Psyllid ID: psy630

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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-------
Protein Sequence
MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWEDKEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS
Secondary Structure (PSIPRED)
ccccccccccEEEEcccccccHHHHHHHHHccccEEEEEEEEcccccccccEEEEEEccHHHHHHHHccccEEEcccccccccccccccccHHHHHHHcccccccccccccccHHHHHHHHHccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccccHHHHHHHHccccccHHHHHHHHHHcccccccccHHHHHHcccccccccccccccccccccccccccccccccccccHHHHHHHHHHccHHHHHHHHHHcccccccccccccHHHHHHHHccccHHHHHHHHHHcccccccccccccHHHHHHHHcccHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccccHHHEEEEEcccccccHHHHHHHHHHHccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHcccccEEcccEEEEcccccccccccHHccccccEEEEEccccccccHHHHHHHHHHcccEEEEEEEEEcccccEEEEcccHHHHHHHHHHccccccccEEEEEccccHHHHcHHHHHHHHHccccccccccccccccccccHHHHcccccccccccccccccccccccccccEEEcccHHHHHHHHHHHcHHHHHHcccHHHHHHHHHHcccccccccccccccHHHHHHcccHHHHHHHHHHHccccEcccccccccHHHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MSNSIRQLNKIfvgnlpwtvSHNELKKFFSEYGQIMNASVmfdkntglskgfgfvtfqnkeavdkvfstdshvlegsrlsiqpsdshNRMAENMEDRFNQACDYLPslvkkldsstlLKFYALYKQAtvgqcnidkpswynmeaKSKYNAWNSLGQMAKSEAMSKYIALLKEVdagwedkeqeeinwdwkpnQKAMSKYIALLNEVdaswedkeqeeinwdesqesgskenegqtkgwVNVSSMindesqlddnEKNIYEWAKEGKLDMLVKQLTKLKdfninqldenglnclhwacdrgHLKVVQHLIEKCgadvnvtdsdgdyglDYAKAIEHTDLIEYLVNSGS
Flexible Loop (DISEMBL)
MSNSIRQLNKifvgnlpwtvSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFStdshvlegsrlsiqpsdsHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWEDKEqeeinwdwkpnqKAMSKYIALLNEVDASWEDKEQEEInwdesqesgskenegqtkgwVNVSSMindesqlddNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS
Low Complexity Region (SEG)
MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWEDKEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS
Disordered region (IsUnstruct)
******QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST****************************FNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDAS***********************************************NIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLV****
Disordered Region (DISOPRED)
******Q****FVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSD***********RFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAW*************KYIALLKEVDA**********************************************************************************IYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG*
Disordered Region (DISEMBL)
MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWE***********************TKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS
Disordered Region (DISPRO)
*****RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDS***M*E***DRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWEDKEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWEDKEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS
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	347	2.2.26 [Sep-21-2011]
Q5RJK8	282	Acyl-CoA-binding domain-c	yes	N/A	0.602	0.741	0.321	6e-32
Q9BR61	282	Acyl-CoA-binding domain-c	yes	N/A	0.599	0.737	0.318	3e-31
A2VDR2	282	Acyl-CoA-binding domain-c	yes	N/A	0.608	0.748	0.315	4e-31
Q9D061	282	Acyl-CoA-binding domain-c	yes	N/A	0.599	0.737	0.312	4e-29
Q4V8X4	300	Acyl-CoA-binding domain-c	yes	N/A	0.625	0.723	0.280	3e-26
Q66JD7	286	Acyl-CoA-binding domain-c	yes	N/A	0.616	0.748	0.266	9e-25
Q4V869	286	Acyl-CoA-binding domain-c	N/A	N/A	0.616	0.748	0.277	3e-24
Q9SM23	338	Acyl-CoA-binding domain-c	yes	N/A	0.533	0.547	0.312	2e-20
Q54GC8	288	Acyl-CoA-binding domain-c	yes	N/A	0.697	0.840	0.301	5e-20
Q9STP8	354	Acyl-CoA-binding domain-c	no	N/A	0.550	0.539	0.289	9e-20

>sp|Q5RJK8|ACBD6_RAT Acyl-CoA-binding domain-containing protein 6 OS=Rattus norvegicus GN=Acbd6 PE=2 SV=1

 Score =  138 bits (348), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 82/255 (32%), Positives = 134/255 (52%), Gaps = 46/255 (18%)

Query: 93  NMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWN 152
           ++ + F +A  ++  LV+      LL  YA YKQ  VG CNI KP++++ E K K+ AW 
Sbjct: 41  SLAELFEKAAAHVQGLVQVASREQLLYLYARYKQVKVGNCNIPKPNFFDFEGKQKWEAWK 100

Query: 153 SLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWED 212
           +LG  + S+AM +YIA +K++D GW                                   
Sbjct: 101 ALGDSSPSQAMQEYIAAVKKLDPGW----------------------------------- 125

Query: 213 KEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVK 272
                 N   S++ G + + G   G   VSS+ ++E+ + + +KNI+++ +E  +D + K
Sbjct: 126 ------NPQVSEKKGKEGSSG--FGGPVVSSLYHEET-IREEDKNIFDYCRENNIDHITK 176

Query: 273 QLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKA 332
            + K K  ++N  DE G   LHWACDRGH ++V+ L++ C A +N  D++G   L YA A
Sbjct: 177 AI-KSKTVDVNMTDEEGRALLHWACDRGHKELVKVLLQ-CEAGINCQDNEGQTALHYAAA 234

Query: 333 IEHTDLIEYLVNSGS 347
            E +D++E L+ SG+
Sbjct: 235 CEFSDIVELLLQSGA 249

Binds long-chain acyl-coenzyme A molecules with a strong preference for unsaturated C18:1-CoA, lower affinity for unsaturated C20:4-CoA, and very weak affinity for saturated C16:0-CoA. Does not bind fatty acids.
Rattus norvegicus (taxid: 10116)

>sp|Q9BR61|ACBD6_HUMAN Acyl-CoA-binding domain-containing protein 6 OS=Homo sapiens GN=ACBD6 PE=1 SV=1

 Score =  136 bits (342), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 81/254 (31%), Positives = 131/254 (51%), Gaps = 46/254 (18%)

Query: 94  MEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNS 153
           + + F +A  +L  L++      LL  YA YKQ  VG CN  KPS+++ E K K+ AW +
Sbjct: 42  LAELFEKAAAHLQGLIQVASREQLLYLYARYKQVKVGNCNTPKPSFFDFEGKQKWEAWKA 101

Query: 154 LGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWEDK 213
           LG  + S+AM +YIA++K++D GW                                    
Sbjct: 102 LGDSSPSQAMQEYIAVVKKLDPGW------------------------------------ 125

Query: 214 EQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQ 273
                N    ++ G + N G   G   +SS+ ++E+ + + +KNI+++ +E  +D + K 
Sbjct: 126 -----NPQIPEKKGKEANTG--FGGPVISSLYHEET-IREEDKNIFDYCRENNIDHITKA 177

Query: 274 LTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAI 333
           + K K+ ++N  DE G   LHWACDRGH ++V  L++   AD+N  D++G   L YA A 
Sbjct: 178 I-KSKNVDVNVKDEEGRALLHWACDRGHKELVTVLLQH-RADINCQDNEGQTALHYASAC 235

Query: 334 EHTDLIEYLVNSGS 347
           E  D++E L+ SG+
Sbjct: 236 EFLDIVELLLQSGA 249

Binds long-chain acyl-coenzyme A molecules with a strong preference for unsaturated C18:1-CoA, lower affinity for unsaturated C20:4-CoA, and very weak affinity for saturated C16:0-CoA. Does not bind fatty acids.

Homo sapiens (taxid: 9606)

>sp|A2VDR2|ACBD6_BOVIN Acyl-CoA-binding domain-containing protein 6 OS=Bos taurus GN=ACBD6 PE=2 SV=1

 Score =  135 bits (341), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 81/257 (31%), Positives = 132/257 (51%), Gaps = 46/257 (17%)

Query: 91  AENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNA 150
           + ++ + F +A ++L  LV+      LL  YA YKQ  VG CN  KPS+++ E K K+ A
Sbjct: 39  SRSLPELFEKAAEHLQGLVQVASREQLLYLYARYKQVKVGNCNTPKPSFFDFEGKQKWEA 98

Query: 151 WNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASW 210
           W +LG  + S+AM +YIA++K++D  W                                 
Sbjct: 99  WKALGDSSPSQAMQEYIAVVKKLDPSW--------------------------------- 125

Query: 211 EDKEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDML 270
                   N    ++ G + N G   G   VSS+ ++E  + + +K+I+++ +E  +D +
Sbjct: 126 --------NPQSPEKKGKEANTG--FGGPVVSSLYHEEI-IREEDKDIFDYCRENNIDHI 174

Query: 271 VKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA 330
            K + K K+ ++N  DE G   LHWACDRGH ++V  L++   AD+N  D++G   L YA
Sbjct: 175 TK-VIKTKNMDVNMKDEEGRTLLHWACDRGHKELVTVLLQY-RADINCQDNEGQTALHYA 232

Query: 331 KAIEHTDLIEYLVNSGS 347
            A E  D++E L+ SG+
Sbjct: 233 AACEFLDIVELLLQSGA 249

Binds long-chain acyl-coenzyme A molecules with a strong preference for unsaturated C18:1-CoA, lower affinity for unsaturated C20:4-CoA, and very weak affinity for saturated C16:0-CoA. Does not bind fatty acids.

Bos taurus (taxid: 9913)

>sp|Q9D061|ACBD6_MOUSE Acyl-CoA-binding domain-containing protein 6 OS=Mus musculus GN=Acbd6 PE=1 SV=2

 Score =  129 bits (323), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 80/256 (31%), Positives = 129/256 (50%), Gaps = 48/256 (18%)

Query: 93  NMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWN 152
           ++ + F +A  ++  LV+      LL  YA +KQ  VG CN  KP++++ E K K+ AW 
Sbjct: 41  SLAELFEKAAAHVQGLVQVASREQLLYLYARFKQVKVGNCNTPKPNFFDFEGKQKWEAWK 100

Query: 153 SLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWED 212
           +LG  + S+AM +YIA +K++D GW                                   
Sbjct: 101 ALGDSSPSQAMQEYIAAVKKLDPGW----------------------------------- 125

Query: 213 KEQEEINWDESQESGSKENEGQTK-GWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLV 271
                      Q S  K  EG +  G   VSS+ ++E+ + + +KNI+++ +E  +D + 
Sbjct: 126 ---------NPQVSEKKGKEGSSGFGGPVVSSLYHEET-IREEDKNIFDYCRENNIDHIA 175

Query: 272 KQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAK 331
           K + K K  ++N  DE G   LHWACDRGH ++V+ L++   A +N  D++G   L YA 
Sbjct: 176 KAI-KSKAADVNMTDEEGRALLHWACDRGHKELVKVLLQY-EAGINCQDNEGQTALHYAA 233

Query: 332 AIEHTDLIEYLVNSGS 347
           A E  D++E L+ SG+
Sbjct: 234 ACEFLDIVELLLQSGA 249

Binds long-chain acyl-coenzyme A molecules with a strong preference for unsaturated C18:1-CoA, lower affinity for unsaturated C20:4-CoA, and very weak affinity for saturated C16:0-CoA. Does not bind fatty acids.

