           HHGYI N+GA PQTWE+P+ +   T   GD DPIDVLEIGE IA  G++ QVKALG++ L
Sbjct: 86  HHGYIHNFGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMAL 145
Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
           +DEG+TDWK+IAI++NDP A KLND+ D+E +FPG L+ATNEWF+IYKIPDGKPEN
Sbjct: 146 LDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPEN 201

>pdb|2IK1|A Chain A, Yeast Inorganic Pyrophosphatase Variant Y93f With Magnesium And Phosphate Length = 286

Iteration: 1
 Score = 58.9 bits (141), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 24/34 (70%), Positives = 31/34 (91%)
Query: 385 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+E+
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEI 59

>pdb|2IK0|A Chain A, Yeast Inorganic Pyrophosphatase Variant E48d With Magnesium And Phosphate Length = 286

Iteration: 1
 Score =  260 bits (664), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 119/176 (67%), Positives = 144/176 (81%)
Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           +S FHDIPLY++ ++ IFNMVV+IPRWTNAK+EI   E LNPI QD KKG LR+V N FP
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVDIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFP 85
Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
           HHGYI NYGA PQTWE+P+ +   T   GD DPIDVLEIGE IA  G++ QVKALG++ L
Sbjct: 86  HHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMAL 145
Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
           +DEG+TDWK+IAI++NDP A KLND+ D+E +FPG L+ATNEWF+IYKIPDGKPEN
Sbjct: 146 LDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPEN 201

>pdb|2IK0|A Chain A, Yeast Inorganic Pyrophosphatase Variant E48d With Magnesium And Phosphate Length = 286

Iteration: 1
 Score = 57.8 bits (138), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 23/34 (67%), Positives = 31/34 (91%)
Query: 385 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
           +S FHDIPLY++ ++ IFNMVV+IPRWTNAK+E+
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVDIPRWTNAKLEI 59

>pdb|117E|A Chain A, The R78k And D117e Active Site Variants Of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies And Mechanistic Implications Length = 286

Iteration: 1
 Score =  259 bits (663), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 119/176 (67%), Positives = 144/176 (81%)
Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+EI   E LNPI QD KKG LR+V N FP
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFP 85
Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
           HHGYI NYGA PQTWE+P+ +   T   GD +PIDVLEIGE IA  G++ QVKALG++ L
Sbjct: 86  HHGYIHNYGAFPQTWEDPNVSHPETKAVGDNEPIDVLEIGETIAYTGQVKQVKALGIMAL 145
Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
           +DEG+TDWK+IAI++NDP A KLND+ D+E +FPG L+ATNEWF+IYKIPDGKPEN
Sbjct: 146 LDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPEN 201

>pdb|117E|A Chain A, The R78k And D117e Active Site Variants Of Saccharomyces Cerevisiae Soluble Inorganic Pyrophosphatase: Structural Studies And Mechanistic Implications Length = 286

Iteration: 1
 Score = 58.9 bits (141), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 24/34 (70%), Positives = 31/34 (91%)
Query: 385 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+E+
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEI 59

>pdb|2IK6|A Chain A, Yeast Inorganic Pyrophosphatase Variant D120e With Magnesium And Phosphate Length = 286

Iteration: 1
 Score =  259 bits (663), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 119/176 (67%), Positives = 144/176 (81%)
Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+EI   E LNPI QD KKG LR+V N FP
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFP 85
Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
           HHGYI NYGA PQTWE+P+ +   T   GD DPI+VLEIGE IA  G++ QVKALG++ L
Sbjct: 86  HHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIEVLEIGETIAYTGQVKQVKALGIMAL 145
Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
           +DEG+TDWK+IAI++NDP A KLND+ D+E +FPG L+ATNEWF+IYKIPDGKPEN
Sbjct: 146 LDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPEN 201

>pdb|2IK6|A Chain A, Yeast Inorganic Pyrophosphatase Variant D120e With Magnesium And Phosphate Length = 286

Iteration: 1
 Score = 58.9 bits (141), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 24/34 (70%), Positives = 31/34 (91%)
Query: 385 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+E+
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEI 59

>pdb|2IK9|A Chain A, Yeast Inorganic Pyrophosphatase Variant D152e With Magnesium And Phosphate Length = 286

Iteration: 1
 Score =  259 bits (663), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 119/176 (67%), Positives = 144/176 (81%)
Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+EI   E LNPI QD KKG LR+V N FP
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFP 85
Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
           HHGYI NYGA PQTWE+P+ +   T   GD DPIDVLEIGE IA  G++ QVKALG++ L
Sbjct: 86  HHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMAL 145
Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
           +DEG+T+WK+IAI++NDP A KLND+ D+E +FPG L+ATNEWF+IYKIPDGKPEN
Sbjct: 146 LDEGETEWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPEN 201

>pdb|2IK9|A Chain A, Yeast Inorganic Pyrophosphatase Variant D152e With Magnesium And Phosphate Length = 286

Iteration: 1
 Score = 58.9 bits (141), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 24/34 (70%), Positives = 31/34 (91%)
Query: 385 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+E+
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEI 59

>pdb|2IK2|A Chain A, Yeast Inorganic Pyrophosphatase Variant D115e With Magnesium And Phosphate Length = 286

Iteration: 1
 Score =  259 bits (663), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 119/176 (67%), Positives = 144/176 (81%)
Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+EI   E LNPI QD KKG LR+V N FP
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFP 85
Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
           HHGYI NYGA PQTWE+P+ +   T   G+ DPIDVLEIGE IA  G++ QVKALG++ L
Sbjct: 86  HHGYIHNYGAFPQTWEDPNVSHPETKAVGENDPIDVLEIGETIAYTGQVKQVKALGIMAL 145
Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
           +DEG+TDWK+IAI++NDP A KLND+ D+E +FPG L+ATNEWF+IYKIPDGKPEN
Sbjct: 146 LDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPEN 201

>pdb|2IK2|A Chain A, Yeast Inorganic Pyrophosphatase Variant D115e With Magnesium And Phosphate Length = 286

Iteration: 1
 Score = 58.9 bits (141), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 24/34 (70%), Positives = 31/34 (91%)
Query: 385 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+E+
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEI 59

>pdb|2IK7|A Chain A, Yeast Inorganic Pyrophosphatase Variant D120n With Magnesium And Phosphate Length = 286

Iteration: 1
 Score =  259 bits (662), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 119/176 (67%), Positives = 144/176 (81%)
Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+EI   E LNPI QD KKG LR+V N FP
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFP 85
Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
           HHGYI NYGA PQTWE+P+ +   T   GD DPI+VLEIGE IA  G++ QVKALG++ L
Sbjct: 86  HHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPINVLEIGETIAYTGQVKQVKALGIMAL 145
Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
           +DEG+TDWK+IAI++NDP A KLND+ D+E +FPG L+ATNEWF+IYKIPDGKPEN
Sbjct: 146 LDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPEN 201

>pdb|2IK7|A Chain A, Yeast Inorganic Pyrophosphatase Variant D120n With Magnesium And Phosphate Length = 286

Iteration: 1
 Score = 58.9 bits (141), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 24/34 (70%), Positives = 31/34 (91%)
Query: 385 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+E+
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEI 59

>pdb|1YPP|A Chain A, Acid Anhydride Hydrolase Length = 286

Iteration: 1
 Score =  259 bits (662), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 119/176 (67%), Positives = 143/176 (81%)
Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+EI   E LNPI QD  KG LR+V N FP
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTAKGKLRFVRNCFP 85
Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
           HHGYI NYGA PQTWE+P+ +   T   GD DPIDVLEIGE IA  G++ QVKALG++ L
Sbjct: 86  HHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMAL 145
Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
           +DEG+TDWK+IAI++NDP A KLND+ D+E +FPG L+ATNEWF+IYKIPDGKPEN
Sbjct: 146 LDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPEN 201

>pdb|1YPP|A Chain A, Acid Anhydride Hydrolase Length = 286

Iteration: 1
 Score = 58.9 bits (141), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 24/34 (70%), Positives = 31/34 (91%)
Query: 385 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
           +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+E+
Sbjct: 26  VSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEI 59

>pdb|1PYP|A Chain A, X-Ray Diffraction Study Of Inorganic Pyrophosphatase From Baker,S Yeast At The 3 Angstroms Resolution (Russian) Length = 285

Iteration: 1
 Score =  248 bits (634), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 115/176 (65%), Positives = 143/176 (81%), Gaps = 1/176 (0%)
Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           +S FHDIPLY++ +D IFNMVVEIPRWTNAK+EI   E LNPI Q+ K G LR+V N FP
Sbjct: 26  VSAFHDIPLYADKEDNIFNMVVEIPRWTNAKLEITKEETLNPIIQNTK-GKLRFVRNCFP 84
Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
           HHGYI NYGA PQTWE+P+ +   T   GD +PIDVL+IGE IA  G++ +VKALG++ L
Sbjct: 85  HHGYIHNYGAFPQTWEDPNVSHPETKAVGDNNPIDVLQIGETIAYTGQVKEVKALGIMAL 144
Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPEN 339
           +DEG+TDWK+IAI++NDP A KLND+ D+E +FPG L+AT+EWF+IYKIPDGKPEN
Sbjct: 145 LDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATDEWFRIYKIPDGKPEN 200

>pdb|1PYP|A Chain A, X-Ray Diffraction Study Of Inorganic Pyrophosphatase From Baker,S Yeast At The 3 Angstroms Resolution (Russian) Length = 285

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 25/34 (73%), Positives = 31/34 (91%)
Query: 385 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
           +S FHDIPLY++ +D IFNMVVEIPRWTNAK+E+
Sbjct: 26  VSAFHDIPLYADKEDNIFNMVVEIPRWTNAKLEI 59

>pdb|1UDE|A Chain A, Crystal Structure Of The Inorganic Pyrophosphatase From The Hyperthermophilic Archaeon Pyrococcus Horikoshii Ot3 Length = 195

Iteration: 1
 Score = 70.5 bits (171), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 48/174 (27%), Positives = 83/174 (47%), Gaps = 27/174 (15%)
Query: 163 LISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVF 222
           +++PFHD+    NV + ++ ++ EIP+ +  K E+           D + G L+    ++
Sbjct: 17  MMNPFHDLEPGPNVPEVVYALI-EIPKGSRNKYEL-----------DKETGLLKLDRVLY 64
Query: 223 PHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIG 282
               Y  +YG +P+TW              DGDP D++ I         II+ + +G+  
Sbjct: 65  TPFHYPVDYGIIPRTWYE------------DGDPFDIMVIMREPTYPLTIIEARPIGLFK 112
Query: 283 LIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGK 336
           +ID G  D+K++A+ V DP      D++D+   F   L     +FK YK  +GK
Sbjct: 113 MIDSGDKDYKVLAVPVEDPYFKDWKDISDVPKAF---LDEIAHFFKRYKELEGK 163

>pdb|3I98|A Chain A, X-Ray Crystallographic Structure Of Inorganic Pyrophosphatase At 298k From Archaeon Thermococcus Thioreducens Length = 178

Iteration: 1
 Score = 69.3 bits (168), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 50/184 (27%), Positives = 86/184 (46%), Gaps = 32/184 (17%)
Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           ++PFH++     V + ++ ++ EIP+ +  K E+           D K G L+    ++ 
Sbjct: 1   MNPFHELEPGPEVPEVVYALI-EIPKGSRNKYEL-----------DKKTGLLKLDRVLYS 48
Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
              Y  +YG +PQTW +            DGDP D++ I         II+ + +G++ +
Sbjct: 49  PFFYPVDYGIIPQTWYD------------DGDPFDIMVIMREPVYPLTIIEARPIGIMKM 96
Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENVLNT 343
            D G  DWK++A+ V DP      D++D+   F   L     +F+ YK   GK      T
Sbjct: 97  EDSGDKDWKVLAVPVEDPYFNDWKDISDVPKAF---LDEIAHFFQRYKELQGK-----TT 148
Query: 344 RVEG 347
           ++EG
Sbjct: 149 KIEG 152

>pdb|3Q46|A Chain A, Magnesium Activated Inorganic Pyrophosphatase From Thermococcus Thioreducens Bound To Hydrolyzed Product At 0.99 Angstrom Resolution Length = 178

Iteration: 1
 Score = 67.4 bits (163), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 49/184 (26%), Positives = 85/184 (46%), Gaps = 32/184 (17%)
Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           ++PFH++     V + ++ ++ EIP+ +  K E+           D   G L+    ++ 
Sbjct: 1   MNPFHELEPGPEVPEVVYALI-EIPKGSRNKYEL-----------DKATGLLKLDRVLYS 48
Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
              Y  +YG +PQTW +            DGDP D++ I         II+ + +G++ +
Sbjct: 49  PFFYPVDYGIIPQTWYD------------DGDPFDIMVIMREPVYPLTIIEARPIGIMKM 96
Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENVLNT 343
            D G  DWK++A+ V DP      D++D+   F   L     +F+ YK   GK      T
Sbjct: 97  EDSGDKDWKVLAVPVEDPYFNDWKDISDVPKAF---LDEIAHFFQRYKELQGK-----TT 148
Query: 344 RVEG 347
           ++EG
Sbjct: 149 KIEG 152

>pdb|3R6E|A Chain A, The Structure Of Thermococcus Thioreducens' Inorganic Pyrophosphatase Bound To Sulfate Length = 178

Iteration: 1
 Score = 65.1 bits (157), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 82/183 (44%), Gaps = 32/183 (17%)
Query: 165 SPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPH 224
           +PFH++     V + ++ ++ EIP+ +  K E+           D K G L+    ++  
Sbjct: 2   NPFHELEPGPEVPEVVYALI-EIPKGSRNKYEL-----------DKKTGLLKLDRVLYSP 49
Query: 225 HGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLI 284
             Y  +YG +PQTW +            DGDP D+  I         II+ + +G+    
Sbjct: 50  FFYPVDYGIIPQTWYD------------DGDPFDIXVIXREPVYPLTIIEARPIGIXKXE 97
Query: 285 DEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENVLNTR 344
           D G  DWK++A+ V DP      D++D+   F   L     +F+ YK   GK      T+
Sbjct: 98  DSGDKDWKVLAVPVEDPYFNDWKDISDVPKAF---LDEIAHFFQRYKELQGK-----TTK 149
Query: 345 VEG 347
           +EG
Sbjct: 150 IEG 152

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 65.1 bits (157), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 42/133 (31%), Positives = 74/133 (55%), Gaps = 29/133 (21%)
Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILK 92
           ++FI  L +  TE+  +E+FG+YG + D +++K+ A G+ +G GF+++  K S+V  ++K
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSF-EKPSSVDEVVK 63
Query: 93  S-----------------NKKPYKGKI---------TEEEFKEHFGQYGDIIDAQLLKNA 126
           +                 +++   GKI           +EF+E F Q+G IIDAQL+ + 
Sbjct: 64  TQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDK 123
Query: 127 D-GKLKGCGFINY 138
           D G+ +G GF+ Y
Sbjct: 124 DTGQSRGFGFVTY 136

>pdb|1TWL|A Chain A, Inorganic Pyrophosphatase From Pyrococcus Furiosus Pfu-264096-001 Length = 186

Iteration: 1
 Score = 63.9 bits (154), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 47/172 (27%), Positives = 78/172 (45%), Gaps = 27/172 (15%)
Query: 165 SPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPH 224
           +PFHD+    +V + ++  ++EIP+ +  K E+           D K G L+    ++  
Sbjct: 10  NPFHDLEPGPDVPEVVYA-IIEIPKGSRNKYEL-----------DKKTGLLKLDRVLYSP 57
Query: 225 HGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLI 284
             Y  +YG +P+TW              D DP D++ I         II+ + +G+  +I
Sbjct: 58  FFYPVDYGIIPRTWYE------------DDDPFDIMVIMREPVYPLTIIEARPIGLFKMI 105
Query: 285 DEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGK 336
           D G  D+K++A+ V DP      D+ D+   F   L     +FK YK   GK
Sbjct: 106 DSGDKDYKVLAVPVEDPYFKDWKDIDDVPKAF---LDEIAHFFKRYKELQGK 154

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 62.0 bits (149), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 51/156 (32%), Positives = 77/156 (49%), Gaps = 30/156 (19%)
Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAI--- 90
           L +  LP  +T++EFK  FG  GDI   +L+++   G+  G GF+NY++   A KAI   
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 91  --LK--------SNKKPYKGKI--------------TEEEFKEHFGQYGDIIDAQ-LLKN 125
             LK        S  +P    I              +++E ++ F QYG II ++ LL  
Sbjct: 67  NGLKLQTKTIKVSYARPSSASIRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQ 126
Query: 126 ADGKLKGCGFINYANKISAVKAILKSN-KKPYKGSE 160
           A G  +G GFI +  +I A +AI   N +KP   +E
Sbjct: 127 ATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAE 162

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 58.9 bits (141), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 47/156 (30%), Positives = 73/156 (46%), Gaps = 30/156 (19%)
Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKS 93
           L +  LP  +T+EEF+  FG  G+I   +L+++   G+  G GF+NY +   A KAI   
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 94  N-------------KKPYKGKI--------------TEEEFKEHFGQYGDIIDAQLL-KN 125
           N              +P    I              T++E ++ F QYG II +++L   
Sbjct: 65  NGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ 124
Query: 126 ADGKLKGCGFINYANKISAVKAILKSN-KKPYKGSE 160
             G  +G GFI +  +I A +AI   N +KP   +E
Sbjct: 125 VTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATE 160

>pdb|3D63|A Chain A, Crystal Structure Of Inorganic Pyrophosphatase From Burkholderia Pseudomallei Length = 196

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 47/156 (30%), Positives = 71/156 (45%), Gaps = 33/156 (21%)
Query: 181 FNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHG--YIWNYGALPQTW 238
           FN+++EIP  +             P+K +  K     V + F   G  Y  NYG +PQT 
Sbjct: 37  FNVIIEIPAQSE------------PVKYEADKALGLLVVDRFIGTGMRYPVNYGFIPQTL 84
Query: 239 ENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINV 298
                        GDGDP+DVL I       G +++ +ALG++ + DE   D K++A+  
Sbjct: 85  S------------GDGDPVDVLVITPFPLLAGSVVRARALGMLKMTDESGVDAKLVAVPH 132
Query: 299 ND--PNAAKLNDVADIETHFPGYLK-ATNEWFKIYK 331
           +   P  A L  + D+    P YLK     +F+ YK
Sbjct: 133 DKVCPMTANLKSIDDV----PAYLKDQIKHFFEQYK 164

>pdb|1QEZ|A Chain A, Sulfolobus Acidocaldarius Inorganic Pyrophosphatase: An Archael Pyrophosphatase. Length = 173

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 41/135 (30%), Positives = 69/135 (51%), Gaps = 25/135 (18%)
Query: 180 IFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWE 239
           + N++VEIP+ +N K E +  E +      IK   + Y +  +P     +NYG +P T E
Sbjct: 12  VVNVLVEIPQGSNIKYEYDDEEGV------IKVDRVLYTSMNYP-----FNYGFIPGTLE 60
Query: 240 NPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAI--N 297
                        DGDP+DVL I       G +I+V+ +G++ + DE   D KI+A+  +
Sbjct: 61  E------------DGDPLDVLVITNYQLYPGSVIEVRPIGILYMKDEEGEDAKIVAVPKD 108
Query: 298 VNDPNAAKLNDVADI 312
             DP+ + + D+ D+
Sbjct: 109 KTDPSFSNIKDINDL 123

>pdb|3LO0|A Chain A, Crystal Structure Of Inorganic Pyrophosphatase From Ehrlichia Chaffeensis Length = 193

Iteration: 1
 Score = 55.5 bits (132), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 42/147 (28%), Positives = 67/147 (45%), Gaps = 17/147 (11%)
Query: 187 IPRWTNAKMEINLNEPLNPIKQDI-KKGNLRYVANVFPHHGYI-WNYGALPQTWENPDET 244
           +P+  N  +EI+ N    P+K +  K+ NL  V    P   Y   NYG +P T       
Sbjct: 33  VPKEINVIIEISQNS--CPVKYEFDKEKNLFCVDRFLPTSMYYPCNYGFIPHTC------ 84
Query: 245 DAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAA 304
                  GDGDP+DVL         G +I+ + +GV+ + DE   D KI+A+  +  +  
Sbjct: 85  ------AGDGDPVDVLVASRFPVMSGAVIRARPVGVLVMHDESGEDVKILAVPTHKVDQY 138
Query: 305 KLNDVADIETHFPGYLKATNEWFKIYK 331
             N++ D       +L + + +F  YK
Sbjct: 139 -YNNIKDYSDFPVSFLNSISHFFTFYK 164

>pdb|2BQX|A Chain A, Inorganic Pyrophosphatase From The Pathogenic Bacterium Helicobacter Pylori-Kinetic And Structural Properties Length = 173

Iteration: 1
 Score = 55.1 bits (131), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 39/151 (25%), Positives = 69/151 (45%), Gaps = 28/151 (18%)
Query: 183 MVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPD 242
           +V+EI + +N K E+           D + G L     ++    Y  NYG +P T     
Sbjct: 17  VVIEISKHSNIKYEL-----------DKESGALMVDRVLYGAQNYPANYGFVPNTL---- 61
Query: 243 ETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVN--D 300
                     DGDP+D L + +   + G +++ + +GV+ + DE   D K+IA+ ++  D
Sbjct: 62  --------GSDGDPVDALVLSDVAFQAGSVVKARLVGVLNMEDESGMDEKLIALPIDKID 113
Query: 301 PNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
           P  + + D+ D+  H    L     +F+ YK
Sbjct: 114 PTHSYVKDIDDLSKH---TLDKIKHFFETYK 141

>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein Cugbp1ab And Its Binding Study With Dna And Rna Length = 187

Iteration: 1
 Score = 55.1 bits (131), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 35/171 (20%), Positives = 75/171 (43%), Gaps = 35/171 (20%)
Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADG---KLKGCGFINYANKISAVKA- 89
           ++F+  +P   +E++ +E F QYG + +  +L++      + KGC F+ +  + +A++A 
Sbjct: 17  KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 90  -------ILKSNKKPYK-----------------------GKITEEEFKEHFGQYGDIID 119
                  +L     P +                        K TE + +  F  +G I +
Sbjct: 77  NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEE 136
Query: 120 AQLLKNADGKLKGCGFINYANKISAVKAILKSNK-KPYKGSENGLISPFHD 169
            ++L+  DG  +GC F+ +  +  A  AI   ++ +  +G  + ++  F D
Sbjct: 137 CRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD 187

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 54.7 bits (130), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 35/171 (20%), Positives = 75/171 (43%), Gaps = 35/171 (20%)
Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADG---KLKGCGFINYANKISAVKA- 89
           ++F+  +P   +E++ +E F QYG + +  +L++      + KGC F+ +  + +A++A 
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 90  -------ILKSNKKPYK-----------------------GKITEEEFKEHFGQYGDIID 119
                  +L     P +                        K TE + +  F  +G I +
Sbjct: 65  NALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEE 124
Query: 120 AQLLKNADGKLKGCGFINYANKISAVKAILKSNK-KPYKGSENGLISPFHD 169
            ++L+  DG  +GC F+ +  +  A  AI   ++ +  +G  + ++  F D
Sbjct: 125 CRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVKFAD 175

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 43/140 (30%), Positives = 69/140 (49%), Gaps = 30/140 (21%)
Query: 32  RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA-- 89
           R RLF+ NLP  ITEE+FK  F +YG+   +++  N D   +G GFI   ++  A  A  
Sbjct: 22  RCRLFVGNLPTDITEEDFKRLFERYGE--PSEVFINRD---RGFGFIRLESRTLAEIAKA 76
Query: 90  -----ILKSNKKPYKGK----------------ITEEEFKEHFGQYGDIIDAQLLKNADG 128
                ILKS  +P + +                ++ E  ++ F Q+G +  A ++ +  G
Sbjct: 77  ELDGTILKS--RPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRG 134
Query: 129 KLKGCGFINYANKISAVKAI 148
           +  G GF+ +A K  A KA+
Sbjct: 135 RATGKGFVEFAAKPPARKAL 154

>pdb|1YGZ|A Chain A, Crystal Structure Of Inorganic Pyrophosphatase From Helicobacter Pylori Length = 173

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 39/151 (25%), Positives = 68/151 (45%), Gaps = 28/151 (18%)
Query: 183 MVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPD 242
           +V+EI + +N K E+           D + G L     ++    Y  NYG +P T     
Sbjct: 17  VVIEISKHSNIKYEL-----------DKESGALXVDRVLYGAQNYPANYGFVPNTL---- 61
Query: 243 ETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVN--D 300
                     DGDP+D L + +   + G +++ + +GV+   DE   D K+IA+ ++  D
Sbjct: 62  --------GSDGDPVDALVLSDVAFQAGSVVKARLVGVLNXEDESGXDEKLIALPIDKID 113
Query: 301 PNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
           P  + + D+ D+  H    L     +F+ YK
Sbjct: 114 PTHSYVKDIDDLSKH---TLDKIKHFFETYK 141

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 52.0 bits (123), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 35/171 (20%), Positives = 73/171 (42%), Gaps = 35/171 (20%)
Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADG---KLKGCGFINYANKISAVKA- 89
           + F+  +P   +E++ +E F QYG + +  +L++      + KGC F+ +  + +A++A 
Sbjct: 5   KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 90  -------ILKSNKKPYKGK-----------------------ITEEEFKEHFGQYGDIID 119
                  +L     P + K                        TE + +  F  +G I +
Sbjct: 65  NALHNXKVLPGXHHPIQXKPADSEKNNAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEE 124
Query: 120 AQLLKNADGKLKGCGFINYANKISAVKAILKSNK-KPYKGSENGLISPFHD 169
            ++L+  DG  +GC F+ +  +  A  AI   ++ +  +G  +  +  F D
Sbjct: 125 CRILRGPDGLSRGCAFVTFTTRAXAQTAIKAXHQAQTXEGCSSPXVVKFAD 175

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 52.0 bits (123), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 38/138 (27%), Positives = 64/138 (46%), Gaps = 26/138 (18%)
Query: 32  RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL 91
           R RLF+ NLP  ITEEE ++ F +YG   +  + K+     KG GFI    +  A  A +
Sbjct: 22  RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKV 76
Query: 92  KSNKKPYKGK---------------------ITEEEFKEHFGQYGDIIDAQLLKNADGKL 130
           + +  P +GK                     ++ E  +E F  +G +  A ++ +  G+ 
Sbjct: 77  ELDNMPLRGKQLRVRFACHSASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRP 136
Query: 131 KGCGFINYANKISAVKAI 148
            G G + ++ K +A KA+
Sbjct: 137 SGKGIVEFSGKPAARKAL 154

>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi) G); A Human Telomeric Repeat Containing 6-Methyl-8-(2- Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi) Length = 195

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 39/154 (25%), Positives = 71/154 (46%), Gaps = 40/154 (25%)
Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILK 92
           +LFI  L F+ T+E  + HF Q+G + D  ++++ + K  +G GF+ YA  +  V A + 
Sbjct: 14  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT-VEEVDAAM- 71
Query: 93  SNKKPYK--GKITE----------------------------EEFKEH-----FGQYGDI 117
            N +P+K  G++ E                            E+ +EH     F QYG I
Sbjct: 72  -NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 130
Query: 118 IDAQLLKN-ADGKLKGCGFINYANKISAVKAILK 150
              +++ +   GK +G  F+ + +  S  K +++
Sbjct: 131 EVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 164

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 39/154 (25%), Positives = 71/154 (46%), Gaps = 40/154 (25%)
Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILK 92
           +LFI  L F+ T+E  + HF Q+G + D  ++++ + K  +G GF+ YA  +  V A + 
Sbjct: 15  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT-VEEVDAAM- 72
Query: 93  SNKKPYK--GKITE----------------------------EEFKEH-----FGQYGDI 117
            N +P+K  G++ E                            E+ +EH     F QYG I
Sbjct: 73  -NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 131
Query: 118 IDAQLLKN-ADGKLKGCGFINYANKISAVKAILK 150
              +++ +   GK +G  F+ + +  S  K +++
Sbjct: 132 EVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165

>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous Cell Carcinoma Antigen Recognized By T Cells 3 Length = 100

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 25/73 (34%), Positives = 41/73 (56%)
Query: 32  RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL 91
           + +LFI  LPF  T+EE +E    +G + D +L+ N  GK KG  ++ Y N+  A +A++
Sbjct: 17  KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVM 76
Query: 92  KSNKKPYKGKITE 104
           K +    K  I +
Sbjct: 77  KMDGMTIKENIIK 89

>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1 (up1) Using Segmental Isotope Labeling Length = 197

Iteration: 1
 Score = 50.1 bits (118), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 39/154 (25%), Positives = 71/154 (46%), Gaps = 40/154 (25%)
Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILK 92
           +LFI  L F+ T+E  + HF Q+G + D  ++++ + K  +G GF+ YA  +  V A + 
Sbjct: 16  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT-VEEVDAAM- 73
Query: 93  SNKKPYK--GKITE----------------------------EEFKEH-----FGQYGDI 117
            N +P+K  G++ E                            E+ +EH     F QYG I
Sbjct: 74  -NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 132
Query: 118 IDAQLLKN-ADGKLKGCGFINYANKISAVKAILK 150
              +++ +   GK +G  F+ + +  S  K +++
Sbjct: 133 EVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 166

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 39/154 (25%), Positives = 71/154 (46%), Gaps = 40/154 (25%)
Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILK 92
           +LFI  L F+ T+E  + HF Q+G + D  ++++ + K  +G GF+ YA  +  V A + 
Sbjct: 15  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT-VEEVDAAM- 72
Query: 93  SNKKPYK--GKITE----------------------------EEFKEH-----FGQYGDI 117
            N +P+K  G++ E                            E+ +EH     F QYG I
Sbjct: 73  -NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 131
Query: 118 IDAQLLKN-ADGKLKGCGFINYANKISAVKAILK 150
              +++ +   GK +G  F+ + +  S  K +++
Sbjct: 132 EVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 165

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 39/154 (25%), Positives = 71/154 (46%), Gaps = 40/154 (25%)
Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILK 92
           +LFI  L F+ T+E  + HF Q+G + D  ++++ + K  +G GF+ YA  +  V A + 
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT-VEEVDAAM- 65
Query: 93  SNKKPYK--GKITE----------------------------EEFKEH-----FGQYGDI 117
            N +P+K  G++ E                            E+ +EH     F QYG I
Sbjct: 66  -NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 124
Query: 118 IDAQLLKN-ADGKLKGCGFINYANKISAVKAILK 150
              +++ +   GK +G  F+ + +  S  K +++
Sbjct: 125 EVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 158

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 39/154 (25%), Positives = 71/154 (46%), Gaps = 40/154 (25%)
Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILK 92
           +LFI  L F+ T+E  + HF Q+G + D  ++++ + K  +G GF+ YA  +  V A + 
Sbjct: 13  KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYAT-VEEVDAAM- 70
Query: 93  SNKKPYK--GKITE----------------------------EEFKEH-----FGQYGDI 117
            N +P+K  G++ E                            E+ +EH     F QYG I
Sbjct: 71  -NARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKI 129
Query: 118 IDAQLLKN-ADGKLKGCGFINYANKISAVKAILK 150
              +++ +   GK +G  F+ + +  S  K +++
Sbjct: 130 EVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 163

>pdb|3D53|A Chain A, 2.2 A Crystal Structure Of Inorganic Pyrophosphatase From Rickettsia Prowazekii Length = 173

Iteration: 1
 Score = 48.5 bits (114), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 35/107 (32%), Positives = 50/107 (46%), Gaps = 16/107 (14%)
Query: 192 NAKMEINLNEPLNPIKQDIKKGNLRYVANVFPH--HGYIWNYGALPQTWENPDETDAHTG 249
           N  +EI +N    PIK +  K +     + F      Y  NYG +P T  N         
Sbjct: 17  NVIIEIPMNS--GPIKYEFDKESGALFVDRFMQTTMSYPCNYGFIPDTLSN--------- 65
Query: 250 QKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAI 296
              DGDP+DVL +       G +I+ +A+GV+ + DE   D KIIA+
Sbjct: 66  ---DGDPVDVLVVAHHPVVPGSVIKCRAIGVLMMEDESGLDEKIIAV 109

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 48.1 bits (113), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           RL + N+PF+  + + ++ FGQ+G I+D +++ N  G  KG GF+ + N   A +A  K 
Sbjct: 17  RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS-KGFGFVTFENSADADRAREKL 75
Query: 94  NKKPYKGKITE 104
           +    +G+  E
Sbjct: 76  HGTVVEGRKIE 86

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 47.8 bits (112), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 23/71 (32%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           RL + N+PF+  + + ++ FGQ+G I+D +++ N  G  KG GF+ + N   A +A  K 
Sbjct: 31  RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS-KGFGFVTFENSADADRAREKL 89
Query: 94  NKKPYKGKITE 104
           +    +G+  E
Sbjct: 90  HGTVVEGRKIE 100

>pdb|3LD3|A Chain A, Crystal Structure Of Inorganic Phosphatase From Anaplasma Phagocytophilum At 1.75a Resolution Length = 199

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 41/154 (26%), Positives = 71/154 (46%), Gaps = 23/154 (14%)
Query: 186 EIPRWTNAKMEINL----NEPLNPIKQDI-KKGNLRYVANVFPHHGYI-WNYGALPQTWE 239
           +I   +NA  E+N+    ++  +P+K +  +K    +V    P   Y   NYG +P T  
Sbjct: 26  DIGSGSNAPEEVNVVIEVSQDSHPVKYEFDEKNGALWVDRFLPTAMYYPCNYGFIPNTI- 84
Query: 240 NPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVN 299
                       GDGDP+DVL +       G +I V+ +GV+ + DE   D K++A+   
Sbjct: 85  -----------AGDGDPVDVLVLARFPVMPGAVICVRPVGVLMMNDEKGEDAKVLAVPAT 133
Query: 300 --DPNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
             D     + + +D+ + F   L + + +F  YK
Sbjct: 134 KVDQYYGNIVNYSDLPSSF---LDSISHFFSFYK 164

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 40/159 (25%), Positives = 70/159 (44%), Gaps = 30/159 (18%)
Query: 32  RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 90
           R  L +  LP  +T++E +  F   G++  A+L+++   G   G GF+NY     A +AI
Sbjct: 2   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 91  -----LKSNKKPYK----------------------GKITEEEFKEHFGQYGDIIDAQ-L 122
                L+   K  K                        +T+++ ++ F ++G II+++ L
Sbjct: 62  NTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVL 121
Query: 123 LKNADGKLKGCGFINYANKISAVKAILKSN-KKPYKGSE 160
           +    G  +G  FI +  +  A +AI   N  KP   SE
Sbjct: 122 VDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSE 160

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 40/159 (25%), Positives = 70/159 (44%), Gaps = 30/159 (18%)
Query: 32  RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 90
           R  L +  LP  +T++E +  F   G++  A+L+++   G   G GF+NY     A +AI
Sbjct: 2   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
Query: 91  -----LKSNKKPYK----------------------GKITEEEFKEHFGQYGDIIDAQ-L 122
                L+   K  K                        +T+++ ++ F ++G II+++ L
Sbjct: 62  NTLNGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVL 121
Query: 123 LKNADGKLKGCGFINYANKISAVKAILKSN-KKPYKGSE 160
           +    G  +G  FI +  +  A +AI   N  KP   SE
Sbjct: 122 VDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSE 160

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 46.6 bits (109), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 21/68 (30%), Positives = 43/68 (63%), Gaps = 1/68 (1%)
Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKS 93
           +F+ N+P++ TEE+ K+ F + G ++  +L+ + + GK KG GF  Y ++ +A+ A+   
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 94  NKKPYKGK 101
           N + + G+
Sbjct: 71  NGREFSGR 78

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 45.4 bits (106), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 24/58 (41%), Positives = 39/58 (67%), Gaps = 1/58 (1%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAIL 91
          +F+ +L  +IT E+ K  F  +G I DA+++K+ A GK KG GF+++ NK+ A  AI+
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 75

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 22/50 (44%), Positives = 34/50 (68%), Gaps = 1/50 (2%)
Query: 101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAIL 149
           +IT E+ K  F  +G I DA+++K+ A GK KG GF+++ NK+ A  AI+
Sbjct: 26  EITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIV 75

>pdb|2UXS|A Chain A, 2.7a Crystal Structure Of Inorganic Pyrophosphatase (rv3628) From Mycobacterium Tuberculosis At Ph 7.5 Length = 169

Iteration: 1
 Score = 45.4 bits (106), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 35/152 (23%), Positives = 65/152 (42%), Gaps = 28/152 (18%)
Query: 181 FNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWEN 240
           F++ +EIP+    K E+           D + G +R    ++    Y  +YG +  T  +
Sbjct: 10  FDVTIEIPKGQRNKYEV-----------DHETGRVRLDRYLYTPMAYPTDYGFIEDTLGD 58
Query: 241 PDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVND 300
                       DGDP+D L +  +    G ++  + +G+  ++DE   D K++ +   D
Sbjct: 59  ------------DGDPLDALVLLPQPVFPGVLVAARPVGMFRMVDEHGGDDKVLCVPAGD 106
Query: 301 PNAAKLNDVADIETHFPGY-LKATNEWFKIYK 331
           P    + D+ D+    P + L A   +F  YK
Sbjct: 107 PRWDHVQDIGDV----PAFELDAIKHFFVHYK 134

>pdb|1SXV|A Chain A, 1.3a Crystal Structure Of Rv3628, Mycobacterium Tuberculosis Inorganic Pyrophosphatase (Ppase) At Ph5.0 Length = 172

Iteration: 1
 Score = 45.4 bits (106), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 35/152 (23%), Positives = 65/152 (42%), Gaps = 28/152 (18%)
Query: 181 FNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWEN 240
           F++ +EIP+    K E+           D + G +R    ++    Y  +YG +  T  +
Sbjct: 13  FDVTIEIPKGQRNKYEV-----------DHETGRVRLDRYLYTPMAYPTDYGFIEDTLGD 61
Query: 241 PDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVND 300
                       DGDP+D L +  +    G ++  + +G+  ++DE   D K++ +   D
Sbjct: 62  ------------DGDPLDALVLLPQPVFPGVLVAARPVGMFRMVDEHGGDDKVLCVPAGD 109
Query: 301 PNAAKLNDVADIETHFPGY-LKATNEWFKIYK 331
           P    + D+ D+    P + L A   +F  YK
Sbjct: 110 PRWDHVQDIGDV----PAFELDAIKHFFVHYK 137

>pdb|1WCF|A Chain A, 1.54 A Crystal Structure Of Rv3628, Mycobacterium Tuberculosis Inorganic Pyrophosphatase (Ppase) At Ph7.0 Length = 171

Iteration: 1
 Score = 45.4 bits (106), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 35/152 (23%), Positives = 65/152 (42%), Gaps = 28/152 (18%)
Query: 181 FNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWEN 240
           F++ +EIP+    K E+           D + G +R    ++    Y  +YG +  T  +
Sbjct: 12  FDVTIEIPKGQRNKYEV-----------DHETGRVRLDRYLYTPMAYPTDYGFIEDTLGD 60
Query: 241 PDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVND 300
                       DGDP+D L +  +    G ++  + +G+  ++DE   D K++ +   D
Sbjct: 61  ------------DGDPLDALVLLPQPVFPGVLVAARPVGMFRMVDEHGGDDKVLCVPAGD 108
Query: 301 PNAAKLNDVADIETHFPGY-LKATNEWFKIYK 331
           P    + D+ D+    P + L A   +F  YK
Sbjct: 109 PRWDHVQDIGDV----PAFELDAIKHFFVHYK 136

>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein M Length = 114

Iteration: 1
 Score = 45.1 bits (105), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 20/56 (35%), Positives = 35/56 (62%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
          +F+ NL +K+  ++ KE F   G ++ A +L++ DGK +G G + +   I AV+AI
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAI 73

>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif Of Nono Length = 99

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/79 (35%), Positives = 40/79 (50%), Gaps = 5/79 (6%)
Query: 32  RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL 91
           R RLF+ NLP  ITEEE ++ F +YG   +  + K+     KG GFI    +  A  A +
Sbjct: 15  RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKV 69
Query: 92  KSNKKPYKGKITEEEFKEH 110
           + +  P +GK     F  H
Sbjct: 70  ELDNMPLRGKQLRVRFACH 88

>pdb|4ECP|A Chain A, X-Ray Crystal Structure Of Inorganic Pyrophosphate Ppa From Mycobacterium Leprae Length = 167

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 36/151 (23%), Positives = 64/151 (42%), Gaps = 26/151 (17%)
Query: 181 FNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWEN 240
           F++ +EIP+    K E+           D K G +R    ++    Y  +YG +  T   
Sbjct: 8   FDVTIEIPKGQRNKYEV-----------DHKTGRVRLDRYLYTPMAYPTDYGFIEDTLGE 56
Query: 241 PDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVND 300
                       DGDP+D L +       G +++ + +G+  ++DE   D K++ + VND
Sbjct: 57  ------------DGDPLDALVLLPEPLFPGVLVEARPVGMFRMVDEHGGDDKVLCVPVND 104
Query: 301 PNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
                ++ + D+ T     L A   +F  YK
Sbjct: 105 HRWDHIHGIIDVPTF---ELDAIKHFFVHYK 132

>pdb|3SW5|A Chain A, Crystal Structure Of Inorganic Pyrophosphatase From Bartonella Henselae Length = 180

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 42/146 (28%), Positives = 63/146 (43%), Gaps = 17/146 (11%)
Query: 188 PRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIW--NYGALPQTWENPDETD 245
           P   N  +E++L     PIK ++ K +     + F +   ++  NYG +P T        
Sbjct: 17  PEDVNVIVEVSLGG--QPIKYEMDKKSGALFVDRFLYTSMVYPGNYGFVPHTLSE----- 69
Query: 246 AHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAK 305
                  DGDPIDVL    R    G +I V  +G + + D+G  D KIIAI        +
Sbjct: 70  -------DGDPIDVLICNTRPLLPGCVINVYPIGALIMEDDGGKDEKIIAIPTPK-LTQR 121
Query: 306 LNDVADIETHFPGYLKATNEWFKIYK 331
            N++ D        LK    +F+ YK
Sbjct: 122 YNNIHDYTDLPEITLKQIEHFFEHYK 147

>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 = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 42/82 (51%), Gaps = 8/82 (9%)
Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKS 93
           L++ NLP  IT+++    FG+YG I+   +L++   G+ +G  F+ Y  +  A +AI   
Sbjct: 16  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 94  N-------KKPYKGKITEEEFK 108
           N        +P   ++ EE  K
Sbjct: 76  NNVIPEGGSQPLSVRLAEEHGK 97

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/65 (38%), Positives = 40/65 (61%), Gaps = 2/65 (3%)
Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQ-LLKNADGKLKGCGFINYANKISAVKAILKS 93
          L++  LP  ++++E ++ F QYG II ++ LL  A G  +G GFI +  +I A +AI   
Sbjct: 4  LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 94 N-KKP 97
          N +KP
Sbjct: 64 NGQKP 68

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 43.5 bits (101), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 42/82 (51%), Gaps = 8/82 (9%)
Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKS 93
           L++ NLP  IT+++    FG+YG I+   +L++   G+ +G  F+ Y  +  A +AI   
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 162
Query: 94  N-------KKPYKGKITEEEFK 108
           N        +P   ++ EE  K
Sbjct: 163 NNVIPEGGSQPLSVRLAEEHGK 184

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/57 (33%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAI 90
           L++ NLP  IT+++    FG+YG I+   +L++   G+ +G  F+ Y  +  A +AI
Sbjct: 92  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 42.4 bits (98), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 23/60 (38%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAI 90
          +  L +  LP  +T++EFK  FG  GDI   +L+++   G+  G GF+NY++   A KAI
Sbjct: 4  KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 32  RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADG-KLKGCGFINYANKISAVKAI 90
           +  +++ NLPF +T  +    F +YG ++   ++K+ D  K KG  FI + +K SA    
Sbjct: 16  KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCT 75
Query: 91  LKSNKKPYKGKITE 104
              N K   G++ +
Sbjct: 76  RAINNKQLFGRVIK 89

>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 4 Rna-Binding Protein Length = 106

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 1/57 (1%)
Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKA 89
          +LFI  +P  + E++ K  F ++G I +  +LK+   G  KGC F+ Y  + SA+KA
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	451
1e9g_A	286	Ppase, inorganic pyrophosphatase; pyrophosphate ph	1e-85
1e9g_A	286	Ppase, inorganic pyrophosphatase; pyrophosphate ph	1e-12
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	5e-30
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	6e-22
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	4e-29
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-14
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-28
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-28
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-15
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-04
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-25
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-16
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-05
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	7e-25
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-15
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-07
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	8e-25
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-23
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-12
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-24
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	4e-15
3q46_A	178	TT-ippase; inorganic pyrophosphatase, hydrolase; H	2e-24
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	6e-24
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-13
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	7e-24
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	4e-14
2prd_A	174	Pyrophosphate phosphohydrolase; 2.00A {Thermus the	7e-23
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-22
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	7e-12
3gvf_A	196	Inorganic pyrophosphatase; structural genomics, hy	3e-21
3ld3_A	199	Inorganic pyrophosphatase; structural genomics, se	3e-21
1sxv_A	172	Inorganic pyrophosphatase; structural genomics, pp	8e-21
2au7_A	175	Inorganic pyrophosphatase; hydrolase, mutant; 1.05	2e-20
3fq3_A	197	Inorganic pyrophosphatase:bacterial/archaeal INOR	3e-20
2bqx_A	173	Inorganic pyrophosphatase; hydrolase; 1.90A {Helic	3e-20
1qez_A	173	Ppase, S-ppase, protein (inorganic pyrophosphatase	1e-19
3d53_A	173	Inorganic pyrophosphatase; seattle structural G ce	2e-19
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-19
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-14
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-19
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	1e-12
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-18
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-11
1x5o_A	114	RNA binding motif, single-stranded interacting pro	4e-18
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-09
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	6e-18
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	7e-13
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	8e-04
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-18
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-11
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-05
3tr4_A	178	Inorganic pyrophosphatase; central intermediary me	1e-17
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-17
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-09
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	5e-17
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-08
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	5e-17
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	3e-10
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	8e-17
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	7e-13
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	9e-17
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-10
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-16
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	6e-09
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-16
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-10
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-16
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	7e-10
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	4e-16
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-09
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-16
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-11
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	6e-16
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	8e-10
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	6e-16
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	6e-09
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	7e-16
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	5e-10
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	7e-16
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	3e-08
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-15
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	6e-09
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-15
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-07
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	2e-15
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	3e-09
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-15
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-08
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-15
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-08
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	4e-15
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-09
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	5e-15
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	4e-08
1x4e_A	85	RNA binding motif, single-stranded interacting pro	5e-15
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-08
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	5e-15
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	6e-15
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	6e-09
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	6e-15
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	8e-08
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	6e-15
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	4e-10
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	7e-15
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-09
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-14
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	7e-09
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	1e-14
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	3e-10
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-14
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	2e-06
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-14
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	6e-09
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-14
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	4e-08
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-14
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-10
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	3e-14
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	9e-08
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	4e-14
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-07
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	9e-14
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-07
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	9e-14
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	2e-07
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-13
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-08
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-13
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	1e-08
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-13
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-07
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-13
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	3e-07
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-13
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	1e-06
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-13
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	7e-06
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	4e-13
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	9e-08
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	4e-13
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	9e-08
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-13
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-06
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	5e-13
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-07
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	5e-13
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-06
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	5e-13
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	2e-07
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	7e-13
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	8e-07
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	7e-13
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-07
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	7e-13
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-07
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	8e-13
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-07
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	8e-13
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	5e-07
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	8e-13
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	8e-07
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	9e-13
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	8e-08
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-12
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	6e-06
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-12
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-07
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-12
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	5e-08
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-12
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	5e-08
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	2e-12
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	9e-08
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-12
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	9e-08
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-12
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	5e-08
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-12
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-08
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-12
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-07
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-12
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-08
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-12
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-07
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	3e-12
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-10
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	3e-12
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	1e-06
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	3e-12
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	5e-08
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	3e-12
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	6e-07
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	3e-12
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-06
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-12
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-07
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	4e-12
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	3e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	4e-12
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-06
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	4e-12
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-06
2dis_A	109	Unnamed protein product; structural genomics, RRM	4e-12
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-06
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	5e-12
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	2e-06
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	5e-12
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-07
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	5e-12
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-05
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	5e-12
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-05
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	6e-12
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	4e-06
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-12
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-07
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	6e-12
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-07
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	7e-12
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-06
1x5p_A	97	Negative elongation factor E; structure genomics,	7e-12
1x5p_A	97	Negative elongation factor E; structure genomics,	6e-10
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-12
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	7e-12
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-06
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	8e-12
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-05
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	8e-12
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-06
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	9e-12
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-06
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	1e-11
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	5e-07
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	1e-11
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	4e-05
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	1e-11
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	8e-07
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-11
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	8e-07
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	2e-11
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	4e-06
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-11
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-07
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-11
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	5e-07
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-11
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-06
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	3e-11
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-05
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-11
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	4e-06
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	4e-11
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	3e-05
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	4e-11
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-06
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	5e-11
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	9e-06
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	5e-11
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	2e-04
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	5e-11
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	6e-06
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	6e-11
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	5e-07
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	7e-11
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	4e-06
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	8e-11
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	6e-07
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	8e-11
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	6e-05
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	1e-10
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	3e-06
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-10
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-07
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-10
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	4e-05
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-10
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	4e-05
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-10
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	4e-06
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-10
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-05
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-10
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-06
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	2e-10
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	1e-06
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-10
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-07
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-06
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-10
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-05
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	4e-10
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	1e-05
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	4e-10
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-05
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	6e-10
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	9e-05
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	6e-10
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	3e-04
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-09
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-04
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-09
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-05
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-09
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-09
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	8e-05
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	6e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	7e-06
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-09
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	5e-04
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-09
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-05
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-09
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	6e-09
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-05
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-05
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	4e-09
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	5e-09
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-06
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	9e-09
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	9e-09
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	1e-04
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-08
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	1e-08
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	7e-04
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	1e-08
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	2e-07
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-08
2div_A	99	TRNA selenocysteine associated protein; structural	2e-08
2div_A	99	TRNA selenocysteine associated protein; structural	1e-04
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	3e-08
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	4e-08
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	5e-08
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	5e-08
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	7e-05
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-07
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	5e-07
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-07
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	8e-07
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-04
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	1e-06
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-06
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	5e-05
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-06
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	5e-06
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	4e-05
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	2e-04
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-04
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	4e-04

>1e9g_A Ppase, inorganic pyrophosphatase; pyrophosphate phosphohydrolase, hydrolase, manganese; HET: PO4; 1.15A {Saccharomyces cerevisiae} SCOP: b.40.5.1 PDB: 1e6a_A* 1wgi_A 1wgj_A 2ihp_A* 8prk_A 2ik6_A 2ik2_A 2ik4_A 117e_A 2ik1_A* 2ik9_A 2ik0_A 2ik7_A 1m38_A 1ypp_A 1huk_A 1huj_A 1pyp_A Length = 286

 Score =  262 bits (672), Expect = 1e-85
 Identities = 121/185 (65%), Positives = 146/185 (78%)

Query: 156 YKGSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNL 215
           Y   +   +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+EI   E LNPI QD KKG L
Sbjct: 18  YIEKDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKL 77

Query: 216 RYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQV 275
           R+V N FPHHGYI NYGA PQTWE+P+ +   T   GD DPIDVLEIGE IA  G++ QV
Sbjct: 78  RFVRNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQV 137

Query: 276 KALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDG 335
           KALG++ L+DEG+TDWK+IAI++NDP A KLND+ D+E +FPG L+ATNEWF+IYKIPDG
Sbjct: 138 KALGIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDG 197

Query: 336 KPENV 340
           KPEN 
Sbjct: 198 KPENQ 202

>1e9g_A Ppase, inorganic pyrophosphatase; pyrophosphate phosphohydrolase, hydrolase, manganese; HET: PO4; 1.15A {Saccharomyces cerevisiae} SCOP: b.40.5.1 PDB: 1e6a_A* 1wgi_A 1wgj_A 2ihp_A* 8prk_A 2ik6_A 2ik2_A 2ik4_A 117e_A 2ik1_A* 2ik9_A 2ik0_A 2ik7_A 1m38_A 1ypp_A 1huk_A 1huj_A 1pyp_A Length = 286

 Score = 67.2 bits (164), Expect = 1e-12
 Identities = 24/39 (61%), Positives = 32/39 (82%)

Query: 380 SENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
            +   +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+E+
Sbjct: 21  KDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEI 59

>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 =  113 bits (286), Expect = 5e-30
 Identities = 29/157 (18%), Positives = 64/157 (40%), Gaps = 34/157 (21%)

Query: 32  RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL---KGCGFINYANKISAVK 88
             ++F+  +P   +E++ +E F QYG + +  +L++        KGC F+ +  + +A++
Sbjct: 3   AIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALE 62

Query: 89  AILKSN---------------------KKPYKGK----------ITEEEFKEHFGQYGDI 117
           A    +                         + +           TE + +  F  +G I
Sbjct: 63  AQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQI 122

Query: 118 IDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
            + ++L+  DG  +GC F+ +  +  A  AI   ++ 
Sbjct: 123 EECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQA 159

>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 = 91.5 bits (228), Expect = 6e-22
 Identities = 22/96 (22%), Positives = 42/96 (43%)

Query: 1   MEKLAKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDII 60
              L   K +         K  + +K +  +  +LFI  +  K TE + +  F  +G I 
Sbjct: 64  QNALHNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIE 123

Query: 61  DAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 96
           + ++L+  DG  +GC F+ +  +  A  AI   ++ 
Sbjct: 124 ECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQA 159

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score =  114 bits (286), Expect = 4e-29
 Identities = 39/165 (23%), Positives = 73/165 (44%), Gaps = 26/165 (15%)

Query: 19  KKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFI 78
           K  ++  +   T+R RLF+ NLP  ITEE+FK  F +YG+  +  + ++     +G GFI
Sbjct: 9   KSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD-----RGFGFI 63

Query: 79  NYANKISAVKAILKSNKKPYKGK---------------------ITEEEFKEHFGQYGDI 117
              ++  A  A  + +    K +                     ++ E  ++ F Q+G +
Sbjct: 64  RLESRTLAEIAKAELDGTILKSRPLRIRFATHGAALTVKNLSPVVSNELLEQAFSQFGPV 123

Query: 118 IDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSENG 162
             A ++ +  G+  G GF+ +A K  A KA+ +     +  +   
Sbjct: 124 EKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTP 168

>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 = 70.9 bits (174), Expect = 5e-14
 Identities = 18/88 (20%), Positives = 37/88 (42%), Gaps = 2/88 (2%)

Query: 14  FKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLK 73
                 + +  +         L +KNL   ++ E  ++ F Q+G +  A ++ +  G+  
Sbjct: 80  GTILKSRPLRIRFATHGAA--LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRAT 137

Query: 74  GCGFINYANKISAVKAILKSNKKPYKGK 101
           G GF+ +A K  A KA+ +     +   
Sbjct: 138 GKGFVEFAAKPPARKALERCGDGAFLLT 165

>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 =  112 bits (283), Expect = 2e-28
 Identities = 34/166 (20%), Positives = 64/166 (38%), Gaps = 28/166 (16%)

Query: 15  KKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKG 74
            ++ +K++E  +     R ++ I+ LP  +T +E  +    Y  +    + K      KG
Sbjct: 5   PEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKY-----KG 58

Query: 75  CGFINYANKISAVKAILKSNKKPYKGK---------------------ITEEEFKEHFGQ 113
             F+   N   A  AI   ++   + +                     +T+++F+E    
Sbjct: 59  TAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRP 118

Query: 114 YGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           +G +    L+ +   G+ KG GF  Y  K SA +A      KP   
Sbjct: 119 FGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGP 164

>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 =  111 bits (280), Expect = 5e-28
 Identities = 33/175 (18%), Positives = 60/175 (34%), Gaps = 37/175 (21%)

Query: 17  KGKK-KIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKG 74
           + ++  ++ +  D      L + NLP  +T+++F+E    +G +    L+ +   G+ KG
Sbjct: 83  RERELSVQLQPTD----ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKG 138

Query: 75  CGFINYANKISAVKAILKSNKKPYKGK------------------------------ITE 104
            GF  Y  K SA +A      KP   +                                +
Sbjct: 139 YGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRCLCVDRLPPGFND 198

Query: 105 EE-FKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            +               QL    DG+LKG   + Y     A +A  +++     G
Sbjct: 199 VDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSLGG 253

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 73.5 bits (181), Expect = 8e-15
 Identities = 15/79 (18%), Positives = 25/79 (31%), Gaps = 1/79 (1%)

Query: 24  RKKPDKTKRGRLFIKNLPFKITEEE-FKEHFGQYGDIIDAQLLKNADGKLKGCGFINYAN 82
           +  P       L +  LP    + +               QL    DG+LKG   + Y  
Sbjct: 176 QLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYET 235

Query: 83  KISAVKAILKSNKKPYKGK 101
              A +A  +++     G 
Sbjct: 236 AEMAEEAQQQADGLSLGGS 254

>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 = 41.9 bits (99), Expect = 2e-04
 Identities = 12/59 (20%), Positives = 21/59 (35%), Gaps = 6/59 (10%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
           +T +E  +    Y  +    + K      KG  F+   N   A  AI   ++   +  E
Sbjct: 34  VTNQEVHDLLSDYE-LKYCFVDKY-----KGTAFVTLLNGEQAEAAINAFHQSRLRERE 86

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  103 bits (258), Expect = 1e-25
 Identities = 32/178 (17%), Positives = 68/178 (38%), Gaps = 40/178 (22%)

Query: 15  KKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLK 73
           ++ G+    +++       R+++ ++ +++ E+  ++ F  +G I    +  ++   K K
Sbjct: 11  QQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHK 70

Query: 74  GCGFINYANKISAVKAILKSNKKPYKGK-------------------------------- 101
           G  F+ Y    +A  A+ + N     G+                                
Sbjct: 71  GFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYV 130

Query: 102 ------ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSN 152
                 +++++ K  F  +G I  A L ++   GK KG GFI Y    S+  A+   N
Sbjct: 131 ASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 77.7 bits (192), Expect = 1e-16
 Identities = 22/98 (22%), Positives = 45/98 (45%), Gaps = 2/98 (2%)

Query: 6   KKKKVKKEFKKKGKKKIERKKPDKTKRG-RLFIKNLPFKITEEEFKEHFGQYGDIIDAQL 64
           +  KV +       + I  +  ++ +   R+++ ++   +++++ K  F  +G I  A L
Sbjct: 98  RNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATL 157

Query: 65  LKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
            ++   GK KG GFI Y    S+  A+   N     G+
Sbjct: 158 ARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQ 195

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 44.6 bits (106), Expect = 2e-05
 Identities = 13/58 (22%), Positives = 25/58 (43%), Gaps = 1/58 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           + E+  ++ F  +G I    +  ++   K KG  F+ Y    +A  A+ + N     G
Sbjct: 40  LGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGG 97

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 99.6 bits (249), Expect = 7e-25
 Identities = 32/154 (20%), Positives = 62/154 (40%), Gaps = 29/154 (18%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKS 93
           L +  LP  +T+ E    F   G I   +++++   G   G  F+++ +++ + +AI   
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65

Query: 94  NKKPYKGK---------------------------ITEEEFKEHFGQYGDIIDAQLLK-N 125
           N    + K                           IT+++    FG+YG I+   +L+  
Sbjct: 66  NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK 125

Query: 126 ADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
             G+ +G  F+ Y  +  A +AI   N    +G 
Sbjct: 126 LTGRPRGVAFVRYNKREEAQEAISALNNVIPEGG 159

>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 = 72.2 bits (178), Expect = 3e-15
 Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 24  RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLK-NADGKLKGCGFINYAN 82
           R   +  K   L++ NLP  IT+++    FG+YG I+   +L+    G+ +G  F+ Y  
Sbjct: 81  RPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNK 140

Query: 83  KISAVKAILKSNKKPYKG 100
           +  A +AI   N    +G
Sbjct: 141 REEAQEAISALNNVIPEG 158

>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 = 49.5 bits (119), Expect = 3e-07
 Identities = 11/60 (18%), Positives = 27/60 (45%), Gaps = 1/60 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
           +T+ E    F   G I   +++++   G   G  F+++ +++ + +AI   N    +   
Sbjct: 15  MTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKR 74

>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 =  102 bits (257), Expect = 8e-25
 Identities = 27/176 (15%), Positives = 58/176 (32%), Gaps = 23/176 (13%)

Query: 5   AKKKKVKKEFKKKGKKKIERKKPDKTKRGR--LFIKNLPFKITEEEFKEHFGQYGDIIDA 62
           +K+   +      G    +  +     R    + +KNLP    + +  ++F   G II  
Sbjct: 12  SKRPLDEGSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHV 71

Query: 63  QLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGKI-------------------T 103
            +  +          I +A    A+ AI K++K   + +I                   T
Sbjct: 72  DVADSLKKN-FRFARIEFARYDGALAAITKTHKVVGQNEIIVSHLTECTLWMTNFPPSYT 130

Query: 104 EEEFKEHFGQYGDI-IDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           +   ++       + +  +L        +   +I+  +K  A   + K N    +G
Sbjct: 131 QRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEG 186

>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 = 98.9 bits (247), Expect = 2e-23
 Identities = 27/177 (15%), Positives = 53/177 (29%), Gaps = 41/177 (23%)

Query: 10  VKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDI-IDAQLLKNA 68
           + K  K  G+ +I      +     L++ N P   T+   ++       + +  +L    
Sbjct: 98  ITKTHKVVGQNEIIVSHLTEC---TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR 154

Query: 69  DGKLKGCGFINYANKISAVKAILKSNKKPYKGK--------------------------- 101
               +   +I+  +K  A   + K N    +G                            
Sbjct: 155 FNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIM 214

Query: 102 --------ITEEEFKEHFGQYGDIIDAQLLKNAD--GKLKGCGFINYANKISAVKAI 148
                   + E   +E F  +G I    +            C F+ + NK SA +A+
Sbjct: 215 IRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 271

>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 = 66.2 bits (162), Expect = 2e-12
 Identities = 18/97 (18%), Positives = 38/97 (39%), Gaps = 5/97 (5%)

Query: 8   KKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEE-FKEHFGQYGDIIDAQLLK 66
             +  +     +K  +R      +   + I+NL  ++ +E   +E F  +G I    +  
Sbjct: 187 YTLVTKVSNPLEKS-KRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPA 245

Query: 67  NAD--GKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
                     C F+ + NK SA +A+ + N+     +
Sbjct: 246 GQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNR 281

>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 = 98.8 bits (247), Expect = 1e-24
 Identities = 44/154 (28%), Positives = 71/154 (46%), Gaps = 29/154 (18%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKS 93
           L +  LP  +T+EEF+  FG  G+I   +L+++   G+  G GF+NY +   A KAI   
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 94  NKKPYKGK---------------------------ITEEEFKEHFGQYGDIIDAQLLK-N 125
           N    + K                           +T++E ++ F QYG II +++L   
Sbjct: 65  NGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQ 124

Query: 126 ADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
             G  +G GFI +  +I A +AI   N +   G+
Sbjct: 125 VTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGA 158

>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 = 72.2 bits (178), Expect = 4e-15
 Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 1/78 (1%)

Query: 24  RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLK-NADGKLKGCGFINYAN 82
           R      +   L++  LP  +T++E ++ F QYG II +++L     G  +G GFI +  
Sbjct: 80  RPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDK 139

Query: 83  KISAVKAILKSNKKPYKG 100
           +I A +AI   N +   G
Sbjct: 140 RIEAEEAIKGLNGQKPSG 157

>3q46_A TT-ippase; inorganic pyrophosphatase, hydrolase; HET: EPE; 0.99A {Thermococcus thioreducens} PDB: 3r6e_A* 3q3l_A 3i98_A 3q4w_A 3q9m_A* 3r5u_A 3r5v_A* 3q5v_A* 1ude_A 1twl_A Length = 178

 Score = 98.5 bits (246), Expect = 2e-24
 Identities = 47/176 (26%), Positives = 76/176 (43%), Gaps = 37/176 (21%)

Query: 166 PFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLR-----YVAN 220
           PFH++     V + +   ++EIP+ +  K E+           D   G L+     Y   
Sbjct: 3   PFHELEPGPEVPE-VVYALIEIPKGSRNKYEL-----------DKATGLLKLDRVLYSPF 50

Query: 221 VFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGV 280
            +P      +YG +PQTW              DGDP D++ I         II+ + +G+
Sbjct: 51  FYPV-----DYGIIPQTWY------------DDGDPFDIMVIMREPVYPLTIIEARPIGI 93

Query: 281 IGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGK 336
           + + D G  DWK++A+ V DP      D++D+   F   L     +F+ YK   GK
Sbjct: 94  MKMEDSGDKDWKVLAVPVEDPYFNDWKDISDVPKAF---LDEIAHFFQRYKELQGK 146

>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 = 96.9 bits (242), Expect = 6e-24
 Identities = 31/163 (19%), Positives = 53/163 (32%), Gaps = 34/163 (20%)

Query: 25  KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKI 84
           +  + T    LFI NL    +  E K    +     D  ++    G  +  G++++ +  
Sbjct: 6   EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAE 65

Query: 85  SAVKAILKSNKKPYKGK-----------------------------ITEEEFKEHFGQYG 115
              KA+ +       G                              ITE+E KE F    
Sbjct: 66  DLEKAL-ELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDAL 124

Query: 116 DIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           +I         DGK KG  +I + ++  A K + +       G
Sbjct: 125 EIRLVS----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG 163

>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 = 67.6 bits (166), Expect = 1e-13
 Identities = 24/83 (28%), Positives = 34/83 (40%), Gaps = 4/83 (4%)

Query: 19  KKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFI 78
           +K   R          L  KNL F ITE+E KE F    +I         DGK KG  +I
Sbjct: 86  EKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSKGIAYI 141

Query: 79  NYANKISAVKAILKSNKKPYKGK 101
            + ++  A K + +       G+
Sbjct: 142 EFKSEADAEKNLEEKQGAEIDGR 164

>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 = 96.8 bits (242), Expect = 7e-24
 Identities = 41/157 (26%), Positives = 77/157 (49%), Gaps = 28/157 (17%)

Query: 31  KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKA 89
           +  ++FI  L +  TE+  +E+FG+YG + D +++K+   G+ +G GF+++    S  + 
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61

Query: 90  ILKSNK----------------KPYKGKI---------TEEEFKEHFGQYGDIIDAQLLK 124
           +   +                 +   GKI           +EF+E F Q+G IIDAQL+ 
Sbjct: 62  VKTQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLML 121

Query: 125 NAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
           + D G+ +G GF+ Y +   AV  + ++    +K  +
Sbjct: 122 DKDTGQSRGFGFVTYDSA-DAVDRVCQNKFIDFKDRK 157

>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 = 69.1 bits (170), Expect = 4e-14
 Identities = 28/84 (33%), Positives = 49/84 (58%), Gaps = 4/84 (4%)

Query: 19  KKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGF 77
           K+ I R + DKT +  +F+  +   +  +EF+E F Q+G IIDAQL+ + D G+ +G GF
Sbjct: 76  KRAIPRDEQDKTGK--IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGF 133

Query: 78  INYANKISAVKAILKSNKKPYKGK 101
           + Y +   AV  + ++    +K +
Sbjct: 134 VTYDSA-DAVDRVCQNKFIDFKDR 156

>2prd_A Pyrophosphate phosphohydrolase; 2.00A {Thermus thermophilus} SCOP: b.40.5.1 Length = 174

 Score = 94.2 bits (235), Expect = 7e-23
 Identities = 36/170 (21%), Positives = 67/170 (39%), Gaps = 37/170 (21%)

Query: 167 FHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLR-----YVANV 221
              +P+     + + +MV+E+PR +  K E            D   G ++       A  
Sbjct: 3   LKSLPVGDKAPE-VVHMVIEVPRGSGNKYEY-----------DPDLGAIKLDRVLPGAQF 50

Query: 222 FPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVI 281
           +P      +YG +P T               DGDP+D L +       G +++V+ +G++
Sbjct: 51  YPG-----DYGFIPSTLA------------EDGDPLDGLVLSTYPLLPGVVVEVRVVGLL 93

Query: 282 GLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
            + DE   D K+I +   D     + D+ D+        +    +F+ YK
Sbjct: 94  LMEDEKGGDAKVIGVVAEDQRLDHIQDIGDVPEGV---KQEIQHFFETYK 140

>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 = 93.1 bits (232), Expect = 3e-22
 Identities = 36/168 (21%), Positives = 70/168 (41%), Gaps = 36/168 (21%)

Query: 20  KKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFI 78
           K    K+P++    +LFI  L F+ T+E  + HF Q+G + D  ++++ +  + +G GF+
Sbjct: 3   KSESPKEPEQL--RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFV 60

Query: 79  NYANKISAVKAILK----------------------------SNKKPYKG----KITEEE 106
            YA       A+                              + KK + G       E  
Sbjct: 61  TYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHH 120

Query: 107 FKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNK 153
            +++F QYG I   +++ +   GK +G  F+ + +  S  K +++   
Sbjct: 121 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH 168

>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 = 63.5 bits (155), Expect = 7e-12
 Identities = 16/88 (18%), Positives = 38/88 (43%), Gaps = 3/88 (3%)

Query: 16  KKGKKKIERKKPDKTKRGR-LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLK 73
           K+   + + ++P      + +F+  +     E   +++F QYG I   +++ +   GK +
Sbjct: 87  KRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKR 146

Query: 74  GCGFINYANKISAVKAILKSNKKPYKGK 101
           G  F+ + +   +V  I+        G 
Sbjct: 147 GFAFVTFDDH-DSVDKIVIQKYHTVNGH 173

>3gvf_A Inorganic pyrophosphatase; structural genomics, hydrolase, S structural genomics center for infectious disease, ssgcid; HET: PGE; 1.75A {Burkholderia pseudomallei 1710B} PDB: 3d63_A* 3eiy_A 3ej0_A* 3ej2_A* 3eiz_A* Length = 196

 Score = 90.1 bits (224), Expect = 3e-21
 Identities = 44/174 (25%), Positives = 71/174 (40%), Gaps = 40/174 (22%)

Query: 166 PFHDIPLYSNVKDKIFNMVVEIPRWT-NAKMEINLNEPLNPIKQDIKKGNLR-----YVA 219
            F ++P   ++    FN+++EIP  +   K E            D   G L         
Sbjct: 23  SFSNVPAGKDLPQ-DFNVIIEIPAQSEPVKYEA-----------DKALGLLVVDRFIGTG 70

Query: 220 NVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALG 279
             +P      NYG +PQT              GDGDP+DVL I       G +++ +ALG
Sbjct: 71  MRYPV-----NYGFIPQTLS------------GDGDPVDVLVITPFPLLAGSVVRARALG 113

Query: 280 VIGLIDEGQTDWKIIAINVND--PNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
           ++ + DE   D K++A+  +   P  A L  + D+  +          +F+ YK
Sbjct: 114 MLKMTDESGVDAKLVAVPHDKVCPMTANLKSIDDVPAYL---KDQIKHFFEQYK 164

>3ld3_A Inorganic pyrophosphatase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, hydrolase; 1.75A {Anaplasma phagocytophilum} PDB: 3lo0_A Length = 199

 Score = 90.1 bits (224), Expect = 3e-21
 Identities = 45/174 (25%), Positives = 71/174 (40%), Gaps = 40/174 (22%)

Query: 166 PFHDIPLYSNVKDKIFNMVVEIPRWT-NAKMEINLNEPLNPIKQDIKKGNLR-----YVA 219
              DI   SN  +   N+V+E+ + +   K E            D K G L        A
Sbjct: 23  NLDDIGSGSNAPE-EVNVVIEVSQDSHPVKYEF-----------DEKNGALWVDRFLPTA 70

Query: 220 NVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALG 279
             +P      NYG +P T              GDGDP+DVL +       G +I V+ +G
Sbjct: 71  MYYPC-----NYGFIPNTIA------------GDGDPVDVLVLARFPVMPGAVICVRPVG 113

Query: 280 VIGLIDEGQTDWKIIAINVN--DPNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
           V+ + DE   D K++A+     D     + + +D+ + F   L + + +F  YK
Sbjct: 114 VLMMNDEKGEDAKVLAVPATKVDQYYGNIVNYSDLPSSF---LDSISHFFSFYK 164

>1sxv_A Inorganic pyrophosphatase; structural genomics, ppase,, hydrolase; 1.30A {Mycobacterium tuberculosis} PDB: 1wcf_A 2uxs_A 4ecp_A Length = 172

 Score = 88.4 bits (220), Expect = 8e-21
 Identities = 35/157 (22%), Positives = 62/157 (39%), Gaps = 36/157 (22%)

Query: 180 IFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLR-----YVANVFPHHGYIWNYGAL 234
            F++ +EIP+    K E+           D + G +R     Y    +P      +YG +
Sbjct: 12  QFDVTIEIPKGQRNKYEV-----------DHETGRVRLDRYLYTPMAYPT-----DYGFI 55

Query: 235 PQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKII 294
             T               DGDP+D L +  +    G ++  + +G+  ++DE   D K++
Sbjct: 56  EDTLG------------DDGDPLDALVLLPQPVFPGVLVAARPVGMFRMVDEHGGDDKVL 103

Query: 295 AINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
            +   DP    + D+ D+       L A   +F  YK
Sbjct: 104 CVPAGDPRWDHVQDIGDVPAFE---LDAIKHFFVHYK 137

>2au7_A Inorganic pyrophosphatase; hydrolase, mutant; 1.05A {Escherichia coli} PDB: 1i40_A 1i6t_A 1igp_A 1obw_A 2au6_A 2au8_A 2au9_A 2auu_A 1mjy_A 1faj_A 1ino_A 1ipw_A 1jfd_A 2eip_A 1mjz_A 1mjx_A 1mjw_A 3i4q_A* Length = 175

 Score = 87.3 bits (217), Expect = 2e-20
 Identities = 38/173 (21%), Positives = 64/173 (36%), Gaps = 40/173 (23%)

Query: 167 FHDIPLYSNVKDKIFNMVVEIPRWT-NAKMEINLNEPLNPIKQDIKKGNLR-----YVAN 220
             ++P   ++ +    +V+EIP      K EI           D + G L        A 
Sbjct: 2   LLNVPAGKDLPE-DIYVVIEIPANADPIKYEI-----------DKESGALFVDQFMSTAM 49

Query: 221 VFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGV 280
            +P      NYG +  T               DGDP+DVL       + G + + + +GV
Sbjct: 50  FYPC-----NYGYINHTLS------------LDGDPVDVLVPTPYPLQPGSVTRCRPVGV 92

Query: 281 IGLIDEGQTDWKIIAINVN--DPNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
           + + DE   D K++A+  +        + DV D+             +F+ YK
Sbjct: 93  LKMTDEAGEDAKLVAVPHSKLSKEYDHIKDVNDLPELL---KAQIAHFFEHYK 142

>3fq3_A Inorganic pyrophosphatase:bacterial/archaeal INOR pyrophosphatase; ssgcid, inorganic phosphatase; 1.90A {Brucella melitensis biovar abortus 230ORGANISM_TAXID} PDB: 3sw5_A Length = 197

 Score = 87.4 bits (217), Expect = 3e-20
 Identities = 47/173 (27%), Positives = 67/173 (38%), Gaps = 40/173 (23%)

Query: 167 FHDIPLYSNVKDKIFNMVVEIPRWT-NAKMEINLNEPLNPIKQDIKKGNLR-----YVAN 220
              I + SN  +   N+++E+P      K E+           D K G L      Y   
Sbjct: 24  IDAISIGSNPPE-DVNVIIEVPVGGQPIKYEM-----------DKKAGALIVDRFLYTPM 71

Query: 221 VFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGV 280
            +P      NYG +P T               DGDPIDVL    R    G +I V+ +GV
Sbjct: 72  TYPG-----NYGFVPHTLS------------EDGDPIDVLVCNTRPLIPGCVINVRPIGV 114

Query: 281 IGLIDEGQTDWKIIAINVN--DPNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
           + + D    D KIIA+          K++D  D+       LK    +F+ YK
Sbjct: 115 LVMEDNSGKDEKIIAVPSPHLTRRYEKIHDYTDMPEIT---LKQIAHFFEHYK 164

>2bqx_A Inorganic pyrophosphatase; hydrolase; 1.90A {Helicobacter pylori} PDB: 1ygz_A 2bqy_A Length = 173

 Score = 86.5 bits (215), Expect = 3e-20
 Identities = 41/172 (23%), Positives = 72/172 (41%), Gaps = 40/172 (23%)

Query: 167 FHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLR-----YVANV 221
              + +  +       +V+EI + +N K E+           D + G L      Y A  
Sbjct: 3   LEKLEVSHDADS--LCVVIEISKHSNIKYEL-----------DKESGALMVDRVLYGAQN 49

Query: 222 FPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVI 281
           +P      NYG +P T               DGDP+D L + +   + G +++ + +GV+
Sbjct: 50  YPA-----NYGFVPNTLG------------SDGDPVDALVLSDVAFQAGSVVKARLVGVL 92

Query: 282 GLIDEGQTDWKIIAI--NVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
            + DE   D K+IA+  +  DP  + + D+ D+  H    L     +F+ YK
Sbjct: 93  NMEDESGMDEKLIALPIDKIDPTHSYVKDIDDLSKHT---LDKIKHFFETYK 141

>1qez_A Ppase, S-ppase, protein (inorganic pyrophosphatase); thermostability, magnesium, hydrolase; 2.70A {Sulfolobus acidocaldarius} SCOP: b.40.5.1 Length = 173

 Score = 85.4 bits (212), Expect = 1e-19
 Identities = 45/170 (26%), Positives = 76/170 (44%), Gaps = 39/170 (22%)

Query: 169 DIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLR-----YVANVFP 223
            +    N  D + N++VEIP+ +N K E            D ++G ++     Y +  +P
Sbjct: 2   KLSPGKNAPD-VVNVLVEIPQGSNIKYEY-----------DDEEGVIKVDRVLYTSMNYP 49

Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
                 NYG +P T E             DGDP+DVL I       G +I+V+ +G++ +
Sbjct: 50  F-----NYGFIPGTLE------------EDGDPLDVLVITNYQLYPGSVIEVRPIGILYM 92

Query: 284 IDEGQTDWKIIAINVN--DPNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
            DE   D KI+A+  +  DP+ + + D+ D+             +F+ YK
Sbjct: 93  KDEEGEDAKIVAVPKDKTDPSFSNIKDINDLPQAT---KNKIVHFFEHYK 139

>3d53_A Inorganic pyrophosphatase; seattle structural G center for infectious disease, ssgcid, hydrolase, magnesium binding; 2.20A {Rickettsia prowazekii} PDB: 3emj_A* Length = 173

 Score = 84.3 bits (209), Expect = 2e-19
 Identities = 42/173 (24%), Positives = 67/173 (38%), Gaps = 41/173 (23%)

Query: 167 FHDIPLYSNVKDKIFNMVVEIPRWT-NAKMEINLNEPLNPIKQDIKKGNLR-----YVAN 220
              I   +N  +   N+++EIP  +   K E            D + G L          
Sbjct: 4   IKKIKAKAN--NNEINVIIEIPMNSGPIKYEF-----------DKESGALFVDRFMQTTM 50

Query: 221 VFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGV 280
            +P      NYG +P T               DGDP+DVL +       G +I+ +A+GV
Sbjct: 51  SYPC-----NYGFIPDTLS------------NDGDPVDVLVVAHHPVVPGSVIKCRAIGV 93

Query: 281 IGLIDEGQTDWKIIAINVN--DPNAAKLNDVADIETHFPGYLKATNEWFKIYK 331
           + + DE   D KIIA+  +  D     + ++ D+        K    +F+ YK
Sbjct: 94  LMMEDESGLDEKIIAVPTSKLDITFDHIKELDDLCEML---KKRIVHFFEHYK 143

>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 = 83.8 bits (208), Expect = 3e-19
 Identities = 27/153 (17%), Positives = 53/153 (34%), Gaps = 35/153 (22%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN------ADGKLKGCGFINYANKISAV 87
           RL++ N+PF ITEE   + F     +                 + K   F+ + +     
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 88  KAILKSNKKPYKGK---------------------------ITEEEFKEHFGQYGDIIDA 120
           +A +  +   ++G+                           + +++ KE    +G +   
Sbjct: 66  QA-MAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAF 124

Query: 121 QLLKNAD-GKLKGCGFINYANKISAVKAILKSN 152
            L+K++  G  KG  F  Y +     +AI   N
Sbjct: 125 NLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN 157

>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 = 71.1 bits (175), Expect = 1e-14
 Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 3/84 (3%)

Query: 21  KIERKKPDKTKRG--RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGF 77
           KI R    +   G  +LFI  LP  + +++ KE    +G +    L+K++  G  KG  F
Sbjct: 81  KIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAF 140

Query: 78  INYANKISAVKAILKSNKKPYKGK 101
             Y +     +AI   N      K
Sbjct: 141 CEYVDINVTDQAIAGLNGMQLGDK 164

>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 = 81.6 bits (202), Expect = 3e-19
 Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 3/74 (4%)

Query: 23 ERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYAN 82
          E +     K   LF+  L  + +EE+    F  +G I +  +L+  DG  KGC F+ +++
Sbjct: 9  ESRGGRDRK---LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSS 65

Query: 83 KISAVKAILKSNKK 96
             A  AI   +  
Sbjct: 66 HTEAQAAIHALHGS 79

>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 = 62.7 bits (153), Expect = 1e-12
 Identities = 15/54 (27%), Positives = 27/54 (50%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
           + +EE+    F  +G I +  +L+  DG  KGC F+ +++   A  AI   +  
Sbjct: 26  QQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGS 79

>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 = 78.9 bits (195), Expect = 3e-18
 Identities = 21/68 (30%), Positives = 38/68 (55%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
            +F+ NL +K+  ++ KE F   G ++ A +L++ DGK +G G + +   I AV+AI   
Sbjct: 17  TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76

Query: 94  NKKPYKGK 101
           N +    +
Sbjct: 77  NGQLLFDR 84

>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 = 59.2 bits (144), Expect = 3e-11
 Identities = 18/58 (31%), Positives = 31/58 (53%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           K+  ++ KE F   G ++ A +L++ DGK +G G + +   I AV+AI   N +    
Sbjct: 26  KVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFD 83

>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 = 78.8 bits (195), Expect = 4e-18
 Identities = 21/90 (23%), Positives = 37/90 (41%), Gaps = 1/90 (1%)

Query: 12  KEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGK 71
              K  G +  +  K  +     L+I NLP  + E+E +     +G +I  ++L+++ G 
Sbjct: 6   SGLKASGVQA-QMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGT 64

Query: 72  LKGCGFINYANKISAVKAILKSNKKPYKGK 101
            +G GF    +       I   N K  K  
Sbjct: 65  SRGVGFARMESTEKCEAVIGHFNGKFIKTP 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 = 54.6 bits (132), Expect = 1e-09
 Identities = 13/57 (22%), Positives = 25/57 (43%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           + E+E +     +G +I  ++L+++ G  +G GF    +       I   N K  K 
Sbjct: 37  MDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKT 93

>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 = 81.2 bits (201), Expect = 6e-18
 Identities = 30/155 (19%), Positives = 61/155 (39%), Gaps = 31/155 (20%)

Query: 28  DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISA 86
                  L++ +L   +TE    E F   G I+  ++ ++    +  G  ++N+     A
Sbjct: 11  PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADA 70

Query: 87  VKAILKSNKKPYKGK-----------------------------ITEEEFKEHFGQYGDI 117
            +A+   N    KGK                             I  +   + F  +G+I
Sbjct: 71  ERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNI 130

Query: 118 IDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 152
           +  +++ + +G  KG GF+++  + +A +AI K N
Sbjct: 131 LSCKVVCDENGS-KGYGFVHFETQEAAERAIEKMN 164

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 66.5 bits (163), Expect = 7e-13
 Identities = 25/117 (21%), Positives = 50/117 (42%), Gaps = 24/117 (20%)

Query: 25  KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKI 84
               K+  G +FIKNL   I  +   + F  +G+I+  +++ + +G  KG GF+++  + 
Sbjct: 96  PSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS-KGYGFVHFETQE 154

Query: 85  SAVKAILKSN----------------KKPYKGK-------ITEEEFKEHFGQYGDII 118
           +A +AI K N                +K  + +           +  ++ G  G I+
Sbjct: 155 AAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFYPYDVPDYAGSSGRIV 211

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 39.6 bits (93), Expect = 8e-04
 Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 1/61 (1%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
            +TE    E F   G I+  ++ ++    +  G  ++N+     A +A+   N    KG 
Sbjct: 26  DVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGK 85

Query: 160 E 160
            
Sbjct: 86  P 86

>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 = 79.9 bits (198), Expect = 7e-18
 Identities = 25/144 (17%), Positives = 54/144 (37%), Gaps = 30/144 (20%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
           L++ NL   ITE+  K++F   G I + +++ + + K     F+ Y     A  A+   N
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62

Query: 95  KKPYKGK-----------------------------ITEEEFKEHFGQYGDIIDAQLLKN 125
            K  +                               + +E  +  F  +   +   ++ +
Sbjct: 63  GKQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWD 122

Query: 126 AD-GKLKGCGFINYANKISAVKAI 148
              G  +G GF+++ ++  A  A+
Sbjct: 123 MQTGSSRGYGFVSFTSQDDAQNAM 146

>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 = 60.2 bits (147), Expect = 4e-11
 Identities = 11/68 (16%), Positives = 30/68 (44%), Gaps = 1/68 (1%)

Query: 24  RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYAN 82
            ++        LF+ +L   + +E  +  F  +   +   ++ +   G  +G GF+++ +
Sbjct: 79  SQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTS 138

Query: 83  KISAVKAI 90
           +  A  A+
Sbjct: 139 QDDAQNAM 146

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 44.4 bits (106), Expect = 1e-05
 Identities = 14/59 (23%), Positives = 27/59 (45%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
           ITE+  K++F   G I + +++ + + K     F+ Y     A  A+   N K  + + 
Sbjct: 12  ITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNI 70

>3tr4_A Inorganic pyrophosphatase; central intermediary metabolism, hydrolase; HET: MSE; 2.00A {Coxiella burnetii} Length = 178

 Score = 79.7 bits (197), Expect = 1e-17
 Identities = 41/161 (25%), Positives = 67/161 (41%), Gaps = 39/161 (24%)

Query: 179 KIFNMVVEIP-RWTNAKMEINLNEPLNPIKQDIKKGNLR-----YVANVFPHHGYIWNYG 232
             FN+++EIP      K E            D + G L        +  +P      NYG
Sbjct: 15  DDFNVIIEIPANGGEVKYEY-----------DKELGFLTVDRFMPTSMRYPC-----NYG 58

Query: 233 ALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWK 292
            +P T               DGDP+DVL +     + G +++V+ALG++ + DE   D K
Sbjct: 59  FVPSTLA------------QDGDPLDVLVLTPVPVQPGVLMRVRALGIMKMEDEAGEDSK 106

Query: 293 IIAINVNDPNA--AKLNDVADIETHFPGYLKATNEWFKIYK 331
           ++A+ V         +  + DI +     L A + +F+ YK
Sbjct: 107 VLAVPVVKACRAYEAIQSLKDISSLL---LDAISHFFERYK 144

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 77.3 bits (191), Expect = 1e-17
 Identities = 19/97 (19%), Positives = 38/97 (39%), Gaps = 7/97 (7%)

Query: 5   AKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQL 64
           +                +  ++  +    RLF++  P  + E E  E FG +G + + ++
Sbjct: 4   SHHHHHHSSGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI 63

Query: 65  LKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
                  L G  F+ +    SA KAI + + K +  +
Sbjct: 64  -------LNGFAFVEFEEAESAAKAIEEVHGKSFANQ 93

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 54.2 bits (131), Expect = 2e-09
 Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 7/57 (12%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           + E E  E FG +G + + ++       L G  F+ +    SA KAI + + K +  
Sbjct: 43  VQESELNEIFGPFGPMKEVKI-------LNGFAFVEFEEAESAAKAIEEVHGKSFAN 92

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 75.4 bits (186), Expect = 5e-17
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 2/75 (2%)

Query: 18 GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD--GKLKGC 75
          G      + P K    ++ ++N+PF+  + E +E F  +G++   +L K     G  +G 
Sbjct: 1  GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60