Mus musculus (taxid: 10090)

>sp|Q4V8X4|ACBD6_DANRE Acyl-CoA-binding domain-containing protein 6 OS=Danio rerio GN=acbd6 PE=2 SV=1

 Score =  119 bits (298), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 74/264 (28%), Positives = 127/264 (48%), Gaps = 47/264 (17%)

Query: 85  DSHNRM-AENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNME 143
           D+  R+   ++E+ F  A D +  LV+      LL  YA +KQ  VG+CN  KP +++ E
Sbjct: 50  DASARLEGADLENEFESAADRVRDLVQTASREQLLYLYARFKQVKVGKCNTSKPGFFDFE 109

Query: 144 AKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALL 203
            + K++AW  LG M+  +AM +Y+  +  +D                             
Sbjct: 110 GQRKWSAWKQLGDMSAEQAMQEYVTCVHALDP---------------------------- 141

Query: 204 NEVDASWEDKEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAK 263
                        E +   S+  G ++  G   G   VSS+  +E ++ + +KNI+++ +
Sbjct: 142 -------------EGSQKSSERRGGEKRTG--FGGPAVSSLYQEE-KIREEDKNIFDYCR 185

Query: 264 EGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDG 323
           E  ++ + K ++  K  ++N  DE G   LHWACDRGH  +V  L++   AD+N  D +G
Sbjct: 186 ENNIEHVSKAISS-KTVDVNTRDEEGRALLHWACDRGHKDLVSLLLQN-NADINSQDDEG 243

Query: 324 DYGLDYAKAIEHTDLIEYLVNSGS 347
              L YA A E  +++E L+ +G+
Sbjct: 244 QTALHYASACEFAEIVELLLKAGA 267

Binds long-chain acyl-coenzyme A molecules with a strong preference for unsaturated C18:1-CoA. Does not bind fatty acids.

Danio rerio (taxid: 7955)

>sp|Q66JD7|ACBD6_XENTR Acyl-CoA-binding domain-containing protein 6 OS=Xenopus tropicalis GN=acbd6 PE=2 SV=1

 Score =  114 bits (286), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 69/259 (26%), Positives = 124/259 (47%), Gaps = 45/259 (17%)

Query: 89  RMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKY 148
           +  E ++ +F QA  ++ ++     +  LL  YA YKQ  VG+CN  KP +++ E K K+
Sbjct: 27  KTEEELQGQFEQAAKHVQNVASVASTEQLLFLYARYKQVKVGRCNTPKPGFFDYEGKKKW 86

Query: 149 NAWNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDA 208
            AW +LG  +  +AM++YI  +K++D  W  +  EE      P+++  + +         
Sbjct: 87  EAWKALGDYSCQQAMNEYIETVKKLDPDWSPQALEE------PHKEPKTTF--------- 131

Query: 209 SWEDKEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLD 268
                                       G   VS +   +  L + +K+I+++ +E  + 
Sbjct: 132 ----------------------------GGPVVSCLYKVQETLREEDKDIFDYCRENNIS 163

Query: 269 MLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLD 328
            +   L+     ++N  D+ G   LHWACDRGH ++V  L+    A +N+ DS+G   L 
Sbjct: 164 RVSHALST-GAIDVNVADDEGRCLLHWACDRGHTQLVSVLLFH-NAHINMQDSEGQTPLH 221

Query: 329 YAKAIEHTDLIEYLVNSGS 347
           YA A E  D+++ L++ G+
Sbjct: 222 YASACEFPDIVDLLLDHGA 240

Binds long-chain acyl-coenzyme A molecules with a strong preference for unsaturated C18:1-CoA. Does not bind fatty acids.

Xenopus tropicalis (taxid: 8364)

>sp|Q4V869|ACBD6_XENLA Acyl-CoA-binding domain-containing protein 6 OS=Xenopus laevis GN=acbd6 PE=2 SV=1

 Score =  112 bits (281), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 72/259 (27%), Positives = 124/259 (47%), Gaps = 45/259 (17%)

Query: 89  RMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKY 148
           +  E ++ +F QA  ++ ++     +  LL  YA YKQ  VG+CN  KP +++ E K K+
Sbjct: 27  KTEEELQCQFEQAAKHVQNVASVASTEQLLYLYARYKQVKVGRCNTPKPGFFDYEGKKKW 86

Query: 149 NAWNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDA 208
            AW +LG  +  +AM++YI  +K++D             DW P                 
Sbjct: 87  EAWKALGDYSHQQAMTEYIETVKKLDP------------DWSP----------------- 117

Query: 209 SWEDKEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLD 268
                        ++ E   KE +    G V VS +   +  L + +K+I+++ +E    
Sbjct: 118 -------------QALEEPYKEPKTTFGGPV-VSCLYKVQETLREEDKDIFDYCRENNHS 163

Query: 269 MLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLD 328
            +   L+     ++N  D+ G + LHWACDRGH ++V  +I    A +N+ DS+G   L 
Sbjct: 164 RVSHALST-GSVDVNVADDEGRSLLHWACDRGHTQLVS-VILFHNAHINMQDSEGQTPLH 221

Query: 329 YAKAIEHTDLIEYLVNSGS 347
           YA A E  D+++ L++ G+
Sbjct: 222 YASACEFPDIVDLLLDHGA 240

Binds long-chain acyl-coenzyme A molecules with a strong preference for unsaturated C18:1-CoA. Does not bind fatty acids.

Xenopus laevis (taxid: 8355)

>sp|Q9SM23|ACBP1_ARATH Acyl-CoA-binding domain-containing protein 1 OS=Arabidopsis thaliana GN=ACBP1 PE=1 SV=2

 Score =  100 bits (248), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 76/243 (31%), Positives = 110/243 (45%), Gaps = 58/243 (23%)

Query: 108 LVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYI 167
           L +K+ +   L+ Y LYK AT G C   +PS   M A++K+ AW  LG M          
Sbjct: 113 LSQKVSNELQLQLYGLYKIATEGPCTAPQPSALKMTARAKWQAWQKLGAM---------- 162

Query: 168 ALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWEDKEQEEINWDESQESG 227
                                  P ++AM KYI L+ ++  +W              E G
Sbjct: 163 -----------------------PPEEAMEKYIDLVTQLYPAW-------------VEGG 186

Query: 228 SKEN--EGQTKGWVN--VSSMINDESQLDDNE---KNIYEWAKEGKLDMLVKQLTKLKDF 280
           SK     G+  G +    SS++ +E    DNE     I+ +A+EG+++ L+K +      
Sbjct: 187 SKRRNRSGEAAGPMGPVFSSLVYEEE--SDNELKIDAIHAFAREGEVENLLKCIEN--GI 242

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
            +N  D  G   LHWA DRGHL V + L++K  ADVN  D++G   L YA   E   L E
Sbjct: 243 PVNARDSEGRTPLHWAIDRGHLNVAEALVDK-NADVNAKDNEGQTSLHYAVVCEREALAE 301

Query: 341 YLV 343
           +LV
Sbjct: 302 FLV 304

Binds medium- and long-chain acyl-CoA esters with very high affinity. Can interact in vitro with arachidonyl-CoA, barely with oleoyl-CoA, but not with palmitoyl-CoA. Confers tolerance and binds to lead ions Pb(2+), probably by promoting lead translocation from roots to shoots. May function as an intracellular carrier of acyl-CoA esters.

Arabidopsis thaliana (taxid: 3702)

>sp|Q54GC8|ACBD6_DICDI Acyl-CoA-binding domain-containing protein 6 homolog OS=Dictyostelium discoideum GN=acbd6 PE=3 SV=1

 Score = 99.0 bits (245), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 80/265 (30%), Positives = 141/265 (53%), Gaps = 23/265 (8%)

Query: 94  MEDRFNQACDYLPSLVKKLDS---STLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNA 150
           +E++F  A DY+ +   KL +      L  Y  YKQAT+G CN   P +Y+   KSK+N+
Sbjct: 6   IENKFKLAVDYITNNSGKLSNIKNEEQLYLYCNYKQATIGDCNTKAPPFYDYIGKSKWNS 65

Query: 151 WNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASW 210
           WNSL  + K  AM+ YI+L+  +  GW+   + E        +   S ++      +   
Sbjct: 66  WNSLKGVEKIVAMNSYISLVNALSPGWDSNIKVE--------RATQSVFLNDEEFKELEK 117

Query: 211 EDKEQEEINWDESQESGSKENEGQTKGWVNVS----SMINDESQLDDNEKNIYE----WA 262
           ++KE++E      +E+G +  + ++K W+       S+++DE+ L+  EKN  +    W 
Sbjct: 118 KEKEEKEELKKLEEENGGEIEKPKSK-WMGPVLSKFSLVDDET-LEKLEKNTKQDLGYWV 175

Query: 263 KEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSD 322
               ++ + K++   K+  IN++DE+G   L WACDRG+ ++ + LIE  G++VNV D +
Sbjct: 176 SVNDIERVKKEIENDKNI-INEVDEDGRTALIWACDRGYFEIAKLLIEN-GSNVNVQDGE 233

Query: 323 GDYGLDYAKAIEHTDLIEYLVNSGS 347
           G   L YA   +  ++ + L++  S
Sbjct: 234 GMTPLHYAVVCDQFEICKLLLSQSS 258

Binds long-chain acyl-coenzyme A molecules with a strong preference for unsaturated C18:1-CoA. Does not bind fatty acids.

Dictyostelium discoideum (taxid: 44689)

>sp|Q9STP8|ACBP2_ARATH Acyl-CoA-binding domain-containing protein 2 OS=Arabidopsis thaliana GN=ACBP2 PE=1 SV=1

 Score = 98.2 bits (243), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 70/242 (28%), Positives = 110/242 (45%), Gaps = 51/242 (21%)

Query: 108 LVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYI 167
           L +K+ S    + Y LYK AT G C   +PS   M A++K+ AW  LG M          
Sbjct: 123 LSQKVPSDVQQQLYGLYKIATEGPCTAPQPSALKMTARAKWQAWQKLGAM---------- 172

Query: 168 ALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWEDKEQEEINWDESQESG 227
                                  P ++AM KYI ++ ++  +W          D   ++G
Sbjct: 173 -----------------------PPEEAMEKYIEIVTQLYPTW---------LDGGVKAG 200

Query: 228 SK------ENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFN 281
           S+       N   T G V  S + ++ES+ +     I+ +A+EG+++ L+K +       
Sbjct: 201 SRGGDDAASNSRGTMGPVFSSLVYDEESENELKIDAIHGFAREGEVENLLKSIES--GIP 258

Query: 282 INQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEY 341
           +N  D  G   LHWA DRGHL + + L++K  ADVN  D++G   L YA   +   + E+
Sbjct: 259 VNARDSEGRTPLHWAIDRGHLNIAKVLVDK-NADVNAKDNEGQTPLHYAVVCDREAIAEF 317

Query: 342 LV 343
           LV
Sbjct: 318 LV 319

Binds medium- and long-chain acyl-CoA esters with very high affinity. Can interact in vitro with palmitoyl-CoA, but not with oleoyl-CoA. Binds to lead ions (Pb). May function as an intracellular carrier of acyl-CoA esters. Required for proper phospholipid and, to a lower extent, galactolipid composition.