Query: 76 GFINYANKISAVKAI 90
          GF+++  K  A KA 
Sbjct: 61 GFVDFITKQDAKKAF 75

>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 = 51.5 bits (124), Expect = 1e-08
 Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 2/50 (4%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD--GKLKGCGFINYANKISAVKAI 148
           +  + E +E F  +G++   +L K     G  +G GF+++  K  A KA 
Sbjct: 26  QANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 75.4 bits (186), Expect = 5e-17
 Identities = 27/78 (34%), Positives = 41/78 (52%), Gaps = 5/78 (6%)

Query: 24  RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANK 83
             +   T+R RLF+ NLP  ITEEE ++ F +YG   +  + K+     KG GFI    +
Sbjct: 7   GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETR 61

Query: 84  ISAVKAILKSNKKPYKGK 101
             A  A ++ +  P +GK
Sbjct: 62  TLAEIAKVELDNMPLRGK 79

>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 = 56.1 bits (136), Expect = 3e-10
 Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 5/57 (8%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           ITEEE ++ F +YG   +  + K+     KG GFI    +  A  A ++ +  P +G
Sbjct: 27  ITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRG 78

>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 = 77.8 bits (192), Expect = 8e-17
 Identities = 27/169 (15%), Positives = 53/169 (31%), Gaps = 55/169 (32%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQL------LKNADGKLKGCGFINYANKISAV 87
           RL++ N+PF ITEE   + F     +           L     + K   F+ + +     
Sbjct: 6   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65

Query: 88  KAILKSNKKPYKGK---------------------------------------------- 101
           +A+   +   ++G+                                              
Sbjct: 66  QAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124

Query: 102 -ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
            + +++ KE    +G +    L+K++  G  KG  F  Y +     +AI
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 173

>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 = 66.2 bits (162), Expect = 7e-13
 Identities = 19/98 (19%), Positives = 32/98 (32%), Gaps = 1/98 (1%)

Query: 5   AKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQL 64
             +                          +LFI  LP  + +++ KE    +G +    L
Sbjct: 87  DYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNL 146

Query: 65  LKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
           +K++  G  KG  F  Y +     +AI   N      K
Sbjct: 147 VKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK 184

>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 = 75.1 bits (185), Expect = 9e-17
 Identities = 24/74 (32%), Positives = 35/74 (47%)

Query: 28  DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAV 87
           +    G+LFI  L  +  E+  K  FG++G I +  L+K+   K +G  FI + N   A 
Sbjct: 3   EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAK 62

Query: 88  KAILKSNKKPYKGK 101
            A    N K   GK
Sbjct: 63  NAAKDMNGKSLHGK 76

>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 = 57.0 bits (138), Expect = 2e-10
 Identities = 18/57 (31%), Positives = 26/57 (45%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
             E+  K  FG++G I +  L+K+   K +G  FI + N   A  A    N K   G
Sbjct: 19  TNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHG 75

>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 = 74.7 bits (184), Expect = 1e-16
 Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 1/87 (1%)

Query: 18  GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCG 76
           G         D T+   +FI+NL F   EE   E   Q+GD+   +++ + D    KGC 
Sbjct: 1   GSSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCA 60

Query: 77  FINYANKISAVKAILKSNKKPYKGKIT 103
           F  +  + +A K +  ++ +   G + 
Sbjct: 61  FAQFMTQEAAQKCLAAASLEAEGGGLK 87

>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 = 52.7 bits (127), Expect = 6e-09
 Identities = 13/55 (23%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKP 155
             EE   E   Q+GD+   +++ + D    KGC F  +  + +A K +  ++ + 
Sbjct: 27  SEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEA 81

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 74.2 bits (183), Expect = 1e-16
 Identities = 24/79 (30%), Positives = 41/79 (51%)

Query: 23  ERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYAN 82
             +     ++ +LFI  LPF  T+EE +E    +G + D +L+ N  GK KG  ++ Y N
Sbjct: 8   VFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYEN 67

Query: 83  KISAVKAILKSNKKPYKGK 101
           +  A +A++K +    K  
Sbjct: 68  ESQASQAVMKMDGMTIKEN 86

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 56.1 bits (136), Expect = 3e-10
 Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 2/62 (3%)

Query: 97  PYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY 156
           P+    T+EE +E    +G + D +L+ N  GK KG  ++ Y N+  A +A++K +    
Sbjct: 26  PFS--CTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTI 83

Query: 157 KG 158
           K 
Sbjct: 84  KE 85

>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 = 73.4 bits (181), Expect = 2e-16
 Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 33  GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAIL 91
           GRLF++NL +  +EE+ ++ F  YG + +     ++   K KG  F+ +     AVKA  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 92  KSNKKPYKG 100
           + + + ++G
Sbjct: 69  EVDGQVFQG 77

>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 = 54.9 bits (133), Expect = 7e-10
 Identities = 14/58 (24%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            +EE+ ++ F  YG + +     ++   K KG  F+ +     AVKA  + + + ++G
Sbjct: 20  SSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQG 77

>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 = 72.7 bits (179), Expect = 4e-16
 Identities = 19/96 (19%), Positives = 45/96 (46%)

Query: 6   KKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLL 65
           + K++  +++                 G+L + NL F +++ + +E F ++G +  A + 
Sbjct: 3   RPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVH 62

Query: 66  KNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
            +  G+  G   +++  K  A+KA+ + N  P  G+
Sbjct: 63  YDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGR 98

>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 = 53.8 bits (130), Expect = 2e-09
 Identities = 13/57 (22%), Positives = 30/57 (52%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           +++ + +E F ++G +  A +  +  G+  G   +++  K  A+KA+ + N  P  G
Sbjct: 41  VSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDG 97

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 72.7 bits (179), Expect = 4e-16
 Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 5/68 (7%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
             +I N+P   TE +    F  +G I+D +         KGC FI Y     A   I+  
Sbjct: 29  TAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE-----KGCCFIKYDTHEQAAVCIVAL 83

Query: 94  NKKPYKGK 101
              P++G+
Sbjct: 84  ANFPFQGR 91

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 59.6 bits (145), Expect = 1e-11
 Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 5/57 (8%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            TE +    F  +G I+D +         KGC FI Y     A   I+     P++G
Sbjct: 39  ATEADLIPLFQNFGFILDFKHYPE-----KGCCFIKYDTHEQAAVCIVALANFPFQG 90

>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 = 72.3 bits (178), Expect = 6e-16
 Identities = 16/73 (21%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 29  KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVK 88
           K     +F+  +  ++ E E +  F +YG + + +++ +  G  KG GF+++ N +   K
Sbjct: 6   KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQK 65

Query: 89  AILKSNKKPYKGK 101
            +   ++  + GK
Sbjct: 66  IV--ESQINFHGK 76

>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 = 54.9 bits (133), Expect = 8e-10
 Identities = 12/49 (24%), Positives = 26/49 (53%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 150
           + E E +  F +YG + + +++ +  G  KG GF+++ N +   K +  
Sbjct: 21  MDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVES 69

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 74.5 bits (183), Expect = 6e-16
 Identities = 16/97 (16%), Positives = 43/97 (44%)

Query: 5   AKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQL 64
           ++ K +  +++                  +L + NL F +++ + +E F ++G +  A +
Sbjct: 61  SRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAV 120

Query: 65  LKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
             +  G+  G   +++  +  A+KA+ +    P  G+
Sbjct: 121 DYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGR 157

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 54.5 bits (131), Expect = 6e-09
 Identities = 11/57 (19%), Positives = 29/57 (50%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           +++ + +E F ++G +  A +  +  G+  G   +++  +  A+KA+ +    P  G
Sbjct: 100 VSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDG 156

>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 = 71.9 bits (177), Expect = 7e-16
 Identities = 20/68 (29%), Positives = 32/68 (47%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
            +F+ NL  ++ EE   E F Q G +    + K+ +GK K  GF+ + +  S   AI   
Sbjct: 18  TVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALL 77

Query: 94  NKKPYKGK 101
           N     G+
Sbjct: 78  NGIRLYGR 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 = 55.3 bits (134), Expect = 5e-10
 Identities = 15/48 (31%), Positives = 24/48 (50%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
           ++ EE   E F Q G +    + K+ +GK K  GF+ + +  S   AI
Sbjct: 27  RVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAI 74

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 71.8 bits (177), Expect = 7e-16
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 27  PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA 86
              +   ++F++NLPF  T +  K+ F + G ++ A +    +GK KGCG + + +   A
Sbjct: 3   SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVA 61

Query: 87  VKAILKSNKKPYKGK 101
            +A    N     G+
Sbjct: 62  ERACRMMNGMKLSGR 76

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 50.3 bits (121), Expect = 3e-08
 Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            T +  K+ F + G ++ A +    +GK KGCG + + +   A +A    N     G
Sbjct: 20  FTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSG 75

>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 = 71.6 bits (176), Expect = 2e-15
 Identities = 15/79 (18%), Positives = 36/79 (45%)

Query: 23  ERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYAN 82
                      +L + NL F +++ + +E F ++G +  A +  +  G+  G   +++  
Sbjct: 26  CGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFER 85

Query: 83  KISAVKAILKSNKKPYKGK 101
           +  A+KA+ +    P  G+
Sbjct: 86  RADALKAMKQYKGVPLDGR 104

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 53.1 bits (128), Expect = 6e-09
 Identities = 11/57 (19%), Positives = 29/57 (50%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           +++ + +E F ++G +  A +  +  G+  G   +++  +  A+KA+ +    P  G
Sbjct: 47  VSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDG 103

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 71.9 bits (176), Expect = 2e-15
 Identities = 19/128 (14%), Positives = 40/128 (31%), Gaps = 23/128 (17%)

Query: 4   LAKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEH----FGQYGDI 59
           + +    K E +      +    P       + I N+  ++ +E+ +          GDI
Sbjct: 1   MKETAAAKFERQHMDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDI 60

Query: 60  IDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGKI----------------- 102
           +D  +  +      G  +I +A + SA   +      P++G                   
Sbjct: 61  LDIVVDLS--DDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQSQVAEDG 118

Query: 103 TEEEFKEH 110
           + E    H
Sbjct: 119 SLEHHHHH 126

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 48.7 bits (116), Expect = 2e-07
 Identities = 12/62 (19%), Positives = 26/62 (41%), Gaps = 6/62 (9%)

Query: 101 KITEEEFKEH----FGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY 156
           ++ +E+ +          GDI+D  +  +      G  +I +A + SA   +      P+
Sbjct: 40  EVPKEKLQALLYALASSQGDILDIVVDLS--DDNSGKAYIVFATQESAQAFVEAFQGYPF 97

Query: 157 KG 158
           +G
Sbjct: 98  QG 99

>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 = 70.9 bits (174), Expect = 2e-15
 Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 2/67 (2%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
           L+I+NLP+KIT EE  + FG+YG I   ++      + +G  ++ Y +   A  A+   +
Sbjct: 11  LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNAVDHLS 68

Query: 95  KKPYKGK 101
                 +
Sbjct: 69  GFNVSNR 75

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 53.5 bits (129), Expect = 3e-09
 Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 2/58 (3%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           KIT EE  + FG+YG I   ++      + +G  ++ Y +   A  A+   +      
Sbjct: 19  KITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNAVDHLSGFNVSN 74

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 70.8 bits (174), Expect = 2e-15
 Identities = 24/96 (25%), Positives = 46/96 (47%), Gaps = 4/96 (4%)

Query: 6   KKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLL 65
                      +G         +K++  RL + N+PF+  + + ++ FGQ+G I+D +++
Sbjct: 6   HHHHHSSGLVPRGSHM---NTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEII 62

Query: 66  KNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
            N  G  KG GF+ + N   A +A  K +    +G+
Sbjct: 63  FNERGS-KGFGFVTFENSADADRAREKLHGTVVEGR 97

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 51.9 bits (125), Expect = 1e-08
 Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
             + + ++ FGQ+G I+D +++ N  G  KG GF+ + N   A +A  K +    +G
Sbjct: 41  FRDPDLRQMFGQFGKILDVEIIFNERGS-KGFGFVTFENSADADRAREKLHGTVVEG 96

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 69.9 bits (172), Expect = 3e-15
 Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 6/79 (7%)

Query: 27  PDKTKRGRLFIKNLPFKITEEEFKEH----FGQYGDIIDAQLLKNADGKLKGCGFINYAN 82
           P+      ++I NL  KI ++E K+     F ++G I+D  + +    K++G  F+ +  
Sbjct: 3   PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKE 60

Query: 83  KISAVKAILKSNKKPYKGK 101
             SA  A+      P+  K
Sbjct: 61  VSSATNALRSMQGFPFYDK 79

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 6/62 (9%)

Query: 101 KITEEEFKEH----FGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY 156
           KI ++E K+     F ++G I+D  + +    K++G  F+ +    SA  A+      P+
Sbjct: 19  KIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPF 76

Query: 157 KG 158
             
Sbjct: 77  YD 78

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 69.8 bits (171), Expect = 4e-15
 Identities = 19/92 (20%), Positives = 42/92 (45%), Gaps = 5/92 (5%)

Query: 18  GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGF 77
           G+  ++    +++    ++IK  P   T ++ KE     G +++ Q+ +      KG  F
Sbjct: 1   GRWILKNDVKNRS----VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIF 56

Query: 78  INYANKISAVKAILKSNKKPYKGKITEEEFKE 109
           + + +  SA K  +++  + YK       FK+
Sbjct: 57  VVFDSIESAKKF-VETPGQKYKETDLLILFKD 87

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 54.0 bits (130), Expect = 2e-09
 Identities = 13/59 (22%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
            T ++ KE     G +++ Q+ +      KG  F+ + +  SA K  +++  + YK ++
Sbjct: 23  ATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKF-VETPGQKYKETD 80

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 70.5 bits (173), Expect = 5e-15
 Identities = 20/102 (19%), Positives = 46/102 (45%), Gaps = 3/102 (2%)

Query: 1   MEKLAKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDII 60
           M+    K       +   +     +K +  KR  +++ N+ +  T ++ + HF   G I 
Sbjct: 6   MQTTHSKMTAGAYTEGPPQPLSAEEKKEIDKR-SVYVGNVDYGSTAQDLEAHFSSCGSIN 64

Query: 61  DAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
              +L +   G  KG  +I +A + ++V A +  ++  ++G+
Sbjct: 65  RITILCDKFSGHPKGYAYIEFAER-NSVDAAVAMDETVFRGR 105

>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 = 50.5 bits (121), Expect = 4e-08
 Identities = 14/58 (24%), Positives = 29/58 (50%), Gaps = 2/58 (3%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            T ++ + HF   G I    +L +   G  KG  +I +A + ++V A +  ++  ++G
Sbjct: 48  STAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAER-NSVDAAVAMDETVFRG 104

>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 = 69.1 bits (170), Expect = 5e-15
 Identities = 15/70 (21%), Positives = 33/70 (47%), Gaps = 1/70 (1%)

Query: 33  GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAIL 91
             L+I+ L    T+++  +    YG I+  + + +    K KG GF+++ +  +A KA+ 
Sbjct: 6   SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65

Query: 92  KSNKKPYKGK 101
                  + +
Sbjct: 66  ALKASGVQAQ 75

>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 = 51.0 bits (123), Expect = 1e-08
 Identities = 12/58 (20%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            T+++  +    YG I+  + + +    K KG GF+++ +  +A KA+        + 
Sbjct: 17  TTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQA 74

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 71.0 bits (174), Expect = 5e-15
 Identities = 27/107 (25%), Positives = 49/107 (45%), Gaps = 11/107 (10%)

Query: 2   EKLAKKKKVKKEFKK-KGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDII 60
            +L K +  ++E +     +  E  +P+      +++KNL   + E++ K  FG+Y D  
Sbjct: 18  RELEKGRISREEMETLSVFRSYEPGEPNCR----IYVKNLAKHVQEKDLKYIFGRYVDFS 73

Query: 61  DAQLLKNAD------GKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
                   D      G++KG  FI   N+ +A KA+ ++N     GK
Sbjct: 74  SETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGK 120

>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 = 69.3 bits (170), Expect = 6e-15
 Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 1/75 (1%)

Query: 27  PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKIS 85
             K     + ++N+PF ++ +E  + F  Y  I  +  L  N  G   G   + + ++  
Sbjct: 10  SGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDE 69

Query: 86  AVKAILKSNKKPYKG 100
           A  A++  N +P   
Sbjct: 70  ATAAVIDLNDRPIGS 84

>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 = 52.3 bits (126), Expect = 6e-09
 Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 3/63 (4%)

Query: 97  PYKGKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVKAILKSNKKP 155
           P+   ++ +E  + F  Y  I  +  L  N  G   G   + + ++  A  A++  N +P
Sbjct: 24  PFT--VSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRP 81

Query: 156 YKG 158
              
Sbjct: 82  IGS 84

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 69.2 bits (170), Expect = 6e-15
 Identities = 23/73 (31%), Positives = 29/73 (39%), Gaps = 4/73 (5%)

Query: 33  GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL----KGCGFINYANKISAVK 88
             LFIKNL F  TEE  K  F + G I    + K  +        G GF+ Y     A K
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 89  AILKSNKKPYKGK 101
           A+ +       G 
Sbjct: 66  ALKQLQGHTVDGH 78

>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 = 49.2 bits (118), Expect = 8e-08
 Identities = 16/61 (26%), Positives = 22/61 (36%), Gaps = 4/61 (6%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKL----KGCGFINYANKISAVKAILKSNKKPYK 157
            TEE  K  F + G I    + K  +        G GF+ Y     A KA+ +       
Sbjct: 17  TTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVD 76

Query: 158 G 158
           G
Sbjct: 77  G 77

>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 = 69.7 bits (171), Expect = 6e-15
 Identities = 21/58 (36%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 90
          +LFI  +P  + E++ K  F ++G I +  +LK+   G  KGC F+ Y  + SA+KA 
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQ 72

>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 = 56.2 bits (136), Expect = 4e-10
 Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 1/48 (2%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAI 148
           + E++ K  F ++G I +  +LK+   G  KGC F+ Y  + SA+KA 
Sbjct: 25  LDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQ 72

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 69.7 bits (171), Expect = 7e-15
 Identities = 11/70 (15%), Positives = 27/70 (38%), Gaps = 1/70 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
            +    L   + E   K+   +YG++ + ++L +    K  G   + + +   A + +  
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 93  SNKKPYKGKI 102
            +     G I
Sbjct: 68  LHLTSVMGNI 77

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 54.3 bits (131), Expect = 1e-09
 Identities = 9/58 (15%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           + E   K+   +YG++ + ++L +    K  G   + + +   A + +   +     G
Sbjct: 18  VRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMG 75

>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 = 68.5 bits (168), Expect = 1e-14
 Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 1/75 (1%)

Query: 27  PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKIS 85
             K     + ++N+PF ++ +E  + F  Y  I  +  L  N  G   G   + + ++  
Sbjct: 10  SGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDE 69

Query: 86  AVKAILKSNKKPYKG 100
           A  A++  N +P   
Sbjct: 70  ATAAVIDLNDRPIGS 84

>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 = 52.3 bits (126), Expect = 7e-09
 Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 3/63 (4%)

Query: 97  PYKGKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVKAILKSNKKP 155
           P+   ++ +E  + F  Y  I  +  L  N  G   G   + + ++  A  A++  N +P
Sbjct: 24  PFT--VSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRP 81

Query: 156 YKG 158
              
Sbjct: 82  IGS 84

>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 = 68.9 bits (169), Expect = 1e-14
 Identities = 13/68 (19%), Positives = 31/68 (45%), Gaps = 5/68 (7%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
            ++   +   +T++  ++ F  +G I++ ++        KG  F+ ++   SA  AI+  
Sbjct: 27  TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSV 81

Query: 94  NKKPYKGK 101
           N    +G 
Sbjct: 82  NGTTIEGH 89

>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 = 56.6 bits (137), Expect = 3e-10
 Identities = 13/57 (22%), Positives = 28/57 (49%), Gaps = 5/57 (8%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           +T++  ++ F  +G I++ ++        KG  F+ ++   SA  AI+  N    +G
Sbjct: 37  LTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEG 88

>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 = 69.1 bits (169), Expect = 2e-14
 Identities = 20/108 (18%), Positives = 42/108 (38%), Gaps = 8/108 (7%)

Query: 15  KKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLK 73
           K    +K  R +        +++K LPF+   +   + F +   + D+  +    +GK  
Sbjct: 8   KSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKAT 67

Query: 74  GCGFINYANKISAVKAILKSNKKPYKG------KITEEEFKEHFGQYG 115
           G GF+ + N+     A+ + +K+           IT++   E      
Sbjct: 68  GEGFVEFRNEADYKAALCR-HKQYMGNRFIQVHPITKKGMLEKIDMIR 114

>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 = 46.0 bits (109), Expect = 2e-06
 Identities = 10/59 (16%), Positives = 25/59 (42%), Gaps = 3/59 (5%)

Query: 97  PYKGKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
           P++     +   + F +   + D+  +    +GK  G GF+ + N+     A+ +  + 
Sbjct: 34  PFE--AENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQY 90

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 68.1 bits (167), Expect = 2e-14
 Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 7/68 (10%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
            LF++NL   +TEE  ++ F Q+G +   +       KLK   FI++  +  AVKA+ + 
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERVK-------KLKDYAFIHFDERDGAVKAMEEM 65

Query: 94  NKKPYKGK 101
           N K  +G+
Sbjct: 66  NGKDLEGE 73

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 52.3 bits (126), Expect = 6e-09
 Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 7/59 (11%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
           +TEE  ++ F Q+G +   +       KLK   FI++  +  AVKA+ + N K  +G  
Sbjct: 23  VTEEILEKAFSQFGKLERVK-------KLKDYAFIHFDERDGAVKAMEEMNGKDLEGEN 74

>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 = 68.5 bits (168), Expect = 2e-14
 Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
            L++KNL  ++TE +    F ++ +     +      G+++G  FI + NK  A +A+  
Sbjct: 27  VLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHL 86

Query: 93  SNKKPYKGK 101
            N     GK
Sbjct: 87  VNGYKLYGK 95

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 50.4 bits (121), Expect = 4e-08
 Identities = 13/59 (22%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           ++TE +    F ++ +     +      G+++G  FI + NK  A +A+   N     G
Sbjct: 36  RVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYG 94

>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 = 66.9 bits (164), Expect = 3e-14
 Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 7/75 (9%)

Query: 28  DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAV 87
           DKT    L++  L   ITE + + HF Q+G+I    +++      + C FI +A + +A 
Sbjct: 9   DKTIT-TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAE 62

Query: 88  KAILKS-NKKPYKGK 101
            A  KS NK    G+
Sbjct: 63  VAAEKSFNKLIVNGR 77

>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 = 56.1 bits (136), Expect = 2e-10
 Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 6/61 (9%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS-NKKPYKGS 159
            ITE + + HF Q+G+I    +++      + C FI +A + +A  A  KS NK    G 
Sbjct: 23  TITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKSFNKLIVNGR 77

Query: 160 E 160
            
Sbjct: 78  R 78

>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 = 67.7 bits (166), Expect = 3e-14
 Identities = 13/92 (14%), Positives = 34/92 (36%), Gaps = 6/92 (6%)

Query: 15  KKKGKKKIERKKPDKTKRGR----LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD- 69
              GK  +     + +   R    +F   L  +I   + ++ F   G + D +++ + + 
Sbjct: 4   GSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNS 63

Query: 70  GKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
            + KG  ++ +     +V   +    +   G 
Sbjct: 64  RRSKGIAYVEFCEI-QSVPLAIGLTGQRLLGV 94

>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 = 49.2 bits (118), Expect = 9e-08
 Identities = 8/59 (13%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           +I   + ++ F   G + D +++ + +  + KG  ++ +     +V   +    +   G
Sbjct: 36  RIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEI-QSVPLAIGLTGQRLLG 93

>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 = 67.3 bits (165), Expect = 4e-14
 Identities = 18/94 (19%), Positives = 51/94 (54%), Gaps = 4/94 (4%)

Query: 12  KEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-G 70
           ++  +    + ++++ ++ ++  LFI  L F+ TEE  + ++ Q+G + D  ++++    
Sbjct: 9   EKTLETVPLERKKREKEQFRK--LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASK 66

Query: 71  KLKGCGFINYANKISAVKAILKSNKKPYKGKITE 104
           + +G GF+ +++  + V A + +      G++ E
Sbjct: 67  RSRGFGFVTFSSM-AEVDAAMAARPHSIDGRVVE 99

>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 = 48.0 bits (115), Expect = 2e-07
 Identities = 10/53 (18%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKK 154
           TEE  + ++ Q+G + D  ++++    + +G GF+ +++      A+      
Sbjct: 40  TEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHS 92

>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 = 66.6 bits (163), Expect = 9e-14
 Identities = 21/85 (24%), Positives = 41/85 (48%), Gaps = 4/85 (4%)

Query: 18  GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCG 76
           G    +++ P+      LFI +LP +  +++  + F  +G+++ A++  +      K  G
Sbjct: 14  GAAGSQKEGPEGAN---LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFG 70

Query: 77  FINYANKISAVKAILKSNKKPYKGK 101
           F++Y N +SA  AI   N      K
Sbjct: 71  FVSYDNPVSAQAAIQSMNGFQIGMK 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 = 48.5 bits (116), Expect = 2e-07
 Identities = 13/58 (22%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
             +++  + F  +G+++ A++  +      K  GF++Y N +SA  AI   N      
Sbjct: 37  FGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGM 94

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 66.1 bits (162), Expect = 9e-14
 Identities = 17/88 (19%), Positives = 45/88 (51%), Gaps = 2/88 (2%)

Query: 18  GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCG 76
               + R     +   ++FI  L ++ T+E  +E+FGQ+G++ +  ++++    + +G G
Sbjct: 11  SSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFG 70

Query: 77  FINYANKISAVKAILKSNKKPYKGKITE 104
           F+ + ++ + V  +L  ++     K  +
Sbjct: 71  FVTFMDQ-AGVDKVLAQSRHELDSKTID 97

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 11/47 (23%), Positives = 29/47 (61%), Gaps = 1/47 (2%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
           T+E  +E+FGQ+G++ +  ++++    + +G GF+ + ++    K +
Sbjct: 38  TQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL 84

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 65.8 bits (161), Expect = 1e-13
 Identities = 15/67 (22%), Positives = 32/67 (47%), Gaps = 5/67 (7%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
           L+++NL    +EE  ++ F         ++      K++   F++++N+  AV+A+   N
Sbjct: 18  LYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAVEAMKALN 72

Query: 95  KKPYKGK 101
            K   G 
Sbjct: 73  GKVLDGS 79

>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 = 50.7 bits (122), Expect = 2e-08
 Identities = 13/58 (22%), Positives = 27/58 (46%), Gaps = 5/58 (8%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
            +EE  ++ F         ++      K++   F++++N+  AV+A+   N K   GS
Sbjct: 27  TSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAVEAMKALNGKVLDGS 79

>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 = 65.3 bits (160), Expect = 2e-13
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 4/76 (5%)

Query: 27  PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKIS 85
           P K+    +++ NLPF +T  +    F +YG ++   ++K+ D  K KG  FI + +K S
Sbjct: 14  PSKST---VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDS 70

Query: 86  AVKAILKSNKKPYKGK 101
           A       N K   G+
Sbjct: 71  AQNCTRAINNKQLFGR 86

>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 = 51.1 bits (123), Expect = 1e-08
 Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           +T  +    F +YG ++   ++K+ D  K KG  FI + +K SA       N K   G
Sbjct: 28  LTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFG 85

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 65.9 bits (161), Expect = 2e-13
 Identities = 21/78 (26%), Positives = 37/78 (47%), Gaps = 1/78 (1%)

Query: 25  KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANK 83
           K+ +  +   LFI +LP + T+ +    F  +G++I A++  +      K  GF+++ N 
Sbjct: 33  KQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNP 92

Query: 84  ISAVKAILKSNKKPYKGK 101
            SA  AI   N      K
Sbjct: 93  DSAQVAIKAMNGFQVGTK 110

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 47.7 bits (114), Expect = 3e-07
 Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 1/48 (2%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
            T+ +    F  +G++I A++  +      K  GF+++ N  SA  AI
Sbjct: 52  FTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAI 99

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 65.0 bits (159), Expect = 2e-13
 Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 27  PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA 86
             K+   RL + N+PF+  + + ++ FGQ+G I+D +++ N  G  KG GF+ + N   A
Sbjct: 10  ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS-KGFGFVTFENSADA 68

Query: 87  VKAILKSNKKPYKGK 101
            +A  K +    +G+
Sbjct: 69  DRAREKLHGTVVEGR 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 = 47.7 bits (114), Expect = 3e-07
 Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
             + + ++ FGQ+G I+D +++ N  G  KG GF+ + N   A +A  K +    +G
Sbjct: 27  FRDPDLRQMFGQFGKILDVEIIFNERGS-KGFGFVTFENSADADRAREKLHGTVVEG 82

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 64.9 bits (159), Expect = 3e-13
 Identities = 21/84 (25%), Positives = 41/84 (48%), Gaps = 1/84 (1%)

Query: 18  GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGF 77
           G       +  + +   L++KNL   I +E  ++ F  +G I  A+++    G+ KG GF
Sbjct: 1   GSSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGF 59

Query: 78  INYANKISAVKAILKSNKKPYKGK 101
           + +++   A KA+ + N +    K
Sbjct: 60  VCFSSPEEATKAVTEMNGRIVATK 83

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 46.1 bits (110), Expect = 1e-06
 Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           I +E  ++ F  +G I  A+++    G+ KG GF+ +++   A KA+ + N +    
Sbjct: 27  IDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVAT 82

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 64.4 bits (157), Expect = 3e-13
 Identities = 15/76 (19%), Positives = 30/76 (39%), Gaps = 2/76 (2%)

Query: 27  PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA 86
           P + +  +L I+N+P  +  E       QYG +   + +            + Y++K  A
Sbjct: 10  PKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVN--TDSETAVVNVTYSSKDQA 67

Query: 87  VKAILKSNKKPYKGKI 102
            +A+ K N    +   
Sbjct: 68  RQALDKLNGFQLENFT 83

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 43.6 bits (103), Expect = 7e-06
 Identities = 10/57 (17%), Positives = 20/57 (35%), Gaps = 2/57 (3%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           +  E       QYG +   + +            + Y++K  A +A+ K N    + 
Sbjct: 27  LQWEVLDSLLVQYGVVESCEQVN--TDSETAVVNVTYSSKDQARQALDKLNGFQLEN 81

>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 = 63.8 bits (156), Expect = 4e-13
 Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 3/79 (3%)

Query: 24  RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYAN 82
           R  PD      L +  L    TE + +E F +YG I D  ++ +    + +G  F+ + N
Sbjct: 9   RANPDPNCC--LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 66

Query: 83  KISAVKAILKSNKKPYKGK 101
              A +A  ++N     G+
Sbjct: 67  VDDAKEAKERANGMELDGR 85

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 48.7 bits (117), Expect = 9e-08
 Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            TE + +E F +YG I D  ++ +    + +G  F+ + N   A +A  ++N     G
Sbjct: 27  TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG 84

>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 = 64.1 bits (157), Expect = 4e-13
 Identities = 17/81 (20%), Positives = 40/81 (49%), Gaps = 4/81 (4%)

Query: 25  KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANK 83
               K+ +  +F+  +P    E E +E+F ++G + +  ++ +A+  + +G GFI + ++
Sbjct: 5   SSGSKSNK--IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDE 62

Query: 84  ISAVKAILKSNKKPYKGKITE 104
             +V   +  +     GK  E
Sbjct: 63  -QSVDQAVNMHFHDIMGKKVE 82

>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 = 49.1 bits (118), Expect = 9e-08
 Identities = 12/48 (25%), Positives = 29/48 (60%), Gaps = 1/48 (2%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
             E E +E+F ++G + +  ++ +A+  + +G GFI + ++ S  +A+
Sbjct: 22  CGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69

>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 = 64.9 bits (158), Expect = 5e-13
 Identities = 23/93 (24%), Positives = 44/93 (47%), Gaps = 8/93 (8%)

Query: 25  KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANK 83
              D    G + ++ LPF  T+EE  + F     + +   L  + +GK+ G  F+ +A++
Sbjct: 35  NSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQ 94

Query: 84  ISAVKAILKSNKKPYKG------KITEEEFKEH 110
             A KA+ K +K+          K ++EE + +
Sbjct: 95  ELAEKALGK-HKERIGHRYIEVFKSSQEEVRSY 126

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 46.4 bits (110), Expect = 2e-06
 Identities = 15/59 (25%), Positives = 30/59 (50%), Gaps = 3/59 (5%)

Query: 97  PYKGKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
           P+    T+EE  + F     + +   L  + +GK+ G  F+ +A++  A KA+ K  ++
Sbjct: 51  PFG--CTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKHKER 107

>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 = 64.2 bits (157), Expect = 5e-13
 Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 1/78 (1%)

Query: 24  RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYAN 82
              PD      L + NL ++ + +  +  F +YG + D  + +       +G  F+ + +
Sbjct: 5   SSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHD 64

Query: 83  KISAVKAILKSNKKPYKG 100
           +  A  A    +     G
Sbjct: 65  RRDAQDAEAAMDGAELDG 82

>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 = 48.0 bits (115), Expect = 2e-07
 Identities = 9/58 (15%), Positives = 22/58 (37%), Gaps = 1/58 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            + +  +  F +YG + D  + +       +G  F+ + ++  A  A    +     G
Sbjct: 25  TSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDG 82

>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 = 64.0 bits (156), Expect = 5e-13
 Identities = 19/80 (23%), Positives = 36/80 (45%), Gaps = 1/80 (1%)

Query: 18 GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCG 76
          G        PD    G + ++ LPF  ++EE  + F     + +   L  +  G+  G  
Sbjct: 1  GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60

Query: 77 FINYANKISAVKAILKSNKK 96
          F+ +A++  A KA+ K  ++
Sbjct: 61 FVQFASQEIAEKALKKHKER 80

>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 = 45.1 bits (107), Expect = 2e-06
 Identities = 13/59 (22%), Positives = 28/59 (47%), Gaps = 3/59 (5%)

Query: 97  PYKGKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
           P+    ++EE  + F     + +   L  +  G+  G  F+ +A++  A KA+ K  ++
Sbjct: 24  PFG--CSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKER 80

>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 = 63.8 bits (156), Expect = 5e-13
 Identities = 20/70 (28%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 33  GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAIL 91
           G+LF+  L F   E+  ++ F +YG I +  ++K+ +  + +G GF+ + N   A  A++
Sbjct: 13  GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72

Query: 92  KSNKKPYKGK 101
             N K   G+
Sbjct: 73  AMNGKSVDGR 82

>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 = 48.0 bits (115), Expect = 2e-07
 Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            E+  ++ F +YG I +  ++K+ +  + +G GF+ + N   A  A++  N K   G
Sbjct: 25  NEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDG 81

>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 = 64.0 bits (156), Expect = 7e-13
 Identities = 18/82 (21%), Positives = 36/82 (43%), Gaps = 8/82 (9%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVKAILKS 93
             I N+PF IT+ +  +         +A  +L + +G+  G   + + N+  A K+    
Sbjct: 18  AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL- 76

Query: 94  NKKPYKG------KITEEEFKE 109
           ++K   G       +T E+ +E
Sbjct: 77  HRKKLNGREAFVHVVTLEDMRE 98

>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 = 46.7 bits (111), Expect = 8e-07
 Identities = 12/63 (19%), Positives = 27/63 (42%), Gaps = 4/63 (6%)

Query: 97  PYKGKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVKAILKSNKKP 155
           P+   IT+ +  +         +A  +L + +G+  G   + + N+  A K+    ++K 
Sbjct: 24  PFS--ITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKK 80

Query: 156 YKG 158
             G
Sbjct: 81  LNG 83

>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 = 63.4 bits (155), Expect = 7e-13
 Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 5/63 (7%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
          +L+I NL   +T ++ ++ FG     +  Q+         G  F++Y ++  A++AI   
Sbjct: 10 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIETL 64

Query: 94 NKK 96
          + K
Sbjct: 65 SGK 67

>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 = 48.4 bits (116), Expect = 1e-07
 Identities = 11/53 (20%), Positives = 25/53 (47%), Gaps = 5/53 (9%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
           +T ++ ++ FG     +  Q+         G  F++Y ++  A++AI   + K
Sbjct: 20  VTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIETLSGK 67

>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 = 64.4 bits (157), Expect = 7e-13
 Identities = 20/98 (20%), Positives = 39/98 (39%), Gaps = 3/98 (3%)

Query: 5   AKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQL 64
                  ++  +  +    R  PD      L +  L    TE + +E F +YG I D  +
Sbjct: 21  MASMTGGQQMGRGSRHVGNRANPDPNCC--LGVFGLSLYTTERDLREVFSKYGPIADVSI 78

Query: 65  LKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
           + +    + +G  F+ + N   A +A  ++N     G+
Sbjct: 79  VYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR 116

>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 = 48.6 bits (116), Expect = 2e-07
 Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
             TE + +E F +YG I D  ++ +    + +G  F+ + N   A +A  ++N     G
Sbjct: 57  YTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG 115

>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 = 65.2 bits (159), Expect = 8e-13
 Identities = 22/98 (22%), Positives = 40/98 (40%), Gaps = 5/98 (5%)

Query: 6   KKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLL 65
             +   + F+   +++ +  K   T    L++ NL F  TEE+  E F + GDI    + 
Sbjct: 17  LSQYRDQHFRGDNEEQEKLLKKSCT----LYVGNLSFYTTEEQIYELFSKSGDIKKIIMG 72

Query: 66  KNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGKI 102
            +       G  F+ Y ++  A  A+   N      +I
Sbjct: 73  LDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRI 110

>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 = 49.0 bits (117), Expect = 2e-07
 Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 1/57 (1%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           TEE+  E F + GDI    +  +       G  F+ Y ++  A  A+   N      
Sbjct: 52  TEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDD 108

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 64.4 bits (157), Expect = 8e-13
 Identities = 17/85 (20%), Positives = 36/85 (42%), Gaps = 1/85 (1%)

Query: 17  KGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGC 75
           +G     R  PD      L + NL ++ + +  +  F +YG + D  + ++    + +G 
Sbjct: 32  RGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGF 91

Query: 76  GFINYANKISAVKAILKSNKKPYKG 100
            F+ + +K  A  A+   +     G
Sbjct: 92  AFVRFHDKRDAEDAMDAMDGAVLDG 116

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 47.8 bits (114), Expect = 5e-07
 Identities = 10/58 (17%), Positives = 25/58 (43%), Gaps = 1/58 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            + +  +  F +YG + D  + ++    + +G  F+ + +K  A  A+   +     G
Sbjct: 59  TSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG 116

>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 = 63.7 bits (155), Expect = 8e-13
 Identities = 13/76 (17%), Positives = 25/76 (32%), Gaps = 7/76 (9%)

Query: 29  KTKRGR--LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA 86
            + R +  +  KNLP      E +E F ++G +    L +           + +   + A
Sbjct: 5   SSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEG-----GITAIVEFLEPLEA 59

Query: 87  VKAILKSNKKPYKGKI 102
            KA        +    
Sbjct: 60  RKAFRHLAYSKFHHVP 75

>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 = 46.7 bits (111), Expect = 8e-07
 Identities = 8/59 (13%), Positives = 17/59 (28%), Gaps = 5/59 (8%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
                E +E F ++G +    L +           + +   + A KA        +   
Sbjct: 21  GTLAAEIQETFSRFGSLGRVLLPEG-----GITAIVEFLEPLEARKAFRHLAYSKFHHV 74

>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 = 63.0 bits (154), Expect = 9e-13
 Identities = 22/68 (32%), Positives = 39/68 (57%), Gaps = 1/68 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
            L++ +L F ITE+  +  F  +G I +  L+K++D G+ KG GFI +++   A +A+ +
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

Query: 93  SNKKPYKG 100
            N     G
Sbjct: 67  LNGFELAG 74

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 49.1 bits (118), Expect = 8e-08
 Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           ITE+  +  F  +G I +  L+K++D G+ KG GFI +++   A +A+ + N     G
Sbjct: 17  ITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAG 74

>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 = 62.7 bits (153), Expect = 1e-12
 Identities = 25/81 (30%), Positives = 35/81 (43%), Gaps = 6/81 (7%)

Query: 22  IERKKPDKTKRG--RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFIN 79
           +E     K  R    L  KNL F ITE+E KE F    +I       + DGK KG  +I 
Sbjct: 4   LEDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIE 59

Query: 80  YANKISAVKAILKSNKKPYKG 100
           + ++  A K + +       G
Sbjct: 60  FKSEADAEKNLEEKQGAEIDG 80

>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 = 43.8 bits (104), Expect = 6e-06
 Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 4/57 (7%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           ITE+E KE F    +I       + DGK KG  +I + ++  A K + +       G
Sbjct: 28  ITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG 80

>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 = 63.1 bits (154), Expect = 1e-12
 Identities = 23/68 (33%), Positives = 39/68 (57%), Gaps = 1/68 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
           RL++ +L F ITE+  +  F  +G I   QL+ +++ G+ KG GFI +++   A KA+ +
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87

Query: 93  SNKKPYKG 100
            N     G
Sbjct: 88  LNGFELAG 95

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 48.1 bits (115), Expect = 2e-07
 Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           ITE+  +  F  +G I   QL+ +++ G+ KG GFI +++   A KA+ + N     G
Sbjct: 38  ITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAG 95

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 61.7 bits (151), Expect = 1e-12
 Identities = 16/72 (22%), Positives = 42/72 (58%), Gaps = 2/72 (2%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
           ++FI  L ++ T+E  +E+FGQ+G++ +  ++++    + +G GF+ + ++ + V  +L 
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ-AGVDKVLA 60

Query: 93  SNKKPYKGKITE 104
            ++     K  +
Sbjct: 61  QSRHELDSKTID 72

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 49.0 bits (118), Expect = 5e-08
 Identities = 12/53 (22%), Positives = 32/53 (60%), Gaps = 1/53 (1%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKK 154
           T+E  +E+FGQ+G++ +  ++++    + +G GF+ + ++    K + +S  +
Sbjct: 13  TQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHE 65

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 62.6 bits (153), Expect = 2e-12
 Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKI 84
          K    K   L +  LP+K TE++ KE+F  +G+++  Q+ K+   G  KG GF+ +    
Sbjct: 9  KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68

Query: 85 SAVKAILKSNK 95
          + VK + + + 
Sbjct: 69 TQVKVMSQRHM 79

>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 = 49.9 bits (120), Expect = 5e-08
 Identities = 16/54 (29%), Positives = 31/54 (57%), Gaps = 1/54 (1%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNK 153
           K TE++ KE+F  +G+++  Q+ K+   G  KG GF+ +    + VK + + + 
Sbjct: 26  KTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHM 79

>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 = 62.6 bits (153), Expect = 2e-12
 Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 1/70 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
            + + NL     E + +E F  +G I    L K+   G+ KG  FI++  +  A +AI  
Sbjct: 17  TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAG 76

Query: 93  SNKKPYKGKI 102
            +   Y   I
Sbjct: 77  VSGFGYDHLI 86

>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 = 49.1 bits (118), Expect = 9e-08
 Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
             E + +E F  +G I    L K+   G+ KG  FI++  +  A +AI   +   Y  
Sbjct: 27  TRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDH 84

>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 = 62.1 bits (152), Expect = 2e-12
 Identities = 16/68 (23%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
            +++ N+ +  T EE + HF   G +    +L +   G  KG  +I +++K  +V+  L 
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSLA 66

Query: 93  SNKKPYKG 100
            ++  ++G
Sbjct: 67  LDESLFRG 74

>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 = 48.7 bits (117), Expect = 9e-08
 Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 2/59 (3%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
             T EE + HF   G +    +L +   G  KG  +I +++K  +V+  L  ++  ++G
Sbjct: 17  GATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK-ESVRTSLALDESLFRG 74

>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 = 62.3 bits (152), Expect = 2e-12
 Identities = 14/68 (20%), Positives = 33/68 (48%), Gaps = 1/68 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
            +++ ++P+  TEE+  +     G +I+ +++ +   G+ KG  FI + +  S+  A+  
Sbjct: 4   VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRN 63

Query: 93  SNKKPYKG 100
            N      
Sbjct: 64  LNGYQLGS 71

>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 = 49.5 bits (119), Expect = 5e-08
 Identities = 13/58 (22%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            TEE+  +     G +I+ +++ +   G+ KG  FI + +  S+  A+   N      
Sbjct: 14  QTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGS 71

>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 = 62.3 bits (152), Expect = 2e-12
 Identities = 21/68 (30%), Positives = 42/68 (61%), Gaps = 1/68 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
            +F+ N+P++ TEE+ K+ F + G ++  +L+ + + GK KG GF  Y ++ +A+ A+  
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 93  SNKKPYKG 100
            N + + G
Sbjct: 70  LNGREFSG 77

>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 = 50.3 bits (121), Expect = 3e-08
 Identities = 21/75 (28%), Positives = 42/75 (56%), Gaps = 5/75 (6%)

Query: 89  AILKSNKKPYKG----KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKIS 143
           A+ +S +  + G    + TEE+ K+ F + G ++  +L+ + + GK KG GF  Y ++ +
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 144 AVKAILKSNKKPYKG 158
           A+ A+   N + + G
Sbjct: 63  ALSAMRNLNGREFSG 77

>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 = 61.8 bits (151), Expect = 2e-12
 Identities = 14/72 (19%), Positives = 41/72 (56%), Gaps = 1/72 (1%)

Query: 26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKI 84
            ++   G++F+  L +  ++++ K++F ++G+++D  +  + + G+ +G GFI + +  
Sbjct: 5  SKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAA 64

Query: 85 SAVKAILKSNKK 96
          S  K + +   +
Sbjct: 65 SVEKVLDQKEHR 76

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 48.3 bits (116), Expect = 1e-07
 Identities = 11/55 (20%), Positives = 32/55 (58%), Gaps = 1/55 (1%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKK 154
             ++++ K++F ++G+++D  +  + + G+ +G GFI + +  S  K + +   +
Sbjct: 22  DTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHR 76

>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 = 61.9 bits (151), Expect = 2e-12
 Identities = 18/81 (22%), Positives = 28/81 (34%), Gaps = 7/81 (8%)

Query: 21  KIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINY 80
           KI   K + T R  L++  L    +       F ++G I     +K          +I Y
Sbjct: 8   KIGYGKANPTTR--LWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQY 60

Query: 81  ANKISAVKAILKSNKKPYKGK 101
            +  +A  A  K    P  G 
Sbjct: 61  ESLDAAQAACAKMRGFPLGGP 81

>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 = 50.3 bits (121), Expect = 3e-08
 Identities = 11/60 (18%), Positives = 19/60 (31%), Gaps = 5/60 (8%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSEN 161
            +       F ++G I     +K          +I Y +  +A  A  K    P  G + 
Sbjct: 29  TSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGGPDR 83

>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 = 62.3 bits (152), Expect = 2e-12
 Identities = 19/82 (23%), Positives = 41/82 (50%), Gaps = 2/82 (2%)

Query: 24  RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYAN 82
                  + G+LF+  L +  T+E  + +F QYG+++D  ++K+    + +G GF+ + +
Sbjct: 8   MNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67

Query: 83  KISAVKAILKSNKKPYKGKITE 104
             + V  +L S      G+  +
Sbjct: 68  P-NCVGTVLASRPHTLDGRNID 88

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 48.8 bits (117), Expect = 1e-07
 Identities = 11/47 (23%), Positives = 26/47 (55%), Gaps = 1/47 (2%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
           T+E  + +F QYG+++D  ++K+    + +G GF+ + +       +
Sbjct: 29  TQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL 75

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 61.9 bits (151), Expect = 3e-12
 Identities = 20/86 (23%), Positives = 36/86 (41%), Gaps = 9/86 (10%)

Query: 25  KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQ--------LLKNAD-GKLKGC 75
                +    +F++ L   +T E   ++F Q G I   +        L  + + GKLKG 
Sbjct: 6   HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE 65

Query: 76  GFINYANKISAVKAILKSNKKPYKGK 101
             +++ +  SA  AI   + K + G 
Sbjct: 66  ATVSFDDPPSAKAAIDWFDGKEFSGN 91

>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 = 46.1 bits (110), Expect = 1e-06
 Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 9/68 (13%)

Query: 102 ITEEEFKEHFGQYGDIIDAQ--------LLKNAD-GKLKGCGFINYANKISAVKAILKSN 152
           +T E   ++F Q G I   +        L  + + GKLKG   +++ +  SA  AI   +
Sbjct: 25  VTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFD 84

Query: 153 KKPYKGSE 160
            K + G+ 
Sbjct: 85  GKEFSGNP 92

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 62.3 bits (152), Expect = 3e-12
 Identities = 19/68 (27%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVK 88
          T   ++F+  LP+  T+   +++F  +GDI +A ++ +   GK +G GF+  A++ +A +
Sbjct: 15 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAER 74

Query: 89 AILKSNKK 96
          A    N  
Sbjct: 75 ACKDPNPI 82

>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 = 50.4 bits (121), Expect = 5e-08
 Identities = 15/53 (28%), Positives = 30/53 (56%), Gaps = 1/53 (1%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKK 154
           T+   +++F  +GDI +A ++ +   GK +G GF+  A++ +A +A    N  
Sbjct: 30  TDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPI 82

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 61.4 bits (150), Expect = 3e-12
 Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 2/70 (2%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD--GKLKGCGFINYANKISAVKAIL 91
           ++ I  L   +T++   E F  YG I    +          KG  ++ + N   A KA+ 
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 92  KSNKKPYKGK 101
             +     G+
Sbjct: 66  HMDGGQIDGQ 75

>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 = 46.0 bits (110), Expect = 6e-07
 Identities = 13/59 (22%), Positives = 22/59 (37%), Gaps = 2/59 (3%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD--GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           +T++   E F  YG I    +          KG  ++ + N   A KA+   +     G
Sbjct: 16  VTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDG 74

>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 = 62.8 bits (153), Expect = 3e-12
 Identities = 16/69 (23%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
            L +  +P  + E + ++ F +YG I   +++ + +  + +G GF+ + +  SA +AI  
Sbjct: 44  NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103

Query: 93  SNKKPYKGK 101
            N      K
Sbjct: 104 LNGFNILNK 112

>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 = 47.0 bits (112), Expect = 1e-06
 Identities = 13/58 (22%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           + E + ++ F +YG I   +++ + +  + +G GF+ + +  SA +AI   N      
Sbjct: 54  VDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN 111

>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 = 63.3 bits (154), Expect = 3e-12
 Identities = 19/101 (18%), Positives = 41/101 (40%), Gaps = 4/101 (3%)

Query: 5   AKKKKVKKEFKKKGKKKIERKKPDKTKR---GRLFIKNLPFKITEEEFKEHFGQYGDIID 61
           +  ++    +++   +  +  +P   +      LF+ ++  +  E+E +E F  YG+I +
Sbjct: 42  SNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKN 101

Query: 62  AQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
             L  +   G  KG   + Y     A+ A    N     G+
Sbjct: 102 IHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQ 142

>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 = 49.1 bits (117), Expect = 3e-07
 Identities = 16/58 (27%), Positives = 23/58 (39%), Gaps = 1/58 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
             E+E +E F  YG+I +  L  +   G  KG   + Y     A+ A    N     G
Sbjct: 84  AQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG 141

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 62.2 bits (151), Expect = 4e-12
 Identities = 20/83 (24%), Positives = 32/83 (38%), Gaps = 4/83 (4%)

Query: 18 GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDA----QLLKNADGKLK 73
          G      +   K  +  + ++ LPF  T EE    FGQ+  I         +   DG+  
Sbjct: 9  GTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPT 68

Query: 74 GCGFINYANKISAVKAILKSNKK 96
          G  F+ +A +  A  A+ K    
Sbjct: 69 GDAFVLFACEEYAQNALRKHKDL 91

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 45.3 bits (107), Expect = 3e-06
 Identities = 16/62 (25%), Positives = 24/62 (38%), Gaps = 6/62 (9%)

Query: 97  PYKGKITEEEFKEHFGQYGDIIDA----QLLKNADGKLKGCGFINYANKISAVKAILKSN 152
           P+    T EE    FGQ+  I         +   DG+  G  F+ +A +  A  A+ K  
Sbjct: 32  PFT--ATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRKHK 89

Query: 153 KK 154
             
Sbjct: 90  DL 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 = 61.7 bits (150), Expect = 4e-12
 Identities = 14/74 (18%), Positives = 31/74 (41%), Gaps = 6/74 (8%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           R+ +  LP   + ++ K+H  + GD+  A + +       G G + +  K     A+ K 
Sbjct: 17  RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR------DGTGVVEFVRKEDMTYAVRKL 70

Query: 94  NKKPYKGKITEEEF 107
           +   ++    E  +
Sbjct: 71  DNTKFRSHEGETAY 84

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 45.2 bits (107), Expect = 2e-06
 Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 6/59 (10%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
            + ++ K+H  + GD+  A + +       G G + +  K     A+ K +   ++  E
Sbjct: 27  GSWQDLKDHMREAGDVCYADVYR------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHE 79

>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 = 61.2 bits (149), Expect = 4e-12
 Identities = 12/62 (19%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
          + ++  PF +TE+   E        +  ++++NA G   G  F++++N+    +A+  + 
Sbjct: 13 VKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNR 71

Query: 95 KK 96
          + 
Sbjct: 72 EY 73

>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 = 45.4 bits (108), Expect = 1e-06
 Identities = 11/58 (18%), Positives = 28/58 (48%), Gaps = 3/58 (5%)

Query: 97  PYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
           P+   +TE+   E        +  ++++NA G   G  F++++N+    +A+  + + 
Sbjct: 19  PFN--VTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNREY 73

>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 = 61.7 bits (150), Expect = 4e-12
 Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 3/69 (4%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDII-DAQLLKNAD--GKLKGCGFINYANKISAVKAI 90
          RLFI  +P     EE  E   +  + + D  +  +A    K +G  F+ Y +  +A  A 
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69

Query: 91 LKSNKKPYK 99
           K      +
Sbjct: 70 RKLMPGRIQ 78

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 45.2 bits (107), Expect = 3e-06
 Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 3/59 (5%)

Query: 102 ITEEEFKEHFGQYGDII-DAQLLKNAD--GKLKGCGFINYANKISAVKAILKSNKKPYK 157
              EE  E   +  + + D  +  +A    K +G  F+ Y +  +A  A  K      +
Sbjct: 20  KKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQ 78

>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 = 61.3 bits (149), Expect = 5e-12
 Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 1/79 (1%)

Query: 18 GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGF 77
          G           T    + ++ LP++ TE +    F      +   +    DG++ G   
Sbjct: 1  GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEAD 59

Query: 78 INYANKISAVKAILKSNKK 96
          + +A    AV A+ K    
Sbjct: 60 VEFATHEDAVAAMAKDKAN 78

>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 = 45.1 bits (107), Expect = 2e-06
 Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 3/58 (5%)

Query: 97  PYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
           PY+   TE +    F      +   +    DG++ G   + +A    AV A+ K    
Sbjct: 24  PYR--ATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKAN 78

>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 = 61.5 bits (150), Expect = 5e-12
 Identities = 21/95 (22%), Positives = 39/95 (41%), Gaps = 5/95 (5%)

Query: 8   KKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN 67
           ++V+ E   + +   +R          LF+ ++  +  E+E +E F  YG+I +  L  +
Sbjct: 6   ERVRNEDDDELEPGPQRSVEGWI----LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLD 61

Query: 68  AD-GKLKGCGFINYANKISAVKAILKSNKKPYKGK 101
              G  KG   + Y     A+ A    N     G+
Sbjct: 62  RRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQ 96

>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 = 48.4 bits (116), Expect = 2e-07
 Identities = 16/58 (27%), Positives = 23/58 (39%), Gaps = 1/58 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
             E+E +E F  YG+I +  L  +   G  KG   + Y     A+ A    N     G
Sbjct: 38  AQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG 95

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 61.5 bits (150), Expect = 5e-12
 Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 33  GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
           G +FIKNL   I  +   + F  +G+I+  +++ + +G  KG GF+++  + +A +AI K
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS-KGYGFVHFETQEAAERAIEK 64

Query: 93  SNKKPYKGK 101
            N      +
Sbjct: 65  MNGMLLNDR 73

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 43.0 bits (102), Expect = 1e-05
 Identities = 14/57 (24%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           I  +   + F  +G+I+  +++ + +G  KG GF+++  + +A +AI K N      
Sbjct: 17  IDNKALYDTFSAFGNILSCKVVCDENGS-KGYGFVHFETQEAAERAIEKMNGMLLND 72

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 61.6 bits (150), Expect = 5e-12
 Identities = 24/100 (24%), Positives = 43/100 (43%), Gaps = 12/100 (12%)

Query: 28  DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDI--------IDAQLLKNAD-GKLKGCGFI 78
           D +    +F++ L   +T E   ++F Q G I            L  + + GKLKG   +
Sbjct: 3   DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATV 62

Query: 79  NYANKISAVKAILKSNKKPYKG---KITEEEFKEHFGQYG 115
           ++ +  SA  AI   + K + G   K++    +  F + G
Sbjct: 63  SFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRADFNRGG 102

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 43.5 bits (103), Expect = 1e-05
 Identities = 18/66 (27%), Positives = 29/66 (43%), Gaps = 9/66 (13%)

Query: 102 ITEEEFKEHFGQYGDI--------IDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSN 152
           +T E   ++F Q G I            L  + + GKLKG   +++ +  SA  AI   +
Sbjct: 19  VTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFD 78

Query: 153 KKPYKG 158
            K + G
Sbjct: 79  GKEFSG 84

>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 = 61.3 bits (149), Expect = 6e-12
 Identities = 17/104 (16%), Positives = 41/104 (39%), Gaps = 12/104 (11%)

Query: 18  GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDI--------IDAQLLKNAD 69
           G         + +    ++++ L   +T ++  + F Q G +            +  + +
Sbjct: 1   GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60

Query: 70  -GKLKGCGFINYANKISAVKAILKSNKKPYKG---KITEEEFKE 109
            GK KG   ++Y +  +A  A+   + K ++G   K++    K 
Sbjct: 61  TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP 104

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 44.7 bits (106), Expect = 4e-06
 Identities = 13/66 (19%), Positives = 29/66 (43%), Gaps = 9/66 (13%)

Query: 102 ITEEEFKEHFGQYGDI--------IDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSN 152
           +T ++  + F Q G +            +  + + GK KG   ++Y +  +A  A+   +
Sbjct: 27  VTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFD 86

Query: 153 KKPYKG 158
            K ++G
Sbjct: 87  GKDFQG 92

>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 = 60.2 bits (147), Expect = 6e-12
 Identities = 12/69 (17%), Positives = 31/69 (44%), Gaps = 1/69 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
            LF+ +L   + +E  +  F  +   +   ++ +   G  +G GF+++ ++  A  A+  
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62

Query: 93  SNKKPYKGK 101
              +   G+
Sbjct: 63  MQGQDLNGR 71

>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 = 46.0 bits (110), Expect = 6e-07
 Identities = 8/48 (16%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
           + +E  +  F  +   +   ++ +   G  +G GF+++ ++  A  A+
Sbjct: 13  VDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 61.1 bits (149), Expect = 6e-12
 Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 2/66 (3%)

Query: 27 PDKTKRG-RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKI 84
          P ++  G  LF+  +  + TEE+  + F +YG+I +  L  +   G LKG   + Y    
Sbjct: 17 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 76

Query: 85 SAVKAI 90
           A  A+
Sbjct: 77 EAQAAM 82

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 48.4 bits (116), Expect = 2e-07
 Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
            TEE+  + F +YG+I +  L  +   G LKG   + Y     A  A+
Sbjct: 35  ATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 82

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 60.3 bits (147), Expect = 7e-12
 Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 7/68 (10%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           +LFI NLP + TE+E +  F QYG +++  +       +K  GF++  +K +A  AI   
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDI-------IKNYGFVHIEDKTAAEDAIRNL 62

Query: 94  NKKPYKGK 101
           +     G 
Sbjct: 63  HHYKLHGV 70

>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 = 45.3 bits (108), Expect = 2e-06
 Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 7/58 (12%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
            TE+E +  F QYG +++  +       +K  GF++  +K +A  AI   +     G 
Sbjct: 20  ATEQEIRSLFEQYGKVLECDI-------IKNYGFVHIEDKTAAEDAIRNLHHYKLHGV 70

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 60.8 bits (148), Expect = 7e-12
 Identities = 15/76 (19%), Positives = 30/76 (39%), Gaps = 8/76 (10%)

Query: 27  PDKTKRGR-LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKIS 85
               ++G  L++      +T    +  F  +G+IID  +        + C F+ Y    S
Sbjct: 9   RRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMES 61

Query: 86  AVKAILKSNKKPYKGK 101
           A +A+ + N    +  
Sbjct: 62  ADQAVAELNGTQVESV 77

>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 = 55.0 bits (133), Expect = 6e-10
 Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 5/57 (8%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           +T    +  F  +G+IID  +        + C F+ Y    SA +A+ + N    + 
Sbjct: 25  MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAELNGTQVES 76

>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 = 64.9 bits (157), Expect = 7e-12
 Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 6/79 (7%)

Query: 27  PDKTKRGRLFIKNLPFKITEEEFKEH----FGQYGDIIDAQLLKNADGKLKGCGFINYAN 82
           P+      ++I NL  KI ++E K+     F Q+G I+D  + ++   K++G  F+ +  
Sbjct: 4   PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRS--LKMRGQAFVIFKE 61

Query: 83  KISAVKAILKSNKKPYKGK 101
             SA  A+      P+  K
Sbjct: 62  VSSATNALRSMQGFPFYDK 80

>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 = 47.2 bits (111), Expect = 5e-06
 Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 6/64 (9%)

Query: 101 KITEEEFKEH----FGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY 156
           KI ++E K+     F Q+G I+D  + ++   K++G  F+ +    SA  A+      P+
Sbjct: 20  KIKKDELKKSLYAIFSQFGQILDILVSRS--LKMRGQAFVIFKEVSSATNALRSMQGFPF 77

Query: 157 KGSE 160
               
Sbjct: 78  YDKP 81

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 44.9 bits (105), Expect = 2e-05
 Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 4/55 (7%)

Query: 36  FIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
           F+ NLP +  E      F Q+    + +L+           F+ + N++ A  A 
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR----HDIAFVEFDNEVQAGAAR 261

>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 = 61.8 bits (150), Expect = 7e-12
 Identities = 15/82 (18%), Positives = 28/82 (34%), Gaps = 1/82 (1%)

Query: 15  KKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKG 74
           +              T    + ++ LP+K TE +    F      +   +    DG++ G
Sbjct: 29  QMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTG 87

Query: 75  CGFINYANKISAVKAILKSNKK 96
              + +A    AV A+ K    
Sbjct: 88  EADVEFATHEEAVAAMSKDRAN 109

>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 = 46.0 bits (109), Expect = 2e-06
 Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 3/58 (5%)

Query: 97  PYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
           PYK   TE +    F      +   +    DG++ G   + +A    AV A+ K    
Sbjct: 55  PYK--ATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSKDRAN 109

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 60.9 bits (148), Expect = 8e-12
 Identities = 18/95 (18%), Positives = 35/95 (36%), Gaps = 8/95 (8%)

Query: 24  RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANK 83
           +  P       + +  +PF   E + ++ F     +    LLK+  G+  G G + + + 
Sbjct: 8   KPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSP 66

Query: 84  ISAVKAILKSNKKPYKG------KITEEEFKEHFG 112
               +A LK N+             TE ++    G
Sbjct: 67  QDTFEA-LKRNRMLMIQRYVEVSPATERQWVAAGG 100

>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 = 42.8 bits (101), Expect = 2e-05
 Identities = 10/58 (17%), Positives = 24/58 (41%), Gaps = 3/58 (5%)

Query: 97  PYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK 154
           P+     E + ++ F     +    LLK+  G+  G G + + +     +A+ ++   
Sbjct: 25  PFS--AMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRNRML 79

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 60.3 bits (147), Expect = 8e-12
 Identities = 13/66 (19%), Positives = 26/66 (39%)

Query: 25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKI 84
          +  + T    LFI NL    +  E K    +     D  ++    G  +  G++++ +  
Sbjct: 10 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAE 69

Query: 85 SAVKAI 90
             KA+
Sbjct: 70 DLEKAL 75

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 7/47 (14%), Positives = 18/47 (38%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
            +  E K    +     D  ++    G  +  G++++ +     KA+
Sbjct: 29  KSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL 75

>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 = 60.8 bits (148), Expect = 9e-12
 Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 2/78 (2%)

Query: 24  RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANK 83
            + P      R+++ NLP  I  ++ ++ F +YG I D  L            F+ + + 
Sbjct: 14  IRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN--RRGGPPFAFVEFEDP 71

Query: 84  ISAVKAILKSNKKPYKGK 101
             A  A+   +   Y G 
Sbjct: 72  RDAEDAVYGRDGYDYDGY 89

>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 = 45.0 bits (107), Expect = 3e-06
 Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 2/59 (3%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
           I  ++ ++ F +YG I D  L            F+ + +   A  A+   +   Y G  
Sbjct: 34  IRTKDIEDVFYKYGAIRDIDLKN--RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYR 90

>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 = 60.3 bits (147), Expect = 1e-11
 Identities = 15/76 (19%), Positives = 27/76 (35%), Gaps = 1/76 (1%)

Query: 26  KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKIS 85
             D  +   L++ NL   +TE    + F Q G     +++           F+ +     
Sbjct: 9   MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN-DPYCFVEFYEHRD 67

Query: 86  AVKAILKSNKKPYKGK 101
           A  A+   N +   GK
Sbjct: 68  AAAALAAMNGRKILGK 83

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 46.9 bits (112), Expect = 5e-07
 Identities = 11/60 (18%), Positives = 20/60 (33%), Gaps = 1/60 (1%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
            +TE    + F Q G     +++           F+ +     A  A+   N +   G E
Sbjct: 26  DVTEVLILQLFSQIGPCKSCKMITEHTSN-DPYCFVEFYEHRDAAAALAAMNGRKILGKE 84

>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 = 59.7 bits (145), Expect = 1e-11
 Identities = 15/70 (21%), Positives = 25/70 (35%), Gaps = 6/70 (8%)

Query: 32  RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL 91
              + +KNLP     +E  +    Y       L      + K   F+   N   A  AI 
Sbjct: 5   SSGILVKNLPQDSNCQEVHDLLKDYD------LKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 92  KSNKKPYKGK 101
             ++  ++GK
Sbjct: 59  MFHQYSFRGK 68

>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 = 41.2 bits (97), Expect = 4e-05
 Identities = 10/59 (16%), Positives = 19/59 (32%), Gaps = 6/59 (10%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
              +E  +    Y       L      + K   F+   N   A  AI   ++  ++G +
Sbjct: 17  SNCQEVHDLLKDYD------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKD 69

>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 = 60.4 bits (147), Expect = 1e-11
 Identities = 26/79 (32%), Positives = 44/79 (55%), Gaps = 1/79 (1%)

Query: 24  RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYAN 82
            +K D +    +F+ +L  +IT E+ K  F  +G I DA+++K+   GK KG GF+++ N
Sbjct: 7   GQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFN 66

Query: 83  KISAVKAILKSNKKPYKGK 101
           K  A  AI +   +   G+
Sbjct: 67  KWDAENAIQQMGGQWLGGR 85

>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 = 46.6 bits (111), Expect = 8e-07
 Identities = 22/58 (37%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           IT E+ K  F  +G I DA+++K+   GK KG GF+++ NK  A  AI +   +   G
Sbjct: 27  ITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGG 84

>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 = 59.9 bits (146), Expect = 1e-11
 Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 1/69 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
            L++  L  ++ ++     F  +GDI D Q+  + +  K +G  F+ +     A  AI  
Sbjct: 14  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDN 73

Query: 93  SNKKPYKGK 101
            N+    G+
Sbjct: 74  MNESELFGR 82

>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 = 46.4 bits (111), Expect = 8e-07
 Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
           ++ ++     F  +GDI D Q+  + +  K +G  F+ +     A  AI
Sbjct: 23  EVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 71

>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 = 59.1 bits (144), Expect = 2e-11
 Identities = 17/68 (25%), Positives = 32/68 (47%), Gaps = 7/68 (10%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           ++F+ N+    T +E +  F + G +I+  +       +K   F++   +  A  AI + 
Sbjct: 11  KIFVGNVSAACTSQELRSLFERRGRVIECDV-------VKDYAFVHMEKEADAKAAIAQL 63

Query: 94  NKKPYKGK 101
           N K  KGK
Sbjct: 64  NGKEVKGK 71

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 44.1 bits (105), Expect = 4e-06
 Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 7/57 (12%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            T +E +  F + G +I+  +       +K   F++   +  A  AI + N K  KG
Sbjct: 21  CTSQELRSLFERRGRVIECDV-------VKDYAFVHMEKEADAKAAIAQLNGKEVKG 70

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 58.6 bits (143), Expect = 2e-11
 Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 2/72 (2%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
           ++F+  L    T E+ K +F Q+G + DA L+ +    + +G GF+ + ++   V+ + +
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE-DIVEKVCE 59

Query: 93  SNKKPYKGKITE 104
            +      K+ E
Sbjct: 60  IHFHEINNKMVE 71

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 47.5 bits (114), Expect = 2e-07
 Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
           T E+ K +F Q+G + DA L+ +    + +G GF+ + ++    K  
Sbjct: 12  TVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC 58

>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 = 58.7 bits (143), Expect = 3e-11
 Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
           L++  L  ++ ++     F  +GDI D Q+  + +  K +G  F+ +     A  AI
Sbjct: 9  VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 66

>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 = 46.4 bits (111), Expect = 5e-07
 Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
           ++ ++     F  +GDI D Q+  + +  K +G  F+ +     A  AI
Sbjct: 18  EVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 66

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 60.2 bits (146), Expect = 3e-11
 Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 1/74 (1%)

Query: 18  GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCG 76
           G           T +  L++  L  ++ ++     F  +GDI D Q+  + +  K +G  
Sbjct: 49  GSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA 108

Query: 77  FINYANKISAVKAI 90
           F+ +     A  AI
Sbjct: 109 FVEFELAEDAAAAI 122

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 47.1 bits (112), Expect = 1e-06
 Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
           ++ ++     F  +GDI D Q+  + +  K +G  F+ +     A  AI
Sbjct: 74  EVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 122

>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 = 58.8 bits (143), Expect = 3e-11
 Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 3/68 (4%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
            L + NL +  TEE  +E F +   I   ++ +N +GK KG  FI +A+   A +A+   
Sbjct: 17  TLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSC 73

Query: 94  NKKPYKGK 101
           NK+  +G+
Sbjct: 74  NKREIEGR 81

>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 = 43.0 bits (102), Expect = 1e-05
 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 3/57 (5%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            TEE  +E F +   I   ++ +N +GK KG  FI +A+   A +A+   NK+  +G
Sbjct: 27  ATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEG 80

>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 = 60.2 bits (146), Expect = 4e-11
 Identities = 13/69 (18%), Positives = 30/69 (43%), Gaps = 1/69 (1%)

Query: 23  ERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYA 81
                D      L + NL ++ + +  +  F +YG + D  + ++    + +G  F+ + 
Sbjct: 61  HHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFH 120

Query: 82  NKISAVKAI 90
           +K  A  A+
Sbjct: 121 DKRDAEDAM 129

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 45.6 bits (108), Expect = 4e-06
 Identities = 9/48 (18%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
            + +  +  F +YG + D  + ++    + +G  F+ + +K  A  A+
Sbjct: 82  TSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 129

>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 = 59.1 bits (143), Expect = 4e-11
 Identities = 15/84 (17%), Positives = 33/84 (39%), Gaps = 6/84 (7%)

Query: 24  RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANK 83
              P +    R+ +  LP   + ++ K+H  + GD+  A + +       G G + +  K
Sbjct: 8   YGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR------DGTGVVEFVRK 61

Query: 84  ISAVKAILKSNKKPYKGKITEEEF 107
                A+ K +   ++    E  +
Sbjct: 62  EDMTYAVRKLDNTKFRSHEGETAY 85

>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 = 42.5 bits (100), Expect = 3e-05
 Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 6/59 (10%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
            + ++ K+H  + GD+  A + +       G G + +  K     A+ K +   ++  E
Sbjct: 28  GSWQDLKDHMREAGDVCYADVYR------DGTGVVEFVRKEDMTYAVRKLDNTKFRSHE 80

>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 = 59.3 bits (144), Expect = 4e-11
 Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
           LF+  +  + TEE+  + F +YG+I +  L  +   G LKG   + Y     A  A+
Sbjct: 24 ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81

>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 = 46.6 bits (111), Expect = 1e-06
 Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
            TEE+  + F +YG+I +  L  +   G LKG   + Y     A  A+
Sbjct: 34  ATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 59.9 bits (145), Expect = 5e-11
 Identities = 13/79 (16%), Positives = 35/79 (44%), Gaps = 3/79 (3%)

Query: 26  KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYG--DIIDAQLLKNAD-GKLKGCGFINYAN 82
              + +R  +++ +  +  T+++  +     G  D+++ +  +N   G+ KG   +  A+
Sbjct: 49  SGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVAS 108

Query: 83  KISAVKAILKSNKKPYKGK 101
           + S  K +     K   G+
Sbjct: 109 ENSVHKLLELLPGKVLNGE 127

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 44.5 bits (105), Expect = 9e-06
 Identities = 12/60 (20%), Positives = 26/60 (43%), Gaps = 3/60 (5%)

Query: 102 ITEEEFKEHFGQYG--DIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            T+++  +     G  D+++ +  +N   G+ KG   +  A++ S  K +     K   G
Sbjct: 67  TTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNG 126

>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 = 58.4 bits (142), Expect = 5e-11
 Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 3/75 (4%)

Query: 18 GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA--DGKLKGC 75
          G       +  K+     F+ NLP+ +TEE  KE F     I   +L +      +LKG 
Sbjct: 1  GSSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGF 59

Query: 76 GFINYANKISAVKAI 90
          G+  + +  S + A+
Sbjct: 60 GYAEFEDLDSLLSAL 74

>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 = 39.9 bits (94), Expect = 2e-04
 Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 5/54 (9%)

Query: 97  PYKGKITEEEFKEHFGQYGDIIDAQLLKNA--DGKLKGCGFINYANKISAVKAI 148
           PY   +TEE  KE F     I   +L +      +LKG G+  + +  S + A+
Sbjct: 24  PYD--VTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 74

>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 = 58.0 bits (141), Expect = 5e-11
 Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 7/68 (10%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           +L + N+    T +E +  F +YG +I+  +       +K   F++      AV+AI   
Sbjct: 12  KLHVGNISPTCTNQELRAKFEEYGPVIECDI-------VKDYAFVHMERAEDAVEAIRGL 64

Query: 94  NKKPYKGK 101
           +   ++GK
Sbjct: 65  DNTEFQGK 72

>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 = 43.4 bits (103), Expect = 6e-06
 Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 11/72 (15%)

Query: 92  KSNKKPYKG----KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 147
           K++ K + G      T +E +  F +YG +I+  +       +K   F++      AV+A
Sbjct: 8   KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDI-------VKDYAFVHMERAEDAVEA 60

Query: 148 ILKSNKKPYKGS 159
           I   +   ++G 
Sbjct: 61  IRGLDNTEFQGK 72

>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 = 57.6 bits (140), Expect = 6e-11
 Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 4/61 (6%)

Query: 30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 89
          +    +F+      +TE+E +E F QYGD++D  + K      +   F+ +A+   A   
Sbjct: 3  SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK----PFRAFAFVTFADDQIAQSL 58

Query: 90 I 90
           
Sbjct: 59 C 59

>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 = 46.4 bits (111), Expect = 5e-07
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 4/47 (8%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
           +TE+E +E F QYGD++D  + K      +   F+ +A+   A    
Sbjct: 17  MTEDELREFFSQYGDVMDVFIPK----PFRAFAFVTFADDQIAQSLC 59

>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 = 58.2 bits (141), Expect = 7e-11
 Identities = 21/87 (24%), Positives = 37/87 (42%), Gaps = 8/87 (9%)

Query: 16  KKGKKKIERKKPDKTKRGRLFIKNLPF-KITEEEFKEHFGQYGDIIDAQLLKNADGKLKG 74
           K     +  K   K+   R+FI NL    + + + +  F +YG +    + K       G
Sbjct: 11  KLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK-------G 63

Query: 75  CGFINYANKISAVKAILKSNKKPYKGK 101
             F+ Y+N+  A  A+L  N +   G+
Sbjct: 64  YAFVQYSNERHARAAVLGENGRVLAGQ 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 = 44.7 bits (106), Expect = 4e-06
 Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 7/59 (11%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
            + + + +  F +YG +    + K       G  F+ Y+N+  A  A+L  N +   G 
Sbjct: 39  LVKKSDVETIFSKYGRVAGCSVHK-------GYAFVQYSNERHARAAVLGENGRVLAGQ 90

>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 = 57.2 bits (139), Expect = 8e-11
 Identities = 13/69 (18%), Positives = 28/69 (40%), Gaps = 4/69 (5%)

Query: 22 IERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYA 81
          +           ++F+      +T EE ++ F QYG+++D  + K      +   F+ +A
Sbjct: 1  MRGSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK----PFRAFAFVTFA 56

Query: 82 NKISAVKAI 90
          +   A    
Sbjct: 57 DDKVAQSLC 65

>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 = 46.4 bits (111), Expect = 6e-07
 Identities = 12/47 (25%), Positives = 23/47 (48%), Gaps = 4/47 (8%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
           +T EE ++ F QYG+++D  + K      +   F+ +A+   A    
Sbjct: 23  MTAEELQQFFCQYGEVVDVFIPK----PFRAFAFVTFADDKVAQSLC 65

>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 = 57.6 bits (140), Expect = 8e-11
 Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 3/81 (3%)

Query: 18 GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA--DGKLKGC 75
                R +  K+     F+ NLP+ +TEE  KE F     I   +L +      +LKG 
Sbjct: 5  HHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGF 63

Query: 76 GFINYANKISAVKAILKSNKK 96
          G+  + +  S + A+  + + 
Sbjct: 64 GYAEFEDLDSLLSALSLNEES 84

>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 = 41.1 bits (97), Expect = 6e-05
 Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 5/60 (8%)

Query: 97  PYKGKITEEEFKEHFGQYGDIIDAQLLKNA--DGKLKGCGFINYANKISAVKAILKSNKK 154
           PY   +TEE  KE F     I   +L +      +LKG G+  + +  S + A+  + + 
Sbjct: 28  PYD--VTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEES 84

>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 = 56.8 bits (138), Expect = 1e-10
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 32  RGRLFIKNLPFKITEEEFKEHFGQYG--DIIDAQLLKNAD-GKLKGCGFINYANKISAVK 88
           R  L+I NL +  T+E+  E     G  DI++ +  +N   G+ KG   +   ++ S+ K
Sbjct: 1   RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 60

Query: 89  AILKSNKKPYKGK 101
            +    K+   G+
Sbjct: 61  LMDLLPKRELHGQ 73

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 44.1 bits (105), Expect = 3e-06
 Identities = 14/60 (23%), Positives = 27/60 (45%), Gaps = 3/60 (5%)

Query: 102 ITEEEFKEHFGQYG--DIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            T+E+  E     G  DI++ +  +N   G+ KG   +   ++ S+ K +    K+   G
Sbjct: 13  TTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHG 72

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 56.4 bits (137), Expect = 1e-10
 Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
           ++F+  L     EE+ +E+FG +G++   +L  +    K +G  FI +  +   VK I++
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEE-EPVKKIME 59

Query: 93  SNKKPYKGKITE 104
                      E
Sbjct: 60  KKYHNVGLSKCE 71

>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 = 47.9 bits (115), Expect = 1e-07
 Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 150
             EE+ +E+FG +G++   +L  +    K +G  FI +  +    K + K
Sbjct: 11  TPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

>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 = 60.1 bits (145), Expect = 1e-10
 Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 3/80 (3%)

Query: 25  KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYG--DIIDAQLLKN-ADGKLKGCGFINYA 81
                 KR  L+I NL +  T+E+  E     G  DI++ +  +N A+G+ KG   +   
Sbjct: 61  VYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVG 120

Query: 82  NKISAVKAILKSNKKPYKGK 101
           ++ S+ K +    K+   G+
Sbjct: 121 SEASSKKLMDLLPKRELHGQ 140

>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 = 43.9 bits (103), Expect = 4e-05
 Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 3/60 (5%)

Query: 102 ITEEEFKEHFGQYG--DIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            T+E+  E     G  DI++ +  +N A+G+ KG   +   ++ S+ K +    K+   G
Sbjct: 80  TTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHG 139

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 57.1 bits (138), Expect = 1e-10
 Identities = 9/88 (10%), Positives = 25/88 (28%), Gaps = 9/88 (10%)

Query: 11 KKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADG 70
                +      +          + I+ L   + E +  E   ++G I    ++     
Sbjct: 4  HHHHHMENYDDPHKTPASPV----VHIRGLIDGVVEADLVEALQEFGPISYVVVMPK--- 56

Query: 71 KLKGCGFINYANKISAVKAILKSNKKPY 98
            K    + + + + A  A+  +     
Sbjct: 57 --KRQALVEFEDVLGACNAVNYAADNQI 82

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 41.3 bits (97), Expect = 4e-05
 Identities = 7/56 (12%), Positives = 19/56 (33%), Gaps = 5/56 (8%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY 156
            + E +  E   ++G I    ++       K    + + + + A  A+  +     
Sbjct: 32  GVVEADLVEALQEFGPISYVVVMPK-----KRQALVEFEDVLGACNAVNYAADNQI 82

>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 = 57.3 bits (139), Expect = 1e-10
 Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 5/81 (6%)

Query: 22  IERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINY 80
           I  +  D T    +++  L  K++E    E F Q G +++  + K+   G+ +G GF+ +
Sbjct: 9   ISERNQDAT----VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF 64

Query: 81  ANKISAVKAILKSNKKPYKGK 101
            ++  A  AI   +     GK
Sbjct: 65  LSEEDADYAIKIMDMIKLYGK 85

>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 = 44.6 bits (106), Expect = 4e-06
 Identities = 14/49 (28%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 148
           K++E    E F Q G +++  + K+   G+ +G GF+ + ++  A  AI
Sbjct: 26  KVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74

>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 = 56.7 bits (137), Expect = 2e-10
 Identities = 10/64 (15%), Positives = 24/64 (37%), Gaps = 5/64 (7%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
          + ++ L   + E +  E   ++G I    ++       K    + + N  SA + +  + 
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAA 72

Query: 95 KKPY 98
            P 
Sbjct: 73 DVPV 76

>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 = 42.5 bits (100), Expect = 2e-05
 Identities = 9/56 (16%), Positives = 20/56 (35%), Gaps = 5/56 (8%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY 156
            + E +  E   ++G I    ++       K    + + N  SA + +  +   P 
Sbjct: 26  SVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADVPV 76

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 57.2 bits (138), Expect = 2e-10
 Identities = 14/79 (17%), Positives = 31/79 (39%), Gaps = 7/79 (8%)

Query: 31  KRGRLFIKNLPFKITEEEF---KEHFGQYGDIIDAQLLKNADGKL----KGCGFINYANK 83
           ++  +F+  L  ++ + E     E+FG++G I    +  +             ++ Y   
Sbjct: 14  QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 73

Query: 84  ISAVKAILKSNKKPYKGKI 102
             A++AI   N     G+ 
Sbjct: 74  EDALRAIQCVNNVVVDGRT 92

>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 = 45.2 bits (107), Expect = 2e-06
 Identities = 12/65 (18%), Positives = 24/65 (36%), Gaps = 7/65 (10%)

Query: 101 KITEEEF---KEHFGQYGDIIDAQLLKNADGKL----KGCGFINYANKISAVKAILKSNK 153
           ++ + E     E+FG++G I    +  +             ++ Y     A++AI   N 
Sbjct: 26  RLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNN 85

Query: 154 KPYKG 158
               G
Sbjct: 86  VVVDG 90

>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 = 56.0 bits (136), Expect = 2e-10
 Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
            +F+ +L  +IT       F  +G I DA+++K+   GK KG GF+++ NK  A  AI +
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 93  SNKKPYKGK 101
              +   G+
Sbjct: 68  MGGQWLGGR 76

>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 = 45.2 bits (108), Expect = 1e-06
 Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           IT       F  +G I DA+++K+   GK KG GF+++ NK  A  AI +   +   G
Sbjct: 18  ITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGG 75

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 58.9 bits (142), Expect = 2e-10
 Identities = 14/74 (18%), Positives = 28/74 (37%), Gaps = 1/74 (1%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKS 93
           L   N P ++TEE F E   + G      + + +   +    G + + +K  A++ +   
Sbjct: 126 LHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFL 185

Query: 94  NKKPYKGKITEEEF 107
           N    K       +
Sbjct: 186 NHYQMKNPNGPYPY 199

>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 = 49.7 bits (118), Expect = 4e-07
 Identities = 13/68 (19%), Positives = 26/68 (38%), Gaps = 5/68 (7%)

Query: 35  LFIKNL-PFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           L +  L   K+  +     F  YG++   + +K+      G   +  A+  +  +AI   
Sbjct: 7   LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAITHL 62

Query: 94  NKKPYKGK 101
           N     G+
Sbjct: 63  NNNFMFGQ 70

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 48.2 bits (114), Expect = 1e-06
 Identities = 12/68 (17%), Positives = 25/68 (36%), Gaps = 3/68 (4%)

Query: 102 ITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
           +TEE F E   + G      + + +   +    G + + +K  A++ +   N    K   
Sbjct: 135 VTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNP- 193

Query: 161 NGLISPFH 168
                P+ 
Sbjct: 194 -NGPYPYT 200

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 56.5 bits (136), Expect = 3e-10
 Identities = 13/84 (15%), Positives = 25/84 (29%), Gaps = 5/84 (5%)

Query: 15 KKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKG 74
                 +   +        + I+ LP  +TE E       +G + +  +LK      K 
Sbjct: 14 LVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KN 68

Query: 75 CGFINYANKISAVKAILKSNKKPY 98
            FI    + +A   +        
Sbjct: 69 QAFIEMNTEEAANTMVNYYTSVTP 92

>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 = 41.4 bits (97), Expect = 6e-05
 Identities = 10/55 (18%), Positives = 18/55 (32%), Gaps = 5/55 (9%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY 156
           +TE E       +G + +  +LK      K   FI    + +A   +        
Sbjct: 43  VTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTP 92

>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 = 55.6 bits (135), Expect = 4e-10
 Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 2/69 (2%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
            +++ NL +  T E+ KE F Q+G + + +L+ + +  K KG GF+    + S  +AI K
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE-SVSEAIAK 61

Query: 93  SNKKPYKGK 101
            +   + G+
Sbjct: 62  LDNTDFMGR 70

>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 = 42.5 bits (101), Expect = 1e-05
 Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 4/63 (6%)

Query: 97  PYKGKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKP 155
            Y    T E+ KE F Q+G + + +L+ + +  K KG GF+    + S  +AI K +   
Sbjct: 10  VYS--ATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE-SVSEAIAKLDNTD 66

Query: 156 YKG 158
           + G
Sbjct: 67  FMG 69

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 55.8 bits (135), Expect = 4e-10
 Identities = 13/68 (19%), Positives = 27/68 (39%), Gaps = 4/68 (5%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           ++++ NL     + E +  F  YG +    + +N      G  F+ + +   A  A+   
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP----PGFAFVEFEDPRDAEDAVRGL 57

Query: 94  NKKPYKGK 101
           + K   G 
Sbjct: 58  DGKVICGS 65

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 41.9 bits (99), Expect = 3e-05
 Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 4/59 (6%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
             + E +  F  YG +    + +N      G  F+ + +   A  A+   + K   GS 
Sbjct: 12  AGKGELERAFSYYGPLRTVWIARNP----PGFAFVEFEDPRDAEDAVRGLDGKVICGSR 66

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 55.2 bits (133), Expect = 6e-10
 Identities = 13/65 (20%), Positives = 23/65 (35%), Gaps = 5/65 (7%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
          + I+ LP  +TE E       +G + +  +LK      K   FI    + +A   +    
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYT 73

Query: 95 KKPYK 99
               
Sbjct: 74 SVTPV 78

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 40.6 bits (95), Expect = 9e-05
 Identities = 10/56 (17%), Positives = 18/56 (32%), Gaps = 5/56 (8%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK 157
           +TE E       +G + +  +LK      K   FI    + +A   +         
Sbjct: 28  VTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPV 78

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 55.0 bits (133), Expect = 6e-10
 Identities = 9/71 (12%), Positives = 27/71 (38%), Gaps = 3/71 (4%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYG--DIIDAQLLKNAD-GKLKGCGFINYANKISAVKAIL 91
           + ++N+      +        Y    + + +L+K+    + +G  F+  ++ + A + + 
Sbjct: 12  IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71

Query: 92  KSNKKPYKGKI 102
                    KI
Sbjct: 72  ILQSLHPPLKI 82

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 7/63 (11%), Positives = 22/63 (34%), Gaps = 3/63 (4%)

Query: 103 TEEEFKEHFGQYG--DIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
             +        Y    + + +L+K+    + +G  F+  ++ + A + +           
Sbjct: 22  VVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLK 81

Query: 160 ENG 162
            +G
Sbjct: 82  IDG 84

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 54.4 bits (131), Expect = 1e-09
 Identities = 14/69 (20%), Positives = 29/69 (42%), Gaps = 7/69 (10%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI--LK 92
           L I+ LP ++TE E       +G + +  +LK      K   F+  A + +A+  +    
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYS 72

Query: 93  SNKKPYKGK 101
           +     + +
Sbjct: 73  AVTPHLRNQ 81

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 39.8 bits (93), Expect = 2e-04
 Identities = 10/56 (17%), Positives = 22/56 (39%), Gaps = 5/56 (8%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY 156
           ++TE E       +G + +  +LK      K   F+  A + +A+  +   +    
Sbjct: 26  EVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTP 76

>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 = 53.9 bits (130), Expect = 1e-09
 Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 8/69 (11%)

Query: 34  RLFIKNLPF-KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
           RLFI NLP   +++E+    F  YG I+   +           GFI + N  S   AI  
Sbjct: 24  RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEX 76

Query: 93  SNKKPYKGK 101
            +++   GK
Sbjct: 77  ESQEMNFGK 85

>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 = 42.3 bits (100), Expect = 2e-05
 Identities = 13/59 (22%), Positives = 23/59 (38%), Gaps = 7/59 (11%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
            +++E+    F  YG I+   +           GFI + N  S   AI   +++   G 
Sbjct: 34  NVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEXESQEMNFGK 85

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 54.4 bits (131), Expect = 2e-09
 Identities = 14/78 (17%), Positives = 31/78 (39%), Gaps = 2/78 (2%)

Query: 24  RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANK 83
                  KR R+ +KNLP   + ++ K+   +         +        G G + + ++
Sbjct: 20  HMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVN--TRDFDGTGALEFPSE 77

Query: 84  ISAVKAILKSNKKPYKGK 101
              V+A+ + N   ++G 
Sbjct: 78  EILVEALERLNNIEFRGS 95

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 54.2 bits (131), Expect = 2e-09
 Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 1/77 (1%)

Query: 25  KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQ-YGDIIDAQLLKNADGKLKGCGFINYANK 83
                     LF+ +L   + +    E F + Y      +++ +  G  KG GF+ + ++
Sbjct: 2   SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDE 61

Query: 84  ISAVKAILKSNKKPYKG 100
           +   +A+ +       G
Sbjct: 62  LEQKRALTECQGAVGLG 78

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 40.7 bits (96), Expect = 8e-05
 Identities = 11/59 (18%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 102 ITEEEFKEHFGQ-YGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
           + +    E F + Y      +++ +  G  KG GF+ + +++   +A+ +       GS
Sbjct: 21  VDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGS 79

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 56.4 bits (136), Expect = 2e-09
 Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 5/68 (7%)

Query: 35  LFIKNL-PFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           L + NL P ++T +     FG YGD+   ++L N     K    +  A+   A  A+   
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHL 61

Query: 94  NKKPYKGK 101
           N     GK
Sbjct: 62  NGHKLHGK 69

>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 = 54.9 bits (132), Expect = 6e-09
 Identities = 18/104 (17%), Positives = 37/104 (35%), Gaps = 11/104 (10%)

Query: 5   AKKKKVKKEFKKKGKKKIERKKPDKTKRG--------RLFIKNLPFKITEEEFKEHFGQY 56
            + ++ +   K  G   + R K   +K           L + N+P  ++EE+ K  F   
Sbjct: 85  REGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSN 144

Query: 57  GDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 100
           G ++        D   +    I   +   AV+A++  +      
Sbjct: 145 GGVVKGFKFFQKD---RKMALIQMGSVEEAVQALIDLHNHDLGE 185

>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 = 45.7 bits (108), Expect = 7e-06
 Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 4/58 (6%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           ++T +     FG YGD+   ++L N     K    +  A+   A  A+   N     G
Sbjct: 15  RVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHG 68

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 54.2 bits (130), Expect = 2e-09
 Identities = 9/77 (11%), Positives = 27/77 (35%), Gaps = 3/77 (3%)

Query: 23 ERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQY---GDIIDAQLLKNADGKLKGCGFIN 79
              P+  +   + ++ LP+  + E+ +           +     +   +G+  G  F+ 
Sbjct: 8  MMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVE 67

Query: 80 YANKISAVKAILKSNKK 96
            ++     A+ K  + 
Sbjct: 68 LESEDDVKLALKKDRES 84

>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 = 38.7 bits (90), Expect = 5e-04
 Identities = 7/61 (11%), Positives = 20/61 (32%), Gaps = 5/61 (8%)

Query: 97  PYKGKITEEEFKEHFGQY---GDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK 153
           P+    + E+ +           +     +   +G+  G  F+   ++     A+ K  +
Sbjct: 26  PWS--CSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALKKDRE 83

Query: 154 K 154
            
Sbjct: 84  S 84

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 53.0 bits (128), Expect = 3e-09
 Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 8/69 (11%)

Query: 34  RLFIKNLPFK-ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
           RLFI NLP K +++E+    F  YG I+   +           GFI + N  S   AI  
Sbjct: 12  RLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIEC 64

Query: 93  SNKKPYKGK 101
            +++   GK
Sbjct: 65  ESQEMNFGK 73

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 41.8 bits (99), Expect = 3e-05
 Identities = 13/59 (22%), Positives = 23/59 (38%), Gaps = 7/59 (11%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
            +++E+    F  YG I+   +           GFI + N  S   AI   +++   G 
Sbjct: 22  NVSKEDLFRIFSPYGHIMQINI-------KNAFGFIQFDNPQSVRDAIECESQEMNFGK 73

>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 = 55.8 bits (134), Expect = 4e-09
 Identities = 20/85 (23%), Positives = 31/85 (36%), Gaps = 5/85 (5%)

Query: 27  PDKTKRGRLFIKNL-PFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKIS 85
                   L + NL P ++T +     FG YGD+   ++L N     K    +  A+   
Sbjct: 29  LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQ 84

Query: 86  AVKAILKSNKKPYKGKITEEEFKEH 110
           A  A+   N     GK       +H
Sbjct: 85  AQLAMSHLNGHKLHGKPIRITLSKH 109

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 55.4 bits (133), Expect = 6e-09
 Identities = 18/103 (17%), Positives = 38/103 (36%), Gaps = 11/103 (10%)

Query: 6   KKKKVKKEFKKKGKKKIERKKPDKTKRGR--------LFIKNLPFKITEEEFKEHFGQYG 57
           + ++ +   K  G   + R K   +K  +        L + N+P  ++EE+ K  F   G
Sbjct: 117 EGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNG 176

Query: 58  DIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 100
            ++        D   +    I   +   AV+A++  +      
Sbjct: 177 GVVKGFKFFQKD---RKMALIQMGSVEEAVQALIDLHNHDLGE 216

>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 = 44.2 bits (104), Expect = 3e-05
 Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 4/59 (6%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
           ++T +     FG YGD+   ++L N     K    +  A+   A  A+   N     G 
Sbjct: 46  RVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGK 100

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 43.1 bits (101), Expect = 8e-05
 Identities = 10/58 (17%), Positives = 22/58 (37%), Gaps = 3/58 (5%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
           ++EE+ K  F   G ++        D   +    I   +   AV+A++  +      +
Sbjct: 163 VSEEDLKVLFSSNGGVVKGFKFFQKD---RKMALIQMGSVEEAVQALIDLHNHDLGEN 217

>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 = 53.0 bits (128), Expect = 4e-09
 Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 33  GRLFIKNLPFKITEEEFKEHFGQYGDIID-AQLLKNAD-GKLKGCGFINYANKISAVKAI 90
             +FI NL  +I E+   + F  +G I+   +++++ D G  KG  FIN+A+  ++  AI
Sbjct: 6   SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65

Query: 91  LKSNKKPYKGK 101
              N +    +
Sbjct: 66  EAMNGQYLCNR 76

>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 = 55.2 bits (132), Expect = 5e-09
 Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 1/76 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
            ++IK  P   T ++ KE     G +++ Q+ +      KG  F+ + +  SA K +   
Sbjct: 111 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETP 170

Query: 94  NKKPYKGKITEEEFKE 109
            +K YK       FK+
Sbjct: 171 GQK-YKETDLLILFKD 185

>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 = 47.5 bits (112), Expect = 2e-06
 Identities = 14/58 (24%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
           T ++ KE     G +++ Q+ +      KG  F+ + +  SA K +    +K YK ++
Sbjct: 122 TLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQK-YKETD 178

>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 = 53.1 bits (127), Expect = 9e-09
 Identities = 9/80 (11%), Positives = 27/80 (33%), Gaps = 3/80 (3%)

Query: 20  KKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQY---GDIIDAQLLKNADGKLKGCG 76
           +      P+  +   + ++ LP+  + E+ +                 +   +G+  G  
Sbjct: 32  RGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEA 91

Query: 77  FINYANKISAVKAILKSNKK 96
           F+   ++     A+ K  + 
Sbjct: 92  FVELGSEDDVKMALKKDRES 111

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 51.6 bits (124), Expect = 9e-09
 Identities = 12/69 (17%), Positives = 27/69 (39%), Gaps = 7/69 (10%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILK 92
            +F+   P  +   +  E+F  +G +    + K+     KG    +   +   A +A+L 
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD-----KGVFAIVEMGDV-GAREAVLS 63

Query: 93  SNKKPYKGK 101
            ++    G 
Sbjct: 64  QSQHSLGGH 72

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 40.0 bits (94), Expect = 1e-04
 Identities = 10/58 (17%), Positives = 23/58 (39%), Gaps = 7/58 (12%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILKSNKKPYKG 158
           +   +  E+F  +G +    + K+     KG    +   +   A +A+L  ++    G
Sbjct: 20  VDSAQLSEYFLAFGPVASVVMDKD-----KGVFAIVEMGDV-GAREAVLSQSQHSLGG 71

>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 = 51.5 bits (124), Expect = 1e-08
 Identities = 20/83 (24%), Positives = 34/83 (40%), Gaps = 6/83 (7%)

Query: 20  KKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFI 78
                 +   +K   LF+K L    TEE  KE F      + A+++ + + G  KG GF+
Sbjct: 5   SSGPNARSQPSKT--LFVKGLSEDTTEETLKESFDG---SVRARIVTDRETGSSKGFGFV 59

Query: 79  NYANKISAVKAILKSNKKPYKGK 101
           ++ ++  A  A          G 
Sbjct: 60  DFNSEEDAKAAKEAMEDGEIDGN 82

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 51.8 bits (124), Expect = 1e-08
 Identities = 15/74 (20%), Positives = 25/74 (33%), Gaps = 3/74 (4%)

Query: 26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQY---GDIIDAQLLKNADGKLKGCGFINYAN 82
          + +      +  + LP+  T E+    F              L N DGK +G   I   +
Sbjct: 5  EEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMES 64

Query: 83 KISAVKAILKSNKK 96
          +    KA+ K    
Sbjct: 65 EQDVQKALEKHRMY 78

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 38.3 bits (89), Expect = 7e-04
 Identities = 14/61 (22%), Positives = 20/61 (32%), Gaps = 5/61 (8%)

Query: 97  PYKGKITEEEFKEHFGQY---GDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK 153
           P+    T E+    F              L N DGK +G   I   ++    KA+ K   
Sbjct: 20  PWS--CTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALEKHRM 77

Query: 154 K 154
            
Sbjct: 78  Y 78

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 54.4 bits (130), Expect = 1e-08
 Identities = 21/109 (19%), Positives = 37/109 (33%), Gaps = 6/109 (5%)

Query: 52  HFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI-LKSNKKPYKGKITEEEFKEH 110
              +  D    +   +    + G G     NK   V  I    N K  K    E   +  
Sbjct: 104 LRTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFV 163

Query: 111 FGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
           F + GDI   + +++     K CGF+ +  + +A  A    + +     
Sbjct: 164 FSRLGDIDRIRYVES-----KNCGFVKFKYQANAEFAKEAMSNQTLLLP 207

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 50.9 bits (121), Expect = 2e-07
 Identities = 14/88 (15%), Positives = 31/88 (35%), Gaps = 14/88 (15%)

Query: 35  LFIKNLPFKIT---------EEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKIS 85
           L++  +   +          E   +  F + GDI   + +++     K CGF+ +  + +
Sbjct: 137 LYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES-----KNCGFVKFKYQAN 191

Query: 86  AVKAILKSNKKPYKGKITEEEFKEHFGQ 113
           A  A    + +       +E      G 
Sbjct: 192 AEFAKEAMSNQTLLLPSDKEWDDRREGT 219

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 51.1 bits (123), Expect = 2e-08
 Identities = 13/58 (22%), Positives = 26/58 (44%), Gaps = 2/58 (3%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
            ++ NLPF   + +    F     I   +L+++ D  K KG  ++ +    S  +A+
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 73

>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 = 50.8 bits (122), Expect = 2e-08
 Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 2/76 (2%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYG-DIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
           L++ +L   + E      F   G  ++  ++++N   G   G  F+ +A+  +A K + K
Sbjct: 12  LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71

Query: 93  SNKKPYKGKITEEEFK 108
            N KP  G    + FK
Sbjct: 72  INGKPLPGATPAKRFK 87

>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 = 40.0 bits (94), Expect = 1e-04
 Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 2/61 (3%)

Query: 102 ITEEEFKEHFGQYG-DIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
           + E      F   G  ++  ++++N   G   G  F+ +A+  +A K + K N KP  G+
Sbjct: 21  MDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGA 80

Query: 160 E 160
            
Sbjct: 81  T 81

>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 = 50.7 bits (121), Expect = 3e-08
 Identities = 9/58 (15%), Positives = 18/58 (31%), Gaps = 7/58 (12%)

Query: 35 LFIKN--LPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
          L + N  L   ++  +      + G +    +  N     K   F  Y     + +A 
Sbjct: 28 LVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAY 80

>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 = 45.7 bits (108), Expect = 2e-06
 Identities = 6/47 (12%), Positives = 14/47 (29%), Gaps = 5/47 (10%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 148
           ++  +      + G +    +  N     K   F  Y     + +A 
Sbjct: 39  VSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAY 80

>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 = 54.1 bits (129), Expect = 4e-08
 Identities = 23/114 (20%), Positives = 50/114 (43%), Gaps = 5/114 (4%)

Query: 1   MEKLAKKKKVKKEFKKKGKKKIERKKPDKTKRGR----LFIKNLPFKITEEEFKEHFGQY 56
           ME+  ++K  +++ + + + K+     D   +G     LF+  + +  TE + +  F  Y
Sbjct: 67  MERKRREKIERRQQEVETELKMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVY 126

Query: 57  GDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGKITEEEFKE 109
           G I    ++ +   GK +G  FI Y ++     A   ++ K   G+    + + 
Sbjct: 127 GPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER 180

>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 = 51.0 bits (122), Expect = 5e-08
 Identities = 13/67 (19%), Positives = 29/67 (43%), Gaps = 4/67 (5%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           ++++ NL     + E +  FG YG +    + +N      G  F+ + +   A  A+ + 
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP----PGFAFVEFEDPRDAADAVREL 130

Query: 94  NKKPYKG 100
           + +   G
Sbjct: 131 DGRTLCG 137

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 50.4 bits (120), Expect = 5e-08
 Identities = 15/72 (20%), Positives = 33/72 (45%), Gaps = 6/72 (8%)

Query: 25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLK---NADGKLKGCGFINYA 81
               +++  +F+  LP  I E+E    F ++G ++     K    +    KG  F+ + 
Sbjct: 3  SGSSGSRK--VFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60

Query: 82 NKISAVKAILKS 93
           + S V+A++ +
Sbjct: 61 EESS-VQALIDA 71

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 41.1 bits (96), Expect = 7e-05
 Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 4/53 (7%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLK---NADGKLKGCGFINYANKISAVKAILKS 151
           I E+E    F ++G ++     K    +    KG  F+ +  + S V+A++ +
Sbjct: 20  IDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESS-VQALIDA 71

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 49.0 bits (117), Expect = 1e-07
 Identities = 15/72 (20%), Positives = 28/72 (38%), Gaps = 1/72 (1%)

Query: 33  GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAIL 91
           G   I +    + ++     F + G +++ +   + A GK KG  F+   +   A K I 
Sbjct: 13  GAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72

Query: 92  KSNKKPYKGKIT 103
             + K    K  
Sbjct: 73  SFHGKRLDLKHR 84

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 47.0 bits (112), Expect = 5e-07
 Identities = 14/75 (18%), Positives = 30/75 (40%), Gaps = 1/75 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYKGSE 160
           + ++     F + G +++ +   + A GK KG  F+   +   A K I   + K      
Sbjct: 24  VLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH 83

Query: 161 NGLISPFHDIPLYSN 175
              +    D+  Y++
Sbjct: 84  RLFLYTMKDVERYNS 98

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 48.3 bits (115), Expect = 1e-07
 Identities = 9/68 (13%), Positives = 23/68 (33%), Gaps = 4/68 (5%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
            +++ NLP      + K    + G +      +      +   F++Y +  +A +A+   
Sbjct: 21  DVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGP----RRRAFLHYPDSAAAQQAVSCL 76

Query: 94  NKKPYKGK 101
                   
Sbjct: 77  QGLRLGTD 84

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 45.8 bits (109), Expect = 8e-07
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 9/76 (11%)

Query: 35  LFIKNLPFKITEEEF-------KEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAV 87
           + + N+P ++  +          + F ++G I +    +  DGK KG  F+ YA+   AV
Sbjct: 4   IVVDNVP-QVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAV 61

Query: 88  KAILKSNKKPYKGKIT 103
            A+  ++      + T
Sbjct: 62  DAVKNADGYKLDKQHT 77

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 99  KGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP 155
           + +  +    + F ++G I +    +  DGK KG  F+ YA+   AV A+  ++   
Sbjct: 16  RLEKLKNVIHKIFSKFGKITNDFYPEE-DGKTKGYIFLEYASPAHAVDAVKNADGYK 71

>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 = 47.4 bits (112), Expect = 1e-06
 Identities = 12/64 (18%), Positives = 29/64 (45%), Gaps = 3/64 (4%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           R+ ++NL + +T +   + F ++G ++        +        + YA+ +SA  A L  
Sbjct: 48  RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ---FQALLQYADPVSAQHAKLSL 104

Query: 94  NKKP 97
           + + 
Sbjct: 105 DGQN 108

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 45.9 bits (109), Expect = 1e-06
 Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 9/77 (11%)

Query: 34  RLFIKNLPFKITEEEF-------KEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA 86
            + + N+P ++  +          + F ++G I +       DGK KG  F+ YA+   A
Sbjct: 17  VIVVDNVP-QVGPDRLEKLKNVIHKIFSKFGKITND-FYPEEDGKTKGYIFLEYASPAHA 74

Query: 87  VKAILKSNKKPYKGKIT 103
           V A+  ++      + T
Sbjct: 75  VDAVKNADGYKLDKQHT 91

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 41.6 bits (98), Expect = 5e-05
 Identities = 16/72 (22%), Positives = 30/72 (41%), Gaps = 1/72 (1%)

Query: 99  KGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           + +  +    + F ++G I +       DGK KG  F+ YA+   AV A+  ++      
Sbjct: 30  RLEKLKNVIHKIFSKFGKITND-FYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDK 88

Query: 159 SENGLISPFHDI 170
                ++ F D 
Sbjct: 89  QHTFRVNLFTDF 100

>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 = 44.7 bits (106), Expect = 2e-06
 Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 7/70 (10%)

Query: 27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN------ADGKLKGCGFINY 80
          P  + R RL++ N+PF ITEE   + F     +                 + K   F+ +
Sbjct: 2  PLGSAR-RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEF 60

Query: 81 ANKISAVKAI 90
           +     +A+
Sbjct: 61 RSVDETTQAM 70

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 45.0 bits (106), Expect = 5e-06
 Identities = 12/64 (18%), Positives = 29/64 (45%), Gaps = 3/64 (4%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
          R+ ++NL + +T +   + F ++G ++        +        + YA+ +SA  A L  
Sbjct: 30 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ---FQALLQYADPVSAQHAKLSL 86

Query: 94 NKKP 97
          + + 
Sbjct: 87 DGQN 90

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 124

 Score = 42.0 bits (98), Expect = 4e-05
 Identities = 13/83 (15%), Positives = 25/83 (30%), Gaps = 4/83 (4%)

Query: 15 KKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKG 74
          K+  +           K   L I+N  + IT +         G +    + K    +   
Sbjct: 8  KRITRPGNTDDPSGGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK----RNGI 63

Query: 75 CGFINYANKISAVKAILKSNKKP 97
             + + + + A KA    N   
Sbjct: 64 QAMVEFESVLCAQKAKAALNGAD 86

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 12/71 (16%), Positives = 33/71 (46%), Gaps = 6/71 (8%)

Query: 35  LFIKNLPFKITEEEFKEH----FGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAI 90
           + + N+ ++++ +E ++     F ++G +   +L  + D +LK    +   N   A+ A+
Sbjct: 12  VQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLK--AVVQMENLQDAIGAV 69

Query: 91  LKSNKKPYKGK 101
              ++     K
Sbjct: 70  NSLHRYKIGSK 80

>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 = 39.5 bits (92), Expect = 3e-04
 Identities = 14/80 (17%), Positives = 31/80 (38%), Gaps = 10/80 (12%)

Query: 19 KKKIERKKPDKTKRGRLFIKNLPF-KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGF 77
          +K  ++++  +     + + NLP    ++    +    YG I +  L++      K   F
Sbjct: 16 QKFDQKQELGRV----IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAF 66

Query: 78 INYANKISAVKAILKSNKKP 97
          I    +  A+  +    KK 
Sbjct: 67 IEMETREDAMAMVDHCLKKA 86

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster} Length = 89

 Score = 38.5 bits (89), Expect = 4e-04
 Identities = 15/73 (20%), Positives = 24/73 (32%), Gaps = 5/73 (6%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
           L +KNL  +I     +    Q+G ++      N     +G     Y  +  A KA +  N
Sbjct: 10  LLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLN-----QGIALCKYTTREEANKAQMALN 64

Query: 95  KKPYKGKITEEEF 107
                      E 
Sbjct: 65  NCVLANTTIFAES 77

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	451
1e9g_A	286	Ppase, inorganic pyrophosphatase; pyrophosphate ph	100.0
3q46_A	178	TT-ippase; inorganic pyrophosphatase, hydrolase; H	100.0
2prd_A	174	Pyrophosphate phosphohydrolase; 2.00A {Thermus the	100.0
3fq3_A	197	Inorganic pyrophosphatase:bacterial/archaeal INOR	100.0
3gvf_A	196	Inorganic pyrophosphatase; structural genomics, hy	100.0
2au7_A	175	Inorganic pyrophosphatase; hydrolase, mutant; 1.05	100.0
3ld3_A	199	Inorganic pyrophosphatase; structural genomics, se	100.0
2bqx_A	173	Inorganic pyrophosphatase; hydrolase; 1.90A {Helic	100.0
3d53_A	173	Inorganic pyrophosphatase; seattle structural G ce	100.0
1sxv_A	172	Inorganic pyrophosphatase; structural genomics, pp	100.0
3tr4_A	178	Inorganic pyrophosphatase; central intermediary me	100.0
1qez_A	173	Ppase, S-ppase, protein (inorganic pyrophosphatase	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.92
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.92
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.92
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.91
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.91
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.9
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.9
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.9
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.87
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.86
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.86
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.85
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.84
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.84
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.84
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.83
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.82
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.82
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.8
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.79
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.65
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.62
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.59
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.57
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.57
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.56
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.56
2div_A	99	TRNA selenocysteine associated protein; structural	99.56
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.55
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.55
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.55
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.55
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.55
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.55
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.55
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.55
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.55
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.55
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.54
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.54
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.54
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.54
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.54
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.54
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.53
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.53
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.53
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.53
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.53
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.53
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.53
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.53
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.53
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.52
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.52
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.52
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.52
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.52
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.52
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.51
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.51
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.51
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.51
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.51
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.51
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.5
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.5
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.5
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.5
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.5
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.5
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.5
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.5
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.5
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.5
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.5
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.49
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.49
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.49
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.49
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.48
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.48
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.48
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.48
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.48
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.48
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.48
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.48
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.48
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.47
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.47
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.47
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.47
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.47
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.47
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.47
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.47
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.47
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.46
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.46
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.46
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.46
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.46
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.45
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.45
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.45
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.44
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.44
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.44
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.44
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.44
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.43
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.43
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.43
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.43
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.43
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.42
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.42
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.42
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.42
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.41
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.4
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.4
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.4
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.4
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.39
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.39
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.39
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.39
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.39
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.38
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.38
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.38
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.37
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.37
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.37
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.36
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.36
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.05
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.36
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.36
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.36
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.35
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.35
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.34
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.34
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.34
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.34
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.34
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.34
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.33
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.33
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.33
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.33
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.33
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.32
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.32
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.32
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.32
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.32
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.32
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.31
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.31
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.31
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.3
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.3
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.3
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.3
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.29
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.29
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.28
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.28
1e9g_A	286	Ppase, inorganic pyrophosphatase; pyrophosphate ph	99.28
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.27
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.27
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.27
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.27
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.26
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.26
1x5p_A	97	Negative elongation factor E; structure genomics,	99.25
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.25
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.25
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.25
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.25
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.24
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.23
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.22
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.2
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.2
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.17
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.16
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.16
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.16
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.14
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.11
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.1
3q46_A	178	TT-ippase; inorganic pyrophosphatase, hydrolase; H	99.08
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.07
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.05
2prd_A	174	Pyrophosphate phosphohydrolase; 2.00A {Thermus the	99.04
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.01
3fq3_A	197	Inorganic pyrophosphatase:bacterial/archaeal INOR	99.0
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.0
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.0
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	98.99
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	98.98
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	98.97
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	98.97
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	98.94
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	98.94
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	98.92
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.91
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.91
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	98.88
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	98.88
3ld3_A	199	Inorganic pyrophosphatase; structural genomics, se	98.87
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	98.87
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	98.86
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	98.86
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	98.86
3gvf_A	196	Inorganic pyrophosphatase; structural genomics, hy	98.85
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	98.85
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	98.84
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	98.83
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	98.83
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.83
2bqx_A	173	Inorganic pyrophosphatase; hydrolase; 1.90A {Helic	98.82
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	98.82
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.81
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	98.81
2div_A	99	TRNA selenocysteine associated protein; structural	98.81
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	98.8
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	98.8
1x5o_A	114	RNA binding motif, single-stranded interacting pro	98.8
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	98.79
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	98.79
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	98.79
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	98.78
3d53_A	173	Inorganic pyrophosphatase; seattle structural G ce	98.78
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	98.78
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.77
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	98.77
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	98.77
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	98.77
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	98.76
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.76
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	98.75
2au7_A	175	Inorganic pyrophosphatase; hydrolase, mutant; 1.05	98.75
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	98.75
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	98.75
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	98.75
1x4e_A	85	RNA binding motif, single-stranded interacting pro	98.74
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	98.74
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	98.74
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	98.74
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	98.74
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	98.73
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	98.73
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	98.73
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	98.73
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	98.73
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	98.73
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	98.73
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	98.73
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	98.73
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	98.73
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	98.73
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	98.73
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	98.72
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	98.72
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.72
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	98.71
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	98.71
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	98.71
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	98.7
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	98.7
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	98.7
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	98.69
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	98.68
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	98.68
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	98.68
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	98.68
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	98.68
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	98.67
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	98.67
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	98.67
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	98.67
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	98.67
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	98.67
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	98.67
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	98.67
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	98.66
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	98.66
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	98.66
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	98.65
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	98.65
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	98.65
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	98.64
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	98.64
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	98.64
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	98.64
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	98.64
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	98.64
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	98.63
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	98.62
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	98.62
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	98.62
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.62
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	98.61
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	98.61
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.6
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	98.6
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	98.6
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	98.6
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	98.59
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	98.59
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	98.59
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	98.58
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	98.58
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.58
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	98.57
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	98.57
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	98.56
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.54
2dis_A	109	Unnamed protein product; structural genomics, RRM	98.54
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	98.53
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	98.53
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.51
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	98.5
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	98.5
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	98.5
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.49
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	98.49
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	98.48
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	98.48
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	98.47
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	98.47
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	97.85
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	98.46
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	98.46
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	98.46
3tr4_A	178	Inorganic pyrophosphatase; central intermediary me	98.46
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	98.46
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	98.45
1x5p_A	97	Negative elongation factor E; structure genomics,	98.45
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	98.45
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	98.44
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	98.44
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.44
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.43
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	98.43
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	98.42
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	98.42
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	98.42
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	98.42
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	98.41
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	98.41
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	98.4
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	98.4
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.4
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	98.4
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	98.4
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	98.4
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	98.39
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	98.39
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	98.36
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	98.35
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	98.34
1qez_A	173	Ppase, S-ppase, protein (inorganic pyrophosphatase	98.33
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	98.32
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	98.29
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	98.23
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	98.23
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	98.22
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	98.21
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	98.2
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	98.2
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	98.19
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.18
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	98.18
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	98.15
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	98.14
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.13
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	98.13
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	98.12
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.06
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	98.04
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	97.76
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	97.3
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	97.29
1sxv_A	172	Inorganic pyrophosphatase; structural genomics, pp	97.24
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	96.98
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	96.95
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.35
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.12
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	95.86
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	94.8
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	93.94
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	93.53
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	93.37
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	91.78
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	91.31
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	88.44
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	81.0

>1e9g_A Ppase, inorganic pyrophosphatase; pyrophosphate phosphohydrolase, hydrolase, manganese; HET: PO4; 1.15A {Saccharomyces cerevisiae} SCOP: b.40.5.1 PDB: 1e6a_A* 1wgi_A 1wgj_A 2ihp_A* 8prk_A 2ik6_A 2ik2_A 2ik4_A 117e_A 2ik1_A* 2ik9_A 2ik0_A 2ik7_A 1m38_A 1ypp_A 1huk_A 1huj_A 1pyp_A

Probab=100.00  E-value=2e-67  Score=510.13  Aligned_cols=221  Identities=57%  Similarity=0.980  Sum_probs=208.9

Q ss_pred             HHHhcCCCcccCCCCCc-ccccccCCccccccccccceeeccCCCCccccccccCCCCCCCcccccCCeeeeecccCCCC
Q psy300          147 AILKSNKKPYKGSENGL-ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHH  225 (451)
Q Consensus       147 Ai~~ln~riy~~~~~G~-iSp~hdiPl~v~~~p~~vn~vvEIPrgS~~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~  225 (451)
                      +..++++|+||.+ +|. +|+||++|++.+..+..+|++||||+||++|||+++++++|||+||.++|++|+++++||++
T Consensus         9 ~~~t~~~r~~~~~-~g~~~sp~hdIp~~~~~~~~~~nvVIEIP~gs~~KyEidk~~~~nPIkqd~k~G~lr~dr~l~~~~   87 (286)
T 1e9g_A            9 AKNTLEYKVYIEK-DGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFPHH   87 (286)
T ss_dssp             ETTSTTCEEEEEE-TTEEECTTTTSCSEEETTTTEEEEEEEECTTCCBCEEECTTSTTCCEEECEETTEECBCCEETTCC
T ss_pred             CCCCcceEEEEEe-CCeecCchhhCCCCCCCCCCEEEEEEEECCCCCeEEEEccCCCCCcchhhhcCCcEEEEeccCCCC
Confidence            3567889999988 476 99999999987655589999999999999999999999999999999999999999999999


Q ss_pred             CCccccCCCCccCCCCCCCCcCCCCCCCCCcceEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecCCccccC
Q psy300          226 GYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAK  305 (451)
Q Consensus       226 ~yp~nYG~iP~T~~~p~~~~~~~~~~~D~DPlD~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~d~~~~~  305 (451)
                      +|||||||||||||||++.++.|+++|||||||||||++.++.||++++|||||+|+|+|+||+|||||||+++||+|++
T Consensus        88 ~YP~NYGfIPqTledp~~~~~~t~~~gDgDPLDVlvi~~~p~~pG~vi~vr~IGvl~MiDege~D~KIIaV~~~Dp~~~~  167 (286)
T 1e9g_A           88 GYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPK  167 (286)
T ss_dssp             SCSSEEEECSSCCCCTTSEETTTTEEBCSSCCEEEECCSSCCCTTCEEEEEEEEEECEEETTEECCEEEEEETTSTTGGG
T ss_pred             CCccCcccCcccccCcccccccCCCCCCCCceEEEEecCccCCCccEEEEEEeEEEEeccCCCCCceEEEEeCCCccccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcccccccCcchHHHHHHHhhhccCCCCCcccc----cCCCcchhhhhhhHHHHHHHHHHhhcccc
Q psy300          306 LNDVADIETHFPGYLKATNEWFKIYKIPDGKPENV----LNTRVEGESSQGFIPGCRGRTEQVVSSRL  369 (451)
Q Consensus       306 i~~~~d~~~~~p~~~~~i~~~F~~yk~~~gk~~~~----~~~~~~~~~~~~~i~~~~~~~~~~i~~~~  369 (451)
                      |+|++||++++|+++++|+|||++||.++||++|.    .+|.|+ +.|+++|++||++|+++++|..
T Consensus       168 i~di~Dl~~~~p~~l~~i~~fF~~YK~leGK~~n~~~~~~~~~~~-~~A~~vI~~~~~~~~~l~~~~~  234 (286)
T 1e9g_A          168 LNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPENQFAFSGEAKNK-KYALDIIKETHDSWKQLIAGKS  234 (286)
T ss_dssp             CCSHHHHHHHSTTHHHHHHHHHHHTTGGGTCCCCEEGGGGCCBCH-HHHHHHHHHHHHHHHHHHTTCC
T ss_pred             CCCHHHhchhhHHHHHHHHHHHHHhcCcCCCCcceeEecCcCCCH-HHHHHHHHHHHHHHHHHhcCCC
Confidence            99999999999999999999999999999999763    577774 6779999999999999999875

>3q46_A TT-ippase; inorganic pyrophosphatase, hydrolase; HET: EPE; 0.99A {Thermococcus thioreducens} SCOP: b.40.5.1 PDB: 3r6e_A* 3q3l_A 3i98_A 3q4w_A 3q9m_A* 3r5u_A 3r5v_A* 3q5v_A* 1ude_A 1twl_A

Probab=100.00  E-value=3.6e-58  Score=419.05  Aligned_cols=175  Identities=26%  Similarity=0.487  Sum_probs=163.8

Q ss_pred             ccccccCCccccccccccceeeccCCCCccccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccCCCCCC
Q psy300          164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDE  243 (451)
Q Consensus       164 iSp~hdiPl~v~~~p~~vn~vvEIPrgS~~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~~~p~~  243 (451)
                      +|+||++|++. ..+..++++||||+||++|||+++           ++|.++++|.+|+++.||+|||||||||     
T Consensus         1 ~spwhdi~~g~-~~p~~~nvvIEIP~gs~~KyE~dk-----------~~g~i~~DR~l~~~~~YP~NYGfIP~Tl-----   63 (178)
T 3q46_A            1 MNPFHELEPGP-EVPEVVYALIEIPKGSRNKYELDK-----------ATGLLKLDRVLYSPFFYPVDYGIIPQTW-----   63 (178)
T ss_dssp             CCTTTTSCSCS-BTTTBCCCEEEECTTCCEEEEECT-----------TTSCEEEEEECSSSCCCSSEEEECTTCC-----
T ss_pred             CCccccCCCCC-CCCCEEEEEEEECCCCCeeEEECC-----------CCCCEEEeecccCCCCCCcccccCCCcc-----
Confidence            58999999975 478999999999999999999986           5688999999999999999999999999     


Q ss_pred             CCcCCCCCCCCCcceEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecCCccccCCCCcccccccCcchHHHH
Q psy300          244 TDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKAT  323 (451)
Q Consensus       244 ~~~~~~~~~D~DPlD~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~d~~~~~i~~~~d~~~~~p~~~~~i  323 (451)
                             ++||||||||||++.++.||++++|||||+|+|+|+||+|||||||+++||+|++|+|++||+++   ++++|
T Consensus        64 -------~~DgDPlDvlvl~~~~~~pG~vi~~r~iGvl~m~Dege~D~KiiaV~~~Dp~~~~i~di~Dl~~~---~l~~i  133 (178)
T 3q46_A           64 -------YDDGDPFDIMVIMREPVYPLTIIEARPIGIMKMEDSGDKDWKVLAVPVEDPYFNDWKDISDVPKA---FLDEI  133 (178)
T ss_dssp             -------BTTTBCCEEEECCSSCCCTTCBC-CEEEEEEEEEETTEECCEEEEECTTCGGGTTCCSGGGSCHH---HHHHH
T ss_pred             -------CCCCCeeEEEEEcCCCCCCceEEEEEEEEEEEeecCCCccceEEEeeCCCccccccCChHHCCHH---HHHHH
Confidence                   58999999999999999999999999999999999999999999999999999999999999864   99999


Q ss_pred             HHHhhhccCCCCCcccccCCCcchhhhhhhHHHHHHHHHHhhc
Q psy300          324 NEWFKIYKIPDGKPENVLNTRVEGESSQGFIPGCRGRTEQVVS  366 (451)
Q Consensus       324 ~~~F~~yk~~~gk~~~~~~~~~~~~~~~~~i~~~~~~~~~~i~  366 (451)
                      +|||++||.++||++++++|.|+ ++|+++|++||++|+++..
T Consensus       134 ~~fF~~YK~legK~v~~~g~~~~-~~A~~~I~~~~~~~~~~~~  175 (178)
T 3q46_A          134 AHFFQRYKELQGKTTKIEGWGNA-EEAKREILRAIEMYKEKFG  175 (178)
T ss_dssp             HHHHHHTTGGGTCCEEEEEEEEH-HHHHHHHHHHHHHHHHC-C
T ss_pred             HHHHHHhcCcCCCceEeccccCH-HHHHHHHHHHHHHHHHHhc
Confidence            99999999999999999999985 7889999999999999654

>2prd_A Pyrophosphate phosphohydrolase; 2.00A {Thermus thermophilus} SCOP: b.40.5.1

Probab=100.00  E-value=1.4e-55  Score=400.99  Aligned_cols=171  Identities=23%  Similarity=0.398  Sum_probs=162.5

Q ss_pred             cccccCCccccccccccceeeccCCCCccccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccCCCCCCC
Q psy300          165 SPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDET  244 (451)
Q Consensus       165 Sp~hdiPl~v~~~p~~vn~vvEIPrgS~~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~~~p~~~  244 (451)
                      |+||++|++.+ .+..+|++||||+||++|||+++           ++|.+++++.+|+++.||+|||||||||      
T Consensus         1 ~~~h~ip~~~~-~p~~~nvvIEIP~gs~~KyE~dk-----------~~g~i~~DR~l~~~~~YP~NYGfIP~Tl------   62 (174)
T 2prd_A            1 ANLKSLPVGDK-APEVVHMVIEVPRGSGNKYEYDP-----------DLGAIKLDRVLPGAQFYPGDYGFIPSTL------   62 (174)
T ss_dssp             CCGGGSCCCTT-TTTEEEEEEEECTTCCEEEEEET-----------TTTEEEEEEECSSSCCCSSEEEECSSCC------
T ss_pred             CCcccCCCCCC-CCCEEEEEEEecCCCCeEEEEec-----------CCCCEEEeeecCCCCcCCcccccccCcc------
Confidence            68999999865 47899999999999999999986           5799999999999999999999999999      


Q ss_pred             CcCCCCCCCCCcceEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecCCccccCCCCcccccccCcchHHHHH
Q psy300          245 DAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATN  324 (451)
Q Consensus       245 ~~~~~~~~D~DPlD~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~d~~~~~i~~~~d~~~~~p~~~~~i~  324 (451)
                            +|||||||||||++.++.||++++||+||+|+|+|+||+|||||||+++||+|++|+|++||+++   ++++|+
T Consensus        63 ------~~DgDPlDvlvl~~~p~~pG~vi~~r~iGvl~m~Dege~D~KiiaV~~~dp~~~~i~di~Dl~~~---~l~~i~  133 (174)
T 2prd_A           63 ------AEDGDPLDGLVLSTYPLLPGVVVEVRVVGLLLMEDEKGGDAKVIGVVAEDQRLDHIQDIGDVPEG---VKQEIQ  133 (174)
T ss_dssp             ------CTTSSCCEEEEECSSCCCTTCEEEEEEEEEEEEEESSCEEEEEEEEETTCGGGTTCCSGGGSCHH---HHHHHH
T ss_pred             ------cCCCCceEEEEECCCCCCCceEEEEEEEEEEEEecCCCCccEEEEEECCCcchhhcCChHHCCHH---HHHHHH
Confidence                  59999999999999999999999999999999999999999999999999999999999999875   999999


Q ss_pred             HHhhhccCCC---CCcccccCCCcchhhhhhhHHHHHHHHHH
Q psy300          325 EWFKIYKIPD---GKPENVLNTRVEGESSQGFIPGCRGRTEQ  363 (451)
Q Consensus       325 ~~F~~yk~~~---gk~~~~~~~~~~~~~~~~~i~~~~~~~~~  363 (451)
                      |||++||.++   ||++++.+|.|+ ++|+++|++||++|++
T Consensus       134 ~fF~~YK~le~k~gK~v~~~gw~~~-~~A~~~I~~~~~~~~~  174 (174)
T 2prd_A          134 HFFETYKALEAKKGKWVKVTGWRDR-KAALEEVRACIARYKG  174 (174)
T ss_dssp             HHHHHTTGGGGGGTCCEEEEEEECH-HHHHHHHHHHHHHHHC
T ss_pred             HHHHHhcCccccCCCceEECcccCH-HHHHHHHHHHHHHHhC
Confidence            9999999999   999999999985 7789999999999974

>3fq3_A Inorganic pyrophosphatase:bacterial/archaeal INOR pyrophosphatase; ssgcid, inorganic phosphatase; 1.90A {Brucella melitensis biovar abortus 230ORGANISM_TAXID} PDB: 3sw5_A

Probab=100.00  E-value=1.4e-54  Score=399.03  Aligned_cols=175  Identities=30%  Similarity=0.385  Sum_probs=160.6

Q ss_pred             CCc-ccccccCCccccccccccceeeccCCC-CccccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccC
Q psy300          161 NGL-ISPFHDIPLYSNVKDKIFNMVVEIPRW-TNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTW  238 (451)
Q Consensus       161 ~G~-iSp~hdiPl~v~~~p~~vn~vvEIPrg-S~~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~  238 (451)
                      .|. +++||++|++.+ .|..++++||||++ |++|||+++           ++|.++.+|.++.++.||+|||||||||
T Consensus        17 ~g~~im~~~~ip~g~~-~p~~vnvvIEIP~g~s~~KyE~dk-----------~~g~i~~DR~l~~~~~YP~NYGfIP~Tl   84 (197)
T 3fq3_A           17 QGPGSMNIDAISIGSN-PPEDVNVIIEVPVGGQPIKYEMDK-----------KAGALIVDRFLYTPMTYPGNYGFVPHTL   84 (197)
T ss_dssp             -----CCGGGSCSCSS-TTSCEEEEEEECTTCCSEEEEEET-----------TTTEEEEEEECCSSBCCSSEEEECTTCC
T ss_pred             CCCCcCCHHHCCCCCC-CCCEEEEEEEecCCCCCEeEEEec-----------CCCCEEEEeecCCCCcCCcccccccCcc
Confidence            566 899999999864 68999999999985 999999986           5688888888999999999999999999


Q ss_pred             CCCCCCCcCCCCCCCCCcceEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecC--CccccCCCCcccccccC
Q psy300          239 ENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVN--DPNAAKLNDVADIETHF  316 (451)
Q Consensus       239 ~~p~~~~~~~~~~~D~DPlD~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~--d~~~~~i~~~~d~~~~~  316 (451)
                                  +|||||||||||++.++.||++++|||||+|+|+|+||.|||||||+++  ||+|++|+|++||++  
T Consensus        85 ------------~~DgDPLDvlvl~~~p~~pG~vi~~r~iGvl~MiDege~D~KIIaVp~~~~dp~~~~i~di~Dlp~--  150 (197)
T 3fq3_A           85 ------------SEDGDPIDVLVCNTRPLIPGCVINVRPIGVLVMEDNSGKDEKIIAVPSPHLTRRYEKIHDYTDMPE--  150 (197)
T ss_dssp             ------------CTTSSCCEEEECCSSCCCTTCEEEEEEEEEEEEEETTEEEEEEEEEECTTTCSTTTTCCSGGGSCH--
T ss_pred             ------------cCCCCceEEEEEcCCCCCCceEEEEEEEEEEEEecCCCCccEEEEEECCCCCchhcccCchHHCCH--
Confidence                        7999999999999999999999999999999999999999999999999  999999999999975  


Q ss_pred             cchHHHHHHHhhhccCCC-CCcccccCCCcchhhhhhhHHHHHHHHHH
Q psy300          317 PGYLKATNEWFKIYKIPD-GKPENVLNTRVEGESSQGFIPGCRGRTEQ  363 (451)
Q Consensus       317 p~~~~~i~~~F~~yk~~~-gk~~~~~~~~~~~~~~~~~i~~~~~~~~~  363 (451)
                       +++++|+|||++||.++ ||++.+.+|.|+ +.|+++|++|+++|++
T Consensus       151 -~~l~~I~~fF~~YK~le~~K~v~v~~~~~~-~~A~~~I~~~~~~~~~  196 (197)
T 3fq3_A          151 -ITLKQIAHFFEHYKDLEPGKWVKIGDWGDE-DYARKFIVEAIERAKG  196 (197)
T ss_dssp             -HHHHHHHHHHHHTTTTSTTCCEEECCCBCH-HHHHHHHHHHHHHHC-
T ss_pred             -HHHHHHHHHHHHhcCcCCCCeEEeCCCCCH-HHHHHHHHHHHHHHhh
Confidence             59999999999999998 899999999995 7789999999999975

>3gvf_A Inorganic pyrophosphatase; structural genomics, hydrolase, S structural genomics center for infectious disease, ssgcid; HET: PGE; 1.75A {Burkholderia pseudomallei 1710B} PDB: 3d63_A* 3eiy_A 3ej0_A* 3ej2_A* 3eiz_A*

Probab=100.00  E-value=1.2e-54  Score=399.06  Aligned_cols=175  Identities=27%  Similarity=0.390  Sum_probs=160.6

Q ss_pred             CCc-ccccccCCccccccccccceeeccCCCCc-cccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccC
Q psy300          161 NGL-ISPFHDIPLYSNVKDKIFNMVVEIPRWTN-AKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTW  238 (451)
Q Consensus       161 ~G~-iSp~hdiPl~v~~~p~~vn~vvEIPrgS~-~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~  238 (451)
                      .|. +++||++|++. ..|..++++||||+||+ +|||+++           ++|.++.+|.++.++.||+|||||||||
T Consensus        17 ~g~~~m~~~~i~~g~-~~p~~vnvvIEIP~gs~~~KyE~dk-----------~~g~i~~DR~l~s~~~YP~NYGfIP~Tl   84 (196)
T 3gvf_A           17 QGPGSMSFSNVPAGK-DLPQDFNVIIEIPAQSEPVKYEADK-----------ALGLLVVDRFIGTGMRYPVNYGFIPQTL   84 (196)
T ss_dssp             ------CGGGSCSCS-BTTTBEEEEEEECTTCCSEEEEEET-----------TTTEEEEEEECTTCCCCSSEEEECTTCC
T ss_pred             cCCCCCchhhCCCCC-CCCCEEEEEEEecCCCCceEEEEec-----------CCCCEEEEeEcCCCccCCcccccccCcc
Confidence            566 88999999975 45899999999999998 9999986           5688888899999999999999999999


Q ss_pred             CCCCCCCcCCCCCCCCCcceEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecCC--ccccCCCCcccccccC
Q psy300          239 ENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVND--PNAAKLNDVADIETHF  316 (451)
Q Consensus       239 ~~p~~~~~~~~~~~D~DPlD~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~d--~~~~~i~~~~d~~~~~  316 (451)
                                  +|||||||||||++.++.||++++|||||+|+|+|+||.|||||||+++|  |+|++|+|++||++  
T Consensus        85 ------------~~DgDPLDvlvl~~~p~~pG~vi~~r~iGvl~M~Dege~D~KIIaVp~~d~~p~~~~i~di~dlp~--  150 (196)
T 3gvf_A           85 ------------SGDGDPVDVLVITPFPLLAGSVVRARALGMLKMTDESGVDAKLVAVPHDKVCPMTANLKSIDDVPA--  150 (196)
T ss_dssp             ------------CTTSSCCEEEECCSSCCCTTCEEEEEEEEEEEEEETTEEEEEEEEEECTTTCGGGTTCCSGGGSCH--
T ss_pred             ------------CCCCCceEEEEecCCccCCeeEEEEEEEEEEEEecCCCcccEEEEEecCCcCchhhhcCchhhCCH--
Confidence                        79999999999999999999999999999999999999999999999998  99999999999975  


Q ss_pred             cchHHHHHHHhhhccCCC-CCcccccCCCcchhhhhhhHHHHHHHHHH
Q psy300          317 PGYLKATNEWFKIYKIPD-GKPENVLNTRVEGESSQGFIPGCRGRTEQ  363 (451)
Q Consensus       317 p~~~~~i~~~F~~yk~~~-gk~~~~~~~~~~~~~~~~~i~~~~~~~~~  363 (451)
                       +++++|+|||++||.++ ||++.+.+|.|+ ++|+++|++|+++|++
T Consensus       151 -~~l~~I~~fF~~YK~le~gK~v~v~gw~~~-~~A~~~I~~~~~~y~~  196 (196)
T 3gvf_A          151 -YLKDQIKHFFEQYKALEKGKWVKVEGWDGI-DAAHKEITDGVANFKK  196 (196)
T ss_dssp             -HHHHHHHHHHHHTTTTSTTCCEEEEEEECH-HHHHHHHHHHHHHHTC
T ss_pred             -HHHHHHHHHHHHhcCcCCCCeEEeccCcCH-HHHHHHHHHHHHHHhC
Confidence             59999999999999999 999999999985 7889999999999974

>2au7_A Inorganic pyrophosphatase; hydrolase, mutant; 1.05A {Escherichia coli} PDB: 1i40_A 1i6t_A 1igp_A 1obw_A 2au6_A 2au8_A 2au9_A 2auu_A 1mjy_A 1faj_A 1ino_A 1ipw_A 1jfd_A 2eip_A 1mjz_A 1mjx_A 1mjw_A 3i4q_A*

Probab=100.00  E-value=1.9e-54  Score=392.99  Aligned_cols=170  Identities=25%  Similarity=0.329  Sum_probs=159.8

Q ss_pred             ccccCCccccccccccceeeccCCCCc-cccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccCCCCCCC
Q psy300          166 PFHDIPLYSNVKDKIFNMVVEIPRWTN-AKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDET  244 (451)
Q Consensus       166 p~hdiPl~v~~~p~~vn~vvEIPrgS~-~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~~~p~~~  244 (451)
                      +||++|++.+ .+..++++||||+||+ +|||+++           ++|.++.+|.+|+++.||+|||||||||      
T Consensus         1 ~~~~ip~~~~-~p~~~nvvIEIP~gs~p~KyE~dk-----------~~g~i~~DR~l~~~~~YP~NYGfIP~Tl------   62 (175)
T 2au7_A            1 SLLNVPAGKD-LPEDIYVVIEIPANADPIKYEIDK-----------ESGALFVDQFMSTAMFYPCNYGYINHTL------   62 (175)
T ss_dssp             CGGGCCSCSB-TTTBEEEEEEECTTCCSEEEEECT-----------TTCCEEEEEECSSSCCCSSEEEECTTCC------
T ss_pred             CcccCCCCCC-CCCEEEEEEEecCCCCceeEEEec-----------CCCCEEEeeecCCCCcCCcCcCccCCcc------
Confidence            4899999864 4789999999999999 9999987           4577777788999999999999999999      


Q ss_pred             CcCCCCCCCCCcceEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecC--CccccCCCCcccccccCcchHHH
Q psy300          245 DAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVN--DPNAAKLNDVADIETHFPGYLKA  322 (451)
Q Consensus       245 ~~~~~~~~D~DPlD~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~--d~~~~~i~~~~d~~~~~p~~~~~  322 (451)
                            +|||||||||||++.++.||++++||+||+|+|+|+||.|||||||+++  ||+|++|+|++||+++   ++++
T Consensus        63 ------~~DgDPlDvlvl~~~p~~pG~vi~~r~iGvl~m~Deg~~D~KiiaV~~~k~dp~~~~i~di~Dl~~~---~l~~  133 (175)
T 2au7_A           63 ------SLDGDPVDVLVPTPYPLQPGSVTRCRPVGVLKMTDEAGEDAKLVAVPHSKLSKEYDHIKDVNDLPEL---LKAQ  133 (175)
T ss_dssp             ------CTTSSCCEEEECCSSCCCTTCEEEEEEEEEEEEEETTEECCEEEEEECTTTCSTTTTCCSGGGSCHH---HHHH
T ss_pred             ------CCCCCceEEEEECCCCCCCceEEEEEEEEEEEeecCCCCccEEEEEeCCCCCcchhhCCChHHCCHH---HHHH
Confidence                  6999999999999999999999999999999999999999999999999  9999999999999876   9999


Q ss_pred             HHHHhhhccCCC-CCcccccCCCcchhhhhhhHHHHHHHHHH
Q psy300          323 TNEWFKIYKIPD-GKPENVLNTRVEGESSQGFIPGCRGRTEQ  363 (451)
Q Consensus       323 i~~~F~~yk~~~-gk~~~~~~~~~~~~~~~~~i~~~~~~~~~  363 (451)
                      |+|||++||.++ ||++++++|.|+ ++|+++|++||++|++
T Consensus       134 i~~fF~~YK~le~gK~v~v~gw~~~-~~A~~~I~~~~~~~~~  174 (175)
T 2au7_A          134 IAHFFEHYKDLEKGKWVKVEGWENA-EAAKAEIVASFERAKN  174 (175)
T ss_dssp             HHHHHHHTTTTSTTCCEEEEEEECH-HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhCccCCCCeEEccccCH-HHHHHHHHHHHHHHHh
Confidence            999999999999 999999999985 7789999999999986

>3ld3_A Inorganic pyrophosphatase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, hydrolase; 1.75A {Anaplasma phagocytophilum} PDB: 3lo0_A

Probab=100.00  E-value=2.4e-54  Score=397.97  Aligned_cols=176  Identities=27%  Similarity=0.364  Sum_probs=157.9

Q ss_pred             CCCc-ccccccCCccccccccccceeeccCCCC-ccccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCcc
Q psy300          160 ENGL-ISPFHDIPLYSNVKDKIFNMVVEIPRWT-NAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQT  237 (451)
Q Consensus       160 ~~G~-iSp~hdiPl~v~~~p~~vn~vvEIPrgS-~~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T  237 (451)
                      .+|+ +++||++|++.+ .|..++++||||+|| ++|||+++           ++|.++++|.+++++.|||||||||||
T Consensus        16 ~~g~~~m~~~~i~~g~~-~p~~vnvvIEIP~gs~~~KyE~dk-----------~~G~l~~DR~l~~~~~YP~NYGfIP~T   83 (199)
T 3ld3_A           16 TQGPGSMNLDDIGSGSN-APEEVNVVIEVSQDSHPVKYEFDE-----------KNGALWVDRFLPTAMYYPCNYGFIPNT   83 (199)
T ss_dssp             ----------CCCSCTT-TTTSEEEEEEECTTCCSEEEEECT-----------TTCCEEEEEECSSSBCCSSEEEECTTC
T ss_pred             cCCCccCChHHCCCCCC-CCCEEEEEEEecCCCCCEEEEEec-----------CCCCEEEEEEcCCCCcCCccccccccc
Confidence            3666 899999999854 689999999999998 59999986           579999999999999999999999999


Q ss_pred             CCCCCCCCcCCCCCCCCCcceEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecC--CccccCCCCccccccc
Q psy300          238 WENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVN--DPNAAKLNDVADIETH  315 (451)
Q Consensus       238 ~~~p~~~~~~~~~~~D~DPlD~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~--d~~~~~i~~~~d~~~~  315 (451)
                      |            +|||||||||||++.++.||++++|||||+|+|+|+||+|||||||+++  ||+|++|+|++||++ 
T Consensus        84 l------------~~DGDPLDvlvl~~~p~~pG~vi~vr~IGvl~MiDege~D~KIIaVp~~~~dp~~~~i~di~Dlp~-  150 (199)
T 3ld3_A           84 I------------AGDGDPVDVLVLARFPVMPGAVICVRPVGVLMMNDEKGEDAKVLAVPATKVDQYYGNIVNYSDLPS-  150 (199)
T ss_dssp             C------------CTTSSCCEEEECCSSCCCTTCEEEEEEEEEEEEEETTEECCEEEEEECTTTCGGGTTCCSGGGSCH-
T ss_pred             c------------cCCCCceEEEEecCCCCCCceEEEEEEEEEEEEecCCCCcceEEEEECCCCCccccccCchHHCCH-
Confidence            9            7999999999999999999999999999999999999999999999999  999999999999975 


Q ss_pred             CcchHHHHHHHhhhccCCC-CCcccccCCCcchhhhhhhHHHHHHHHHH
Q psy300          316 FPGYLKATNEWFKIYKIPD-GKPENVLNTRVEGESSQGFIPGCRGRTEQ  363 (451)
Q Consensus       316 ~p~~~~~i~~~F~~yk~~~-gk~~~~~~~~~~~~~~~~~i~~~~~~~~~  363 (451)
                        +++++|+|||++||.++ ||++.+.+|.|+ ++|+++|++|+++|++
T Consensus       151 --~~l~~I~~fF~~YK~le~gK~v~v~gw~~~-~~A~~~I~~~~~~~~~  196 (199)
T 3ld3_A          151 --SFLDSISHFFSFYKKLEKDKFVSVGCWQDA-ASAKELIRSAIIAAKK  196 (199)
T ss_dssp             --HHHHHHHHHHHHTTTTSTTCCEEEEEEEEH-HHHHHHHHHHHHHHHC
T ss_pred             --HHHHHHHHHHHHhcCcCCCceEEecCCCCH-HHHHHHHHHHHHHHHh
Confidence              59999999999999998 799999999985 7889999999999986

>2bqx_A Inorganic pyrophosphatase; hydrolase; 1.90A {Helicobacter pylori} PDB: 1ygz_A 2bqy_A

Probab=100.00  E-value=2.5e-54  Score=392.38  Aligned_cols=169  Identities=25%  Similarity=0.438  Sum_probs=156.6

Q ss_pred             ccccCCccccccccccceeeccCCCCccccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccCCCCCCCC
Q psy300          166 PFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETD  245 (451)
Q Consensus       166 p~hdiPl~v~~~p~~vn~vvEIPrgS~~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~~~p~~~~  245 (451)
                      +||++|++.+  +..+|++||||+||++|||+++           ++|.+++++.+|+++.||+|||||||||       
T Consensus         2 ~~~~ip~~~~--p~~~nvvIEIP~gs~~KyE~dk-----------~~g~i~~DR~l~~~~~YP~NYGfIP~Tl-------   61 (173)
T 2bqx_A            2 NLEKLEVSHD--ADSLCVVIEISKHSNIKYELDK-----------ESGALMVDRVLYGAQNYPANYGFVPNTL-------   61 (173)
T ss_dssp             -----CCCEE--TTEEEEEEEECTTCSEEEEECT-----------TTCCEEEEEECSSSCCCSSEEEECSSCC-------
T ss_pred             CcccCCCCCC--CCeEEEEEEECCCCCeEEEEec-----------CCCCEEEeeecCCCCcCccccccccccc-------
Confidence            6999999875  8899999999999999999986           5799999999999999999999999999       


Q ss_pred             cCCCCCCCCCcceEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecC--CccccCCCCcccccccCcchHHHH
Q psy300          246 AHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVN--DPNAAKLNDVADIETHFPGYLKAT  323 (451)
Q Consensus       246 ~~~~~~~D~DPlD~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~--d~~~~~i~~~~d~~~~~p~~~~~i  323 (451)
                           +|||||||||||++.++.||++++|||||+|+|+|+||+|||||||+++  ||+|++|++++||+++   ++++|
T Consensus        62 -----~~DgDPlDvlvl~~~p~~~G~vi~~r~iGvl~m~D~g~~D~KiiaV~~~k~dp~~~~i~di~Dl~~~---~l~~i  133 (173)
T 2bqx_A           62 -----GSDGDPVDALVLSDVAFQAGSVVKARLVGVLNMEDESGMDEKLIALPIDKIDPTHSYVKDIDDLSKH---TLDKI  133 (173)
T ss_dssp             -----CTTSSCCEEEECCSSCCCTTCEEEEEEEEEEEEEETTEEEEEEEEEECTTTCCTTTTCCSGGGSCHH---HHHHH
T ss_pred             -----CCCCCceEEEEECCCCCCCceEEEEEEEEEEEeccCCCCccEEEEEeCCCCCcchhhcCChhHCCHH---HHHHH
Confidence                 7999999999999999999999999999999999999999999999999  9999999999999876   99999


Q ss_pred             HHHhhhccCCC-CCcccccCCCcchhhhhhhHHHHHHHHHH
Q psy300          324 NEWFKIYKIPD-GKPENVLNTRVEGESSQGFIPGCRGRTEQ  363 (451)
Q Consensus       324 ~~~F~~yk~~~-gk~~~~~~~~~~~~~~~~~i~~~~~~~~~  363 (451)
                      +|||++||.++ ||++++.+|.|+ ++|+++|++||++|++
T Consensus       134 ~~fF~~YK~le~gK~v~~~g~~~~-~~A~~~I~~~~~~~~~  173 (173)
T 2bqx_A          134 KHFFETYKDLEPNKWVKVKGFENK-ESAIKVLEKAIKAYQG  173 (173)
T ss_dssp             HHHHHHTTTTSTTCCEEEEEEEEH-HHHHHHHHHHHHHHC-
T ss_pred             HHHHHHhccccCCCceeeCcCcCH-HHHHHHHHHHHHHHhC
Confidence            99999999999 999999999985 7789999999999974

>3d53_A Inorganic pyrophosphatase; seattle structural G center for infectious disease, ssgcid, hydrolase, magnesium binding; 2.20A {Rickettsia prowazekii} PDB: 3emj_A*

Probab=100.00  E-value=7.6e-54  Score=388.44  Aligned_cols=166  Identities=28%  Similarity=0.386  Sum_probs=158.7

Q ss_pred             ccccCCccccccccccceeeccCCCCc-cccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccCCCCCCC
Q psy300          166 PFHDIPLYSNVKDKIFNMVVEIPRWTN-AKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDET  244 (451)
Q Consensus       166 p~hdiPl~v~~~p~~vn~vvEIPrgS~-~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~~~p~~~  244 (451)
                      +||++|++.+  +..++++||||+||+ +|||+++           ++|.+++++.+|+++.||+|||||||||      
T Consensus         3 ~~~~ip~~~~--p~~~nvvIEIP~gs~p~KyE~dk-----------~~g~i~~DR~l~~~~~YP~NYGfIP~Tl------   63 (173)
T 3d53_A            3 FIKKIKAKAN--NNEINVIIEIPMNSGPIKYEFDK-----------ESGALFVDRFMQTTMSYPCNYGFIPDTL------   63 (173)
T ss_dssp             CGGGSCSCSS--TTCEEEEEEECTTCCSEEEEECT-----------TTCCEEEEEECCSSCCCSSEEEECTTCC------
T ss_pred             chhhCCCCCC--CCeEEEEEEeCCCCCceeEEEec-----------CCCCEEEeeecCCCCcCCcccchhhCCc------
Confidence            6999999875  889999999999999 9999986           5789999999999999999999999999      


Q ss_pred             CcCCCCCCCCCcceEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecC--CccccCCCCcccccccCcchHHH
Q psy300          245 DAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVN--DPNAAKLNDVADIETHFPGYLKA  322 (451)
Q Consensus       245 ~~~~~~~~D~DPlD~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~--d~~~~~i~~~~d~~~~~p~~~~~  322 (451)
                            +|||||||||||++.++.||++++||+||+|+|+|+||+|||||||+++  ||+|++|++++||+++   ++++
T Consensus        64 ------~~DgDPlDvlvl~~~p~~~G~vi~~r~iGvl~m~Dege~D~KiiaV~~~k~dp~~~~i~di~Dl~~~---~l~~  134 (173)
T 3d53_A           64 ------SNDGDPVDVLVVAHHPVVPGSVIKCRAIGVLMMEDESGLDEKIIAVPTSKLDITFDHIKELDDLCEM---LKKR  134 (173)
T ss_dssp             ------CTTSSCCEEEECCSSCCCTTCEEEEEEEEEEEEEETTEEEEEEEEEECTTTCGGGTTCCSGGGSCHH---HHHH
T ss_pred             ------cCCCCceEEEEECCCccCCceEEEEEEEEEEEEccCCCccceEEEEeCCCCCcchhhcCChhHCCHH---HHHH
Confidence                  6999999999999999999999999999999999999999999999999  9999999999999875   9999


Q ss_pred             HHHHhhhccCCC-CCcccccCCCcchhhhhhhHHHHHHH
Q psy300          323 TNEWFKIYKIPD-GKPENVLNTRVEGESSQGFIPGCRGR  360 (451)
Q Consensus       323 i~~~F~~yk~~~-gk~~~~~~~~~~~~~~~~~i~~~~~~  360 (451)
                      |+|||++||.++ ||++++.+|.|+ ++|+++|++||+|
T Consensus       135 i~~fF~~YK~le~gK~v~v~gw~~~-~~A~~~I~~~~~~  172 (173)
T 3d53_A          135 IVHFFEHYKDLEKGKWVKVTGWGDK-VKAETLIKEGIDR  172 (173)
T ss_dssp             HHHHHHHTTTTSTTCCEEEEEEECH-HHHHHHHHHHHHC
T ss_pred             HHHHHHHHcCccCCCcEEEccCcCH-HHHHHHHHHHHhc
Confidence            999999999999 999999999985 7789999999985

>1sxv_A Inorganic pyrophosphatase; structural genomics, ppase,, hydrolase; 1.30A {Mycobacterium tuberculosis} PDB: 1wcf_A 2uxs_A 4ecp_A

Probab=100.00  E-value=1.4e-53  Score=385.51  Aligned_cols=158  Identities=23%  Similarity=0.399  Sum_probs=150.8

Q ss_pred             cccceeeccCCCCccccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccCCCCCCCCcCCCCCCCCCcce
Q psy300          179 KIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPID  258 (451)
Q Consensus       179 ~~vn~vvEIPrgS~~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~~~p~~~~~~~~~~~D~DPlD  258 (451)
                      -.++++||||+||++|||+|+           ++|+++++|.+|+++.||+|||||||||            +|||||||
T Consensus        11 ~~~nvvIEIP~gs~~KyE~Dk-----------~~G~l~~DR~l~~~~~YP~NYGfIP~Tl------------~~DGDPlD   67 (172)
T 1sxv_A           11 MQFDVTIEIPKGQRNKYEVDH-----------ETGRVRLDRYLYTPMAYPTDYGFIEDTL------------GDDGDPLD   67 (172)
T ss_dssp             CCEEEEEEECTTCCEEC-CCT-----------TTCCCCCCEECSSSCCCSSEEEEETTCC------------CTTSSCCE
T ss_pred             eEEEEEEEECCCCCeEEEEEc-----------CCCCEEEEeecCCCCCCCcCcCccCCcc------------CCCCCCeE
Confidence            458999999999999999975           6899999999999999999999999999            69999999


Q ss_pred             EEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecCCccccCCCCcccccccCcchHHHHHHHhhhccCCC-CCc
Q psy300          259 VLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPD-GKP  337 (451)
Q Consensus       259 ~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~d~~~~~i~~~~d~~~~~p~~~~~i~~~F~~yk~~~-gk~  337 (451)
                      ||||++.++.||++++|||||+|+|+|+||.|||||||+++||+|++|+|++||+++   ++++|+|||++||.++ ||+
T Consensus        68 vlvl~~~p~~pG~vi~~r~iGvl~m~Dege~D~KIIaVp~~Dp~~~~i~di~Dlp~~---~l~~I~~fF~~YK~le~gK~  144 (172)
T 1sxv_A           68 ALVLLPQPVFPGVLVAARPVGMFRMVDEHGGDDKVLCVPAGDPRWDHVQDIGDVPAF---ELDAIKHFFVHYKDLEPGKF  144 (172)
T ss_dssp             EEECCSSCCCTTCEEEEEEEEEEEEEETTEECCEEEEEETTCGGGTTCCSGGGSCHH---HHHHHHHHHHHTTTTSTTCC
T ss_pred             EEEEcCCCcCCceEEEEEEEEEEEecCCCCCCCEEEEEeCCCCCccccCChHHCCHH---HHHHHHHHHHHhcCcCCCCe
Confidence            999999999999999999999999999999999999999999999999999999986   9999999999999999 999


Q ss_pred             ccccCCCcchhhhhhhHHHHHHHHHH
Q psy300          338 ENVLNTRVEGESSQGFIPGCRGRTEQ  363 (451)
Q Consensus       338 ~~~~~~~~~~~~~~~~i~~~~~~~~~  363 (451)
                      +.+.+|.|+ ++|+++|++|+++|++
T Consensus       145 v~v~gw~~~-~~A~~~I~~~~~~~~~  169 (172)
T 1sxv_A          145 VKAADWVDR-AEAEAEVQRSVERFKA  169 (172)
T ss_dssp             EEEEEEECH-HHHHHHHHHHHHHHHC
T ss_pred             EEeCCCCCH-HHHHHHHHHHHHHHHH
Confidence            999999986 7779999999999987

>3tr4_A Inorganic pyrophosphatase; central intermediary metabolism, hydrolase; HET: MSE; 2.00A {Coxiella burnetii} SCOP: b.40.5.0

Probab=100.00  E-value=2.2e-53  Score=387.12  Aligned_cols=167  Identities=26%  Similarity=0.351  Sum_probs=154.7

Q ss_pred             ccCCccccccccccceeeccCCCCc-cccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccCCCCCCCCc
Q psy300          168 HDIPLYSNVKDKIFNMVVEIPRWTN-AKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETDA  246 (451)
Q Consensus       168 hdiPl~v~~~p~~vn~vvEIPrgS~-~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~~~p~~~~~  246 (451)
                      |++|++.+.  ..++++||||+||+ +|||+++           ++|.++.+|.++.++.||+|||||||||        
T Consensus         6 h~ip~g~~~--~~vnvvIEIP~gs~~~KyE~dk-----------~~g~i~~DR~l~~~~~YP~NYGfIP~Tl--------   64 (178)
T 3tr4_A            6 FLVSAGKGI--DDFNVIIEIPANGGEVKYEYDK-----------ELGFLTVDRFMPTSMRYPCNYGFVPSTL--------   64 (178)
T ss_dssp             --CCCEEET--TEEEEEEEECTTCCSEEEEEET-----------TTTEEEEEEECCSSBCCSSEEEECTTCC--------
T ss_pred             ccCCCCCCC--CEEEEEEEecCCCCcEEEEEec-----------CCCcEEEEEecCcCccCCccccccCCcc--------
Confidence            889998643  89999999999999 9999986           4688888888888999999999999999        


Q ss_pred             CCCCCCCCCcceEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecC--CccccCCCCcccccccCcchHHHHH
Q psy300          247 HTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVN--DPNAAKLNDVADIETHFPGYLKATN  324 (451)
Q Consensus       247 ~~~~~~D~DPlD~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~--d~~~~~i~~~~d~~~~~p~~~~~i~  324 (451)
                          +|||||||||||++.++.||++++|||||+|+|+|+||+|||||||+++  ||+|++|+|++||++   +++++|+
T Consensus        65 ----~~DgDPlDvlvl~~~p~~pG~vi~~r~iGvl~m~Dege~D~KiIaVp~~~~dp~~~~i~di~dl~~---~~l~~i~  137 (178)
T 3tr4_A           65 ----AQDGDPLDVLVLTPVPVQPGVLMRVRALGIMKMEDEAGEDSKVLAVPVVKACRAYEAIQSLKDISS---LLLDAIS  137 (178)
T ss_dssp             ----CTTSSCCEEEECCSSCCCTTCEEEEEEEEEEEEEETTEECCEEEEEECTTTCGGGTTCCSGGGSCH---HHHHHHH
T ss_pred             ----cCCCCceEEEEECCCCCCCeeEEEEEEEEEEEeccCCCCcceEEEEEcCCCCchhhhcCchhhCCH---HHHHHHH
Confidence                7999999999999999999999999999999999999999999999999  899999999999975   5999999


Q ss_pred             HHhhhccCCC-CCcccccCCCcchhhhhhhHHHHHHHHHH
Q psy300          325 EWFKIYKIPD-GKPENVLNTRVEGESSQGFIPGCRGRTEQ  363 (451)
Q Consensus       325 ~~F~~yk~~~-gk~~~~~~~~~~~~~~~~~i~~~~~~~~~  363 (451)
                      |||++||.++ ||++++.+|.|+ +.|+++|++||++|++
T Consensus       138 ~fF~~YK~le~gK~v~~~g~~~~-~~A~~~I~~~~~~~~~  176 (178)
T 3tr4_A          138 HFFERYKDLEPNKWAKVKGWEDK-EAAKKEFEASIVRFKE  176 (178)
T ss_dssp             HHHHHTTTTSTTCCEEEEEEECH-HHHHHHHHHHHHHHHC
T ss_pred             HHHHHHcCcCCCceeEeccCcCH-HHHHHHHHHHHHHHHh
Confidence            9999999998 699999999985 7889999999999986

>1qez_A Ppase, S-ppase, protein (inorganic pyrophosphatase); thermostability, magnesium, hydrolase; 2.70A {Sulfolobus acidocaldarius} SCOP: b.40.5.1

Probab=100.00  E-value=3e-53  Score=384.94  Aligned_cols=160  Identities=28%  Similarity=0.450  Sum_probs=152.5

Q ss_pred             cccccceeeccCCCCccccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccCCCCCCCCcCCCCCCCCCc
Q psy300          177 KDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDP  256 (451)
Q Consensus       177 ~p~~vn~vvEIPrgS~~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~~~p~~~~~~~~~~~D~DP  256 (451)
                      .|..+|++||||+||++|||+++           ++|.+++++.+|+++.||+|||||||||            +|||||
T Consensus         9 ~p~~~nvvIEIP~gs~~KyE~dk-----------~~g~l~~DR~l~~~~~YP~NYGfIP~Tl------------~~DgDP   65 (173)
T 1qez_A            9 APDVVNVLVEIPQGSNIKYEYDD-----------EEGVIKVDRVLYTSMNYPFNYGFIPGTL------------EEDGDP   65 (173)
T ss_dssp             TTTSEEEEEEECTTCCEEEEEET-----------TTTEEEEEEECSSSBCCSSEEEECTTCC------------CTTSSC
T ss_pred             CCCeEEEEEEECCCCCeEEEEec-----------CCCCEEEEeecCCCCcCCcccccccccc------------CCCCCc
Confidence            45789999999999999999986           5799999999999999999999999999            699999


Q ss_pred             ceEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecC--CccccCCCCcccccccCcchHHHHHHHhhhccCCC
Q psy300          257 IDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVN--DPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPD  334 (451)
Q Consensus       257 lD~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~--d~~~~~i~~~~d~~~~~p~~~~~i~~~F~~yk~~~  334 (451)
                      ||||||++.++.||++++|||||+|+|+|+||+|||||||+++  ||+|++|+|++||+++   ++++|+|||++||.++
T Consensus        66 lDvlvl~~~p~~~G~vi~~r~iGvl~m~Dege~D~KiiaV~~~k~dp~~~~i~di~Dl~~~---~l~~i~~fF~~YK~le  142 (173)
T 1qez_A           66 LDVLVITNYQLYPGSVIEVRPIGILYMKDEEGEDAKIVAVPKDKTDPSFSNIKDINDLPQA---TKNKIVHFFEHYKELE  142 (173)
T ss_dssp             CEEEECCSSCCCTTCEEEEEEEEEEEEEETTEEEEEEEEEECTTTCGGGTTCCSGGGSCHH---HHHHHHHHHHHTTTTS
T ss_pred             eEEEEECCCCCCCccEEEEEEEEEEEeecCCCcccEEEEEeCCCCCcchhhcCChHHCCHH---HHHHHHHHHHHhcccc
Confidence            9999999999999999999999999999999999999999999  9999999999999875   9999999999999999


Q ss_pred             -CCcccccCCCcchhhhhhhHHHHHHHHHH
Q psy300          335 -GKPENVLNTRVEGESSQGFIPGCRGRTEQ  363 (451)
Q Consensus       335 -gk~~~~~~~~~~~~~~~~~i~~~~~~~~~  363 (451)
                       ||++++.+|.|+ ++|+++|++||++|++
T Consensus       143 ~gK~v~~~gw~~~-~~A~~~I~~~~~~~~~  171 (173)
T 1qez_A          143 PGKYVKISGWGSA-TEAKNRIQLAIKRVSG  171 (173)
T ss_dssp             TTCCEEEEEEECH-HHHHHHHHHHHHHHC-
T ss_pred             CCCceEEccccCH-HHHHHHHHHHHHHHHh
Confidence             999999999985 7789999999999987

>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=99.92  E-value=9.8e-25  Score=196.67  Aligned_cols=127  Identities=24%  Similarity=0.517  Sum_probs=117.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CC--CceeEEEEEEccHHHHHHHHHhcCCccCCC-------
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DG--KLKGCGFINYANKISAVKAILKSNKKPYKG-------  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg--~skG~aFV~F~~~~~A~~Al~~lng~~f~G-------  100 (451)
                      +.++|||+|||.++++++|+++|++||+|.+++++++. +|  +++|||||+|.+.++|.+|+..+++..+.+       
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            57899999999999999999999999999999999998 44  899999999999999999999999876542       


Q ss_pred             ------------------------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 ------------------------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ------------------------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                                              .+|+++|+++|++||.|.++.++++++|.++|||||+|.+.++|.+|+..+|++.+
T Consensus        82 ~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~  161 (175)
T 3nmr_A           82 MKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQT  161 (175)
T ss_dssp             EEECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCC
T ss_pred             EccccccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcc
Confidence                                    37999999999999999999999998899999999999999999999999998765


Q ss_pred             c
Q psy300          157 K  157 (451)
Q Consensus       157 ~  157 (451)
                      .
T Consensus       162 ~  162 (175)
T 3nmr_A          162 M  162 (175)
T ss_dssp             C
T ss_pred             c
Confidence            3

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.92  E-value=5e-25  Score=207.48  Aligned_cols=127  Identities=22%  Similarity=0.409  Sum_probs=116.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC-------
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG-------  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G-------  100 (451)
                      ..++++|||+|||.++++++|+++|++||+|.+|++++++ +|+++|||||+|.+.++|.+|+..+++..+.|       
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            3467899999999999999999999999999999999998 89999999999999999999999999877665       


Q ss_pred             ----------------------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 ----------------------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ----------------------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                                            .+|+++|+++|++||.|.++.++++. +.++|||||+|.+.++|.+|+..||+..+
T Consensus        92 ~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~-~~~~g~~fV~f~~~~~a~~Ai~~lng~~~  168 (213)
T 4f02_A           92 SQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGMLL  168 (213)
T ss_dssp             CCCCTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TEEEEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             ccccccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC-CCCceEEEEEeCCHHHHHHHHHHhCCCEE
Confidence                                  37999999999999999999999985 44799999999999999999999998764

>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=99.92  E-value=2.9e-24  Score=191.84  Aligned_cols=126  Identities=33%  Similarity=0.590  Sum_probs=118.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC---------
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG---------  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G---------  100 (451)
                      +.++|||+|||.++++++|+++|++||+|.++++++++ +|+++|||||+|.+.++|.+|+..++|..+.|         
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            36899999999999999999999999999999999998 99999999999999999999999999877765         


Q ss_pred             ------------------CCcHHHHHHHhcccCcceeeEEeeCC-CCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 ------------------KITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ------------------~~tee~L~~~F~~fG~V~~v~v~~d~-~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                                        .+++++|+++|++||.|.++.++.++ +|.++|||||+|.+.++|.+|+..+|++.+
T Consensus        81 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~  155 (167)
T 1fxl_A           81 PSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKP  155 (167)
T ss_dssp             CCCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             CCcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCcc
Confidence                              37999999999999999999999874 788999999999999999999999998765

>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=99.91  E-value=2.8e-24  Score=192.64  Aligned_cols=126  Identities=24%  Similarity=0.489  Sum_probs=118.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC---------
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG---------  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G---------  100 (451)
                      +.++|||+|||.++++++|+++|++||+|.++++++++ +|+++|||||+|.+.++|.+|+..++|..+.|         
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            57899999999999999999999999999999999987 89999999999999999999999999877765         


Q ss_pred             ------------------CCcHHHHHHHhcccCcceeeEEeeCC-CCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 ------------------KITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ------------------~~tee~L~~~F~~fG~V~~v~v~~d~-~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                                        .+++++|+++|++||.|.++.++++. +|.++|||||+|.+.++|.+|+..+|++.+
T Consensus        82 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  156 (168)
T 1b7f_A           82 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIP  156 (168)
T ss_dssp             CCSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             CCcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEe
Confidence                              37999999999999999999999985 889999999999999999999999998765

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.91  E-value=4.1e-24  Score=190.68  Aligned_cols=124  Identities=20%  Similarity=0.377  Sum_probs=116.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC------------
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG------------  100 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G------------  100 (451)
                      ++|||+|||.++++++|+++|++||+|.+++++++++|+++|||||+|.+.++|.+|+..++|..+.|            
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            58999999999999999999999999999999999989999999999999999999999999887765            


Q ss_pred             -----------------CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 -----------------KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 -----------------~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                                       .+++++|+++|++||.|.++.++.+ .+|.++|||||+|.+.++|.+|+..+|++.+
T Consensus        81 ~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  154 (166)
T 3md3_A           81 QSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDL  154 (166)
T ss_dssp             CCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc
Confidence                             3799999999999999999999988 6789999999999999999999999998765

>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=99.90  E-value=2.5e-23  Score=191.28  Aligned_cols=126  Identities=25%  Similarity=0.533  Sum_probs=113.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC------
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG------  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G------  100 (451)
                      +....++|||+|||.++++++|+++|++||.|.++++++++ +|.++|||||+|.+.++|.+|+.. ++..+.|      
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~   87 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPK   87 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeee
Confidence            44578899999999999999999999999999999999997 899999999999999999999986 5444433      


Q ss_pred             ---------------------------CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcC
Q psy300          101 ---------------------------KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSN  152 (451)
Q Consensus       101 ---------------------------~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln  152 (451)
                                                 .+|+++|+++|++||.|.++.++.+ .+|.++|||||+|.+.++|.+|+.. +
T Consensus        88 ~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~  166 (196)
T 1l3k_A           88 RAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-K  166 (196)
T ss_dssp             ECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-S
T ss_pred             cccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-C
Confidence                                       3799999999999999999999998 4789999999999999999999986 4


Q ss_pred             CCc
Q psy300          153 KKP  155 (451)
Q Consensus       153 ~ri  155 (451)
                      +..
T Consensus       167 ~~~  169 (196)
T 1l3k_A          167 YHT  169 (196)
T ss_dssp             CCE
T ss_pred             CcE
Confidence            543

>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=99.90  E-value=9.9e-24  Score=189.11  Aligned_cols=125  Identities=28%  Similarity=0.593  Sum_probs=112.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHh---cCCccCCC------
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILK---SNKKPYKG------  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~---lng~~f~G------  100 (451)
                      +.++|||+|||.++++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|+..   ++|+.+..      
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~~~~~   81 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPR   81 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHSCCEETTEECCCEECCCH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhcccccCCeEcccccccch
Confidence            56899999999999999999999999999999999997 899999999999999999999996   44443321      


Q ss_pred             ----------------CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 ----------------KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ----------------~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                                      .+++++|+++|++||.|.++.++.+ .+|.++|||||+|.+.++|.+|+. +++..+
T Consensus        82 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~  153 (167)
T 2cjk_A           82 DEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDF  153 (167)
T ss_dssp             HHHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECS
T ss_pred             hhccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEe
Confidence                            4899999999999999999999988 578999999999999999999997 666544

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.90  E-value=3e-23  Score=193.66  Aligned_cols=126  Identities=25%  Similarity=0.450  Sum_probs=115.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC---------
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG---------  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G---------  100 (451)
                      ..++|||+|||.++++++|+++|++||.|.+++++++. +|+++|||||+|.+.++|.+|+..+++..+.|         
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            56899999999999999999999999999999999987 89999999999999999999999999877665         


Q ss_pred             -----------------------------CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHh
Q psy300          101 -----------------------------KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILK  150 (451)
Q Consensus       101 -----------------------------~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~  150 (451)
                                                   .+++++|+++|++||.|.++.++++ .+|+++|||||+|.+.++|.+|+..
T Consensus       107 ~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~  186 (216)
T 2qfj_A          107 NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS  186 (216)
T ss_dssp             CCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             CccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHH
Confidence                                         3799999999999999999999998 5789999999999999999999999


Q ss_pred             cCCCcc
Q psy300          151 SNKKPY  156 (451)
Q Consensus       151 ln~riy  156 (451)
                      +|++.+
T Consensus       187 l~g~~~  192 (216)
T 2qfj_A          187 MNLFDL  192 (216)
T ss_dssp             HTTCBC
T ss_pred             ccCCEe
Confidence            998765

>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=99.87  E-value=1.6e-21  Score=190.40  Aligned_cols=127  Identities=24%  Similarity=0.321  Sum_probs=119.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC--------
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG--------  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G--------  100 (451)
                      ...++|||+|||.++++++|+++|++||.|.+++++++. +|.++|||||+|.+.++|.+|+..++|..+.|        
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a  172 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT  172 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            356899999999999999999999999999999999987 99999999999999999999999999877765        


Q ss_pred             ----------------------C-CcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 ----------------------K-ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ----------------------~-~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                                            . +++++|+++|+.||.|.++.++++++|.++|||||+|.+.++|.+|+..+|++.+
T Consensus       173 ~~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~  251 (284)
T 3smz_A          173 DAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEMAEEAQQQADGLSL  251 (284)
T ss_dssp             CGGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHHHHHHHHHhCCCcc
Confidence                                  2 3899999999999999999999998999999999999999999999999998876

>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=99.86  E-value=7.7e-22  Score=191.41  Aligned_cols=126  Identities=30%  Similarity=0.495  Sum_probs=115.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC-------
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG-------  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G-------  100 (451)
                      ...+.++|||+|||.++|+++|+++|++||.|.++++.+     ++|||||+|.+.++|.+|+..++|..+.|       
T Consensus        18 ~~~~~~~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           18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR-----DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            445778999999999999999999999999999999964     48999999999999999999999987766       


Q ss_pred             --------------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcccC
Q psy300          101 --------------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  158 (451)
Q Consensus       101 --------------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~~  158 (451)
                                    .+|+++|+++|++||.|.++.++.+.+|+++|||||+|.+.++|.+|+..+|+..++.
T Consensus        93 a~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~  164 (261)
T 3sde_A           93 ATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDGAFLL  164 (261)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHSCEES
T ss_pred             cccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEe
Confidence                          3799999999999999999999999999999999999999999999999996655543

>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=99.86  E-value=1.8e-21  Score=175.11  Aligned_cols=120  Identities=25%  Similarity=0.442  Sum_probs=109.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccC----C-------CeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQY----G-------DIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK   99 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~----G-------~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~   99 (451)
                      +.++|||+|||.++++++|+++|++|    |       .|.++++.     +++|||||+|.+.++|.+|+ .++|..+.
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~-----~~~g~afV~f~~~~~A~~A~-~~~~~~~~   76 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN-----QDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE-----TTTTEEEEEESSHHHHHHHG-GGTTCEET
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec-----CCCCEEEEEeCCHHHHHHHH-HhCCcEec
Confidence            57899999999999999999999999    6       77777764     45899999999999999999 89887766