Arabidopsis thaliana (taxid: 3702)

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	347
242009252	511	conserved hypothetical protein [Pediculu	0.798	0.542	0.360	4e-53
350406915	240	PREDICTED: acyl-CoA-binding domain-conta	0.599	0.866	0.361	1e-36
340721725	262	PREDICTED: acyl-CoA-binding domain-conta	0.680	0.900	0.344	3e-36
383857939	479	PREDICTED: uncharacterized protein LOC10	0.585	0.423	0.349	6e-36
380028990	483	PREDICTED: putative ankyrin repeat prote	0.582	0.418	0.362	6e-36
307174126	233	Acyl-CoA-binding domain-containing prote	0.585	0.871	0.333	6e-35
307195671	238	Acyl-CoA-binding domain-containing prote	0.587	0.857	0.349	1e-34
332031342	240	Acyl-CoA-binding domain-containing prote	0.613	0.887	0.314	4e-33
322797576	296	hypothetical protein SINV_80899 [Solenop	0.639	0.75	0.300	2e-32
260795083	251	hypothetical protein BRAFLDRAFT_69053 [B	0.602	0.832	0.319	3e-32

>gi|242009252|ref|XP_002425404.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212509213|gb|EEB12666.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score =  214 bits (546), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 125/347 (36%), Positives = 181/347 (52%), Gaps = 70/347 (20%)

Query: 1   MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
           MSN I+ L K+FV NLP+TV   E KK+F  +G+++ A V+FD  TG SKG+GF+ ++N+
Sbjct: 218 MSN-IKALKKLFVSNLPYTVGKREFKKYFETFGKVIYADVIFDWKTGFSKGYGFILYKNE 276

Query: 61  EAVDKVFSTDSHVLEGSRLSIQPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKF 120
            ++  V S+  H LEG RL                     A  ++ ++V  L    LL+F
Sbjct: 277 SSLKSVMSSQPHTLEGGRLV--------------------ASSHVKNIVGNLTKEQLLEF 316

Query: 121 YALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWEDK 180
           YA YKQA  G CN  KP WY    K K+ AW +L  M                       
Sbjct: 317 YAHYKQAIEGPCNKPKPYWYEFSEKQKWEAWTNLNDMD---------------------- 354

Query: 181 EQEEINWDWKPNQKAMSKYIALLNEVDASWEDKEQEEINWDESQESGSKENEGQTKGWVN 240
                      +  AM KYI LLN++D  W DK    +               +T+GWV+
Sbjct: 355 -----------SNLAMEKYIKLLNDIDPEWNDKPVSNV---------------KTQGWVH 388

Query: 241 VSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRG 300
            S M N++  +++++K +++W KEG LD  VK LT   +  IN+LDE+GL  LHWA DRG
Sbjct: 389 HSCMENNDEVIEESKKTVFDWVKEGNLDK-VKALTSNINLEINKLDESGLGLLHWASDRG 447

Query: 301 HLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
           ++ VV++L+E+  ADVN+ D  G   L +A   E+ D+  YL+ SG+
Sbjct: 448 NINVVKYLVEELKADVNLRDGTGQTPLHFAVICEYDDVANYLIESGA 494

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350406915|ref|XP_003487922.1| PREDICTED: acyl-CoA-binding domain-containing protein 6-like [Bombus impatiens]

 Score =  160 bits (404), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 94/260 (36%), Positives = 137/260 (52%), Gaps = 52/260 (20%)

Query: 88  NRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSK 147
           N +  N+E  FN+A  YL SL  +L+S+ LLKFYALYKQAT+G CNI KP+WY M+A+ K
Sbjct: 10  NDIKMNLEKTFNKATIYLQSLASELNSTELLKFYALYKQATIGPCNISKPNWYQMQARQK 69

Query: 148 YNAWNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVD 207
           ++AW SL  M+  +AM+ Y+  L +++  WE   Q E N                     
Sbjct: 70  WDAWKSLNDMSCDDAMNNYVLELSKLNPNWEQDAQSESN--------------------- 108

Query: 208 ASWEDKEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKL 267
                      NW                  V +S +IN E ++ D +K   +W KEG  
Sbjct: 109 -----------NW------------------VAISRLINMEDEISDTDKTFLDWVKEGH- 138

Query: 268 DMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGL 327
           D  V++L   +  + N  D  GL  +HWA DRGHL++++ LI+K GA V+  D DG   L
Sbjct: 139 DEKVQELLNKEPKHANLTDSEGLLPIHWAADRGHLRIIEQLIKK-GASVDSQDEDGQTPL 197

Query: 328 DYAKAIEHTDLIEYLVNSGS 347
            YA +  H D+++YL++ G+
Sbjct: 198 HYAASCGHLDVVKYLLSIGA 217

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340721725|ref|XP_003399266.1| PREDICTED: acyl-CoA-binding domain-containing protein 6-like [Bombus terrestris]

 Score =  158 bits (400), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 102/296 (34%), Positives = 149/296 (50%), Gaps = 60/296 (20%)

Query: 52  FGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDSHNRMAENMEDRFNQACDYLPSLVKK 111
           +GFV F +K  V  V + D HVL+  +LSI  ++    + E+   +F      + SL  +
Sbjct: 4   YGFVEFYDKAVVTFVLNKD-HVLDDGKLSI--TEGLKYLHEDSVKQF-----LIKSLASE 55

Query: 112 LDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLK 171
           L+S+ LLKFYALYKQAT+G CNI KP+WY M+A+ K+ AW SL  M+  +AM+ Y+  L 
Sbjct: 56  LNSTELLKFYALYKQATIGPCNISKPNWYQMQARQKWEAWKSLNDMSCDDAMNNYVLELS 115

Query: 172 EVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWEDKEQEEINWDESQESGSKEN 231
           + +  WE   Q E N                                NW           
Sbjct: 116 KFNPNWEQDAQSESN--------------------------------NW----------- 132

Query: 232 EGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLN 291
                  V +S +IN E ++ D +K   +W KEG  D  V++L   +  + N  D  GL 
Sbjct: 133 -------VAISRLINMEDEISDTDKTFLDWVKEGH-DEKVQELLNKEPKHANLTDSEGLL 184

Query: 292 CLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
            +HWA DRGHL +++ LI++ GA VN  D DG   L YA +  H D++ YL++ G+
Sbjct: 185 PIHWAADRGHLTIIEQLIKR-GASVNSQDEDGQTPLHYAASCGHLDVVTYLLSIGA 239

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383857939|ref|XP_003704461.1| PREDICTED: uncharacterized protein LOC100882258 [Megachile rotundata]

 Score =  157 bits (398), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 89/255 (34%), Positives = 135/255 (52%), Gaps = 52/255 (20%)

Query: 93  NMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWN 152
           N+ED F++A  +L SL  +L+S+ LLKFYALYKQAT+G C+  KP+WY +EA+ K+ AW 
Sbjct: 252 NLEDIFDKAAHHLQSLASELNSTELLKFYALYKQATIGPCDTSKPNWYQIEARQKWEAWK 311

Query: 153 SLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWED 212
           +L  M+   AM+ YI  L ++D  WE+  + E N                          
Sbjct: 312 NLNDMSHDTAMNSYIQELTKLDPNWEENIKSESN-------------------------- 345

Query: 213 KEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVK 272
                                    WV VS +IN E +++D +K   +W KEG  +  V+
Sbjct: 346 ------------------------SWVAVSCLINTEEEINDIDKTFLDWVKEGH-EGKVQ 380

Query: 273 QLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKA 332
           +L   +   +N +D  GL  +HWA DRGHL +++ LI+K GA++N  D DG   L YA +
Sbjct: 381 ELLDKEPRLVNSMDTEGLLPIHWAADRGHLGIIEQLIKK-GANINSQDEDGQSPLHYAAS 439

Query: 333 IEHTDLIEYLVNSGS 347
             H D+++YL++ G+
Sbjct: 440 CGHLDVVKYLLSIGA 454

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380028990|ref|XP_003698166.1| PREDICTED: putative ankyrin repeat protein FPV014-like [Apis florea]

 Score =  157 bits (397), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 92/254 (36%), Positives = 137/254 (53%), Gaps = 52/254 (20%)

Query: 94  MEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNS 153
           +E  FN+A  YL  L  +L+S+ LLKFYALYKQAT+G CNI KP+WY M+A+ K+ AW S
Sbjct: 259 LEKTFNKATHYLQLLASELNSAELLKFYALYKQATIGPCNISKPNWYQMQARQKWEAWKS 318

Query: 154 LGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWEDK 213
           L  M+  +AM+ YI              QE                   L +++ +WE+ 
Sbjct: 319 LNNMSCDDAMNNYI--------------QE-------------------LTKLNPNWEEN 345

Query: 214 EQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQ 273
            Q E                 +  WV +S  IN E +++D +K   +W KEG+ + + + 
Sbjct: 346 VQSE-----------------SSNWVAISRFINMEDEINDVDKTFLDWIKEGQEEKVQEL 388

Query: 274 LTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAI 333
           L K  +  IN++D  GL  +HWA DRGHLK+++ LI+K GA +N  D  G   L YA + 
Sbjct: 389 LDKEPNL-INKMDSEGLLPIHWAADRGHLKIIEQLIKK-GASINSQDEGGQTPLHYAASC 446

Query: 334 EHTDLIEYLVNSGS 347
            H D+++YL++ G+
Sbjct: 447 GHLDVVKYLISIGA 460

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307174126|gb|EFN64784.1| Acyl-CoA-binding domain-containing protein 6 [Camponotus floridanus]

 Score =  154 bits (389), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 85/255 (33%), Positives = 138/255 (54%), Gaps = 52/255 (20%)

Query: 93  NMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWN 152
           ++E+ FN+A  YL +LV +LDS  LL FY LYKQATVG C+I +P+WY ++AK K+ AW 
Sbjct: 7   DLEESFNRAAKYLQTLVSELDSGQLLGFYGLYKQATVGPCDIPRPNWYQVQAKHKWEAWK 66

Query: 153 SLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWED 212
           +LG M++  AM+ Y+  + +++  WE++E+ +      P   ++SK              
Sbjct: 67  NLGDMSREAAMANYVHAIAKINPSWEEEEKAD-----SPGWTSVSK-------------- 107

Query: 213 KEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVK 272
                                          + N +++L D +K   +W KEG  +  V+
Sbjct: 108 -------------------------------LSNTDTELRDTDKTFLDWVKEGN-EAKVR 135

Query: 273 QLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKA 332
           ++   +   +N  DE+GL  +HWA DRGH+K+V++LI   GA+VN  D DG   L YA +
Sbjct: 136 EILNGEPMLVNMQDEDGLLPIHWAADRGHVKIVEYLI-GSGANVNSQDRDGQTPLHYAAS 194

Query: 333 IEHTDLIEYLVNSGS 347
             HT+ ++ L++SG+
Sbjct: 195 CGHTEAVKCLLSSGA 209

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307195671|gb|EFN77513.1| Acyl-CoA-binding domain-containing protein 6 [Harpegnathos saltator]

 Score =  153 bits (387), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 89/255 (34%), Positives = 135/255 (52%), Gaps = 51/255 (20%)

Query: 93  NMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWN 152
           ++EDRFN+A  Y+ SLV +LD+  LL FYALYKQATVG CNI +P+WY ++A  KY AW 
Sbjct: 10  DLEDRFNRASKYMQSLVSELDTDHLLTFYALYKQATVGPCNISRPNWYQVQAVRKYEAWK 69

Query: 153 SLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWED 212
            LG M++                                 + AM+ YI ++  V+ SWE 
Sbjct: 70  KLGDMSQ---------------------------------EIAMANYIDVIARVNPSWE- 95

Query: 213 KEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVK 272
              EE  ++ES            +GW +VS + N ++ L D EK   +W KEG  +  V+
Sbjct: 96  ---EEAKFEES------------RGWTSVSKLPNTDAALKDTEKTFLDWLKEGN-EAKVR 139

Query: 273 QLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKA 332
           ++   +     ++D+ GL  +HWA DRGH+ +++ LIE+ G D+N  D +    L YA  
Sbjct: 140 EMVSKEPGLSGRMDDIGLLPIHWAADRGHVGILKFLIEQ-GVDLNSLDLEEQTPLHYAAG 198

Query: 333 IEHTDLIEYLVNSGS 347
             H + + YL++ G+
Sbjct: 199 CGHMEAVRYLLSIGA 213

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332031342|gb|EGI70855.1| Acyl-CoA-binding domain-containing protein 6 [Acromyrmex echinatior]

 Score =  148 bits (374), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 83/264 (31%), Positives = 140/264 (53%), Gaps = 51/264 (19%)

Query: 84  SDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNME 143
           SD  +    ++E+ FN+A  YL +LV +LDS  LL FY LYKQATVG C+I +P+WY M+
Sbjct: 4   SDLESEPLTDLEETFNRASKYLQTLVSELDSGQLLAFYGLYKQATVGPCDIPRPNWYQMQ 63

Query: 144 AKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALL 203
           AK K+ AW +LG M++  AM+ YI  +++++  W+++E                      
Sbjct: 64  AKHKWEAWKNLGDMSRETAMTNYIHGIEKINPTWDEEE---------------------- 101

Query: 204 NEVDASWEDKEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAK 263
                                ++GS++       W+  S +    ++L+D +K   +W K
Sbjct: 102 --------------------AKAGSQQ-------WIVFSKLSYGNAELNDEDKTFLDWIK 134

Query: 264 EGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDG 323
           EG  +  V++    +   +N+ DE G++ +HWA DRG+L ++ +LI K GA++N  D  G
Sbjct: 135 EGN-EAKVREFLSGEPALVNKPDEEGMHPIHWAADRGYLGILDYLI-KNGANINSRDQYG 192