Q ss_pred             C---------------------------CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhc
Q psy300          100 G---------------------------KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKS  151 (451)
Q Consensus       100 G---------------------------~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~l  151 (451)
                      |                           .+++++|+++|++||.|.++.++++ .+|.++|||||+|.+.++|.+|+..+
T Consensus        77 g~~i~v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l  156 (172)
T 2g4b_A           77 GQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL  156 (172)
T ss_dssp             TEECEEECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHH
T ss_pred             CceeeecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHc
Confidence            5                           3799999999999999999999998 48999999999999999999999999


Q ss_pred             CCCcc
Q psy300          152 NKKPY  156 (451)
Q Consensus       152 n~riy  156 (451)
                      |+..+
T Consensus       157 ~g~~~  161 (172)
T 2g4b_A          157 NGMQL  161 (172)
T ss_dssp             TTCEE
T ss_pred             CCCEE
Confidence            98765

>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=99.85  E-value=1.7e-21  Score=190.96  Aligned_cols=128  Identities=16%  Similarity=0.171  Sum_probs=107.4

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC------
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG------  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G------  100 (451)
                      ....+.++|||+|||.++++++|+++|++||+|.+|+++++..+ ++|||||+|.+.++|.+|+. ++|..+.|      
T Consensus        36 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~A~~A~~-~~~~~~~g~~i~v~  113 (292)
T 2ghp_A           36 TRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK-NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVS  113 (292)
T ss_dssp             ------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS-SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC-CcEEEEEEECCHHHHHHHHH-hCCcEeCCcEEEEE
Confidence            34567899999999999999999999999999999999998755 58999999999999999994 88877766      


Q ss_pred             --------------CCcHHHHHHHhcccC-cceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 --------------KITEEEFKEHFGQYG-DIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 --------------~~tee~L~~~F~~fG-~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                                    .+++++|+++|++|| .|.++.++++..|.++|||||+|.+.++|.+|+..+++..+
T Consensus       114 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~  184 (292)
T 2ghp_A          114 HLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKI  184 (292)
T ss_dssp             ECCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             ECCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEe
Confidence                          479999999999999 99999999987788999999999999999999999988654

>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=99.84  E-value=6.9e-21  Score=178.85  Aligned_cols=122  Identities=19%  Similarity=0.298  Sum_probs=107.8

Q ss_pred             CCCceEEEcCCC-CCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC--------
Q psy300           30 TKRGRLFIKNLP-FKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG--------  100 (451)
Q Consensus        30 ~~~~~lfVgnLp-~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G--------  100 (451)
                      .+.++|||+||| .++++++|+++|++||.|.+|+++++    ++|||||+|.+.++|.+|++.|||..+.|        
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            367899999999 89999999999999999999999865    47999999999999999999887643221        


Q ss_pred             --------------------------------------------------------CCcHHHHHHHhcccCcc--eeeEE
Q psy300          101 --------------------------------------------------------KITEEEFKEHFGQYGDI--IDAQL  122 (451)
Q Consensus       101 --------------------------------------------------------~~tee~L~~~F~~fG~V--~~v~v  122 (451)
                                                                              .+|+++|+++|++||.|  .++++
T Consensus        78 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~  157 (205)
T 3tyt_A           78 KQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKV  157 (205)
T ss_dssp             SCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEE
T ss_pred             cCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEE
Confidence                                                                    25899999999999999  88998


Q ss_pred             eeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          123 LKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       123 ~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      +.+. +.++|||||+|.+.++|.+|+..||+..+
T Consensus       158 ~~~~-~~~~g~gfV~f~~~~~A~~Ai~~lng~~~  190 (205)
T 3tyt_A          158 FSGK-SERSSSGLLEWDSKSDALETLGFLNHYQM  190 (205)
T ss_dssp             CSCC-SSSSEEEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             EcCC-CCCceEEEEEeCCHHHHHHHHHHhCCCCc
Confidence            8875 55679999999999999999999998765

>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=99.84  E-value=2.7e-21  Score=188.79  Aligned_cols=121  Identities=26%  Similarity=0.425  Sum_probs=111.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC---------
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG---------  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G---------  100 (451)
                      .++++|||+|||.++++++|+++|++|| |.++.+     ++++|||||+|.+.++|.+|+..++|..+.|         
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~-----~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~   93 (284)
T 3smz_A           20 RNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-----DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP   93 (284)
T ss_dssp             HCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE-----ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE-----ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC
Confidence            3678999999999999999999999999 999988     5678999999999999999999999987766         


Q ss_pred             ------------CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 ------------KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ------------~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                                  .+++++|+++|++||.|.++.++.+ .+|.++|||||+|.+.++|.+|+..+++..+
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~  162 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPL  162 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEe
Confidence                        3799999999999999999999987 5789999999999999999999999988654

>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=99.84  E-value=9.1e-21  Score=185.82  Aligned_cols=126  Identities=19%  Similarity=0.295  Sum_probs=110.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCC-CeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC--------
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYG-DIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG--------  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G-~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G--------  100 (451)
                      ...++|||+|||.++++++|+++|++|| .|.+++++++..|.++|||||+|.+.++|.+|+..++|..+.|        
T Consensus       115 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  194 (292)
T 2ghp_A          115 LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS  194 (292)
T ss_dssp             CCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            4688999999999999999999999999 9999999998888999999999999999999999998876644        


Q ss_pred             --------------------------C-CcHHHHHHHhcccCcceeeEEeeCCC--CCccceEEEEecchHHHHHHHHhc
Q psy300          101 --------------------------K-ITEEEFKEHFGQYGDIIDAQLLKNAD--GKLKGCGFINYANKISAVKAILKS  151 (451)
Q Consensus       101 --------------------------~-~tee~L~~~F~~fG~V~~v~v~~d~~--g~srG~gFV~F~s~e~A~~Ai~~l  151 (451)
                                                . +++++|+++|++||.|.++.++++..  |.++|||||+|.+.++|.+|+ .+
T Consensus       195 ~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l  273 (292)
T 2ghp_A          195 NPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QM  273 (292)
T ss_dssp             CCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GG
T ss_pred             CCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-Hh
Confidence                                      4 89999999999999999999999866  999999999999999999999 99


Q ss_pred             CCCcc
Q psy300          152 NKKPY  156 (451)
Q Consensus       152 n~riy  156 (451)
                      |++.+
T Consensus       274 ~g~~~  278 (292)
T 2ghp_A          274 NRSLL  278 (292)
T ss_dssp             TTEEE
T ss_pred             cCCEE
Confidence            98764

>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=99.83  E-value=1.2e-21  Score=177.13  Aligned_cols=124  Identities=24%  Similarity=0.305  Sum_probs=108.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC-------
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG-------  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G-------  100 (451)
                      .....++|||+|||.++++++|+++|++||.+..+.+....+|+++|||||+|.+.++|.+|+ +++|..+.|       
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~v~~   87 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVFGNEIKLEK   87 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHH-HGGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHH-hcCCCEeCCeEEEEec
Confidence            455789999999999999999999999999877633333348899999999999999999999 598877766       


Q ss_pred             ----------------------CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 ----------------------KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ----------------------~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                                            .+++++|+++|++||.|..+    ..++.++|||||+|.+.++|.+|+..+|++.+
T Consensus        88 ~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~  161 (175)
T 1fje_B           88 PKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI  161 (175)
T ss_dssp             CCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEE
T ss_pred             CCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEE
Confidence                                  37999999999999988766    56788999999999999999999999988664

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.82  E-value=3.9e-20  Score=170.18  Aligned_cols=120  Identities=24%  Similarity=0.444  Sum_probs=106.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccC----C-------CeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQY----G-------DIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK   99 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~----G-------~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~   99 (451)
                      ..++|||+|||.++++++|+++|++|    |       .|.++.+     ++++|||||+|.+.++|.+|+ .+||..+.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~-----~~~~g~afV~F~~~~~A~~Al-~l~g~~~~   76 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI-----NQDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE-----ETTTTEEEEEESCSHHHHHHG-GGTTEEET
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe-----cCCCCEEEEEeCCHHHHHHHH-HhcCCEEc
Confidence            57899999999999999999999999    5       5666655     466999999999999999999 78876543


Q ss_pred             C-----------------------------------------------CCcHHHHHHHhcccCcceeeEEeeCC-CCCcc
Q psy300          100 G-----------------------------------------------KITEEEFKEHFGQYGDIIDAQLLKNA-DGKLK  131 (451)
Q Consensus       100 G-----------------------------------------------~~tee~L~~~F~~fG~V~~v~v~~d~-~g~sr  131 (451)
                      |                                               .+++++|+++|++||.|.++.++.++ +|.++
T Consensus        77 g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~  156 (198)
T 2yh0_A           77 GQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSK  156 (198)
T ss_dssp             TEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEE
T ss_pred             CceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcc
Confidence            3                                               26999999999999999999999984 89999


Q ss_pred             ceEEEEecchHHHHHHHHhcCCCcc
Q psy300          132 GCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       132 G~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      |||||+|.+.++|.+|+..+|+..+
T Consensus       157 g~afV~f~~~~~a~~A~~~l~g~~~  181 (198)
T 2yh0_A          157 GYAFCEYVDINVTDQAIAGLNGMQL  181 (198)
T ss_dssp             EEEEEEESSSSHHHHHHHHHTTCEE
T ss_pred             eEEEEEECCHHHHHHHHHHcCCCEE
Confidence            9999999999999999999988664

>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=99.82  E-value=1.2e-19  Score=176.88  Aligned_cols=124  Identities=23%  Similarity=0.379  Sum_probs=110.3

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHH----HHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC--
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFK----EHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG--  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~----~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G--  100 (451)
                      .+..+.++|||+|||.++++++|+    ++|++||.|.+|++++  +|+++|||||+|.+.++|.+|+..+||..+.|  
T Consensus         4 ~~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~--~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC--CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            345678999999999999999976    8999999999999876  78899999999999999999998887754322  


Q ss_pred             --------------------------------------------------------------------------------
Q psy300          101 --------------------------------------------------------------------------------  100 (451)
Q Consensus       101 --------------------------------------------------------------------------------  100 (451)
                                                                                                      
T Consensus        82 l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~  161 (282)
T 3pgw_A           82 MRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQP  161 (282)
T ss_pred             EEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCC
Confidence                                                                                            


Q ss_pred             --------------------------------------------------------CCcHHHHHHHhcccCcceeeEEee
Q psy300          101 --------------------------------------------------------KITEEEFKEHFGQYGDIIDAQLLK  124 (451)
Q Consensus       101 --------------------------------------------------------~~tee~L~~~F~~fG~V~~v~v~~  124 (451)
                                                                              .+++++|+++|++||.|.++.++.
T Consensus       162 ~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~  241 (282)
T 3pgw_A          162 PYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVP  241 (282)
T ss_pred             CCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEec
Confidence                                                                    258999999999999999999997


Q ss_pred             CCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          125 NADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       125 d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++    +|||||+|.+.++|.+|+..+|++.+
T Consensus       242 ~~----~g~afV~f~~~~~A~~A~~~l~g~~~  269 (282)
T 3pgw_A          242 GR----HDIAFVEFDNEVQAGAARDALQGFKI  269 (282)
T ss_pred             CC----CcEEEEEeCCHHHHHHHHHHcCCcEe
Confidence            63    58999999999999999999998765

>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=99.80  E-value=4.3e-19  Score=168.66  Aligned_cols=120  Identities=22%  Similarity=0.336  Sum_probs=107.4

Q ss_pred             CCCCceEEEcCCCC-CCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC-------
Q psy300           29 KTKRGRLFIKNLPF-KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG-------  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~-~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G-------  100 (451)
                      ..++++|||+|||. ++++++|+++|++||.|.+++++++.    +|||||+|.+.++|.+|+..++|..+.|       
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~  106 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL  106 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEEC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            45789999999999 99999999999999999999998874    7899999999999999999887754432       


Q ss_pred             -------------------------------------------------------CCcHHHHHHHhcccC-cceeeEEee
Q psy300          101 -------------------------------------------------------KITEEEFKEHFGQYG-DIIDAQLLK  124 (451)
Q Consensus       101 -------------------------------------------------------~~tee~L~~~F~~fG-~V~~v~v~~  124 (451)
                                                                             .+++++|+++|++|| .|.++.++.
T Consensus       107 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~  186 (229)
T 2adc_A          107 SKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ  186 (229)
T ss_dssp             CSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECS
T ss_pred             ecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEE
Confidence                                                                   258999999999999 999999965


Q ss_pred             CCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          125 NADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       125 d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      +    ++|||||+|.+.++|.+|+..+|++.+
T Consensus       187 ~----~~g~afV~f~~~~~A~~Ai~~l~g~~~  214 (229)
T 2adc_A          187 K----DRKMALIQMGSVEEAVQALIDLHNHDL  214 (229)
T ss_dssp             S----STTCEEEEESSHHHHHHHHHHHTTCBS
T ss_pred             C----CCcEEEEEECCHHHHHHHHHHHCCCcc
Confidence            3    379999999999999999999998765

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.79  E-value=2.6e-19  Score=165.35  Aligned_cols=118  Identities=22%  Similarity=0.343  Sum_probs=106.0

Q ss_pred             CCceEEEcCCCC-CCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC---------
Q psy300           31 KRGRLFIKNLPF-KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG---------  100 (451)
Q Consensus        31 ~~~~lfVgnLp~-~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G---------  100 (451)
                      .+++|||+|||. ++++++|+++|++||.|.++++++++    +|||||+|.+.++|.+|+..++|..+.|         
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            468999999999 99999999999999999999998764    7899999999999999999887754433         


Q ss_pred             -----------------------------------------------------CCcHHHHHHHhcccC-cceeeEEeeCC
Q psy300          101 -----------------------------------------------------KITEEEFKEHFGQYG-DIIDAQLLKNA  126 (451)
Q Consensus       101 -----------------------------------------------------~~tee~L~~~F~~fG-~V~~v~v~~d~  126 (451)
                                                                           .+++++|+++|++|| .|.++.++.+ 
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-  156 (198)
T 1qm9_A           78 HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-  156 (198)
T ss_dssp             CCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-
T ss_pred             CCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-
Confidence                                                                 258999999999999 9999999764 


Q ss_pred             CCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          127 DGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       127 ~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                         ++|+|||+|.+.++|.+|+..+|++.+
T Consensus       157 ---~~g~afV~f~~~~~A~~A~~~l~g~~~  183 (198)
T 1qm9_A          157 ---DRKMALIQMGSVEEAVQALIDLHNHDL  183 (198)
T ss_dssp             ---TSSCEEEECSSHHHHHHHHHHHTSSCC
T ss_pred             ---CCcEEEEEeCCHHHHHHHHHHhcCCcc
Confidence               279999999999999999999998775

>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=99.65  E-value=3.5e-16  Score=129.86  Aligned_cols=72  Identities=28%  Similarity=0.502  Sum_probs=67.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .+.++|||+|||.++|+++|+++|++||+|.++++++++ +|+++|||||+|.+.++|.+|++.|||..+.|+
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr   89 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSK   89 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            356899999999999999999999999999999999998 899999999999999999999999999888773

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.62  E-value=1.7e-15  Score=128.15  Aligned_cols=71  Identities=14%  Similarity=0.209  Sum_probs=67.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .+.++|||+|||.++++++|+++|++||.|.++++++++ ||+++|||||+|.+.++|.+|++.|||+.+.|
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~g   75 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMG   75 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            467899999999999999999999999999999999998 89999999999999999999999999998876

>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=99.59  E-value=7.1e-15  Score=122.24  Aligned_cols=75  Identities=24%  Similarity=0.425  Sum_probs=69.6

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .......++|||+|||.++++++|+++|++||.|.+++++++++|+++|||||+|.+.++|.+|+..|||..+.|
T Consensus         9 ~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   83 (105)
T 2dnh_A            9 ESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMP   83 (105)
T ss_dssp             CCSCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCT
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCC
Confidence            334457899999999999999999999999999999999999999999999999999999999999999988775

>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=99.57  E-value=6.5e-15  Score=124.63  Aligned_cols=86  Identities=28%  Similarity=0.451  Sum_probs=78.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC-------
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK-------  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~-------  101 (451)
                      ....++|||+|||.++++++|+++|++||.|.+++++++  +.++|||||+|.+.++|.+|+..+||..+.|+       
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   82 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS--TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC--CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            446789999999999999999999999999999999865  56699999999999999999999999999883       


Q ss_pred             ------------CcHHHHHHHhcccCc
Q psy300          102 ------------ITEEEFKEHFGQYGD  116 (451)
Q Consensus       102 ------------~tee~L~~~F~~fG~  116 (451)
                                  .++++|.++|++||.
T Consensus        83 ~~~~~~~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           83 NANRAFQKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             CHHHHTTTSCHHHHHHHHHHHHHHHCC
T ss_pred             cCChhhhhhhHhHhHHHHHHHHHHhCC
Confidence                        478999999999986

>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=99.57  E-value=2.9e-15  Score=121.49  Aligned_cols=69  Identities=26%  Similarity=0.457  Sum_probs=63.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCC--CeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYG--DIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G--~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .+|||+|||.++++++|+++|++||  .|.++++++++ +|+++|||||+|.+.++|.+|++.|||..+.|+
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr   73 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQ   73 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCE
Confidence            5899999999999999999999999  99999999997 999999999999999999999999999988884

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=7.5e-15  Score=122.77  Aligned_cols=73  Identities=23%  Similarity=0.406  Sum_probs=67.9

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      +....++|||+|||.++|+++|+++|++||+|.+|+++++++|+++|||||+|.+.++|.+|+. +++..+.|+
T Consensus         7 ~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr   79 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKET   79 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCCTTT
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEECCE
Confidence            3446789999999999999999999999999999999999889999999999999999999999 899888885

>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=99.56  E-value=1.1e-14  Score=116.68  Aligned_cols=71  Identities=31%  Similarity=0.491  Sum_probs=66.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .+.++|||+|||.++++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|+..+||..+.|
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   75 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGG   75 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            467899999999999999999999999999999999997 99999999999999999999999999987776

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.56  E-value=1.2e-14  Score=119.60  Aligned_cols=74  Identities=23%  Similarity=0.424  Sum_probs=69.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeE-EEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDII-DAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~-~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .....++|||+|||.++++++|+++|++||.|. ++++++++ +|+++|||||+|.+.++|.+|+..|||..+.|+
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   80 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGA   80 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCC
Confidence            345789999999999999999999999999999 99999997 999999999999999999999999999887764

>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=99.55  E-value=1.5e-14  Score=114.92  Aligned_cols=69  Identities=17%  Similarity=0.440  Sum_probs=65.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..+|||+|||.++++++|+++|++||+|.++++++++ +|+++|||||+|.+.++|.+|+..+||..+.|
T Consensus         1 t~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g   70 (83)
T 3md1_A            1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNG   70 (83)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCC
Confidence            3689999999999999999999999999999999996 89999999999999999999999999988766

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=2.2e-14  Score=118.31  Aligned_cols=74  Identities=32%  Similarity=0.547  Sum_probs=69.0

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....+.++|||+|||.++++++|+++|++||.|.+++++++++|+++|||||+|.+.++|.+|+..+||..+.|
T Consensus        12 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   85 (100)
T 2do4_A           12 STSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKE   85 (100)
T ss_dssp             SSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSS
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            34557889999999999999999999999999999999999999999999999999999999999999987765

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.55  E-value=3e-15  Score=123.45  Aligned_cols=70  Identities=10%  Similarity=0.267  Sum_probs=64.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCC--eEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCcc
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGD--IIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKP   97 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~--I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~   97 (451)
                      ....+.+|||+|||+++|+++|+++|++||.  +.+|++++|+ +|++||||||+|.+.++|.+|++.+||..
T Consensus         5 ~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~   77 (95)
T 2lkz_A            5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLH   77 (95)
T ss_dssp             SSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSS
T ss_pred             cCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCC
Confidence            3457899999999999999999999999995  6799999998 89999999999999999999999999863

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.55  E-value=3.5e-15  Score=123.74  Aligned_cols=70  Identities=17%  Similarity=0.286  Sum_probs=67.2

Q ss_pred             CCceEEEcCCCC------CCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           31 KRGRLFIKNLPF------KITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        31 ~~~~lfVgnLp~------~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..++|||+|||.      ++++++|+++|++||.|.++++++++ ||+++|||||+|.+.++|.+|+..|||..+.|
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g   81 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDL   81 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSS
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCC
Confidence            468999999999      99999999999999999999999998 79999999999999999999999999999987

>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=99.55  E-value=9e-15  Score=124.33  Aligned_cols=69  Identities=28%  Similarity=0.516  Sum_probs=63.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..++|||+|||.++++++|+++|++||.|.+|+++++. +.++|||||+|.+.++|.+|++.|+|..+.|
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~-~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g   72 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGMLLND   72 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TEEEEEEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC-CCCCceEEEEECCHHHHHHHHHHcCCCEECC
Confidence            46789999999999999999999999999999999985 4589999999999999999999999988776

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=6.3e-15  Score=117.81  Aligned_cols=72  Identities=21%  Similarity=0.413  Sum_probs=67.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .+.++|||+|||.++++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|+..|||..+.|+
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   75 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQ   75 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeE
Confidence            477899999999999999999999999999999999987 899999999999999999999999999887763

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.55  E-value=2.4e-14  Score=118.78  Aligned_cols=74  Identities=16%  Similarity=0.336  Sum_probs=69.3

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhcc-CCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCcc-CCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQ-YGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP-YKG  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~-~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~-f~G  100 (451)
                      .+..+.++|||+|||.++++++|+++|++ ||.|.+++++++.+|+++|||||+|.+.++|.+|+..+++.. +.|
T Consensus         4 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g   79 (104)
T 2dhg_A            4 GSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGS   79 (104)
T ss_dssp             CCSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSS
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCC
Confidence            34557899999999999999999999999 999999999999999999999999999999999999999988 776

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=2.2e-14  Score=118.98  Aligned_cols=74  Identities=26%  Similarity=0.478  Sum_probs=68.6

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      +....+.++|||+|||.++++++|+++|++||.|.+++++++ +|.++|||||+|.+.++|.+|+..||+..+.|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   82 (103)
T 2d9p_A            9 RITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVAT   82 (103)
T ss_dssp             CCCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSS
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            344558899999999999999999999999999999999999 99999999999999999999999999987765

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=1.6e-14  Score=117.58  Aligned_cols=75  Identities=23%  Similarity=0.385  Sum_probs=69.3

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..+..+.++|||+|||.++++++|+++|++||.|.++++++++ +++++|||||+|.+.++|.+|+..|||..+.|
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   84 (95)
T 2cqc_A            9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDG   84 (95)
T ss_dssp             CCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            3345578899999999999999999999999999999999997 79999999999999999999999999987776

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=1.8e-14  Score=119.92  Aligned_cols=74  Identities=26%  Similarity=0.409  Sum_probs=68.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ...+.++|||+|||.++++++|+++|++||.|.++.+++++ +|.++|||||+|.+.++|.+|+..+||..+.|+
T Consensus        19 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   93 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ   93 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCc
Confidence            34467899999999999999999999999999999999997 899999999999999999999999999887763

>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=99.54  E-value=1e-14  Score=116.32  Aligned_cols=73  Identities=23%  Similarity=0.383  Sum_probs=68.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ..+.++|||+|||.++++++|+++|++||+|.++++++++ +|+++|||||+|.+.++|.+|++.+||..+.|+
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   77 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGR   77 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            3578999999999999999999999999999999999986 899999999999999999999999999888763

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.54  E-value=2.6e-14  Score=117.77  Aligned_cols=75  Identities=27%  Similarity=0.372  Sum_probs=70.0

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEE--------EEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCcc
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIID--------AQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKP   97 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~--------i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~   97 (451)
                      ......++|||+|||.++++++|+++|++||.|.+        +++++++ +|+++|||||+|.+.++|.+|++.|||..
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~   87 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKE   87 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCB
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCE
Confidence            34567899999999999999999999999999999        9999997 89999999999999999999999999998


Q ss_pred             CCCC
Q psy300           98 YKGK  101 (451)
Q Consensus        98 f~G~  101 (451)
                      +.|+
T Consensus        88 ~~g~   91 (99)
T 2la6_A           88 FSGN   91 (99)
T ss_dssp             SSSS
T ss_pred             eCCc
Confidence            8874

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=2.5e-14  Score=116.57  Aligned_cols=71  Identities=30%  Similarity=0.550  Sum_probs=67.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .+.++|||+|||.++++++|+++|++||.|.++++++++ +++++|||||+|.+.++|.+|+..+|+..+.|
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   74 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAG   74 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCC
Confidence            467899999999999999999999999999999999987 89999999999999999999999999987765

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.54  E-value=2e-15  Score=123.18  Aligned_cols=69  Identities=17%  Similarity=0.398  Sum_probs=62.5

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCC-CeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcC-CccCCC
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFGQYG-DIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSN-KKPYKG  100 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~~~G-~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~ln-g~~f~G  100 (451)
                      +++|||+|||.++|+++|+++|++|| +|.+|++++++ +|.++|||||+|.+.++|.+|++.++ +..+.|
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~g   72 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILG   72 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECC
Confidence            46899999999999999999999999 79999999997 89999999999999999999998874 444544

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.54  E-value=2.2e-14  Score=118.97  Aligned_cols=73  Identities=25%  Similarity=0.396  Sum_probs=68.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      +..+.++|||+|||.++++++|+++|++||.|.+|++++++ +|+++|||||+|.+.++|.+|+..||+..+.|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   84 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDH   84 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCC
Confidence            45578999999999999999999999999999999999997 89999999999999999999999999987665

>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=99.54  E-value=3.1e-14  Score=119.79  Aligned_cols=76  Identities=30%  Similarity=0.527  Sum_probs=70.3

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .....+.++|||+|||.++++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|++.++|..+.|+
T Consensus        20 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~   96 (108)
T 2jrs_A           20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGR   96 (108)
T ss_dssp             CCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSS
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            4455678999999999999999999999999999999999987 899999999999999999999999999888774

>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=99.53  E-value=2.4e-14  Score=118.99  Aligned_cols=74  Identities=22%  Similarity=0.385  Sum_probs=69.1

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .+....++|||+|||.++++++|+++|++||.|.++++++++ +++++|||||+|.+.++|.+|+..|++..+.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   84 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYG   84 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSS
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            345578999999999999999999999999999999999998 89999999999999999999999999987765

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.53  E-value=1.2e-14  Score=115.39  Aligned_cols=69  Identities=23%  Similarity=0.388  Sum_probs=64.2

Q ss_pred             CceEEEcCCCCCC------CHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           32 RGRLFIKNLPFKI------TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        32 ~~~lfVgnLp~~v------te~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .++|||+|||.++      ++++|+++|++||+|.+++++ ..+|+++|||||+|.+.++|.+|+..|||..+.|+
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~   75 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   75 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSS
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCc
Confidence            3789999999999      779999999999999999987 35899999999999999999999999999999885

>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=99.53  E-value=1.6e-14  Score=118.38  Aligned_cols=70  Identities=20%  Similarity=0.413  Sum_probs=66.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      +.++|||+|||.++++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|+..+||..+.|
T Consensus         1 P~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   71 (96)
T 2x1f_A            1 PSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGS   71 (96)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            46899999999999999999999999999999999997 89999999999999999999999999987766

>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=99.53  E-value=2e-14  Score=117.21  Aligned_cols=73  Identities=27%  Similarity=0.368  Sum_probs=68.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .....++|||+|||.++++++|+++|++||+|.+++++++++|+++|||||+|.+.++|.+|+..+|+..+.|
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   84 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYG   84 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            3456789999999999999999999999999999999999899999999999999999999999999988776

>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=99.53  E-value=2e-14  Score=118.20  Aligned_cols=72  Identities=28%  Similarity=0.551  Sum_probs=67.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..+.++|||+|||.++++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|+..+||..+.|
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   77 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQG   77 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            4578899999999999999999999999999999999998 99999999999999999999999999987765

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.53  E-value=3.9e-14  Score=119.82  Aligned_cols=75  Identities=35%  Similarity=0.556  Sum_probs=69.6

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..+..+.++|||+|||.++++++|+++|++||.|.+|++++++ +|.++|||||+|.+.++|.+|+..|+|..+.|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   84 (115)
T 2dgo_A            9 KKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGG   84 (115)
T ss_dssp             CCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETT
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            3445678999999999999999999999999999999999997 99999999999999999999999999987765

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=3.4e-14  Score=116.91  Aligned_cols=72  Identities=22%  Similarity=0.495  Sum_probs=67.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .....++|||+|||.++++++|+++|++||.|.++++++++ +++++|||||+|.+.++|.+|++ +++..+.|
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g   78 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMG   78 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECC
Confidence            44578999999999999999999999999999999999987 89999999999999999999998 89887765

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=1.7e-14  Score=119.58  Aligned_cols=74  Identities=19%  Similarity=0.387  Sum_probs=68.8

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .+..+.++|||+|||.++++++|+++|++||.|.++.+++++ +++++|||||+|.+.++|.+|+..|||..+.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   82 (103)
T 2dnm_A            8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDG   82 (103)
T ss_dssp             SCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTT
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            345578999999999999999999999999999999999987 79999999999999999999999999987765

>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=99.53  E-value=4.6e-14  Score=119.16  Aligned_cols=75  Identities=24%  Similarity=0.471  Sum_probs=70.0

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ......++|||+|||.++++++|+++|++||.|.+++++++.+|.++|||||+|.+.++|.+|+..|||..+.|+
T Consensus        20 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~   94 (114)
T 1x5o_A           20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTP   94 (114)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCC
Confidence            344577899999999999999999999999999999999999999999999999999999999999999988764

>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=99.52  E-value=3.5e-14  Score=113.97  Aligned_cols=72  Identities=21%  Similarity=0.596  Sum_probs=65.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...+.++|||+|||.++++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|++. ++..+.|
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~~g   79 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ-KEHRLDG   79 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS-SCEEETT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh-CCCEECC
Confidence            34578899999999999999999999999999999999997 899999999999999999999965 5555555

>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=99.52  E-value=3.9e-14  Score=118.15  Aligned_cols=76  Identities=24%  Similarity=0.503  Sum_probs=70.0

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .....+.++|||+|||.++++++|+++|++||.|.+++++++.+|+++|||||+|.+.++|.+|+..|||..+.|+
T Consensus        23 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   98 (107)
T 3ulh_A           23 GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGR   98 (107)
T ss_dssp             -CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCc
Confidence            3345678999999999999999999999999999999999999999999999999999999999999999887763

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.52  E-value=1.7e-14  Score=116.81  Aligned_cols=78  Identities=19%  Similarity=0.228  Sum_probs=71.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC------CcH
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK------ITE  104 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~------~te  104 (451)
                      ....|||+||++++|+++|+++|.+||+|.++++..     ++|||||+|.++++|.+|++.||+..+.|+      .++
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~-----~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~e   80 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL-----NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPSE   80 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCCH
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC-----CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECCH
Confidence            577999999999999999999999999999999964     699999999999999999999999999985      588


Q ss_pred             HHHHHHhcc
Q psy300          105 EEFKEHFGQ  113 (451)
Q Consensus       105 e~L~~~F~~  113 (451)
                      .++..+|++
T Consensus        81 ~~~~~~~~~   89 (89)
T 2wbr_A           81 NEVQSIMQH   89 (89)
T ss_dssp             HHHHHHHCC
T ss_pred             HHHHHHhhC
Confidence            888888753

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.52  E-value=3.4e-14  Score=118.35  Aligned_cols=75  Identities=27%  Similarity=0.587  Sum_probs=68.9

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeEC-C-CCCceeEEEEEEccHHHHHHHHHhc-CCccCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-A-DGKLKGCGFINYANKISAVKAILKS-NKKPYKG  100 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d-~-tg~skG~aFV~F~~~~~A~~Al~~l-ng~~f~G  100 (451)
                      .......++|||+|||.++++++|+++|++||.|.+|+++++ . +++++|||||+|.+.++|.+|+..+ |+..+.|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g   86 (107)
T 2cph_A            9 VPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYG   86 (107)
T ss_dssp             SCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSS
T ss_pred             cccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECC
Confidence            334567899999999999999999999999999999999998 4 9999999999999999999999999 8887765

>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=99.52  E-value=2.3e-14  Score=120.26  Aligned_cols=74  Identities=24%  Similarity=0.363  Sum_probs=68.5

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....+.++|||+|||.++++++|+++|++||.|.+++++++. +|.++|||||+|.+.++|.+|+..|||..+.|
T Consensus        21 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   95 (110)
T 1oo0_B           21 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG   95 (110)
T ss_dssp             CCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            344567899999999999999999999999999999999987 89999999999999999999999999987765

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.52  E-value=3.1e-14  Score=115.78  Aligned_cols=74  Identities=27%  Similarity=0.510  Sum_probs=68.8

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....+.++|||+|||.++++++|+++|++||+|.++++++++ +++++|||||+|.+.++|.+|++.+|+..+.|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   85 (94)
T 2e5h_A           11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFG   85 (94)
T ss_dssp             SCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETT
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCC
Confidence            345578899999999999999999999999999999999987 79999999999999999999999999988776

>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=99.51  E-value=3.8e-14  Score=120.00  Aligned_cols=75  Identities=24%  Similarity=0.422  Sum_probs=69.1

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .......++|||+|||.++++++|+++|++||.|.++++++++ +++++|||||+|.+.++|.+|+..||+..+.|
T Consensus        19 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   94 (115)
T 2cpz_A           19 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGM   94 (115)
T ss_dssp             CCCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CcCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECC
Confidence            3345567899999999999999999999999999999999998 99999999999999999999999999987765

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.51  E-value=2.1e-14  Score=117.31  Aligned_cols=71  Identities=27%  Similarity=0.434  Sum_probs=66.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEE-EEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i-~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .+.++|||+|||.++++++|+++|++||.|.++ ++++++ +|.++|||||+|.+.++|.+|+..+||..+.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   75 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCN   75 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            468899999999999999999999999999999 999985 99999999999999999999999999987654

>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=99.51  E-value=4.7e-14  Score=118.29  Aligned_cols=73  Identities=27%  Similarity=0.495  Sum_probs=67.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcC------CccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSN------KKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~ln------g~~f~G  100 (451)
                      +..+.++|||+|||.++++++|+++|++||.|.+|++++++ +|.++|||||+|.+.++|.+|+..+|      +..+.|
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            45578899999999999999999999999999999999997 89999999999999999999999999      776665

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.51  E-value=8.5e-14  Score=112.75  Aligned_cols=72  Identities=28%  Similarity=0.557  Sum_probs=67.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ..+.++|||+|||.++++++|+++|++||.|.+++++++ +|+++|||||+|.+.++|.+|+..|++..+.|+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~-~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~   76 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKLSGR   76 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTB
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-CCCcceEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            457789999999999999999999999999999999985 889999999999999999999999999887763

>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=99.51  E-value=4e-14  Score=120.60  Aligned_cols=72  Identities=32%  Similarity=0.498  Sum_probs=67.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....++|||+|||.++++++|+++|++||.|.++.++.+.+|+++|||||+|.+.++|.+|+..|||..+.|
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g   75 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHG   75 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            346789999999999999999999999999999999999899999999999999999999999999987765

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.51  E-value=4.6e-14  Score=124.03  Aligned_cols=88  Identities=11%  Similarity=0.245  Sum_probs=76.5

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCC---eEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC--
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGD---IIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK--  101 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~---I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~--  101 (451)
                      ......++|||+|||+++|+++|+++|++||.   |.+|++++++.|+++|||||+|.+.++|.+|+. +|+..+.|+  
T Consensus        39 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i  117 (136)
T 2hgl_A           39 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESMGHRYI  117 (136)
T ss_dssp             SSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEE
Confidence            34456789999999999999999999999999   899999999889999999999999999999999 999988885  


Q ss_pred             ----CcHHHHHHHhcccC
Q psy300          102 ----ITEEEFKEHFGQYG  115 (451)
Q Consensus       102 ----~tee~L~~~F~~fG  115 (451)
                          .+..++....+..|
T Consensus       118 ~V~~a~~~e~~~~~~~~~  135 (136)
T 2hgl_A          118 EVFKSHRTEMDWVLKHSG  135 (136)
T ss_dssp             EEEECCHHHHHHHHTTSC
T ss_pred             EEEECChHHHHHHHhhcC
Confidence                35566666555544

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.50  E-value=6.3e-14  Score=118.20  Aligned_cols=73  Identities=29%  Similarity=0.462  Sum_probs=68.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .....++|||+|||.++++++|+++|++||.|.+++++++++|+++|||||+|.+.++|.+|+..||+..+.|
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   83 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFD   83 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            3456789999999999999999999999999999999999999999999999999999999999999987765

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.50  E-value=4.7e-14  Score=119.85  Aligned_cols=76  Identities=26%  Similarity=0.380  Sum_probs=69.8

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .....+.++|||+|||.++++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|+..+||..+.|+
T Consensus        34 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  110 (118)
T 2khc_A           34 QIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTK  110 (118)
T ss_dssp             SCCCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCE
Confidence            3445577999999999999999999999999999999999987 899999999999999999999999999887763

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=3.7e-14  Score=117.26  Aligned_cols=73  Identities=27%  Similarity=0.577  Sum_probs=68.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...+.++|||+|||.++++++|+++|++||.|.++++++++ +++++|||||+|.+.++|.+|+..||+..+.|
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   81 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDG   81 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTS
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            34577899999999999999999999999999999999987 89999999999999999999999999987765

>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=99.50  E-value=4.7e-14  Score=113.47  Aligned_cols=68  Identities=22%  Similarity=0.508  Sum_probs=65.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .++|||+|||.++++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|+ .++|..+.|
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g   74 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRG   74 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECC
Confidence            5799999999999999999999999999999999997 9999999999999999999999 999988776

>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=99.50  E-value=3e-14  Score=118.65  Aligned_cols=71  Identities=30%  Similarity=0.571  Sum_probs=66.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPY   98 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f   98 (451)
                      .....++|||+|||.++++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|+..||+..+
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~   80 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKT   80 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcc
Confidence            45578999999999999999999999999999999999987 899999999999999999999999999765

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.50  E-value=7.7e-14  Score=115.73  Aligned_cols=73  Identities=16%  Similarity=0.312  Sum_probs=66.6

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .....+.++|||+|||.++++++|+++|++|| |.++++++++ +|+++|||||+|.+.++|.+|+ .+|+..+.|
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g   82 (103)
T 2dng_A            9 ELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGD   82 (103)
T ss_dssp             CCCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETT
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECC
Confidence            33455789999999999999999999999997 9999999998 8999999999999999999999 899977655

>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=99.50  E-value=4.9e-14  Score=122.48  Aligned_cols=76  Identities=22%  Similarity=0.392  Sum_probs=70.1

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ..+..+.++|||+|||.++++++|+++|++||+|.++++++++ +|+++|||||+|.+.++|.+|+..+||..+.|+
T Consensus        40 ~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~  116 (129)
T 2kxn_B           40 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR  116 (129)
T ss_dssp             SSCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            3445678899999999999999999999999999999999987 899999999999999999999999999888773

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.50  E-value=2.3e-14  Score=111.71  Aligned_cols=67  Identities=24%  Similarity=0.428  Sum_probs=63.5

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        34 ~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      +|||+|||.++++++|+++|++||+|.++++++++ +|+++|||||+|.+.++|++|++ +++..+.|+
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~   68 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNK   68 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCE
Confidence            58999999999999999999999999999999987 89999999999999999999997 899888774

>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=99.50  E-value=9.4e-14  Score=115.10  Aligned_cols=74  Identities=31%  Similarity=0.640  Sum_probs=67.2

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .......++|||+|||.++++++|+++|++||.|.+++++++..+ ++|||||+|.+.++|.+|+..|++..+.|
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g   82 (103)
T 2cq3_A            9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEG   82 (103)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            344567899999999999999999999999999999999988654 89999999999999999999999987765

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.50  E-value=6.7e-14  Score=116.66  Aligned_cols=74  Identities=26%  Similarity=0.429  Sum_probs=67.3

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEE-EEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIID-AQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~-i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .+....++|||+|||+++++++|+++|++||.|.+ ++++++.+|+++|||||+|.+.++|.+|+.. ++..+.|+
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr   84 (104)
T 1wg5_A           10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERIGHR   84 (104)
T ss_dssp             SSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CcchhCCc
Confidence            34457789999999999999999999999999987 8898888999999999999999999999998 88877764

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.50  E-value=5.1e-14  Score=126.48  Aligned_cols=71  Identities=18%  Similarity=0.349  Sum_probs=66.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCC--CeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYG--DIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G--~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ..++|||+|||.++++++|+++|++||  .|.++++++|+ +|+++|||||+|.+.++|.+|+..|||..+.|+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr  127 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGE  127 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            468999999999999999999999999  99999999997 999999999999999999999999999988874

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=4.7e-14  Score=118.90  Aligned_cols=75  Identities=19%  Similarity=0.352  Sum_probs=68.7

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeE--------EEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCc
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDII--------DAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKK   96 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~--------~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~   96 (451)
                      ..+....++|||+|||.++++++|+++|++||.|.        .+++++++ +|+++|||||+|.+.++|.+|+..|||.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   88 (113)
T 2cpe_A            9 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   88 (113)
T ss_dssp             CCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             cccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCC
Confidence            34556789999999999999999999999999999        69999996 8999999999999999999999999998


Q ss_pred             cCCC
Q psy300           97 PYKG  100 (451)
Q Consensus        97 ~f~G  100 (451)
                      .+.|
T Consensus        89 ~~~g   92 (113)
T 2cpe_A           89 DFQG   92 (113)
T ss_dssp             EETT
T ss_pred             ccCC
Confidence            7765

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.49  E-value=2.3e-14  Score=112.08  Aligned_cols=68  Identities=24%  Similarity=0.599  Sum_probs=63.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ++|||+|||.++++++|+++|++||+|.++++++++ +|+++|||||+|.+.++|.+|+..++ ..+.|+
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~   69 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSK   69 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCE
Confidence            589999999999999999999999999999999987 89999999999999999999999988 777664

>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=99.49  E-value=5.3e-14  Score=116.61  Aligned_cols=71  Identities=30%  Similarity=0.633  Sum_probs=67.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ..++|||+|||.++++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|+..+||..+.|+
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   78 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGR   78 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSS
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCc
Confidence            46899999999999999999999999999999999987 899999999999999999999999999888763

>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=99.49  E-value=6.6e-14  Score=116.33  Aligned_cols=72  Identities=28%  Similarity=0.473  Sum_probs=66.0

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-C-CCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-D-GKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-t-g~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....+.++|||+|||.++++++|+++|++|| |.++++++++ + |+++|||||+|.+.++|.+|+ .+++..+.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g   83 (104)
T 1wi8_A           10 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGN   83 (104)
T ss_dssp             CCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETT
T ss_pred             CCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCC
Confidence            3455779999999999999999999999999 9999999987 5 999999999999999999999 999987665

>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=99.48  E-value=4e-14  Score=113.48  Aligned_cols=70  Identities=23%  Similarity=0.358  Sum_probs=65.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCC-ceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGK-LKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~-skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..++|||+|||.++++++|+++|++||.|.+++++++. ++. ++|||||+|.+.++|.+|+..+||..+.|
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   74 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDG   74 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECC
Confidence            56899999999999999999999999999999999887 444 89999999999999999999999988776

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.48  E-value=8.8e-14  Score=115.67  Aligned_cols=73  Identities=22%  Similarity=0.556  Sum_probs=67.8

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....+.++|||+|||.++++++|+++|++||.|.+|++++++ +++++|||||+|.+.++|.+|+.. ++..+.|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g   84 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDG   84 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECC
Confidence            345678999999999999999999999999999999999997 899999999999999999999998 8887776

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.48  E-value=4.9e-14  Score=117.71  Aligned_cols=72  Identities=22%  Similarity=0.359  Sum_probs=66.0

Q ss_pred             CCCCceEEEcCCCCCC------CHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           29 KTKRGRLFIKNLPFKI------TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~v------te~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ....++|||+|||.++      ++++|+++|++||.|.+++++ ..+|+++|||||+|.+.++|.+|+..|||..+.|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~   89 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   89 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTT
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            4457899999999999      789999999999999999998 35899999999999999999999999999988874

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=3.3e-14  Score=117.56  Aligned_cols=72  Identities=24%  Similarity=0.375  Sum_probs=67.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..+.++|||+|||.++++++|+++|++||.|.++++++++ +++++|||||+|.+.++|.+|+..||+..+.|
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   81 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG   81 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            4578899999999999999999999999999999999986 89999999999999999999999999987665

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.48  E-value=9.1e-14  Score=117.78  Aligned_cols=74  Identities=27%  Similarity=0.560  Sum_probs=67.7

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .......++|||+|||.++++++|+++|++||.|.++++++++ +++++|||||+|.+.++|.+|+..+++ .+.|
T Consensus        11 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g   85 (116)
T 2cqd_A           11 SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDG   85 (116)
T ss_dssp             CCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETT
T ss_pred             CcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCC
Confidence            4455678999999999999999999999999999999999987 899999999999999999999999987 5554

>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=99.48  E-value=4.5e-14  Score=115.86  Aligned_cols=73  Identities=22%  Similarity=0.380  Sum_probs=67.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .....++|||+|||.++++++|+++|++||.|.++.++.++ +|+++|||||+|.+.++|.+|++.+||..+.|
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   84 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGS   84 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCC
Confidence            44567899999999999999999999999999988888776 89999999999999999999999999987766

>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=99.48  E-value=5.6e-14  Score=125.39  Aligned_cols=95  Identities=17%  Similarity=0.258  Sum_probs=80.7

Q ss_pred             EEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCC------------------------------------ccCCC----
Q psy300           61 DAQLLKNADGKLKGCGFINYANKISAVKAILKSNK------------------------------------KPYKG----  100 (451)
Q Consensus        61 ~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng------------------------------------~~f~G----  100 (451)
                      +++++++. .+++|||||+|.+.++|++|+..+++                                    ++|.|    
T Consensus         2 ~~kl~ln~-~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~   80 (158)
T 2kn4_A            2 QYKLILNG-KTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTY   80 (158)
T ss_dssp             EEEEEEEC-SSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESCCT
T ss_pred             cEEEEecC-ccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCccccccccccccccccccCCCCCCEEEEeCCCC
Confidence            46677764 36899999999999999999977542                                    12222    


Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++++ .+|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        81 ~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~  137 (158)
T 2kn4_A           81 RTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL  137 (158)
T ss_dssp             TCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEES
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            4799999999999999999999998 4799999999999999999999999988654

>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=99.48  E-value=8.7e-14  Score=115.90  Aligned_cols=72  Identities=19%  Similarity=0.395  Sum_probs=64.9

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .....++|||+|||+++++++|+++|++||.+ +++++++++|+++|||||+|.+.++|++|+. +|+..+.|+
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr   82 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHR   82 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCCCeECCc
Confidence            34567899999999999999999999999955 9999999999999999999999999999994 788877763

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.48  E-value=8.4e-14  Score=114.24  Aligned_cols=71  Identities=32%  Similarity=0.438  Sum_probs=65.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC----CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA----DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~----tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .+.++|||+|||.++++++|+++|++||.|.+++++++.    +++++|||||+|.+.++|.+|+..|||..+.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   77 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDG   77 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCC
Confidence            467899999999999999999999999999999999875    34899999999999999999999999987765

>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=99.47  E-value=4.7e-14  Score=121.29  Aligned_cols=74  Identities=19%  Similarity=0.375  Sum_probs=65.8

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeE-CCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLK-NADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~-d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ......++|||+|||.++++++|+++|++||.|.++.++. +.+|+++|||||+|.+.++|.+|+. +|+..+.|+
T Consensus        20 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr   94 (124)
T 1wel_A           20 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNR   94 (124)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTS
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCc
Confidence            3445678999999999999999999999999998855544 4599999999999999999999999 999998884

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.47  E-value=9.9e-14  Score=121.23  Aligned_cols=75  Identities=21%  Similarity=0.409  Sum_probs=69.0

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .......++|||+|||.++++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|+..+||..+.|
T Consensus        36 ~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g  111 (139)
T 1u6f_A           36 NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN  111 (139)
T ss_dssp             SCCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSS
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            3445567899999999999999999999999999999999987 89999999999999999999999999987765

>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=99.47  E-value=9.3e-14  Score=119.35  Aligned_cols=74  Identities=26%  Similarity=0.402  Sum_probs=68.8

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....+.++|||+|||.++++++|+++|++||.|.+|.++++. +|.++|||||+|.+.++|.+|+..|||..+.|
T Consensus        17 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   91 (126)
T 3ex7_B           17 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMG   91 (126)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCC
Confidence            345567899999999999999999999999999999999997 99999999999999999999999999987765

>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=99.47  E-value=2.8e-14  Score=115.23  Aligned_cols=69  Identities=28%  Similarity=0.560  Sum_probs=65.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .++|||+|||.++++++|+++|++||+|.++++++++ +|+++|||||+|.+.+ |.+|+..+||..+.|+
T Consensus         1 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~   70 (90)
T 2ki2_A            1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGR   70 (90)
T ss_dssp             CEEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSS
T ss_pred             CcEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCe
Confidence            3689999999999999999999999999999999987 8999999999999999 9999999999988774

>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=99.47  E-value=3.8e-14  Score=115.49  Aligned_cols=73  Identities=22%  Similarity=0.394  Sum_probs=65.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ....++|||+|||.++++++|+++|++||.|.++.++.++ +|+++|||||+|.+.++|.+|+..+|+..+.|+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr   85 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSR   85 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCc
Confidence            3456899999999999999999999999999989888876 899999999999999999999999999888763

>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=99.47  E-value=3.8e-14  Score=119.77  Aligned_cols=70  Identities=17%  Similarity=0.367  Sum_probs=65.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...++|||+|||.++++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|+ .+|+..+.|
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g   93 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLG   93 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCC
Confidence            346899999999999999999999999999999999988 7999999999999999999999 999988776

>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=99.47  E-value=1.4e-13  Score=114.11  Aligned_cols=73  Identities=19%  Similarity=0.291  Sum_probs=65.7

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ......++|||+|||.++++++|+++|++||.|.+|+++++..+ ++|||||+|.+.++|.+|+..|++..+.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~~g   82 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILG   82 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC-CCCEEEEEECCHHHHHHHHHHhCCCCcCC
Confidence            34557899999999999999999999999999999999998533 79999999999999999999999986654

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.47  E-value=1.7e-13  Score=111.00  Aligned_cols=71  Identities=21%  Similarity=0.418  Sum_probs=66.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .....++|||+|||.++++++|+++|++| .|.+++++++.+|+++|||||+|.+.++|.+|+. +||..+.|
T Consensus         6 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~g   76 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYMGG   76 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEETT
T ss_pred             CCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCceeCC
Confidence            34567899999999999999999999999 9999999999999999999999999999999999 99988776

>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=99.47  E-value=1.8e-13  Score=122.16  Aligned_cols=75  Identities=25%  Similarity=0.308  Sum_probs=68.9

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .......++|||+|||.++++++|+++|++||.|.+|++++++ ++.++|||||+|.+.++|.+|+..||+..+.|
T Consensus        33 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  108 (156)
T 1h2v_Z           33 EKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDD  108 (156)
T ss_dssp             CTTTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETT
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            3344578999999999999999999999999999999999998 89999999999999999999999999987655

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.46  E-value=1.4e-13  Score=118.16  Aligned_cols=73  Identities=21%  Similarity=0.462  Sum_probs=68.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .....++|||+|||.++++++|+++|++||.|.+++++++.+|+++|||||+|.+.++|.+|+..+||..+.|
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  103 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDG  103 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            4456789999999999999999999999999999999998899999999999999999999999999987766

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.46  E-value=4.1e-14  Score=122.94  Aligned_cols=72  Identities=14%  Similarity=0.248  Sum_probs=66.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEE--EEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCc----cCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIID--AQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKK----PYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~--i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~----~f~G  100 (451)
                      .....++|||+|||.++++++|+++|++||.|.+  |++++++ +|+++|||||+|.+. +|.+|+..|||.    .+.|
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~g   97 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDG   97 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGG
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCC
Confidence            3457789999999999999999999999999977  9999998 999999999999999 999999999998    6655

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.46  E-value=1.4e-13  Score=117.59  Aligned_cols=73  Identities=10%  Similarity=0.255  Sum_probs=67.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCC---eEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGD---IIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~---I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .....++|||+|||+++++++|+++|++||.   |.+|+++++++|+++|||||+|.+.++|.+|+. +++..+.|+
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr   88 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESMGHR   88 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEETTE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeECCe
Confidence            3456789999999999999999999999999   899999999899999999999999999999999 899887773

>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=99.46  E-value=1.1e-13  Score=115.95  Aligned_cols=84  Identities=19%  Similarity=0.236  Sum_probs=72.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCC---eEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC---
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGD---IIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK---  101 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~---I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~---  101 (451)
                      .....++|||+|||+++++++|+++|++||.   |.++++++++.|+++|||||+|.+.++|.+|+. +++..+.|+   
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~   85 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVE   85 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEE
Confidence            4457789999999999999999999999998   899999999889999999999999999999999 899888874   


Q ss_pred             ---CcHHHHHHHhc
Q psy300          102 ---ITEEEFKEHFG  112 (451)
Q Consensus       102 ---~tee~L~~~F~  112 (451)
                         .+..++.....
T Consensus        86 V~~a~~~~~~~~~~   99 (107)
T 2lmi_A           86 VYEINNEDVDALMK   99 (107)
T ss_dssp             CEECCHHHHHHHHH
T ss_pred             EEECCHHHHHHHHH
Confidence               34455554443

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.46  E-value=1.4e-13  Score=119.57  Aligned_cols=73  Identities=21%  Similarity=0.332  Sum_probs=64.8

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHH----HHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFK----EHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~----~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .+..+.++|||+|||.++++++|+    ++|++||.|.+|.+.  .+++++|||||+|.+.++|.+|+..|||..+.|+
T Consensus        24 ~~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~--~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr  100 (127)
T 2a3j_A           24 PHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD--LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGN  100 (127)
T ss_dssp             CCCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEEC--CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEec--cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCC
Confidence            345568899999999999999876    699999999998875  3788999999999999999999999999988774

>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=99.45  E-value=7.3e-14  Score=115.52  Aligned_cols=73  Identities=27%  Similarity=0.466  Sum_probs=63.9

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC--CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA--DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~--tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ......++|||+|||.++++++|+++|++|| |.+++++++.  +|+++|||||+|.+.++|.+|+ .++|..+.|+
T Consensus        14 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~   88 (100)
T 2j76_E           14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNR   88 (100)
T ss_dssp             ------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTB
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCe
Confidence            3455789999999999999999999999999 9999999986  8999999999999999999999 8999988774

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.45  E-value=9.8e-14  Score=116.75  Aligned_cols=74  Identities=30%  Similarity=0.619  Sum_probs=67.4

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .......++|||+|||.++++++|+++|++||.|.+++++++.. .++|||||+|.+.++|.+|+..++|..+.|
T Consensus        23 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g   96 (109)
T 2err_A           23 TENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREKLHGTVVEG   96 (109)
T ss_dssp             CSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT-BCTTEEEEECCCSHHHHHHHHHHTTCEETT
T ss_pred             ccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC-CCceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            44456789999999999999999999999999999999998854 489999999999999999999999988776

>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=99.45  E-value=3.4e-13  Score=111.70  Aligned_cols=66  Identities=30%  Similarity=0.585  Sum_probs=61.5

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHh
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILK   92 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~   92 (451)
                      ....+.++|||+|||.++++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|+..
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~   76 (103)
T 2cqg_A           10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ   76 (103)
T ss_dssp             CCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS
T ss_pred             CccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc
Confidence            345577899999999999999999999999999999999997 899999999999999999999984

>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=99.44  E-value=1.3e-13  Score=113.10  Aligned_cols=71  Identities=14%  Similarity=0.264  Sum_probs=65.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHH----HHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFK----EHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~----~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .....++|||+|||.++++++|+    ++|++||.|.++++++++.+  +|||||+|.+.++|.+|+..+||..+.|
T Consensus         5 ~~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~g~~~~g   79 (96)
T 2dgx_A            5 SSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYKIGS   79 (96)
T ss_dssp             CCSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            45577899999999999999999    99999999999999988755  8999999999999999999999987765

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=1.6e-13  Score=118.48  Aligned_cols=81  Identities=26%  Similarity=0.345  Sum_probs=69.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCe----EEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC----
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDI----IDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK----  101 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I----~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~----  101 (451)
                      ...++|||+|||+++++++|+++|++||.|    .+|+|+++.+|+++|||||+|.+.++|.+|+.. ++..+.|+    
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~V   99 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIEL   99 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEEE
Confidence            467899999999999999999999999985    689999999999999999999999999999986 88777764    


Q ss_pred             --CcHHHHHHHh
Q psy300          102 --ITEEEFKEHF  111 (451)
Q Consensus       102 --~tee~L~~~F  111 (451)
                        .+..++....
T Consensus       100 ~~a~~~e~~~~~  111 (123)
T 2dha_A          100 FRSTAAEVQQVL  111 (123)
T ss_dssp             EEECHHHHHHHH
T ss_pred             EECCHHHHHHHH
Confidence              3445555444

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.44  E-value=1.3e-13  Score=116.09  Aligned_cols=72  Identities=21%  Similarity=0.535  Sum_probs=62.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...+.++|||+|||.++++++|+++|++||.|.+|++++++ +|+++|||||+|.+.++|.+|+..++ ..+.|
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~-~~l~g   93 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDS   93 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSC-EEETT
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCC-CcCCC
Confidence            44567899999999999999999999999999999999997 89999999999999999999998764 54444

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.44  E-value=2.1e-13  Score=118.82  Aligned_cols=74  Identities=23%  Similarity=0.380  Sum_probs=68.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ...+.++|||+|||.++++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|+..+||..+.|+
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~  133 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGR  133 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            45578999999999999999999999999999999999986 899999999999999999999999999877763

>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=99.44  E-value=2.2e-13  Score=121.53  Aligned_cols=72  Identities=18%  Similarity=0.371  Sum_probs=67.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....++|||+|||.++++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|+..|||..+.|
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g  139 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG  139 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            4457899999999999999999999999999999999997 99999999999999999999999999987765

>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=99.43  E-value=1.2e-13  Score=116.98  Aligned_cols=71  Identities=20%  Similarity=0.278  Sum_probs=66.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCe-EEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDI-IDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I-~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..+.++|||+|||.++++++|+++|++||.| .+|+++++++|+++|||||+|.+.++|.+|+.. |+..+.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~g   83 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKLNG   83 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEETT
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCccCC
Confidence            4467899999999999999999999999999 899999999999999999999999999999987 8877776

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A

Probab=99.43  E-value=6.6e-14  Score=109.03  Aligned_cols=67  Identities=22%  Similarity=0.397  Sum_probs=61.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        34 ~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      +|||+|||.++++++|+++|++||+|.++++++++ +|+++|||||+|.+.++|.+|++. ++..+.|+
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~   68 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLS   68 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTB
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCE
Confidence            69999999999999999999999999999999987 899999999999999999999985 77767663

>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=99.43  E-value=2.1e-13  Score=114.02  Aligned_cols=72  Identities=25%  Similarity=0.348  Sum_probs=65.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCC-eEEEEEe-ECC-CCCceeEEEEEEccHHHHHHHHHhcC--CccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGD-IIDAQLL-KNA-DGKLKGCGFINYANKISAVKAILKSN--KKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~-I~~i~l~-~d~-tg~skG~aFV~F~~~~~A~~Al~~ln--g~~f~G  100 (451)
                      ..+.++|||+|||.++++++|+++|++||. |.++.++ .+. +|+++|||||+|.+.++|.+|+..++  +..+.|
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g   81 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWG   81 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTT
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecC
Confidence            346789999999999999999999999998 9999998 666 78999999999999999999999996  466665

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.43  E-value=2.1e-13  Score=116.78  Aligned_cols=69  Identities=22%  Similarity=0.515  Sum_probs=65.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..++|||+|||.++++++|+++|++||.|.++++++++ +|.++|||||+|.+.++|.+|+ .+||..+.|
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g  104 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRG  104 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECC
Confidence            45899999999999999999999999999999999986 9999999999999999999999 899987765

>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=99.43  E-value=1.3e-13  Score=115.11  Aligned_cols=67  Identities=18%  Similarity=0.158  Sum_probs=60.2

Q ss_pred             CCCCCCCCceEEEcCCCC-CCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCc
Q psy300           25 KKPDKTKRGRLFIKNLPF-KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK   96 (451)
Q Consensus        25 ~~~~~~~~~~lfVgnLp~-~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~   96 (451)
                      +.....+.++|||+|||. ++++++|+++|++||.|.+++++++     +|||||+|.+.++|.+|+..|++.
T Consensus         8 ~~~~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~   75 (102)
T 1x4d_A            8 QKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTT   75 (102)
T ss_dssp             CCCCCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHS
T ss_pred             CCCCCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHHcCC
Confidence            344455789999999999 9999999999999999999999865     689999999999999999988864

>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=99.42  E-value=4.5e-13  Score=120.90  Aligned_cols=72  Identities=25%  Similarity=0.376  Sum_probs=66.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..+.++|||+|||.++++++|+++|++||.|.+|.++++. +|.++|||||+|.+.++|.+|+..|||..+.|
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g  141 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMG  141 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            4456789999999999999999999999999999999997 99999999999999999999999999987765

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.42  E-value=3.1e-13  Score=128.80  Aligned_cols=71  Identities=28%  Similarity=0.482  Sum_probs=66.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCC--CeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYG--DIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G--~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ..++|||+|||.++++++|+++|++||  .|.+|+|++++ +|+++|||||+|.+.++|.+||..||+..|.|+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr  140 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQ  140 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTB
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCE
Confidence            567899999999999999999999999  99999999997 999999999999999999999999999988774

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.42  E-value=2.8e-13  Score=113.67  Aligned_cols=67  Identities=21%  Similarity=0.289  Sum_probs=60.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCC--ccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK--KPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng--~~f~G  100 (451)
                      ..+.++|||+|||.++++++|+++|++||.|.+++++++     ||||||+|.+.++|.+|+..+++  ..+.|
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~G   81 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRG   81 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTSCCEETT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            446789999999999999999999999999999999865     79999999999999999998764  45555

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.42  E-value=1.5e-13  Score=113.74  Aligned_cols=69  Identities=20%  Similarity=0.565  Sum_probs=62.8

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...++|||+|||.++++++|+++|++||.|.+++++++++|+++|||||+|.+.++|.+|+.  ++..+.|
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g   75 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE--SQINFHG   75 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT--CCCEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh--CCCeECC
Confidence            35689999999999999999999999999999999999999999999999999999999998  5544444

>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=99.41  E-value=2.6e-13  Score=114.40  Aligned_cols=74  Identities=19%  Similarity=0.341  Sum_probs=66.5

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHH---HHhccCCCeEEEEEeECC-C---CCceeEEEEEEccHHHHHHHHHhcCCccCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFK---EHFGQYGDIIDAQLLKNA-D---GKLKGCGFINYANKISAVKAILKSNKKPYK   99 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~---~~F~~~G~I~~i~l~~d~-t---g~skG~aFV~F~~~~~A~~Al~~lng~~f~   99 (451)
                      ......++|||+|||.++++++|+   ++|++||+|.+++++++. +   ++++|||||+|.+.++|.+|+..|||..+.
T Consensus        10 ~r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   89 (111)
T 2cpi_A           10 VRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVD   89 (111)
T ss_dssp             CCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             ccccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEEC
Confidence            345567899999999999999999   999999999999999886 3   356799999999999999999999998877


Q ss_pred             C
Q psy300          100 G  100 (451)
Q Consensus       100 G  100 (451)
                      |
T Consensus        90 g   90 (111)
T 2cpi_A           90 G   90 (111)
T ss_dssp             T
T ss_pred             C
Confidence            6

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.40  E-value=7.3e-13  Score=110.92  Aligned_cols=73  Identities=23%  Similarity=0.430  Sum_probs=65.2

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .......++|||+|||.++++++|+++|++||.|.++++..  ++.++|||||+|.+.++|.+|++.||+..+.|
T Consensus        16 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   88 (109)
T 1x4a_A           16 GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN--RRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDG   88 (109)
T ss_dssp             CCCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECC--SSSSSCCEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEE--CCCCCcEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            33455778999999999999999999999999999999954  46689999999999999999999999987765

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=4.5e-13  Score=110.54  Aligned_cols=70  Identities=31%  Similarity=0.443  Sum_probs=63.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .....++|||+|||.++++++|+++|++||.|   +++++.+++++|||||+|.+.++|.+|+..+|+..+.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   80 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEG   80 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            45578999999999999999999999999987   66667789999999999999999999999999987665

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.40  E-value=2.7e-13  Score=114.58  Aligned_cols=69  Identities=19%  Similarity=0.386  Sum_probs=64.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ..++|||+|||+++++++|+++|++| .|.+|+|+++++|+++|||||+|.+.++|.+|+ .+|+..+.|+
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr   83 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQR   83 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEETTE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeECCe
Confidence            45799999999999999999999999 899999999989999999999999999999999 6898877764

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.40  E-value=3.3e-13  Score=114.32  Aligned_cols=69  Identities=23%  Similarity=0.539  Sum_probs=64.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..++|||+|||.++++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|+.. ++..+.|
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g   95 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDG   95 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECC
Confidence            45899999999999999999999999999999999997 899999999999999999999988 8776655

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.39  E-value=2.5e-13  Score=115.12  Aligned_cols=69  Identities=23%  Similarity=0.414  Sum_probs=61.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-C---CCceeEEEEEEccHHHHHHHHHhc---CCccC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-D---GKLKGCGFINYANKISAVKAILKS---NKKPY   98 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-t---g~skG~aFV~F~~~~~A~~Al~~l---ng~~f   98 (451)
                      ....++|||+|||.++++++|+++|++||+|. +.++.+. +   |+++|||||+|.+.++|.+|+..+   +|+.+
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~~~G~~~   80 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLY   80 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEEETTEEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhhcCCcEE
Confidence            44678999999999999999999999999999 8887776 4   799999999999999999999988   55543

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.39  E-value=1.9e-13  Score=119.56  Aligned_cols=74  Identities=20%  Similarity=0.416  Sum_probs=68.6

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .+..+.++|||+|||.++++++|+++|++||.|.++++++++ +++++|||||+|.+.++|.+|+..|||..+.|
T Consensus        42 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g  116 (135)
T 2lea_A           42 PDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDG  116 (135)
T ss_dssp             SSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            344567899999999999999999999999999999999987 89999999999999999999999999988776

>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=99.39  E-value=5.9e-13  Score=114.22  Aligned_cols=70  Identities=20%  Similarity=0.290  Sum_probs=61.4

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCC--ccCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK--KPYKG  100 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng--~~f~G  100 (451)
                      .....+.++|||+|||.++++++|+++|++||.|.+++++++     ||||||+|.+.++|.+|+..+++  ..+.|
T Consensus        25 ~~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-----kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~G   96 (119)
T 2ad9_A           25 RSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTSVTPVLRG   96 (119)
T ss_dssp             TSCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-----GTEEEEECSCHHHHHHHHHHHHHHCCCBTT
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            344557889999999999999999999999999999999865     89999999999999999998874  34444

>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=99.39  E-value=9.2e-13  Score=104.97  Aligned_cols=68  Identities=31%  Similarity=0.506  Sum_probs=62.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhc-CCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS-NKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~l-ng~~f~G  100 (451)
                      .....++|||+|||.++++++|+++|++||.|.++++++     ++|||||+|.+.++|.+|+..+ ++..+.|
T Consensus         8 ~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~-----~kg~afV~f~~~~~A~~a~~~l~~~~~~~g   76 (85)
T 2ytc_A            8 EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ-----RQQCAFIQFATRQAAEVAAEKSFNKLIVNG   76 (85)
T ss_dssp             SCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG-----GGTEEEEEESSHHHHHHHHHTTTTTCEETT
T ss_pred             CCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC-----CCCEEEEEECCHHHHHHHHHHhcCCeeECC
Confidence            445778999999999999999999999999999999986     4899999999999999999998 8887776

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.39  E-value=6e-13  Score=110.65  Aligned_cols=65  Identities=14%  Similarity=0.247  Sum_probs=59.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCcc
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP   97 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~   97 (451)
                      ...++++|||+|||.++++++|+++|++||.|.++++++     +||||||+|.+.++|.+|+..+++..
T Consensus        17 ~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~-----~kg~AFVef~~~~~A~~Av~~ln~~~   81 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP-----KKRQALVEFEDVLGACNAVNYAADNQ   81 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHHHSC
T ss_pred             cCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc-----CCCEEEEEECCHHHHHHHHHHhcCCC
Confidence            445788999999999999999999999999999999985     48999999999999999999998764

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.38  E-value=7.9e-13  Score=114.58  Aligned_cols=72  Identities=29%  Similarity=0.498  Sum_probs=64.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeE--EEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDII--DAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~--~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .....++|||+|||+++++++|+++|++| .|.  +|+++++++|+++|||||+|.+.++|.+|+.. ++..+.|+
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR  111 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKERIGHR  111 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTCCBTTB
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCCEECCE
Confidence            44567899999999999999999999999 677  89999998899999999999999999999985 66777664

>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=99.38  E-value=2.9e-13  Score=119.35  Aligned_cols=72  Identities=19%  Similarity=0.394  Sum_probs=64.4

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .....++|||+|||+++++++|+++|++|| |.+|+|+++++|+++|||||+|.+.++|.+|+ .+|+..+.|+
T Consensus        42 ~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR  113 (139)
T 2hgn_A           42 QSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANMQHR  113 (139)
T ss_dssp             ---CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSSSSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEECCE
Confidence            344678999999999999999999999999 67999999989999999999999999999999 7898887764

>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=99.38  E-value=9.4e-13  Score=108.30  Aligned_cols=69  Identities=38%  Similarity=0.605  Sum_probs=63.0

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....+.++|||+|||.++++++|+++|++||.|.++++.++     +|||||+|.+.++|.+|+..|+|..+.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~-----kg~afV~f~~~~~a~~a~~~l~g~~~~g   78 (99)
T 2cpj_A           10 KTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRG   78 (99)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTT
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC-----CCEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            34567889999999999999999999999999999999754     8999999999999999999999987765

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.37  E-value=1.6e-12  Score=104.96  Aligned_cols=66  Identities=32%  Similarity=0.576  Sum_probs=61.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...+.++|||+|||.++++++|+++|++||.|.+++++       +|||||+|.+.++|.+|+..+|+..+.|
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g   69 (90)
T 2dnq_A            4 GSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHYKLHG   69 (90)
T ss_dssp             CSSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE-------TTEEEEEESSHHHHHHHHHHHTTCBCSS
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhcCCccCC
Confidence            34578999999999999999999999999999999997       6899999999999999999999987765

>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=99.37  E-value=2.9e-13  Score=110.68  Aligned_cols=71  Identities=25%  Similarity=0.471  Sum_probs=63.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHH----HHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFK----EHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~----~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      +..+.++|||+|||.++++++|+    ++|++||.|.++++.+  +|.++|||||+|.+.++|.+|+..+||..+.|
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   78 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYD   78 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc--CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECC
Confidence            34578999999999999999999    9999999999998863  67889999999999999999999999987765

>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=99.37  E-value=1.5e-12  Score=108.94  Aligned_cols=64  Identities=14%  Similarity=0.209  Sum_probs=58.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCc
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK   96 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~   96 (451)
                      ...+.++|||+|||.++++++|+++|++||.|.++.++++     ||||||+|.+.++|.+|+..+++.
T Consensus        11 ~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~   74 (104)
T 1wex_A           11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADV   74 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHS
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccC
Confidence            3456789999999999999999999999999999998753     899999999999999999988754

>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=99.36  E-value=1.8e-12  Score=106.16  Aligned_cols=67  Identities=19%  Similarity=0.292  Sum_probs=61.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK   99 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~   99 (451)
                      ...+.++|||+|||.++++++|+++|++||.|.++.+.++     +|||||+|.+.++|.+|+..||+..+.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~   79 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLG   79 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC-----CCEEEEEECCHHHHHHHHHHHCCCEeC
Confidence            3456789999999999999999999999999999999754     789999999999999999999998776

>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=99.36  E-value=1.5e-12  Score=109.03  Aligned_cols=66  Identities=20%  Similarity=0.449  Sum_probs=61.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....++|||+|||.++++++|+++|++||.|.+++++.+      |||||+|.+.++|++|++.||+..+.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~g   77 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRS   77 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHHHHHHHSSSEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHHHHHHHHCcCCccC
Confidence            456789999999999999999999999999999999875      899999999999999999999987766

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.05  E-value=5.7e-14  Score=119.17  Aligned_cols=72  Identities=28%  Similarity=0.387  Sum_probs=67.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEE--------EEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIID--------AQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYK   99 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~--------i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~   99 (451)
                      ..+.++|||+|||.++++++|+++|++||.|.+        +++++++ +|+++|||||+|.+.++|.+|+..|||..+.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            457789999999999999999999999999999        8999986 8999999999999999999999999998777


Q ss_pred             C
Q psy300          100 G  100 (451)
Q Consensus       100 G  100 (451)
                      |
T Consensus        84 g   84 (116)
T 2lcw_A           84 G   84 (116)
Confidence            6

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.36  E-value=1.2e-12  Score=107.86  Aligned_cols=67  Identities=28%  Similarity=0.504  Sum_probs=62.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....++|||+|||.++++++|+++|++||.|.++++.     +++|||||+|.+.++|.+|+..+||..+.|
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~-----~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   90 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY-----PEKGCCFIKYDTHEQAAVCIVALANFPFQG   90 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE-----TTTTEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe-----cCCCEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            4457899999999999999999999999999999997     468999999999999999999999988876

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.36  E-value=1.5e-13  Score=113.40  Aligned_cols=70  Identities=20%  Similarity=0.190  Sum_probs=63.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....++|||+|||.++++++|+++|++||.|.+ .++++. +|+++|||||+|.+.++|.+|++ +||..+.|
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g   84 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFG   84 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECC
Confidence            446789999999999999999999999999888 566665 89999999999999999999998 99988776

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.36  E-value=1.9e-12  Score=106.85  Aligned_cols=71  Identities=27%  Similarity=0.398  Sum_probs=63.5

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....+.++|||+|||.++++++|+++|+.|+   +++++++. +++++|||||+|.+.++|.+|+..||+..+.|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   81 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDG   81 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            3455789999999999999999999999874   67888886 89999999999999999999999999987654

>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=99.35  E-value=2e-12  Score=107.70  Aligned_cols=69  Identities=22%  Similarity=0.288  Sum_probs=59.7

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcC--CccCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN--KKPYKG  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~ln--g~~f~G  100 (451)
                      ....+.++|||+|||.++++++|+++|++||.|.++.++++     ||||||+|.+.++|.+|+..++  +..+.|
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~G   80 (101)
T 2cq1_A           10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRN   80 (101)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETT
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            34457789999999999999999999999999999998864     8999999999999999999764  333444

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.35  E-value=3.4e-12  Score=113.03  Aligned_cols=75  Identities=16%  Similarity=0.423  Sum_probs=69.4

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ....+.++|||+|||.++++++|+++|++||.|.+++++++. +|.++|||||+|.+.++|.+|+..+||..+.|+
T Consensus        82 ~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  157 (166)
T 3md3_A           82 SSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGR  157 (166)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCc
Confidence            345567899999999999999999999999999999999996 899999999999999999999999999888763

>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=99.34  E-value=2.8e-12  Score=114.74  Aligned_cols=73  Identities=25%  Similarity=0.512  Sum_probs=67.6

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .....++|||+|||.++++++|+++|++||.|.+++++++.+|+++|||||+|.+.++|.+|+..|||..+.+
T Consensus        91 ~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~  163 (175)
T 3nmr_A           91 NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTME  163 (175)
T ss_dssp             SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTSCCCT
T ss_pred             ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHHHHHHHHhcCCcccC
Confidence            3446789999999999999999999999999999999999999999999999999999999999999976653

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.34  E-value=2e-12  Score=106.00  Aligned_cols=70  Identities=14%  Similarity=0.224  Sum_probs=62.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .....++|||+|||.++++++|+++|++||.|. ++++.   ++++|||||+|.+.++|.+|+..|||..+.|+
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~---~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   84 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW---QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTD   84 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE---ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSS
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc---CCCCcEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            344678999999999999999999999999996 66664   47899999999999999999999999988763

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.34  E-value=1.6e-12  Score=119.00  Aligned_cols=71  Identities=21%  Similarity=0.495  Sum_probs=67.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ..++|||+|||.++++++|+++|++||.|.+|.++.+.+|.++|||||+|.+.++|.+|+..+||..+.|+
T Consensus        87 ~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr  157 (177)
T 2f3j_A           87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGR  157 (177)
T ss_dssp             TCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCE
Confidence            46899999999999999999999999999999999988999999999999999999999999999888763

>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=99.34  E-value=1.5e-12  Score=109.85  Aligned_cols=70  Identities=24%  Similarity=0.430  Sum_probs=62.0

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeE----EEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDII----DAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~----~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...+.++|||+|||.++++++|+++|++||.|.    .+++.   +|+++|||||+|.+.++|.+|+..|+|..+.|
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~---~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   94 (115)
T 2cpx_A           21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM---TGRMRGQAFITFPNKEIAWQALHLVNGYKLYG   94 (115)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE---CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC---CCccceEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            345678999999999999999999999999994    44444   88999999999999999999999999987765

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.34  E-value=7.7e-13  Score=109.15  Aligned_cols=64  Identities=20%  Similarity=0.351  Sum_probs=60.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ++|||+|||.++++++|+++|++||+|.+++++++    ++|||||+|.+.++|.+|+..|+|..+.|
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g   64 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLDGKVICG   64 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS----SSSEEEEECSSHHHHHHHHHHHHHSCSSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC----CCCEEEEEECCHHHHHHHHHHHCCCeECC
Confidence            58999999999999999999999999999999876    78999999999999999999999987765

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.34  E-value=1.1e-12  Score=113.25  Aligned_cols=68  Identities=19%  Similarity=0.228  Sum_probs=61.2

Q ss_pred             ceEEEcCC----CCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEcc----HHH----HHHHHH--hcCCcc
Q psy300           33 GRLFIKNL----PFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYAN----KIS----AVKAIL--KSNKKP   97 (451)
Q Consensus        33 ~~lfVgnL----p~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~----~~~----A~~Al~--~lng~~   97 (451)
                      ++|||+||    |+.+++.+|+++|++||+|.++.++.|+ ||+|+|||||+|.+    +++    |.+|+.  .++|..
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    9999999999999999999999999999 99999999999996    433    788888  788888


Q ss_pred             CCC
Q psy300           98 YKG  100 (451)
Q Consensus        98 f~G  100 (451)
                      +.|
T Consensus        83 I~G   85 (136)
T 2j8a_A           83 IMG   85 (136)
T ss_dssp             ETT
T ss_pred             ecC
Confidence            877

>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=99.33  E-value=2.7e-12  Score=105.61  Aligned_cols=69  Identities=29%  Similarity=0.513  Sum_probs=60.7

Q ss_pred             CCCCCCCCceEEEcCCCC-CCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           25 KKPDKTKRGRLFIKNLPF-KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        25 ~~~~~~~~~~lfVgnLp~-~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .....+..++|||+|||. ++++++|+++|++||.|.++++.       +|||||+|.+.++|.+|+..+||..+.|
T Consensus        15 ~~~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (97)
T 2xnq_A           15 VPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEMNFG   84 (97)
T ss_dssp             ----CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHTTSEETT
T ss_pred             ccCCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            344566789999999998 99999999999999999999983       7999999999999999999999987766

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.33  E-value=8.8e-13  Score=111.79  Aligned_cols=70  Identities=20%  Similarity=0.327  Sum_probs=63.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCC-CeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYG-DIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G-~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ....++|||+|||.++++++|+++|++|| .|..+.+..   +.++|||||+|.+.++|.+|+..|||..+.|+
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~---~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr   95 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT---RDFDGTGALEFPSEEILVEALERLNNIEFRGS   95 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS---CSSSCCEEEEESSHHHHHHHHHHTTTEEETTE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc---CCCCCEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            34678999999999999999999999999 899998853   35899999999999999999999999988773

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.33  E-value=2.6e-12  Score=105.18  Aligned_cols=66  Identities=30%  Similarity=0.548  Sum_probs=59.5

Q ss_pred             CCCCCceEEEcCCCC-CCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPF-KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~-~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      +..+.++|||+|||. ++++++|+++|++||.|.++++.       +|||||+|.+.++|.+|+..++|..+.|
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g   72 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEMNFG   72 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE-------TTEEEEEESCHHHHHHHHHHHTCSSCBT
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCeeCC
Confidence            345789999999998 99999999999999999999984       7899999999999999999999987765

>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=99.33  E-value=1.2e-12  Score=111.18  Aligned_cols=68  Identities=21%  Similarity=0.346  Sum_probs=59.7

Q ss_pred             CCCCCceEEEcCCCCC-CCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCc--cCCC
Q psy300           28 DKTKRGRLFIKNLPFK-ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK--PYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~-vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~--~f~G  100 (451)
                      ...+.++|||+|||.+ +++++|+++|++||.|.++++++     ++|||||+|.+.++|.+|+..+++.  .+.|
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~-----~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~G   91 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR-----MKSQAFIEMETREDAMAMVDHCLKKALWFQG   91 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHHHSCCCSSS
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            3557889999999998 99999999999999999999974     4899999999999999999988643  3444

>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=99.33  E-value=1.1e-12  Score=110.69  Aligned_cols=65  Identities=18%  Similarity=0.277  Sum_probs=60.4

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..++|||+|||.++++++|+++|++||.|.+|.+++     ++|||||+|.+.++|.+|+..|||..+.|
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   73 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKFHH   73 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBSSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC-----CCCEEEEEeCCHHHHHHHHHHhCCCEECC
Confidence            467999999999999999999999999999999864     58999999999999999999999987776

>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=99.32  E-value=2.1e-12  Score=108.25  Aligned_cols=68  Identities=21%  Similarity=0.491  Sum_probs=62.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .....++|||+|||.++++++|+++|++||.|.+++++++     +|||||+|.+.++|.+|+..|+|..+.|
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~~g   88 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEG   88 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            3457789999999999999999999999999999999875     8999999999999999999999987765

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.32  E-value=9.2e-13  Score=107.53  Aligned_cols=68  Identities=32%  Similarity=0.457  Sum_probs=61.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..+.++|||+|||.++++++|+++|++||.|..+    ..+|.++|||||+|.+.++|.+|+..++|..+.|
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   80 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG   80 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            4467899999999999999999999999988766    3488999999999999999999999999987765

>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=4.2e-12  Score=113.56  Aligned_cols=73  Identities=26%  Similarity=0.388  Sum_probs=68.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ....++|||+|||.++++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|+..|||..+.|+
T Consensus        91 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  164 (172)
T 2g4b_A           91 LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK  164 (172)
T ss_dssp             CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCe
Confidence            3457899999999999999999999999999999999997 999999999999999999999999999888763

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.32  E-value=2.7e-12  Score=107.89  Aligned_cols=67  Identities=28%  Similarity=0.615  Sum_probs=61.3

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ......++|||+|||.++++++|+++|++||.|.+++++       +|||||+|.+.++|.+|+..|||..+.|
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-------kg~afV~f~~~~~A~~Ai~~l~g~~~~g   92 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKSFAN   92 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            345678999999999999999999999999999999997       7899999999999999999999988776

>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=99.32  E-value=2.8e-12  Score=113.60  Aligned_cols=71  Identities=18%  Similarity=0.340  Sum_probs=64.9

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ......++|||+|||.++++++|+++|++||.|.+++++++    ++|||||+|.+.++|.+|+..|||..+.|+
T Consensus        68 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~  138 (150)
T 2i2y_A           68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDGRTLCGC  138 (150)
T ss_dssp             SSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS----SCSEEEEEESSHHHHHHHHHHHSSSCSSSS
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC----CCcEEEEEECCHHHHHHHHHHcCCCEECCe
Confidence            34557799999999999999999999999999999999876    689999999999999999999999888764

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.32  E-value=5.3e-12  Score=103.75  Aligned_cols=68  Identities=22%  Similarity=0.426  Sum_probs=61.0

Q ss_pred             CCCCCCCceEEEcCCCCCCCHHHHHHHhccC--CCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           26 KPDKTKRGRLFIKNLPFKITEEEFKEHFGQY--GDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~--G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .....+.++|||+|||.++++++|+++|++|  |.|.++++.       +|||||+|.+.++|.+|+..|||..+.|
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~~g   78 (99)
T 2cpd_A            9 EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI-------RDYAFVHFSNREDAVEAMKALNGKVLDG   78 (99)
T ss_dssp             CSCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHSSEEETT
T ss_pred             ccccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe-------CCeEEEEeCCHHHHHHHHHHhCCCEeCC
Confidence            3445578999999999999999999999999  899999874       6799999999999999999999987765

>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=99.31  E-value=5.6e-12  Score=111.70  Aligned_cols=73  Identities=32%  Similarity=0.605  Sum_probs=68.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ....++|||+|||.++++++|+++|++||.|.+++++++. +|+++|||||+|.+.++|.+|+..+||..+.|+
T Consensus        85 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~  158 (167)
T 1fxl_A           85 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGA  158 (167)
T ss_dssp             GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC
T ss_pred             cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCC
Confidence            4467899999999999999999999999999999999987 999999999999999999999999999988874

>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=99.31  E-value=8e-12  Score=111.15  Aligned_cols=73  Identities=30%  Similarity=0.626  Sum_probs=68.8

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .....++|||+|||.++++++|+++|++||.|.+++++++. +|+++|||||+|.+.++|.+|+..+||..+.|
T Consensus        85 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  158 (168)
T 1b7f_A           85 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEG  158 (168)
T ss_dssp             STTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTT
T ss_pred             ccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecC
Confidence            34567899999999999999999999999999999999998 99999999999999999999999999998876

>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=99.31  E-value=1.9e-12  Score=109.93  Aligned_cols=66  Identities=20%  Similarity=0.439  Sum_probs=59.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ...++|||+|||.++++++|+++|++||.|.++.++.+      |||||+|.+.++|.+|++.||+..+.|+
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~~gr   79 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKFRSH   79 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBCCCT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            45789999999999999999999999999999999765      8999999999999999999999988873

>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=99.30  E-value=1.6e-12  Score=110.66  Aligned_cols=66  Identities=14%  Similarity=0.115  Sum_probs=59.3

Q ss_pred             CCCCCceEEE--cCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccC
Q psy300           28 DKTKRGRLFI--KNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY   98 (451)
Q Consensus        28 ~~~~~~~lfV--gnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f   98 (451)
                      ...+.++|||  +||+.++++++|+++|++||.|.++.++.     +||||||+|.+.++|.+|+..|||+.+
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~-----~rgfaFV~f~~~~~A~~Ai~~lnG~~~   88 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEV   88 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT-----TCSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEE
Confidence            3446789999  77999999999999999999999998863     379999999999999999999999865

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.30  E-value=7.9e-12  Score=115.93  Aligned_cols=71  Identities=27%  Similarity=0.502  Sum_probs=67.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...++|||+|||.++++++|+++|++||.|.+++++++. +|+++|||||+|.+.++|.+|+..|||..+.|
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g  194 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGG  194 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSS
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCC
Confidence            356899999999999999999999999999999999997 99999999999999999999999999988766

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.30  E-value=9.4e-12  Score=101.37  Aligned_cols=67  Identities=10%  Similarity=0.285  Sum_probs=59.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ....++|||+|||.++++++|+++|++||.|.+|  +.+. +|+   ||||+|.+.++|.+|+. ++|..+.|+
T Consensus         5 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~   72 (94)
T 2e5g_A            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGH   72 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCE
Confidence            3467899999999999999999999999999987  4454 555   99999999999999999 999888773

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.30  E-value=5.2e-12  Score=102.42  Aligned_cols=67  Identities=22%  Similarity=0.480  Sum_probs=60.7

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ......++|||+|||.++++++|+++|++||.|.+++++       ++||||+|.+.++|.+|+..||+..+.|
T Consensus         5 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~~g   71 (92)
T 2dgt_A            5 SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV-------KDYAFVHMERAEDAVEAIRGLDNTEFQG   71 (92)
T ss_dssp             CCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC-------SSEEEEEESCHHHHHHHHHHHTTEEETT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE-------CCEEEEEECCHHHHHHHHHHhCCCeeCC
Confidence            345578999999999999999999999999999999997       4499999999999999999999987654

>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=99.29  E-value=4.7e-12  Score=106.21  Aligned_cols=65  Identities=29%  Similarity=0.547  Sum_probs=59.8

Q ss_pred             CCCCceEEEcCCCCC-CCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFK-ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~-vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....++|||+|||.+ +++++|+++|++||.|.++.+       ++|||||+|.+.++|.+|+..|++..+.|
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~A~~~l~g~~~~g   89 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGENGRVLAG   89 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-------ETTEEEEECSSSHHHHHHHHHHTTCEETT
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-------eCCEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            345689999999999 999999999999999999998       58999999999999999999999987765

>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=99.29  E-value=6.2e-12  Score=130.79  Aligned_cols=72  Identities=24%  Similarity=0.448  Sum_probs=67.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..+.++|||+|||.++|+++|.++|++||.|.+|.|+.+. +|.++|||||+|.+.++|.+||..|||..|.|
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~g  171 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDG  171 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECC
Confidence            3456899999999999999999999999999999999997 99999999999999999999999999988776

>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=99.28  E-value=2e-12  Score=113.56  Aligned_cols=73  Identities=29%  Similarity=0.473  Sum_probs=62.9

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEE------EEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDA------QLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i------~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...+.++|||+|||.++++++|+++|++||.|.++      .+....+|+++|||||+|.+.++|.+|+..|||..+.|
T Consensus        41 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g  119 (143)
T 3egn_A           41 PGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFG  119 (143)
T ss_dssp             CCSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCC
Confidence            35578899999999999999999999999998774      12112379999999999999999999999999987765

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.28  E-value=5.2e-12  Score=101.99  Aligned_cols=66  Identities=24%  Similarity=0.435  Sum_probs=60.3

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...+.++|||+|||.++++++|+++|++||.|.+++++       ++||||+|.+.++|.+|+..|||..+.|
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~~g   70 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV-------KDYAFVHMEKEADAKAAIAQLNGKEVKG   70 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            34578899999999999999999999999999999997       4499999999999999999999987765

>1e9g_A Ppase, inorganic pyrophosphatase; pyrophosphate phosphohydrolase, hydrolase, manganese; HET: PO4; 1.15A {Saccharomyces cerevisiae} SCOP: b.40.5.1 PDB: 1e6a_A* 1wgi_A 1wgj_A 2ihp_A* 8prk_A 2ik6_A 2ik2_A 2ik4_A 117e_A 2ik1_A* 2ik9_A 2ik0_A 2ik7_A 1m38_A 1ypp_A 1huk_A 1huj_A 1pyp_A

Probab=99.28  E-value=1.4e-12  Score=126.55  Aligned_cols=45  Identities=53%  Similarity=0.994  Sum_probs=41.6

Q ss_pred             CCCccCCccCCCccccCCCCEEEEEEeecCCCccceeeeccccce
Q psy300          381 ENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMR  425 (451)
Q Consensus       381 ~~~~~s~~hd~~l~~~~~~~~~~~~~e~p~~~~~k~e~~~~~~~~  425 (451)
                      +|+++||||||||+++....+|||||||||||++||||.+++++|
T Consensus        22 ~g~~~sp~hdIp~~~~~~~~~~nvVIEIP~gs~~KyEidk~~~~n   66 (286)
T 1e9g_A           22 DGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLN   66 (286)
T ss_dssp             TTEEECTTTTSCSEEETTTTEEEEEEEECTTCCBCEEECTTSTTC
T ss_pred             CCeecCchhhCCCCCCCCCCEEEEEEEECCCCCeEEEEccCCCCC
Confidence            488999999999998876689999999999999999999999874

>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=99.27  E-value=4.8e-12  Score=101.11  Aligned_cols=66  Identities=24%  Similarity=0.516  Sum_probs=60.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccC----C-------CeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQY----G-------DIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY   98 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~----G-------~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f   98 (451)
                      .+.++|||+|||.++++++|+++|++|    |       .|.++++.++     +|||||+|.+.++|.+|+ .+||..+
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-----kg~afV~f~~~~~a~~A~-~l~g~~~   77 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAM-AFDGIIF   77 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-----SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-----CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            467899999999999999999999999    8       9999998754     899999999999999999 9999988


Q ss_pred             CCC
Q psy300           99 KGK  101 (451)
Q Consensus        99 ~G~  101 (451)
                      .|+
T Consensus        78 ~g~   80 (87)
T 2hzc_A           78 QGQ   80 (87)
T ss_dssp             TTE
T ss_pred             CCe
Confidence            773

>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=99.27  E-value=6.1e-12  Score=104.24  Aligned_cols=66  Identities=33%  Similarity=0.521  Sum_probs=60.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...+.++|||+|||.++++++|+++|++||.|.+++++       +|||||+|.+.++|.+|+..||+..+.|
T Consensus         7 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~~g   72 (103)
T 2dgu_A            7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL-------KDYAFIHFDERDGAVKAMEEMNGKDLEG   72 (103)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEeCCHHHHHHHHHHHCCCccCC
Confidence            34567899999999999999999999999999999986       5699999999999999999999987655

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.27  E-value=6.4e-12  Score=102.47  Aligned_cols=71  Identities=20%  Similarity=0.235  Sum_probs=61.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEE-EeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQ-LLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~-l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .....++|||+|||.++++++|+++|++||.|.+++ ++.++   ..|.|||+|.+.++|.+|+..|||..+.|+
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~---~~~~afV~f~~~~~a~~Ai~~l~g~~~~g~   82 (96)
T 2e44_A           11 KRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS---ETAVVNVTYSSKDQARQALDKLNGFQLENF   82 (96)
T ss_dssp             CCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSS---SSEEEEEEESSHHHHHHHHHHHTTCBCSSC
T ss_pred             CCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEECCHHHHHHHHHHhCCCEECCc
Confidence            445678999999999999999999999999999995 77764   123399999999999999999999888763

>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=99.27  E-value=1.1e-11  Score=115.00  Aligned_cols=68  Identities=24%  Similarity=0.413  Sum_probs=62.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .++|||+|||.++++++|+++|++||+|.+|+++++.+|+++|||||+|.+.++|.+|+..++. .+.|
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~~-~~~G  176 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQ-KYKE  176 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTTC-EETT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCCC-eECC
Confidence            5899999999999999999999999999999999998999999999999999999999987653 5555

>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=99.26  E-value=4.4e-12  Score=102.16  Aligned_cols=65  Identities=22%  Similarity=0.332  Sum_probs=60.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...++|||+|||.++++++|+++|++| .|.++++.     +++|||||+|.+.++|.+|+..+||..+.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   67 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRG   67 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            467899999999999999999999999 99999884     679999999999999999999999987776

>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=99.26  E-value=7e-12  Score=101.62  Aligned_cols=57  Identities=23%  Similarity=0.507  Sum_probs=50.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHH
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVK   88 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~   88 (451)
                      ...+.++|||+|||.++++++|+++|++||.|.+++++++    ++|||||+|.+.++|.+
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~~   63 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQS   63 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHHH
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHHH
Confidence            4557889999999999999999999999999999999874    79999999999999873

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.25  E-value=1.7e-11  Score=100.45  Aligned_cols=66  Identities=23%  Similarity=0.419  Sum_probs=59.5

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...+.++|||+||  ++++++|+++|++||.|.++.+.     +++|||||+|.+.++|.+|+..|++..+.|
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   76 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD-----PPRNCAFVTYEKMESADQAVAELNGTQVES   76 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE-----TTTTEEEEEESSHHHHHHHHHHTTTEEETT
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec-----CCCCEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            3446789999996  99999999999999999999984     568999999999999999999999987765

>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=99.25  E-value=4e-12  Score=103.20  Aligned_cols=66  Identities=24%  Similarity=0.438  Sum_probs=58.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCC-eEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCC-ccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGD-IIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK-KPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~-I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng-~~f~G  100 (451)
                      ....++|||+|||.++++++|+++|++||. |..+.+.      ++|||||+|.+.++|.+|+..+|| ..+.|
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g   72 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHG   72 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETT
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHHHHHHHccCCeeECC
Confidence            457789999999999999999999999999 6666653      589999999999999999999999 66655

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.25  E-value=1.4e-11  Score=112.72  Aligned_cols=71  Identities=25%  Similarity=0.398  Sum_probs=67.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...++|||+|||.++++++|+++|++||.|.++++++++ +|.++|||||+|.+.++|.+|+..|||..+.|
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g  183 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGD  183 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECC
Confidence            567899999999999999999999999999999999997 99999999999999999999999999987765

>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=99.25  E-value=1.7e-11  Score=111.92  Aligned_cols=70  Identities=20%  Similarity=0.454  Sum_probs=64.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...++|||+|||.++++++|+++|++||.|.+++++++. +|.++|||||+|.+.++|.+|+.. ++..+.|
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G  172 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNG  172 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETT
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECC
Confidence            356899999999999999999999999999999999997 899999999999999999999986 6766655

>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=99.25  E-value=7e-12  Score=111.57  Aligned_cols=70  Identities=30%  Similarity=0.607  Sum_probs=65.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ..++|||+|||.++++++|+++|++||.|.+++++++. +|.++|||||+|.+.++|.+|++ +++..+.|+
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~  156 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDR  156 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSS
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCe
Confidence            46799999999999999999999999999999999987 89999999999999999999998 788877764

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.24  E-value=1.3e-11  Score=115.60  Aligned_cols=69  Identities=28%  Similarity=0.508  Sum_probs=64.0

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..++|||+|||.++++++|+++|++||.|.+++++++. +.++|||||+|.+.++|.+|++.|||..+.|
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~-~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g  170 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGMLLND  170 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC-CCCceEEEEEeCCHHHHHHHHHHhCCCEECC
Confidence            45799999999999999999999999999999999985 4489999999999999999999999987776

>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=99.23  E-value=2.2e-11  Score=109.95  Aligned_cols=69  Identities=17%  Similarity=0.324  Sum_probs=62.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .....+|||+||++++++++|+++|++||.|.+|++...   +++|||||+|.+.++|.+|++.|||..+.|
T Consensus        43 ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k---~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g  111 (164)
T 1sjr_A           43 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDGQNIYN  111 (164)
T ss_dssp             CCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES---SSCEEEEEEESCHHHHHHHHHHSTTBCSSS
T ss_pred             CCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC---CCCCEEEEEECCHHHHHHHHHHhCCCEecC
Confidence            345578999999999999999999999999999999754   368999999999999999999999998865

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.22  E-value=3.1e-11  Score=101.11  Aligned_cols=72  Identities=19%  Similarity=0.270  Sum_probs=64.0

Q ss_pred             CCCceEEEcCCCC-----CCCHHHHHHHhccCCCeEEEEEeECC--CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           30 TKRGRLFIKNLPF-----KITEEEFKEHFGQYGDIIDAQLLKNA--DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        30 ~~~~~lfVgnLp~-----~vte~~L~~~F~~~G~I~~i~l~~d~--tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .+++.|+|+||..     +-++++|++.|++||.|.++.+++++  +++++|||||+|.+.++|.+|+..|||+.|.|+
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            4678999999962     23789999999999999999999986  478999999999999999999999999999885

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.20  E-value=5.4e-11  Score=102.70  Aligned_cols=63  Identities=19%  Similarity=0.208  Sum_probs=57.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeE-EEEEEccHHHHHHHHHhcCCccCCC
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~-aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      -.|||+||++.+++++|+++|++||.|.+|++...     .|| |||+|.+.++|.+|++.|||..+.|
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g   89 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR-----NGIQAMVEFESVLCAQKAKAALNGADIYA   89 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES-----SSEEEEEEESSHHHHHHHHHHHTTCCCBT
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEecC
Confidence            45789999999999999999999999999999753     286 9999999999999999999998875

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.20  E-value=2.8e-11  Score=105.21  Aligned_cols=67  Identities=18%  Similarity=0.348  Sum_probs=60.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeE-EEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~-aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...-+|||+||++.+|+++|+++|++||.|.+|++...    ++|+ |||+|.+.++|.+|++.|||..+.|
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g   93 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYN   93 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE----TTEEEEEEEESCHHHHHHHHHHHTTCEEET
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC----CCCcEEEEEECCHHHHHHHHHHcCCCeecC
Confidence            45568999999999999999999999999999998764    3677 9999999999999999999987765

>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=99.17  E-value=1.7e-11  Score=98.49  Aligned_cols=56  Identities=27%  Similarity=0.532  Sum_probs=51.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHH
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA   89 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~A   89 (451)
                      .+.++|||+|||.++++++|+++|++||.|.+++++++    ++|||||+|.+.++|++|
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~~   58 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSL   58 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHT
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC----CCCEEEEEECCHHHHHHH
Confidence            46789999999999999999999999999999999764    789999999999998754

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.16  E-value=7.7e-11  Score=96.30  Aligned_cols=63  Identities=17%  Similarity=0.308  Sum_probs=54.8

Q ss_pred             CCCce-EEEcCCCCCCCHHH----HHHHhccC-CCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           30 TKRGR-LFIKNLPFKITEEE----FKEHFGQY-GDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        30 ~~~~~-lfVgnLp~~vte~~----L~~~F~~~-G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      +++.+ |||+|||.++++++    |+++|++| |+|.+|      +|   |+|||.|.+.++|.+|++.|+|..+.|+
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr   74 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI------TG---CSAILRFINQDSAERAQKRMENEDVFGN   74 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSS
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE------ec---CEEEEEECCHHHHHHHHHHhcCCccCCc
Confidence            34555 99999999999988    55899999 599988      34   9999999999999999999999887764

>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=99.16  E-value=5.3e-11  Score=105.29  Aligned_cols=83  Identities=22%  Similarity=0.361  Sum_probs=71.8

Q ss_pred             CCceeEEEEEEccHHHHHHHHHhc-CCcc--------------------------------------CCC----CCcHHH
Q psy300           70 GKLKGCGFINYANKISAVKAILKS-NKKP--------------------------------------YKG----KITEEE  106 (451)
Q Consensus        70 g~skG~aFV~F~~~~~A~~Al~~l-ng~~--------------------------------------f~G----~~tee~  106 (451)
                      ..-+|+++++|.+.++|++|+..+ ||..                                      |.|    .+|+++
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~~   89 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTE   89 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCCEEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCHH
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCCceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHHH
Confidence            456899999999999999999888 4332                                      222    479999


Q ss_pred             HHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          107 FKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       107 L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      |+++|++||.|.++.++++    ++|||||+|.+.++|.+|+..+|+..+
T Consensus        90 l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~  135 (150)
T 2i2y_A           90 LERAFGYYGPLRSVWVARN----PPGFAFVEFEDPRDAADAVRELDGRTL  135 (150)
T ss_dssp             HHHHHHHHSCEEEEEECSS----SCSEEEEEESSHHHHHHHHHHHSSSCS
T ss_pred             HHHHHHhhCCEEEEEEeeC----CCcEEEEEECCHHHHHHHHHHcCCCEE
Confidence            9999999999999999886    589999999999999999999988664

>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=99.16  E-value=2.5e-11  Score=113.52  Aligned_cols=71  Identities=20%  Similarity=0.292  Sum_probs=64.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCe--EEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDI--IDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I--~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .+.++|||+|||.++++++|+++|++||.|  .+++++.+. +.++|+|||+|.+.++|.+|+..|||..+.|+
T Consensus       121 ~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~-~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~  193 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK-SERSSSGLLEWDSKSDALETLGFLNHYQMKNP  193 (205)
T ss_dssp             CCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC-SSSSEEEEEECSSHHHHHHHHHHHTTCEECCS
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC-CCCceEEEEEeCCHHHHHHHHHHhCCCCccCC
Confidence            356789999999999999999999999999  899998775 55679999999999999999999999988774

>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=99.11  E-value=1.1e-10  Score=112.57  Aligned_cols=66  Identities=27%  Similarity=0.473  Sum_probs=62.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCc
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK   96 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~   96 (451)
                      +.++|||+|||.++++++|+++|++||.|.+++++++.+|+++|||||+|.+.++|.+|+..+|+.
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~  160 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDG  160 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHS
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCC
Confidence            567999999999999999999999999999999999999999999999999999999999999544

>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=99.10  E-value=8.8e-11  Score=105.45  Aligned_cols=68  Identities=32%  Similarity=0.457  Sum_probs=61.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....++|||+|||.++++++|+++|++||.|..+    ..+|.++|||||+|.+.++|.+|+..|||..+.|
T Consensus        96 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g  163 (175)
T 1fje_B           96 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG  163 (175)
T ss_dssp             TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETT
T ss_pred             cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            3467899999999999999999999999988766    5589999999999999999999999999987776

>3q46_A TT-ippase; inorganic pyrophosphatase, hydrolase; HET: EPE; 0.99A {Thermococcus thioreducens} SCOP: b.40.5.1 PDB: 3r6e_A* 3q3l_A 3i98_A 3q4w_A 3q9m_A* 3r5u_A 3r5v_A* 3q5v_A* 1ude_A 1twl_A

Probab=99.08  E-value=4.5e-11  Score=108.73  Aligned_cols=52  Identities=25%  Similarity=0.409  Sum_probs=41.4

Q ss_pred             cCCccCCCccccCCCCEEEEEEeecCCCccceeeeccccceEEEEEeeCCCCchh
Q psy300          385 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLYLVCFNLPSPLGY  439 (451)
Q Consensus       385 ~s~~hd~~l~~~~~~~~~~~~~e~p~~~~~k~e~~~~~~~~~~~~~~~~~~~~~~  439 (451)
                      +|||||||+..+ ...+|||||||||||++|+|+.++...  ..+--+|.++.+|
T Consensus         1 ~spwhdi~~g~~-~p~~~nvvIEIP~gs~~KyE~dk~~g~--i~~DR~l~~~~~Y   52 (178)
T 3q46_A            1 MNPFHELEPGPE-VPEVVYALIEIPKGSRNKYELDKATGL--LKLDRVLYSPFFY   52 (178)
T ss_dssp             CCTTTTSCSCSB-TTTBCCCEEEECTTCCEEEEECTTTSC--EEEEEECSSSCCC
T ss_pred             CCccccCCCCCC-CCCEEEEEEEECCCCCeeEEECCCCCC--EEEeecccCCCCC
Confidence            599999999765 478999999999999999999998653  3333456666665

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.07  E-value=1.5e-10  Score=110.90  Aligned_cols=65  Identities=20%  Similarity=0.374  Sum_probs=60.6

Q ss_pred             CCCCceEEEcCCCCCC---------CHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccC
Q psy300           29 KTKRGRLFIKNLPFKI---------TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY   98 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~v---------te~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f   98 (451)
                      ....++|||+|||.++         ++++|+++|++||+|.+|+++.     ++|||||+|.+.++|+.|+..|+|..+
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~-----~kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE-----SKNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG-----GGTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC-----CCCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            4568899999999998         7999999999999999999985     489999999999999999999999888

>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=99.05  E-value=4.6e-11  Score=99.86  Aligned_cols=65  Identities=22%  Similarity=0.489  Sum_probs=57.9

Q ss_pred             EcCCCCCCCHHHHHHHh------------ccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           37 IKNLPFKITEEEFKEHF------------GQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        37 VgnLp~~vte~~L~~~F------------~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      +.|||.++++++|++.|            ++||+|.+++++++.+++++|||||+|.+.++|.+|+..|||+.|.|+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr   96 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ   96 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCE
Confidence            56777778888777666            999999999999988889999999999999999999999999998875

>2prd_A Pyrophosphate phosphohydrolase; 2.00A {Thermus thermophilus} SCOP: b.40.5.1

Probab=99.04  E-value=1.8e-10  Score=104.46  Aligned_cols=51  Identities=22%  Similarity=0.354  Sum_probs=42.3

Q ss_pred             CCccCCCccccCCCCEEEEEEeecCCCccceeeeccccceEEEEEeeCCCCchh
Q psy300          386 SPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLYLVCFNLPSPLGY  439 (451)
Q Consensus       386 s~~hd~~l~~~~~~~~~~~~~e~p~~~~~k~e~~~~~~~~~~~~~~~~~~~~~~  439 (451)
                      |||||||+..+. ...|||||||||||++|||+.++.  +...+-..|.+++.|
T Consensus         1 ~~~h~ip~~~~~-p~~~nvvIEIP~gs~~KyE~dk~~--g~i~~DR~l~~~~~Y   51 (174)
T 2prd_A            1 ANLKSLPVGDKA-PEVVHMVIEVPRGSGNKYEYDPDL--GAIKLDRVLPGAQFY   51 (174)
T ss_dssp             CCGGGSCCCTTT-TTEEEEEEEECTTCCEEEEEETTT--TEEEEEEECSSSCCC
T ss_pred             CCcccCCCCCCC-CCEEEEEEEecCCCCeEEEEecCC--CCEEEeeecCCCCcC
Confidence            899999998775 589999999999999999999875  344455667777665

>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=99.01  E-value=3.1e-10  Score=114.13  Aligned_cols=69  Identities=14%  Similarity=0.128  Sum_probs=61.3

Q ss_pred             CCCCCCCceEEEcC--CCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCC
Q psy300           26 KPDKTKRGRLFIKN--LPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK   99 (451)
Q Consensus        26 ~~~~~~~~~lfVgn--Lp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~   99 (451)
                      +....++.+|||+|  |+.++|+++|+++|++||.|.++.+.+     +||||||+|.+.++|++|++.|||+.+.
T Consensus        12 ~~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~   82 (345)
T 3tht_A           12 ETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVV   82 (345)
T ss_dssp             CCCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             eecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCccc
Confidence            44466889999999  588999999999999999999987753     5899999999999999999999998774

>3fq3_A Inorganic pyrophosphatase:bacterial/archaeal INOR pyrophosphatase; ssgcid, inorganic phosphatase; 1.90A {Brucella melitensis biovar abortus 230ORGANISM_TAXID} PDB: 3sw5_A

Probab=99.00  E-value=2.8e-10  Score=104.67  Aligned_cols=58  Identities=21%  Similarity=0.227  Sum_probs=42.1

Q ss_pred             CCCCCccCCccCCCccccCCCCEEEEEEeecC-CCccceeeeccccceEEEEEeeCCCCchh
Q psy300          379 GSENGLISPFHDIPLYSNVKDKIFNMVVEIPR-WTNAKMEVGNAMEMRLYLVCFNLPSPLGY  439 (451)
Q Consensus       379 ~~~~~~~s~~hd~~l~~~~~~~~~~~~~e~p~-~~~~k~e~~~~~~~~~~~~~~~~~~~~~~  439 (451)
                      ..+|++||+|||||+..+ ..++||||||||| ||++|+|+.++.  +...+--.|.++++|
T Consensus        15 ~~~g~~im~~~~ip~g~~-~p~~vnvvIEIP~g~s~~KyE~dk~~--g~i~~DR~l~~~~~Y   73 (197)
T 3fq3_A           15 QTQGPGSMNIDAISIGSN-PPEDVNVIIEVPVGGQPIKYEMDKKA--GALIVDRFLYTPMTY   73 (197)
T ss_dssp             -------CCGGGSCSCSS-TTSCEEEEEEECTTCCSEEEEEETTT--TEEEEEEECCSSBCC
T ss_pred             ccCCCCcCCHHHCCCCCC-CCCEEEEEEEecCCCCCEeEEEecCC--CCEEEEeecCCCCcC
Confidence            356899999999999876 3689999999998 799999999875  555555566677666

>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=99.00  E-value=8e-10  Score=107.16  Aligned_cols=69  Identities=19%  Similarity=0.276  Sum_probs=62.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCC-C
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK-G  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~-G  100 (451)
                      .....++|||+|||.++++++|+++|++||.|.+++++.++    +|||||+|.+.++|.+|+..|||..+. |
T Consensus       203 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~g  272 (282)
T 3pgw_A          203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR----HDIAFVEFDNEVQAGAARDALQGFKITQN  272 (282)
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC----CcEEEEEeCCHHHHHHHHHHcCCcEeCCC
Confidence            34467899999999999999999999999999999998653    589999999999999999999998877 5

>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=99.00  E-value=4.9e-10  Score=92.53  Aligned_cols=56  Identities=29%  Similarity=0.534  Sum_probs=52.4

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|.++.++++ .+|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        30 ~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~   86 (99)
T 4fxv_A           30 NMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRL   86 (99)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEE
Confidence            5899999999999999999999998 5689999999999999999999999998765

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=98.99  E-value=3e-10  Score=99.14  Aligned_cols=82  Identities=12%  Similarity=0.221  Sum_probs=51.7

Q ss_pred             EEEEEEccHHHHHHHHHhcCCccCCC--------------------------CCcHHHHHHHhcccCcceeeEEeeC-CC
Q psy300           75 CGFINYANKISAVKAILKSNKKPYKG--------------------------KITEEEFKEHFGQYGDIIDAQLLKN-AD  127 (451)
Q Consensus        75 ~aFV~F~~~~~A~~Al~~lng~~f~G--------------------------~~tee~L~~~F~~fG~V~~v~v~~d-~~  127 (451)
                      +.|.+|.+...+..|+..++|..-.|                          .+|+++|+++|++||.|..+.++.+ .+
T Consensus         6 ~~~~~~~~~~~~~~a~~~~~g~~~~g~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~   85 (135)
T 2lea_A            6 HHHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYT   85 (135)
T ss_dssp             -----------------------------CCSCCSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSS
T ss_pred             cccccccCCCchhhhhhhccCCCCCCCCCCCcCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCC
Confidence            56777888888888888877643222                          4799999999999999999999987 47


Q ss_pred             CCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          128 GKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       128 g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++|||||+|.+.++|.+|+..+|+..+
T Consensus        86 g~~~G~afV~F~~~~~A~~Ai~~l~g~~i  114 (135)
T 2lea_A           86 KESRGFAFVRFHDKRDAEDAMDAMDGAVL  114 (135)
T ss_dssp             SSCCSCCEEECSCHHHHHHHHTTTTTCCS
T ss_pred             CccceEEEEEECCHHHHHHHHHHcCCCEE
Confidence            89999999999999999999999988764

>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=98.98  E-value=1.4e-09  Score=91.56  Aligned_cols=70  Identities=16%  Similarity=0.260  Sum_probs=59.0

Q ss_pred             CCCCCceEEEcCCCCCCC-----------HHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCc
Q psy300           28 DKTKRGRLFIKNLPFKIT-----------EEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK   96 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vt-----------e~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~   96 (451)
                      ...+.++|+|+||.....           +++|+++|++||.|.++.+ .+.  .++|||||+|.+.++|.+|+..|||.
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~--~~~G~afV~f~~~~~A~~Ai~~lng~   87 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR--HPDGVASVSFRDPEEADYCIQTLDGR   87 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT--CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC--CCCEEEEEEECCHHHHHHHHHHcCCC
Confidence            445788999999944332           5899999999999999966 443  48999999999999999999999998


Q ss_pred             cCCC
Q psy300           97 PYKG  100 (451)
Q Consensus        97 ~f~G  100 (451)
                      .|.|
T Consensus        88 ~~~g   91 (112)
T 2dit_A           88 WFGG   91 (112)
T ss_dssp             EETT
T ss_pred             EECC
Confidence            7765

>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=98.97  E-value=4.9e-10  Score=93.73  Aligned_cols=72  Identities=15%  Similarity=0.289  Sum_probs=62.3

Q ss_pred             CCCceEEEcCC--CCCCC--------HHHHHHHhccCCCeEEEEEeECCC---CCceeEEEEEEccHHHHHHHHHhcCCc
Q psy300           30 TKRGRLFIKNL--PFKIT--------EEEFKEHFGQYGDIIDAQLLKNAD---GKLKGCGFINYANKISAVKAILKSNKK   96 (451)
Q Consensus        30 ~~~~~lfVgnL--p~~vt--------e~~L~~~F~~~G~I~~i~l~~d~t---g~skG~aFV~F~~~~~A~~Al~~lng~   96 (451)
                      .+++.|.+.|+  |.++.        +++|++.|++||+|.+++++++..   ++++|+|||+|.+.++|.+|+..|||+
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  44443        368999999999999999998863   468999999999999999999999999


Q ss_pred             cCCCC
Q psy300           97 PYKGK  101 (451)
Q Consensus        97 ~f~G~  101 (451)
                      .|.|+
T Consensus        83 ~f~GR   87 (105)
T 3v4m_A           83 KFANR   87 (105)
T ss_dssp             EETTE
T ss_pred             EeCCC
Confidence            99885

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=98.97  E-value=7.4e-10  Score=93.30  Aligned_cols=56  Identities=14%  Similarity=0.263  Sum_probs=52.3

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCC-CCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~-~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++++|+++|++||.|.++.+++|+ +++++|||||+|.+.++|.+|+..+|++.+
T Consensus        17 ~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~   73 (110)
T 3s8s_A           17 NVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSV   73 (110)
T ss_dssp             TCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEE
Confidence            58999999999999999999999984 699999999999999999999999998765

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.94  E-value=8.9e-10  Score=91.75  Aligned_cols=61  Identities=21%  Similarity=0.356  Sum_probs=53.5

Q ss_pred             CccCCC----CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           95 KKPYKG----KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        95 g~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .++|.|    .+|+++|+++|++||.|.++.+++++.|.++|||||+|.+.++|.+|+. +++..+
T Consensus        12 ~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~   76 (103)
T 1s79_A           12 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKY   76 (103)
T ss_dssp             GCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHT-SSCCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHH-cCCCEE
Confidence            345554    5899999999999999999999998779999999999999999999998 776554

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=98.94  E-value=1.2e-09  Score=100.28  Aligned_cols=67  Identities=18%  Similarity=0.325  Sum_probs=61.6

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCC-CeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCC-C
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYG-DIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK-G  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G-~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~-G  100 (451)
                      .+.++|||+|||.++++++|+++|++|| .|.+++++.+    ++|+|||+|.+.++|.+|+..+||..+. |
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g  186 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGEN  186 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST----TSSCEEEECSSHHHHHHHHHHHTSSCCSSC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC----CCcEEEEEeCCHHHHHHHHHHhcCCccCCC
Confidence            4578999999999999999999999999 9999999754    3799999999999999999999999887 5

>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=98.92  E-value=1.2e-09  Score=88.09  Aligned_cols=56  Identities=25%  Similarity=0.420  Sum_probs=51.5

Q ss_pred             CCcHHHHHHHhcccC--cceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYG--DIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG--~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||  .|.++.++.+ .+|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        12 ~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~   70 (90)
T 3p5t_L           12 WTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKREL   70 (90)
T ss_dssp             TCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCS
T ss_pred             CCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCee
Confidence            579999999999999  9999999998 5899999999999999999999999998765

>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=98.91  E-value=2e-09  Score=91.95  Aligned_cols=71  Identities=20%  Similarity=0.333  Sum_probs=62.2

Q ss_pred             CCceEEEcCCC--CCC---CHHHHHHHhccCCCeEEEEEeECC-----CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           31 KRGRLFIKNLP--FKI---TEEEFKEHFGQYGDIIDAQLLKNA-----DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        31 ~~~~lfVgnLp--~~v---te~~L~~~F~~~G~I~~i~l~~d~-----tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      +++.|+++|+-  .++   -+++|++.|++||+|.+++++++.     +++++|++||+|.+.++|.+|+..|||+.|.|
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            67899999993  222   368999999999999999999875     35688999999999999999999999999988


Q ss_pred             C
Q psy300          101 K  101 (451)
Q Consensus       101 ~  101 (451)
                      +
T Consensus        99 R   99 (118)
T 3ue2_A           99 R   99 (118)
T ss_dssp             E
T ss_pred             c
Confidence            5

>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=98.91  E-value=2.2e-09  Score=101.43  Aligned_cols=67  Identities=18%  Similarity=0.325  Sum_probs=61.3

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCC-CeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCC-C
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYG-DIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK-G  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G-~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~-G  100 (451)
                      .+.++|||+|||.++++++|+++|++|| .|.+++++.+    ++|||||+|.+.++|.+|+..+||..+. |
T Consensus       149 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g  217 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGEN  217 (229)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS----STTCEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC----CCcEEEEEECCHHHHHHHHHHHCCCccCCC
Confidence            3578999999999999999999999999 9999999653    4789999999999999999999998887 5

>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=98.88  E-value=5.6e-10  Score=116.05  Aligned_cols=61  Identities=23%  Similarity=0.422  Sum_probs=55.1

Q ss_pred             ccCCC----CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           96 KPYKG----KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        96 ~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+|    .+|+++|.++|++||.|..|.|+.+ .+|.++|||||+|.+.++|.+|+..||+..+
T Consensus       104 ~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i  169 (437)
T 3pgw_S          104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKI  169 (437)
T ss_pred             EEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEE
Confidence            45665    4799999999999999999999988 5789999999999999999999999998765

>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=98.88  E-value=1.3e-09  Score=92.09  Aligned_cols=55  Identities=24%  Similarity=0.482  Sum_probs=50.4

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|++||.|.+++++++. +.++|||||+|.+.++|.+|+..+++..+
T Consensus        16 ~~te~~L~~~F~~~G~v~~v~i~~d~-~~~kg~afV~f~~~~~A~~Ai~~l~~~~~   70 (115)
T 4f25_A           16 SIDNKALYDTFSAFGNILSCKVVCDE-NGSKGYGFVHFETQEAAERAIEKMNGMLL   70 (115)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEEEEEET-TEEEEEEEEEESCHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHhccCCEEEEEEeecC-CCCCceEEEEECCHHHHHHHHHHcCCCEE
Confidence            58999999999999999999999985 45899999999999999999999988654

>3ld3_A Inorganic pyrophosphatase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, hydrolase; 1.75A {Anaplasma phagocytophilum} PDB: 3lo0_A

Probab=98.87  E-value=1.2e-09  Score=100.56  Aligned_cols=58  Identities=22%  Similarity=0.183  Sum_probs=36.6

Q ss_pred             CCCCCccCCccCCCccccCCCCEEEEEEeecCCC-ccceeeeccccceEEEEEeeCCCCchh
Q psy300          379 GSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWT-NAKMEVGNAMEMRLYLVCFNLPSPLGY  439 (451)
Q Consensus       379 ~~~~~~~s~~hd~~l~~~~~~~~~~~~~e~p~~~-~~k~e~~~~~~~~~~~~~~~~~~~~~~  439 (451)
                      ..+|++|++|||||+..+ ...++|||||||||| ++|+|+.++.  +...+--.|.++++|
T Consensus        15 ~~~g~~~m~~~~i~~g~~-~p~~vnvvIEIP~gs~~~KyE~dk~~--G~l~~DR~l~~~~~Y   73 (199)
T 3ld3_A           15 QTQGPGSMNLDDIGSGSN-APEEVNVVIEVSQDSHPVKYEFDEKN--GALWVDRFLPTAMYY   73 (199)
T ss_dssp             -----------CCCSCTT-TTTSEEEEEEECTTCCSEEEEECTTT--CCEEEEEECSSSBCC
T ss_pred             ccCCCccCChHHCCCCCC-CCCEEEEEEEecCCCCCEEEEEecCC--CCEEEEEEcCCCCcC
Confidence            467889999999999866 368999999999998 6999999876  444444456666655

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=98.87  E-value=8.9e-10  Score=89.39  Aligned_cols=54  Identities=17%  Similarity=0.433  Sum_probs=49.3

Q ss_pred             CCcHHHHHHHhcccC-cceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCC
Q psy300          101 KITEEEFKEHFGQYG-DIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKK  154 (451)
Q Consensus       101 ~~tee~L~~~F~~fG-~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~r  154 (451)
                      ++|+++|+++|++|| .|.+++++++ .+|.++|||||+|.+.++|.+|+..+++.
T Consensus        12 ~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~   67 (91)
T 2lxi_A           12 AATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHS   67 (91)
T ss_dssp             SCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTE
T ss_pred             CCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCC
Confidence            589999999999999 7999999988 56899999999999999999999887543

>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=98.86  E-value=3.7e-09  Score=87.33  Aligned_cols=56  Identities=27%  Similarity=0.504  Sum_probs=53.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.++++.++|||||+|.+.++|.+|+..+|+..+
T Consensus        26 ~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   81 (105)
T 2dnh_A           26 QQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQT   81 (105)
T ss_dssp             TCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCC
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCcc
Confidence            57999999999999999999999998899999999999999999999999998765

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=98.86  E-value=2.1e-09  Score=84.84  Aligned_cols=53  Identities=26%  Similarity=0.442  Sum_probs=49.2

Q ss_pred             cHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       103 tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++|+++|++||.|.++.++ ..+|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        20 t~~~l~~~F~~~G~i~~v~i~-~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~   72 (81)
T 2krb_A           20 LKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKL   72 (81)
T ss_dssp             HHHHHHHHHHTTCCEEEEECC-CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCC
T ss_pred             HHHHHHHHHhhcCCeEEEEec-CCCCcEeEEEEEEECCHHHHHHHHHHhcCccc
Confidence            679999999999999999988 45789999999999999999999999998776

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=98.86  E-value=1.5e-09  Score=89.43  Aligned_cols=56  Identities=20%  Similarity=0.317  Sum_probs=51.5

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCC-CCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~-~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.+++++ +|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        23 ~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~   79 (100)
T 3ns6_A           23 PVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRL   79 (100)
T ss_dssp             HHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBS
T ss_pred             HHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCccc
Confidence            35789999999999999999999885 599999999999999999999999998765

>3gvf_A Inorganic pyrophosphatase; structural genomics, hydrolase, S structural genomics center for infectious disease, ssgcid; HET: PGE; 1.75A {Burkholderia pseudomallei 1710B} PDB: 3d63_A* 3eiy_A 3ej0_A* 3ej2_A* 3eiz_A*

Probab=98.85  E-value=2.1e-09  Score=98.83  Aligned_cols=58  Identities=22%  Similarity=0.373  Sum_probs=39.4

Q ss_pred             CCCCCccCCccCCCccccCCCCEEEEEEeecCCCc-cceeeeccccceEEEEEeeCCCCchh
Q psy300          379 GSENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTN-AKMEVGNAMEMRLYLVCFNLPSPLGY  439 (451)
Q Consensus       379 ~~~~~~~s~~hd~~l~~~~~~~~~~~~~e~p~~~~-~k~e~~~~~~~~~~~~~~~~~~~~~~  439 (451)
                      ..+|++|++|||||+..+. ..++||||||||||+ +|+|+.++.  +...+---|.+++.|
T Consensus        15 ~~~g~~~m~~~~i~~g~~~-p~~vnvvIEIP~gs~~~KyE~dk~~--g~i~~DR~l~s~~~Y   73 (196)
T 3gvf_A           15 QTQGPGSMSFSNVPAGKDL-PQDFNVIIEIPAQSEPVKYEADKAL--GLLVVDRFIGTGMRY   73 (196)
T ss_dssp             --------CGGGSCSCSBT-TTBEEEEEEECTTCCSEEEEEETTT--TEEEEEEECTTCCCC
T ss_pred             cccCCCCCchhhCCCCCCC-CCEEEEEEEecCCCCceEEEEecCC--CCEEEEeEcCCCccC
Confidence            3568899999999997664 589999999999998 999999876  344444445666555

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=98.85  E-value=1.6e-09  Score=88.93  Aligned_cols=54  Identities=11%  Similarity=0.281  Sum_probs=49.5

Q ss_pred             CCcHHHHHHHhcccCc--ceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCC
Q psy300          101 KITEEEFKEHFGQYGD--IIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKK  154 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~--V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~r  154 (451)
                      .+|+++|+++|++||.  +.++++++| .+|+++|||||+|.+.++|.+|+..+|+.
T Consensus        20 ~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~   76 (95)
T 2lkz_A           20 HTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSL   76 (95)
T ss_dssp             TCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSS
T ss_pred             cCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCC
Confidence            5899999999999995  678999988 56899999999999999999999999875

>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=98.84  E-value=4.7e-09  Score=85.00  Aligned_cols=56  Identities=29%  Similarity=0.358  Sum_probs=52.6

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+++++++|||||+|.+.++|.+|+..+|+..+
T Consensus        27 ~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~   82 (95)
T 2ywk_A           27 RVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRL   82 (95)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            58999999999999999999999998899999999999999999999999988654

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=98.83  E-value=3.9e-09  Score=88.24  Aligned_cols=54  Identities=22%  Similarity=0.297  Sum_probs=50.4

Q ss_pred             cHHHHHHHhcccCcceeeEEeeCC--CCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          103 TEEEFKEHFGQYGDIIDAQLLKNA--DGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       103 tee~L~~~F~~fG~V~~v~v~~d~--~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++|++.|++||.|.++.+++++  +++++|||||+|.+.++|.+|+..|||+.|
T Consensus        26 ~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~   81 (105)
T 2pe8_A           26 LEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYF   81 (105)
T ss_dssp             CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             HHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEE
Confidence            689999999999999999999874  368999999999999999999999999987

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.83  E-value=5e-09  Score=85.85  Aligned_cols=56  Identities=30%  Similarity=0.479  Sum_probs=52.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+++|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        28 ~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~   83 (100)
T 2do4_A           28 SCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTI   83 (100)
T ss_dssp             TCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEES
T ss_pred             CCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEE
Confidence            57999999999999999999999998899999999999999999999999988654

>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=98.83  E-value=2.6e-09  Score=89.07  Aligned_cols=54  Identities=20%  Similarity=0.367  Sum_probs=49.3

Q ss_pred             cHHHHHHHh-cccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          103 TEEEFKEHF-GQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       103 tee~L~~~F-~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++|++.| ++||.|.++.++++.+++++|||||+|.+.++|.+|+..+||+.+
T Consensus        39 ~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~   93 (104)
T 1jmt_A           39 FFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWF   93 (104)
T ss_dssp             HHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEE
T ss_pred             HHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEE
Confidence            446777777 999999999999988889999999999999999999999999876

>2bqx_A Inorganic pyrophosphatase; hydrolase; 1.90A {Helicobacter pylori} PDB: 1ygz_A 2bqy_A

Probab=98.82  E-value=2.3e-09  Score=97.18  Aligned_cols=49  Identities=18%  Similarity=0.266  Sum_probs=34.7

Q ss_pred             CccCCCccccCCCCEEEEEEeecCCCccceeeeccccceEEEEEeeCCCCchh
Q psy300          387 PFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLYLVCFNLPSPLGY  439 (451)
Q Consensus       387 ~~hd~~l~~~~~~~~~~~~~e~p~~~~~k~e~~~~~~~~~~~~~~~~~~~~~~  439 (451)
                      +|||||+..+  ...|||||||||||++|||+.++.  +...+--+|.+++.|
T Consensus         2 ~~~~ip~~~~--p~~~nvvIEIP~gs~~KyE~dk~~--g~i~~DR~l~~~~~Y   50 (173)
T 2bqx_A            2 NLEKLEVSHD--ADSLCVVIEISKHSNIKYELDKES--GALMVDRVLYGAQNY   50 (173)
T ss_dssp             -----CCCEE--TTEEEEEEEECTTCSEEEEECTTT--CCEEEEEECSSSCCC
T ss_pred             CcccCCCCCC--CCeEEEEEEECCCCCeEEEEecCC--CCEEEeeecCCCCcC
Confidence            7999999988  689999999999999999999874  444444456566554

>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=98.82  E-value=6.5e-09  Score=82.64  Aligned_cols=56  Identities=36%  Similarity=0.557  Sum_probs=52.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+ .++.++|||||+|.+.++|.+|+..+|+..+
T Consensus        17 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~   73 (87)
T 3bs9_A           17 EITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWL   73 (87)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEE
Confidence            5899999999999999999999998 5889999999999999999999999988654

>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=98.81  E-value=6.7e-09  Score=81.79  Aligned_cols=56  Identities=14%  Similarity=0.421  Sum_probs=52.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+ .++.++|||||+|.+.++|.+|+..+|+..+
T Consensus        12 ~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~   68 (83)
T 3md1_A           12 NVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDL   68 (83)
T ss_dssp             TCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCee
Confidence            5799999999999999999999988 6789999999999999999999999988764

>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=98.81  E-value=6e-09  Score=88.33  Aligned_cols=56  Identities=30%  Similarity=0.461  Sum_probs=53.0

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+.+|.++|||||+|.+.++|.+|+..+|+..+
T Consensus        18 ~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~   73 (116)
T 2fy1_A           18 ETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSL   73 (116)
T ss_dssp             TCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBC
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEE
Confidence            58999999999999999999999988999999999999999999999999998765

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.81  E-value=5.3e-09  Score=85.44  Aligned_cols=62  Identities=24%  Similarity=0.462  Sum_probs=54.9

Q ss_pred             CccCCC----CCcHHHHHHHhcccCcce-eeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           95 KKPYKG----KITEEEFKEHFGQYGDII-DAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        95 g~~f~G----~~tee~L~~~F~~fG~V~-~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .++|.|    .+++++|+++|++||.|. ++.++++ .+++++|||||+|.+.++|.+|+..+|+..+
T Consensus        10 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~   77 (99)
T 2div_A           10 ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPL   77 (99)
T ss_dssp             SEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCcc
Confidence            344555    479999999999999999 9999998 4789999999999999999999999998765

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.80  E-value=8.3e-09  Score=85.05  Aligned_cols=55  Identities=16%  Similarity=0.401  Sum_probs=52.4

Q ss_pred             CCcHHHHHHHhcc-cCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCc
Q psy300          101 KITEEEFKEHFGQ-YGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP  155 (451)
Q Consensus       101 ~~tee~L~~~F~~-fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~ri  155 (451)
                      .+|+++|+++|++ ||.|.++.++.+++|.++|||||+|.+.++|.+|+..+++..
T Consensus        20 ~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~   75 (104)
T 2dhg_A           20 DVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAV   75 (104)
T ss_dssp             TCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCC
T ss_pred             CCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCc
Confidence            5899999999999 999999999999899999999999999999999999999866

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.80  E-value=9.7e-09  Score=83.10  Aligned_cols=56  Identities=30%  Similarity=0.523  Sum_probs=51.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.++++ .+++++|||||+|.+.++|.+|+..+|+..+
T Consensus        16 ~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~   72 (95)
T 2dnz_A           16 NITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFEL   72 (95)
T ss_dssp             TCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCS
T ss_pred             CCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCee
Confidence            5899999999999999999999988 4689999999999999999999999988654

>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=98.80  E-value=9e-09  Score=86.37  Aligned_cols=56  Identities=21%  Similarity=0.435  Sum_probs=53.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.++++.++|||||+|.+.++|.+|+..+|++.+
T Consensus        36 ~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~   91 (114)
T 1x5o_A           36 SMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFI   91 (114)
T ss_dssp             TCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCC
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            57999999999999999999999998899999999999999999999999998765

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=98.79  E-value=9e-09  Score=84.21  Aligned_cols=56  Identities=30%  Similarity=0.363  Sum_probs=52.0

Q ss_pred             CCcHHHHHHHhcccCccee--------eEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIID--------AQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~--------v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.+        +.++.+ .+|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        24 ~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A           24 NVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            5899999999999999999        999988 5789999999999999999999999998765

>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=98.79  E-value=6.5e-09  Score=84.90  Aligned_cols=56  Identities=23%  Similarity=0.412  Sum_probs=52.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCC-CCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~-~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.++ ++.++|||||+|.+.++|.+|+..+|+..+
T Consensus        19 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~   75 (99)
T 1whw_A           19 TSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVF   75 (99)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEES
T ss_pred             CCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEE
Confidence            58999999999999999999999885 889999999999999999999999988654

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=98.79  E-value=5.8e-09  Score=80.71  Aligned_cols=55  Identities=24%  Similarity=0.377  Sum_probs=49.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCC-CCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~-~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.++ +|+++|||||+|.+.++|.+|+. +++..+
T Consensus        10 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~   65 (75)
T 2mss_A           10 NTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEI   65 (75)
T ss_dssp             SCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCS
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEE
Confidence            58999999999999999999999884 78999999999999999999987 777654

>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=98.78  E-value=7.7e-09  Score=85.68  Aligned_cols=56  Identities=21%  Similarity=0.450  Sum_probs=52.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+.+|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        40 ~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~   95 (107)
T 3ulh_A           40 GVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPL   95 (107)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEe
Confidence            58999999999999999999999998999999999999999999999999988764

>3d53_A Inorganic pyrophosphatase; seattle structural G center for infectious disease, ssgcid, hydrolase, magnesium binding; 2.20A {Rickettsia prowazekii} PDB: 3emj_A*

Probab=98.78  E-value=3.9e-09  Score=95.50  Aligned_cols=49  Identities=20%  Similarity=0.289  Sum_probs=41.3

Q ss_pred             CccCCCccccCCCCEEEEEEeecCCCc-cceeeeccccceEEEEEeeCCCCchh
Q psy300          387 PFHDIPLYSNVKDKIFNMVVEIPRWTN-AKMEVGNAMEMRLYLVCFNLPSPLGY  439 (451)
Q Consensus       387 ~~hd~~l~~~~~~~~~~~~~e~p~~~~-~k~e~~~~~~~~~~~~~~~~~~~~~~  439 (451)
                      +|||||+..+  ...|||||||||||+ +|+|+.++.  +...+-.+|.+++.|
T Consensus         3 ~~~~ip~~~~--p~~~nvvIEIP~gs~p~KyE~dk~~--g~i~~DR~l~~~~~Y   52 (173)
T 3d53_A            3 FIKKIKAKAN--NNEINVIIEIPMNSGPIKYEFDKES--GALFVDRFMQTTMSY   52 (173)
T ss_dssp             CGGGSCSCSS--TTCEEEEEEECTTCCSEEEEECTTT--CCEEEEEECCSSCCC
T ss_pred             chhhCCCCCC--CCeEEEEEEeCCCCCceeEEEecCC--CCEEEeeecCCCCcC
Confidence            7999999887  689999999999999 999999875  455555667777666

>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=98.78  E-value=4.2e-09  Score=92.59  Aligned_cols=60  Identities=18%  Similarity=0.282  Sum_probs=52.3

Q ss_pred             CccCCC----CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           95 KKPYKG----KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        95 g~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .++|.+    .+|+++|+++|++|| +.++.++.+++|+++|||||+|.+.++|.+|+ .+|+..+
T Consensus        47 ~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al-~~~g~~l  110 (139)
T 2hgn_A           47 HCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAM-SKDRANM  110 (139)
T ss_dssp             CCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHT-TCCSCSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHH-hhCCCEE
Confidence            345665    489999999999999 67999999988999999999999999999999 7777554

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.77  E-value=2.9e-08  Score=82.30  Aligned_cols=60  Identities=17%  Similarity=0.210  Sum_probs=51.1

Q ss_pred             CceEEEcCCC-------CCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCC
Q psy300           32 RGRLFIKNLP-------FKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK   95 (451)
Q Consensus        32 ~~~lfVgnLp-------~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng   95 (451)
                      ..+|-|.-.+       .++++++|+++|++||.|.+|+++    ++++|||||+|.+.++|.+|+..+++
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~----~~~rGfaFVeF~~~~~A~~Ai~~~~~   76 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS----SKKPGTAVVEFATVKAAELAVQNEVG   76 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE----SSSSSEEEEEESCHHHHHHHHHTCCB
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc----cCCCCEEEEEECCHHHHHHHHHhcCC
Confidence            4566666443       468999999999999999999997    47899999999999999999987554

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.77  E-value=9.2e-09  Score=84.69  Aligned_cols=55  Identities=27%  Similarity=0.558  Sum_probs=51.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|..+.++.+ ++.++|||||+|.+.++|.+|+..+|+..+
T Consensus        26 ~~t~~~l~~~F~~~G~i~~v~i~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~   80 (103)
T 2d9p_A           26 GIDDERLRKAFSPFGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIV   80 (103)
T ss_dssp             TCCHHHHHHTTTTTSCEEEEEEEEC-SSSEEEEEEEEESSHHHHHHHHHHHTTCBS
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEEcC-CCCcCEEEEEEECCHHHHHHHHHHhCCCEe
Confidence            5899999999999999999999998 899999999999999999999999988764

>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=98.77  E-value=6.1e-09  Score=82.42  Aligned_cols=56  Identities=23%  Similarity=0.393  Sum_probs=52.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++++ .+++++|||||+|.+.++|.+|+..+|+..+
T Consensus        18 ~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~   74 (85)
T 3mdf_A           18 EVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL   74 (85)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEE
Confidence            5799999999999999999999887 6788999999999999999999999988764

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=98.77  E-value=1.2e-08  Score=84.39  Aligned_cols=56  Identities=29%  Similarity=0.471  Sum_probs=51.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+ .+|.++|||||+|.+.++|.+|+..+|+..+
T Consensus        34 ~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~   90 (106)
T 1p27_B           34 EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL   90 (106)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBS
T ss_pred             CCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEE
Confidence            5799999999999999999999988 5689999999999999999999999988654

>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=98.76  E-value=9.3e-09  Score=84.87  Aligned_cols=56  Identities=25%  Similarity=0.384  Sum_probs=52.0

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCC-CCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~-~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.++.++ ++.++|||||+|.+.++|.+|+..+|+..+
T Consensus        26 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~   82 (105)
T 1x5u_A           26 KVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKL   82 (105)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBC
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeE
Confidence            57999999999999999999999984 789999999999999999999999988654

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.76  E-value=1.1e-08  Score=85.72  Aligned_cols=56  Identities=32%  Similarity=0.507  Sum_probs=52.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+++++++|||||+|.+.++|.+|+..+|+..+
T Consensus        26 ~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~   81 (114)
T 2do0_A           26 KVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLL   81 (114)
T ss_dssp             TCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            58999999999999999999999998899999999999999999999999988654

>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=98.75  E-value=9e-09  Score=83.73  Aligned_cols=56  Identities=23%  Similarity=0.391  Sum_probs=51.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+ .+|.++|||||+|.+.++|.+|+..+|+..+
T Consensus        13 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   69 (96)
T 2x1f_A           13 DQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQL   69 (96)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeE
Confidence            5799999999999999999999988 4689999999999999999999999988654

>2au7_A Inorganic pyrophosphatase; hydrolase, mutant; 1.05A {Escherichia coli} PDB: 1i40_A 1i6t_A 1igp_A 1obw_A 2au6_A 2au8_A 2au9_A 2auu_A 1mjy_A 1faj_A 1ino_A 1ipw_A 1jfd_A 2eip_A 1mjz_A 1mjx_A 1mjw_A 3i4q_A*

Probab=98.75  E-value=5.8e-09  Score=94.54  Aligned_cols=50  Identities=18%  Similarity=0.292  Sum_probs=42.6

Q ss_pred             CccCCCccccCCCCEEEEEEeecCCCc-cceeeeccccceEEEEEeeCCCCchh
Q psy300          387 PFHDIPLYSNVKDKIFNMVVEIPRWTN-AKMEVGNAMEMRLYLVCFNLPSPLGY  439 (451)
Q Consensus       387 ~~hd~~l~~~~~~~~~~~~~e~p~~~~-~k~e~~~~~~~~~~~~~~~~~~~~~~  439 (451)
                      +|||||+..+. ...|||||||||||+ +|+|+.+++  +...+-..|.+++.|
T Consensus         1 ~~~~ip~~~~~-p~~~nvvIEIP~gs~p~KyE~dk~~--g~i~~DR~l~~~~~Y   51 (175)
T 2au7_A            1 SLLNVPAGKDL-PEDIYVVIEIPANADPIKYEIDKES--GALFVDQFMSTAMFY   51 (175)
T ss_dssp             CGGGCCSCSBT-TTBEEEEEEECTTCCSEEEEECTTT--CCEEEEEECSSSCCC
T ss_pred             CcccCCCCCCC-CCEEEEEEEecCCCCceeEEEecCC--CCEEEeeecCCCCcC
Confidence            69999998775 589999999999999 999999987  666666777777766

>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=98.75  E-value=1.4e-08  Score=81.07  Aligned_cols=55  Identities=24%  Similarity=0.450  Sum_probs=51.0

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+ .+++++|||||+|.+.++|.+|+ .+|+..+
T Consensus        17 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~   72 (89)
T 3ucg_A           17 GATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLF   72 (89)
T ss_dssp             TCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEE
T ss_pred             CCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEE
Confidence            5799999999999999999999998 47899999999999999999999 9988664

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=98.75  E-value=4.9e-09  Score=90.62  Aligned_cols=59  Identities=12%  Similarity=0.151  Sum_probs=52.9

Q ss_pred             CccCCC----CCcHHHHHHHhcccCccee--eEEeeCC-CCCccceEEEEecchHHHHHHHHhcCCC
Q psy300           95 KKPYKG----KITEEEFKEHFGQYGDIID--AQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKK  154 (451)
Q Consensus        95 g~~f~G----~~tee~L~~~F~~fG~V~~--v~v~~d~-~g~srG~gFV~F~s~e~A~~Ai~~ln~r  154 (451)
                      .++|.|    .+|+++|+++|++||.|..  +++++|+ +|+++|||||+|.+. +|.+|+..+|+.
T Consensus        24 ~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~   89 (131)
T 2m2b_A           24 DTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQAL   89 (131)
T ss_dssp             CEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCC
Confidence            455666    4799999999999999977  9999986 899999999999999 999999999886

>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=98.75  E-value=1.1e-08  Score=84.14  Aligned_cols=56  Identities=30%  Similarity=0.591  Sum_probs=52.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.++.+ .+|.++|||||+|.+.++|.+|+..+|+..+
T Consensus        19 ~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~   75 (104)
T 1p1t_A           19 EATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREF   75 (104)
T ss_dssp             TSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSC
T ss_pred             cCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCee
Confidence            5899999999999999999999988 5789999999999999999999999998765

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.74  E-value=5.9e-09  Score=82.71  Aligned_cols=56  Identities=21%  Similarity=0.422  Sum_probs=51.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+ .++.++|||||+|.+.++|.+|+..+|+..+
T Consensus        16 ~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~   72 (85)
T 1x4e_A           16 GTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGV   72 (85)
T ss_dssp             TCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeE
Confidence            5799999999999999999999988 5789999999999999999999999987654

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.74  E-value=1.5e-08  Score=82.73  Aligned_cols=55  Identities=20%  Similarity=0.424  Sum_probs=50.3

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+ .+++++|||||+|.+.++|.+|+. +++..+
T Consensus        21 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~   76 (99)
T 2dgs_A           21 NCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDI   76 (99)
T ss_dssp             SCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBS
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEE
Confidence            5899999999999999999999988 468899999999999999999998 877654

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.74  E-value=1.1e-08  Score=82.95  Aligned_cols=56  Identities=27%  Similarity=0.468  Sum_probs=52.0

Q ss_pred             CCcHHHHHHHhcccCcceee-EEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDA-QLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v-~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+ .++++ .++.++|||||+|.+.++|.+|+..+|+..+
T Consensus        16 ~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~   73 (96)
T 1x5t_A           16 EIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYL   73 (96)
T ss_dssp             TCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEE
T ss_pred             CCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEE
Confidence            57999999999999999999 99988 6889999999999999999999999988654

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.74  E-value=1e-08  Score=84.37  Aligned_cols=56  Identities=14%  Similarity=0.341  Sum_probs=51.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.++.+ .++.++|||||+|.+.++|.+|+..+|+..+
T Consensus        24 ~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~   80 (103)
T 2dnm_A           24 RTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAEL   80 (103)
T ss_dssp             TCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCB
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEE
Confidence            5799999999999999999999987 4588999999999999999999999988664

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.74  E-value=1.2e-08  Score=83.84  Aligned_cols=56  Identities=25%  Similarity=0.516  Sum_probs=51.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.++++ .++.++|||||+|.+.++|.+|+..+|+..+
T Consensus        23 ~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~   79 (102)
T 1x5s_A           23 DTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSV   79 (102)
T ss_dssp             TCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCT
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEE
Confidence            5899999999999999999999987 4788999999999999999999999988764

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.73  E-value=1.3e-08  Score=82.31  Aligned_cols=56  Identities=25%  Similarity=0.440  Sum_probs=51.6

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.++.+ .+++++|||||+|.+.++|.+|+..+|+..+
T Consensus        26 ~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~   82 (95)
T 2cqc_A           26 YTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL   82 (95)
T ss_dssp             SCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             CCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEE
Confidence            5899999999999999999999988 4588999999999999999999999988654

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.73  E-value=1.2e-08  Score=83.96  Aligned_cols=56  Identities=29%  Similarity=0.482  Sum_probs=52.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.++++ .++.++|||||+|.+.++|.+|+..+|+..+
T Consensus        26 ~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~   82 (103)
T 2cq0_A           26 DTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGY   82 (103)
T ss_dssp             TCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCee
Confidence            5899999999999999999999998 5789999999999999999999999988664

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.73  E-value=1.3e-08  Score=82.16  Aligned_cols=56  Identities=27%  Similarity=0.478  Sum_probs=51.5

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.++.+ .++.++|||||+|.+.++|.+|+..+|+..+
T Consensus        27 ~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~   83 (94)
T 2e5h_A           27 SLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQL   83 (94)
T ss_dssp             TSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEE
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCee
Confidence            5899999999999999999999987 4588999999999999999999999988654

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=98.73  E-value=9.2e-09  Score=87.61  Aligned_cols=61  Identities=25%  Similarity=0.482  Sum_probs=53.9

Q ss_pred             CccCCC----CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           95 KKPYKG----KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        95 g~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .++|.|    .+++++|+++|++||.|.++.++.+ .+|.++|||||+|.+.++|.+|+ .+|+..+
T Consensus        37 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~  102 (124)
T 2jwn_A           37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVF  102 (124)
T ss_dssp             TEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeE
Confidence            445555    5899999999999999999999988 57899999999999999999999 8987654

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.73  E-value=1.2e-08  Score=79.07  Aligned_cols=52  Identities=23%  Similarity=0.607  Sum_probs=49.0

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcC
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSN  152 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln  152 (451)
                      .+++++|+++|++||.|.++.++++ .+|+++|||||+|.+.++|.+|+..++
T Consensus        11 ~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~   63 (77)
T 1uaw_A           11 QTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR   63 (77)
T ss_dssp             SCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC
Confidence            5899999999999999999999988 468999999999999999999999987

>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=98.73  E-value=1.5e-08  Score=84.69  Aligned_cols=56  Identities=32%  Similarity=0.519  Sum_probs=52.0

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++++ .+|+++|||||+|.+.++|.+|+..+++..+
T Consensus        37 ~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i   93 (108)
T 2jrs_A           37 NITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFEL   93 (108)
T ss_dssp             SCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCS
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEE
Confidence            5899999999999999999999987 5788999999999999999999999988654

>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=98.73  E-value=9.9e-09  Score=82.28  Aligned_cols=55  Identities=29%  Similarity=0.545  Sum_probs=50.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++++ .+|+++|||||+|.+.+ |.+|+..+|+..+
T Consensus        12 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~   67 (90)
T 2ki2_A           12 SATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDF   67 (90)
T ss_dssp             TSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCC
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEE
Confidence            5899999999999999999999988 46899999999999999 9999999998765

>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=98.73  E-value=1.4e-08  Score=85.45  Aligned_cols=56  Identities=23%  Similarity=0.433  Sum_probs=52.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCC-CCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~-~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.++ +++++|||||+|.+.++|.+|+..+|+..+
T Consensus        36 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~   92 (115)
T 2cpz_A           36 EFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQI   92 (115)
T ss_dssp             SCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEE
Confidence            57999999999999999999999985 789999999999999999999999988654

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=98.73  E-value=7.9e-09  Score=85.80  Aligned_cols=53  Identities=26%  Similarity=0.442  Sum_probs=49.2

Q ss_pred             cHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       103 tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      |+++|+++|++||.|.++.++ ..+|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        34 t~~~l~~~F~~~G~v~~v~i~-~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~   86 (105)
T 2nlw_A           34 LKNVIHKIFSKFGKITNDFYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKL   86 (105)
T ss_dssp             HHHHHHHHHGGGSCEEEEECC-CBTTBSCCEEEEEECSSSHHHHHHHHCSSEEC
T ss_pred             HHHHHHHHHhcCCCEEEEEee-CCCCCeeeEEEEEECCHHHHHHHHHHhCCccc
Confidence            789999999999999999998 46789999999999999999999999998765

>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=98.73  E-value=1.1e-08  Score=84.53  Aligned_cols=56  Identities=30%  Similarity=0.591  Sum_probs=51.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+ .+++++|||||+|.+.++|.+|+..+|+..+
T Consensus        24 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~   80 (106)
T 2dgp_A           24 NLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKT   80 (106)
T ss_dssp             TCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCC
T ss_pred             CCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcc
Confidence            5899999999999999999999987 4689999999999999999999999998654

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.73  E-value=1.3e-08  Score=84.11  Aligned_cols=56  Identities=25%  Similarity=0.488  Sum_probs=51.6

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCC--CCCccceEEEEecchHHHHHHHHhc-CCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNA--DGKLKGCGFINYANKISAVKAILKS-NKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~--~g~srG~gFV~F~s~e~A~~Ai~~l-n~riy  156 (451)
                      .+++++|+++|++||.|..+.++++.  ++.++|||||+|.+.++|.+|+..+ |+..+
T Consensus        26 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~   84 (107)
T 2cph_A           26 QANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHL   84 (107)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBS
T ss_pred             cCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeE
Confidence            57999999999999999999999874  7889999999999999999999999 77654

>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=98.73  E-value=1.4e-08  Score=84.06  Aligned_cols=54  Identities=20%  Similarity=0.372  Sum_probs=48.4

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||. .++.++.+++++++|||||+|.+.++|.+|+ .+|+..+
T Consensus        26 ~~te~~l~~~F~~~G~-~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~   79 (102)
T 1wez_A           26 RATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAM-AKDKANM   79 (102)
T ss_dssp             TCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHH-TTSSCCS
T ss_pred             CCCHHHHHHHHHHcCc-eEEEEEECCCCCEeeEEEEEECCHHHHHHHH-HhCCCeE
Confidence            5899999999999995 4999999989999999999999999999999 4676543

>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=98.72  E-value=7.3e-09  Score=86.54  Aligned_cols=54  Identities=15%  Similarity=0.281  Sum_probs=49.5

Q ss_pred             cHHHHHHHhcccCcceeeEEeeCCC---CCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          103 TEEEFKEHFGQYGDIIDAQLLKNAD---GKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       103 tee~L~~~F~~fG~V~~v~v~~d~~---g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++|++.|++||.|.++.+++++.   ++++|+|||+|.+.++|.+|+..|||+.|
T Consensus        28 ~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~f   84 (105)
T 3v4m_A           28 IVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF   84 (105)
T ss_dssp             HHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             HHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCEe
Confidence            5689999999999999999998753   36899999999999999999999999987

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=98.72  E-value=1.8e-08  Score=84.56  Aligned_cols=56  Identities=39%  Similarity=0.615  Sum_probs=52.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.++++ .++.++|||||+|.+.++|.+|+..+|+..+
T Consensus        26 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~   82 (115)
T 2dgo_A           26 EITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWL   82 (115)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            5799999999999999999999998 4889999999999999999999999988654

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=98.72  E-value=2e-08  Score=80.70  Aligned_cols=55  Identities=25%  Similarity=0.445  Sum_probs=51.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++++ +++++|||||+|.+.++|.+|+..+|+..+
T Consensus        19 ~~t~~~l~~~f~~~G~v~~~~i~~~-~g~~~g~afV~f~~~~~a~~a~~~l~g~~~   73 (92)
T 2dgv_A           19 DFTWKMLKDKFNECGHVLYADIKME-NGKSKGCGVVKFESPEVAERACRMMNGMKL   73 (92)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEEEEES-SSCEEEEEEEEESSHHHHHHHHHHHTTCCB
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEEcc-CCCcceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            5799999999999999999999985 788999999999999999999999988664

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=98.71  E-value=1.6e-08  Score=86.31  Aligned_cols=56  Identities=18%  Similarity=0.417  Sum_probs=52.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+++|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        46 ~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~  101 (124)
T 2kt5_A           46 GVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPL  101 (124)
T ss_dssp             SCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEES
T ss_pred             CCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEE
Confidence            57999999999999999999999988899999999999999999999999988654

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=98.71  E-value=7.4e-09  Score=83.64  Aligned_cols=51  Identities=18%  Similarity=0.193  Sum_probs=47.3

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|.+||+|.++.+..     ++|||||+|.+.++|.+|+..||+..+
T Consensus        18 ~~te~~L~~lF~q~G~V~~~~l~~-----~kGfaFVey~~~~eA~~Ai~~Ln~~~l   68 (89)
T 2wbr_A           18 QIDGPTLRTLCMQHGPLVSFHPYL-----NQGIALCKYTTREEANKAQMALNNCVL   68 (89)
T ss_dssp             TCCCHHHHHHHHHHSCEEEEEEET-----TTTEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             cCCHHHHHHHHHhhCCEEEEEEcC-----CCcEEEEEECCHHHHHHHHHHhcCCEE
Confidence            589999999999999999999975     599999999999999999999998664

>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=98.71  E-value=1.6e-08  Score=83.81  Aligned_cols=55  Identities=24%  Similarity=0.334  Sum_probs=49.9

Q ss_pred             CCcHHHHHHHhcccCccee-eEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIID-AQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~-v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|.. +.++.+.+|+++|||||+|.+.++|.+|+.. ++..+
T Consensus        26 ~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~   81 (104)
T 1wg5_A           26 GCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKK-HKERI   81 (104)
T ss_dssp             TCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTT-TTCCS
T ss_pred             CCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-Ccchh
Confidence            5899999999999999987 8888888999999999999999999999987 76543

>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=98.70  E-value=2.6e-08  Score=86.08  Aligned_cols=56  Identities=25%  Similarity=0.440  Sum_probs=51.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.++++ .+++++|||||+|.+.++|.+|+..+|+..+
T Consensus        57 ~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i  113 (129)
T 2kxn_B           57 YTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL  113 (129)
T ss_dssp             SCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCS
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            4799999999999999999999988 5688999999999999999999999998665

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=98.70  E-value=1.8e-08  Score=90.08  Aligned_cols=62  Identities=23%  Similarity=0.300  Sum_probs=55.9

Q ss_pred             CccCCC----CCcHHHHHHHhcccC--cceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           95 KKPYKG----KITEEEFKEHFGQYG--DIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        95 g~~f~G----~~tee~L~~~F~~fG--~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .++|.|    .+|+++|+++|++||  .|.++.++.| .+|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        56 ~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~  124 (156)
T 3n9u_C           56 AAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVL  124 (156)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEE
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEE
Confidence            456666    589999999999999  9999999998 5899999999999999999999999998765

>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=98.70  E-value=1.1e-08  Score=83.99  Aligned_cols=60  Identities=27%  Similarity=0.466  Sum_probs=53.0

Q ss_pred             CccCCC----CCcHHHHHHHhcccCcceeeEEeeCC--CCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           95 KKPYKG----KITEEEFKEHFGQYGDIIDAQLLKNA--DGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        95 g~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d~--~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .++|.|    .+++++|+++|++|| |.++.+++++  +|+++|||||+|.+.++|.+|+ .+++..+
T Consensus        20 ~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~   85 (100)
T 2j76_E           20 YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESL   85 (100)
T ss_dssp             CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCB
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEE
Confidence            445555    479999999999999 9999999885  7999999999999999999999 8988764

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=98.69  E-value=1.9e-08  Score=84.92  Aligned_cols=56  Identities=25%  Similarity=0.379  Sum_probs=52.0

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++++ .+|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        51 ~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~  107 (118)
T 2khc_A           51 EFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQV  107 (118)
T ss_dssp             TCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEE
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEE
Confidence            5899999999999999999999987 5789999999999999999999999988664

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.68  E-value=1.2e-08  Score=83.77  Aligned_cols=56  Identities=23%  Similarity=0.393  Sum_probs=51.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+ .+++++|||||+|.+.++|.+|+..+|+..+
T Consensus        23 ~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~   79 (102)
T 2cqb_A           23 EVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL   79 (102)
T ss_dssp             SCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEE
T ss_pred             CCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            5799999999999999999999987 6788999999999999999999999988654

>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=98.68  E-value=2.6e-08  Score=79.25  Aligned_cols=50  Identities=22%  Similarity=0.578  Sum_probs=46.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHh
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILK  150 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~  150 (451)
                      .+++++|+++|++||.|.++.++.+ .+|+++|||||+|.+.++|.+|+..
T Consensus        22 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~   72 (87)
T 3s7r_A           22 DTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ   72 (87)
T ss_dssp             TCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS
T ss_pred             CCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh
Confidence            5899999999999999999999988 4689999999999999999999966

>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=98.68  E-value=2e-08  Score=83.65  Aligned_cols=56  Identities=27%  Similarity=0.411  Sum_probs=51.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+ .+|.++|||||+|.+.++|.+|+..+|+..+
T Consensus        37 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~   93 (110)
T 1oo0_B           37 EAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEI   93 (110)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEE
Confidence            5799999999999999999999987 5789999999999999999999999988654

>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=98.68  E-value=1.6e-08  Score=81.77  Aligned_cols=56  Identities=21%  Similarity=0.363  Sum_probs=51.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.++.+ .+++++|||||+|.+.++|.+|+..+|+..+
T Consensus        26 ~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~   82 (95)
T 2ek1_A           26 TVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPI   82 (95)
T ss_dssp             TCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeE
Confidence            5899999999999999999988876 6788999999999999999999999988764

>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=98.68  E-value=2.4e-08  Score=89.73  Aligned_cols=56  Identities=27%  Similarity=0.411  Sum_probs=52.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.++.+ .+|.++|||||+|.+.++|.+|+..+|+..+
T Consensus        83 ~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~  139 (165)
T 1rk8_A           83 EAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEI  139 (165)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEE
Confidence            5799999999999999999999998 5889999999999999999999999988654

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.67  E-value=2.6e-08  Score=82.26  Aligned_cols=60  Identities=22%  Similarity=0.545  Sum_probs=53.0

Q ss_pred             ccCCC----CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           96 KPYKG----KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        96 ~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|.+    .+++++|+++|++||.|.++.++++ .++.++|||||+|.+.++|.+|+.. ++..+
T Consensus        18 ~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~   82 (105)
T 2dh8_A           18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTL   82 (105)
T ss_dssp             EECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEE
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeE
Confidence            44554    5799999999999999999999998 5789999999999999999999998 77554

>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=98.67  E-value=1.8e-08  Score=82.07  Aligned_cols=56  Identities=21%  Similarity=0.363  Sum_probs=51.0

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.++.+ .+|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        26 ~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~   82 (98)
T 2cqp_A           26 TVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPI   82 (98)
T ss_dssp             TCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEE
T ss_pred             CCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCee
Confidence            5899999999999999998888776 6789999999999999999999999988654

>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=98.67  E-value=3e-08  Score=81.60  Aligned_cols=55  Identities=29%  Similarity=0.596  Sum_probs=50.4

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+..+ ++|||||+|.+.++|.+|+..+|+..+
T Consensus        26 ~~t~~~l~~~f~~~G~v~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~   80 (103)
T 2cq3_A           26 RFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVV   80 (103)
T ss_dssp             TCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEecCCC-CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            5899999999999999999999988654 899999999999999999999988654

>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=98.67  E-value=2.3e-08  Score=83.28  Aligned_cols=52  Identities=23%  Similarity=0.445  Sum_probs=49.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcC
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSN  152 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln  152 (451)
                      .+++++|+++|++||.|.++.++.+ .++.++|||||+|.+.++|.+|+..+|
T Consensus        26 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~   78 (111)
T 1x4h_A           26 DSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAAS   78 (111)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhc
Confidence            5799999999999999999999988 568899999999999999999999998

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=98.67  E-value=2.1e-08  Score=85.20  Aligned_cols=55  Identities=9%  Similarity=0.250  Sum_probs=50.7

Q ss_pred             CCcHHHHHHHhcccCc---ceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGD---IIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~---V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|+.||.   |..++++.++.|+++|||||+|.+.++|.+|+. +|+..+
T Consensus        28 ~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~   85 (118)
T 2db1_A           28 SCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK-KDRESM   85 (118)
T ss_dssp             TCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGG-GTTEEE
T ss_pred             CCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCeE
Confidence            5899999999999999   899999999789999999999999999999999 877543

>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=98.67  E-value=1.7e-08  Score=88.36  Aligned_cols=55  Identities=9%  Similarity=0.238  Sum_probs=51.0

Q ss_pred             CCcHHHHHHHhcccCc---ceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGD---IIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~---V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|++||.   |.++.+++++.|+++|||||+|.+.++|.+|+. +|+..+
T Consensus        55 ~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~-~~g~~l  112 (136)
T 2hgl_A           55 SCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALK-KDRESM  112 (136)
T ss_dssp             TCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHT-TTEEES
T ss_pred             CCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHh-cCCCEE
Confidence            5899999999999999   899999999779999999999999999999999 887654

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.67  E-value=2.1e-08  Score=81.68  Aligned_cols=56  Identities=27%  Similarity=0.324  Sum_probs=50.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCC----CCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNA----DGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~----~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.++.++    ++.++|||||+|.+.++|.+|+..+|+..+
T Consensus        16 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~   75 (98)
T 2cpf_A           16 STTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTV   75 (98)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEE
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCee
Confidence            58999999999999999999999874    348899999999999999999999988654

>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=98.67  E-value=2.2e-08  Score=84.00  Aligned_cols=55  Identities=16%  Similarity=0.395  Sum_probs=50.5

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCC-CCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~-~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.++.++ ++.++|||||+|.+.++|.+|+ .+|+..+
T Consensus        36 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~   91 (114)
T 2cq4_A           36 RIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRL   91 (114)
T ss_dssp             TCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEE
T ss_pred             CCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEe
Confidence            58999999999999999999999884 5889999999999999999999 9987654

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=98.66  E-value=1.7e-08  Score=83.00  Aligned_cols=49  Identities=24%  Similarity=0.643  Sum_probs=47.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHH
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL  149 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~  149 (451)
                      .+++++|+++|++||.|.++.++.+++|+++|||||+|.+.++|.+|+.
T Consensus        20 ~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~   68 (102)
T 2xs2_A           20 RMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE   68 (102)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT
T ss_pred             CCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh
Confidence            5799999999999999999999999889999999999999999999998

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.66  E-value=2.1e-08  Score=84.36  Aligned_cols=54  Identities=20%  Similarity=0.405  Sum_probs=49.4

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|+.| .|.++.++.++.|+++|||||+|.+.++|.+|+ .+|+..+
T Consensus        27 ~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al-~~~~~~~   80 (109)
T 2dnn_A           27 SAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEAL-KRNRMLM   80 (109)
T ss_dssp             SCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHH-HTTTEEE
T ss_pred             CCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHH-hcCCCeE
Confidence            58999999999999 899999999988999999999999999999999 6776543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.66  E-value=2.3e-08  Score=83.65  Aligned_cols=55  Identities=27%  Similarity=0.550  Sum_probs=50.4

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+.. .++|||||+|.+.++|.+|+..+|+..+
T Consensus        40 ~~te~~l~~~F~~~G~i~~v~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~   94 (109)
T 2err_A           40 RFRDPDLRQMFGQFGKILDVEIIFNER-GSKGFGFVTFENSADADRAREKLHGTVV   94 (109)
T ss_dssp             TCCHHHHHHHGGGTCCCSCEEECCBTT-BCTTEEEEECCCSHHHHHHHHHHTTCEE
T ss_pred             cCCHHHHHHHHHhcCCEEEEEEEECCC-CCceEEEEEECCHHHHHHHHHHcCCCEE
Confidence            589999999999999999999998854 4899999999999999999999988764

>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=98.65  E-value=2.1e-08  Score=83.51  Aligned_cols=55  Identities=22%  Similarity=0.241  Sum_probs=50.4

Q ss_pred             CCcHHHHHHHhcccCc---ceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGD---IIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~---V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|+.||.   |.++.++.++.|+++|||||+|.+.++|.+|+. +|+..+
T Consensus        22 ~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~-~~~~~~   79 (107)
T 2lmi_A           22 SCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYM   79 (107)
T ss_dssp             SCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHT-TTTCCS
T ss_pred             CCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHH-hCccee
Confidence            5899999999999998   999999998779999999999999999999999 877543

>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=98.65  E-value=1.6e-08  Score=85.85  Aligned_cols=51  Identities=16%  Similarity=0.197  Sum_probs=46.3

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++++|+++|++||.|.++.++.+     +|||||+|.+.++|.+|+..||++.+
T Consensus        38 ~~te~~L~~~F~~fG~v~~v~i~~~-----rgfaFV~f~~~~~A~~Ai~~lnG~~~   88 (114)
T 2cq2_A           38 GVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEV   88 (114)
T ss_dssp             TCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEE
Confidence            4799999999999999999888653     79999999999999999999999754

>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=98.65  E-value=2.1e-08  Score=84.52  Aligned_cols=55  Identities=16%  Similarity=0.174  Sum_probs=50.6

Q ss_pred             CCcHHHHHHHhcccCcc-eeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDI-IDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V-~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.| ..+.++.+++|+++|||||+|.+.++|.+|+.. |+..+
T Consensus        26 ~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~-~~~~~   81 (114)
T 2cpy_A           26 SITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL-HRKKL   81 (114)
T ss_dssp             TSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGG-CSEEE
T ss_pred             cCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHh-CCCcc
Confidence            58999999999999999 899999998999999999999999999999987 76543

>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=98.64  E-value=3e-08  Score=84.66  Aligned_cols=56  Identities=29%  Similarity=0.471  Sum_probs=52.0

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|.++.++.+ .++.++|||||+|.+.++|.+|+..+|+..+
T Consensus        33 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~   89 (126)
T 3ex7_B           33 EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL   89 (126)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBS
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCee
Confidence            5799999999999999999999988 4889999999999999999999999988764

>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=98.64  E-value=1.9e-08  Score=77.68  Aligned_cols=53  Identities=25%  Similarity=0.449  Sum_probs=48.0

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCC
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKK  154 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~r  154 (451)
                      .+++++|+++|++||.|.++.++.+ .+|.++|||||+|.+.++|.+|+.. ++.
T Consensus        10 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~   63 (75)
T 1iqt_A           10 DTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYH   63 (75)
T ss_dssp             SCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSC
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCC
Confidence            5899999999999999999999887 5688999999999999999999986 443

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.64  E-value=2.9e-08  Score=83.10  Aligned_cols=56  Identities=21%  Similarity=0.333  Sum_probs=51.7

Q ss_pred             CCcHHHHHHHhcccCcce--------eeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDII--------DAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~--------~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.        .+.++.+ .+++++|||||+|.+.++|.+|+..+|+..+
T Consensus        26 ~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           26 SVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             TCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            589999999999999999        6999988 6789999999999999999999999988764

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=98.64  E-value=2.5e-08  Score=86.66  Aligned_cols=56  Identities=23%  Similarity=0.429  Sum_probs=51.6

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|+.||.|.++.++++ .+++++|||||+|.+.++|.+|+..+|+..+
T Consensus        53 ~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~  109 (139)
T 1u6f_A           53 TVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNI  109 (139)
T ss_dssp             TCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEEC
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            5899999999999999999999988 4688999999999999999999999988654

>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=98.64  E-value=3e-08  Score=81.61  Aligned_cols=55  Identities=16%  Similarity=0.243  Sum_probs=49.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++++..+ ++|||||+|.+.++|.+|+..+|+..+
T Consensus        26 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~-~~g~afV~f~~~~~a~~A~~~l~g~~~   80 (103)
T 2cqi_A           26 DVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKI   80 (103)
T ss_dssp             TCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             cCCHHHHHHHHHhcCCEeEEEEEecCCC-CCCEEEEEECCHHHHHHHHHHhCCCCc
Confidence            5799999999999999999999998544 699999999999999999999988654

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.64  E-value=3.8e-08  Score=79.05  Aligned_cols=54  Identities=20%  Similarity=0.417  Sum_probs=50.6

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++| .|.++.++++.+|+++|||||+|.+.++|.+|+. +|+..+
T Consensus        21 ~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~   74 (91)
T 2dgw_A           21 NVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALK-CNREYM   74 (91)
T ss_dssp             SCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHH-SCSEEE
T ss_pred             CCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHH-hCCcee
Confidence            58999999999999 9999999999889999999999999999999999 988654

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.63  E-value=2.5e-08  Score=85.71  Aligned_cols=70  Identities=24%  Similarity=0.246  Sum_probs=55.8

Q ss_pred             HHHHHHHh-cCCccCCC----CCcHHHHHHHhcccCcc----eeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCc
Q psy300           85 SAVKAILK-SNKKPYKG----KITEEEFKEHFGQYGDI----IDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP  155 (451)
Q Consensus        85 ~A~~Al~~-lng~~f~G----~~tee~L~~~F~~fG~V----~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~ri  155 (451)
                      .+.+.+.. -..++|.+    ++|+++|+++|++||.|    ..+.++.+.+|+++|||||+|.+.++|.+|+.. |+..
T Consensus        13 ~~~~~~~~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~   91 (123)
T 2dha_A           13 EVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRK-HKDL   91 (123)
T ss_dssp             HHHHHHHCCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTT-TTEE
T ss_pred             hHHhhccCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHh-CCCe
Confidence            34444432 22345555    58999999999999875    799999998999999999999999999999986 6544

>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=98.62  E-value=2e-08  Score=79.89  Aligned_cols=56  Identities=21%  Similarity=0.331  Sum_probs=50.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCC-CC-CccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNA-DG-KLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~-~g-~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+. ++ +++|||||+|.+.++|.+|+..+|+..+
T Consensus        15 ~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~   72 (88)
T 4a8x_A           15 NVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQI   72 (88)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeE
Confidence            58999999999999999999998874 33 3899999999999999999999988765

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.62  E-value=2.5e-08  Score=83.41  Aligned_cols=48  Identities=21%  Similarity=0.231  Sum_probs=44.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCC
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK  153 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~  153 (451)
                      ++|+++|+++|++||.|.++.++++     +|||||+|++.++|..|+..+++
T Consensus        27 ~vte~dL~~lF~~fG~V~~v~i~~~-----kGfaFVeF~~~~~A~~Ai~~l~~   74 (105)
T 1sjq_A           27 DVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTS   74 (105)
T ss_dssp             TSCHHHHHHHHHHHCCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhcc
Confidence            5899999999999999999999976     89999999999999999998764

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.62  E-value=4.8e-08  Score=80.39  Aligned_cols=54  Identities=15%  Similarity=0.299  Sum_probs=49.3

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCC-CCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~-~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++|| |.++.+++++ +++++|||||+|.+.++|.+|+ .+|+..+
T Consensus        26 ~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~   80 (103)
T 2dng_A           26 NTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALL   80 (103)
T ss_dssp             TCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeE
Confidence            579999999999997 9999999984 6899999999999999999999 8987654

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=98.62  E-value=8.2e-08  Score=81.44  Aligned_cols=79  Identities=16%  Similarity=0.253  Sum_probs=62.3

Q ss_pred             CCCceEEEcCCCCCCC----------HHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCC
Q psy300           30 TKRGRLFIKNLPFKIT----------EEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK   99 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vt----------e~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~   99 (451)
                      .+++.|.+.|+=....          +++|++.|++||.|.++.+.++   .++|++||+|.+.++|.+|+..|||+.|.
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~---~~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKN---SAQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTT---CTTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecC---CCcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            3567888888832211          2578999999999999999665   25899999999999999999999999999


Q ss_pred             CC------CcHHHHHHHh
Q psy300          100 GK------ITEEEFKEHF  111 (451)
Q Consensus       100 G~------~tee~L~~~F  111 (451)
                      |+      ..++...+.|
T Consensus        82 GR~i~v~~~~~~~y~~~f   99 (114)
T 3s6e_A           82 GKMITAAYVPLPTYHNLF   99 (114)
T ss_dssp             TEECEEEEECHHHHHHHC
T ss_pred             CEEEEEEEEcHHHHHHhC
Confidence            96      3555555444

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=98.61  E-value=4.7e-08  Score=81.77  Aligned_cols=52  Identities=23%  Similarity=0.607  Sum_probs=48.5

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcC
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSN  152 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln  152 (451)
                      .+++++|+++|++||.|.++.++++ .+|.++|||||+|.+.++|.+|+..++
T Consensus        36 ~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~   88 (109)
T 2rs2_A           36 QTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR   88 (109)
T ss_dssp             TCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSC
T ss_pred             CCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCC
Confidence            5899999999999999999999998 468999999999999999999998874

>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=98.61  E-value=3.8e-08  Score=81.18  Aligned_cols=54  Identities=28%  Similarity=0.487  Sum_probs=49.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCC-C-CCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNA-D-GKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~-~-g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++|| |.++.++.++ + ++++|||||+|.+.++|.+|+ .+|+..+
T Consensus        26 ~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~   81 (104)
T 1wi8_A           26 DVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESL   81 (104)
T ss_dssp             SCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEE
T ss_pred             cCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEe
Confidence            579999999999999 9999999885 3 899999999999999999999 9987654

>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=98.60  E-value=2.4e-08  Score=85.25  Aligned_cols=54  Identities=20%  Similarity=0.307  Sum_probs=49.3