Query: 324 DYGLDYAKAIEHTDLIEYLVNSGS 347
              L Y  + +H D ++YL++ G+
Sbjct: 193 QTALHYVVSCDHVDAVKYLLSIGA 216

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322797576|gb|EFZ19620.1| hypothetical protein SINV_80899 [Solenopsis invicta]

 Score =  146 bits (368), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 82/273 (30%), Positives = 136/273 (49%), Gaps = 51/273 (18%)

Query: 75  EGSRLSIQPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNI 134
           E   + I  SD  +    ++E+ FN+A  YL +LV +LDS  LL FY LYKQATVG C+ 
Sbjct: 51  ESLEILIPESDFESESLTDLEETFNRAAKYLQTLVSELDSGQLLAFYGLYKQATVGPCDT 110

Query: 135 DKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQK 194
            +P+WY ++AK K+ AW +LG M +  AM+ YI  +  ++  W+                
Sbjct: 111 PRPNWYQVQAKQKWEAWKNLGDMDRETAMTNYIQGIARINPAWD---------------- 154

Query: 195 AMSKYIALLNEVDASWEDKEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDN 254
                                            ++E + ++  W+  S +  D  +L+D 
Sbjct: 155 ---------------------------------AEEMKAESSQWIVFSKLSYDNVELNDE 181

Query: 255 EKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGA 314
           +K   +W KEG     V++    +   +++ DE G++ +HWA DRG+L+++ +LI K GA
Sbjct: 182 DKTFLDWIKEGNA-AKVREFLSSEPALVDKPDEEGMHPIHWAADRGYLEILDYLI-KSGA 239

Query: 315 DVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
           +VN  D  G   L Y  + +H D ++YL++ G+
Sbjct: 240 NVNSRDQYGQTALHYVVSCDHVDAVKYLLSIGA 272

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|260795083|ref|XP_002592536.1| hypothetical protein BRAFLDRAFT_69053 [Branchiostoma floridae] gi|229277756|gb|EEN48547.1| hypothetical protein BRAFLDRAFT_69053 [Branchiostoma floridae]

 Score =  145 bits (365), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 82/257 (31%), Positives = 129/257 (50%), Gaps = 48/257 (18%)

Query: 91  AENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNA 150
           + N+ D F QA D++ ++  +L +  LL  YA YKQ  VG+CN  KP +++ + K K++A
Sbjct: 9   SSNLADVFQQAVDHVATIAPQLSADQLLYLYARYKQVNVGRCNTAKPGFFDFQGKQKWDA 68

Query: 151 WNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASW 210
           WNSLG MA+ +AM++Y+  +++ D  WE            P +   SK  + +  V    
Sbjct: 69  WNSLGGMAQDQAMTEYVDGVRKADPTWE------------PREGGDSKKTSFMGPV---- 112

Query: 211 EDKEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDML 270
                                         VS+M  +E  + D  K  ++W KEG    +
Sbjct: 113 ------------------------------VSTMSFEEEYISDKNKTAFDWCKEGNTKQM 142

Query: 271 VKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA 330
            + L+   D +INQ D  GL+ LHWACDRGH  VV+ L+ K  A++N+ D DG   L YA
Sbjct: 143 ARLLSN-GDADINQQDSEGLSLLHWACDRGHEDVVRELL-KHKANINIQDEDGQTPLHYA 200

Query: 331 KAIEHTDLIEYLVNSGS 347
              E   +++ L++S +
Sbjct: 201 ATCEFLSIVQLLLDSSA 217

Source: Branchiostoma floridae

Species: Branchiostoma floridae

Genus: Branchiostoma

Family: Branchiostomidae

Phylum: Chordata

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	347
DICTYBASE|DDB_G0290237	288	acbd6 "acyl-CoA-binding domain	0.700	0.843	0.314	2.4e-28
UNIPROTKB|F1PLQ8	282	ACBD6 "Uncharacterized protein	0.628	0.773	0.303	5.5e-22
RGD|1305030	282	Acbd6 "acyl-CoA binding domain	0.449	0.553	0.36	7e-22
UNIPROTKB|A2VDR2	282	ACBD6 "Acyl-CoA-binding domain	0.449	0.553	0.348	1.9e-21
UNIPROTKB|E1C483	268	ACBD6 "Uncharacterized protein	0.449	0.582	0.348	3e-21
UNIPROTKB|Q9BR61	282	ACBD6 "Acyl-CoA-binding domain	0.449	0.553	0.342	3.9e-21
UNIPROTKB|F1S683	282	ACBD6 "Uncharacterized protein	0.668	0.822	0.285	1e-20
MGI|MGI:1919732	282	Acbd6 "acyl-Coenzyme A binding	0.449	0.553	0.354	2.7e-20
FB|FBgn0064117	90	CG33714 [Drosophila melanogast	0.227	0.877	0.506	4.4e-20
UNIPROTKB|G3N0L6	221	ACBD6 "Acyl-CoA-binding domain	0.270	0.425	0.382	2.6e-19

DICTYBASE|DDB_G0290237 acbd6 "acyl-CoA-binding domain-containing protein 6" [Dictyostelium discoideum (taxid:44689)]

 Score = 316 (116.3 bits), Expect = 2.4e-28, P = 2.4e-28
 Identities = 83/264 (31%), Positives = 145/264 (54%)

Query:    94 MEDRFNQACDYLPSLVKKLDS---STLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNA 150
             +E++F  A DY+ +   KL +      L  Y  YKQAT+G CN   P +Y+   KSK+N+
Sbjct:     6 IENKFKLAVDYITNNSGKLSNIKNEEQLYLYCNYKQATIGDCNTKAPPFYDYIGKSKWNS 65

Query:   151 WNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASW 210
             WNSL  + K  AM+ YI+L+  +  GW+   + E     +  Q           E++   
Sbjct:    66 WNSLKGVEKIVAMNSYISLVNALSPGWDSNIKVE-----RATQSVFLNDEEF-KELEKK- 118

Query:   211 EDKEQEEINWDESQESGSKENEGQTKGWVN--VS--SMINDES--QLDDNEK-NIYEWAK 263
             E +E+EE+   E +E+G +  + ++K W+   +S  S+++DE+  +L+ N K ++  W  
Sbjct:   119 EKEEKEELKKLE-EENGGEIEKPKSK-WMGPVLSKFSLVDDETLEKLEKNTKQDLGYWVS 176

Query:   264 EGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDG 323
                ++ + K++   K+  IN++DE+G   L WACDRG+ ++ + LIE  G++VNV D +G
Sbjct:   177 VNDIERVKKEIENDKNI-INEVDEDGRTALIWACDRGYFEIAKLLIEN-GSNVNVQDGEG 234

Query:   324 DYGLDYAKAIEHTDLIEYLVNSGS 347
                L YA   +  ++ + L++  S
Sbjct:   235 MTPLHYAVVCDQFEICKLLLSQSS 258

GO:0000062 "fatty-acyl-CoA binding" evidence=IEA

GO:0008289 "lipid binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|F1PLQ8 ACBD6 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 256 (95.2 bits), Expect = 5.5e-22, P = 5.5e-22
 Identities = 70/231 (30%), Positives = 116/231 (50%)

Query:    93 NMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWN 152
             ++ + F QA  +L  LV+      LL  YA YKQ  VG CN  KPS+++ E K K+ AW 
Sbjct:    41 SLAELFEQAAAHLQGLVQVASREQLLYLYARYKQVKVGNCNTPKPSFFDFEGKQKWEAWK 100

Query:   153 SLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWED 212
             +LG  + S+AM +YIA++K++D GW  +  E+   +   N       ++ L   +     
Sbjct:   101 ALGDSSPSQAMQEYIAVVKKLDPGWNPQSPEKKGKE--ANTGFGGPVVSSLYHEEII--- 155

Query:   213 KEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVK 272
             +E+++  +D  +E+     +  TK    + S   D +  D+  + +  WA +     LV 
Sbjct:   156 REEDKNIFDYCRENNI---DHVTKV---IRSKNVDVNMKDEEGRTLLHWACDRGHKELVT 209

Query:   273 QLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDG 323
              L + K  +IN  D+ G   LH+A     L +V+ L++  GAD  + D DG
Sbjct:   210 VLLRYKA-DINCQDDEGQTALHYAAACEFLDIVELLLQS-GADPTLRDQDG 258

GO:0000062 "fatty-acyl-CoA binding" evidence=IEA

RGD|1305030 Acbd6 "acyl-CoA binding domain containing 6" [Rattus norvegicus (taxid:10116)]

 Score = 255 (94.8 bits), Expect = 7.0e-22, P = 7.0e-22
 Identities = 63/175 (36%), Positives = 102/175 (58%)

Query:   177 WEDKEQEEINW----DWKPNQKAMSKYIALLNEVDASWEDKEQEEINWDESQESGSKENE 232
             +E K++ E  W    D  P+Q AM +YIA + ++D  W        N   S++ G KE  
Sbjct:    90 FEGKQKWEA-WKALGDSSPSQ-AMQEYIAAVKKLDPGW--------NPQVSEKKG-KEGS 138

Query:   233 GQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNC 292
                 G V VSS+ ++E+ + + +KNI+++ +E  +D + K + K K  ++N  DE G   
Sbjct:   139 SGFGGPV-VSSLYHEET-IREEDKNIFDYCRENNIDHITKAI-KSKTVDVNMTDEEGRAL 195

Query:   293 LHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
             LHWACDRGH ++V+ L++ C A +N  D++G   L YA A E +D++E L+ SG+
Sbjct:   196 LHWACDRGHKELVKVLLQ-CEAGINCQDNEGQTALHYAAACEFSDIVELLLQSGA 249

GO:0000062 "fatty-acyl-CoA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

GO:0008289 "lipid binding" evidence=IEA

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|A2VDR2 ACBD6 "Acyl-CoA-binding domain-containing protein 6" [Bos taurus (taxid:9913)]

 Score = 251 (93.4 bits), Expect = 1.9e-21, P = 1.9e-21
 Identities = 61/175 (34%), Positives = 101/175 (57%)

Query:   177 WEDKEQEEINW----DWKPNQKAMSKYIALLNEVDASWEDKEQEEINWDESQESGSKENE 232
             +E K++ E  W    D  P+Q AM +YIA++ ++D SW  +  E+         G + N 
Sbjct:    90 FEGKQKWEA-WKALGDSSPSQ-AMQEYIAVVKKLDPSWNPQSPEK--------KGKEANT 139

Query:   233 GQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNC 292
             G   G   VSS+ ++E  + + +K+I+++ +E  +D + K + K K+ ++N  DE G   
Sbjct:   140 GF--GGPVVSSLYHEEI-IREEDKDIFDYCRENNIDHITKVI-KTKNMDVNMKDEEGRTL 195

Query:   293 LHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
             LHWACDRGH ++V  L++   AD+N  D++G   L YA A E  D++E L+ SG+
Sbjct:   196 LHWACDRGHKELVTVLLQY-RADINCQDNEGQTALHYAAACEFLDIVELLLQSGA 249

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008289 "lipid binding" evidence=IEA

GO:0000062 "fatty-acyl-CoA binding" evidence=IEA

UNIPROTKB|E1C483 ACBD6 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 249 (92.7 bits), Expect = 3.0e-21, P = 3.0e-21
 Identities = 61/175 (34%), Positives = 99/175 (56%)

Query:   177 WEDKEQEEINW----DWKPNQKAMSKYIALLNEVDASWEDKEQEEINWDESQESGSKENE 232
             +E K++ E  W    D  P+Q AM +Y+A + ++D SW           ++ E   KE++
Sbjct:    76 FEGKQKWEA-WKALGDTSPHQ-AMQEYVATVKKLDPSWNP---------QTTEKRGKESK 124

Query:   233 GQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNC 292
                 G V VSS+  +E+ + + +KNI+++ +E  +D + K +   K  ++N  DE G   
Sbjct:   125 TAFGGPV-VSSLYQEET-IREEDKNIFDYCRENNIDYVTKAIQS-KKVDVNVADEEGRAL 181