Q ss_pred             cHHHHHHHhcccCcceeeEEeeCC-----CCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          103 TEEEFKEHFGQYGDIIDAQLLKNA-----DGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       103 tee~L~~~F~~fG~V~~v~v~~d~-----~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++|++.|++||.|.++.+++++     +++++|++||+|.+.++|.+|+..|||+.|
T Consensus        38 leedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f   96 (118)
T 3ue2_A           38 LEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWF   96 (118)
T ss_dssp             HHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             HHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEE
Confidence            468999999999999999999873     356789999999999999999999999987

>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=98.60  E-value=5e-08  Score=83.33  Aligned_cols=55  Identities=18%  Similarity=0.340  Sum_probs=48.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEe-eCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLL-KNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~-~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|..+.++ .+.+|+++|||||+|.+.++|.+|+. +|+..+
T Consensus        36 ~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~   91 (124)
T 1wel_A           36 EAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYM   91 (124)
T ss_dssp             TCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCS
T ss_pred             CCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeE
Confidence            58999999999999999985554 45789999999999999999999999 888664

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.60  E-value=4.5e-08  Score=82.36  Aligned_cols=53  Identities=28%  Similarity=0.566  Sum_probs=49.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCC
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNK  153 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~  153 (451)
                      .+++++|+++|++||.|.++.++++ .+++++|||||+|.+.++|.+|+..+++
T Consensus        28 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~   81 (116)
T 2cqd_A           28 HTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP   81 (116)
T ss_dssp             SCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC
T ss_pred             CCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC
Confidence            5799999999999999999999988 5689999999999999999999999886

>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=98.60  E-value=3.7e-08  Score=82.55  Aligned_cols=56  Identities=20%  Similarity=0.363  Sum_probs=50.1

Q ss_pred             CCcHHHHH---HHhcccCcceeeEEeeCC----CCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFK---EHFGQYGDIIDAQLLKNA----DGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~---~~F~~fG~V~~v~v~~d~----~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+   ++|++||.|..+.++++.    +++++|||||+|.+.++|.+|+..+|+..+
T Consensus        26 ~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~   88 (111)
T 2cpi_A           26 RLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVV   88 (111)
T ss_dssp             TTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             CCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEE
Confidence            58999999   999999999999998874    236779999999999999999999988764

>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=98.59  E-value=5e-08  Score=92.67  Aligned_cols=61  Identities=26%  Similarity=0.438  Sum_probs=55.3

Q ss_pred             ccCCC----CCcHHHHHHHhcccC--cceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           96 KPYKG----KITEEEFKEHFGQYG--DIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        96 ~~f~G----~~tee~L~~~F~~fG--~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+|    .+|+++|+++|++||  .|.+|.|+++ .+++++|||||+|.+.++|.+|+..+|+..+
T Consensus        70 ~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~  137 (229)
T 3q2s_C           70 ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKREL  137 (229)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCB
T ss_pred             EEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeE
Confidence            45665    579999999999999  9999999998 5899999999999999999999999998765

>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=98.59  E-value=3.8e-08  Score=80.20  Aligned_cols=54  Identities=17%  Similarity=0.271  Sum_probs=49.5

Q ss_pred             CCcHHHHH----HHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFK----EHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~----~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+    ++|++||.|.++.++.++.+  +|||||+|.+.++|.+|+..+|+..+
T Consensus        20 ~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--rg~afV~f~~~~~A~~Ai~~l~g~~~   77 (96)
T 2dgx_A           20 RLSRKELQQLLQEAFARHGKVKSVELSPHTDY--QLKAVVQMENLQDAIGAVNSLHRYKI   77 (96)
T ss_dssp             TSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--TCCEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             CCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--CeEEEEEECCHHHHHHHHHHhCCCEE
Confidence            57999999    99999999999999988655  89999999999999999999988654

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=98.59  E-value=5.9e-08  Score=83.83  Aligned_cols=54  Identities=20%  Similarity=0.302  Sum_probs=47.0

Q ss_pred             CCcHHHHH----HHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFK----EHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~----~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++++|+    ++|++||.|.++.+.+  +++++|||||+|.+.++|..|+..+|+..+
T Consensus        40 ~~~e~~L~~~L~~~F~~~G~I~~v~i~~--~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l   97 (127)
T 2a3j_A           40 EVPKEKLQALLYALASSQGDILDIVVDL--SDDNSGKAYIVFATQESAQAFVEAFQGYPF   97 (127)
T ss_dssp             TSCHHHHHHHHHHHHHHHSCEEEEEECC--CCSSCCCEEEEESSHHHHHHHHHHSTTCCC
T ss_pred             CCCHHHHHHHHHHHhccCCCeEEEEecc--CCCcCCEEEEEECCHHHHHHHHHHHCCCEe
Confidence            46787765    7999999999988754  578899999999999999999999998765

>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=98.58  E-value=7.3e-08  Score=85.46  Aligned_cols=56  Identities=25%  Similarity=0.279  Sum_probs=51.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCC-CCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~-~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|..|.++.+. ++.++|||||+|.+.++|.+|+..+|+..+
T Consensus        50 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~  106 (156)
T 1h2v_Z           50 YTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRL  106 (156)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEE
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            58999999999999999999999984 688999999999999999999999987654

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=98.58  E-value=4.5e-08  Score=84.70  Aligned_cols=56  Identities=23%  Similarity=0.393  Sum_probs=51.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.++++ .+++++|||||+|.+.++|.+|+..+|+..+
T Consensus        74 ~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~  130 (140)
T 2ku7_A           74 EVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL  130 (140)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEE
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEE
Confidence            5799999999999999999999988 6789999999999999999999999988654

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.58  E-value=6.9e-08  Score=79.97  Aligned_cols=50  Identities=18%  Similarity=0.338  Sum_probs=45.2

Q ss_pred             CCCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCC
Q psy300          100 GKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK  153 (451)
Q Consensus       100 G~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~  153 (451)
                      ..+++++|+++|++||.|.++.++    ++++|||||+|.+.++|..|+..+++
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~----~~~rGfaFVeF~~~~~A~~Ai~~~~~   76 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS----SKKPGTAVVEFATVKAAELAVQNEVG   76 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE----SSSSSEEEEEESCHHHHHHHHHTCCB
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc----cCCCCEEEEEECCHHHHHHHHHhcCC
Confidence            368999999999999999999998    36799999999999999999998654

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.57  E-value=2.4e-08  Score=84.14  Aligned_cols=56  Identities=23%  Similarity=0.410  Sum_probs=47.9

Q ss_pred             CccCCC----CCcHHHHHHHhcccCcceeeEEeeCC-C---CCccceEEEEecchHHHHHHHHhc
Q psy300           95 KKPYKG----KITEEEFKEHFGQYGDIIDAQLLKNA-D---GKLKGCGFINYANKISAVKAILKS  151 (451)
Q Consensus        95 g~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d~-~---g~srG~gFV~F~s~e~A~~Ai~~l  151 (451)
                      .++|.|    .+++++|+++|++||.|. +.++.+. +   |+++|||||+|.+.++|.+|+..+
T Consensus         9 ~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~   72 (114)
T 2dnl_A            9 RKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDAC   72 (114)
T ss_dssp             CCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHS
T ss_pred             CEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhh
Confidence            345554    589999999999999999 7777653 3   789999999999999999999988

>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=98.57  E-value=8.2e-08  Score=78.91  Aligned_cols=50  Identities=32%  Similarity=0.632  Sum_probs=47.0

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHh
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILK  150 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~  150 (451)
                      .+++++|+++|++||.|..+.++.+ .++.++|||||+|.+.++|.+|+..
T Consensus        26 ~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~   76 (103)
T 2cqg_A           26 KTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ   76 (103)
T ss_dssp             SCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS
T ss_pred             cCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc
Confidence            5899999999999999999999998 4689999999999999999999985

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.56  E-value=6.5e-08  Score=81.37  Aligned_cols=55  Identities=20%  Similarity=0.491  Sum_probs=49.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.++.+ .++.++|||||+|.+.++|.+|+.. ++..+
T Consensus        38 ~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~   93 (116)
T 1x4b_A           38 ETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSI   93 (116)
T ss_dssp             CCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEE
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEE
Confidence            5899999999999999999999998 5689999999999999999999987 66543

>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=98.54  E-value=3.6e-08  Score=81.99  Aligned_cols=48  Identities=19%  Similarity=0.164  Sum_probs=44.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCC
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK  153 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~  153 (451)
                      ++|+++|+++|++||.|.++.++++     +|||||+|++.++|..|+..+++
T Consensus        27 ~~te~dL~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~   74 (102)
T 1x4d_A           27 KNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTT   74 (102)
T ss_dssp             SSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHhcCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHHcC
Confidence            6789999999999999999999876     68999999999999999999875

>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=98.54  E-value=7.2e-08  Score=80.01  Aligned_cols=52  Identities=21%  Similarity=0.282  Sum_probs=47.6

Q ss_pred             CCcHHHHHHHhcccCc-ceeeEEe-eC-CCCCccceEEEEecchHHHHHHHHhcC
Q psy300          101 KITEEEFKEHFGQYGD-IIDAQLL-KN-ADGKLKGCGFINYANKISAVKAILKSN  152 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~-V~~v~v~-~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln  152 (451)
                      .+++++|+++|++||. |.++.++ .+ .+|.++|||||+|.+.++|.+|+..++
T Consensus        19 ~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~   73 (109)
T 2dis_A           19 MKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLM   73 (109)
T ss_dssp             TSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTT
T ss_pred             cCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhh
Confidence            5899999999999998 9999998 55 467899999999999999999999995

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=98.53  E-value=9.1e-08  Score=87.24  Aligned_cols=56  Identities=18%  Similarity=0.417  Sum_probs=52.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+.++.++|||||+|.+.++|.+|+..+|+..+
T Consensus        99 ~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l  154 (177)
T 2f3j_A           99 GVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPL  154 (177)
T ss_dssp             CCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBC
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            57999999999999999999999988899999999999999999999999988754

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=98.53  E-value=7e-08  Score=79.94  Aligned_cols=49  Identities=14%  Similarity=0.333  Sum_probs=45.4

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCC
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK  154 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~r  154 (451)
                      ++|+++|+++|++||.|.++.++++     ||||||+|++.++|.+|+..+++.
T Consensus        32 ~~te~~L~~lF~~fG~V~~v~i~~~-----kg~AFVef~~~~~A~~Av~~ln~~   80 (100)
T 3r27_A           32 GVVEADLVEALQEFGPISYVVVMPK-----KRQALVEFEDVLGACNAVNYAADN   80 (100)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHS
T ss_pred             CCCHHHHHHHHhccCCEEEEEEEcC-----CCEEEEEECCHHHHHHHHHHhcCC
Confidence            5899999999999999999999864     899999999999999999998764

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.51  E-value=2.7e-07  Score=78.96  Aligned_cols=70  Identities=14%  Similarity=0.133  Sum_probs=60.0

Q ss_pred             CCCCCCCceEEEcCCCCC-CCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEcc-HHHHHHHHHhcC--CccCCC
Q psy300           26 KPDKTKRGRLFIKNLPFK-ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYAN-KISAVKAILKSN--KKPYKG  100 (451)
Q Consensus        26 ~~~~~~~~~lfVgnLp~~-vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~-~~~A~~Al~~ln--g~~f~G  100 (451)
                      +......+-|||+||+.+ ++.++|+++|++||+|.+|.+.++.+     .|||.|.+ +.+|..|+..+|  +..+.|
T Consensus        12 ~~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~-----tgfVrf~~~~~~A~~av~~ln~~~~~i~g   85 (121)
T 1owx_A           12 SLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK-----EGIILFKEKAKEALGKAKDANNGNLQLRN   85 (121)
T ss_dssp             CCSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS-----EEEEEESSCHHHHHHHHHHTTTSCBCTTS
T ss_pred             cccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC-----EEEEEECCChHHHHHHHHHhhcCCcEEeC
Confidence            345678899999999999 99999999999999999999987642     59999999 799999999985  444544

>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=98.50  E-value=1.4e-07  Score=78.50  Aligned_cols=54  Identities=20%  Similarity=0.354  Sum_probs=48.6

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.+..+  +.++|||||+|.+.++|.+|+..+|+..+
T Consensus        33 ~~t~~~l~~~F~~~G~v~~~~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~   86 (109)
T 1x4a_A           33 DIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDY   86 (109)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEEC--CCCCcEEEEEECCHHHHHHHHHHcCCCEE
Confidence            5799999999999999999999664  45799999999999999999999988654

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=98.50  E-value=7.9e-08  Score=78.71  Aligned_cols=52  Identities=19%  Similarity=0.330  Sum_probs=48.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|.++.++.+    ++|||||+|.+.++|.+|+..+++..+
T Consensus        11 ~~t~~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~A~~~l~g~~~   62 (101)
T 2hvz_A           11 GAGKGELERAFSYYGPLRTVWIARN----PPGFAFVEFEDPRDAEDAVRGLDGKVI   62 (101)
T ss_dssp             SCSHHHHHHHHHHHCCCSEEEEESS----SSSEEEEECSSHHHHHHHHHHHHHSCS
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEeeC----CCCEEEEEECCHHHHHHHHHHHCCCeE
Confidence            5899999999999999999999987    689999999999999999999987654

>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=98.50  E-value=2.2e-07  Score=83.66  Aligned_cols=54  Identities=17%  Similarity=0.301  Sum_probs=48.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCccc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK  157 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~  157 (451)
                      .+|+++|+++|++||.|.++.+..+   .++|||||+|.+.++|..|+..||++.+.
T Consensus        57 ~vted~L~~~Fs~fG~V~~V~i~~k---~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~  110 (164)
T 1sjr_A           57 PVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDGQNIY  110 (164)
T ss_dssp             CCCHHHHHHHHHHHSCEEEEEEEES---SSCEEEEEEESCHHHHHHHHHHSTTBCSS
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEEeC---CCCCEEEEEECCHHHHHHHHHHhCCCEec
Confidence            5899999999999999999999764   25899999999999999999999998764

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=98.49  E-value=8.8e-08  Score=81.24  Aligned_cols=51  Identities=16%  Similarity=0.277  Sum_probs=46.7

Q ss_pred             cHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       103 tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++|++.|++||.|.++.+.++.   ++|||||+|.+.++|.+|+..|||+.|
T Consensus        30 l~edl~~~f~kfG~V~~v~i~~~~---~~G~~fV~f~~~e~A~~Ai~~lnG~~f   80 (114)
T 3s6e_A           30 IKDDVIEECNKHGGVIHIYVDKNS---AQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             HHHHHHHHHTTTTCCSEEEECTTC---TTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             HHHHHHHHHhccCCEEEEEEecCC---CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            458999999999999999997763   589999999999999999999999987

>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=98.49  E-value=1.2e-07  Score=79.64  Aligned_cols=51  Identities=16%  Similarity=0.228  Sum_probs=46.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.+++     ++|||||+|.+.++|.+|+..+|++.+
T Consensus        21 ~~te~~L~~~F~~~G~i~~v~i~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~   71 (111)
T 1whx_A           21 GTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKF   71 (111)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBS
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEeC-----CCCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            579999999999999999999875     489999999999999999999998765

>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=98.48  E-value=1.5e-07  Score=76.84  Aligned_cols=51  Identities=33%  Similarity=0.533  Sum_probs=47.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.++++     +|||||+|.+.++|.+|+..+++..+
T Consensus        26 ~~t~~~l~~~F~~~G~i~~v~~~~~-----kg~afV~f~~~~~a~~a~~~l~g~~~   76 (99)
T 2cpj_A           26 DITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPL   76 (99)
T ss_dssp             TCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCB
T ss_pred             CCCHHHHHHHHhhcCCeEEEEEecC-----CCEEEEEECCHHHHHHHHHHhCCCEe
Confidence            5899999999999999999999865     89999999999999999999988764

>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=98.48  E-value=2e-07  Score=78.11  Aligned_cols=54  Identities=26%  Similarity=0.412  Sum_probs=49.3

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+  +.++|||||+|.+.++|.+|+..+|+..+
T Consensus        19 ~~t~~~l~~~F~~~G~v~~v~i~~~--~~~~g~afV~f~~~~~A~~A~~~l~g~~~   72 (115)
T 3lqv_A           19 KITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNAVDHLSGFNV   72 (115)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEEEECS--TTTTTCEEEEESSHHHHHHHHHHHTTCBS
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEeeC--CCCCcEEEEEECCHHHHHHHHHHcCCCEE
Confidence            5799999999999999999999875  45699999999999999999999998765

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.47  E-value=1.1e-07  Score=77.87  Aligned_cols=53  Identities=34%  Similarity=0.449  Sum_probs=47.3

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|   .++.+.+++++|||||+|.+.++|.+|+..+|+..+
T Consensus        26 ~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~   78 (101)
T 2fc9_A           26 SATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREI   78 (101)
T ss_dssp             TCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEE
T ss_pred             CCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            58999999999999987   566667889999999999999999999999987654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=98.47  E-value=1.2e-07  Score=81.81  Aligned_cols=56  Identities=21%  Similarity=0.253  Sum_probs=47.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecc----hHH----HHHHHH--hcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYAN----KIS----AVKAIL--KSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s----~e~----A~~Ai~--~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.| .+|+|+|||||+|.+    +++    |.+|+.  .+|+..+
T Consensus        17 ~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~I   83 (136)
T 2j8a_A           17 NIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCFI   83 (136)
T ss_dssp             CCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEEE
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCee
Confidence            4799999999999999999999999 578999999999996    333    788888  6776654

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=97.85  E-value=1.9e-08  Score=84.85  Aligned_cols=61  Identities=28%  Similarity=0.333  Sum_probs=53.6

Q ss_pred             ccCCC----CCcHHHHHHHhcccCccee--------eEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           96 KPYKG----KITEEEFKEHFGQYGDIID--------AQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        96 ~~f~G----~~tee~L~~~F~~fG~V~~--------v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|.+    .+++++|+++|++||.|..        +.++.+ .+++++|||||+|.+.++|.+|+..+|+..+
T Consensus         9 ~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   82 (116)
T 2lcw_A            9 TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   82 (116)
Confidence            44555    4799999999999999998        888887 5689999999999999999999999988654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=98.46  E-value=9.7e-08  Score=80.55  Aligned_cols=53  Identities=11%  Similarity=0.215  Sum_probs=47.6

Q ss_pred             CCcHHHHHHHhcccC-cceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYG-DIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG-~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++++|+++|++|| .|..+.+..+   .++|||||+|.+.++|.+|+..+|+..+
T Consensus        39 ~~te~dL~~~F~~~G~~v~~v~i~~~---~~rGfaFV~F~~~e~A~~Ai~~lng~~l   92 (111)
T 2jvr_A           39 GCSWQDLKDLARENSLETTFSSVNTR---DFDGTGALEFPSEEILVEALERLNNIEF   92 (111)
T ss_dssp             CCCHHHHHHHHHHHTCCCSEEECSSC---SSSCCEEEEESSHHHHHHHHHHTTTEEE
T ss_pred             CCCHHHHHHHHHHhCCeeEEEEEEcC---CCCCEEEEEECCHHHHHHHHHHcCCCEE
Confidence            589999999999999 8999988643   4799999999999999999999998765

>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=98.46  E-value=2.1e-07  Score=73.53  Aligned_cols=51  Identities=35%  Similarity=0.582  Sum_probs=46.4

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhc-CCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS-NKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~l-n~riy  156 (451)
                      .+++++|+++|++||.|.++.++++     +|||||+|.+.++|.+|+..+ ++..+
T Consensus        23 ~~t~~~l~~~f~~~G~i~~~~~~~~-----kg~afV~f~~~~~A~~a~~~l~~~~~~   74 (85)
T 2ytc_A           23 TITETDLRNHFYQFGEIRTITVVQR-----QQCAFIQFATRQAAEVAAEKSFNKLIV   74 (85)
T ss_dssp             TSCHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHTTTTTCEE
T ss_pred             CCCHHHHHHHHHhCCCEeEEEEECC-----CCEEEEEECCHHHHHHHHHHhcCCeeE
Confidence            5899999999999999999999974     899999999999999999998 76554

>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=98.46  E-value=1.6e-07  Score=81.04  Aligned_cols=57  Identities=28%  Similarity=0.389  Sum_probs=49.0

Q ss_pred             ccCCC----CCcHHHHHHHhcccCcce--eeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCC
Q psy300           96 KPYKG----KITEEEFKEHFGQYGDII--DAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK  154 (451)
Q Consensus        96 ~~f~G----~~tee~L~~~F~~fG~V~--~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~r  154 (451)
                      ++|.|    ++|+++|+++|++| .|.  ++.++.++.|+++|||||+|.+.++|.+|+.. ++.
T Consensus        44 ~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~-~~~  106 (126)
T 2hgm_A           44 FVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGK-HKE  106 (126)
T ss_dssp             EEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTT-TTC
T ss_pred             EEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHH-CCC
Confidence            44554    58999999999999 566  89999987799999999999999999999986 443

>3tr4_A Inorganic pyrophosphatase; central intermediary metabolism, hydrolase; HET: MSE; 2.00A {Coxiella burnetii} SCOP: b.40.5.0

Probab=98.46  E-value=1.3e-07  Score=85.84  Aligned_cols=47  Identities=21%  Similarity=0.343  Sum_probs=35.8

Q ss_pred             cCCCccccCCCCEEEEEEeecCCCc-cceeeeccccceEEEEEeeCCCCchh
Q psy300          389 HDIPLYSNVKDKIFNMVVEIPRWTN-AKMEVGNAMEMRLYLVCFNLPSPLGY  439 (451)
Q Consensus       389 hd~~l~~~~~~~~~~~~~e~p~~~~-~k~e~~~~~~~~~~~~~~~~~~~~~~  439 (451)
                      ||||+..+.  .++||||||||||+ +|+|+.++.  +...+---|.++++|
T Consensus         6 h~ip~g~~~--~~vnvvIEIP~gs~~~KyE~dk~~--g~i~~DR~l~~~~~Y   53 (178)
T 3tr4_A            6 FLVSAGKGI--DDFNVIIEIPANGGEVKYEYDKEL--GFLTVDRFMPTSMRY   53 (178)
T ss_dssp             --CCCEEET--TEEEEEEEECTTCCSEEEEEETTT--TEEEEEEECCSSBCC
T ss_pred             ccCCCCCCC--CEEEEEEEecCCCCcEEEEEecCC--CcEEEEEecCcCccC
Confidence            999999876  99999999999999 999999975  444444445666554

>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=98.46  E-value=1.2e-07  Score=78.87  Aligned_cols=49  Identities=16%  Similarity=0.274  Sum_probs=44.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCC
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKK  154 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~r  154 (451)
                      .+++++|+++|++||.|.++.++++     +|||||+|.+.++|.+|+..+++.
T Consensus        26 ~~te~~L~~~F~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~~   74 (104)
T 1wex_A           26 SVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAADV   74 (104)
T ss_dssp             SCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHS
T ss_pred             CCCHHHHHHHHHhCCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhccC
Confidence            5899999999999999999999864     899999999999999999988653

>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=98.45  E-value=2.1e-07  Score=75.60  Aligned_cols=51  Identities=20%  Similarity=0.312  Sum_probs=46.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.+.++     +|||||+|.+.++|.+|+..+|+..+
T Consensus        28 ~~t~~~l~~~F~~~G~v~~v~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~   78 (97)
T 1why_A           28 NTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPL   78 (97)
T ss_dssp             SCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBC
T ss_pred             CCCHHHHHHHHHhcCCeeEEEEeCC-----CCEEEEEECCHHHHHHHHHHHCCCEe
Confidence            5899999999999999999999865     78999999999999999999988764

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.45  E-value=2.1e-07  Score=75.71  Aligned_cols=51  Identities=25%  Similarity=0.473  Sum_probs=46.6

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.+.     +++|||||+|.+.++|.+|+..+|+..+
T Consensus        24 ~~t~~~l~~~F~~~G~i~~v~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~   74 (97)
T 1x5p_A           24 DMTPTLLRGAFSPFGNIIDLSMD-----PPRNCAFVTYEKMESADQAVAELNGTQV   74 (97)
T ss_dssp             SCCHHHHHHHHTTTSCEEEEEEE-----TTTTEEEEEESSHHHHHHHHHHTTTEEE
T ss_pred             CCCHHHHHHHHhhCCCEEEEEec-----CCCCEEEEEECCHHHHHHHHHHhCCCeE
Confidence            58999999999999999999985     4589999999999999999999988654

>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=98.45  E-value=1.9e-07  Score=77.70  Aligned_cols=50  Identities=20%  Similarity=0.429  Sum_probs=46.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.++.+      |||||+|.+.++|.+|+..+|+..+
T Consensus        26 ~~t~~~l~~~F~~~G~i~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~   75 (108)
T 1x4c_A           26 SGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKF   75 (108)
T ss_dssp             SCCHHHHHHHHGGGSCEEEEEEETT------TEEEEEESSHHHHHHHHHHSSSEEE
T ss_pred             CCCHHHHHHHHHhcCCEeEEEEecC------CEEEEEECCHHHHHHHHHHHCcCCc
Confidence            5899999999999999999999876      8999999999999999999988765

>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=98.44  E-value=7.9e-08  Score=80.54  Aligned_cols=56  Identities=21%  Similarity=0.378  Sum_probs=47.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|..+.+..+ .+++++|||||+|.+.++|.+|+..+|+..+
T Consensus        36 ~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~   92 (115)
T 2cpx_A           36 RVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKL   92 (115)
T ss_dssp             TCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBC
T ss_pred             CCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEe
Confidence            5799999999999999966544332 3788999999999999999999999988654

>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=98.44  E-value=1.9e-07  Score=78.81  Aligned_cols=50  Identities=20%  Similarity=0.429  Sum_probs=46.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+      |||||+|.+.++|.+|+..||+..+
T Consensus        27 ~~t~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~   76 (115)
T 3beg_B           27 SGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKF   76 (115)
T ss_dssp             SCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBC
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEecC------CEEEEEECCHHHHHHHHHHhCCCEE
Confidence            5899999999999999999999875      8999999999999999999998765

>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=98.44  E-value=1.4e-07  Score=80.61  Aligned_cols=48  Identities=21%  Similarity=0.231  Sum_probs=44.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCC
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK  153 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~  153 (451)
                      ++|+++|+++|++||.|.++.++++     +|||||+|++.++|.+|+..+++
T Consensus        42 ~vte~dL~~lF~~fG~V~~v~i~~~-----kG~AFVeF~~~e~A~~Ai~~l~~   89 (119)
T 2ad9_A           42 DVTEGEVISLGLPFGKVTNLLMLKG-----KNQAFIEMNTEEAANTMVNYYTS   89 (119)
T ss_dssp             TCCHHHHHHHHTTTSCCCEEEEEGG-----GTEEEEECSCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhcc
Confidence            5899999999999999999999986     89999999999999999998864

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=98.43  E-value=2.3e-07  Score=75.95  Aligned_cols=51  Identities=29%  Similarity=0.479  Sum_probs=46.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.+.+     ++|||||+|.+.++|.+|+..+|+..+
T Consensus        38 ~~~~~~l~~~f~~~G~i~~~~~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~   88 (101)
T 2la4_A           38 FATEADLIPLFQNFGFILDFKHYP-----EKGCCFIKYDTHEQAAVCIVALANFPF   88 (101)
T ss_dssp             TCCHHHHHHHHHTTSCCSEEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             ccCHHHHHHHHHhCCCEEEEEEec-----CCCEEEEEECCHHHHHHHHHHhCCCeE
Confidence            579999999999999999999984     489999999999999999999988664

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=98.43  E-value=2.4e-07  Score=80.37  Aligned_cols=53  Identities=17%  Similarity=0.333  Sum_probs=47.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccce-EEEEecchHHHHHHHHhcCCCccc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILKSNKKPYK  157 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~-gFV~F~s~e~A~~Ai~~ln~riy~  157 (451)
                      .+|+++|+++|++||.|.++.++.+    ++|| |||+|.+.++|.+|+..|||+.+.
T Consensus        39 ~vte~~L~~lFs~yG~V~~V~i~~~----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~   92 (130)
T 3zzy_A           39 PVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIY   92 (130)
T ss_dssp             CCCHHHHHHHHTTSSCEEEEEEEEE----TTEEEEEEEESCHHHHHHHHHHHTTCEEE
T ss_pred             CCCHHHHHHHHhCcCCEEEEEEEcC----CCCcEEEEEECCHHHHHHHHHHcCCCeec
Confidence            5899999999999999999998864    3677 999999999999999999987653

>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=98.42  E-value=1.7e-07  Score=77.68  Aligned_cols=47  Identities=21%  Similarity=0.299  Sum_probs=43.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcC
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN  152 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln  152 (451)
                      .+++++|+++|++||.|.++.++++     +|||||+|.+.++|.+|+..++
T Consensus        26 ~~te~~L~~~F~~fG~v~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~   72 (101)
T 2cq1_A           26 EVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYS   72 (101)
T ss_dssp             TCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhc
Confidence            5899999999999999999999875     8999999999999999999774

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=98.42  E-value=3.8e-07  Score=74.09  Aligned_cols=49  Identities=24%  Similarity=0.452  Sum_probs=45.5

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.+.       +|||||+|.+.++|.+|+..+|+..+
T Consensus        22 ~~t~~~l~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~A~~~l~g~~~   70 (96)
T 2kvi_A           22 NVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIECESQEMN   70 (96)
T ss_dssp             CCCHHHHHHHHTTTCCCCEEEEE-------TTEEEEEESCHHHHHHHHHHHTCSSC
T ss_pred             cCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCee
Confidence            58999999999999999999984       78999999999999999999998765

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.42  E-value=3.6e-07  Score=73.19  Aligned_cols=49  Identities=29%  Similarity=0.561  Sum_probs=45.3

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++       +|||||+|.+.++|.+|+..+|+..+
T Consensus        19 ~~t~~~l~~~F~~~G~i~~v~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~   67 (90)
T 2dnq_A           19 EATEQEIRSLFEQYGKVLECDII-------KNYGFVHIEDKTAAEDAIRNLHHYKL   67 (90)
T ss_dssp             SCCHHHHHHHHHTSSCEEEEEEE-------TTEEEEEESSHHHHHHHHHHHTTCBC
T ss_pred             CCCHHHHHHHHHhCCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHhcCCcc
Confidence            58999999999999999999997       68999999999999999999988654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.41  E-value=3.7e-07  Score=78.52  Aligned_cols=52  Identities=17%  Similarity=0.220  Sum_probs=46.6

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccce-EEEEecchHHHHHHHHhcCCCccc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILKSNKKPYK  157 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~-gFV~F~s~e~A~~Ai~~ln~riy~  157 (451)
                      .+++++|+++|++||.|.++.++..     .|| |||+|.+.++|..|+..|||+.+.
T Consensus        36 ~vt~~~L~~~Fs~yG~V~~v~i~~~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~   88 (124)
T 2e5i_A           36 PITVDVLYTVCNPVGKVQRIVIFKR-----NGIQAMVEFESVLCAQKAKAALNGADIY   88 (124)
T ss_dssp             CCCHHHHHHHHTTTSCEEEEEEEES-----SSEEEEEEESSHHHHHHHHHHHTTCCCB
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCEec
Confidence            5899999999999999999999763     386 999999999999999999987653

>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=98.41  E-value=2.9e-07  Score=77.22  Aligned_cols=51  Identities=14%  Similarity=0.247  Sum_probs=45.3

Q ss_pred             cHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       103 tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++|+++|++||.|.++.+ .++  .++|||||+|.+.++|.+|+..+|++.+
T Consensus        39 ~e~~l~~~f~~~G~v~~v~i-~~~--~~~G~afV~f~~~~~A~~Ai~~lng~~~   89 (112)
T 2dit_A           39 IREDLRVECSKFGQIRKLLL-FDR--HPDGVASVSFRDPEEADYCIQTLDGRWF   89 (112)
T ss_dssp             HHHHHHHHGGGTSCCSEEEE-ETT--CTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             HHHHHHHHHHccCCEeEEEE-ecC--CCCEEEEEEECCHHHHHHHHHHcCCCEE
Confidence            56899999999999999966 443  3799999999999999999999998765

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.40  E-value=3.2e-07  Score=74.64  Aligned_cols=52  Identities=13%  Similarity=0.204  Sum_probs=46.4

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|. +.++.+   .++|||||+|.+.++|.+|+..+|+..+
T Consensus        30 ~~t~~~l~~~F~~~G~v~-~~~~~~---~~~g~afV~f~~~~~a~~A~~~l~g~~~   81 (97)
T 2e5j_A           30 DARVSDLKRALRELGSVP-LRLTWQ---GPRRRAFLHYPDSAAAQQAVSCLQGLRL   81 (97)
T ss_dssp             TCCHHHHHHHHHHTTCCC-SEEEEE---TTTTEEEEECSSHHHHHHHHHHHTTCCS
T ss_pred             cCcHHHHHHHHHhcCCEE-EEEEcC---CCCcEEEEEECCHHHHHHHHHHhCCCEE
Confidence            589999999999999997 677654   6799999999999999999999998765

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.40  E-value=6.2e-08  Score=79.38  Aligned_cols=54  Identities=13%  Similarity=0.135  Sum_probs=47.3

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.. .++.+ .+|+++|||||+|.+.++|.+|+. +|+..+
T Consensus        28 ~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~   82 (101)
T 1fj7_A           28 NKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKV   82 (101)
T ss_dssp             TSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCB
T ss_pred             CCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEE
Confidence            5899999999999999988 55444 578899999999999999999998 987654

>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=98.40  E-value=1.7e-07  Score=79.24  Aligned_cols=47  Identities=19%  Similarity=0.265  Sum_probs=43.6

Q ss_pred             CcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCC
Q psy300          102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK  153 (451)
Q Consensus       102 ~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~  153 (451)
                      +++++|+++|++||.|.++.++++     +|||||+|.+.++|..|+..+++
T Consensus        38 ~te~~L~~lF~~fG~V~~v~i~~~-----kg~aFVef~~~~~A~~Ai~~l~~   84 (112)
T 1x4f_A           38 YSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLK   84 (112)
T ss_dssp             CCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHhcCCEEEEEEecC-----CCEEEEEECCHHHHHHHHHHhcc
Confidence            899999999999999999999853     89999999999999999998864

>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=98.40  E-value=3.4e-07  Score=84.53  Aligned_cols=59  Identities=20%  Similarity=0.335  Sum_probs=52.3

Q ss_pred             CccCCC----CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCC
Q psy300           95 KKPYKG----KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK  153 (451)
Q Consensus        95 g~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~  153 (451)
                      .++|.|    .+|+++|+++|++||.|.+++++++.++.++|||||+|.+.++|.+|+..++.
T Consensus       110 ~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~~  172 (193)
T 2voo_A          110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQ  172 (193)
T ss_dssp             TEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTTC
T ss_pred             CEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCCC
Confidence            345544    58999999999999999999999998899999999999999999999987654

>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=98.40  E-value=9.7e-08  Score=77.42  Aligned_cols=54  Identities=28%  Similarity=0.530  Sum_probs=48.6

Q ss_pred             CCcHHHHH----HHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFK----EHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~----~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+    ++|++||.|.++.+++  +|.++|||||+|.+.++|.+|+..+|+..+
T Consensus        19 ~~~~~~l~~~l~~~f~~~G~i~~v~i~~--~~~~~g~afV~f~~~~~A~~A~~~l~g~~~   76 (97)
T 1nu4_A           19 KIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPF   76 (97)
T ss_dssp             TSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHHHHHhCCCEEEEEEEc--CCCcCcEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            57999999    9999999999998874  467899999999999999999999988654

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=98.40  E-value=2.8e-07  Score=76.96  Aligned_cols=55  Identities=27%  Similarity=0.579  Sum_probs=48.7

Q ss_pred             CccCCC----CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           95 KKPYKG----KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        95 g~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .++|.|    .+++++|+++|++||.|..+.++       +|||||+|.+.++|.+|+..+|+..+
T Consensus        32 ~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~-------kg~afV~f~~~~~A~~Ai~~l~g~~~   90 (108)
T 2jvo_A           32 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-------NGFAFVEFEEAESAAKAIEEVHGKSF   90 (108)
T ss_dssp             SEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE-------TTEEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEECCHHHHHHHHHHcCCCEE
Confidence            345555    47999999999999999999998       78999999999999999999998765

>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=98.39  E-value=2.8e-07  Score=76.65  Aligned_cols=51  Identities=24%  Similarity=0.555  Sum_probs=47.4

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++++     +|||||+|.+.++|.+|+..+++..+
T Consensus        36 ~~t~~~l~~~F~~~G~i~~v~i~~~-----~g~afV~f~~~~~a~~A~~~l~g~~~   86 (109)
T 1x4g_A           36 GLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTI   86 (109)
T ss_dssp             CCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEeCC-----CCEEEEEECCHHHHHHHHHHcCCCEE
Confidence            5799999999999999999999986     89999999999999999999988654

>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=98.39  E-value=3.9e-07  Score=74.41  Aligned_cols=49  Identities=24%  Similarity=0.466  Sum_probs=45.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.+.       +|||||+|.+.++|.+|+..+|+..+
T Consensus        34 ~~t~~~L~~~F~~~G~v~~v~i~-------~g~afV~f~~~~~A~~Ai~~l~g~~~   82 (97)
T 2xnq_A           34 NVSKEDLFRIFSPYGHIMQINIK-------NAFGFIQFDNPQSVRDAIEXESQEMN   82 (97)
T ss_dssp             CCCHHHHHHHHGGGSCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHTTSEE
T ss_pred             cCCHHHHHHHHHhcCCEEEEEEe-------CCEEEEEECCHHHHHHHHHHcCCCEE
Confidence            57999999999999999999983       79999999999999999999988764

>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=98.36  E-value=3.3e-07  Score=73.80  Aligned_cols=42  Identities=29%  Similarity=0.615  Sum_probs=38.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHH
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVK  146 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~  146 (451)
                      ++|+++|+++|++||.|.++.++++    ++|||||+|.+.++|.+
T Consensus        22 ~~te~~L~~~F~~~G~i~~v~i~~~----srGfaFV~F~~~~~A~~   63 (89)
T 3d2w_A           22 DMTAEELQQFFCQYGEVVDVFIPKP----FRAFAFVTFADDKVAQS   63 (89)
T ss_dssp             TCCHHHHHHHHTTTSCEEEEECCSS----CCSEEEEEESCHHHHHH
T ss_pred             CCCHHHHHHHHhccCCEEEEEEeeC----CCCEEEEEECCHHHHHH
Confidence            5899999999999999999999875    79999999999999884

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.35  E-value=2e-07  Score=75.52  Aligned_cols=52  Identities=31%  Similarity=0.427  Sum_probs=46.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+    ..++.++|||||+|.+.++|.+|+..+++..+
T Consensus        27 ~~t~~~l~~~F~~~g~v~~~----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~   78 (96)
T 1fjc_A           27 NITEDELKEVFEDALEIRLV----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI   78 (96)
T ss_dssp             SCCHHHHHHHHCSEEEECCE----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEE
T ss_pred             CCCHHHHHHHHhhCCcEEEe----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            58999999999999998776    45678999999999999999999999987654

>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=98.34  E-value=3e-07  Score=80.23  Aligned_cols=56  Identities=29%  Similarity=0.481  Sum_probs=47.8

Q ss_pred             CCcHHHHHHHhcccCcceee------EEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDA------QLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v------~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|..+      .+....+|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        56 ~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~  117 (143)
T 3egn_A           56 HVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVL  117 (143)
T ss_dssp             TCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEE
T ss_pred             CCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEe
Confidence            58999999999999999886      122224788999999999999999999999988764

>1qez_A Ppase, S-ppase, protein (inorganic pyrophosphatase); thermostability, magnesium, hydrolase; 2.70A {Sulfolobus acidocaldarius} SCOP: b.40.5.1

Probab=98.33  E-value=4.3e-07  Score=82.16  Aligned_cols=47  Identities=30%  Similarity=0.418  Sum_probs=37.3

Q ss_pred             ccCCccCCCccccCCCCEEEEEEeecCCCccceeeeccccceEEEEEeeCCCCchh
Q psy300          384 LISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLYLVCFNLPSPLGY  439 (451)
Q Consensus       384 ~~s~~hd~~l~~~~~~~~~~~~~e~p~~~~~k~e~~~~~~~~~~~~~~~~~~~~~~  439 (451)
                      .||++|++|       ..|||||||||||++|||+.++.  +...+-.+|.+++.|
T Consensus         2 ~i~~g~~~p-------~~~nvvIEIP~gs~~KyE~dk~~--g~l~~DR~l~~~~~Y   48 (173)
T 1qez_A            2 KLSPGKNAP-------DVVNVLVEIPQGSNIKYEYDDEE--GVIKVDRVLYTSMNY   48 (173)
T ss_dssp             CCCSCTTTT-------TSEEEEEEECTTCCEEEEEETTT--TEEEEEEECSSSBCC
T ss_pred             CcCCCCCCC-------CeEEEEEEECCCCCeEEEEecCC--CCEEEEeecCCCCcC
Confidence            368888877       57999999999999999999975  444455667777665

>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=98.32  E-value=5e-07  Score=75.21  Aligned_cols=55  Identities=24%  Similarity=0.526  Sum_probs=48.4

Q ss_pred             CccCCC----C-CcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           95 KKPYKG----K-ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        95 g~~f~G----~-~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .++|.+    . +++++|+++|++||.|..+.+       ++|||||+|.+.++|.+|+..+|+..+
T Consensus        28 ~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i-------~~g~afV~f~~~~~A~~A~~~l~g~~~   87 (110)
T 1wf1_A           28 SRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV-------HKGYAFVQYSNERHARAAVLGENGRVL   87 (110)
T ss_dssp             SEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE-------ETTEEEEECSSSHHHHHHHHHHTTCEE
T ss_pred             cEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE-------eCCEEEEEECCHHHHHHHHHHcCCCEE
Confidence            445555    4 899999999999999999998       489999999999999999999988664

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=98.29  E-value=4.6e-07  Score=86.60  Aligned_cols=50  Identities=22%  Similarity=0.386  Sum_probs=46.6

Q ss_pred             cHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCccc
Q psy300          103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK  157 (451)
Q Consensus       103 tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~  157 (451)
                      ++++|+++|++||.|++++++.+     +|||||+|.+.++|..|+..|+++.++
T Consensus       156 tEe~L~~~F~~fG~I~~v~v~~~-----kG~AFV~F~~~~~Ae~A~~am~g~~l~  205 (240)
T 3u1l_A          156 IESRIRFVFSRLGDIDRIRYVES-----KNCGFVKFKYQANAEFAKEAMSNQTLL  205 (240)
T ss_dssp             HHHHHHHHHHTTSCEEEEEEEGG-----GTEEEEEESSHHHHHHHHHHHTTCCCC
T ss_pred             cHHHHHHHHHccCCEEEEEEECC-----CCEEEEEeCCHHHHHHHHHHhCCCEEe
Confidence            69999999999999999999864     899999999999999999999998763

>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=98.23  E-value=8.6e-07  Score=72.86  Aligned_cols=49  Identities=33%  Similarity=0.518  Sum_probs=44.6

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|..+.++       +|||||+|.+.++|.+|+..+|+..+
T Consensus        22 ~~t~~~l~~~F~~~G~i~~v~~~-------~~~afV~f~~~~~a~~A~~~l~g~~~   70 (103)
T 2dgu_A           22 TVTEEILEKAFSQFGKLERVKKL-------KDYAFIHFDERDGAVKAMEEMNGKDL   70 (103)
T ss_dssp             TCCHHHHHHHHHHHSCEEEEEEC-------SSCEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             CCCHHHHHHHHHhcCCEEEEEEE-------CCEEEEEeCCHHHHHHHHHHHCCCcc
Confidence            57999999999999999999987       46999999999999999999987654

>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=98.23  E-value=1.1e-06  Score=69.47  Aligned_cols=50  Identities=20%  Similarity=0.389  Sum_probs=45.4

Q ss_pred             CCcHHHHHHHhccc----C-------cceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQY----G-------DIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~f----G-------~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++|    |       .|.++.+.++     +|||||+|.+.++|.+|+ .+|+..+
T Consensus        17 ~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~-----kg~afV~f~~~~~a~~A~-~l~g~~~   77 (87)
T 2hzc_A           17 GITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEFRSVDETTQAM-AFDGIIF   77 (87)
T ss_dssp             TCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS-----SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC-----CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            57999999999999    8       8999988865     899999999999999999 9988764

>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=98.22  E-value=8.9e-07  Score=70.68  Aligned_cols=50  Identities=18%  Similarity=0.213  Sum_probs=45.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++| .|.++.+.     +++|||||+|.+.++|.+|+..+|+..+
T Consensus        16 ~~t~~~l~~~F~~~-~v~~~~i~-----~~~g~afV~f~~~~~a~~Ai~~l~g~~~   65 (88)
T 1wg1_A           16 DSNCQEVHDLLKDY-DLKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSF   65 (88)
T ss_dssp             SCCHHHHHHHTCSS-CCCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEE
T ss_pred             CCCHHHHHHHHhhC-CeEEEEEe-----CCCcEEEEEECCHHHHHHHHHHhCCCeE
Confidence            58999999999999 99999985     5699999999999999999999988764

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.21  E-value=1.3e-06  Score=70.18  Aligned_cols=49  Identities=24%  Similarity=0.533  Sum_probs=44.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.+++       +||||+|.+.++|.+|+..+|+..+
T Consensus        21 ~~t~~~l~~~F~~~G~v~~v~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~   69 (92)
T 2dgt_A           21 TCTNQELRAKFEEYGPVIECDIVK-------DYAFVHMERAEDAVEAIRGLDNTEF   69 (92)
T ss_dssp             SCCHHHHHHHHHTTSCCCEEEECS-------SEEEEEESCHHHHHHHHHHHTTEEE
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEEC-------CEEEEEECCHHHHHHHHHHhCCCee
Confidence            579999999999999999999974       4999999999999999999988654

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.20  E-value=1.5e-06  Score=70.95  Aligned_cols=53  Identities=26%  Similarity=0.390  Sum_probs=46.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|+.|+   .+.++.+ .+++++|||||+|.+.++|.+|+..+|+..+
T Consensus        26 ~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~   79 (102)
T 2fc8_A           26 DTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEI   79 (102)
T ss_dssp             TCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             ccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeE
Confidence            579999999999874   6677776 5788999999999999999999999988654

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.20  E-value=1.3e-06  Score=69.87  Aligned_cols=49  Identities=24%  Similarity=0.422  Sum_probs=44.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.+++       +||||+|.+.++|.+|+..+|+..+
T Consensus        20 ~~t~~~l~~~F~~~G~v~~~~~~~-------~~afV~f~~~~~a~~A~~~l~g~~~   68 (90)
T 2dnp_A           20 ACTSQELRSLFERRGRVIECDVVK-------DYAFVHMEKEADAKAAIAQLNGKEV   68 (90)
T ss_dssp             TCCHHHHHHHHHHHSCEEEEEECS-------SCEEEEESCHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHcCCCEEEEEEEC-------CEEEEEECCHHHHHHHHHHhCCCEE
Confidence            579999999999999999999974       4999999999999999999988654

>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=98.19  E-value=8.9e-07  Score=71.21  Aligned_cols=50  Identities=22%  Similarity=0.408  Sum_probs=43.3

Q ss_pred             CCcHHHHHHHhcccCc-ceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCC-Ccc
Q psy300          101 KITEEEFKEHFGQYGD-IIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK-KPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~-V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~-riy  156 (451)
                      .+++++|+++|++||. |..+.+.      ++|||||+|.+.++|.+|+..+|+ ..+
T Consensus        19 ~~t~~~l~~~F~~~G~vv~~~~~~------~~g~afV~f~~~~~A~~A~~~l~g~~~~   70 (93)
T 2cqh_A           19 AVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVEL   70 (93)
T ss_dssp             TCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEE
T ss_pred             CCCHHHHHHHHHHcCCceEEEEEc------CCCEEEEEECCHHHHHHHHHHccCCeeE
Confidence            5799999999999999 6666663      489999999999999999999988 443

>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=98.18  E-value=2.6e-06  Score=79.78  Aligned_cols=58  Identities=21%  Similarity=0.315  Sum_probs=52.5

Q ss_pred             CCHHHHHHHhccCCCeEEEEEeECC-----CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           44 ITEEEFKEHFGQYGDIIDAQLLKNA-----DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        44 vte~~L~~~F~~~G~I~~i~l~~d~-----tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      -.+++|++.|++||.|.++.+.++.     +++++|++||+|.+.++|.+|+..|||+.|.|+
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr  203 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGR  203 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCe
Confidence            4567899999999999999998653     458999999999999999999999999999986

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=98.18  E-value=1.1e-06  Score=88.28  Aligned_cols=53  Identities=13%  Similarity=0.137  Sum_probs=47.5

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcccC
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  158 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~~  158 (451)
                      ++|+++|+++|++||.|.++.+..     +||||||+|++.++|.+|+..|||+....
T Consensus        31 ~~te~~L~~~F~~~G~V~~v~~~~-----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~   83 (345)
T 3tht_A           31 GVSRNQLLPVLEKCGLVDALLMPP-----NKPYSFARYRTTEESKRAYVTLNGKEVVD   83 (345)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEECCT-----TCSEEEEEESSHHHHHHHHHHTTTCEEEC
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEeC-----CCCEEEEEECCHHHHHHHHHHhCCCcccc
Confidence            389999999999999999887754     48999999999999999999999987643

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.15  E-value=2.9e-06  Score=68.40  Aligned_cols=51  Identities=8%  Similarity=0.252  Sum_probs=42.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++ +....+++   ||||+|.+.++|.+|+. +|+..+
T Consensus        19 ~~t~~~l~~~F~~~G~v~~v-~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~   69 (94)
T 2e5g_A           19 GVDSAQLSEYFLAFGPVASV-VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSL   69 (94)
T ss_dssp             TCCHHHHHHHGGGTSCEEEE-EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEE
T ss_pred             CCCHHHHHHHHHhcCCeEEE-EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEE
Confidence            58999999999999999987 33223443   99999999999999999 987654

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.14  E-value=2.8e-06  Score=68.53  Aligned_cols=53  Identities=19%  Similarity=0.210  Sum_probs=45.8

Q ss_pred             CCcHHHHHHHhcccCcceeeE-EeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQ-LLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~-v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.+++ ++.++.   .|.|||+|.+.++|.+|+..+|+..+
T Consensus        26 ~~t~~~l~~~F~~~G~v~~~~~i~~~~~---~~~afV~f~~~~~a~~Ai~~l~g~~~   79 (96)
T 2e44_A           26 HLQWEVLDSLLVQYGVVESCEQVNTDSE---TAVVNVTYSSKDQARQALDKLNGFQL   79 (96)
T ss_dssp             SSCHHHHHHHHHHHSCEEEEEEECCSSS---SEEEEEEESSHHHHHHHHHHHTTCBC
T ss_pred             CCCHHHHHHHHHhcCCeEEEEEeecCCC---CCEEEEEECCHHHHHHHHHHhCCCEE
Confidence            589999999999999999995 777632   34499999999999999999998764

>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=98.13  E-value=2.5e-06  Score=79.88  Aligned_cols=55  Identities=20%  Similarity=0.279  Sum_probs=49.9

Q ss_pred             CcHHHHHHHhcccCcceeeEEeeCC-----CCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          102 ITEEEFKEHFGQYGDIIDAQLLKNA-----DGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       102 ~tee~L~~~F~~fG~V~~v~v~~d~-----~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      -.+++|++.|++||.|.++.++++.     +++++|++||+|.+.++|.+|+..|||+.|
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~  200 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWF  200 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBS
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceE
Confidence            4678999999999999999998652     448999999999999999999999999988

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.13  E-value=2.5e-06  Score=69.45  Aligned_cols=49  Identities=22%  Similarity=0.424  Sum_probs=44.1

Q ss_pred             CCcHHHHHHHhccc--CcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQY--GDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~f--G~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++|  |.|..+.+.       +|||||+|.+.++|.+|+..+|+..+
T Consensus        26 ~~t~~~l~~~F~~~g~g~v~~~~~~-------~g~afV~f~~~~~A~~A~~~l~g~~~   76 (99)
T 2cpd_A           26 STSEEMIEKEFNNIKPGAVERVKKI-------RDYAFVHFSNREDAVEAMKALNGKVL   76 (99)
T ss_dssp             TCCHHHHHHHHHTTSTTCEEEEEEC-------SSEEEEEESSHHHHHHHHHHHSSEEE
T ss_pred             CCCHHHHHHHHHhcCCcceEEEEEe-------CCeEEEEeCCHHHHHHHHHHhCCCEe
Confidence            58999999999999  889888764       67999999999999999999988754

>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=98.12  E-value=1.2e-06  Score=69.77  Aligned_cols=43  Identities=33%  Similarity=0.661  Sum_probs=39.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHH
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA  147 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~A  147 (451)
                      .+++++|+++|++||.|.++.++++    ++|||||+|.+.++|.+|
T Consensus        16 ~~te~~l~~~F~~~G~i~~v~i~~~----~~g~afV~f~~~~~a~~~   58 (88)
T 1wf0_A           16 DMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFADDQIAQSL   58 (88)
T ss_dssp             SSCHHHHHHHSTTTSCCCEEECCSS----CCSCCEEECSCHHHHHHT
T ss_pred             CCCHHHHHHHHHHcCCeeEEEEecC----CCCEEEEEECCHHHHHHH
Confidence            5899999999999999999999875    689999999999999754

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.06  E-value=4.6e-06  Score=67.44  Aligned_cols=64  Identities=14%  Similarity=0.338  Sum_probs=53.7

Q ss_pred             CCCCceEEEcCCC----CCCCH----HHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLP----FKITE----EEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp----~~vte----~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .++..||+|.-.|    .++-.    .+|.+.|++||.|..++++.+.       +||+|.+.++|.+|++ |||..+.|
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~-------~fVtF~d~~sAlaAi~-mnG~~v~G   75 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK-------MWVTFLEGSSALNVLS-LNGKELLN   75 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS-------EEEEESSHHHHHHGGG-GTTCEETT
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC-------EEEEECChHHHHHHHh-cCCeEeCC
Confidence            3567899998776    24444    6789999999999999998762       8999999999999998 99987776

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.04  E-value=5.9e-06  Score=67.41  Aligned_cols=49  Identities=14%  Similarity=0.255  Sum_probs=41.3

Q ss_pred             CCcHHH----HHHHhcccC-cceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcccC
Q psy300          101 KITEEE----FKEHFGQYG-DIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  158 (451)
Q Consensus       101 ~~tee~----L~~~F~~fG-~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~~  158 (451)
                      ++++++    |+++|++|| .|.++      ++   |+|||+|.+.++|.+|+..|++..+++
T Consensus        20 ~~~~~~lk~~L~~lF~~yGG~Vl~V------tg---G~AfV~F~~~esA~~A~~~l~G~~l~g   73 (96)
T 2diu_A           20 NKDGKSVSNRLRRLSDNCGGKVLSI------TG---CSAILRFINQDSAERAQKRMENEDVFG   73 (96)
T ss_dssp             TSCHHHHHHHHHHHHHTTTCCEEEC------CT---TCEEEEESSHHHHHHHHHHHTTCCSSS
T ss_pred             cCCHHHHHHHHHHHHHHcCCeeEEE------ec---CEEEEEECCHHHHHHHHHHhcCCccCC
Confidence            466666    668999995 99988      23   999999999999999999999987654

>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=97.76  E-value=9.3e-06  Score=66.01  Aligned_cols=66  Identities=15%  Similarity=0.253  Sum_probs=55.3

Q ss_pred             CCCCCceEEEcCCCCC-----CCH----HHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccC
Q psy300           28 DKTKRGRLFIKNLPFK-----ITE----EEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY   98 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~-----vte----~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f   98 (451)
                      -.++..||+|.-++.+     +-.    .+|.+.|++||.|..+++..++       +||+|.+.++|.+|++ |+|..+
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~-------~fVtF~d~~sAl~AI~-ldG~~v   82 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ-------MLVTFADSHSALSVLD-VDGMKV   82 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE-------EEEECSCSHHHHHHHH-GGGSEE
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc-------EEEEEcChHHHHHHHh-cCCeee
Confidence            3567889999988743     323    4689999999999999999772       9999999999999998 999888


Q ss_pred             CCC
Q psy300           99 KGK  101 (451)
Q Consensus        99 ~G~  101 (451)
                      .|+
T Consensus        83 ~Gr   85 (95)
T 1ufw_A           83 KGR   85 (95)
T ss_dssp             TTE
T ss_pred             CCe
Confidence            774

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.30  E-value=0.00022  Score=60.77  Aligned_cols=46  Identities=20%  Similarity=0.288  Sum_probs=41.7

Q ss_pred             CcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecc-hHHHHHHHHhcC
Q psy300          102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYAN-KISAVKAILKSN  152 (451)
Q Consensus       102 ~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s-~e~A~~Ai~~ln  152 (451)
                      +++++|+++|++||.|.+|.+.+++.     .|||+|.+ .++|..|+.++|
T Consensus        31 ~sredLke~F~~~G~V~~Vd~~~g~~-----tgfVrf~~~~~~A~~av~~ln   77 (121)
T 1owx_A           31 TCREDLHILFSNHGEIKWIDFVRGAK-----EGIILFKEKAKEALGKAKDAN   77 (121)
T ss_dssp             CCHHHHHHHTCSSCCEEEEECCTTCS-----EEEEEESSCHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHhcCCEEEEEEecCCC-----EEEEEECCChHHHHHHHHHhh
Confidence            79999999999999999999998743     59999999 789999999885

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.29  E-value=0.00018  Score=58.01  Aligned_cols=44  Identities=18%  Similarity=0.446  Sum_probs=39.8

Q ss_pred             HHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          105 EEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       105 e~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|.+.|++||.|..+++..++       +||+|.+.++|.+|+. ||+..+
T Consensus        30 ~~L~~~F~~~G~Vi~vr~~~d~-------~fVtF~d~~sAlaAi~-mnG~~v   73 (91)
T 2dnr_A           30 DELLQQFASFGEVILIRFVEDK-------MWVTFLEGSSALNVLS-LNGKEL   73 (91)
T ss_dssp             HHHHHHHHTTCCEEEEEECSSS-------EEEEESSHHHHHHGGG-GTTCEE
T ss_pred             HHHHHHHHhCCCeEEEEEecCC-------EEEEECChHHHHHHHh-cCCeEe
Confidence            6799999999999999999873       8999999999999998 998765

>1sxv_A Inorganic pyrophosphatase; structural genomics, ppase,, hydrolase; 1.30A {Mycobacterium tuberculosis} PDB: 1wcf_A 2uxs_A 4ecp_A

Probab=97.24  E-value=7.2e-05  Score=67.42  Aligned_cols=23  Identities=30%  Similarity=0.511  Sum_probs=19.6

Q ss_pred             CEEEEEEeecCCCccceeeeccc
Q psy300          400 KIFNMVVEIPRWTNAKMEVGNAM  422 (451)
Q Consensus       400 ~~~~~~~e~p~~~~~k~e~~~~~  422 (451)
                      -.|||||||||||++|+|+.++.
T Consensus        11 ~~~nvvIEIP~gs~~KyE~Dk~~   33 (172)
T 1sxv_A           11 MQFDVTIEIPKGQRNKYEVDHET   33 (172)
T ss_dssp             CCEEEEEEECTTCCEEC-CCTTT
T ss_pred             eEEEEEEEECCCCCeEEEEEcCC
Confidence            57999999999999999997653

>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=96.98  E-value=0.00037  Score=56.55  Aligned_cols=44  Identities=18%  Similarity=0.357  Sum_probs=40.0

Q ss_pred             HHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          105 EEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       105 e~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|.+.|++||.|..+++..++       +||+|.+.++|.+|+. ||+..+
T Consensus        39 ~~L~~~F~~~G~Vilvr~v~d~-------~fVtF~d~~sAl~AI~-ldG~~v   82 (95)
T 1ufw_A           39 TELMQTLGSYGTIVLVRINQGQ-------MLVTFADSHSALSVLD-VDGMKV   82 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETTE-------EEEECSCSHHHHHHHH-GGGSEE
T ss_pred             HHHHHHHHHCCCEEEEEEecCc-------EEEEEcChHHHHHHHh-cCCeee
Confidence            5699999999999999999873       8999999999999998 988765

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=96.95  E-value=0.0017  Score=54.03  Aligned_cols=77  Identities=18%  Similarity=0.182  Sum_probs=65.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccC-----CCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC--
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQY-----GDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK--  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~-----G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~--  101 (451)
                      ....++|=+=|||..+++..|+.+.+.+     |.+..+.+..|     -|-|+|+|.+...|-+|.-+++|..|.|+  
T Consensus        18 ~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pD-----H~GAivef~d~~~AgKasLaL~G~ef~gr~L   92 (117)
T 2l9w_A           18 KELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSD-----FNGAIIIFRDSKFAAKMLMILNGSQFQGKVI   92 (117)
T ss_dssp             TTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT-----TTEEEEECSCHHHHHHHHHHHSSEEETTEEE
T ss_pred             ccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecC-----CCceEEEEccchhhHHHHhhcCCeeecCeEE
Confidence            3356788889999999999999999999     99999999877     44599999999999999999999999985  


Q ss_pred             --CcHHHHHHH
Q psy300          102 --ITEEEFKEH  110 (451)
Q Consensus       102 --~tee~L~~~  110 (451)
                        .|-.+|...
T Consensus        93 r~gTv~eL~~~  103 (117)
T 2l9w_A           93 RSGTINDMKRY  103 (117)
T ss_dssp             EEECHHHHHHH
T ss_pred             EecCHHHHHhc
Confidence              355555544

>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=96.35  E-value=0.013  Score=47.23  Aligned_cols=68  Identities=16%  Similarity=0.259  Sum_probs=56.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-C-CC-ceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-D-GK-LKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-t-g~-skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ++|-|++||+++|++++.+.++....+.....+... + +. .-+-|+|.|.+.+++..-.+.++|..|..
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D   72 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEc
Confidence            578999999999999999999999887777776654 2 22 23569999999999999999999988874

>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=96.12  E-value=0.015  Score=47.32  Aligned_cols=56  Identities=14%  Similarity=0.336  Sum_probs=46.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN   94 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~ln   94 (451)
                      -..-+++ ++|+.+...||..+|+.||.| .|+.+.|      ..|||.|.+++.|..|+..+.
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidD------TsAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDD------TSAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEET------TEEEEECSCHHHHHHHHHHHH
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcC------CeEEEEecCHHHHHHHHHhcc
Confidence            3344555 999999999999999999954 5777765      369999999999999998664

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=95.86  E-value=0.014  Score=47.61  Aligned_cols=53  Identities=15%  Similarity=0.317  Sum_probs=45.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcC
Q psy300           34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN   94 (451)
Q Consensus        34 ~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~ln   94 (451)
                      -+++ ++|+.+...||..+|+.|| -..|+.+-|      ..|||.|.+++.|..|+..+.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidD------TsAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDD------TSAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEET------TEEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcC------CeEEEEecCHHHHHHHHHhcc
Confidence            3445 9999999999999999999 456888766      369999999999999998765

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=94.80  E-value=0.17  Score=41.52  Aligned_cols=57  Identities=16%  Similarity=0.252  Sum_probs=48.2

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhcc-----CCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHh
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQ-----YGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK   92 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~-----~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~   92 (451)
                      .....+|.|.|||.++.++.|.-+|+.     =|+|.++....       +-|+|+|.+.+.|++.++.
T Consensus         5 ~~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-------~~AvItF~d~~va~rVL~k   66 (104)
T 2dhx_A            5 SSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-------CGGVLTFREPADAERVLAQ   66 (104)
T ss_dssp             CCCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-------TEEEEEESSHHHHHHHHTC
T ss_pred             ccCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-------CcEEEEEcChHHHHHHhcC
Confidence            446789999999999999999999986     25788887742       4689999999999999876

>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=93.94  E-value=0.065  Score=44.05  Aligned_cols=66  Identities=26%  Similarity=0.290  Sum_probs=53.7

Q ss_pred             CCceEEEcCCCCCC-CH----HHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           31 KRGRLFIKNLPFKI-TE----EEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        31 ~~~~lfVgnLp~~v-te----~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      -.++|+|.||+.++ ..    +.++.+|.+|+++.+....+.     =+-.-|.|.++++|.+|...|++..|.|+
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS-----FRRirv~F~~~~~A~~AR~~Lh~~~f~g~   74 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLHKTEFLGK   74 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTSTTSEETTE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCc-----ceEEEEEeCChHHHHHHHHHhccceecCc
Confidence            45789999998765 22    567999999999988877754     22367999999999999999999988874

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=93.53  E-value=0.054  Score=44.02  Aligned_cols=70  Identities=13%  Similarity=0.089  Sum_probs=49.1

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC--CCCc-eeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA--DGKL-KGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~--tg~s-kG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .+-+|-|+.||+.+|++++.+.++..-++.....+...  .+.+ -+-|||.|.+.++...-.+.++|..|..
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D   80 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLD   80 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEEC
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEe
Confidence            34589999999999999987777765443322222222  1211 2458999999999888888888887764

>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=93.37  E-value=0.14  Score=43.07  Aligned_cols=65  Identities=20%  Similarity=0.297  Sum_probs=51.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....+-|-|-+.|+.. -..+...|++||.|.+....   +  ...+-.|.|.++.+|++||.+ ||+.+.|
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~---~--~~NWihI~Y~s~~~A~rAL~k-NG~ii~g   85 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS---N--TGNWMHIRYQSKLQARKALSK-DGRIFGE   85 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC---S--SSSEEEEEESSHHHHHHHHTT-TTCEETT
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC---C--CCCeEEEEeCCHHHHHHHHHh-CCeEecC
Confidence            3456788888999884 67788999999999988762   2  245889999999999999975 7776655

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=91.78  E-value=0.075  Score=55.06  Aligned_cols=57  Identities=19%  Similarity=0.241  Sum_probs=42.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHh
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK   92 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~   92 (451)
                      ..++|||. .|..+++.+|.++|++||+|.++.+-.+ .   .-|+.|+|.+.+++..++..
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~-~---g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYES-F---GLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECS-S---SEEEEEECC---CCHHHHSS
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEcc-C---CeEEEEEeCCHHHHHHHHhc
Confidence            46899998 7999999999999999999999887643 2   25999999999998877643

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=91.31  E-value=0.41  Score=39.72  Aligned_cols=53  Identities=15%  Similarity=0.190  Sum_probs=47.5

Q ss_pred             CCCCcHHHHHHHhccc-----CcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           99 KGKITEEEFKEHFGQY-----GDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        99 ~G~~tee~L~~~F~~f-----G~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ...+++..++.+.+++     |.+..+.+..|     -|-|+|+|.+...|.+|...++|..|
T Consensus        30 pDtvndarIr~lve~~~~i~~g~i~KI~L~pD-----H~GAivef~d~~~AgKasLaL~G~ef   87 (117)
T 2l9w_A           30 SDKVSPSLICQFLQEEIHINEKDIRKILLVSD-----FNGAIIIFRDSKFAAKMLMILNGSQF   87 (117)
T ss_dssp             CTTCCHHHHHHHHHHHTCCCTTTCSEEEEETT-----TTEEEEECSCHHHHHHHHHHHSSEEE
T ss_pred             CCCCCHHHHHHHHhhhhccCccceeEEEEecC-----CCceEEEEccchhhHHHHhhcCCeee
Confidence            4578999999999999     99999999887     34599999999999999999999876

>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=88.44  E-value=0.53  Score=39.60  Aligned_cols=48  Identities=25%  Similarity=0.405  Sum_probs=38.4

Q ss_pred             cHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          103 TEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       103 tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .-..+...|++||.|.+.....     ...+..|.|.++.+|.+|+.. |++++
T Consensus        36 ~~~~VL~~F~~~G~Iv~~~~~~-----~~NWihI~Y~s~~~A~rAL~k-NG~ii   83 (119)
T 1wwh_A           36 SASYILLQFAQYGNILKHVMSN-----TGNWMHIRYQSKLQARKALSK-DGRIF   83 (119)
T ss_dssp             GHHHHHHHHHTTSCEEEEEECS-----SSSEEEEEESSHHHHHHHHTT-TTCEE
T ss_pred             HHHHHHHHHHhhCcEEEeccCC-----CCCeEEEEeCCHHHHHHHHHh-CCeEe
Confidence            3467788999999999877621     257899999999999999966 66654

>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=81.00  E-value=2.2  Score=34.89  Aligned_cols=56  Identities=25%  Similarity=0.304  Sum_probs=44.5

Q ss_pred             cCCCCCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCccc
Q psy300           97 PYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK  157 (451)
Q Consensus        97 ~f~G~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~  157 (451)
                      +|...--.+.++++|..|+.+......+.     =.-..|.|.+.++|.+|...+++..+.
T Consensus        17 vF~~~~lk~~~e~Lf~~~~~~~tF~~lkS-----FRRirv~F~~~~~A~~AR~~Lh~~~f~   72 (104)
T 1wey_A           17 VFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLHKTEFL   72 (104)
T ss_dssp             GGSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTSTTSEET
T ss_pred             HcCCHHHHHHHHHHHHhhCcCcceeecCc-----ceEEEEEeCChHHHHHHHHHhccceec
Confidence            34433345789999999999998888875     224689999999999999999987663

---

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	451
d1e9ga_	284	b.40.5.1 (A:) Inorganic pyrophosphatase {Baker's y	2e-69
d1e9ga_	284	b.40.5.1 (A:) Inorganic pyrophosphatase {Baker's y	6e-13
d1twla_	173	b.40.5.1 (A:) Inorganic pyrophosphatase {Pyrococcu	2e-43
d1twla_	173	b.40.5.1 (A:) Inorganic pyrophosphatase {Pyrococcu	2e-08
d2prda_	174	b.40.5.1 (A:) Inorganic pyrophosphatase {Thermus t	1e-37
d2prda_	174	b.40.5.1 (A:) Inorganic pyrophosphatase {Thermus t	9e-06
d1i40a_	175	b.40.5.1 (A:) Inorganic pyrophosphatase {Escherich	1e-35
d1i40a_	175	b.40.5.1 (A:) Inorganic pyrophosphatase {Escherich	4e-05
d1qeza_	170	b.40.5.1 (A:) Inorganic pyrophosphatase {Archaeon	8e-35
d1qeza_	170	b.40.5.1 (A:) Inorganic pyrophosphatase {Archaeon	1e-06
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-14
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	8e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	6e-14
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	9e-06
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-04
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-13
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	6e-06
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-12
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-06
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-11
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-05
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-11
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-06
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	6e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	5e-05
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	9e-11
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-04
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	9e-11
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	1e-10
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-04
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-10
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	0.002
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-10
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	7e-05
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-10
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-04
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	4e-10
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	4e-10
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	5e-04
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 6e-10
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 4e-07
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	6e-10
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-04
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	6e-10
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	4e-04
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	9e-10
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-04
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	1e-09
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-09
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-09
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-09
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	3e-09
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	4e-09
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	5e-09
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	7e-09
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	7e-09
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	0.003
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-09
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-08
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-08
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-08
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	2e-08
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-08
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-08
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-08
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	3e-08
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	6e-08
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	9e-08
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	9e-08
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-04
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	9e-08
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	9e-08
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	2e-07
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-07
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-07
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-07
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	3e-07
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	4e-07
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	4e-07
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	4e-07
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	1e-06
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	1e-06
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	1e-06
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	3e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	3e-06
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	4e-06
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	4e-06
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	5e-06
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	7e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	9e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-05
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	2e-05
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-05
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	4e-05
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	4e-05
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	4e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	6e-05
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	0.003
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	8e-05
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	1e-04
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	1e-04
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	2e-04
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-04
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	4e-04
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	7e-04
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	9e-04
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	0.002

>d1e9ga_ b.40.5.1 (A:) Inorganic pyrophosphatase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 284

class: All beta proteins
fold: OB-fold
superfamily: Inorganic pyrophosphatase
family: Inorganic pyrophosphatase
domain: Inorganic pyrophosphatase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  219 bits (560), Expect = 2e-69
 Identities = 120/183 (65%), Positives = 145/183 (79%)

Query: 159 SENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYV 218
            +   +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+EI   E LNPI QD KKG LR+V
Sbjct: 21  KDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFV 80

Query: 219 ANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKAL 278
            N FPHHGYI NYGA PQTWE+P+ +   T   GD DPIDVLEIGE IA  G++ QVKAL
Sbjct: 81  RNCFPHHGYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKAL 140

Query: 279 GVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPE 338
           G++ L+DEG+TDWK+IAI++NDP A KLND+ D+E +FPG L+ATNEWF+IYKIPDGKPE
Sbjct: 141 GIMALLDEGETDWKVIAIDINDPLAPKLNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPE 200

Query: 339 NVL 341
           N  
Sbjct: 201 NQF 203

>d1e9ga_ b.40.5.1 (A:) Inorganic pyrophosphatase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 284

class: All beta proteins
fold: OB-fold
superfamily: Inorganic pyrophosphatase
family: Inorganic pyrophosphatase
domain: Inorganic pyrophosphatase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 66.9 bits (163), Expect = 6e-13
 Identities = 24/39 (61%), Positives = 32/39 (82%)

Query: 380 SENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
            +   +S FHDIPLY++ ++ IFNMVVEIPRWTNAK+E+
Sbjct: 21  KDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEI 59

>d1twla_ b.40.5.1 (A:) Inorganic pyrophosphatase {Pyrococcus furiosus [TaxId: 2261]} Length = 173

class: All beta proteins
fold: OB-fold
superfamily: Inorganic pyrophosphatase
family: Inorganic pyrophosphatase
domain: Inorganic pyrophosphatase
species: Pyrococcus furiosus [TaxId: 2261]

 Score =  148 bits (374), Expect = 2e-43
 Identities = 46/177 (25%), Positives = 77/177 (43%), Gaps = 27/177 (15%)

Query: 165 SPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPH 224
           +PFHD+    +V  ++   ++EIP+ +  K E+           D K G L+    ++  
Sbjct: 1   NPFHDLEPGPDV-PEVVYAIIEIPKGSRNKYEL-----------DKKTGLLKLDRVLYSP 48

Query: 225 HGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLI 284
             Y  +YG +P+TW                DP D++ I         II+ + +G+  +I
Sbjct: 49  FFYPVDYGIIPRTWYED------------DDPFDIMVIMREPVYPLTIIEARPIGLFKMI 96

Query: 285 DEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENVL 341
           D G  D+K++A+ V DP      D+ D+      +L     +FK YK   GK   V 
Sbjct: 97  DSGDKDYKVLAVPVEDPYFKDWKDIDDVP---KAFLDEIAHFFKRYKELQGKEIIVE 150

>d1twla_ b.40.5.1 (A:) Inorganic pyrophosphatase {Pyrococcus furiosus [TaxId: 2261]} Length = 173

class: All beta proteins
fold: OB-fold
superfamily: Inorganic pyrophosphatase
family: Inorganic pyrophosphatase
domain: Inorganic pyrophosphatase
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 51.5 bits (123), Expect = 2e-08
 Identities = 10/33 (30%), Positives = 20/33 (60%), Gaps = 1/33 (3%)

Query: 386 SPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV 418
           +PFHD+    +V  ++   ++EIP+ +  K E+
Sbjct: 1   NPFHDLEPGPDV-PEVVYAIIEIPKGSRNKYEL 32

>d2prda_ b.40.5.1 (A:) Inorganic pyrophosphatase {Thermus thermophilus [TaxId: 274]} Length = 174

class: All beta proteins
fold: OB-fold
superfamily: Inorganic pyrophosphatase
family: Inorganic pyrophosphatase
domain: Inorganic pyrophosphatase
species: Thermus thermophilus [TaxId: 274]

 Score =  133 bits (335), Expect = 1e-37
 Identities = 39/181 (21%), Positives = 72/181 (39%), Gaps = 29/181 (16%)

Query: 167 FHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHG 226
              +P+     + + +MV+E+PR +  K E            D   G ++    +     
Sbjct: 3   LKSLPVGDKAPE-VVHMVIEVPRGSGNKYEY-----------DPDLGAIKLDRVLPGAQF 50

Query: 227 YIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDE 286
           Y  +YG +P T               DGDP+D L +       G +++V+ +G++ + DE
Sbjct: 51  YPGDYGFIPSTLAE------------DGDPLDGLVLSTYPLLPGVVVEVRVVGLLLMEDE 98

Query: 287 GQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENVLNTRVE 346
              D K+I +   D     + D+ D+     G  +    +F+ YK  + K       +V 
Sbjct: 99  KGGDAKVIGVVAEDQRLDHIQDIGDV---PEGVKQEIQHFFETYKALEAKKGKW--VKVT 153

Query: 347 G 347
           G
Sbjct: 154 G 154

>d2prda_ b.40.5.1 (A:) Inorganic pyrophosphatase {Thermus thermophilus [TaxId: 274]} Length = 174

class: All beta proteins
fold: OB-fold
superfamily: Inorganic pyrophosphatase
family: Inorganic pyrophosphatase
domain: Inorganic pyrophosphatase
species: Thermus thermophilus [TaxId: 274]

 Score = 43.7 bits (103), Expect = 9e-06
 Identities = 13/61 (21%), Positives = 26/61 (42%), Gaps = 5/61 (8%)

Query: 388 FHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAM-EMRLYLVCFNL---PSPLGYLQLN 443
              +P+     + + +MV+E+PR +  K E    +  ++L  V       P   G++   
Sbjct: 3   LKSLPVGDKAPE-VVHMVIEVPRGSGNKYEYDPDLGAIKLDRVLPGAQFYPGDYGFIPST 61

Query: 444 L 444
           L
Sbjct: 62  L 62

>d1i40a_ b.40.5.1 (A:) Inorganic pyrophosphatase {Escherichia coli [TaxId: 562]} Length = 175

class: All beta proteins
fold: OB-fold
superfamily: Inorganic pyrophosphatase
family: Inorganic pyrophosphatase
domain: Inorganic pyrophosphatase
species: Escherichia coli [TaxId: 562]

 Score =  128 bits (322), Expect = 1e-35
 Identities = 35/177 (19%), Positives = 66/177 (37%), Gaps = 26/177 (14%)

Query: 167 FHDIPLYSNVKDKIFNMVVEIPRWT-NAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHH 225
             ++P   ++ +    +V+EIP      K EI           D + G L     +    
Sbjct: 2   LLNVPAGKDLPE-DIYVVIEIPANADPIKYEI-----------DKESGALFVDRFMSTAM 49

Query: 226 GYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLID 285
            Y  NYG +  T               DGDP+DVL       + G + + + +GV+ + D
Sbjct: 50  FYPCNYGYINHTLSL------------DGDPVDVLVPTPYPLQPGSVTRCRPVGVLKMTD 97

Query: 286 EGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGKPENVLN 342
           E   D K++A+  +  +  + + + D+             +F+ YK  +      + 
Sbjct: 98  EAGEDAKLVAVPHSKLS-KEYDHIKDVNDLPELLKAQIAHFFEHYKDLEKGKWVKVE 153

>d1i40a_ b.40.5.1 (A:) Inorganic pyrophosphatase {Escherichia coli [TaxId: 562]} Length = 175

class: All beta proteins
fold: OB-fold
superfamily: Inorganic pyrophosphatase
family: Inorganic pyrophosphatase
domain: Inorganic pyrophosphatase
species: Escherichia coli [TaxId: 562]

 Score = 41.8 bits (98), Expect = 4e-05
 Identities = 7/32 (21%), Positives = 15/32 (46%), Gaps = 2/32 (6%)

Query: 388 FHDIPLYSNVKDKIFNMVVEIPRWT-NAKMEV 418
             ++P   ++ +    +V+EIP      K E+
Sbjct: 2   LLNVPAGKDLPE-DIYVVIEIPANADPIKYEI 32

>d1qeza_ b.40.5.1 (A:) Inorganic pyrophosphatase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]} Length = 170

class: All beta proteins
fold: OB-fold
superfamily: Inorganic pyrophosphatase
family: Inorganic pyrophosphatase
domain: Inorganic pyrophosphatase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

 Score =  125 bits (315), Expect = 8e-35
 Identities = 43/173 (24%), Positives = 75/173 (43%), Gaps = 31/173 (17%)

Query: 164 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFP 223
           +SP  + P        + N++VEIP+ +N K E            D ++G ++    ++ 
Sbjct: 2   LSPGKNAP-------DVVNVLVEIPQGSNIKYEY-----------DDEEGVIKVDRVLYT 43

Query: 224 HHGYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGL 283
              Y +NYG +P T E             DGDP+DVL I       G +I+V+ +G++ +
Sbjct: 44  SMNYPFNYGFIPGTLEE------------DGDPLDVLVITNYQLYPGSVIEVRPIGILYM 91

Query: 284 IDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPDGK 336
            DE   D KI+A+  +       +++ DI             +F+ YK  +  
Sbjct: 92  KDEEGEDAKIVAVPKDK-TDPSFSNIKDINDLPQATKNKIVHFFEHYKELEPG 143

>d1qeza_ b.40.5.1 (A:) Inorganic pyrophosphatase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]} Length = 170

class: All beta proteins
fold: OB-fold
superfamily: Inorganic pyrophosphatase
family: Inorganic pyrophosphatase
domain: Inorganic pyrophosphatase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

 Score = 46.5 bits (110), Expect = 1e-06
 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 11/61 (18%)

Query: 385 ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEV----GNAMEMRLYLVCFNLPSPLGYL 440
           +SP  + P        + N++VEIP+ +N K E     G     R+     N P   G++
Sbjct: 2   LSPGKNAP-------DVVNVLVEIPQGSNIKYEYDDEEGVIKVDRVLYTSMNYPFNYGFI 54

Query: 441 Q 441
            
Sbjct: 55  P 55

>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 = 66.1 bits (161), Expect = 2e-14
 Identities = 18/69 (26%), Positives = 38/69 (55%)

Query: 33  GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
           G+L + NL F +++ + +E F ++G +  A +  +  G+  G   +++  K  A+KA+ +
Sbjct: 1   GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 60

Query: 93  SNKKPYKGK 101
            N  P  G+
Sbjct: 61  YNGVPLDGR 69

>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 = 44.5 bits (105), Expect = 8e-07
 Identities = 13/58 (22%), Positives = 30/58 (51%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            +++ + +E F ++G +  A +  +  G+  G   +++  K  A+KA+ + N  P  G
Sbjct: 11  GVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDG 68

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 67.7 bits (164), Expect = 6e-14
 Identities = 33/163 (20%), Positives = 66/163 (40%), Gaps = 36/163 (22%)

Query: 25  KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANK 83
           K+P++ ++  LFI  L F+ T+E  + HF Q+G + D  ++++ +  + +G GF+ YA  
Sbjct: 1   KEPEQLRK--LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 58

Query: 84  ISAVKAILKSNKKPYKGK--------------------------------ITEEEFKEHF 111
                A+     K                                       E   +++F
Sbjct: 59  EEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYF 118

Query: 112 GQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNK 153
            QYG I   +++ +   GK +G  F+ + +  S  K +++   
Sbjct: 119 EQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH 161

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.8 bits (102), Expect = 9e-06
 Identities = 15/86 (17%), Positives = 38/86 (44%), Gaps = 1/86 (1%)

Query: 11  KKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD- 69
             E K+   ++  ++        ++F+  +     E   +++F QYG I   +++ +   
Sbjct: 76  VVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGS 135

Query: 70  GKLKGCGFINYANKISAVKAILKSNK 95
           GK +G  F+ + +  S  K +++   
Sbjct: 136 GKKRGFAFVTFDDHDSVDKIVIQKYH 161

>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 = 38.8 bits (89), Expect = 4e-04
 Identities = 25/164 (15%), Positives = 51/164 (31%), Gaps = 15/164 (9%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKGS 159
           + T+E  + HF Q+G + D  ++++ +  + +G GF+ YA       A+     K     
Sbjct: 17  ETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRV 76

Query: 160 ENGLISPFHDIPLYSNVKDKIFN-MVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYV 218
                +   +          +    V  I   T      +  E    I+           
Sbjct: 77  VEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV--------IE 128

Query: 219 ANVFPHHGYIWNYGALPQTWENPDETDA---HTGQKGDGDPIDV 259
                  G    +  +  T+++ D  D          +G   +V
Sbjct: 129 IMTDRGSGKKRGFAFV--TFDDHDSVDKIVIQKYHTVNGHNCEV 170

>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 = 63.0 bits (153), Expect = 3e-13
 Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 3/78 (3%)

Query: 27  PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD--GKLKGCGFINYANKI 84
           P K    ++ ++N+PF+  + E +E F  +G++   +L K     G  +G GF+++  K 
Sbjct: 3   PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 62

Query: 85  SAVKAILK-SNKKPYKGK 101
            A KA     +     G+
Sbjct: 63  DAKKAFNALCHSTHLYGR 80

>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 = 42.2 bits (99), Expect = 6e-06
 Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 3/61 (4%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD--GKLKGCGFINYANKISAVKAILK-SNKKPYK 157
           +  + E +E F  +G++   +L K     G  +G GF+++  K  A KA     +     
Sbjct: 19  QANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLY 78

Query: 158 G 158
           G
Sbjct: 79  G 79

>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 = 59.9 bits (145), Expect = 3e-12
 Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 1/68 (1%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLK-GCGFINYANKISAVKAILKS 93
           L++ +L   +TE    E F   G I+  ++ ++   +   G  ++N+     A +A+   
Sbjct: 3   LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 62

Query: 94  NKKPYKGK 101
           N    KGK
Sbjct: 63  NFDVIKGK 70

>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 = 43.4 bits (102), Expect = 2e-06
 Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLK-GCGFINYANKISAVKAILKSNKKPYKG 158
            +TE    E F   G I+  ++ ++   +   G  ++N+     A +A+   N    KG
Sbjct: 11  DVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKG 69

>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 = 58.4 bits (141), Expect = 1e-11
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 1/74 (1%)

Query: 28  DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISA 86
           +  K   L++ NLP  IT+++    FG+YG I+   +L++          F+ Y  +  A
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 61

Query: 87  VKAILKSNKKPYKG 100
            +AI   N    +G
Sbjct: 62  QEAISALNNVIPEG 75

>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 = 41.1 bits (96), Expect = 1e-05
 Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILKSNKKPYKGS 159
            IT+++    FG+YG I+   +L++          F+ Y  +  A +AI   N    +G 
Sbjct: 17  TITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGG 76

Query: 160 E 160
            
Sbjct: 77  S 77

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.2 bits (138), Expect = 4e-11
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 8/78 (10%)

Query: 25  KKPDKTKRGRLFIKNL-PFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANK 83
           K   ++   R+FI NL    + + + +  F +YG I+   +        KG  F+ Y N+
Sbjct: 8   KTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNE 60

Query: 84  ISAVKAILKSNKKPYKGK 101
            +A  A+   + +   G+
Sbjct: 61  RNARAAVAGEDGRMIAGQ 78

>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 = 42.2 bits (99), Expect = 7e-06
 Identities = 12/57 (21%), Positives = 25/57 (43%), Gaps = 7/57 (12%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           + + + +  F +YG I+   + K       G  F+ Y N+ +A  A+   + +   G
Sbjct: 28  VKKSDVEAIFSKYGKIVGCSVHK-------GFAFVQYVNERNARAAVAGEDGRMIAG 77

>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 = 57.3 bits (138), Expect = 6e-11
 Identities = 27/114 (23%), Positives = 44/114 (38%), Gaps = 22/114 (19%)

Query: 25  KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKI 84
           + P +  R  L+I+NLP+KIT EE  + FG+YG I   +       + +G  ++ Y +  
Sbjct: 1   RLPPEVNR-ILYIRNLPYKITAEEMYDIFGKYGPIRQIR--VGNTPETRGTAYVVYEDIF 57

Query: 85  SAVKAILKSNKKPYKGKI-------------------TEEEFKEHFGQYGDIID 119
            A  A    +      +                     EE+ K    +YG   D
Sbjct: 58  DAKNACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTD 111

>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 = 40.4 bits (94), Expect = 5e-05
 Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 2/58 (3%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           KIT EE  + FG+YG I   +       + +G  ++ Y +   A  A    +      
Sbjct: 18  KITAEEMYDIFGKYGPIRQIR--VGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCN 73

>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 = 55.4 bits (133), Expect = 9e-11
 Identities = 15/69 (21%), Positives = 39/69 (56%), Gaps = 2/69 (2%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILK 92
           ++FI  L ++ T+E  +E+FGQ+G++ +  ++++    + +G GF+ + ++    K +  
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-A 60

Query: 93  SNKKPYKGK 101
            ++     K
Sbjct: 61  QSRHELDSK 69

>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 = 38.0 bits (88), Expect = 1e-04
 Identities = 12/55 (21%), Positives = 33/55 (60%), Gaps = 1/55 (1%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKK 154
           + T+E  +E+FGQ+G++ +  ++++    + +G GF+ + ++    K + +S  +
Sbjct: 11  QTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHE 65

>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 = 56.2 bits (135), Expect = 9e-11
 Identities = 22/83 (26%), Positives = 45/83 (54%), Gaps = 2/83 (2%)

Query: 20  KKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFI 78
             +ERKK +K +  +LFI  L F+ TEE  + ++ Q+G + D  ++++ A  + +G GF+
Sbjct: 8   VPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFV 67

Query: 79  NYANKISAVKAILKSNKKPYKGK 101
            +++      A+  +      G+
Sbjct: 68  TFSSMAEVDAAM-AARPHSIDGR 89

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 55.0 bits (132), Expect = 1e-10
 Identities = 15/69 (21%), Positives = 32/69 (46%), Gaps = 1/69 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILK 92
            L +  LP  +T+ E    F   G I   +++++   G   G  F+++ +++ + +AI  
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 93  SNKKPYKGK 101
            N    + K
Sbjct: 64  LNGITVRNK 72

>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 = 37.7 bits (87), Expect = 2e-04
 Identities = 11/58 (18%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           +T+ E    F   G I   +++++   G   G  F+++ +++ + +AI   N    + 
Sbjct: 14  MTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRN 71

>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 = 55.4 bits (133), Expect = 2e-10
 Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 29  KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVK 88
           K+  G +FIKNL   I  +   + F  +G+I+  +++ + +G  KG GF+++  + +A +
Sbjct: 5   KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS-KGYGFVHFETQEAAER 63

Query: 89  AILKSNKKPYKGK 101
           AI K N      +
Sbjct: 64  AIEKMNGMLLNDR 76

>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 = 35.0 bits (80), Expect = 0.002
 Identities = 14/58 (24%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            I  +   + F  +G+I+  +++ + +G  KG GF+++  + +A +AI K N      
Sbjct: 19  SIDNKALYDTFSAFGNILSCKVVCDENGS-KGYGFVHFETQEAAERAIEKMNGMLLND 75

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 2e-10
 Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 2/69 (2%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLK--GCGFINYANKISAVKAILK 92
           +FI NL  +I E+   + F  +G I+    +          G  FIN+A+  ++  AI  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 93  SNKKPYKGK 101
            N +    +
Sbjct: 61  MNGQYLCNR 69

>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 = 39.0 bits (90), Expect = 7e-05
 Identities = 13/59 (22%), Positives = 23/59 (38%), Gaps = 2/59 (3%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLK--GCGFINYANKISAVKAILKSNKKPYKG 158
           I E+   + F  +G I+    +          G  FIN+A+  ++  AI   N +    
Sbjct: 10  IDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCN 68

>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 = 54.7 bits (131), Expect = 2e-10
 Identities = 23/71 (32%), Positives = 29/71 (40%), Gaps = 4/71 (5%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD----GKLKGCGFINYANKISAVKAI 90
           LFIKNL F  TEE  K  F + G I    + K  +        G GF+ Y     A KA+
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 91  LKSNKKPYKGK 101
            +       G 
Sbjct: 61  KQLQGHTVDGH 71

>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 = 38.1 bits (88), Expect = 2e-04
 Identities = 16/62 (25%), Positives = 22/62 (35%), Gaps = 4/62 (6%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNAD----GKLKGCGFINYANKISAVKAILKSNKKPY 156
             TEE  K  F + G I    + K  +        G GF+ Y     A KA+ +      
Sbjct: 9   STTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTV 68

Query: 157 KG 158
            G
Sbjct: 69  DG 70

>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 = 54.2 bits (130), Expect = 4e-10
 Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 30  TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 89
           T+R RLF+ NLP  ITEEE ++ F +YG   +  + K+        GFI    +  A  A
Sbjct: 6   TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG-----FGFIRLETRTLAEIA 60

Query: 90  ILKSNKKPYKGK 101
            ++ +  P +GK
Sbjct: 61  KVELDNMPLRGK 72

>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 = 54.2 bits (130), Expect = 4e-10
 Identities = 19/70 (27%), Positives = 30/70 (42%), Gaps = 1/70 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILK 92
            L++ NL F  TEE+  E F + GDI    +  +       G  F+ Y ++  A  A+  
Sbjct: 9   TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 68

Query: 93  SNKKPYKGKI 102
            N      +I
Sbjct: 69  INGTRLDDRI 78

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.9 bits (85), Expect = 5e-04
 Identities = 14/59 (23%), Positives = 22/59 (37%), Gaps = 1/59 (1%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
             TEE+  E F + GDI    +  +       G  F+ Y ++  A  A+   N      
Sbjct: 18  YTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDD 76

>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 = 54.3 bits (130), Expect = 6e-10
 Identities = 15/89 (16%), Positives = 37/89 (41%)

Query: 19  KKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFI 78
           +   +     ++    + ++    +  EE F E   +YG++ +  +  N    L G  ++
Sbjct: 14  QNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYV 73

Query: 79  NYANKISAVKAILKSNKKPYKGKITEEEF 107
            +  +  A KA++  N + + G+    E 
Sbjct: 74  KFRREEDAEKAVIDLNNRWFNGQPIHAEL 102

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Splicing factor U2AF subunits
domain: U2AF35 (35 KDa subunit)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 4e-07
 Identities = 14/58 (24%), Positives = 28/58 (48%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
           +  EE F E   +YG++ +  +  N    L G  ++ +  +  A KA++  N + + G
Sbjct: 38  EFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNG 95

>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 = 53.5 bits (128), Expect = 6e-10
 Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 31  KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLK-GCGFINYANKISAVKA 89
           +   L++  LP  +T++E ++ F QYG II +++L +    +  G GFI +  +I A +A
Sbjct: 5   RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 64

Query: 90  ILKSNKKPYKGK 101
           I   N +   G 
Sbjct: 65  IKGLNGQKPSGA 76

>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 = 37.3 bits (86), Expect = 3e-04
 Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLK-GCGFINYANKISAVKAILKSNKKPYKGS 159
            +T++E ++ F QYG II +++L +    +  G GFI +  +I A +AI   N +   G+
Sbjct: 17  TMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGA 76

Query: 160 E 160
            
Sbjct: 77  T 77

>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 = 53.8 bits (129), Expect = 6e-10
 Identities = 12/87 (13%), Positives = 35/87 (40%), Gaps = 8/87 (9%)

Query: 15  KKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKG 74
           + + +  + +  P       ++   +   +T++  ++ F  +G I++ ++          
Sbjct: 4   QLRFEDVVNQSSPKNC---TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG----- 55

Query: 75  CGFINYANKISAVKAILKSNKKPYKGK 101
             F+ ++   SA  AI+  N    +G 
Sbjct: 56  YSFVRFSTHESAAHAIVSVNGTTIEGH 82

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.3 bits (86), Expect = 4e-04
 Identities = 11/58 (18%), Positives = 26/58 (44%), Gaps = 5/58 (8%)

Query: 101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            +T++  ++ F  +G I++ ++            F+ ++   SA  AI+  N    +G
Sbjct: 29  GLTDQLMRQTFSPFGQIMEIRVFPEKG-----YSFVRFSTHESAAHAIVSVNGTTIEG 81

>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 = 53.2 bits (127), Expect = 9e-10
 Identities = 14/74 (18%), Positives = 29/74 (39%), Gaps = 7/74 (9%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLK------NADGKLKGCGFINYANKISAV 87
           RL++ N+PF ITEE   + F     +                 + K   F+ + +     
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 88  KAILKSNKKPYKGK 101
           +A+   +   ++G+
Sbjct: 63  QAMAF-DGIIFQGQ 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 = 37.0 bits (85), Expect = 5e-04
 Identities = 8/59 (13%), Positives = 16/59 (27%), Gaps = 6/59 (10%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLK------NADGKLKGCGFINYANKISAVKAILKSNKK 154
           ITEE   + F     +                 + K   F+ + +     +A+      
Sbjct: 13  ITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGII 71

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.1 bits (127), Expect = 1e-09
 Identities = 23/74 (31%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 28  DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAV 87
            K+   RL + N+PF+  + + ++ FGQ+G I+D +++ N  G  KG GF+ + N   A 
Sbjct: 7   SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS-KGFGFVTFENSADAD 65

Query: 88  KAILKSNKKPYKGK 101
           +A  K +    +G+
Sbjct: 66  RAREKLHGTVVEGR 79

>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 = 52.8 bits (126), Expect = 1e-09
 Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 3/79 (3%)

Query: 24  RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKG-CGFINYAN 82
           R  PD      L +  L    TE + +E F +YG I D  ++ +   +      F+ + N
Sbjct: 3   RANPDPNCC--LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 60

Query: 83  KISAVKAILKSNKKPYKGK 101
              A +A  ++N     G+
Sbjct: 61  VDDAKEAKERANGMELDGR 79

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 1e-09
 Identities = 17/75 (22%), Positives = 30/75 (40%), Gaps = 2/75 (2%)

Query: 27  PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA 86
           P      R+++ NLP  I  ++ ++ F +YG I D  L            F+ + +   A
Sbjct: 9   PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKN--RRGGPPFAFVEFEDPRDA 66

Query: 87  VKAILKSNKKPYKGK 101
             A+   +   Y G 
Sbjct: 67  EDAVYGRDGYDYDGY 81

>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 = 51.6 bits (123), Expect = 3e-09
 Identities = 15/76 (19%), Positives = 33/76 (43%), Gaps = 1/76 (1%)

Query: 27  PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKG-CGFINYANKIS 85
            ++ +   +++  L  K++E    E F Q G +++  + K+         GF+ + ++  
Sbjct: 4   SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED 63

Query: 86  AVKAILKSNKKPYKGK 101
           A  AI   +     GK
Sbjct: 64  ADYAIKIMDMIKLYGK 79

>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 = 51.3 bits (122), Expect = 3e-09
 Identities = 24/71 (33%), Positives = 38/71 (53%), Gaps = 1/71 (1%)

Query: 32  RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAI 90
           +  L +  LP  +T+EEF+  FG  G+I   +L+++   G+  G GF+NY +   A KAI
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 91  LKSNKKPYKGK 101
              N    + K
Sbjct: 62  NTLNGLRLQTK 72

>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 = 51.2 bits (122), Expect = 4e-09
 Identities = 18/69 (26%), Positives = 29/69 (42%), Gaps = 1/69 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVKAILK 92
           +LFI  LP  + +++ KE    +G +     +  +A G  KG  F  Y +     +AI  
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 93  SNKKPYKGK 101
            N      K
Sbjct: 63  LNGMQLGDK 71

>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 = 50.8 bits (121), Expect = 5e-09
 Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 3/73 (4%)

Query: 25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANK 83
          K+P++ ++  LFI  L F+ T+E  + HF Q+G + D  ++++ +  + +G GF+ YA  
Sbjct: 1  KEPEQLRK--LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 58

Query: 84 ISAVKAILKSNKK 96
               A+     K
Sbjct: 59 EEVDAAMNARPHK 71

>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 = 50.8 bits (121), Expect = 7e-09
 Identities = 12/88 (13%), Positives = 36/88 (40%), Gaps = 2/88 (2%)

Query: 15  KKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADG-KLK 73
           K   ++ ++   P++     +F   L  +I   + ++ F   G + D +++ + +  + K
Sbjct: 1   KSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK 60

Query: 74  GCGFINYANKISAVKAILKSNKKPYKGK 101
           G  ++ +     +V   +    +   G 
Sbjct: 61  GIAYVEFCEI-QSVPLAIGLTGQRLLGV 87

>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 = 51.2 bits (122), Expect = 7e-09
 Identities = 12/64 (18%), Positives = 29/64 (45%), Gaps = 3/64 (4%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
          R+ ++NL + +T +   + F ++G ++            +    + YA+ +SA  A L  
Sbjct: 9  RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSL 65

Query: 94 NKKP 97
          + + 
Sbjct: 66 DGQN 69

>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 = 35.0 bits (80), Expect = 0.003
 Identities = 9/54 (16%), Positives = 22/54 (40%), Gaps = 3/54 (5%)

Query: 102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP 155
           +T +   + F ++G ++            +    + YA+ +SA  A L  + + 
Sbjct: 19  VTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDGQN 69

>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 = 50.0 bits (119), Expect = 9e-09
 Identities = 16/70 (22%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILK 92
           ++FI  L +  T+++ K++F ++G+++D  L  +      +G GF+ +    S  K +  
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-D 59

Query: 93  SNKKPYKGKI 102
             +    GK+
Sbjct: 60  QKEHKLNGKV 69

>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 = 49.6 bits (118), Expect = 1e-08
 Identities = 13/64 (20%), Positives = 28/64 (43%), Gaps = 1/64 (1%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILK 92
          ++F+  L     EE+ +E+FG +G++   +L  +     +    FI +  +    K + K
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 93 SNKK 96
              
Sbjct: 61 KYHN 64

>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 = 50.1 bits (119), Expect = 1e-08
 Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 1/70 (1%)

Query: 33  GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAIL 91
           GRLF++NL +  +EE+ ++ F  YG + +     ++  K  KG  F+ +     AVKA  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 92  KSNKKPYKGK 101
           + + + ++G+
Sbjct: 69  EVDGQVFQGR 78

>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 = 49.7 bits (118), Expect = 1e-08
 Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 4/77 (5%)

Query: 26  KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKI 84
           KP  T    + ++N+PF ++ +E  + F  Y  I  +  L  N  G   G   + + ++ 
Sbjct: 6   KPGPTI---IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRD 62

Query: 85  SAVKAILKSNKKPYKGK 101
            A  A++  N +P   +
Sbjct: 63  EATAAVIDLNDRPIGSR 79

>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 = 49.7 bits (118), Expect = 2e-08
 Identities = 25/81 (30%), Positives = 37/81 (45%), Gaps = 8/81 (9%)

Query: 25  KKPDKTKRGR----LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINY 80
           + P  +K+ R    L  KNL F ITE+E KE F    +I         DGK KG  +I +
Sbjct: 5   EDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEF 60

Query: 81  ANKISAVKAILKSNKKPYKGK 101
            ++  A K + +       G+
Sbjct: 61  KSEADAEKNLEEKQGAEIDGR 81

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.3 bits (117), Expect = 2e-08
 Identities = 15/74 (20%), Positives = 27/74 (36%), Gaps = 1/74 (1%)

Query: 28  DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAV 87
           D  +   L++ NL   +TE    + F Q G     +++           F+ +     A 
Sbjct: 4   DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE-HTSNDPYCFVEFYEHRDAA 62

Query: 88  KAILKSNKKPYKGK 101
            A+   N +   GK
Sbjct: 63  AALAAMNGRKILGK 76

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.2 bits (117), Expect = 2e-08
 Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 3/73 (4%)

Query: 24 RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYAN 82
          ++   KT    L +  LP+K TE++ KE+F  +G+++  Q+ K+      KG GF+ +  
Sbjct: 2  KRAVQKTSD--LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTE 59

Query: 83 KISAVKAILKSNK 95
            + VK + + + 
Sbjct: 60 YETQVKVMSQRHM 72

>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 = 48.9 bits (116), Expect = 3e-08
 Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 2/74 (2%)

Query: 29  KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAV 87
            TKR  L++  L  ++ ++     F  +GDI D Q+  + + +  +G  F+ +     A 
Sbjct: 3   TTKR-VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 61

Query: 88  KAILKSNKKPYKGK 101
            AI   N+    G+
Sbjct: 62  AAIDNMNESELFGR 75

>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 = 48.9 bits (116), Expect = 3e-08
 Identities = 20/88 (22%), Positives = 39/88 (44%), Gaps = 4/88 (4%)

Query: 15  KKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIID-AQLLKNADGKLK 73
           +  G    +++ P+      LFI +LP +  +++  + F  +G+++     +       K
Sbjct: 4   QSIGAAGSQKEGPEGAN---LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 60

Query: 74  GCGFINYANKISAVKAILKSNKKPYKGK 101
             GF++Y N +SA  AI   N      K
Sbjct: 61  CFGFVSYDNPVSAQAAIQSMNGFQIGMK 88

>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 = 47.8 bits (113), Expect = 6e-08
 Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 5/63 (7%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
          +L+I NL   +T ++ ++ FG     +  Q+         G  F++Y ++  A++AI   
Sbjct: 3  KLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-----LLKSGYAFVDYPDQNWAIRAIETL 57

Query: 94 NKK 96
          + K
Sbjct: 58 SGK 60

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (112), Expect = 9e-08
 Identities = 15/72 (20%), Positives = 33/72 (45%), Gaps = 5/72 (6%)

Query: 30  TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 89
           +    L+++NL    +EE  ++ F         ++      K++   F++++N+  AV+A
Sbjct: 6   SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAVEA 60

Query: 90  ILKSNKKPYKGK 101
           +   N K   G 
Sbjct: 61  MKALNGKVLDGS 72

>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 = 47.9 bits (113), Expect = 9e-08
 Identities = 17/74 (22%), Positives = 27/74 (36%), Gaps = 10/74 (13%)

Query: 34  RLFIKNLPFKITEE-----EFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVK 88
            L        +  E     +F+  F  Y      Q  K+          IN++N +SA  
Sbjct: 7   GLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAAD 61

Query: 89  AILKSNKKPYKGKI 102
           A L+ +K  + GK 
Sbjct: 62  ARLRLHKTEFLGKE 75

>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 = 39.0 bits (90), Expect = 1e-04
 Identities = 16/65 (24%), Positives = 26/65 (40%), Gaps = 5/65 (7%)

Query: 94  NKKPYKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK 153
           N   +    T  +F+  F  Y      Q  K+          IN++N +SA  A L+ +K
Sbjct: 14  NDDVFSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLHK 68

Query: 154 KPYKG 158
             + G
Sbjct: 69  TEFLG 73

>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 = 47.8 bits (113), Expect = 9e-08
 Identities = 15/69 (21%), Positives = 24/69 (34%), Gaps = 3/69 (4%)

Query: 34 RLFIKNLPFKITEEEFKEHFGQYGDI---IDAQLLKNADGKLKGCGFINYANKISAVKAI 90
          RLFI  +P     EE  E   +  +    +          K +G  F+ Y +  +A  A 
Sbjct: 3  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 91 LKSNKKPYK 99
           K      +
Sbjct: 63 RKLMPGRIQ 71

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (112), Expect = 9e-08
 Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 4/80 (5%)

Query: 24  RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYAN 82
           R+  D      + + NL     E + +E F  +G I    L K+   G+ KG  FI++  
Sbjct: 3   RRADDNAT---IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHR 59

Query: 83  KISAVKAILKSNKKPYKGKI 102
           +  A +AI   +   Y   I
Sbjct: 60  REDAARAIAGVSGFGYDHLI 79

>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 = 46.7 bits (110), Expect = 2e-07
 Identities = 20/70 (28%), Positives = 38/70 (54%), Gaps = 1/70 (1%)

Query: 33  GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGK-LKGCGFINYANKISAVKAIL 91
           G+LF+  L F   E+  ++ F +YG I +  ++K+ + +  +G GF+ + N   A  A++
Sbjct: 6   GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 65

Query: 92  KSNKKPYKGK 101
             N K   G+
Sbjct: 66  AMNGKSVDGR 75

>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 = 46.6 bits (110), Expect = 2e-07
 Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 10/80 (12%)

Query: 26  KPDKTKRGRLFIKNLPFKITEEEFKEH----FGQYGDIIDAQLLKNADGKLKGCGFINYA 81
           +P+ T    ++I NL  KI ++E K+     F ++G I+D  + ++     +G  F+ + 
Sbjct: 1   RPNHT----IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM--RGQAFVIFK 54

Query: 82  NKISAVKAILKSNKKPYKGK 101
              SA  A+      P+  K
Sbjct: 55  EVSSATNALRSMQGFPFYDK 74

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.0 bits (111), Expect = 2e-07
 Identities = 14/78 (17%), Positives = 28/78 (35%), Gaps = 1/78 (1%)

Query: 24  RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANK 83
            + P        F+ NLP+ +TEE  KE F            + ++ +            
Sbjct: 8   SRLPKSPPY-TAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFED 66

Query: 84  ISAVKAILKSNKKPYKGK 101
           + ++ + L  N++    K
Sbjct: 67  LDSLLSALSLNEESLGNK 84

>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 = 46.3 bits (109), Expect = 2e-07
 Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 1/82 (1%)

Query: 28  DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAV 87
           +  K   ++IK  P   T ++ KE     G +++ Q+ +      KG  F+ + +  SA 
Sbjct: 2   NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAK 61

Query: 88  KAILKSNKKPYKGKITEEEFKE 109
           K + ++  + YK       FK+
Sbjct: 62  KFV-ETPGQKYKETDLLILFKD 82

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 46.3 bits (109), Expect = 2e-07
 Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 2/77 (2%)

Query: 27  PDKTKRGR-LFIKNLPFKITEEEFKEHFGQYGDII-DAQLLKNADGKLKGCGFINYANKI 84
           P ++  G  LF+ ++  +  E+E +E F  YG+I      L    G  KG   + Y    
Sbjct: 1   PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 60

Query: 85  SAVKAILKSNKKPYKGK 101
            A+ A    N     G+
Sbjct: 61  QALAAKEALNGAEIMGQ 77

>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 = 46.3 bits (109), Expect = 3e-07
 Identities = 14/84 (16%), Positives = 34/84 (40%), Gaps = 9/84 (10%)

Query: 27  PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN---------ADGKLKGCGF 77
            + +    ++++ L   +T ++  + F Q G +   +               GK KG   
Sbjct: 3   DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDAT 62

Query: 78  INYANKISAVKAILKSNKKPYKGK 101
           ++Y +  +A  A+   + K ++G 
Sbjct: 63  VSYEDPPTAKAAVEWFDGKDFQGS 86

>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 = 46.3 bits (109), Expect = 4e-07
 Identities = 19/76 (25%), Positives = 40/76 (52%), Gaps = 2/76 (2%)

Query: 22 IERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADG-KLKGCGFINY 80
          +   + D T   ++F+  LP+  T+   +++F  +GDI +A ++ +    K +G GF+  
Sbjct: 1  MHGSQKDTTFT-KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTM 59

Query: 81 ANKISAVKAILKSNKK 96
          A++ +A +A    N  
Sbjct: 60 ADRAAAERACKDPNPI 75

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 4e-07
 Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 6/68 (8%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
            +F+      +TE+E +E F QYGD++D  + K          F+ +A+   A       
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR----AFAFVTFADDQIAQSLC--G 60

Query: 94  NKKPYKGK 101
                KG 
Sbjct: 61  EDLIIKGI 68

>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 = 45.1 bits (106), Expect = 4e-07
 Identities = 16/69 (23%), Positives = 32/69 (46%), Gaps = 2/69 (2%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFINYANKISAVKAILK 92
           ++F+  L    T E+ K +F Q+G + DA L+ +      +G GF+ + ++    K   +
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-E 59

Query: 93  SNKKPYKGK 101
            +      K
Sbjct: 60  IHFHEINNK 68

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 44.0 bits (103), Expect = 1e-06
 Identities = 11/69 (15%), Positives = 24/69 (34%), Gaps = 1/69 (1%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDII-DAQLLKNADGKLKGCGFINYANKISAVKAILK 92
            L++ N P   T+   ++       +    +L        +   +I+  +K  A   + K
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 93  SNKKPYKGK 101
            N    +G 
Sbjct: 63  LNGLKIEGY 71

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.0 bits (103), Expect = 1e-06
 Identities = 13/68 (19%), Positives = 22/68 (32%), Gaps = 6/68 (8%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
            + +KNLP     +E  +    Y                    F+   N   A  AI   
Sbjct: 7   GILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNK------RTAFVTLLNGEQAQNAIQMF 60

Query: 94  NKKPYKGK 101
           ++  ++GK
Sbjct: 61  HQYSFRGK 68

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 44.2 bits (103), Expect = 1e-06
 Identities = 15/79 (18%), Positives = 29/79 (36%), Gaps = 2/79 (2%)

Query: 18 GKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGF 77
          G   +E  +        LFI NL    +  E K    +     D  ++    G  +  G+
Sbjct: 1  GSHMVEGSESTTPFN--LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGY 58

Query: 78 INYANKISAVKAILKSNKK 96
          +++ +     KA+  +  K
Sbjct: 59 VDFESAEDLEKALELTGLK 77

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.6 bits (102), Expect = 3e-06
 Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 1/87 (1%)

Query: 15  KKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKG 74
           K  G +    K+ ++     L+I NLP  + E+E +     +G +I  ++L+++ G  +G
Sbjct: 2   KASGVQAQMAKQQEQDPT-NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRG 60

Query: 75  CGFINYANKISAVKAILKSNKKPYKGK 101
            GF    +       I   N K  K  
Sbjct: 61  VGFARMESTEKCEAVIGHFNGKFIKTP 87

>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 = 44.1 bits (103), Expect = 3e-06
 Identities = 19/98 (19%), Positives = 48/98 (48%), Gaps = 3/98 (3%)

Query: 5   AKKKKVKKEFKKKGKKKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQL 64
           A+ ++++++ ++         +PD  +   L +  +P  + E + ++ F +YG I   ++
Sbjct: 17  AQLQQLQQQQQQHIPPTQMNPEPDVLRN--LMVNYIPTTVDEVQLRQLFERYGPIESVKI 74

Query: 65  LKNADG-KLKGCGFINYANKISAVKAILKSNKKPYKGK 101
           + + +  + +G GF+ + +  SA +AI   N      K
Sbjct: 75  VCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNK 112

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 42.9 bits (100), Expect = 4e-06
 Identities = 14/79 (17%), Positives = 31/79 (39%), Gaps = 7/79 (8%)

Query: 31  KRGRLFIKNLPFKITEEE---FKEHFGQYGDIIDAQLLKNADGK----LKGCGFINYANK 83
           ++  +F+  L  ++ + E     E+FG++G I    +  +             ++ Y   
Sbjct: 7   QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRS 66

Query: 84  ISAVKAILKSNKKPYKGKI 102
             A++AI   N     G+ 
Sbjct: 67  EDALRAIQCVNNVVVDGRT 85

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.4 bits (99), Expect = 4e-06
 Identities = 15/69 (21%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNAD-GKLKGCGFINYANKISAVKAILKS 93
           L+I+ L    T+++  +    YG I+  + + +    K KG GF+++ +  +A KA+   
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 94  NKKPYKGKI 102
                + ++
Sbjct: 61  KASGVQAQM 69

>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 = 42.7 bits (100), Expect = 5e-06
 Identities = 18/81 (22%), Positives = 28/81 (34%), Gaps = 7/81 (8%)

Query: 21  KIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINY 80
           KI   K + T R  L++  L    +       F ++G I     +K          +I Y
Sbjct: 8   KIGYGKANPTTR--LWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS-----FAYIQY 60

Query: 81  ANKISAVKAILKSNKKPYKGK 101
            +  +A  A  K    P  G 
Sbjct: 61  ESLDAAQAACAKMRGFPLGGP 81

>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 = 42.9 bits (100), Expect = 6e-06
 Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 1/79 (1%)

Query: 25  KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANK 83
             PD    G + ++ LPF  ++EE  + F     + +   L  +  G+  G  F+ +A++
Sbjct: 8   NSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQ 67

Query: 84  ISAVKAILKSNKKPYKGKI 102
             A KA+ K  ++     I
Sbjct: 68  EIAEKALKKHKERIGHRYI 86

>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 = 42.5 bits (99), Expect = 7e-06
 Identities = 20/79 (25%), Positives = 38/79 (48%), Gaps = 2/79 (2%)

Query: 27  PDKTKRGR-LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLK-GCGFINYANKI 84
           P     G+ +FI+NL F   EE   E   Q+GD+   +++ + D +   GC F  +  + 
Sbjct: 2   PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 61

Query: 85  SAVKAILKSNKKPYKGKIT 103
           +A K +  ++ +   G + 
Sbjct: 62  AAQKCLAAASLEAEGGGLK 80

>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 = 42.1 bits (98), Expect = 9e-06
 Identities = 22/77 (28%), Positives = 43/77 (55%), Gaps = 2/77 (2%)

Query: 26  KPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKI 84
             D++ R  +F+ N+P++ TEE+ K+ F + G ++    +     GK KG GF  Y ++ 
Sbjct: 3   AVDRSLR-SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQE 61

Query: 85  SAVKAILKSNKKPYKGK 101
           +A+ A+   N + + G+
Sbjct: 62  TALSAMRNLNGREFSGR 78

>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 = 41.3 bits (96), Expect = 2e-05
 Identities = 9/64 (14%), Positives = 23/64 (35%), Gaps = 5/64 (7%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
          + ++ L   + E +  E   ++G I    ++            + + N  SA + +  + 
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR-----QALVEFENIDSAKECVTFAA 72

Query: 95 KKPY 98
            P 
Sbjct: 73 DVPV 76

>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 = 41.0 bits (95), Expect = 2e-05
 Identities = 18/87 (20%), Positives = 39/87 (44%), Gaps = 8/87 (9%)

Query: 30  TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVK 88
           + +    I N+PF IT+ +  +         +A  +L + +G+  G   + + N+  A K
Sbjct: 6   SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARK 65

Query: 89  AILKSNKKPYKG------KITEEEFKE 109
           +  + ++K   G       +T E+ +E
Sbjct: 66  SE-RLHRKKLNGREAFVHVVTLEDMRE 91

>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 = 40.1 bits (93), Expect = 3e-05
 Identities = 12/69 (17%), Positives = 28/69 (40%), Gaps = 2/69 (2%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGC-GFINYANKISAVKAILK 92
           ++F+  +     E   +++F QYG I   +++ +     K    F+ + +   +V  I+ 
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKIVI 62

Query: 93  SNKKPYKGK 101
                  G 
Sbjct: 63  QKYHTVNGH 71

>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 = 39.5 bits (91), Expect = 4e-05
 Identities = 14/76 (18%), Positives = 26/76 (34%), Gaps = 6/76 (7%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
           + I+ LP  +T +E  +    Y              K KG  F+   N   A  AI   +
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYELKYC------FVDKYKGTAFVTLLNGEQAEAAINTFH 54

Query: 95  KKPYKGKITEEEFKEH 110
           +   + +    + +  
Sbjct: 55  QSRLRERELSVQLQPT 70

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.1 bits (93), Expect = 4e-05
 Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 6/75 (8%)

Query: 27  PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISA 86
           P +    R+ +  LP   + ++ K+H  + GD+  A + K+      G G + Y  K   
Sbjct: 10  PTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD------GMGMVEYLRKEDM 63

Query: 87  VKAILKSNKKPYKGK 101
             A+ K +   ++  
Sbjct: 64  EYALRKLDDTKFRSH 78

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 39.4 bits (91), Expect = 4e-05
 Identities = 15/62 (24%), Positives = 27/62 (43%), Gaps = 1/62 (1%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
          + +KNLP    + +  ++F   G II   +  +          I +A    A+ AI K++
Sbjct: 3  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN-FRFARIEFARYDGALAAITKTH 61

Query: 95 KK 96
          K 
Sbjct: 62 KV 63

>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 = 39.9 bits (93), Expect = 6e-05
 Identities = 13/102 (12%), Positives = 32/102 (31%), Gaps = 18/102 (17%)

Query: 24  RKKPDKTKRGRLFIKNL-----------PFKITEEEFKEHFGQYGDIIDAQLLKNADGKL 72
           R + ++     + IKN+                 E+ +    ++G I         D   
Sbjct: 4   RMRHERV----VIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKL---LLFDRHP 56

Query: 73  KGCGFINYANKISAVKAILKSNKKPYKGKITEEEFKEHFGQY 114
            G   +++ +   A   I   + + + G+    +  +    Y
Sbjct: 57  DGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDY 98

>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 = 34.9 bits (80), Expect = 0.003
 Identities = 8/55 (14%), Positives = 19/55 (34%), Gaps = 3/55 (5%)

Query: 104 EEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG 158
            E+ +    ++G I         D    G   +++ +   A   I   + + + G
Sbjct: 33  REDLRVECSKFGQIRKL---LLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGG 84

>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 = 39.3 bits (91), Expect = 8e-05
 Identities = 9/67 (13%), Positives = 20/67 (29%), Gaps = 5/67 (7%)

Query: 30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKA 89
          T+   +    L   ++  +      + G +    +  N         F  Y     + +A
Sbjct: 18 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP-----YSFARYRTTEESKRA 72

Query: 90 ILKSNKK 96
           +  N K
Sbjct: 73 YVTLNGK 79

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (89), Expect = 1e-04
 Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 3/63 (4%)

Query: 35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
          L + N+P  ++EE+ K  F   G ++          K +    I   +   AV+A++  +
Sbjct: 13 LHLSNIPPSVSEEDLKVLFSSNGGVVKG---FKFFQKDRKMALIQMGSVEEAVQALIDLH 69

Query: 95 KKP 97
             
Sbjct: 70 NHD 72

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.1 bits (88), Expect = 1e-04
 Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 7/68 (10%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
            L++      +T    +  F  +G+IID  +        + C F+ Y    SA +A+ + 
Sbjct: 7   TLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAEL 59

Query: 94  NKKPYKGK 101
           N    +  
Sbjct: 60  NGTQVESV 67

>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 = 38.6 bits (89), Expect = 2e-04
 Identities = 11/68 (16%), Positives = 23/68 (33%), Gaps = 6/68 (8%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKIS-AVKAILKS 93
            F  +L  +   E+    F  +G+I     ++         G I +  K   A+     +
Sbjct: 14  KFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEALGKAKDA 68

Query: 94  NKKPYKGK 101
           N    + +
Sbjct: 69  NNGNLQLR 76

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.0 bits (87), Expect = 3e-04
 Identities = 12/73 (16%), Positives = 23/73 (31%), Gaps = 5/73 (6%)

Query: 35  LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN 94
           +  KNLP      E +E F ++G +           +      + +   + A KA     
Sbjct: 13  ILAKNLPAGTLAAEIQETFSRFGSLGRVL-----LPEGGITAIVEFLEPLEARKAFRHLA 67

Query: 95  KKPYKGKITEEEF 107
              +       E+
Sbjct: 68  YSKFHHVPLYLEW 80

>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 = 37.2 bits (85), Expect = 4e-04
 Identities = 13/68 (19%), Positives = 30/68 (44%), Gaps = 6/68 (8%)

Query: 34  RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS 93
           R+ +  LP   + ++ K+H  + GD+  A + ++      G G + +  K     A+ K 
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKL 55

Query: 94  NKKPYKGK 101
           +   ++  
Sbjct: 56  DNTKFRSH 63

>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 = 37.0 bits (85), Expect = 7e-04
 Identities = 14/72 (19%), Positives = 26/72 (36%), Gaps = 1/72 (1%)

Query: 25 KKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKI 84
               T    + ++ LP++ TE +    F     +         DG++ G   + +A   
Sbjct: 8  SSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHI-EIGPDGRVTGEADVEFATHE 66

Query: 85 SAVKAILKSNKK 96
           AV A+ K    
Sbjct: 67 DAVAAMAKDKAN 78

>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 = 36.7 bits (84), Expect = 7e-04
 Identities = 19/83 (22%), Positives = 34/83 (40%), Gaps = 5/83 (6%)

Query: 20  KKIERKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKL-KGCGFI 78
                 +P+K     L++KNL  ++TE +    F ++ +     +         +G  FI
Sbjct: 10  SSYNPGEPNKV----LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFI 65

Query: 79  NYANKISAVKAILKSNKKPYKGK 101
            + NK  A +A+   N     GK
Sbjct: 66  TFPNKEIAWQALHLVNGYKLYGK 88

>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 = 36.7 bits (84), Expect = 9e-04
 Identities = 19/78 (24%), Positives = 30/78 (38%), Gaps = 5/78 (6%)

Query: 34  RLFIKNL-PFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK 92
            L + NL P ++T +     FG YGD+   ++L N          +  A+   A  A+  
Sbjct: 4   VLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK----ENALVQMADGNQAQLAMSH 59

Query: 93  SNKKPYKGKITEEEFKEH 110
            N     GK       +H
Sbjct: 60  LNGHKLHGKPIRITLSKH 77

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 35.1 bits (80), Expect = 0.002
 Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 4/74 (5%)

Query: 31  KRGRLFIKNLPFKITEEE-FKEHFGQYGDIIDAQLLKNADG--KLKGCGFINYANKISAV 87
           +   + I+NL  ++ +E   +E F  +G I    +            C F+ + NK SA 
Sbjct: 3   EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 62

Query: 88  KAILKSNKKPYKGK 101
           +A+ + N+     +
Sbjct: 63  RAL-QMNRSLLGNR 75

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	451
d1e9ga_	284	Inorganic pyrophosphatase {Baker's yeast (Saccharo	100.0
d1twla_	173	Inorganic pyrophosphatase {Pyrococcus furiosus [Ta	100.0
d2prda_	174	Inorganic pyrophosphatase {Thermus thermophilus [T	100.0
d1qeza_	170	Inorganic pyrophosphatase {Archaeon Sulfolobus aci	100.0
d1i40a_	175	Inorganic pyrophosphatase {Escherichia coli [TaxId	100.0
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.87
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.66
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.65
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.65
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.64
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.64
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.64
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.64
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.63
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.63
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.62
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.62
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.62
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.61
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.61
d1e9ga_	284	Inorganic pyrophosphatase {Baker's yeast (Saccharo	99.61
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.61
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.6
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.6
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.6
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.6
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.6
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.59
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.59
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.58
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.58
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.58
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.57
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.57
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.57
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.56
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.56
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.55
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.55
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.54
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.53
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.53
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.53
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.52
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.52
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.51
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.51
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.5
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.49
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.47
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.47
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.46
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.46
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.45
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.45
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.45
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.45
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.44
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.44
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.43
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.42
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.42
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.42
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.41
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.41
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.41
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.4
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.39
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.38
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.38
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.38
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.37
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.37
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.36
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.34
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.34
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.34
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.32
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.31
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.29
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.29
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.29
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.25
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.24
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.23
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.22
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	99.21
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.15
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.14
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.13
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.11
d1twla_	173	Inorganic pyrophosphatase {Pyrococcus furiosus [Ta	99.1
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.07
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.04
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.0
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.0
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	98.99
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	98.98
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	98.97
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	98.97
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	98.97
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	98.96
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	98.96
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	98.94
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	98.93
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	98.93
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	98.93
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	98.92
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	98.91
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	98.91
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	98.91
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.91
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	98.9
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.9
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.89
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	98.89
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	98.89
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	98.88
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.88
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.87
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	98.84
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	98.84
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	98.84
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	98.83
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.82
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	98.8
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	98.8
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	98.79
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	98.78
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	98.78
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	98.78
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.77
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	98.76
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	98.74
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	98.74
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	98.73
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	98.72
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.72
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	98.7
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.69
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.69
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	98.68
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	98.67
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	98.67
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	98.64
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	98.64
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.59
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.59
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	98.57
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	98.57
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	98.56
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	98.55
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	98.54
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.52
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	98.52
d1qeza_	170	Inorganic pyrophosphatase {Archaeon Sulfolobus aci	98.52
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	98.5
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	98.47
d2prda_	174	Inorganic pyrophosphatase {Thermus thermophilus [T	98.46
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.46
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	98.43
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	98.42
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	98.4
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	98.4
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	98.4
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	98.39
d1i40a_	175	Inorganic pyrophosphatase {Escherichia coli [TaxId	98.38
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	98.37
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	98.37
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	98.35
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.34
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.34
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	98.33
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	98.31
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.29
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	98.27
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	98.24
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.24
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.24
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	98.21
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	98.15
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.12
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.44
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	89.03
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	84.24
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	83.62

>d1e9ga_ b.40.5.1 (A:) Inorganic pyrophosphatase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Inorganic pyrophosphatase
family: Inorganic pyrophosphatase
domain: Inorganic pyrophosphatase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=2.9e-71  Score=531.92  Aligned_cols=223  Identities=57%  Similarity=0.974  Sum_probs=213.1

Q ss_pred             HHHhcCCCcccCCCCCc-ccccccCCccccccccccceeeccCCCCccccccccCCCCCCCcccccCCeeeeecccCCCC
Q psy300          147 AILKSNKKPYKGSENGL-ISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHH  225 (451)
Q Consensus       147 Ai~~ln~riy~~~~~G~-iSp~hdiPl~v~~~p~~vn~vvEIPrgS~~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~  225 (451)
                      +..++++|+||.. +|. +|||||+|++.+..+..+||+||||+||++|||+++++.+|||+||.++|++|+++++||++
T Consensus         9 ~~~t~~yr~~~~~-~g~~iSp~HDIPl~~d~~~~~~nvVVEIPrgsn~KyEi~ke~~~npIkqD~k~G~lr~~r~l~~~~   87 (284)
T d1e9ga_           9 AKNTLEYKVYIEK-DGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPIIQDTKKGKLRFVRNCFPHH   87 (284)
T ss_dssp             ETTSTTCEEEEEE-TTEEECTTTTSCSEEETTTTEEEEEEEECTTCCBCEEECTTSTTCCEEECEETTEECBCCEETTCC
T ss_pred             CCCCcceeEEEcc-CCcccCccccCCCCCCCCCCEEEEEEEeCCCCCeeEEECcCCCCCceeeeccCCCEEEEeccCCCC
Confidence            3467899999985 677 99999999998778889999999999999999999999999999999999999999999999


Q ss_pred             CCccccCCCCccCCCCCCCCcCCCCCCCCCcceEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecCCccccC
Q psy300          226 GYIWNYGALPQTWENPDETDAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAK  305 (451)
Q Consensus       226 ~yp~nYG~iP~T~~~p~~~~~~~~~~~D~DPlD~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~d~~~~~  305 (451)
                      +||||||||||||+||++.++.++++|||||||||||++.++.+|+|++|||||+|+|+|+||+|||||||+++||++++
T Consensus        88 ~YP~NYGfIPqTwedp~~~~~~~~~~GDgDPLDVlvi~~~~~~~G~Vv~vk~lGvL~miDeGE~D~KIIaV~~~Dp~~~~  167 (284)
T d1e9ga_          88 GYIHNYGAFPQTWEDPNVSHPETKAVGDNDPIDVLEIGETIAYTGQVKQVKALGIMALLDEGETDWKVIAIDINDPLAPK  167 (284)
T ss_dssp             SCSSEEEECSSCCCCTTSEETTTTEEBCSSCCEEEECCSSCCCTTCEEEEEEEEEECEEETTEECCEEEEEETTSTTGGG
T ss_pred             CCCcccccCcccccCcccccccccccCCCCCeeEEEecccccccceEEEEEEEEEEEeccCCCccceEEEeecCCccccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcccccccCcchHHHHHHHhhhccCCCCCcccccCCCcchh---hhhhhHHHHHHHHHHhhccccC
Q psy300          306 LNDVADIETHFPGYLKATNEWFKIYKIPDGKPENVLNTRVEGE---SSQGFIPGCRGRTEQVVSSRLE  370 (451)
Q Consensus       306 i~~~~d~~~~~p~~~~~i~~~F~~yk~~~gk~~~~~~~~~~~~---~~~~~i~~~~~~~~~~i~~~~~  370 (451)
                      +++|+||++++|+++++|++||++||.++||++|.++|+|+++   .|+++|++||++|++|++|...
T Consensus       168 ~ndI~Dv~~~~p~~l~~i~~fF~~YK~~eGK~~n~~~~~g~~~~k~~A~~iI~e~h~~wk~li~g~~~  235 (284)
T d1e9ga_         168 LNDIEDVEKYFPGLLRATNEWFRIYKIPDGKPENQFAFSGEAKNKKYALDIIKETHDSWKQLIAGKSS  235 (284)
T ss_dssp             CCSHHHHHHHSTTHHHHHHHHHHHTTGGGTCCCCEEGGGGCCBCHHHHHHHHHHHHHHHHHHHTTCCS
T ss_pred             cCChhhhhhhCHHHHHHHHHHHHHhcCCCCCceeEeeccCcccCHHHHHHHHHHHHHHHHHHhcCcCC
Confidence            9999999999999999999999999999999999999998655   4689999999999999999764

>d1twla_ b.40.5.1 (A:) Inorganic pyrophosphatase {Pyrococcus furiosus [TaxId: 2261]}

class: All beta proteins
fold: OB-fold
superfamily: Inorganic pyrophosphatase
family: Inorganic pyrophosphatase
domain: Inorganic pyrophosphatase
species: Pyrococcus furiosus [TaxId: 2261]

Probab=100.00  E-value=5.9e-55  Score=396.20  Aligned_cols=171  Identities=27%  Similarity=0.481  Sum_probs=161.4

Q ss_pred             cccccCCccccccccccceeeccCCCCccccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccCCCCCCC
Q psy300          165 SPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDET  244 (451)
Q Consensus       165 Sp~hdiPl~v~~~p~~vn~vvEIPrgS~~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~~~p~~~  244 (451)
                      |||||+|++.+ .+..++++||||+||++|||+++           ++|.+++++.++.++.||+|||||||||      
T Consensus         1 ~pwhdi~~~~~-~p~~vn~viEIP~gs~~KyE~dk-----------~~g~~~~dr~l~~~~~yP~nYGfiP~T~------   62 (173)
T d1twla_           1 NPFHDLEPGPD-VPEVVYAIIEIPKGSRNKYELDK-----------KTGLLKLDRVLYSPFFYPVDYGIIPRTW------   62 (173)
T ss_dssp             CHHHHSCSCSB-TTTBEEEEEEECTTCSEEEEECT-----------TTCCEEEEEECSSSCCCSSEEEECTTCC------
T ss_pred             CCccCCCCCCC-CCCeEEEEEEECCCCCcCEEEcc-----------CCCceeeeeecCCCccCCcccceeeccc------
Confidence            68999999764 57899999999999999999986           6788999999999999999999999999      


Q ss_pred             CcCCCCCCCCCcceEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecCCccccCCCCcccccccCcchHHHHH
Q psy300          245 DAHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATN  324 (451)
Q Consensus       245 ~~~~~~~~D~DPlD~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~d~~~~~i~~~~d~~~~~p~~~~~i~  324 (451)
                            ++||||||+|||++.++.+|++++|||||+|+|+|+||.|||||||+++||.+++++|++||++   +++++|+
T Consensus        63 ------~~DgDPLDvlvl~~~~~~~G~vv~~r~iG~l~m~D~ge~D~Kiiav~~~dp~~~~i~~i~dl~~---~~l~~I~  133 (173)
T d1twla_          63 ------YEDDDPFDIMVIMREPVYPLTIIEARPIGLFKMIDSGDKDYKVLAVPVEDPYFKDWKDIDDVPK---AFLDEIA  133 (173)
T ss_dssp             ------BCCB-CCEEEECCSSCCCTTCEEEEEEEEEEEEEETTEECCEEEEEETTCGGGTTCCSGGGSCH---HHHHHHH
T ss_pred             ------cCCCCCchheeccccccCCceEEEEEEEEEEEeccCCCccceEEEEecCCchhhccCChHHCCH---HHHHHHH
Confidence                  5899999999999999999999999999999999999999999999999999999999999986   5999999


Q ss_pred             HHhhhccCCCCCcccccCCCcchhhhhhhHHHHHHHHHH
Q psy300          325 EWFKIYKIPDGKPENVLNTRVEGESSQGFIPGCRGRTEQ  363 (451)
Q Consensus       325 ~~F~~yk~~~gk~~~~~~~~~~~~~~~~~i~~~~~~~~~  363 (451)
                      +||++||.++||++++++|.|+ ++|+++|++||++|++
T Consensus       134 ~fF~~YK~~egK~v~v~g~~~~-~~A~k~I~~~~~~y~~  171 (173)
T d1twla_         134 HFFKRYKELQGKEIIVEGWEGA-EAAKREILRAIEMYKE  171 (173)
T ss_dssp             HHHHHTTGGGTCCEEEEEEEEH-HHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCCCCCceEEcCccCH-HHHHHHHHHHHHHHHh
Confidence            9999999999999999999986 7889999999999987

>d2prda_ b.40.5.1 (A:) Inorganic pyrophosphatase {Thermus thermophilus [TaxId: 274]}

class: All beta proteins
fold: OB-fold
superfamily: Inorganic pyrophosphatase
family: Inorganic pyrophosphatase
domain: Inorganic pyrophosphatase
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=4.5e-52  Score=377.55  Aligned_cols=169  Identities=24%  Similarity=0.412  Sum_probs=156.4

Q ss_pred             ccccCCccccccccccceeeccCCCCccccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccCCCCCCCC
Q psy300          166 PFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETD  245 (451)
Q Consensus       166 p~hdiPl~v~~~p~~vn~vvEIPrgS~~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~~~p~~~~  245 (451)
                      .++++|++. .+|..++++||||+||++|||+++           ++|.++.++.++.++.||||||||||||       
T Consensus         2 ~l~~ip~g~-~~p~~vn~viEIP~gs~~KyE~d~-----------~~g~~~~dr~l~~~~~yP~nYGfiP~T~-------   62 (174)
T d2prda_           2 NLKSLPVGD-KAPEVVHMVIEVPRGSGNKYEYDP-----------DLGAIKLDRVLPGAQFYPGDYGFIPSTL-------   62 (174)
T ss_dssp             CGGGSCCCT-TTTTEEEEEEEECTTCCEEEEEET-----------TTTEEEEEEECSSSCCCSSEEEECSSCC-------
T ss_pred             CHhHCCCCC-CCCCEEEEEEEECCCCCccEEEcc-----------CCCcEEEEeecCCCCcCCCCcceecccc-------
Confidence            578899875 467899999999999999999986           5677888888888899999999999999       


Q ss_pred             cCCCCCCCCCcceEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecCCccccCCCCcccccccCcchHHHHHH
Q psy300          246 AHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVNDPNAAKLNDVADIETHFPGYLKATNE  325 (451)
Q Consensus       246 ~~~~~~~D~DPlD~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~d~~~~~i~~~~d~~~~~p~~~~~i~~  325 (451)
                           ++||||||+|||++.++.+|++++|||||+|+|+|+||.|||||||+.+||++++|+|++||+   |+++++|++
T Consensus        63 -----~~DgDPLDvlvl~~~~~~~G~vv~~r~iG~l~m~D~ge~D~KiIaV~~~dp~~~~i~di~dl~---~~~l~~I~~  134 (174)
T d2prda_          63 -----AEDGDPLDGLVLSTYPLLPGVVVEVRVVGLLLMEDEKGGDAKVIGVVAEDQRLDHIQDIGDVP---EGVKQEIQH  134 (174)
T ss_dssp             -----CTTSSCCEEEEECSSCCCTTCEEEEEEEEEEEEEESSCEEEEEEEEETTCGGGTTCCSGGGSC---HHHHHHHHH
T ss_pred             -----cCCCCCeEEEeecccccccccEEEEEEEEEEEEeeCCCCcceEEEEeCCCCcccccCChHHCC---HHHHHHHHH
Confidence                 589999999999999999999999999999999999999999999999999999999999996   469999999


Q ss_pred             HhhhccCCC---CCcccccCCCcchhhhhhhHHHHHHHHH
Q psy300          326 WFKIYKIPD---GKPENVLNTRVEGESSQGFIPGCRGRTE  362 (451)
Q Consensus       326 ~F~~yk~~~---gk~~~~~~~~~~~~~~~~~i~~~~~~~~  362 (451)
                      ||++||.++   ||++.+.+|.++ ++|+++|++||++|+
T Consensus       135 fF~~YK~le~k~~k~v~~~g~~d~-~~A~~iI~~~~~~yk  173 (174)
T d2prda_         135 FFETYKALEAKKGKWVKVTGWRDR-KAALEEVRACIARYK  173 (174)
T ss_dssp             HHHHTTGGGGGGTCCEEEEEEECH-HHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCcCCCCCEEEEccccCH-HHHHHHHHHHHHHhC
Confidence            999999998   566889999985 788999999999997

>d1qeza_ b.40.5.1 (A:) Inorganic pyrophosphatase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: All beta proteins
fold: OB-fold
superfamily: Inorganic pyrophosphatase
family: Inorganic pyrophosphatase
domain: Inorganic pyrophosphatase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=100.00  E-value=4.5e-51  Score=369.87  Aligned_cols=158  Identities=28%  Similarity=0.462  Sum_probs=149.3

Q ss_pred             ccccceeeccCCCCccccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccCCCCCCCCcCCCCCCCCCcc
Q psy300          178 DKIFNMVVEIPRWTNAKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETDAHTGQKGDGDPI  257 (451)
Q Consensus       178 p~~vn~vvEIPrgS~~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~~~p~~~~~~~~~~~D~DPl  257 (451)
                      |..++++||||+||++|||+++           ++|.+++++.++.++.||||||||||||            ++|||||
T Consensus         9 p~~vn~viEIP~gs~~KyE~d~-----------~~g~~~~dr~l~~~~~yP~nYGfiP~T~------------~~DgDPL   65 (170)
T d1qeza_           9 PDVVNVLVEIPQGSNIKYEYDD-----------EEGVIKVDRVLYTSMNYPFNYGFIPGTL------------EEDGDPL   65 (170)
T ss_dssp             TTSEEEEEEECTTCCEEEEEET-----------TTTEEEEEEECSSSBCCSSEEEECTTCC------------CTTSSCC
T ss_pred             CCeEEEEEEECCCCCeeEEEcc-----------CCCceEEEeeccccccCCcceeeeeccc------------cCCCCcc
Confidence            4679999999999999999986           5788999999999999999999999999            5899999


Q ss_pred             eEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecC--CccccCCCCcccccccCcchHHHHHHHhhhccCCC-
Q psy300          258 DVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVN--DPNAAKLNDVADIETHFPGYLKATNEWFKIYKIPD-  334 (451)
Q Consensus       258 D~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~--d~~~~~i~~~~d~~~~~p~~~~~i~~~F~~yk~~~-  334 (451)
                      |+|||++.++.||++++|||||+|.|+|+||.|||||||+++  ||++++|+|++||++   +++++|+|||++||.++ 
T Consensus        66 Dvlvl~~~~~~~G~vv~~r~iG~l~m~D~ge~D~KiiaVp~~~~d~~~~~i~di~dl~~---~~l~~I~~fF~~YK~le~  142 (170)
T d1qeza_          66 DVLVITNYQLYPGSVIEVRPIGILYMKDEEGEDAKIVAVPKDKTDPSFSNIKDINDLPQ---ATKNKIVHFFEHYKELEP  142 (170)
T ss_dssp             EEEECCSSCCCTTCEEEEEEEEEEEEEETTEEEEEEEEEECTTTCGGGTTCCSGGGSCH---HHHHHHHHHHHHTTTTST
T ss_pred             eeeeecccccCCcEEEEEEEeEEEEcccCCCCceEEEEEeccccchhhcccCChHHCCH---HHHHHHHHHHHHhhccCC
Confidence            999999999999999999999999999999999999999988  899999999999965   59999999999999998 


Q ss_pred             CCcccccCCCcchhhhhhhHHHHHHHHH
Q psy300          335 GKPENVLNTRVEGESSQGFIPGCRGRTE  362 (451)
Q Consensus       335 gk~~~~~~~~~~~~~~~~~i~~~~~~~~  362 (451)
                      ||++++.+|.|+ ++|.++|++||+||+
T Consensus       143 ~K~v~v~g~~~~-~~A~~~I~~s~~ry~  169 (170)
T d1qeza_         143 GKYVKISGWGSA-TEAKNRIQLAIKRVS  169 (170)
T ss_dssp             TCCEEEEEEECH-HHHHHHHHHHHHHHC
T ss_pred             CCeEEEccccCH-HHHHHHHHHHHHHhc
Confidence            899999999986 778999999999996

>d1i40a_ b.40.5.1 (A:) Inorganic pyrophosphatase {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Inorganic pyrophosphatase
family: Inorganic pyrophosphatase
domain: Inorganic pyrophosphatase
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=4e-50  Score=365.24  Aligned_cols=169  Identities=25%  Similarity=0.315  Sum_probs=156.0

Q ss_pred             cccCCccccccccccceeeccCCCCc-cccccccCCCCCCCcccccCCeeeeecccCCCCCCccccCCCCccCCCCCCCC
Q psy300          167 FHDIPLYSNVKDKIFNMVVEIPRWTN-AKMEINLNEPLNPIKQDIKKGNLRYVANVFPHHGYIWNYGALPQTWENPDETD  245 (451)
Q Consensus       167 ~hdiPl~v~~~p~~vn~vvEIPrgS~-~K~E~~k~~~~npI~qD~~~g~~r~~~~l~p~~~yp~nYG~iP~T~~~p~~~~  245 (451)
                      ++++|++. ..|..++++||||+||+ +|||+++           ++|.++.++.++.++.||+|||||||||       
T Consensus         2 l~dip~~~-~~p~~vn~vIEIP~gs~~~KyE~dk-----------~~g~~~~dr~l~~~~~yP~nYGfiP~T~-------   62 (175)
T d1i40a_           2 LLNVPAGK-DLPEDIYVVIEIPANADPIKYEIDK-----------ESGALFVDRFMSTAMFYPCNYGYINHTL-------   62 (175)
T ss_dssp             GGGCCSCS-BTTTBEEEEEEECTTCCSEEEEECT-----------TTCCEEEEEECSSSCCCSSEEEECTTCC-------
T ss_pred             ccccCCCC-CCCCEEEEEEEecCCCCceeEEEec-----------cCCCEEEEEeccccccCCCcCCcccccc-------
Confidence            68899985 45789999999999996 6999986           5788888888999999999999999999       


Q ss_pred             cCCCCCCCCCcceEEEeccccCCCccEEEEEEeeeeeeecCCCccceEEEEecC--CccccCCCCcccccccCcchHHHH
Q psy300          246 AHTGQKGDGDPIDVLEIGERIAKRGEIIQVKALGVIGLIDEGQTDWKIIAINVN--DPNAAKLNDVADIETHFPGYLKAT  323 (451)
Q Consensus       246 ~~~~~~~D~DPlD~~~~~~~~~~~G~v~~vr~lG~l~~~d~~e~D~Kii~v~~~--d~~~~~i~~~~d~~~~~p~~~~~i  323 (451)
                           +|||||||+|||++.++.+|++++|||||+|+|+|+||.|||||||+++  ||.+++|+|++||++   +++++|
T Consensus        63 -----~~DgDPLDvlvl~~~~~~~G~vv~~r~iG~l~~~D~ge~D~Kii~V~~~~~~~~~~~i~dl~dl~~---~~l~~I  134 (175)
T d1i40a_          63 -----SLDGDPVDVLVPTPYPLQPGSVTRCRPVGVLKMTDEAGEDAKLVAVPHSKLSKEYDHIKDVNDLPE---LLKAQI  134 (175)
T ss_dssp             -----CTTSSCCEEEECCSSCCCTTCEEEEEEEEEEEEEETTEEEEEEEEEECTTTCSTTTTCCSGGGSCH---HHHHHH
T ss_pred             -----cCCCCCeeEEEEeccccccceEEEEEEEEEEEEecCCCcccceEEeecccCcccccccCChhHCCH---HHHHHH
Confidence                 6999999999999999999999999999999999999999999999987  789999999999975   599999


Q ss_pred             HHHhhhccCCC-CCcccccCCCcchhhhhhhHHHHHHHHHH
Q psy300          324 NEWFKIYKIPD-GKPENVLNTRVEGESSQGFIPGCRGRTEQ  363 (451)
Q Consensus       324 ~~~F~~yk~~~-gk~~~~~~~~~~~~~~~~~i~~~~~~~~~  363 (451)
                      ++||++||.++ ||++.+.+|.|+ ++|.++|++||++|++
T Consensus       135 ~~fF~~YK~le~~k~v~v~g~~~~-~~A~~~I~~~~~~yk~  174 (175)
T d1i40a_         135 AHFFEHYKDLEKGKWVKVEGWENA-EAAKAEIVASFERAKN  174 (175)
T ss_dssp             HHHHHHTTTTSTTCCEEEEEEECH-HHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHcCcCCCCceEECcccCH-HHHHHHHHHHHHHHhc
Confidence            99999999998 788999999985 7789999999999986

>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=99.87  E-value=4.3e-22  Score=180.23  Aligned_cols=123  Identities=26%  Similarity=0.551  Sum_probs=109.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCcc------------
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKP------------   97 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~------------   97 (451)
                      ..++|||+|||+++|+++|+++|++||.|.++.++++. +|.++|||||+|.+.++|.+|+...++..            
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhh
Confidence            34799999999999999999999999999999999987 99999999999999999999998765432            


Q ss_pred             ----------------CCC----CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCC
Q psy300           98 ----------------YKG----KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKK  154 (451)
Q Consensus        98 ----------------f~G----~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~r  154 (451)
                                      |.|    .+|+++|+++|+.||.|..+.++.+ .+|.++|||||+|.+.++|.+|+. +++.
T Consensus        85 ~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~  161 (183)
T d1u1qa_          85 REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYH  161 (183)
T ss_dssp             TTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCE
T ss_pred             cccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCC
Confidence                            111    4899999999999999999999987 568999999999999999999996 4543

>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=99.66  E-value=1.6e-16  Score=126.38  Aligned_cols=71  Identities=32%  Similarity=0.624  Sum_probs=67.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ..++|||+|||.++++++|+++|++||+|.++++++++ +|+++|||||+|.+.++|.+|++.|||..+.|+
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~   76 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGA   76 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCC
Confidence            45789999999999999999999999999999999987 899999999999999999999999999998874

>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=99.65  E-value=1.3e-16  Score=126.08  Aligned_cols=72  Identities=24%  Similarity=0.392  Sum_probs=68.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .+.++|||+|||.++|+++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|+..|||..+.|+
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr   79 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR   79 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCE
Confidence            457899999999999999999999999999999999987 899999999999999999999999999988774

>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=99.65  E-value=2.5e-16  Score=125.12  Aligned_cols=71  Identities=31%  Similarity=0.630  Sum_probs=67.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...++|||+|||.++++++|+++|++||+|.++++++++ +|+++|||||+|.+.++|.+|++.+||..+.|
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   75 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEG   75 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCC
Confidence            356789999999999999999999999999999999987 89999999999999999999999999988876

>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=99.64  E-value=3.4e-16  Score=123.20  Aligned_cols=70  Identities=34%  Similarity=0.589  Sum_probs=66.3

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .++|||+|||.++++++|+++|++||+|.+++++++. +|+++|||||+|.+.++|++|++.|||..+.|+
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~   72 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTK   72 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            5689999999999999999999999999999999987 899999999999999999999999999988773

>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=99.64  E-value=2.9e-16  Score=123.36  Aligned_cols=69  Identities=23%  Similarity=0.404  Sum_probs=65.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .+|||+|||+++|+++|+++|++||+|.++++++++ +|+++|||||+|.++++|.+|++.|+|..+.|+
T Consensus         1 aslfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr   70 (80)
T d1cvja1           1 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGK   70 (80)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCE
Confidence            379999999999999999999999999999999988 899999999999999999999999999888763

>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=99.64  E-value=1.6e-16  Score=125.18  Aligned_cols=69  Identities=20%  Similarity=0.408  Sum_probs=65.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      +++|||+|||.++++++|+++|++||+|.++++++++ +|+++|||||+|.+.++|++|++.|||..+.|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g   71 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRN   71 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECC
Confidence            5789999999999999999999999999999999987 89999999999999999999999999988776

>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=99.64  E-value=2.8e-16  Score=127.06  Aligned_cols=73  Identities=23%  Similarity=0.391  Sum_probs=68.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ....++|||+|||.++++++|+++|++||+|.++++++++ +|.++|||||+|.+.++|.+|++.|||..+.|+
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~   79 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGK   79 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSC
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCE
Confidence            3456899999999999999999999999999999999987 899999999999999999999999999988773

>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=99.63  E-value=5.3e-16  Score=124.09  Aligned_cols=73  Identities=25%  Similarity=0.377  Sum_probs=67.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ..+.++|||+|||.++++++|+++|++||+|.++++++++ +|+++|||||+|.+.++|++|+..+||..+.|+
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~   77 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQ   77 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCE
Confidence            4467899999999999999999999999999999999987 899999999999999999999999999888763

>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=99.63  E-value=5.3e-16  Score=125.43  Aligned_cols=71  Identities=27%  Similarity=0.351  Sum_probs=67.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..+++|||+|||.++++++|+++|++||+|.++++++++ +|.++|||||+|.+.++|..|++.|||..+.|
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g   76 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDD   76 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECC
Confidence            367899999999999999999999999999999999988 89999999999999999999999999987776

>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=99.62  E-value=9.9e-16  Score=125.66  Aligned_cols=73  Identities=25%  Similarity=0.480  Sum_probs=68.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ....++|||+|||.++++++|+++|++||.|.++++..+.++.++|||||+|.+.++|.+|++.|||+.+.|+
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr   87 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTP   87 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCC
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCc
Confidence            3456899999999999999999999999999999999988999999999999999999999999999999874

>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=99.62  E-value=3.2e-16  Score=122.54  Aligned_cols=69  Identities=26%  Similarity=0.570  Sum_probs=65.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .+|||+|||+++++++|+++|++||+|.++++.++++|+++|||||+|.+.++|.+|++.+||+.+.|+
T Consensus         1 grl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~   69 (78)
T d1no8a_           1 GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGR   69 (78)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            479999999999999999999999999999999999999999999999999999999999999988773

>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=99.62  E-value=4e-16  Score=124.06  Aligned_cols=69  Identities=28%  Similarity=0.428  Sum_probs=65.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .+|||+|||.++|+++|+++|++||+|.++++++|+ +|+++|||||+|.++++|..|+..+||..+.|+
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~   71 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK   71 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSS
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            479999999999999999999999999999999997 899999999999999999999999999988873

>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=99.61  E-value=7.4e-16  Score=123.72  Aligned_cols=72  Identities=25%  Similarity=0.403  Sum_probs=67.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..+.++|||+|||.++++++|+++|++||+|.++++++++ +|.++|||||+|.+.++|.+|++.|||..+.|
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g   77 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDH   77 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETT
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECC
Confidence            3466899999999999999999999999999999999987 89999999999999999999999999987776

>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=99.61  E-value=7.1e-16  Score=125.97  Aligned_cols=72  Identities=28%  Similarity=0.551  Sum_probs=67.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....++|||+|||.++++++|+++|++||+|.++++++++ +|+++|||||+|.+.++|.+|++.||+..+.|
T Consensus         5 ~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   77 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQG   77 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSS
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECC
Confidence            4567899999999999999999999999999999999987 89999999999999999999999999988876

>d1e9ga_ b.40.5.1 (A:) Inorganic pyrophosphatase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All beta proteins
fold: OB-fold
superfamily: Inorganic pyrophosphatase
family: Inorganic pyrophosphatase
domain: Inorganic pyrophosphatase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.61  E-value=1e-16  Score=152.42  Aligned_cols=48  Identities=50%  Similarity=0.912  Sum_probs=44.7

Q ss_pred             CCCCccCCccCCCccccCCCCEEEEEEeecCCCccceeeeccccceEE
Q psy300          380 SENGLISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLY  427 (451)
Q Consensus       380 ~~~~~~s~~hd~~l~~~~~~~~~~~~~e~p~~~~~k~e~~~~~~~~~~  427 (451)
                      .+|++|||||||||+++..+++||||||||||||+||||+|++++|-.
T Consensus        21 ~~g~~iSp~HDIPl~~d~~~~~~nvVVEIPrgsn~KyEi~ke~~~npI   68 (284)
T d1e9ga_          21 KDGKPVSAFHDIPLYADKENNIFNMVVEIPRWTNAKLEITKEETLNPI   68 (284)
T ss_dssp             ETTEEECTTTTSCSEEETTTTEEEEEEEECTTCCBCEEECTTSTTCCE
T ss_pred             cCCcccCccccCCCCCCCCCCEEEEEEEeCCCCCeeEEECcCCCCCce
Confidence            368899999999999998899999999999999999999999998843

>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=99.61  E-value=2.5e-16  Score=123.07  Aligned_cols=68  Identities=22%  Similarity=0.598  Sum_probs=64.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      |+|||+|||.++++++|+++|++||.|.++++++|+ +|+++|||||+|.++++|.+|++ +++..+.|+
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr   69 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSK   69 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCe
Confidence            689999999999999999999999999999999998 89999999999999999999997 688888774

>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=99.60  E-value=8.9e-16  Score=124.34  Aligned_cols=73  Identities=26%  Similarity=0.580  Sum_probs=66.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC--CCCceeEEEEEEccHHHHHHHHHhc-CCccCCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA--DGKLKGCGFINYANKISAVKAILKS-NKKPYKGK  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~--tg~skG~aFV~F~~~~~A~~Al~~l-ng~~f~G~  101 (451)
                      ....++|||+|||.++++++|+++|++||.|.+++++++.  +|+++|||||+|.+.++|.+|+..| ||..+.|+
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr   80 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGR   80 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCE
Confidence            3466889999999999999999999999999999998875  7999999999999999999999998 88877763

>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=99.60  E-value=3e-16  Score=125.75  Aligned_cols=70  Identities=23%  Similarity=0.376  Sum_probs=66.5

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..++|||+|||.++++++|+++|++||+|.++++++++ +|+++|||||+|.+.++|.+|+..+||..+.|
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g   74 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG   74 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETT
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECC
Confidence            56799999999999999999999999999999999988 89999999999999999999999999987766

>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=99.60  E-value=3e-16  Score=129.02  Aligned_cols=70  Identities=17%  Similarity=0.345  Sum_probs=65.6

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ..++|||+|||.++++++|+++|++||+|.+++++++. +|+++|||||+|.+.++|.+|+. +||..|.|+
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~   87 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGV   87 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCE
Confidence            45789999999999999999999999999999999987 89999999999999999999995 999988873

>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=99.60  E-value=1.2e-15  Score=120.95  Aligned_cols=70  Identities=27%  Similarity=0.583  Sum_probs=64.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      +.++|||+|||.++++++|+++|++||.|.++++++|+ +|+++|||||+|.++++|.+|++ +++..+.|+
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr   75 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGR   75 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCE
Confidence            45799999999999999999999999999999999998 89999999999999999999997 477766663

>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=99.60  E-value=1.3e-15  Score=122.45  Aligned_cols=65  Identities=31%  Similarity=0.599  Sum_probs=60.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhc
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKS   93 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~l   93 (451)
                      ....++|||+|||+++|+++|+++|++||+|.++++++|+ +|+++|||||+|.++++|.+|++.+
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~   70 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR   70 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC
Confidence            3466899999999999999999999999999999999998 8999999999999999999999853

>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=99.59  E-value=1.1e-15  Score=118.67  Aligned_cols=67  Identities=25%  Similarity=0.599  Sum_probs=62.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        34 ~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      +|||+|||+++++++|+++|++||+|.++++++++ +|+++|||||+|.++++|.+|++ +++..+.|+
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr   68 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGK   68 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTB
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCC
Confidence            59999999999999999999999999999999988 89999999999999999999997 677777764

>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=99.59  E-value=1.5e-15  Score=124.82  Aligned_cols=72  Identities=25%  Similarity=0.422  Sum_probs=67.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .++.++|||+|||.++++++|+++|++||.|.+++++.+. +|.++|||||+|.+.++|.+|++.|||..+.|
T Consensus        15 ~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g   87 (102)
T d2cpza1          15 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGM   87 (102)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECC
Confidence            3466789999999999999999999999999999999987 89999999999999999999999999987776

>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=99.58  E-value=1.4e-15  Score=125.19  Aligned_cols=71  Identities=30%  Similarity=0.633  Sum_probs=66.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ..++|||+|||.++++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|++.|||..+.|+
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~   78 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGR   78 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSS
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCE
Confidence            34689999999999999999999999999999999987 899999999999999999999999999988774

>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=99.58  E-value=2.1e-15  Score=126.11  Aligned_cols=85  Identities=28%  Similarity=0.429  Sum_probs=73.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC--------
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK--------  101 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~--------  101 (451)
                      ..+++|||+|||.++++++|+++|++||.|.+|++..  ++.++|||||+|.+.++|..|+..|||..+.|+        
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~--~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN--TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC--STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc--cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            3567999999999999999999999999999999875  467799999999999999999999999998883        


Q ss_pred             -----------CcHHHHHHHhcccCc
Q psy300          102 -----------ITEEEFKEHFGQYGD  116 (451)
Q Consensus       102 -----------~tee~L~~~F~~fG~  116 (451)
                                 ..++++..+.++||.
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~g~  108 (114)
T d2f9da1          83 ANRAFQKMDTKKKEEQLKLLKEKYGI  108 (114)
T ss_dssp             HHHHTTTSCHHHHHHHHHHHHHHHCC
T ss_pred             CCchhhhhHHHHHHHHHHHHHHHhCC
Confidence                       245666666666664

>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=99.58  E-value=2.1e-15  Score=130.55  Aligned_cols=72  Identities=21%  Similarity=0.375  Sum_probs=67.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....++|||+|||.++++++|+++|++||.|.++++++++ +|+++|||||+|.+.++|.+|++.|||..+.|
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~g  111 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN  111 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECC
Confidence            3455789999999999999999999999999999999987 89999999999999999999999999988876

>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=99.57  E-value=1.6e-15  Score=121.56  Aligned_cols=71  Identities=28%  Similarity=0.609  Sum_probs=66.4

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...++|||+|||+++++++|+++|++||.|..+.++++. +|.++|||||+|.+.++|.+|+..|+|..+.|
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g   74 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDG   74 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTS
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECC
Confidence            356789999999999999999999999999999998876 89999999999999999999999999987766

>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=99.57  E-value=2.2e-15  Score=124.07  Aligned_cols=71  Identities=28%  Similarity=0.581  Sum_probs=64.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....++|||+|||.++++++|+++|++||+|.++++++++ +|+++|||||+|.+.++|.+|++.+|+ .+.|
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~G   78 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDG   78 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETT
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCC
Confidence            3456789999999999999999999999999999999987 899999999999999999999998876 3444

>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=99.57  E-value=9.7e-16  Score=117.67  Aligned_cols=68  Identities=22%  Similarity=0.451  Sum_probs=64.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCCC
Q psy300           35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGKI  102 (451)
Q Consensus        35 lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~~  102 (451)
                      |||+|||.++++++|+++|++||+|.++++.+++ ++.++|||||+|.+.++|.+|++.|||+.+.|+.
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~   69 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQM   69 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEES
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            7999999999999999999999999999999987 8999999999999999999999999999998753

>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=99.56  E-value=4.8e-15  Score=117.75  Aligned_cols=70  Identities=24%  Similarity=0.411  Sum_probs=64.9

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ..++|||+|||.++|+++|+++|+.||+|.++++.++.+|+++|||||+|.++++|.+|++ +++..|.|+
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~   74 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKET   74 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTE
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCE
Confidence            4579999999999999999999999999999999998899999999999999999999995 688877763

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=1.4e-15  Score=118.19  Aligned_cols=66  Identities=23%  Similarity=0.402  Sum_probs=60.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        34 ~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      +|||+|||+++|+++|+++|++||+|.++++++++ +|+++|||||+|.+.++|.+|++. ++..+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~-~~~~i~g   67 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGL   67 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTT
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCCEECC
Confidence            69999999999999999999999999999999997 899999999999999999999975 4444544

>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=99.55  E-value=7.2e-15  Score=114.68  Aligned_cols=69  Identities=20%  Similarity=0.463  Sum_probs=64.1

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .++|||+|||+++|+++|+++|++||.|..+.+..++ ++.++|||||+|.++++|.+|+. ++|..+.|+
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr   71 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGH   71 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTE
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCE
Confidence            4799999999999999999999999999999999987 89999999999999999999985 799888774

>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=99.55  E-value=2e-15  Score=118.51  Aligned_cols=69  Identities=16%  Similarity=0.182  Sum_probs=59.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ++|||+|||.++|+++|+++|++||+|..+.++.+. +|+++|||||+|.+.++|.+|++.|||..+.|+
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~   71 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGY   71 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCE
Confidence            699999999999999999999999999988887765 899999999999999999999999999988773

>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=99.54  E-value=5.7e-15  Score=116.99  Aligned_cols=67  Identities=34%  Similarity=0.510  Sum_probs=61.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CC---CceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DG---KLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        35 lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg---~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      |||+|||.++++++|+++|++||+|.++++++++ ++   +++|||||+|.+.++|.+|++.+||..+.|+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~   71 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGH   71 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTE
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            7999999999999999999999999999999876 33   5799999999999999999999999888773

>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=99.53  E-value=1.4e-14  Score=116.88  Aligned_cols=72  Identities=32%  Similarity=0.660  Sum_probs=65.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .....++|||+|||.++++++|+++|++||+|.+++++++..+ ++|||||+|.+.++|.+|+..|||..+.|
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~~Ai~~l~~~~~~g   78 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVVEG   78 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHHHHHHHcCCCEECC
Confidence            3446778999999999999999999999999999999988644 79999999999999999999999988876

>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=99.53  E-value=7.8e-15  Score=117.60  Aligned_cols=71  Identities=18%  Similarity=0.280  Sum_probs=64.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..+.++|||+|||.++++++|+++|++||+|.+++++++..+ ++|||||+|.+.++|.+|+..++|..+.|
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~-~~~~afV~f~~~~~A~~A~~~l~~~~~~g   75 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKILG   75 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc-cceeeEEEECCHHHHHHHHHHcCCCEECC
Confidence            456779999999999999999999999999999999988633 38999999999999999999999987776

>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=99.53  E-value=3.8e-15  Score=117.49  Aligned_cols=66  Identities=29%  Similarity=0.469  Sum_probs=61.5

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeEEE-EEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           35 LFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        35 lfVgnLp~~vte~~L~~~F~~~G~I~~i-~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      |||+|||.++++++|+++|++||.|.++ ++++++ +|+++|||||+|.+.++|.+|++.++|..+.|
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~g   68 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCN   68 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETT
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECC
Confidence            7999999999999999999999998765 788887 89999999999999999999999999987766

>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=99.52  E-value=5e-15  Score=118.52  Aligned_cols=69  Identities=28%  Similarity=0.516  Sum_probs=63.7

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..++|||+|||.++++++|+++|++||.|.+++++.+.. .++|||||+|.+.++|.+|++.|||..+.|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g   75 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLLND   75 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT-BCCSCEEEEESCHHHHHHHTTSSSEEEETT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC-CCcceeEEEECCHHHHHHHHHHcCCCEECC
Confidence            456899999999999999999999999999999998853 478999999999999999999999988876

>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=99.52  E-value=6.5e-15  Score=113.62  Aligned_cols=67  Identities=24%  Similarity=0.428  Sum_probs=63.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           34 RLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        34 ~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      +|||+|||+++|+++|+++|++||.|.++.+++++ +|.++|||||+|.+.++|.+|++ +||..+.|+
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr   68 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNK   68 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTB
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCe
Confidence            59999999999999999999999999999998887 89999999999999999999996 999988874

>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=99.51  E-value=9e-15  Score=120.44  Aligned_cols=68  Identities=24%  Similarity=0.547  Sum_probs=63.0

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .++|||+|||+++++++|+++|++||.|.++.|++++ ++.++|||||+|.+.++|.+|++ +++..+.|
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G   88 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDG   88 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETT
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECC
Confidence            4789999999999999999999999999999999987 88999999999999999999985 67776666

>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=99.51  E-value=2e-14  Score=116.48  Aligned_cols=70  Identities=26%  Similarity=0.463  Sum_probs=64.1

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPY   98 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f   98 (451)
                      ..+.++|||+|||.++++++|+++|++||+|.++.++.+. ++.++|||||+|.+.++|.+|++.+|+...
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~   75 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAE   75 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTT
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccc
Confidence            4467899999999999999999999999999999999887 889999999999999999999999886543

>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=99.50  E-value=7.8e-15  Score=116.64  Aligned_cols=71  Identities=23%  Similarity=0.387  Sum_probs=61.2

Q ss_pred             CCCceEEEcCCCCCCC-HHHHHHHhccCCCeEEEEEeECC--CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           30 TKRGRLFIKNLPFKIT-EEEFKEHFGQYGDIIDAQLLKNA--DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vt-e~~L~~~F~~~G~I~~i~l~~d~--tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .+.++|||+|||.+++ +++|+++|++||.|.++++.++.  +|+++|||||+|.+.++|.+|++ +||..+.|+
T Consensus         2 ~e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr   75 (86)
T d2ghpa3           2 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNR   75 (86)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTE
T ss_pred             CCCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCE
Confidence            3578999999999986 56699999999999999997753  89999999999999999999995 999888773

>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=99.49  E-value=1.2e-14  Score=116.38  Aligned_cols=72  Identities=19%  Similarity=0.395  Sum_probs=64.4

Q ss_pred             CCCceEEEcCCCCCCCHHHH---HHHhccCCCeEEEEEeECC-CCC---ceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEF---KEHFGQYGDIIDAQLLKNA-DGK---LKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L---~~~F~~~G~I~~i~l~~d~-tg~---skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .+.++|||+|||+++++++|   .++|++||+|.++.+++++ ++.   ++|||||+|.+.++|.+|++.|||..+.|+
T Consensus         6 iq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr   84 (89)
T d2cpia1           6 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   84 (89)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             EecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCE
Confidence            45678999999999999999   6789999999999999986 443   459999999999999999999999998874

>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=99.47  E-value=2.8e-14  Score=115.66  Aligned_cols=66  Identities=26%  Similarity=0.349  Sum_probs=60.8

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCC-eEEEEEeECC--CCCceeEEEEEEccHHHHHHHHHhcCCcc
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFGQYGD-IIDAQLLKNA--DGKLKGCGFINYANKISAVKAILKSNKKP   97 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~~~G~-I~~i~l~~d~--tg~skG~aFV~F~~~~~A~~Al~~lng~~   97 (451)
                      +++|||+|||.++++++|+++|++||+ |.+++++++.  +|+++|||||+|.+.++|.+|++.|++..
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~   69 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGR   69 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCC
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCC
Confidence            479999999999999999999999996 9999999875  68999999999999999999999987643

>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=99.47  E-value=6.9e-14  Score=110.24  Aligned_cols=70  Identities=17%  Similarity=0.274  Sum_probs=63.0

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .+.+++++|||+|||.++++++|.++|++||+|.+++++++    .+|||||+|.+.++|.+|+..|+|..+.+
T Consensus         3 ~~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~~~   72 (83)
T d2b0ga1           3 TEQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN----RHDIAFVEFTTELQSNAAKEALQGFKITP   72 (83)
T ss_dssp             CCCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT----TCSCEEEEESSHHHHHHHHHHHTTCBSST
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc----cceeEEEecCCHHHHHHHHHHhCCcEeCC
Confidence            34567889999999999999999999999999999999754    47899999999999999999999987753

>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=99.46  E-value=4.2e-14  Score=115.26  Aligned_cols=72  Identities=19%  Similarity=0.360  Sum_probs=64.6

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeE--------EEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDII--------DAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYK   99 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~--------~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~   99 (451)
                      ....++|||+|||.++++++|+++|++||+|.        .+.+.++. +|+++|||||+|.+.++|.+|++.+||..|.
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            45678999999999999999999999999984        45666666 7999999999999999999999999998887


Q ss_pred             C
Q psy300          100 G  100 (451)
Q Consensus       100 G  100 (451)
                      |
T Consensus        85 g   85 (101)
T d2cpea1          85 G   85 (101)
T ss_dssp             T
T ss_pred             C
Confidence            6

>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=99.46  E-value=3.9e-15  Score=119.79  Aligned_cols=72  Identities=19%  Similarity=0.190  Sum_probs=65.5

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .....+|||+|||.++++++|+++|++||.|.+++++.+.+|+++|||||+|.+.++|.+|++ +||..+.|+
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~   81 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGN   81 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTE
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCE
Confidence            335679999999999999999999999999999998877799999999999999999999995 899888773

>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=99.45  E-value=5.5e-14  Score=111.70  Aligned_cols=67  Identities=40%  Similarity=0.658  Sum_probs=62.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .+.++|||+|||.++++++|+++|++||+|.++++.++     +|||||+|.+.++|.+|+..|||..+.|+
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~-----k~~afV~f~~~~~A~~A~~~l~g~~i~g~   72 (86)
T d2cpja1           6 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPLRGK   72 (86)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCBTTB
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc-----cceEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            45678999999999999999999999999999999854     78999999999999999999999988873

>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=99.45  E-value=5.9e-14  Score=111.20  Aligned_cols=73  Identities=22%  Similarity=0.382  Sum_probs=65.3

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEE-EEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIID-AQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~-i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      .+..++|||+|||+++++++|+++|+.||.+.. +.+..+.+|+++|+|||+|.+.++|.+|++.+|++.+.|+
T Consensus         6 ~p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr   79 (86)
T d2cqpa1           6 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSR   79 (86)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCE
Confidence            345678999999999999999999999999876 4666667999999999999999999999999999988763

>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=99.45  E-value=7.9e-14  Score=107.93  Aligned_cols=67  Identities=21%  Similarity=0.265  Sum_probs=60.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ++|||+|||+++++++|+++|++||+|.++++.+++.+. +|||||+|.++++|.+|+. ++++.+.|+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~-~~~afV~F~~~~~a~~Al~-~~~~~i~g~   67 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN-FRFARIEFARYDGALAAIT-KTHKVVGQN   67 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS-SEEEEEEESSHHHHHHHHT-TTTCEETTE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc-ceEEEEEEcchHHhHHHHH-hcCcEECCE
Confidence            589999999999999999999999999999999987554 5799999999999999984 899888773

>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=99.45  E-value=1.6e-14  Score=118.18  Aligned_cols=73  Identities=25%  Similarity=0.393  Sum_probs=67.4

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ..++++|||+|||.++++++|+++|++||.|..+.++.+. +|+++|||||+|.+.++|.+|+..|||..+.|+
T Consensus        15 ~~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~   88 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGK   88 (102)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCE
Confidence            3467899999999999999999999999999999988876 899999999999999999999999999887763

>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=99.44  E-value=1.2e-13  Score=111.65  Aligned_cols=71  Identities=23%  Similarity=0.414  Sum_probs=63.7

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      .....++|||+|||+++++++|+++|++||.|..+.+.++  +.++|||||+|.+.++|.+|++.||+..|.|
T Consensus        10 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~--~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g   80 (95)
T d1x4aa1          10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDG   80 (95)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEETT
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc--ccccceEEEEECCHHHHHHHHHHhCCCEECC
Confidence            3456779999999999999999999999999999887544  5678999999999999999999999998876

>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=99.44  E-value=7.3e-14  Score=113.34  Aligned_cols=66  Identities=21%  Similarity=0.503  Sum_probs=61.7

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      +..++|||+|||.++++++|+++|++||+|.+++++++     +|||||+|.+.++|.+|+..|||+.+.|
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~-----kg~afV~f~~~~~A~~Ai~~l~~~~i~g   81 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTIEG   81 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            45679999999999999999999999999999999865     8999999999999999999999988876

>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=99.43  E-value=6.5e-14  Score=116.02  Aligned_cols=65  Identities=18%  Similarity=0.277  Sum_probs=60.2

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..++|||+|||.++++++|+++|++||+|.+|.|.     .++|||||+|.+.++|.+|++.|||..|.|
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~-----~~kg~afV~f~~~~~A~~A~~~lng~~~~g   73 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP-----EGGITAIVEFLEPLEARKAFRHLAYSKFHH   73 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC-----SSSSCEEEEESCHHHHHHHHHHHTTCBSSS
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee-----ccCceEEEEEcCHHHHHHHHHHHcCCccCC
Confidence            55799999999999999999999999999999884     358999999999999999999999998876

>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=99.42  E-value=7.9e-14  Score=110.94  Aligned_cols=63  Identities=21%  Similarity=0.449  Sum_probs=58.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ++|||+|||+++++++|+++|++||+|.++++.+      .|||||+|.+.++|++|+..|||..|.|+
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~l~g~~~~g~   63 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYR------DGTGVVEFVRKEDMTYAVRKLDNTKFRSH   63 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECT------TSEEEEEESSHHHHHHHHHHHTTCBCCCT
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccc------cceeeEEeCCHHHHHHHHHHhCCCEECCc
Confidence            4799999999999999999999999999999864      38999999999999999999999999873

>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=99.42  E-value=1.3e-13  Score=114.00  Aligned_cols=69  Identities=17%  Similarity=0.324  Sum_probs=62.8

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..+..+|||+|||.++|+++|+++|++||.|.++.++++   +++|||||+|.+.++|.+|+..+||..+.+
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~---~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~   72 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDGQNIYN   72 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEE---TTEEEEEEEESCHHHHHHHHHHHHSCCSST
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEee---CCCCeEEEEECCHHHHHHHHHHHCCCEecc
Confidence            446779999999999999999999999999999999876   468999999999999999999999987753