Query:   293 LHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
             LHWACDRGH ++V  L++   ADVN  D +G   L YA A E +D++E L+ SG+
Sbjct:   182 LHWACDRGHKELVSVLLQHA-ADVNSQDGEGQTALHYASACEFSDIVELLLQSGA 235

GO:0000062 "fatty-acyl-CoA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|Q9BR61 ACBD6 "Acyl-CoA-binding domain-containing protein 6" [Homo sapiens (taxid:9606)]

 Score = 248 (92.4 bits), Expect = 3.9e-21, P = 3.9e-21
 Identities = 60/175 (34%), Positives = 101/175 (57%)

Query:   177 WEDKEQEEINW----DWKPNQKAMSKYIALLNEVDASWEDKEQEEINWDESQESGSKENE 232
             +E K++ E  W    D  P+Q AM +YIA++ ++D  W  +  E+         G + N 
Sbjct:    90 FEGKQKWEA-WKALGDSSPSQ-AMQEYIAVVKKLDPGWNPQIPEK--------KGKEANT 139

Query:   233 GQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNC 292
             G   G   +SS+ ++E+ + + +KNI+++ +E  +D + K + K K+ ++N  DE G   
Sbjct:   140 GF--GGPVISSLYHEET-IREEDKNIFDYCRENNIDHITKAI-KSKNVDVNVKDEEGRAL 195

Query:   293 LHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
             LHWACDRGH ++V  L++   AD+N  D++G   L YA A E  D++E L+ SG+
Sbjct:   196 LHWACDRGHKELVTVLLQH-RADINCQDNEGQTALHYASACEFLDIVELLLQSGA 249

GO:0000062 "fatty-acyl-CoA binding" evidence=IEA

GO:0008289 "lipid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|F1S683 ACBD6 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 244 (91.0 bits), Expect = 1.0e-20, P = 1.0e-20
 Identities = 71/249 (28%), Positives = 121/249 (48%)

Query:    76 GSRLSIQPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNID 135
             G   S+Q  ++    + ++ + F +A  +L  LV+      LL  YA YKQ  VG CN  
Sbjct:    26 GDAESLQSPETE--ASRSLTELFEKAAAHLQGLVQVASREQLLYLYARYKQVKVGNCNTP 83

Query:   136 KPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKA 195
             KPS+++ E K K+ AW +LG  + S+AM +YIA++K++D  W  +  E+   +   N   
Sbjct:    84 KPSFFDFEGKQKWEAWKALGDSSPSQAMQEYIAVVKKLDPDWNPQLPEKKGKE--TNTGF 141

Query:   196 MSKYIALLNEVDASWEDKEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNE 255
                 ++ L   +     +E+++  +D  +E+     +  TK    + S   D +  D+  
Sbjct:   142 GGPVVSSLYHEEII---REEDKNIFDYCRENNI---DHITKV---IKSKNVDVNMKDEEG 192

Query:   256 KNIYEWAKE-GKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGA 314
             + +  WA + G  D++   L    D  IN  D  G   LH+A     L +V+ L++  GA
Sbjct:   193 RALLHWACDRGHKDLVTVLLQYRAD--INSQDNEGQTALHYAAACEFLDIVELLLQ-AGA 249

Query:   315 DVNVTDSDG 323
             D  + D DG
Sbjct:   250 DATLRDQDG 258

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000062 "fatty-acyl-CoA binding" evidence=IEA

MGI|MGI:1919732 Acbd6 "acyl-Coenzyme A binding domain containing 6" [Mus musculus (taxid:10090)]

 Score = 240 (89.5 bits), Expect = 2.7e-20, P = 2.7e-20
 Identities = 62/175 (35%), Positives = 100/175 (57%)

Query:   177 WEDKEQEEINW----DWKPNQKAMSKYIALLNEVDASWEDKEQEEINWDESQESGSKENE 232
             +E K++ E  W    D  P+Q AM +YIA + ++D  W        N   S++ G KE  
Sbjct:    90 FEGKQKWEA-WKALGDSSPSQ-AMQEYIAAVKKLDPGW--------NPQVSEKKG-KEGS 138

Query:   233 GQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNC 292
                 G V VSS+ ++E+ + + +KNI+++ +E  +D + K + K K  ++N  DE G   
Sbjct:   139 SGFGGPV-VSSLYHEET-IREEDKNIFDYCRENNIDHIAKAI-KSKAADVNMTDEEGRAL 195

Query:   293 LHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
             LHWACDRGH ++V+ L++   A +N  D++G   L YA A E  D++E L+ SG+
Sbjct:   196 LHWACDRGHKELVKVLLQY-EAGINCQDNEGQTALHYAAACEFLDIVELLLQSGA 249

GO:0000062 "fatty-acyl-CoA binding" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0005737 "cytoplasm" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0008289 "lipid binding" evidence=IEA

FB|FBgn0064117 CG33714 [Drosophila melanogaster (taxid:7227)]

 Score = 238 (88.8 bits), Expect = 4.4e-20, P = 4.4e-20
 Identities = 40/79 (50%), Positives = 63/79 (79%)

Query:     6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
             + +++IFVGNLPWTV H EL+ +F E+G++++A+V+FDK TG SKG+GFV+F +  A++K
Sbjct:    12 KSVHRIFVGNLPWTVGHQELRGYFREFGRVVSANVIFDKRTGCSKGYGFVSFNSLTALEK 71

Query:    66 VFSTDSHVLEGSRLSIQPS 84
             + +   H+LEG+ L+IQ S
Sbjct:    72 IENEQKHILEGNYLNIQKS 90

GO:0003729 "mRNA binding" evidence=ISS

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|G3N0L6 ACBD6 "Acyl-CoA-binding domain-containing protein 6" [Bos taurus (taxid:9913)]

 Score = 203 (76.5 bits), Expect = 2.6e-19, Sum P(2) = 2.6e-19
 Identities = 36/94 (38%), Positives = 58/94 (61%)

Query:    91 AENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNA 150
             + ++ + F +A ++L  LV+      LL  YA YKQ  VG CN  KPS+++ E K K+ A
Sbjct:    39 SRSLPELFEKAAEHLQGLVQVASREQLLYLYARYKQVKVGNCNTPKPSFFDFEGKQKWEA 98

Query:   151 WNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEE 184
             W +LG  + S+AM +YIA++K++D  W  +  E+
Sbjct:    99 WKALGDSSPSQAMQEYIAVVKKLDPSWNPQSPEK 132

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000062 "fatty-acyl-CoA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5RJK8	ACBD6_RAT	No assigned EC number	0.3215	0.6023	0.7411	yes	N/A
Q54GC8	ACBD6_DICDI	No assigned EC number	0.3018	0.6974	0.8402	yes	N/A
A2VDR2	ACBD6_BOVIN	No assigned EC number	0.3151	0.6080	0.7482	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	347
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-27
pfam00887	87	pfam00887, ACBP, Acyl CoA binding protein	2e-25
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	7e-22
cd00435	85	cd00435, ACBP, Acyl CoA binding protein (ACBP) bin	1e-21
smart00360	73	smart00360, RRM, RNA recognition motif	1e-21
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-20
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	5e-19
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	7e-19
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	7e-19
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	3e-18
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	1e-17
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	8e-17
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	2e-16
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-16
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	7e-16
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	1e-15
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	2e-15
COG4281	87	COG4281, ACB, Acyl-CoA-binding protein [Lipid meta	2e-15
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	3e-15
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	4e-15
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	7e-15
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	7e-15
PTZ00458	90	PTZ00458, PTZ00458, acyl CoA binding protein; Prov	1e-14
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	2e-14
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	2e-14
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	2e-14
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-14
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	3e-14
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	7e-14
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	8e-14
cd00204	126	cd00204, ANK, ankyrin repeats; ankyrin repeats med	8e-14
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	9e-14
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	1e-13
cd00204	126	cd00204, ANK, ankyrin repeats; ankyrin repeats med	2e-13
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	2e-13
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	2e-13
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	4e-13
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	1e-12
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-12
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-12
cd00204	126	cd00204, ANK, ankyrin repeats; ankyrin repeats med	3e-12
pfam12796	91	pfam12796, Ank_2, Ankyrin repeats (3 copies)	3e-12
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	3e-12
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	3e-12
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	5e-12
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	8e-12
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	8e-12
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	9e-12
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	9e-12
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	1e-11
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	2e-11
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	2e-11
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	2e-11
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-11
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	4e-11
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	5e-11
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	6e-11
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	7e-11
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	9e-11
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	1e-10
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	1e-10
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-10
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	1e-10
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	1e-10
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	1e-10
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	1e-10
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	2e-10
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-10
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	2e-10
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	3e-10
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	3e-10
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	4e-10
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	4e-10
pfam13637	54	pfam13637, Ank_4, Ankyrin repeats (many copies)	5e-10
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	5e-10
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-10
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	7e-10
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	8e-10
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	8e-10
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	9e-10
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-09
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	1e-09
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	1e-09
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	1e-09
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	1e-09
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	1e-09
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-09
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	1e-09
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	1e-09
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	2e-09
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-09
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-09
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	2e-09
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	2e-09
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	2e-09
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-09
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	2e-09
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	3e-09
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	4e-09
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	4e-09
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	4e-09
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	4e-09
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	6e-09
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	6e-09
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	8e-09
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	8e-09
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	8e-09
pfam12796	91	pfam12796, Ank_2, Ankyrin repeats (3 copies)	1e-08
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	1e-08
pfam13857	56	pfam13857, Ank_5, Ankyrin repeats (many copies)	1e-08
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	1e-08
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-08
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	1e-08
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	1e-08
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	2e-08
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	2e-08
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	2e-08
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	2e-08
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	2e-08
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	3e-08
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	3e-08
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	4e-08
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	5e-08
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	5e-08
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	5e-08
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	6e-08
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	7e-08
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	7e-08
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	7e-08
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	8e-08
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	8e-08
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	9e-08
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-07
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-07
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	1e-07
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	1e-07
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	2e-07
pfam00023	33	pfam00023, Ank, Ankyrin repeat	2e-07
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	2e-07
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	2e-07
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-07
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-07
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	4e-07
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	4e-07
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	4e-07
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	4e-07
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	4e-07
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	5e-07
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	5e-07
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	6e-07
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	7e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-06
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	1e-06
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	1e-06
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-06
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	1e-06
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	1e-06
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	1e-06
cd12646	77	cd12646, RRM_SRSF7, RNA recognition motif in verte	2e-06
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-06
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	2e-06
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	2e-06
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	2e-06
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	2e-06
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	3e-06
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	3e-06
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	3e-06
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	3e-06
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	4e-06
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-06
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	5e-06
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	5e-06
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	5e-06
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	6e-06
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	6e-06
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	7e-06
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	7e-06
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	8e-06
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	8e-06
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	9e-06
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	9e-06
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-05
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	1e-05
COG0666	235	COG0666, Arp, FOG: Ankyrin repeat [General functio	1e-05
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	1e-05
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	1e-05
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	1e-05
pfam12796	91	pfam12796, Ank_2, Ankyrin repeats (3 copies)	2e-05
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-05
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-05
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	2e-05
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	2e-05
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	2e-05
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	2e-05
PHA03100	422	PHA03100, PHA03100, ankyrin repeat protein; Provis	2e-05
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	3e-05
smart00248	30	smart00248, ANK, ankyrin repeats	3e-05
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	3e-05
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	3e-05
pfam13606	30	pfam13606, Ank_3, Ankyrin repeat	3e-05
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	3e-05
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	3e-05
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	4e-05
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	5e-05
cd12645	81	cd12645, RRM_SRSF3, RNA recognition motif in verte	5e-05
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	5e-05
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	5e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	7e-05
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	7e-05
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	7e-05
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	7e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	8e-05
cd12659	76	cd12659, RRM2_hnRNPM, RNA recognition motif 2 in v	9e-05
cd12452	88	cd12452, RRM_ARP_like, RNA recognition motif in ye	9e-05
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	9e-05
cd12473	85	cd12473, RRM2_MSSP1, RNA recognition motif 2 found	9e-05
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	9e-05
pfam13637	54	pfam13637, Ank_4, Ankyrin repeats (many copies)	1e-04
COG0666	235	COG0666, Arp, FOG: Ankyrin repeat [General functio	1e-04
cd12591	80	cd12591, RRM2_p54nrb, RNA recognition motif 2 in v	1e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	1e-04
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	1e-04
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	1e-04
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	1e-04
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-04
cd12536	85	cd12536, RRM1_RBM39, RNA recognition motif 1 in ve	2e-04
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	2e-04
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	2e-04
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	2e-04
cd12475	88	cd12475, RRM2_RBMS3, RNA recognition motif 2 found	2e-04
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	2e-04
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	2e-04
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	2e-04
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	2e-04
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	2e-04
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	2e-04
cd12474	86	cd12474, RRM2_MSSP2, RNA recognition motif 2 found	3e-04
PTZ00322	664	PTZ00322, PTZ00322, 6-phosphofructo-2-kinase/fruct	3e-04
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	3e-04
cd12537	85	cd12537, RRM1_RBM23, RNA recognition motif 1 in ve	3e-04
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	4e-04
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	4e-04
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	4e-04
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	4e-04
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	4e-04
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	5e-04
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	5e-04
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	5e-04
cd12421	74	cd12421, RRM1_PTBP1_hnRNPL_like, RNA recognition m	5e-04
cd12603	71	cd12603, RRM_hnRNPC, RNA recognition motif in vert	5e-04
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	5e-04
cd12753	85	cd12753, RRM1_RBM10, RNA recognition motif 1 in ve	6e-04
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	6e-04
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	6e-04
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	7e-04
cd12604	76	cd12604, RRM_RALY, RNA recognition motif in verteb	8e-04
cd12660	76	cd12660, RRM2_MYEF2, RNA recognition motif 2 in ve	9e-04
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	0.001
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	0.001
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	0.002
cd12403	75	cd12403, RRM1_NCL, RNA recognition motif 1 in vert	0.002
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	0.002
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	0.002
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	0.002
cd12444	112	cd12444, RRM1_CPEBs, RNA recognition motif 1 in cy	0.002
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	0.002
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	0.002
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	0.002
cd12471	75	cd12471, RRM1_MSSP2, RNA recognition motif 1 in ve	0.003
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	0.003
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	0.003
cd12267	77	cd12267, RRM_YRA1_MLO3, RNA recognition motif in y	0.004
cd12523	78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	0.004
cd12607	67	cd12607, RRM2_RBM4, RNA recognition motif 2 in ver	0.004
cd12356	79	cd12356, RRM_PPARGC1B, RNA recognition motif in pe	0.004

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

 Score =  102 bits (256), Expect = 2e-27
 Identities = 36/73 (49%), Positives = 56/73 (76%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+FVGNLPWTV   ELK++FS++G++ + +V FDK TGLSKG+GFV+F +++ ++     
Sbjct: 1  KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 70 DSHVLEGSRLSIQ 82
            H+LEG++L +Q
Sbjct: 61 QKHILEGNKLQVQ 73

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

>gnl|CDD|216174 pfam00887, ACBP, Acyl CoA binding protein

 Score = 97.6 bits (244), Expect = 2e-25
 Identities = 32/87 (36%), Positives = 51/87 (58%), Gaps = 2/87 (2%)

Query: 94  MEDRFNQACDYLPSLVK--KLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAW 151
           +E+ F  A  ++  L K  +  +   LK YALYKQAT G  N  +P  +++  K+K++AW
Sbjct: 1   LEEEFEAAVKFVKKLPKDGRPSNEEKLKLYALYKQATEGDVNTPRPGMFDVIGKAKWDAW 60

Query: 152 NSLGQMAKSEAMSKYIALLKEVDAGWE 178
             L  M+K EAM KY+ L++E+   + 
Sbjct: 61  KKLKGMSKEEAMKKYVELVEELVEKYG 87

Length = 87

>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 = 87.4 bits (217), Expect = 7e-22
 Identities = 33/74 (44%), Positives = 53/74 (71%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          KIFVG LP  V+  E K++FS++G++++A +M D +TG S+GFGFVTF ++ AV++VFS 
Sbjct: 1  KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 70 DSHVLEGSRLSIQP 83
              L G ++ ++ 
Sbjct: 61 GMLELGGKQVEVKR 74

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

>gnl|CDD|238248 cd00435, ACBP, Acyl CoA binding protein (ACBP) binds thiol esters of long fatty acids and coenzyme A in a one-to-one binding mode with high specificity and affinity

 Score = 87.4 bits (217), Expect = 1e-21
 Identities = 32/85 (37%), Positives = 56/85 (65%)

Query: 94  MEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNS 153
           +++ F  A + +  L  K  +   L+ Y+LYKQATVG CN ++P  ++++ ++K++AWNS
Sbjct: 1   LQEEFEAAAEKVKKLKTKPSNEEKLQLYSLYKQATVGDCNTERPGMFDLKGRAKWDAWNS 60

Query: 154 LGQMAKSEAMSKYIALLKEVDAGWE 178
           L  M+K +AM  YIA ++E+ A + 
Sbjct: 61  LKGMSKEDAMKAYIAKVEELIAKYA 85

Acyl-CoAs are important intermediates in fatty lipid synthesis and fatty acid degradation and play a role in regulation of intermediary metabolism and gene regulation. The suggested role of ACBP is to act as a intracellular acyl-CoA transporter and pool former. ACBPs are present in a large group of eukaryotic species and several tissue-specific isoforms have been detected. Length = 85

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

 Score = 86.5 bits (215), Expect = 1e-21
 Identities = 27/73 (36%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           +FVGNLP   +  EL++ FS++G++ +  ++ DK TG SKGF FV F+++E  +K    
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 70 -DSHVLEGSRLSI 81
           +   L+G  L +
Sbjct: 61 LNGKELDGRPLKV 73

Length = 73

>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 = 84.2 bits (209), Expect = 1e-20
 Identities = 29/66 (43%), Positives = 46/66 (69%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          +F+G L W  +   L+++FS+YG++++  +M D  TG S+GFGFVTF +  +VDKV +  
Sbjct: 1  LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 71 SHVLEG 76
           HVL+G
Sbjct: 61 PHVLDG 66

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

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

 Score = 80.0 bits (198), Expect = 5e-19
 Identities = 28/73 (38%), Positives = 52/73 (71%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          KIFVG LP+  + + L+K+FS++G+I  A V+ D+ TG S+G+GFVTF++KE+ ++    
Sbjct: 2  KIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKD 61

Query: 70 DSHVLEGSRLSIQ 82
           + +++G + ++ 
Sbjct: 62 PNPIIDGRKANVN 74

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

 Score = 79.7 bits (197), Expect = 7e-19
 Identities = 27/74 (36%), Positives = 49/74 (66%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
           KIFVG LP  V+  +L+K+FS++G +    VM+D      +GFGF+TF+++++VD+V +
Sbjct: 3  KKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVN 62

Query: 69 TDSHVLEGSRLSIQ 82
             H + G ++ ++
Sbjct: 63 EHFHDINGKKVEVK 76

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

 Score = 79.6 bits (197), Expect = 7e-19
 Identities = 22/57 (38%), Positives = 37/57 (64%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
           ++VGNLP+ V+  +LK  F ++G++ +A V+ D+ TG S+GFGFV  +  E  +  
Sbjct: 1  NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAA 57

This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. . Length = 78

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

 Score = 77.6 bits (192), Expect = 3e-18
 Identities = 27/70 (38%), Positives = 40/70 (57%), Gaps = 2/70 (2%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST- 69
          +FVGNLP   +  +LK  FS++G I +  ++ D  TG SKGF FV F+++E  +K     
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 70 DSHVLEGSRL 79
          +   L G  L
Sbjct: 60 NGKELGGREL 69

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

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

 Score = 75.9 bits (187), Expect = 1e-17
 Identities = 29/69 (42%), Positives = 46/69 (66%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          KIFVG L    + +++KK+FS++G++ +A +MFDK T   +GFGFVTF++++ VDKV   
Sbjct: 1  KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60

Query: 70 DSHVLEGSR 78
            H +    
Sbjct: 61 HFHEINNKM 69

This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 74.1 bits (182), Expect = 8e-17
 Identities = 28/74 (37%), Positives = 46/74 (62%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+FVG L W  +   L+++FS+YG++++  +M DK T  S+GFGFV F++   V  V + 
Sbjct: 1  KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60

Query: 70 DSHVLEGSRLSIQP 83
            H L+G  +  +P
Sbjct: 61 GPHTLDGRTIDPKP 74

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

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

 Score = 73.1 bits (180), Expect = 2e-16
 Identities = 27/70 (38%), Positives = 44/70 (62%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+FVG L   V+  +L+++FS+YG + +  ++ DK TG  +GF FVTF + + VDK+   
Sbjct: 1  KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

Query: 70 DSHVLEGSRL 79
            H + G R+
Sbjct: 61 KYHTINGHRV 70

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

 Score = 72.7 bits (179), Expect = 2e-16
 Identities = 28/75 (37%), Positives = 48/75 (64%), Gaps = 1/75 (1%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          N+IFVG +P   +  EL+ FFS +G + +  ++ D+  G+SKG+GFVTF+ +E  +K+ +
Sbjct: 3  NRIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKILA 61

Query: 69 TDSHVLEGSRLSIQP 83
            +    G +L+I P
Sbjct: 62 MGNLNFRGKKLNIGP 76

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

 Score = 72.3 bits (178), Expect = 2e-16
 Identities = 26/73 (35%), Positives = 45/73 (61%), Gaps = 2/73 (2%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST- 69
          +FVGNLP   +  +L++ FS++G+I +  ++ DK+ G SKGF FV F++ E  +K     
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKD-GKSKGFAFVEFESPEDAEKALEAL 59

Query: 70 DSHVLEGSRLSIQ 82
          +   L+G +L + 
Sbjct: 60 NGKELDGRKLKVS 72

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

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

 Score = 71.0 bits (175), Expect = 7e-16
 Identities = 24/72 (33%), Positives = 44/72 (61%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          +FVGNLP+ +   EL+K F + G +    ++ D+ TG+ KGFG+V F+ K++V      +
Sbjct: 2  VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLN 61

Query: 71 SHVLEGSRLSIQ 82
             L+G ++ ++
Sbjct: 62 GIKLKGRKIRVK 73

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

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

 Score = 70.5 bits (173), Expect = 1e-15
 Identities = 28/69 (40%), Positives = 44/69 (63%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          +F+G L W  +   L+++FS++G+I    VM D  T  S+GFGFVTF +  +VDKV +  
Sbjct: 1  MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60

Query: 71 SHVLEGSRL 79
           H L+G ++
Sbjct: 61 PHELDGKKI 69

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

 Score = 70.0 bits (171), Expect = 2e-15
 Identities = 27/67 (40%), Positives = 45/67 (67%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+FVG L W  S  +LK +F+++G++ + ++  D NTG S+GFGF+ F++  +V+KV   
Sbjct: 1  KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

Query: 70 DSHVLEG 76
            H L+G
Sbjct: 61 KEHRLDG 67

This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 75

>gnl|CDD|226731 COG4281, ACB, Acyl-CoA-binding protein [Lipid metabolism]

 Score = 70.3 bits (172), Expect = 2e-15
 Identities = 30/83 (36%), Positives = 50/83 (60%)

Query: 94  MEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNS 153
           +  RF QA   +  L +K  +  LLK YAL+KQ +VG  + +KP ++++  + KY AW  
Sbjct: 2   LSTRFEQAQTDVKELSEKPSNDELLKLYALFKQGSVGDNDGEKPGFFDIVGRYKYEAWAG 61

Query: 154 LGQMAKSEAMSKYIALLKEVDAG 176
           L   ++ +A  +YIAL++E+ A 
Sbjct: 62  LKGKSQEDARQEYIALVEELKAK 84

Length = 87

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

 Score = 69.8 bits (171), Expect = 3e-15
 Identities = 27/78 (34%), Positives = 47/78 (60%)

Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
          QL K+FVG L    S + L++ F+ YG++    VM D NT  S+GFGF+TF + +  D+ 
Sbjct: 1  QLCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEA 60

Query: 67 FSTDSHVLEGSRLSIQPS 84
               H ++G+++ ++ +
Sbjct: 61 MEAQPHSIDGNQIELKRA 78

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

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

 Score = 69.3 bits (170), Expect = 4e-15
 Identities = 24/73 (32%), Positives = 44/73 (60%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          KIFVG L    +  +++++F ++G I+   +  DK T   +GF F+TF ++E V K+  T
Sbjct: 1  KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60

Query: 70 DSHVLEGSRLSIQ 82
            HV+ G ++ ++
Sbjct: 61 QFHVIGGKKVEVK 73

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

 Score = 68.4 bits (167), Expect = 7e-15
 Identities = 26/66 (39%), Positives = 45/66 (68%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          +FVG L W  +  +LK++FS++G++++ ++  D  TG S+GFGFV F++  +V+KV    
Sbjct: 1  MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 71 SHVLEG 76
           H L+G
Sbjct: 61 EHKLDG 66

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

>gnl|CDD|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 = 68.4 bits (168), Expect = 7e-15
 Identities = 26/75 (34%), Positives = 44/75 (58%), Gaps = 1/75 (1%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVF 67
          NK+FV  L    +  EL+  FS++G++    +M D  TG S+GFGFVTF++ ++A   + 
Sbjct: 2  NKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

Query: 68 STDSHVLEGSRLSIQ 82
            +   LEG  + ++
Sbjct: 62 DLNGKELEGRVIKVE 76

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

>gnl|CDD|185637 PTZ00458, PTZ00458, acyl CoA binding protein; Provisional

 Score = 68.3 bits (167), Expect = 1e-14
 Identities = 31/90 (34%), Positives = 48/90 (53%), Gaps = 2/90 (2%)

Query: 94  MEDRFNQACDYLPSLVKK--LDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAW 151
           M D F +   ++ SL K   L     L  Y  YKQ+TVG CNI +PS +  + + KY AW
Sbjct: 1   MADLFEECVSFINSLPKTVNLSVEIKLDLYKYYKQSTVGNCNIKEPSMFKYQDRKKYEAW 60

Query: 152 NSLGQMAKSEAMSKYIALLKEVDAGWEDKE 181
            S+  + + +A  +Y+ ++ E+   WE  E
Sbjct: 61  KSIENLNREDAKKRYVEIVTELFPNWEKGE 90

Length = 90

>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 = 67.6 bits (165), Expect = 2e-14
 Identities = 24/66 (36%), Positives = 47/66 (71%), Gaps = 1/66 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          +F+G L W  + + L+++F ++G++ + +VM D  TG S+GFGF+TF+  ++V++V   +
Sbjct: 1  MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKE 60

Query: 71 SHVLEG 76
           H+L+G
Sbjct: 61 -HILDG 65

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

 Score = 67.4 bits (165), Expect = 2e-14
 Identities = 27/67 (40%), Positives = 42/67 (62%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+F+G L +  + + LK +FS++G+I +  VM D NT  S+GFGFVTF +   VD   + 
Sbjct: 1  KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 70 DSHVLEG 76
            H ++G
Sbjct: 61 RPHKVDG 67

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

 Score = 67.0 bits (164), Expect = 2e-14
 Identities = 28/77 (36%), Positives = 43/77 (55%), Gaps = 1/77 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           + V  LPW  +  +LK +FS +G+++   V  D  TG SKGFGFV F + E   KV S 
Sbjct: 1  DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ 60

Query: 70 DSHVLEGSRLSIQPSDS 86
            H+++G    ++  +S
Sbjct: 61 -RHMIDGRWCDVKIPNS 76

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

 Score = 66.9 bits (164), Expect = 3e-14
 Identities = 28/80 (35%), Positives = 44/80 (55%), Gaps = 6/80 (7%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV---- 66
          +F+ NLP+  +  ELK+ FS++G++  A ++ DK TG SKG  FV F+ KE+  K     
Sbjct: 3  VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 67 --FSTDSHVLEGSRLSIQPS 84
                   L+G RL +  +
Sbjct: 63 DNAEDSGLSLDGRRLIVTLA 82

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

>gnl|CDD|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 = 66.5 bits (163), Expect = 3e-14
 Identities = 19/52 (36%), Positives = 35/52 (67%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
          +FVGN+P+  +  +L + FSE G +++  ++ D++TG  KG+GF  F++ E 
Sbjct: 1  VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIET 52

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

 Score = 65.9 bits (160), Expect = 7e-14
 Identities = 31/74 (41%), Positives = 45/74 (60%), Gaps = 2/74 (2%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+F+G L W  S + L+ +FS++G+I    VM D  T  S+GFGFVTF +  +VDKV + 
Sbjct: 1  KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60

Query: 70 DSHVLEGSRLSIQP 83
            H L+    +I P
Sbjct: 61 PHHELDSK--TIDP 72

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

>gnl|CDD|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 = 65.4 bits (160), Expect = 8e-14
 Identities = 28/71 (39%), Positives = 41/71 (57%), Gaps = 2/71 (2%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          ++FV NLP+T +  EL++ F  +G+I    +  DK T  SKGF FV+F   E   K +S 
Sbjct: 1  RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSE 60

Query: 70 -DSHVLEGSRL 79
           D  + +G RL
Sbjct: 61 LDGSIFQG-RL 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|238125 cd00204, ANK, ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins

 Score = 67.0 bits (164), Expect = 8e-14
 Identities = 32/86 (37%), Positives = 49/86 (56%), Gaps = 3/86 (3%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
           A  G L++ VK L +    ++N  D +G   LH A   GHL++V+ L+EK GADVN  D 
Sbjct: 15  ASNGHLEV-VKLLLENGA-DVNAKDNDGRTPLHLAAKNGHLEIVKLLLEK-GADVNARDK 71

Query: 322 DGDYGLDYAKAIEHTDLIEYLVNSGS 347
           DG+  L  A    + D+++ L+  G+
Sbjct: 72  DGNTPLHLAARNGNLDVVKLLLKHGA 97

The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats. Length = 126

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

 Score = 65.3 bits (160), Expect = 9e-14
 Identities = 24/64 (37%), Positives = 38/64 (59%), Gaps = 4/64 (6%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE----AVDKV 66
          +FV NLP+  +  +L++FFSE G I    V+ DK +   +GFG+VTF  +E    A+++ 
Sbjct: 2  LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 67 FSTD 70
            T 
Sbjct: 62 KKTK 65

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

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

 Score = 65.0 bits (159), Expect = 1e-13
 Identities = 26/73 (35%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE-AVDKVFST 69
          +F+ +LP   +  +L + F+ +G +++A V  DKNTG SK FGFV++ N E A   + + 
Sbjct: 1  LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 70 DSHVLEGSRLSIQ 82
          +   + G RL +Q
Sbjct: 61 NGFQVGGKRLKVQ 73

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

>gnl|CDD|238125 cd00204, ANK, ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins

 Score = 65.9 bits (161), Expect = 2e-13
 Identities = 30/82 (36%), Positives = 46/82 (56%), Gaps = 3/82 (3%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
           AK G L++ VK L +    ++N  D++G   LH A   G+L VV+ L++  GADVN  D 
Sbjct: 48  AKNGHLEI-VKLLLEKGA-DVNARDKDGNTPLHLAARNGNLDVVKLLLKH-GADVNARDK 104

Query: 322 DGDYGLDYAKAIEHTDLIEYLV 343
           DG   L  A    H ++++ L+
Sbjct: 105 DGRTPLHLAAKNGHLEVVKLLL 126

The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats. Length = 126

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

 Score = 64.6 bits (157), Expect = 2e-13
 Identities = 27/66 (40%), Positives = 43/66 (65%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          +F+G L W  +  +LK +FS++G++++ ++  D  TG S+GFGFV F+  E+VDKV    
Sbjct: 1  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 71 SHVLEG 76
           H L G
Sbjct: 61 EHKLNG 66

This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 74

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

 Score = 64.3 bits (156), Expect = 2e-13
 Identities = 26/67 (38%), Positives = 43/67 (64%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+F+G L W  S  +L ++ S +G++++ ++  D  TG S+GFGFV F++  +VDKV   
Sbjct: 1  KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60

Query: 70 DSHVLEG 76
            H L+G
Sbjct: 61 KEHKLDG 67

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

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

 Score = 63.5 bits (154), Expect = 4e-13
 Identities = 26/66 (39%), Positives = 41/66 (62%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+F+G L W  +   L+++F ++G++    VM D  T  S+GFGFVTF ++  VDKV + 
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 70 DSHVLE 75
            H L+
Sbjct: 62 SRHELD 67

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

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

 Score = 62.4 bits (152), Expect = 1e-12
 Identities = 24/56 (42%), Positives = 36/56 (64%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           +FVGNL W+V    LK  F ++G ++ A V+ D+ TG S+GFG+V F++ E   K
Sbjct: 1  TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKK 56

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

 Score = 62.2 bits (151), Expect = 1e-12
 Identities = 29/73 (39%), Positives = 43/73 (58%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+FVG L   V   +L + FS++G +  A V+ DK TG  +GFGFV FQN ++ DK    
Sbjct: 1  KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60

Query: 70 DSHVLEGSRLSIQ 82
            H + G R+ ++
Sbjct: 61 KFHPINGHRVEVK 73

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

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

 Score = 61.8 bits (151), Expect = 2e-12
 Identities = 26/58 (44%), Positives = 36/58 (62%), Gaps = 1/58 (1%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
            ++V NL   +   +LK+ F +YG+I +A VM D + G SKGFGFV F+N EA  K 
Sbjct: 2  TNVYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKA 58

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|238125 cd00204, ANK, ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins

 Score = 62.8 bits (153), Expect = 3e-12
 Identities = 27/64 (42%), Positives = 37/64 (57%), Gaps = 1/64 (1%)

Query: 283 NQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYL 342
           N  DE+G   LH A   GHL+VV+ L+E  GADVN  D+DG   L  A    H ++++ L
Sbjct: 1   NARDEDGRTPLHLAASNGHLEVVKLLLEN-GADVNAKDNDGRTPLHLAAKNGHLEIVKLL 59

Query: 343 VNSG 346
           +  G
Sbjct: 60  LEKG 63

The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats. Length = 126

>gnl|CDD|205076 pfam12796, Ank_2, Ankyrin repeats (3 copies)

 Score = 61.9 bits (151), Expect = 3e-12
 Identities = 30/86 (34%), Positives = 49/86 (56%), Gaps = 5/86 (5%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
           AK G L++ VK L + K  ++N  D +    LH A   G+L++V+ L+E  GADVN  D 
Sbjct: 5   AKNGNLEL-VKLLLE-KGADVNLGDTD--TALHLAARNGNLEIVKLLLEH-GADVNAKDK 59

Query: 322 DGDYGLDYAKAIEHTDLIEYLVNSGS 347
           DG+  L  A    + ++++ L+  G+
Sbjct: 60  DGNTALHLAARNGNLEIVKLLLEHGA 85

Length = 91

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

 Score = 61.2 bits (149), Expect = 3e-12
 Identities = 23/68 (33%), Positives = 41/68 (60%), Gaps = 1/68 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTF-QNKEAVDKVFST 69
          ++V  LP T++  EL+  FS YG+I+ + ++ D  TGLS+G GF+ F +  EA   + + 
Sbjct: 3  LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL 62

Query: 70 DSHVLEGS 77
          +  +  G+
Sbjct: 63 NGTIPPGA 70

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|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA

 Score = 61.0 bits (149), Expect = 3e-12
 Identities = 24/56 (42%), Positives = 35/56 (62%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          K+FVG LP T +  +++  F EYG I   +++ DK+TG SKG  FV F ++E   K
Sbjct: 1  KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQK 56

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

 Score = 60.6 bits (147), Expect = 5e-12
 Identities = 27/77 (35%), Positives = 47/77 (61%), Gaps = 2/77 (2%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          N+IFVG + +  + N+L+KFFS+YG +    ++ D+  G+SKG+GFVTF+ +E   K+  
Sbjct: 3  NRIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQKILQ 61