>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=99.42  E-value=1e-13  Score=115.52  Aligned_cols=77  Identities=19%  Similarity=0.380  Sum_probs=65.8

Q ss_pred             cCCCCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEE-EeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           24 RKKPDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQ-LLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        24 ~~~~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~-l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      +.+.......+|||+|||+++|+++|+++|+.||.+..+. +..+.+|.++|||||+|.+.++|.+|+. +||..+.|+
T Consensus        10 ~~~~~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR   87 (112)
T d1wela1          10 RSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNR   87 (112)
T ss_dssp             CCSSCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTS
T ss_pred             CCCCCCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCE
Confidence            3344455677999999999999999999999999987654 4455699999999999999999999985 899999885

>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=99.41  E-value=1.9e-13  Score=112.06  Aligned_cols=70  Identities=29%  Similarity=0.487  Sum_probs=61.7

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC--CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA--DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~--tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..+.++|||+|||.++++++|+++|++|| +.+++++.+.  +|+++|||||+|.+.++|++|+ .+|+..+.|
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~g   83 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGN   83 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETT
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECC
Confidence            34668999999999999999999999999 7788887765  7899999999999999998776 589887776

>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=99.41  E-value=3.6e-13  Score=110.57  Aligned_cols=73  Identities=23%  Similarity=0.377  Sum_probs=63.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeEC-CCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d-~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      +......|||+|||+++++++|+++|+.+|.+....++.+ .+++++|||||+|.++++|++|+. +++..+.|+
T Consensus        11 ~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR   84 (104)
T d1wg5a_          11 DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHR   84 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSS
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcce
Confidence            4446678999999999999999999999999887655554 499999999999999999999985 888877764

>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=99.41  E-value=2.6e-13  Score=111.12  Aligned_cols=72  Identities=19%  Similarity=0.395  Sum_probs=64.2

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ......+|||+|||+++|+++|+++|+.+|. .++.++++.+|.++|||||+|.+.++|++|++ +|++.+.|+
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR   82 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANMQHR   82 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSS
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEECCE
Confidence            3456679999999999999999999999984 57888888899999999999999999999985 899888774

>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=99.40  E-value=1.9e-13  Score=112.91  Aligned_cols=66  Identities=27%  Similarity=0.377  Sum_probs=60.5

Q ss_pred             CceEEEcCCCC-CCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           32 RGRLFIKNLPF-KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        32 ~~~lfVgnLp~-~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      +++|||+|||+ .+++++|+++|++||.|.+++++++    .+|||||+|.+.++|.+|++.+||..+.|+
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~----~kg~afV~f~~~~~A~~ai~~lng~~l~g~   68 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN----KKENALVQMADGNQAQLAMSHLNGHKLHGK   68 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCT----TSCCEEEEESCHHHHHHHHHHHTTCBCSSS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEec----ccceEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            67999999965 5999999999999999999999876    378999999999999999999999988764

>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=99.39  E-value=7.3e-14  Score=109.42  Aligned_cols=64  Identities=27%  Similarity=0.460  Sum_probs=57.4

Q ss_pred             CceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCcc-CCC
Q psy300           32 RGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP-YKG  100 (451)
Q Consensus        32 ~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~-f~G  100 (451)
                      +++|||+|||.++++++|+++|++||.|.++++.+     ++|||||+|.+.++|.+|++.|||.. +.|
T Consensus         1 mn~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~-----~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G   65 (80)
T d2cqha1           1 MNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----KSGYAFVDYPDQNWAIRAIETLSGKVELHG   65 (80)
T ss_dssp             CCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-----ETTEEEECCSCHHHHHHHHHHHTTTCEETT
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec-----ccceEEEEECCHHHHHHHHHHhCCCeEECC
Confidence            46899999999999999999999999998777654     48999999999999999999999864 665

>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=99.38  E-value=3.8e-13  Score=109.11  Aligned_cols=67  Identities=21%  Similarity=0.322  Sum_probs=61.9

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..+.++|||+|||.++++++|+++|++||+|.++++.++     ++||||+|.+.++|.+|++.||+..+.|
T Consensus        14 ~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~-----~~~afV~f~~~~~A~~A~~~l~~~~i~g   80 (97)
T d1whya_          14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPLGG   80 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBCSS
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc-----ccEEEeccCCHHHHHHHHHHhCCCEeCC
Confidence            346789999999999999999999999999999999754     7899999999999999999999988876

>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=99.38  E-value=1.1e-13  Score=110.99  Aligned_cols=68  Identities=26%  Similarity=0.479  Sum_probs=61.1

Q ss_pred             CCceEEEcCCCCCCCHHHHH----HHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFK----EHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~----~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ++++|||+|||.++++++|+    ++|++||+|.+|++.+  +++++|||||+|.+.++|.+|++.+||..+.|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~--~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g   73 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPFYD   73 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee--eccCCCceEEEECCHHHHHHHHHHhCCCEECC
Confidence            57899999999999999885    4689999999988743  67789999999999999999999999988776

>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=99.38  E-value=2.1e-13  Score=110.40  Aligned_cols=68  Identities=32%  Similarity=0.447  Sum_probs=61.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..+.++|||+|||.++++++|+++|++||.|..++.    +++++|||||+|.+.++|.+|++.|||..+.|
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g   80 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDG   80 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee----cCccccEEEEEeCCHHHHHHHHHHcCCCEECC
Confidence            445689999999999999999999999998866542    78899999999999999999999999988776

>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=99.37  E-value=5.7e-13  Score=105.92  Aligned_cols=67  Identities=19%  Similarity=0.322  Sum_probs=59.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK   99 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~   99 (451)
                      +++++|||+|||.++++++|+++|++||.|.++.+..   ++++|||||+|.+.++|.+|+..|+|..+.
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~---~~~~~~afV~f~~~~~A~~A~~~l~~~~i~   74 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF---QKDRKMALIQMGSVEEAVQALIDLHNHDLG   74 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC---SSSTTCEEEEESSHHHHHHHHHHHTTCBSS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee---ecccceeEEEECCHHHHHHHHHhccCCEec
Confidence            4678999999999999999999999999998887654   356789999999999999999999997663

>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=99.37  E-value=2.3e-13  Score=111.50  Aligned_cols=79  Identities=23%  Similarity=0.335  Sum_probs=66.8

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEE-EEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC------Cc
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDA-QLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK------IT  103 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i-~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~------~t  103 (451)
                      ...+|||+|||+++++++|+++|+.||.+..+ .+..+.+|+++|||||+|.+.++|++|++ +|+..|.|+      ++
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECC
Confidence            45679999999999999999999999998764 55555699999999999999999999996 899988884      35


Q ss_pred             HHHHHHH
Q psy300          104 EEEFKEH  110 (451)
Q Consensus       104 ee~L~~~  110 (451)
                      .++..+.
T Consensus        86 ~~~~~~~   92 (103)
T d2cpya1          86 LEDMREI   92 (103)
T ss_dssp             HHHHHHH
T ss_pred             HHHhhhh
Confidence            5555554

>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=99.36  E-value=4.9e-13  Score=108.79  Aligned_cols=65  Identities=26%  Similarity=0.550  Sum_probs=58.4

Q ss_pred             CCCCceEEEcCCC-CCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLP-FKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp-~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ....++|||+||| ..+++++|+++|++||+|.++++       ++|||||+|.+.++|.+|++.|||+.+.|
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i-------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g   77 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVAGEDGRMIAG   77 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE-------ETEEEEEEESSHHHHHHHHHTTTTCEETT
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE-------eCCeEEEEECCHHHHHHHHHHcCCCEECC
Confidence            3456789999997 57889999999999999999998       47999999999999999999999987766

>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=99.34  E-value=1.2e-12  Score=106.50  Aligned_cols=67  Identities=22%  Similarity=0.410  Sum_probs=61.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ....++|||+|||.++++++|+++|++||+|.++.+.+      +|||||+|.+.++|++|++.|||..|.|+
T Consensus        12 ~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~lng~~~~g~   78 (98)
T d1wg4a_          12 RRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK------DGMGMVEYLRKEDMEYALRKLDDTKFRSH   78 (98)
T ss_dssp             CSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET------TTEEEEEESSHHHHHHHHHHHSSEEEECT
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc------cceEEEEECCHHHHHHHHHHhCCCEeCCe
Confidence            34567899999999999999999999999999999853      58999999999999999999999988873

>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=99.34  E-value=6.8e-13  Score=103.44  Aligned_cols=65  Identities=23%  Similarity=0.415  Sum_probs=59.0

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ...++|||+|++  +|+++|+++|++||.|.++++.+     ++|||||+|.+.++|.+|+..|||..+.|+
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~-----~~~~afV~f~~~~~A~~Ai~~lng~~~~g~   67 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP-----PRNCAFVTYEKMESADQAVAELNGTQVESV   67 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET-----TTTEEEEECSSHHHHHHHHHHHTTCBCSSC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeecc-----CCCEEEEEEcccHHHHHHHHHhCCCEECCE
Confidence            356799999985  89999999999999999999864     478999999999999999999999988873

>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=99.34  E-value=1.2e-12  Score=103.47  Aligned_cols=65  Identities=23%  Similarity=0.384  Sum_probs=59.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..++|||+|||.++++++|+++|++||.|..+.+.     +++|||||+|.+.++|.+|+..|||..+.|
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~-----~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g   71 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK-----KIRDYAFVHFSNREDAVEAMKALNGKVLDG   71 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE-----ECSSEEEEEESSHHHHHHHHHHHSSEEETT
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc-----cccEEEEEEeCCHHHHHHHHHHcCCCEECC
Confidence            45799999999999999999999999999887774     458999999999999999999999988776

>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=99.32  E-value=1.9e-12  Score=102.85  Aligned_cols=69  Identities=22%  Similarity=0.288  Sum_probs=60.0

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcC--CccCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN--KKPYKG  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~ln--g~~f~G  100 (451)
                      .+..++++|||+|||.++++++|+++|++||.|.++++.++     +|||||+|.+.++|.+|++.++  +..+.|
T Consensus         3 ~~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~-----~~~afV~f~~~e~A~~a~~~~~~~~~~~~g   73 (88)
T d2cq1a1           3 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYSAVTPHLRN   73 (88)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHHSCCEETT
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc-----ceEEEEEeCCHHHHHHHHHHHccCCCccCC
Confidence            45678999999999999999999999999999999998754     6899999999999999998654  444444

>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=99.31  E-value=1.3e-12  Score=106.30  Aligned_cols=70  Identities=17%  Similarity=0.288  Sum_probs=60.0

Q ss_pred             CCCCCCceEEEcCCCCC-CCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHH--hcCCccCCCC
Q psy300           27 PDKTKRGRLFIKNLPFK-ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL--KSNKKPYKGK  101 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~-vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~--~lng~~f~G~  101 (451)
                      +.....++|||+|||.+ +|+++|.++|++||.|.+++++++     +|||||+|.+.++|.+|++  .+++..+.|+
T Consensus        13 ~~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~-----k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr   85 (99)
T d1x4fa1          13 QKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDHCLKKALWFQGR   85 (99)
T ss_dssp             CSSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHHHHHSCCCSSSS
T ss_pred             cCCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec-----CCcEEEEecchHHHHHHHHHHhcCCceECCE
Confidence            34456789999999985 899999999999999999999754     7899999999999999997  4666666663

>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=99.29  E-value=2.6e-12  Score=99.16  Aligned_cols=61  Identities=23%  Similarity=0.384  Sum_probs=54.4

Q ss_pred             EEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           35 LFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        35 lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      |||+|||+++++++|+++|++|| +..+.+     ++++|||||+|.+.++|.+|+..|||..+.|+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~-----~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~   61 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV-----DKYKGTAFVTLLNGEQAEAAINTFHQSRLRER   61 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE-----ETTTTEEEEEESSHHHHHHHHHHHTTEESSSC
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee-----cccceeEEEEECCHHHHHHHHHHhCCccCCCC
Confidence            79999999999999999999999 444443     46799999999999999999999999988773

>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=99.29  E-value=7.6e-13  Score=105.35  Aligned_cols=65  Identities=25%  Similarity=0.440  Sum_probs=56.2

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ...++|||+|||.++++++|+++|++||.|.++++.    +.++|||||+|.+.++|++|+.  ++..+.|
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~----~~~~gfafV~f~~~~~a~~a~~--~~~~i~g   67 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP----KPFRAFAFVTFADDQIAQSLCG--EDLIIKG   67 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC----SSCCSCCEEECSCHHHHHHTTT--CEEEETT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe----eccCceEEEEECCHHHHHHHHh--CCCEECC
Confidence            467899999999999999999999999999999874    3578999999999999999975  4544444

>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=99.29  E-value=1.2e-12  Score=104.20  Aligned_cols=65  Identities=20%  Similarity=0.295  Sum_probs=55.9

Q ss_pred             CCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           30 TKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        30 ~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ..+++|||+|||.++++++|+++|++||. ..+.+     ++++|||||+|.+.++|.+|+..||+..+.|
T Consensus         3 s~s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~~-----~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G   67 (88)
T d1wg1a_           3 SGSSGILVKNLPQDSNCQEVHDLLKDYDL-KYCYV-----DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRG   67 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSCC-CCEEE-----EGGGTEEEECCSCHHHHHHHHHHHTTEEETT
T ss_pred             CCCCEEEEeCCCCccChHHHHHHHHhcCc-eeeee-----eccCCceEEEECCHHHHHHHHHHhCCCEECC
Confidence            45689999999999999999999999992 22332     4578999999999999999999999987665

>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=99.25  E-value=1.2e-11  Score=101.25  Aligned_cols=63  Identities=14%  Similarity=0.221  Sum_probs=57.1

Q ss_pred             CCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCC
Q psy300           28 DKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK   95 (451)
Q Consensus        28 ~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng   95 (451)
                      ...++++|||+|||.++++++|.++|++||.|.++++.++     +|+|||+|.+.++|.+|+..+++
T Consensus        11 ~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~-----k~~AfV~f~~~e~A~~ai~~~~~   73 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAAD   73 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHH
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec-----ceeEEEEeCCHHHHHHHHHHHcC
Confidence            3457889999999999999999999999999999999754     78999999999999999987754

>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=99.24  E-value=1.8e-13  Score=109.40  Aligned_cols=68  Identities=21%  Similarity=0.338  Sum_probs=59.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeE-----C-CCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLK-----N-ADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~-----d-~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ++|||+|||.++|+++|+++|++||.+.++.+..     + .+++++|||||+|.+.++|.+|+. |||..+.|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr   75 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQ   75 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSS
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCE
Confidence            6899999999999999999999999987765532     2 267889999999999999999984 999999884

>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=99.23  E-value=1.4e-11  Score=109.98  Aligned_cols=73  Identities=19%  Similarity=0.424  Sum_probs=65.9

Q ss_pred             CCCCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-CCCceeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           27 PDKTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-DGKLKGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ......++|||+|||.++++++|+++|+.||.|..+.++.+. +|+++|||||+|.+.++|.+|++ +++..+.|
T Consensus        92 ~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G  165 (183)
T d1u1qa_          92 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNG  165 (183)
T ss_dssp             TTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETT
T ss_pred             ccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECC
Confidence            345567899999999999999999999999999999999987 89999999999999999999997 57766665

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.22  E-value=4.3e-12  Score=103.66  Aligned_cols=67  Identities=15%  Similarity=0.142  Sum_probs=59.2

Q ss_pred             CCCCCceEEEc--CCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCC
Q psy300           28 DKTKRGRLFIK--NLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK   99 (451)
Q Consensus        28 ~~~~~~~lfVg--nLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~   99 (451)
                      ...+.+++||+  |||.++|+++|+++|++||.|.+++++++     +|||||+|.+.++|.+|+..|||+.+.
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~-----k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC-----ccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            34567889995  59999999999999999999999988754     789999999999999999999997653

>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=99.21  E-value=5.6e-13  Score=109.69  Aligned_cols=69  Identities=20%  Similarity=0.352  Sum_probs=65.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      +.++|++++.++++++|+++|++||+|.+|+|+++.+|+++|||||+|.+.++|.+|++.|||+.|.|+
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr   96 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ   96 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCE
Confidence            568888999999999999999999999999999888999999999999999999999999999999885

>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=99.15  E-value=2.4e-11  Score=96.81  Aligned_cols=67  Identities=16%  Similarity=0.117  Sum_probs=57.7

Q ss_pred             CCCCceEEEcCCCCC-CCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhc--CCccCCC
Q psy300           29 KTKRGRLFIKNLPFK-ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS--NKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~-vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~l--ng~~f~G  100 (451)
                      ..+++.|||+|||.. +|++||.++|++||.|.++.++++     +++|||+|.+.++|..|+..+  ++..+.|
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~-----k~~afV~f~~~~~A~~A~~~l~~~~~~~~g   74 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYTTTPALVFG   74 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHHHSCCEETT
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc-----ceEEEEEEcchhhHHHHHHHHhhCCCccCC
Confidence            447789999999986 889999999999999999999765     679999999999999999866  4444554

>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=99.14  E-value=1.3e-11  Score=95.75  Aligned_cols=56  Identities=21%  Similarity=0.450  Sum_probs=53.4

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++++|+++|++||.|.+++++.+++|+++|||||+|.+.++|.+|+..+|++.+
T Consensus        11 ~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l   66 (78)
T d1no8a_          11 GVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPL   66 (78)
T ss_dssp             TCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEE
Confidence            58999999999999999999999999999999999999999999999999998765

>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=99.13  E-value=4.3e-11  Score=99.49  Aligned_cols=67  Identities=18%  Similarity=0.160  Sum_probs=59.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccH-HHHHHHHHhcCCccCCC
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANK-ISAVKAILKSNKKPYKG  100 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~-~~A~~Al~~lng~~f~G  100 (451)
                      ......+||||||.++|+++|+++|++||+|.+|.++++     +|||||.|.++ ++|..|+..+++..+.+
T Consensus         8 ~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~-----kg~gfV~F~~~~~~A~~a~~~~~~~~l~~   75 (113)
T d1owxa_           8 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEALGKAKDANNGNLQL   75 (113)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT-----CSEEEEEESSCHHHHHHHHHHTTTSCBCT
T ss_pred             CCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC-----CceEEEEecCcHHHHHHHHHHhcCCceec
Confidence            334567799999999999999999999999999999854     89999999996 67899999999887765

>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=99.11  E-value=1.3e-11  Score=101.22  Aligned_cols=68  Identities=25%  Similarity=0.275  Sum_probs=59.5

Q ss_pred             CCCCceEEEcCCCCCC-CH----HHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           29 KTKRGRLFIKNLPFKI-TE----EEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~v-te----~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ....++|||+||+.++ ++    ++|+++|++||.|.++++++     ++|||||+|.+.++|.+|+..|||..+.|+
T Consensus         2 ~~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k-----~~~~afV~f~~~~~A~~Ai~~lng~~~~g~   74 (104)
T d1weya_           2 SSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK-----SFKRVRINFSNPLSAADARLRLHKTEFLGK   74 (104)
T ss_dssp             CSCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET-----TTTEEEEECSSTTHHHHHHHTSTTSEETTE
T ss_pred             CCCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec-----CCCEEEEEECCHHHHHHHHHHhcccccCCC
Confidence            3567899999999886 33    56999999999999999974     588999999999999999999999988763

>d1twla_ b.40.5.1 (A:) Inorganic pyrophosphatase {Pyrococcus furiosus [TaxId: 2261]}

class: All beta proteins
fold: OB-fold
superfamily: Inorganic pyrophosphatase
family: Inorganic pyrophosphatase
domain: Inorganic pyrophosphatase
species: Pyrococcus furiosus [TaxId: 2261]

Probab=99.10  E-value=1.8e-11  Score=109.23  Aligned_cols=50  Identities=26%  Similarity=0.376  Sum_probs=39.6

Q ss_pred             CCccCCCccccCCCCEEEEEEeecCCCccceeeeccccceEEEEEeeCCCCch
Q psy300          386 SPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLYLVCFNLPSPLG  438 (451)
Q Consensus       386 s~~hd~~l~~~~~~~~~~~~~e~p~~~~~k~e~~~~~~~~~~~~~~~~~~~~~  438 (451)
                      |||||||++.+. .+++||||||||||++|+|++++......  -..|.+|+.
T Consensus         1 ~pwhdi~~~~~~-p~~vn~viEIP~gs~~KyE~dk~~g~~~~--dr~l~~~~~   50 (173)
T d1twla_           1 NPFHDLEPGPDV-PEVVYAIIEIPKGSRNKYELDKKTGLLKL--DRVLYSPFF   50 (173)
T ss_dssp             CHHHHSCSCSBT-TTBEEEEEEECTTCSEEEEECTTTCCEEE--EEECSSSCC
T ss_pred             CCccCCCCCCCC-CCeEEEEEEECCCCCcCEEEccCCCceee--eeecCCCcc
Confidence            899999998765 57999999999999999999998876443  334444443

>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=99.07  E-value=8.6e-11  Score=92.51  Aligned_cols=56  Identities=34%  Similarity=0.611  Sum_probs=52.6

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|.+++++++ .+|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        17 ~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~   73 (85)
T d1fxla2          17 TMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKP   73 (85)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             CCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEe
Confidence            5899999999999999999999998 4689999999999999999999999998776

>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=99.04  E-value=1.3e-10  Score=91.56  Aligned_cols=56  Identities=25%  Similarity=0.378  Sum_probs=52.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|++||.|.++++++| .+|.++|||||+|.+.++|..|+..+|+..+
T Consensus        12 ~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l   68 (85)
T d2u2fa_          12 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL   68 (85)
T ss_dssp             SCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCC
T ss_pred             CCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEE
Confidence            5899999999999999999999998 5699999999999999999999999988664

>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=99.00  E-value=1.5e-10  Score=90.50  Aligned_cols=64  Identities=19%  Similarity=0.287  Sum_probs=55.3

Q ss_pred             CCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCCCC
Q psy300           31 KRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYKGK  101 (451)
Q Consensus        31 ~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~G~  101 (451)
                      ..+.|+|+|+|++.+++.| +.|++||+|.++++.     +++|||||+|.++++|++|++ +||+.+.|+
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~-----~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~   66 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS-----NTGNWMHIRYQSKLQARKALS-KDGRIFGES   66 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC-----SSSSEEEEEESSHHHHHHHHT-TTTCEETTT
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEec-----CCCCEEEEEEcccHHHHHHHh-cCCCeECCc
Confidence            4568999999999986555 689999999999874     458999999999999999995 899988875

>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=99.00  E-value=2.5e-10  Score=88.69  Aligned_cols=56  Identities=20%  Similarity=0.344  Sum_probs=52.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|.+++++++ .+|+++|||||+|.++++|..|+..+|+..+
T Consensus        11 ~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~   67 (80)
T d1cvja1          11 DVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVI   67 (80)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEE
T ss_pred             cCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEE
Confidence            5899999999999999999999998 4689999999999999999999999998765

>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=98.99  E-value=1.1e-10  Score=95.61  Aligned_cols=56  Identities=23%  Similarity=0.420  Sum_probs=53.4

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.|+++.+|+++|||||+|.+.++|.+|+..+||+.|
T Consensus        38 ~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~   93 (104)
T d1jmta_          38 EFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWF   93 (104)
T ss_dssp             HHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEE
T ss_pred             hhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEE
Confidence            46889999999999999999999988999999999999999999999999999987

>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=98.98  E-value=4.1e-10  Score=88.38  Aligned_cols=56  Identities=29%  Similarity=0.593  Sum_probs=52.4

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.+++++++ .+|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        17 ~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   73 (85)
T d1b7fa2          17 TITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIP   73 (85)
T ss_dssp             TCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             CCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEe
Confidence            5899999999999999999999987 5789999999999999999999999998765

>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=98.97  E-value=2.5e-10  Score=89.16  Aligned_cols=56  Identities=25%  Similarity=0.440  Sum_probs=52.3

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|.++.++++ .+++++|||||+|.+.++|.+|+..+|+..+
T Consensus        20 ~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~   76 (83)
T d2cqca1          20 YTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL   76 (83)
T ss_dssp             SCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             CCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEE
Confidence            5899999999999999999999988 4689999999999999999999999998765

>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=98.97  E-value=1e-10  Score=90.05  Aligned_cols=53  Identities=25%  Similarity=0.449  Sum_probs=48.3

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCC
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNK  153 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~  153 (451)
                      ++|+++|+++|++||.|.++.++++ .+++++|||||+|.+.++|.+|+...++
T Consensus        10 ~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~~~   63 (75)
T d1x0fa1          10 DTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYH   63 (75)
T ss_dssp             SCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSC
T ss_pred             CCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhCCC
Confidence            5899999999999999999999988 5789999999999999999999976443

>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=98.97  E-value=2.2e-10  Score=91.70  Aligned_cols=61  Identities=26%  Similarity=0.416  Sum_probs=54.6

Q ss_pred             ccCCC----CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           96 KPYKG----KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        96 ~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|.|    .+|+++|+++|++||.|.++.++++ .+|.++|||||+|.+.++|.+|+..+|+..+
T Consensus        11 tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~   76 (93)
T d1x5ua1          11 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKL   76 (93)
T ss_dssp             EEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEE
Confidence            45555    5799999999999999999999987 5789999999999999999999999998764

>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=98.96  E-value=4.9e-10  Score=90.93  Aligned_cols=62  Identities=23%  Similarity=0.435  Sum_probs=56.3

Q ss_pred             ccCCC----CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCccc
Q psy300           96 KPYKG----KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK  157 (451)
Q Consensus        96 ~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy~  157 (451)
                      ++|.|    ++++++|+++|++||.|..+.+..+.++.++|||||+|.+.++|.+|+..+||+.+.
T Consensus        20 ~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~   85 (101)
T d1x5oa1          20 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIK   85 (101)
T ss_dssp             EEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCC
T ss_pred             EEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEEC
Confidence            35555    589999999999999999999999888999999999999999999999999998763

>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=98.96  E-value=4.3e-10  Score=88.94  Aligned_cols=56  Identities=27%  Similarity=0.411  Sum_probs=52.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|.+++++++ .+|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        18 ~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l   74 (88)
T d1rk8a_          18 EAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEI   74 (88)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEE
Confidence            5899999999999999999999997 5789999999999999999999999988654

>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=98.94  E-value=3e-10  Score=88.41  Aligned_cols=56  Identities=20%  Similarity=0.399  Sum_probs=51.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|.++.++++ .+|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        13 ~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~   69 (82)
T d1b7fa1          13 DMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITV   69 (82)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEE
Confidence            5899999999999999999999987 5789999999999999999999999998654

>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=98.93  E-value=3.7e-10  Score=86.65  Aligned_cols=54  Identities=22%  Similarity=0.525  Sum_probs=48.6

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKP  155 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~ri  155 (451)
                      ++|+++|+++|++||.|.++.++++ .+++++|||||+|.+.++|.+|+. +++..
T Consensus        10 ~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~   64 (75)
T d1hd0a_          10 DTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHK   64 (75)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCC
T ss_pred             cCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCE
Confidence            5899999999999999999999987 568999999999999999999997 45443

>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=98.93  E-value=2.3e-10  Score=90.77  Aligned_cols=62  Identities=24%  Similarity=0.417  Sum_probs=54.8

Q ss_pred             CccCCC----CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           95 KKPYKG----KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        95 g~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ..+|.|    .+++++|+++|++||.|.++.++++ .+|.++|||||+|.+.++|.+|+..+|+..+
T Consensus         6 ~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i   72 (89)
T d2cqba1           6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL   72 (89)
T ss_dssp             SCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEE
T ss_pred             cEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEE
Confidence            345555    5799999999999999999999987 4689999999999999999999999987654

>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=98.93  E-value=5.4e-10  Score=88.71  Aligned_cols=56  Identities=29%  Similarity=0.482  Sum_probs=52.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++++ .+|.++|||||+|.+.++|.+|+..+|+..+
T Consensus        19 ~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~   75 (90)
T d2cq0a1          19 DTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGY   75 (90)
T ss_dssp             TCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEE
Confidence            5899999999999999999999998 5689999999999999999999999998654

>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=98.92  E-value=8.7e-10  Score=88.10  Aligned_cols=56  Identities=25%  Similarity=0.277  Sum_probs=52.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|.++.++++ .++.++|||||+|.+.++|..|+..+|+..+
T Consensus        18 ~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~   74 (93)
T d1h2vz_          18 YTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRL   74 (93)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEE
T ss_pred             CCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEE
Confidence            5899999999999999999999987 5688999999999999999999999998765

>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=98.91  E-value=6.2e-10  Score=85.94  Aligned_cols=55  Identities=20%  Similarity=0.573  Sum_probs=49.4

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|++||.|.++.+++| .+|+++|||||+|.+.++|.+|+. +++..+
T Consensus        11 ~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i   66 (77)
T d1uawa_          11 QTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHEL   66 (77)
T ss_dssp             SCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCC
T ss_pred             cCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEE
Confidence            5799999999999999999999998 468999999999999999999996 566543

>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=98.91  E-value=4.6e-10  Score=88.96  Aligned_cols=63  Identities=25%  Similarity=0.516  Sum_probs=55.3

Q ss_pred             CCccCCC----CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           94 NKKPYKG----KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        94 ng~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++|.|    ++++++|+++|++||.|..+.++.+ .+|.++|||||+|.++++|..|+..+|+..+
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~   72 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSV   72 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCT
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEE
Confidence            3556666    5799999999999999999998875 6788999999999999999999999988654

>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=98.91  E-value=8.1e-10  Score=85.81  Aligned_cols=56  Identities=36%  Similarity=0.602  Sum_probs=51.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.+++++++ .+|.++|||||+|.+.++|..|+..+|+..+
T Consensus        13 ~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~   69 (82)
T d1fxla1          13 NMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRL   69 (82)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEE
Confidence            5899999999999999999999987 5689999999999999999999999988654

>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=98.91  E-value=5.7e-10  Score=87.54  Aligned_cols=59  Identities=25%  Similarity=0.540  Sum_probs=51.3

Q ss_pred             ccCCC----CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCc
Q psy300           96 KPYKG----KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKP  155 (451)
Q Consensus        96 ~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~ri  155 (451)
                      ++|.|    .+|+++|+++|++||.|.++.+++| .+|+++|||||+|.+.++|.+|+.. ++..
T Consensus         8 ~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~-~~~~   71 (84)
T d1l3ka1           8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHK   71 (84)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCE
T ss_pred             EEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHh-CCCE
Confidence            45555    5899999999999999999999998 4699999999999999999999975 4433

>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=98.90  E-value=7.3e-10  Score=90.22  Aligned_cols=56  Identities=30%  Similarity=0.591  Sum_probs=51.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++++ .+|+++|||||+|.+.++|..|+..+|+..+
T Consensus        19 ~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~   75 (104)
T d1p1ta_          19 EATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREF   75 (104)
T ss_dssp             TSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSC
T ss_pred             cCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEE
Confidence            5899999999999999999999987 5789999999999999999999999988654

>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=98.90  E-value=7.7e-10  Score=86.96  Aligned_cols=60  Identities=22%  Similarity=0.347  Sum_probs=52.5

Q ss_pred             ccCCC----CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           96 KPYKG----KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        96 ~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|.|    ++|+++|+++|+.||.|.++.+.++++|+++|||||+|.+.++|.+|+. +++..+
T Consensus         8 tvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~-~~~~~~   71 (85)
T d1zh5a2           8 SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE-TPGQKY   71 (85)
T ss_dssp             EEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHT-CCCCEE
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHH-HCCCEE
Confidence            45554    5899999999999999999999999899999999999999999999985 566544

>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=98.89  E-value=8.1e-10  Score=88.47  Aligned_cols=56  Identities=25%  Similarity=0.495  Sum_probs=50.6

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC--CCCCccceEEEEecchHHHHHHHHhc-CCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN--ADGKLKGCGFINYANKISAVKAILKS-NKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d--~~g~srG~gFV~F~s~e~A~~Ai~~l-n~riy  156 (451)
                      .+++++|+++|++||.|.++.++++  .+|+++|||||+|.+.++|.+|+..+ |+..+
T Consensus        19 ~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~   77 (94)
T d2cpha1          19 QANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHL   77 (94)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBS
T ss_pred             CCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEE
Confidence            5899999999999999999999876  46899999999999999999999998 66543

>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=98.89  E-value=4.6e-10  Score=85.18  Aligned_cols=58  Identities=21%  Similarity=0.407  Sum_probs=53.1

Q ss_pred             CCCCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           99 KGKITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        99 ~G~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ..++|+++|+++|++||.|..+.+.++ .++.++|||||+|.+.++|.+|+..+|++.+
T Consensus         7 p~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~   65 (72)
T d1x4ea1           7 QPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGV   65 (72)
T ss_dssp             CTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTC
T ss_pred             CCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEE
Confidence            346899999999999999999999887 5688999999999999999999999998876

>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=98.89  E-value=7.7e-10  Score=89.92  Aligned_cols=60  Identities=15%  Similarity=0.347  Sum_probs=53.2

Q ss_pred             ccCCC----CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           96 KPYKG----KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        96 ~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|.|    .+++++|+++|+.||.|.+++++++ .+|+++|||||+|.+.++|.+|+ .+|+..+
T Consensus        20 tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~-~l~g~~~   84 (101)
T d2cq4a1          20 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRL   84 (101)
T ss_dssp             EEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEE
T ss_pred             EEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHH-HHCCCEE
Confidence            45555    5899999999999999999999998 57999999999999999999999 5887654

>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=98.88  E-value=9.5e-10  Score=87.48  Aligned_cols=51  Identities=31%  Similarity=0.618  Sum_probs=47.6

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKS  151 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~l  151 (451)
                      ++|+++|+++|++||.|.++.+++| .+|+++|||||+|.+.++|.+|+...
T Consensus        19 ~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~   70 (90)
T d2cqga1          19 KTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR   70 (90)
T ss_dssp             SCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC
T ss_pred             CCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC
Confidence            5899999999999999999999998 46999999999999999999999754

>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=98.88  E-value=9.6e-10  Score=88.75  Aligned_cols=56  Identities=23%  Similarity=0.398  Sum_probs=52.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+ .+++++|||||+|.+.++|..|+..+|+..+
T Consensus        19 ~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~   75 (99)
T d1whwa_          19 TSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVF   75 (99)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEES
T ss_pred             cCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEE
Confidence            5899999999999999999999987 5789999999999999999999999998764

>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=98.87  E-value=1.1e-09  Score=85.73  Aligned_cols=56  Identities=27%  Similarity=0.354  Sum_probs=50.0

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCC----CCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNAD----GKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~----g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|++||.|.++.+++++.    +.++|||||+|.+.++|.+|+..+|+..+
T Consensus         9 ~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~   68 (85)
T d2cpfa1           9 STTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTV   68 (85)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEE
T ss_pred             CCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            689999999999999999999988632    24799999999999999999999998764

>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=98.84  E-value=1.2e-09  Score=93.61  Aligned_cols=56  Identities=23%  Similarity=0.429  Sum_probs=52.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|.++.++++ .+|+++|||||+|.+.++|..|+..+|+..+
T Consensus        53 ~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~  109 (139)
T d1u6fa1          53 TVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNI  109 (139)
T ss_dssp             TCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEEC
T ss_pred             CCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEE
Confidence            5899999999999999999999987 5689999999999999999999999998765

>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=98.84  E-value=1.7e-09  Score=84.25  Aligned_cols=56  Identities=27%  Similarity=0.468  Sum_probs=49.8

Q ss_pred             CCcHHHHHHHhcccCcceee-EEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDA-QLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v-~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|++||.|.++ .++++ .+|+++|||||+|.+.++|.+|+..+++..+
T Consensus         9 ~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~   66 (83)
T d1x5ta1           9 EIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYL   66 (83)
T ss_dssp             TCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEE
T ss_pred             cCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEE
Confidence            58999999999999998765 67777 5789999999999999999999999988654

>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=98.84  E-value=1.8e-09  Score=87.66  Aligned_cols=56  Identities=23%  Similarity=0.434  Sum_probs=52.0

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.+ .+|.++|||||+|.+.++|..|+..+|+..+
T Consensus        29 ~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~   85 (102)
T d2cpza1          29 EFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQI   85 (102)
T ss_dssp             SCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEE
Confidence            5899999999999999999999887 6789999999999999999999999998764

>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=98.83  E-value=1.5e-09  Score=88.35  Aligned_cols=54  Identities=28%  Similarity=0.543  Sum_probs=50.0

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCC
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKK  154 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~r  154 (451)
                      ++++++|+++|++||.|.++.++++ .+|+++|||||+|.+.++|.+|+..+++.
T Consensus        21 ~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~   75 (103)
T d2cqda1          21 HTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPI   75 (103)
T ss_dssp             SCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCE
T ss_pred             cCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCCc
Confidence            5899999999999999999999988 56899999999999999999999988753

>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=98.82  E-value=1.4e-09  Score=84.26  Aligned_cols=56  Identities=13%  Similarity=0.089  Sum_probs=46.4

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|++||.|..+.++.+ .+|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        12 ~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~   68 (81)
T d2ghpa1          12 SYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKI   68 (81)
T ss_dssp             TCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             cCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEE
Confidence            5899999999999999998888665 6789999999999999999999999998765

>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=98.80  E-value=2.4e-09  Score=86.61  Aligned_cols=70  Identities=17%  Similarity=0.356  Sum_probs=59.5

Q ss_pred             CCCCceEEEcCC--CCCCC---------HHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCcc
Q psy300           29 KTKRGRLFIKNL--PFKIT---------EEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP   97 (451)
Q Consensus        29 ~~~~~~lfVgnL--p~~vt---------e~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~   97 (451)
                      ....++|+|+|+  |.++.         +++|++.|++||.|.++++..+   .++|+|||+|.+.++|.+|+..|||..
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~---~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT---CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC---CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            457889999999  55432         2679999999999999988654   567999999999999999999999999


Q ss_pred             CCCC
Q psy300           98 YKGK  101 (451)
Q Consensus        98 f~G~  101 (451)
                      |.|+
T Consensus        82 ~~gr   85 (99)
T d2dita1          82 FGGR   85 (99)
T ss_dssp             ETTE
T ss_pred             ECCE
Confidence            8874

>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=98.80  E-value=1.8e-09  Score=82.28  Aligned_cols=55  Identities=24%  Similarity=0.383  Sum_probs=49.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|++||.+..+.++.+ .++.++|||||+|.+.++|.+|+. +|+..+
T Consensus        10 ~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l   65 (75)
T d2msta_          10 NTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEI   65 (75)
T ss_dssp             SCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCB
T ss_pred             CCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEE
Confidence            5899999999999999999999876 468899999999999999999985 887765

>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=98.79  E-value=2.3e-09  Score=88.51  Aligned_cols=54  Identities=26%  Similarity=0.386  Sum_probs=49.4

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++++..+  +.++|||||+|.+.++|..|+..+|+..+
T Consensus        18 ~~te~~l~~~F~~~G~v~~i~~~~~--~~~kG~afV~f~~~~~A~~Ai~~l~g~~~   71 (114)
T d2f9da1          18 KITAEEMYDIFGKYGPIRQIRVGNT--PETRGTAYVVYEDIFDAKNACDHLSGFNV   71 (114)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEEEECS--TTTTTEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHhhcCCeEeeccccc--CCcCCeEEEEECCHHHHHHHHHHhCCCEE
Confidence            5899999999999999999999864  56799999999999999999999998775

>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=98.78  E-value=4e-09  Score=84.08  Aligned_cols=55  Identities=29%  Similarity=0.596  Sum_probs=50.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.++.++.+ ++|||||+|.+.++|.+|+..+|+..+
T Consensus        22 ~~t~~~L~~~F~~~G~v~~v~~~~~~~~-~kg~afV~f~~~~~a~~Ai~~l~~~~~   76 (93)
T d2cq3a1          22 RFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRAREKLHGTVV   76 (93)
T ss_dssp             TCCHHHHHHHGGGTSCEEEEEEECCTTT-TCCEEEEEESCHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHhhcceeeeccccccccC-CcceeEEEECCHHHHHHHHHHcCCCEE
Confidence            5899999999999999999999988544 799999999999999999999988654

>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=98.78  E-value=3.2e-09  Score=81.75  Aligned_cols=55  Identities=22%  Similarity=0.448  Sum_probs=48.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|++||.|..+.++.+ .++.++|||||+|.+.++|.+|+ .+++..+
T Consensus        13 ~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al-~~~~~~l   68 (79)
T d1l3ka2          13 DTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTV   68 (79)
T ss_dssp             TCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHH-HCSCCEE
T ss_pred             cCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHH-HhCCCEE
Confidence            5899999999999999999999887 57889999999999999888888 4777654

>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=98.78  E-value=1.8e-09  Score=85.43  Aligned_cols=60  Identities=22%  Similarity=0.453  Sum_probs=52.5

Q ss_pred             ccCCC----CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           96 KPYKG----KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        96 ~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|.+    .+++++|+++|++||.|.++.++.+.. .++|||||+|.+.++|.+|+..+|+..+
T Consensus        10 ~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~-~~kg~afV~f~~~~~A~~Ai~~l~g~~~   73 (89)
T d1cvja2          10 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-GSKGYGFVHFETQEAAERAIEKMNGMLL   73 (89)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT-BCCSCEEEEESCHHHHHHHTTSSSEEEE
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC-CCcceeEEEECCHHHHHHHHHHcCCCEE
Confidence            35555    589999999999999999999998854 4789999999999999999999988654

>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=98.77  E-value=3e-09  Score=86.75  Aligned_cols=72  Identities=14%  Similarity=0.280  Sum_probs=61.2

Q ss_pred             CCCceEEEcCC--CCCCC--------HHHHHHHhccCCCeEEEEEeECC---CCCceeEEEEEEccHHHHHHHHHhcCCc
Q psy300           30 TKRGRLFIKNL--PFKIT--------EEEFKEHFGQYGDIIDAQLLKNA---DGKLKGCGFINYANKISAVKAILKSNKK   96 (451)
Q Consensus        30 ~~~~~lfVgnL--p~~vt--------e~~L~~~F~~~G~I~~i~l~~d~---tg~skG~aFV~F~~~~~A~~Al~~lng~   96 (451)
                      .+++.|.++|+  |.++.        .+||++.|++||.|.++.+.++.   ...+.|++||+|.+.++|.+|+..|||+
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            46788999999  55443        25689999999999999998865   2345799999999999999999999999


Q ss_pred             cCCCC
Q psy300           97 PYKGK  101 (451)
Q Consensus        97 ~f~G~  101 (451)
                      .|.|+
T Consensus        82 ~f~gR   86 (104)
T d1o0pa_          82 KFANR   86 (104)
T ss_dssp             CSSSS
T ss_pred             EECCe
Confidence            99996

>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=98.76  E-value=2.8e-09  Score=86.87  Aligned_cols=60  Identities=22%  Similarity=0.535  Sum_probs=51.8

Q ss_pred             CccCCC----CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCc
Q psy300           95 KKPYKG----KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKP  155 (451)
Q Consensus        95 g~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~ri  155 (451)
                      .++|.|    .+++++|+++|++||.|..+.+++| .++.++|||||+|.+.++|.+|+. +++..
T Consensus        21 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~   85 (103)
T d1x4ba1          21 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHS   85 (103)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEE
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCe
Confidence            356666    5899999999999999999999997 467899999999999999999985 56554

>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=98.74  E-value=3.2e-09  Score=84.10  Aligned_cols=55  Identities=16%  Similarity=0.243  Sum_probs=49.5

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|++||.|.++.++++..+ .+|||||+|.+.++|..|+..+++..+
T Consensus        19 ~~te~~l~~~F~~~G~i~~v~i~~d~~~-~~~~afV~f~~~~~A~~A~~~l~~~~~   73 (90)
T d2cqia1          19 DVTEVLILQLFSQIGPCKSCKMITEHTS-NDPYCFVEFYEHRDAAAALAAMNGRKI   73 (90)
T ss_dssp             TCCHHHHHHHHHHHSCEEEEEEECCCCS-SCCEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             CCCHHHHHHHHHhcCCceeeeeecccCc-cceeeEEEECCHHHHHHHHHHcCCCEE
Confidence            5899999999999999999999987543 489999999999999999999988654

>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=98.74  E-value=4.8e-09  Score=83.94  Aligned_cols=60  Identities=20%  Similarity=0.385  Sum_probs=52.8

Q ss_pred             ccCCC----CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCc
Q psy300           96 KPYKG----KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKP  155 (451)
Q Consensus        96 ~~f~G----~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~ri  155 (451)
                      ++|.|    ++|+++|+++|++||.|.++.+..+ .++.++|||||+|.+.++|.+|+..+++..
T Consensus        10 tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~   74 (98)
T d1x4ha1          10 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEA   74 (98)
T ss_dssp             CEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTT
T ss_pred             EEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHccccc
Confidence            45555    5899999999999999999999886 567899999999999999999999998654

>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=98.73  E-value=6e-09  Score=80.45  Aligned_cols=51  Identities=25%  Similarity=0.482  Sum_probs=47.0

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|.++.+.++     +|||||+|.+.++|..|+..+|+..+
T Consensus        14 ~~te~~L~~~F~~~G~I~~v~~~~~-----~~~afV~f~~~~~A~~Ai~~lng~~~   64 (79)
T d2bz2a1          14 DMTPTLLRGAFSPFGNIIDLSMDPP-----RNCAFVTYEKMESADQAVAELNGTQV   64 (79)
T ss_dssp             SCCHHHHHHHHSTTCCCSCEEEETT-----TTEEEEECSSHHHHHHHHHHHTTCBC
T ss_pred             CCCHHHHHHHHhccCccceeeeccC-----CCEEEEEEcccHHHHHHHHHhCCCEE
Confidence            3799999999999999999999865     78999999999999999999998765

>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=98.72  E-value=5.9e-09  Score=85.37  Aligned_cols=53  Identities=17%  Similarity=0.320  Sum_probs=48.5

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|++||.|.++.++.+   +++|||||+|.+.++|..|+..+|++.+
T Consensus        18 ~vte~~L~~~F~~~G~i~~~~i~~~---~~~g~aFV~f~~~e~A~~Ai~~ln~~~l   70 (108)
T d2adba1          18 PVTLDVLHQIFSKFGTVLKIITFTK---NNQFQALLQYADPVSAQHAKLSLDGQNI   70 (108)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEE---TTEEEEEEEESCHHHHHHHHHHHHSCCS
T ss_pred             CCCHHHHHHHHccCCcEEEEEEEee---CCCCeEEEEECCHHHHHHHHHHHCCCEe
Confidence            5899999999999999999999876   3589999999999999999999988754

>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=98.72  E-value=4.7e-09  Score=82.42  Aligned_cols=55  Identities=24%  Similarity=0.395  Sum_probs=45.2

Q ss_pred             CCc-HHHHHHHhcccCcceeeEEeeC--CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KIT-EEEFKEHFGQYGDIIDAQLLKN--ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~t-ee~L~~~F~~fG~V~~v~v~~d--~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      +++ +++|+++|++||.|.+++++.+  .+++++|||||+|.+.++|.+|+. +|+..+
T Consensus        15 ~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~   72 (86)
T d2ghpa3          15 ELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLL   72 (86)
T ss_dssp             TTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEE
T ss_pred             CcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEE
Confidence            344 5669999999999999999764  478899999999999999999995 887664

>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=98.70  E-value=6.4e-09  Score=84.94  Aligned_cols=52  Identities=25%  Similarity=0.353  Sum_probs=48.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|.++.+++++    +|||||+|++.++|.+|+..+|+..+
T Consensus        14 ~~te~~L~~~F~~fG~I~~v~i~~~~----kg~afV~f~~~~~A~~ai~~lng~~l   65 (109)
T d2adca1          14 RVTPQSLFILFGVYGDVQRVKILFNK----KENALVQMADGNQAQLAMSHLNGHKL   65 (109)
T ss_dssp             TCCHHHHHHHHHHHTCEEEEEECCTT----SCCEEEEESCHHHHHHHHHHHTTCBC
T ss_pred             cCCHHHHHHHHhhccccceEEEEecc----cceEEEEECCHHHHHHHHHHhCCCEE
Confidence            47999999999999999999999873    78999999999999999999998765

>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=98.69  E-value=6.2e-09  Score=81.91  Aligned_cols=50  Identities=20%  Similarity=0.429  Sum_probs=46.3

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.+.++      |||||+|.+.++|.+|+..||+..+
T Consensus        11 ~~~~~~l~~~F~~~G~v~~~~i~~~------g~afV~f~~~~~a~~Ai~~l~g~~~   60 (87)
T d3begb1          11 SGSWQDLKDHMREAGDVCYADVYRD------GTGVVEFVRKEDMTYAVRKLDNTKF   60 (87)
T ss_dssp             SCCTTHHHHHHGGGSCEEEEEECTT------SEEEEEESSHHHHHHHHHHHTTCBC
T ss_pred             cCCHHHHHHHHhhhccccccccccc------ceeeEEeCCHHHHHHHHHHhCCCEE
Confidence            5899999999999999999998753      8999999999999999999999876

>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=98.69  E-value=1.3e-09  Score=86.76  Aligned_cols=55  Identities=13%  Similarity=0.139  Sum_probs=50.5

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|.++.++.+.+|+++|||||+|.+.++|.+|+. +|+..+
T Consensus        24 ~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~   78 (91)
T d1fjeb1          24 NKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKV   78 (91)
T ss_dssp             TSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEE
T ss_pred             cchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHh-cCCcEE
Confidence            5899999999999999999999887889999999999999999999995 887654

>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=98.68  E-value=5.7e-09  Score=82.55  Aligned_cols=56  Identities=20%  Similarity=0.361  Sum_probs=48.8

Q ss_pred             CCcHHHH---HHHhcccCcceeeEEeeCC-CC---CccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEF---KEHFGQYGDIIDAQLLKNA-DG---KLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L---~~~F~~fG~V~~v~v~~d~-~g---~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++++|   .++|++||.|.++.+++++ ++   .++|||||+|.+.++|.+|+..+|+..+
T Consensus        19 ~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~   81 (89)
T d2cpia1          19 RLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVV   81 (89)
T ss_dssp             TTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEE
T ss_pred             ccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEE
Confidence            5789999   7789999999999999874 22   3459999999999999999999998776

>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=98.67  E-value=9.4e-09  Score=80.42  Aligned_cols=56  Identities=21%  Similarity=0.348  Sum_probs=50.6

Q ss_pred             CCcHHHHHHHhcccCccee-eEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIID-AQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~-v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++++|+++|+.||.+.. +.+..+++++++|+|||+|.+.++|.+|+..+|++.+
T Consensus        20 ~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l   76 (86)
T d2cqpa1          20 TVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPI   76 (86)
T ss_dssp             TCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEE
T ss_pred             CCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEE
Confidence            6899999999999999876 4566678899999999999999999999999998765

>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=98.67  E-value=5.7e-09  Score=83.56  Aligned_cols=54  Identities=22%  Similarity=0.282  Sum_probs=48.7

Q ss_pred             CCcHHHHHHHhcccCc-ceeeEEeeCC--CCCccceEEEEecchHHHHHHHHhcCCC
Q psy300          101 KITEEEFKEHFGQYGD-IIDAQLLKNA--DGKLKGCGFINYANKISAVKAILKSNKK  154 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~-V~~v~v~~d~--~g~srG~gFV~F~s~e~A~~Ai~~ln~r  154 (451)
                      .+++++|+++|++||. |.++.++++.  +++++|||||+|.++++|..|+..+++.
T Consensus        12 ~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~   68 (96)
T d2disa1          12 MKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPG   68 (96)
T ss_dssp             TSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTC
T ss_pred             cCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCC
Confidence            5899999999999996 8999998873  5789999999999999999999998754

>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=98.64  E-value=1.5e-08  Score=79.60  Aligned_cols=51  Identities=33%  Similarity=0.533  Sum_probs=47.6

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++++|+++|++||.|.++.+.++     +|||||+|.+.++|.+|+..+|+..+
T Consensus        19 ~~~~~~l~~~F~~~G~i~~i~~~~~-----k~~afV~f~~~~~A~~A~~~l~g~~i   69 (86)
T d2cpja1          19 DITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELDNMPL   69 (86)
T ss_dssp             TCCHHHHHHHTSTTCCCSEEEEETT-----TTEEEEECSSSHHHHHHHHHHTTCCB
T ss_pred             CCCHHHHHHHHHHhCCceEeeeecc-----cceEEEEECCHHHHHHHHHHhCCCEE
Confidence            5899999999999999999999876     78999999999999999999998765

>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=98.64  E-value=1.2e-08  Score=81.85  Aligned_cols=51  Identities=24%  Similarity=0.555  Sum_probs=47.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.+++++++     +|||||+|.+.++|.+|+..+|++.+
T Consensus        29 ~~te~~L~~~F~~fG~i~~v~i~~~-----kg~afV~f~~~~~A~~Ai~~l~~~~i   79 (96)
T d1x4ga1          29 GLTDQLMRQTFSPFGQIMEIRVFPE-----KGYSFVRFSTHESAAHAIVSVNGTTI   79 (96)
T ss_dssp             CCCHHHHHHHHHHHSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHHhCCceEEEEEec-----ceEEEEEECCHHHHHHHHHHhCCCEE
Confidence            5899999999999999999999976     89999999999999999999988765

>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=98.59  E-value=4e-08  Score=75.04  Aligned_cols=54  Identities=19%  Similarity=0.217  Sum_probs=47.5

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++++|+++|++||.|..++++.++.+. ++||||+|.+.++|.+|+ .+|++.+
T Consensus        11 ~~t~~~l~~~F~~~G~I~~v~~~~~~~~~-~~~afV~F~~~~~a~~Al-~~~~~~i   64 (75)
T d2ghpa2          11 SYNQNKVYKYFKHCGPIIHVDVADSLKKN-FRFARIEFARYDGALAAI-TKTHKVV   64 (75)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEEEEECTTSS-SEEEEEEESSHHHHHHHH-TTTTCEE
T ss_pred             CCCHHHHHHHHhcCCceEEEEEEeecccc-ceEEEEEEcchHHhHHHH-HhcCcEE
Confidence            58999999999999999999999886554 579999999999999998 5777654

>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=98.59  E-value=1.9e-08  Score=82.20  Aligned_cols=51  Identities=16%  Similarity=0.228  Sum_probs=46.6

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.+.+     ++|||||+|.+.++|.+|+..||+..+
T Consensus        21 ~~t~~~L~~~F~~fG~I~~v~l~~-----~kg~afV~f~~~~~A~~A~~~lng~~~   71 (111)
T d1whxa_          21 GTLAAEIQETFSRFGSLGRVLLPE-----GGITAIVEFLEPLEARKAFRHLAYSKF   71 (111)
T ss_dssp             TCCHHHHHHHHHTTSCEEEEECCS-----SSSCEEEEESCHHHHHHHHHHHTTCBS
T ss_pred             CCCHHHHHhhhhccCCccEEEeec-----cCceEEEEEcCHHHHHHHHHHHcCCcc
Confidence            589999999999999999998854     489999999999999999999998775

>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=98.57  E-value=1.1e-08  Score=82.49  Aligned_cols=56  Identities=21%  Similarity=0.378  Sum_probs=51.4

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++++|+++|++||.|..+.+..+ .+|+++|||||+|.+.++|.+|+..+|+..+
T Consensus        29 ~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~   85 (102)
T d2cpxa1          29 RVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKL   85 (102)
T ss_dssp             TCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBC
T ss_pred             CCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEE
Confidence            5899999999999999999999876 5789999999999999999999999988654

>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=98.57  E-value=2.5e-08  Score=80.24  Aligned_cols=49  Identities=22%  Similarity=0.491  Sum_probs=44.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|.++.+       ++|||||+|.+.++|.+|+..+|++.+
T Consensus        27 ~~~~~~L~~~F~~~G~i~~~~i-------~rg~aFV~f~~~~~A~~Ai~~lng~~~   75 (98)
T d1wf2a_          27 VVKKSDVEAIFSKYGKIVGCSV-------HKGFAFVQYVNERNARAAVAGEDGRMI   75 (98)
T ss_dssp             TCCHHHHHHSSTTSSCEEEEEE-------ETEEEEEEESSHHHHHHHHHTTTTCEE
T ss_pred             cCCHHHHHHHHhhcCCEEEEEE-------eCCeEEEEECCHHHHHHHHHHcCCCEE
Confidence            3678899999999999999998       379999999999999999999998765

>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=98.56  E-value=3.3e-08  Score=79.43  Aligned_cols=56  Identities=21%  Similarity=0.333  Sum_probs=48.0

Q ss_pred             CCcHHHHHHHhcccCccee--------eEEeeC-CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIID--------AQLLKN-ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~--------v~v~~d-~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|++||.|..        +.+..+ .+|+++|||||+|.++++|.+|+..+|+..+
T Consensus        19 ~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1          19 SVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             TCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            5899999999999999853        344454 4688999999999999999999999998765

>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=98.55  E-value=1.4e-08  Score=78.47  Aligned_cols=50  Identities=24%  Similarity=0.441  Sum_probs=45.9

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP  155 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~ri  155 (451)
                      ++|+++|+++|++||.|.++.+.+.     +|||||+|.+.++|.+|+..+|++.
T Consensus        12 ~~te~~L~~~F~~~G~i~~~~~~~~-----rg~aFV~f~~~~~A~~Ai~~lng~~   61 (80)
T d2cqha1          12 AVTADDLRQLFGDRKLPLAGQVLLK-----SGYAFVDYPDQNWAIRAIETLSGKV   61 (80)
T ss_dssp             TCCHHHHHHHHHHTTCCCSSCEEEE-----TTEEEECCSCHHHHHHHHHHHTTTC
T ss_pred             CCCHHHHHHHHHHhCcEEEeEEecc-----cceEEEEECCHHHHHHHHHHhCCCe
Confidence            5899999999999999998888765     8999999999999999999998764

>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=98.54  E-value=2.4e-08  Score=80.83  Aligned_cols=51  Identities=16%  Similarity=0.197  Sum_probs=47.1

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|++||.|..+.++++     +|||||+|.+.++|..|+..|||+..
T Consensus        31 ~vte~~L~~~F~~~G~i~~i~~~~~-----k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          31 GVSRNQLLPVLEKCGLVDALLMPPN-----KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             TCCHHHHHHHHHHHSCEEEEECCTT-----CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCHHHHHHHHHhhCcccEEeeccC-----ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            6899999999999999999998865     78999999999999999999998754

>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=98.52  E-value=4.2e-08  Score=78.24  Aligned_cols=54  Identities=20%  Similarity=0.354  Sum_probs=48.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|..+.+..+  +.++|||||+|.+.++|..|+..+|+..+
T Consensus        25 ~~t~~~l~~~F~~~G~v~~~~~~~~--~~~~g~afV~f~~~e~a~~Ai~~l~g~~~   78 (95)
T d1x4aa1          25 DIRTKDIEDVFYKYGAIRDIDLKNR--RGGPPFAFVEFEDPRDAEDAVYGRDGYDY   78 (95)
T ss_dssp             TCCHHHHHHHHGGGSCEEEEEECCS--SSSSCCEEEEESCHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHhcCCceEEEEeccc--ccccceEEEEECCHHHHHHHHHHhCCCEE
Confidence            5899999999999999999887654  34689999999999999999999998765

>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=98.52  E-value=6.6e-08  Score=75.07  Aligned_cols=52  Identities=13%  Similarity=0.211  Sum_probs=47.3

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|.++|++||.|.+++++++    .+|||||+|.+.++|..|+..+++..+
T Consensus        19 ~~t~~~l~~~f~~~G~i~~v~~~~~----~~g~afV~f~~~~~A~~A~~~l~g~~~   70 (83)
T d2b0ga1          19 ETNEMMLSMLFNQFPGFKEVRLVPN----RHDIAFVEFTTELQSNAAKEALQGFKI   70 (83)
T ss_dssp             TCCHHHHHHHHTTSTTEEEEEECTT----TCSCEEEEESSHHHHHHHHHHHTTCBS
T ss_pred             CCCHHHHHhhhccCccEEEeeeecc----cceeEEEecCCHHHHHHHHHHhCCcEe
Confidence            5899999999999999999999865    378999999999999999999988654

>d1qeza_ b.40.5.1 (A:) Inorganic pyrophosphatase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: All beta proteins
fold: OB-fold
superfamily: Inorganic pyrophosphatase
family: Inorganic pyrophosphatase
domain: Inorganic pyrophosphatase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=98.52  E-value=3.8e-08  Score=87.06  Aligned_cols=47  Identities=30%  Similarity=0.418  Sum_probs=37.3

Q ss_pred             ccCCccCCCccccCCCCEEEEEEeecCCCccceeeeccccceEEEEEeeCCCCchh
Q psy300          384 LISPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLYLVCFNLPSPLGY  439 (451)
Q Consensus       384 ~~s~~hd~~l~~~~~~~~~~~~~e~p~~~~~k~e~~~~~~~~~~~~~~~~~~~~~~  439 (451)
                      .||||||.|       +++||||||||||++|+|++++...  ..+--.|.+++.|
T Consensus         1 ~i~p~~~~p-------~~vn~viEIP~gs~~KyE~d~~~g~--~~~dr~l~~~~~y   47 (170)
T d1qeza_           1 KLSPGKNAP-------DVVNVLVEIPQGSNIKYEYDDEEGV--IKVDRVLYTSMNY   47 (170)
T ss_dssp             CCCSCTTTT-------TSEEEEEEECTTCCEEEEEETTTTE--EEEEEECSSSBCC
T ss_pred             CcCCCCCCC-------CeEEEEEEECCCCCeeEEEccCCCc--eEEEeeccccccC
Confidence            489999999       6899999999999999999987643  4444455665554

>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=98.50  E-value=6.2e-08  Score=78.27  Aligned_cols=54  Identities=20%  Similarity=0.356  Sum_probs=47.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|+.|| +..+.++.+.++.++|||||+|.+.++|.+|+. +|+..+
T Consensus        26 ~~te~dl~~~F~~~~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i   79 (102)
T d1weza_          26 RATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA-KDKANM   79 (102)
T ss_dssp             TCCHHHHHHSSCSCC-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHT-TSSCCS
T ss_pred             cCCHHHHHHHHhccC-cceeeeEEecCCcceEEEEEEECCHHHHHHHHH-cCCCEE
Confidence            589999999999998 457888888889999999999999999999975 787664

>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=98.47  E-value=9.2e-08  Score=76.51  Aligned_cols=51  Identities=20%  Similarity=0.312  Sum_probs=47.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++++|+++|++||.|..+++.++     ++||||+|.+.++|..|+..+|+..+
T Consensus        28 ~~t~~~l~~~f~~~G~i~~~~~~~~-----~~~afV~f~~~~~A~~A~~~l~~~~i   78 (97)
T d1whya_          28 NTSLAALAREFDRFGSIRTIDHVKG-----DSFAYIQYESLDAAQAACAKMRGFPL   78 (97)
T ss_dssp             SCCHHHHHHHHHTTSCEEEEEECSS-----SCCEEEEESSHHHHHHHHHHHTTCBC
T ss_pred             CCCHHHHHHHHHhhcccceEeeecc-----ccEEEeccCCHHHHHHHHHHhCCCEe
Confidence            5899999999999999999999865     78999999999999999999998765

>d2prda_ b.40.5.1 (A:) Inorganic pyrophosphatase {Thermus thermophilus [TaxId: 274]}

class: All beta proteins
fold: OB-fold
superfamily: Inorganic pyrophosphatase
family: Inorganic pyrophosphatase
domain: Inorganic pyrophosphatase
species: Thermus thermophilus [TaxId: 274]

Probab=98.46  E-value=7.5e-08  Score=85.37  Aligned_cols=51  Identities=22%  Similarity=0.354  Sum_probs=40.8

Q ss_pred             CCccCCCccccCCCCEEEEEEeecCCCccceeeeccccceEEEEEeeCCCCchh
Q psy300          386 SPFHDIPLYSNVKDKIFNMVVEIPRWTNAKMEVGNAMEMRLYLVCFNLPSPLGY  439 (451)
Q Consensus       386 s~~hd~~l~~~~~~~~~~~~~e~p~~~~~k~e~~~~~~~~~~~~~~~~~~~~~~  439 (451)
                      |-+|+||+..+. .+++||||||||||++|||+.++  .++.-+-..|+++..|
T Consensus         1 ~~l~~ip~g~~~-p~~vn~viEIP~gs~~KyE~d~~--~g~~~~dr~l~~~~~y   51 (174)
T d2prda_           1 ANLKSLPVGDKA-PEVVHMVIEVPRGSGNKYEYDPD--LGAIKLDRVLPGAQFY   51 (174)
T ss_dssp             CCGGGSCCCTTT-TTEEEEEEEECTTCCEEEEEETT--TTEEEEEEECSSSCCC
T ss_pred             CCHhHCCCCCCC-CCEEEEEEEECCCCCccEEEccC--CCcEEEEeecCCCCcC
Confidence            457999997554 58999999999999999999975  6777666667666554

>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=98.46  E-value=6.8e-08  Score=78.02  Aligned_cols=55  Identities=18%  Similarity=0.165  Sum_probs=47.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEE-eeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v-~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|+.||.+..+.+ +.+.+|+++|||||+|.+.++|.+|+. +|+..+
T Consensus        19 ~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i   74 (103)
T d2cpya1          19 SITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKL   74 (103)
T ss_dssp             TSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEE
T ss_pred             CCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeE
Confidence            6899999999999999887544 456889999999999999999999995 777654

>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=98.43  E-value=1.5e-07  Score=73.74  Aligned_cols=53  Identities=19%  Similarity=0.319  Sum_probs=46.3

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.|..+.+...   +++|||||+|++.++|.+|+..+++...
T Consensus        21 ~~te~~l~~~F~~~G~v~~~~~~~~---~~~~~afV~f~~~~~A~~A~~~l~~~~i   73 (88)
T d2adca2          21 SVSEEDLKVLFSSNGGVVKGFKFFQ---KDRKMALIQMGSVEEAVQALIDLHNHDL   73 (88)
T ss_dssp             TCCHHHHHHHHHTTSCCEEEEEECS---SSTTCEEEEESSHHHHHHHHHHHTTCBS
T ss_pred             CCCHHHHHHHhhccCCEEEEEEeee---cccceeEEEECCHHHHHHHHHhccCCEe
Confidence            5899999999999999988777654   3588999999999999999999988643

>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=98.42  E-value=1.1e-07  Score=76.26  Aligned_cols=50  Identities=24%  Similarity=0.411  Sum_probs=46.3

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++++|+++|++||.|.++.+.+      +|||||+|.+.++|.+|+..+|+..+
T Consensus        26 ~~~~~~L~~~F~~~G~v~~~~i~~------~g~afV~f~~~~~a~~Ai~~lng~~~   75 (98)
T d1wg4a_          26 SGSWQDLKDHMREAGDVCYADVQK------DGMGMVEYLRKEDMEYALRKLDDTKF   75 (98)
T ss_dssp             SCCHHHHHHHHTTSSCEEEEEEET------TTEEEEEESSHHHHHHHHHHHSSEEE
T ss_pred             CCCHHHHHHHHHhhcccccccccc------cceEEEEECCHHHHHHHHHHhCCCEe
Confidence            589999999999999999999864      58999999999999999999998876

>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=98.40  E-value=1.6e-07  Score=75.60  Aligned_cols=50  Identities=14%  Similarity=0.286  Sum_probs=45.8

Q ss_pred             HHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          104 EEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       104 ee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      +++|++.|++||.|..+.+..+   .++|||||+|.+.++|.+|+..+|++.|
T Consensus        33 ~edv~~~~~~~G~V~~v~~~~~---~~~G~~fV~f~~~e~A~~A~~~lng~~~   82 (99)
T d2dita1          33 REDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWF   82 (99)
T ss_dssp             HHHHHHHGGGTSCCSEEEEETT---CTTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             HHHHHHHhcCcccEEEEeccCC---CCccEEEEEECCHHHHHHHHHHhCCcEE
Confidence            5889999999999999988765   4589999999999999999999999987

>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=98.40  E-value=1.9e-07  Score=75.48  Aligned_cols=55  Identities=22%  Similarity=0.322  Sum_probs=46.6

Q ss_pred             CCcHHHHHHHhcccCcceeeEEe-eCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLL-KNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~-~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|+.+|.+....++ .+.+++++|||||+|.++++|.+|+. +|+..+
T Consensus        26 ~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i   81 (104)
T d1wg5a_          26 GCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERI   81 (104)
T ss_dssp             TCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCS
T ss_pred             CCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEE
Confidence            58999999999999998875554 45788999999999999999998885 766543

>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=98.40  E-value=1.3e-07  Score=76.46  Aligned_cols=54  Identities=28%  Similarity=0.465  Sum_probs=45.0

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeC--CCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKN--ADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d--~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|++|| +.++.++.+  .+++++|||||+|.+.++|.+|+ .+|+..+
T Consensus        26 ~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~   81 (104)
T d1wi8a_          26 DVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESL   81 (104)
T ss_dssp             SCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEE
T ss_pred             cCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEE
Confidence            589999999999999 677777665  46889999999999999997666 5877554

>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=98.39  E-value=1.4e-07  Score=76.59  Aligned_cols=54  Identities=26%  Similarity=0.339  Sum_probs=47.3

Q ss_pred             CCCCCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300           98 YKGKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus        98 f~G~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      +.-..+.++|+++|++||.|.++.++++     +|||||+|.+.++|.+|+..||++.+
T Consensus        18 ~~~d~~k~~l~~lF~~~G~i~~~~~~k~-----~~~afV~f~~~~~A~~Ai~~lng~~~   71 (104)
T d1weya_          18 FSESETRAKFESLFRTYDKDTTFQYFKS-----FKRVRINFSNPLSAADARLRLHKTEF   71 (104)
T ss_dssp             GSTTTHHHHHHHHHHTTCSSCEEEEETT-----TTEEEEECSSTTHHHHHHHTSTTSEE
T ss_pred             cCcHHHHHHHHHHhcccccceEEEEecC-----CCEEEEEECCHHHHHHHHHHhccccc
Confidence            3334566889999999999999999864     88999999999999999999999876

>d1i40a_ b.40.5.1 (A:) Inorganic pyrophosphatase {Escherichia coli [TaxId: 562]}

class: All beta proteins
fold: OB-fold
superfamily: Inorganic pyrophosphatase
family: Inorganic pyrophosphatase
domain: Inorganic pyrophosphatase
species: Escherichia coli [TaxId: 562]

Probab=98.38  E-value=1.1e-07  Score=84.28  Aligned_cols=49  Identities=18%  Similarity=0.291  Sum_probs=38.9

Q ss_pred             ccCCCccccCCCCEEEEEEeecCCCc-cceeeeccccceEEEEEeeCCCCchh
Q psy300          388 FHDIPLYSNVKDKIFNMVVEIPRWTN-AKMEVGNAMEMRLYLVCFNLPSPLGY  439 (451)
Q Consensus       388 ~hd~~l~~~~~~~~~~~~~e~p~~~~-~k~e~~~~~~~~~~~~~~~~~~~~~~  439 (451)
                      +||||++.+. .+++|||||||+||+ +|+|+.++  .+...+-..|++|+.|
T Consensus         2 l~dip~~~~~-p~~vn~vIEIP~gs~~~KyE~dk~--~g~~~~dr~l~~~~~y   51 (175)
T d1i40a_           2 LLNVPAGKDL-PEDIYVVIEIPANADPIKYEIDKE--SGALFVDRFMSTAMFY   51 (175)
T ss_dssp             GGGCCSCSBT-TTBEEEEEEECTTCCSEEEEECTT--TCCEEEEEECSSSCCC
T ss_pred             ccccCCCCCC-CCEEEEEEEecCCCCceeEEEecc--CCCEEEEEeccccccC
Confidence            6999998776 579999999999995 89999985  4555556666666655

>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=98.37  E-value=4.7e-08  Score=77.27  Aligned_cols=54  Identities=28%  Similarity=0.530  Sum_probs=45.8

Q ss_pred             CCcHHHHH----HHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFK----EHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~----~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++++|+    ++|++||.|.++.+.+  +++++|||||+|.+.++|.+|+..+|+..+
T Consensus        14 ~~t~~dl~~~l~~~f~~~G~i~~i~~~~--~~~~~g~afV~F~~~~~A~~A~~~~~~~~~   71 (91)
T d1nu4a_          14 KIKKDELKKSLHAIFSRFGQILDILVSR--SLKMRGQAFVIFKEVSSATNALRSMQGFPF   71 (91)
T ss_dssp             TSCHHHHHHHHHHHHGGGSCEEEEECCH--HHHHTTCEEEEESSHHHHHHHHHHHTTCEE
T ss_pred             CCCHHHHHHHHHHHhcccccccceEEee--eccCCCceEEEECCHHHHHHHHHHhCCCEE
Confidence            57888876    4689999999988764  456799999999999999999999987654

>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=98.37  E-value=1.9e-07  Score=71.05  Aligned_cols=50  Identities=22%  Similarity=0.315  Sum_probs=42.8

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++++++|+++|++|| +..+.+     ++++|||||+|.+.++|.+|+..+|++.+
T Consensus         9 ~~t~~~l~~~F~~~g-~~~~~~-----~~~~g~afv~f~~~~~A~~Ai~~ln~~~~   58 (75)
T d1wi6a1           9 DVTNQEVHDLLSDYE-LKYCFV-----DKYKGTAFVTLLNGEQAEAAINTFHQSRL   58 (75)
T ss_dssp             TCCHHHHHHHTTTSC-EEEEEE-----ETTTTEEEEEESSHHHHHHHHHHHTTEES
T ss_pred             cCCHHHHHHHHhccc-ccceee-----cccceeEEEEECCHHHHHHHHHHhCCccC
Confidence            589999999999999 444443     34689999999999999999999998775

>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=98.35  E-value=2.5e-07  Score=76.09  Aligned_cols=51  Identities=18%  Similarity=0.257  Sum_probs=45.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecch-HHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANK-ISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~-e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|.++.++++     +|||||+|.+. ++|..|+..+++...
T Consensus        22 ~~tee~Lk~~F~~fG~V~~v~i~~~-----kg~gfV~F~~~~~~A~~a~~~~~~~~l   73 (113)
T d1owxa_          22 QTCREDLHILFSNHGEIKWIDFVRG-----AKEGIILFKEKAKEALGKAKDANNGNL   73 (113)
T ss_dssp             SCCHHHHHHHTCSSCCEEEEECCTT-----CSEEEEEESSCHHHHHHHHHHTTTSCB
T ss_pred             CCCHHHHHHHHHhcCChheEEEecC-----CceEEEEecCcHHHHHHHHHHhcCCce
Confidence            5899999999999999999999875     79999999986 788999999987653

>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=98.34  E-value=1.9e-07  Score=76.64  Aligned_cols=55  Identities=18%  Similarity=0.316  Sum_probs=47.5

Q ss_pred             CCcHHHHHHHhcccCcceeeEE-eeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQL-LKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v-~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ++|+++|+++|+.||.+..+.+ ..+.+|.++|||||+|.+.++|.+|+. +|+..+
T Consensus        29 ~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i   84 (112)
T d1wela1          29 EAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYM   84 (112)
T ss_dssp             TCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCS
T ss_pred             cCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcC
Confidence            5899999999999999877655 456789999999999999999998885 887654

>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=98.34  E-value=2.9e-07  Score=74.54  Aligned_cols=54  Identities=15%  Similarity=0.281  Sum_probs=47.9

Q ss_pred             cHHHHHHHhcccCcceeeEEeeCCC---CCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          103 TEEEFKEHFGQYGDIIDAQLLKNAD---GKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       103 tee~L~~~F~~fG~V~~v~v~~d~~---g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      ..++|++.|++||.|.++.++++..   ....|++||+|.+.++|.+|+..|||+.|
T Consensus        27 i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~f   83 (104)
T d1o0pa_          27 IVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKF   83 (104)
T ss_dssp             HHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCCS
T ss_pred             HHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCEE
Confidence            4578999999999999999988643   33569999999999999999999999998

>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=98.33  E-value=2.9e-07  Score=71.69  Aligned_cols=51  Identities=22%  Similarity=0.332  Sum_probs=45.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++||.+..+.+.+     ++|||||+|.+.++|..|+..+|+..+
T Consensus        19 ~~te~~l~~~F~~~g~i~~~~~~~-----~rg~afV~f~~~~~A~~Ai~~l~~~~i   69 (86)
T d2cpda1          19 STSEEMIEKEFNNIKPGAVERVKK-----IRDYAFVHFSNREDAVEAMKALNGKVL   69 (86)
T ss_dssp             TCCHHHHHHHHHTTSTTCEEEEEE-----CSSEEEEEESSHHHHHHHHHHHSSEEE
T ss_pred             CCCHHHHHHhhcccceeeeEEEcc-----ccEEEEEEeCCHHHHHHHHHHcCCCEE
Confidence            589999999999999998887754     489999999999999999999988654

>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=98.31  E-value=1.8e-07  Score=74.61  Aligned_cols=52  Identities=31%  Similarity=0.422  Sum_probs=45.7

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.|..+.    .++.++|||||+|.+.++|.+|+..+|+..+
T Consensus        27 ~~te~~l~~~F~~~g~v~~~~----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~   78 (96)
T d1fjca_          27 NITEDELKEVFEDALEIRLVS----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEI   78 (96)
T ss_dssp             SCCHHHHHHHHCSEEEECCEE----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEE
T ss_pred             CCCHHHHHHHHHhcccceeee----ecCccccEEEEEeCCHHHHHHHHHHcCCCEE
Confidence            589999999999999987654    2567899999999999999999999987654

>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=98.29  E-value=2.7e-07  Score=74.05  Aligned_cols=45  Identities=18%  Similarity=0.267  Sum_probs=41.6

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHh
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILK  150 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~  150 (451)
                      .+|+++|.++|++||.|.++.++++     +|||||+|.+.++|.+|+..
T Consensus        30 ~~te~~l~~~F~~fG~V~~v~~~~~-----k~~afV~f~~~~~A~~Ai~~   74 (99)
T d1x4fa1          30 GYSDSAVLKLAEPYGKIKNYILMRM-----KSQAFIEMETREDAMAMVDH   74 (99)
T ss_dssp             SCCSHHHHTTTTTTSCCSEEEEETT-----TTEEEEECSSHHHHHHHHHH
T ss_pred             ccCHHHHHhhhccccceeEEEEeec-----CCcEEEEecchHHHHHHHHH
Confidence            4799999999999999999999875     78999999999999999974

>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=98.27  E-value=3.4e-07  Score=74.04  Aligned_cols=48  Identities=17%  Similarity=0.292  Sum_probs=44.0

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCC
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNK  153 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~  153 (451)
                      .+|+++|+++|++||.|..+.+.++     +|+|||+|.+.++|..|+..++.
T Consensus        26 ~~te~~l~~~F~~fG~I~~~~~~~~-----k~~AfV~f~~~e~A~~ai~~~~~   73 (104)
T d1wexa_          26 SVVEADLVEALEKFGTICYVMMMPF-----KRQALVEFENIDSAKECVTFAAD   73 (104)
T ss_dssp             SCCHHHHHHHHTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHhhhhcccceEEEEEec-----ceeEEEEeCCHHHHHHHHHHHcC
Confidence            6899999999999999999999865     78999999999999999987753

>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=98.24  E-value=3.6e-07  Score=71.64  Aligned_cols=50  Identities=16%  Similarity=0.183  Sum_probs=42.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+++++|+++|++|| +..+.+.     .++|||||+|.+.++|.+|+..+|+..+
T Consensus        16 ~~t~~~l~~lF~~~G-~~~~~~~-----~~kg~afV~f~~~~~A~~Ai~~ln~~~~   65 (88)
T d1wg1a_          16 DSNCQEVHDLLKDYD-LKYCYVD-----RNKRTAFVTLLNGEQAQNAIQMFHQYSF   65 (88)
T ss_dssp             SCCHHHHHHHTCSSC-CCCEEEE-----GGGTEEEECCSCHHHHHHHHHHHTTEEE
T ss_pred             ccChHHHHHHHHhcC-ceeeeee-----ccCCceEEEECCHHHHHHHHHHhCCCEE
Confidence            589999999999999 3334443     4589999999999999999999998764

>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=98.24  E-value=6e-08  Score=76.40  Aligned_cols=55  Identities=15%  Similarity=0.135  Sum_probs=47.0

Q ss_pred             CCcHHHHHHHhcccCcceeeEEee------CCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLK------NADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~------d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .+|+++|+++|++||.+..+.+..      ..+++++|||||+|.+.++|.+|+ ++|+..+
T Consensus        12 ~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~-~l~g~~~   72 (90)
T d1u2fa_          12 GITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFDGIIF   72 (90)
T ss_dssp             TCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGG-GGSSCCS
T ss_pred             ccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHH-hhCCcEE
Confidence            589999999999999988877643      245778999999999999999998 5988765

>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=98.24  E-value=3.9e-07  Score=71.69  Aligned_cols=48  Identities=21%  Similarity=0.209  Sum_probs=43.4

Q ss_pred             CCCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcC
Q psy300          100 GKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN  152 (451)
Q Consensus       100 G~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln  152 (451)
                      +.+|+++|.++|++||.|.++.++++     +++|||+|++.++|..|+..++
T Consensus        19 ~~~t~~eL~~lF~~fG~I~~i~i~~~-----k~~afV~f~~~~~A~~A~~~l~   66 (89)
T d1x4da1          19 GKNLRYQLLQLVEPFGVISNHLILNK-----INEAFIEMATTEDAQAAVDYYT   66 (89)
T ss_dssp             SSSHHHHHHTTTGGGSCEEEEEECSS-----SSCEEEEESSHHHHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHhhCCeEEEEeecc-----ceEEEEEEcchhhHHHHHHHHh
Confidence            45799999999999999999999876     6799999999999999998663

>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=98.21  E-value=6.2e-07  Score=70.10  Aligned_cols=47  Identities=21%  Similarity=0.299  Sum_probs=43.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcC
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSN  152 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln  152 (451)
                      .+++++|+++|++||.|.++.+.++     +|||||+|.+.++|.+|+..++
T Consensus        19 ~~t~~~L~~~f~~~G~i~~v~~~~~-----~~~afV~f~~~e~A~~a~~~~~   65 (88)
T d2cq1a1          19 EVTETEVIALGLPFGKVTNILMLKG-----KNQAFLELATEEAAITMVNYYS   65 (88)
T ss_dssp             TCCHHHHHHTTTTTSCEEEEEEETT-----TTEEEEEESSHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHhccccccccccccc-----ceEEEEEeCCHHHHHHHHHHHc
Confidence            5899999999999999999999865     6899999999999999998764

>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=98.15  E-value=4.2e-07  Score=71.18  Aligned_cols=45  Identities=31%  Similarity=0.593  Sum_probs=40.2

Q ss_pred             CCcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHH
Q psy300          101 KITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAIL  149 (451)
Q Consensus       101 ~~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~  149 (451)
                      .+|+++|+++|++||.|.++++..    .++|||||+|.+.++|.+|+.
T Consensus        16 ~~te~~L~~~F~~~G~v~~v~~~~----~~~gfafV~f~~~~~a~~a~~   60 (88)
T d1wf0a_          16 DMTEDELREFFSQYGDVMDVFIPK----PFRAFAFVTFADDQIAQSLCG   60 (88)
T ss_dssp             SSCHHHHHHHSTTTSCCCEEECCS----SCCSCCEEECSCHHHHHHTTT
T ss_pred             CCCHHHHHHHHHHcCCceEEEEee----ccCceEEEEECCHHHHHHHHh
Confidence            589999999999999999987754    358999999999999999974

>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=98.12  E-value=1.3e-06  Score=67.48  Aligned_cols=48  Identities=23%  Similarity=0.378  Sum_probs=40.3

Q ss_pred             CcHHHHHHHhcccCcceeeEEeeCCCCCccceEEEEecchHHHHHHHHhcCCCcc
Q psy300          102 ITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPY  156 (451)
Q Consensus       102 ~tee~L~~~F~~fG~V~~v~v~~d~~g~srG~gFV~F~s~e~A~~Ai~~ln~riy  156 (451)
                      .++ ++.++|++||.|.++++.++     +|||||+|.++++|.+|+. +||+.+
T Consensus        16 ~~~-~il~~F~~~G~I~~~~~~~~-----~~~~fV~f~~~~~A~~Al~-~nG~~~   63 (81)
T d1wwha1          16 SAS-YILLQFAQYGNILKHVMSNT-----GNWMHIRYQSKLQARKALS-KDGRIF   63 (81)
T ss_dssp             GHH-HHHHHHHTTSCEEEEEECSS-----SSEEEEEESSHHHHHHHHT-TTTCEE
T ss_pred             HHH-HHHHHHHhhhhhheEEecCC-----CCEEEEEEcccHHHHHHHh-cCCCeE
Confidence            454 55568999999999987644     7999999999999999995 888776

>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=96.44  E-value=0.0054  Score=47.49  Aligned_cols=68  Identities=16%  Similarity=0.236  Sum_probs=56.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECC-C-CCc-eeEEEEEEccHHHHHHHHHhcCCccCCC
Q psy300           33 GRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNA-D-GKL-KGCGFINYANKISAVKAILKSNKKPYKG  100 (451)
Q Consensus        33 ~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~-t-g~s-kG~aFV~F~~~~~A~~Al~~lng~~f~G  100 (451)
                      ++|-|+.||+++|++++.+.++..|++........+ + +.+ -.-|+|.|.+.++...-.+.++|..|..
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            689999999999999999999999998888777654 2 222 3569999999999988888888887753

>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=89.03  E-value=0.55  Score=36.10  Aligned_cols=58  Identities=16%  Similarity=0.328  Sum_probs=47.0

Q ss_pred             CCCCceEEEcCCCCCCCHHHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhc
Q psy300           29 KTKRGRLFIKNLPFKITEEEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKS   93 (451)
Q Consensus        29 ~~~~~~lfVgnLp~~vte~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~l   93 (451)
                      ...+..||.-.+|..+...||.++|+.||.|. |..+.|      --|||.-.+.++|+.++..+
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIdd------TSa~V~L~~~e~~~~v~~~~   69 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDD------TSAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEET------TEEEEECSCHHHHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecC------ceEEEEecCHHHHHHHHHHh
Confidence            44566889889999999999999999999975 444443      25999999999998887643

>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=84.24  E-value=0.82  Score=32.95  Aligned_cols=50  Identities=18%  Similarity=0.242  Sum_probs=40.7

Q ss_pred             HHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCccCC
Q psy300           48 EFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKPYK   99 (451)
Q Consensus        48 ~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~f~   99 (451)
                      -|.+.|+++|+|.++.+....+|..  .|-|...+..+|.-|+..+++..+.
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG   61 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHTDYQL--KAVVQMENLQDAIGAVNSLHRYKIG   61 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCCSTTC--CEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             HHHHHHHhheeEEEEEEEeccCCcE--EEEEEcCCHHHHHHHHHHHHHHhcC
Confidence            3577899999999999866545543  5899999999999999999876544

>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=83.62  E-value=0.52  Score=35.76  Aligned_cols=66  Identities=17%  Similarity=0.268  Sum_probs=49.2

Q ss_pred             CCCCCCceEEEcCCCCCCCH---------HHHHHHhccCCCeEEEEEeECCCCCceeEEEEEEccHHHHHHHHHhcCCcc
Q psy300           27 PDKTKRGRLFIKNLPFKITE---------EEFKEHFGQYGDIIDAQLLKNADGKLKGCGFINYANKISAVKAILKSNKKP   97 (451)
Q Consensus        27 ~~~~~~~~lfVgnLp~~vte---------~~L~~~F~~~G~I~~i~l~~d~tg~skG~aFV~F~~~~~A~~Al~~lng~~   97 (451)
                      ...++..+|.|.=...+..+         .+|.+.|+.||+|.-+|++.+       -..|+|.+-..|.+|++ ++|..
T Consensus        10 ~qGPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d-------~mwVTF~dG~SAL~al~-l~g~~   81 (95)
T d1ufwa_          10 FQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG-------QMLVTFADSHSALSVLD-VDGMK   81 (95)
T ss_dssp             CCCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT-------EEEEECSCSHHHHHHHH-GGGSE
T ss_pred             ccCCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC-------eEEEEECCcHHHHHHhc-cCCeE
Confidence            34567788888644433322         367889999999999999855       68899999999999986 56665


Q ss_pred             CCC
Q psy300           98 YKG  100 (451)
Q Consensus        98 f~G  100 (451)
                      +.|
T Consensus        82 v~G   84 (95)
T d1ufwa_          82 VKG   84 (95)
T ss_dssp             ETT
T ss_pred             Ecc
Confidence            554