Query: 69 -TDSHVLEGSRLSIQPS 84
            +       +L+I  +
Sbjct: 62 EANRLCFRDKKLNIGQA 78

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

 Score = 60.1 bits (146), Expect = 8e-12
 Identities = 28/75 (37%), Positives = 44/75 (58%), Gaps = 1/75 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE-AVDKVFS 68
          ++FV NLP++   ++L+K FS++G++    V  DK +G SKGF +V F + E AV     
Sbjct: 4  RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKE 63

Query: 69 TDSHVLEGSRLSIQP 83
           D  V +G  + I P
Sbjct: 64 LDGKVFQGRLIHILP 78

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

 Score = 62.0 bits (150), Expect = 8e-12
 Identities = 29/87 (33%), Positives = 49/87 (56%), Gaps = 2/87 (2%)

Query: 1   MSNSIRQLN-KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN 59
           M  S+R ++ K+F+G L W      L+  F+ +G +++A V+ D+ TG S+GFGFV F +
Sbjct: 26  MLGSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFND 85

Query: 60  KEAVDKVFS-TDSHVLEGSRLSIQPSD 85
           + A     S  D   L G  + + P++
Sbjct: 86  EGAATAAISEMDGKELNGRHIRVNPAN 112

Length = 144

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

 Score = 64.6 bits (156), Expect = 9e-12
 Identities = 28/102 (27%), Positives = 57/102 (55%), Gaps = 1/102 (0%)

Query: 2   SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
             S  + N +FVGNLP+ V+  +L++ F ++G +    ++ D+ TG S+GF FV F+++E
Sbjct: 109 QKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEE 168

Query: 62  AVDK-VFSTDSHVLEGSRLSIQPSDSHNRMAENMEDRFNQAC 102
           + +K +   +   LEG  L +Q +   ++    + +  + + 
Sbjct: 169 SAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASF 210

Length = 306

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

 Score = 59.5 bits (145), Expect = 9e-12
 Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 3/70 (4%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF-ST 69
          ++V NLP +V+  +L++FFS YG++    ++ +K+    +GF FV F + E  +      
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58

Query: 70 DSHVLEGSRL 79
          +  VL+G  L
Sbjct: 59 NGLVLDGRTL 68

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

>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 = 59.2 bits (144), Expect = 1e-11
 Identities = 23/66 (34%), Positives = 43/66 (65%), Gaps = 1/66 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          +FV NL ++V  +EL+K FS+ G+I +  ++ +   G SKG+ +V F+N+E+V +    D
Sbjct: 2  VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEALKLD 60

Query: 71 SHVLEG 76
            +++G
Sbjct: 61 RELIKG 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|241016 cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins

 Score = 58.9 bits (142), Expect = 2e-11
 Identities = 26/63 (41%), Positives = 43/63 (68%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          KIFVG L    +  ++K++F ++G++ +A +MFDK T   +GFGFVTF++++ V+KV   
Sbjct: 1  KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 70 DSH 72
            H
Sbjct: 61 HFH 63

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 59.0 bits (143), Expect = 2e-11
 Identities = 28/76 (36%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          ++F+ NL +T +  +L+K FS+YG +    +  DK T   KGF FVT+   E   K F+ 
Sbjct: 4  RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAE 63

Query: 70 -DSHVLEGSRLSIQPS 84
           D  V +G  L + PS
Sbjct: 64 LDGTVFQGRLLHLLPS 79

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

 Score = 58.9 bits (142), Expect = 2e-11
 Identities = 28/83 (33%), Positives = 47/83 (56%), Gaps = 2/83 (2%)

Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
          QL K+F+G L +  +   L+  F ++G + +  VM D NT  S+GFGFVT+ + E VD  
Sbjct: 1  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAA 60

Query: 67 FSTDSHVLEGSRLSIQPSDSHNR 89
           +   H ++G    ++P  + +R
Sbjct: 61 MNARPHKVDGR--VVEPKRAVSR 81

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

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

 Score = 58.9 bits (143), Expect = 2e-11
 Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 1/71 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          +FVGNL W+   ++L++FF E G++++  +  D + G SKGFG V F  +E   K     
Sbjct: 2  LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALEKS 60

Query: 71 SHVLEGSRLSI 81
             L G  + +
Sbjct: 61 GEELLGREIRV 71

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

>gnl|CDD|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 = 58.2 bits (141), Expect = 4e-11
 Identities = 28/81 (34%), Positives = 45/81 (55%), Gaps = 4/81 (4%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+FVG +P  +   +L+  F ++G+I   +V+ DK TG+ KG  F+T+  +E+  K  S 
Sbjct: 7  KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESALKAQSA 66

Query: 70 --DSHVLEGSRLSIQ--PSDS 86
            +   L G    IQ  P+DS
Sbjct: 67 LHEQKTLPGMNRPIQVKPADS 87

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

 Score = 57.8 bits (139), Expect = 5e-11
 Identities = 27/63 (42%), Positives = 42/63 (66%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          KIFVG L       ++K++F ++G++ +A +MFDK T   +GFGFVTF+N++ V+KV   
Sbjct: 5  KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEI 64

Query: 70 DSH 72
            H
Sbjct: 65 HFH 67

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 79

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

 Score = 57.4 bits (139), Expect = 6e-11
 Identities = 20/62 (32%), Positives = 33/62 (53%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          +FVGNL +    + + + F EYG+I +  +  D ++G  KGFG+V F ++EA        
Sbjct: 1  LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 71 SH 72
            
Sbjct: 61 GG 62

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

 Score = 57.3 bits (139), Expect = 7e-11
 Identities = 25/69 (36%), Positives = 38/69 (55%), Gaps = 1/69 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSE-YGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          IFVG+L   V+   L++ F   Y  +  A V+ D  TG SKG+GFV F +++  D+  + 
Sbjct: 4  IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 70 DSHVLEGSR 78
           + V   SR
Sbjct: 64 MNGVYCSSR 72

This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 80

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

 Score = 57.4 bits (138), Expect = 9e-11
 Identities = 22/70 (31%), Positives = 39/70 (55%)

Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
          Q  K+F+G L +  +   L+ ++ ++G++ +  VM D  +  S+GFGFVTF     VD  
Sbjct: 1  QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAA 60

Query: 67 FSTDSHVLEG 76
           +   H ++G
Sbjct: 61 MAARPHTIDG 70

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

 Score = 57.2 bits (138), Expect = 1e-10
 Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK-EAVDKVFST 69
          ++V NLP  ++ +EL+K F  YG I+  +++ DK+TGL +G  FV +  + EA   + S 
Sbjct: 3  LYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSL 62

Query: 70 DSHVLEGSRLSIQ 82
          +  +  GS + + 
Sbjct: 63 NGTIPPGSTMPLS 75

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

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 17/73 (23%), Positives = 39/73 (53%), Gaps = 6/73 (8%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
           K+FVG L   ++  +L+++FS++G++ +  +         + F FVTF + E    +  
Sbjct: 1  RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP-----FRAFAFVTFADPEVAQSLCG 55

Query: 69 TDSHVLEGSRLSI 81
           + H+++G  + +
Sbjct: 56 -EDHIIKGVSVHV 67

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|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 = 57.2 bits (138), Expect = 1e-10
 Identities = 23/55 (41%), Positives = 35/55 (63%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVD 64
          K+F+G L +  +   L++ FS+YGQI    V+ D+ T  S+GFGFVTF+N +   
Sbjct: 2  KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAK 56

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|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 57.6 bits (139), Expect = 1e-10
 Identities = 20/54 (37%), Positives = 33/54 (61%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVD 64
          +FV NLP+  +   L   FS++G +  A  + DK+TG +KG GFV F+++   +
Sbjct: 4  LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYN 57

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

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

 Score = 56.1 bits (136), Expect = 1e-10
 Identities = 21/71 (29%), Positives = 38/71 (53%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          IFVGN+ +  +  EL++ F   G I   +++ DK TG  KGF ++ F +K +V+     +
Sbjct: 2  IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLN 61

Query: 71 SHVLEGSRLSI 81
               G ++ +
Sbjct: 62 ESEFRGRQIKV 72

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

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

 Score = 56.6 bits (137), Expect = 1e-10
 Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF-S 68
          ++FVGNLP  ++ +ELK+FF E+G ++   +      G    FGFV F + EAV K+  +
Sbjct: 5  QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64

Query: 69 TDSHVLEGSRLSIQP 83
             +     RL+++ 
Sbjct: 65 KPIYFRGDHRLNVEE 79

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|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 = 56.5 bits (137), Expect = 1e-10
 Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 4/78 (5%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASV-MFDKNTGLSKGFGFVTFQNKEAVDKVF 67
           K+ V N+P+  +  EL++ FS +GQ+   SV +  K  G  +GF FV F  K+      
Sbjct: 1  TKLIVRNVPFEATKKELRELFSPFGQVK--SVRLPKKFDGSHRGFAFVEFVTKQEAQNAM 58

Query: 68 STDSHV-LEGSRLSIQPS 84
                 L G  L ++ +
Sbjct: 59 EALKSTHLYGRHLVLEYA 76

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

 Score = 56.6 bits (136), Expect = 2e-10
 Identities = 26/70 (37%), Positives = 41/70 (58%)

Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
          QL K+F+G L +  + + L++ F ++G + +  VM D  T  S+GFGFVT+   E VD  
Sbjct: 1  QLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA 60

Query: 67 FSTDSHVLEG 76
           S   H ++G
Sbjct: 61 MSARPHKVDG 70

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

 Score = 56.5 bits (137), Expect = 2e-10
 Identities = 22/52 (42%), Positives = 32/52 (61%), Gaps = 1/52 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
           ++V NL  ++    L++ FS +G I +A VM D+  G SKGFGFV F + E
Sbjct: 3  NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDEK-GRSKGFGFVCFSSPE 53

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

 Score = 56.1 bits (135), Expect = 2e-10
 Identities = 24/67 (35%), Positives = 39/67 (58%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          KIFVG +      + L+ +F +YG+I    +M D+ +G  +GF FVTF + ++VDK+   
Sbjct: 2  KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 61

Query: 70 DSHVLEG 76
            H + G
Sbjct: 62 KYHTVNG 68

This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 77

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

 Score = 55.4 bits (134), Expect = 3e-10
 Identities = 29/72 (40%), Positives = 41/72 (56%), Gaps = 2/72 (2%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST- 69
          IFV NLP++V+  +LK  F E G ++ A V  D N G SKGFG V F++ E   +     
Sbjct: 1  IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTD-NDGRSKGFGTVLFESPEDAQRAIEMF 59

Query: 70 DSHVLEGSRLSI 81
          + + LEG  L +
Sbjct: 60 NGYDLEGRELEV 71

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

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

 Score = 55.7 bits (134), Expect = 3e-10
 Identities = 19/58 (32%), Positives = 38/58 (65%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          ++V  LP T++  EL++ FS+YG+I+ + ++ D+ TG+S+G GF+ F  +   ++   
Sbjct: 3  LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

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|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 = 55.2 bits (133), Expect = 4e-10
 Identities = 19/51 (37%), Positives = 36/51 (70%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          +FVGN+P+  +  +LK  FSE G +++  +++D+ TG  KG+GF  ++++E
Sbjct: 1  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQE 51

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

 Score = 55.6 bits (133), Expect = 4e-10
 Identities = 23/57 (40%), Positives = 40/57 (70%), Gaps = 1/57 (1%)

Query: 4  SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
          SIR  N ++V  LP T++  EL++ FS+YG+I+ + ++ D+ TG+S+G GF+ F  +
Sbjct: 2  SIRDAN-LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKR 57

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|222277 pfam13637, Ank_4, Ankyrin repeats (many copies)

 Score = 54.2 bits (131), Expect = 5e-10
 Identities = 20/55 (36%), Positives = 33/55 (60%), Gaps = 1/55 (1%)

Query: 289 GLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLV 343
           G   LH A   G L++V++L+EK G D+N TD DG+  L  A    + ++++ L+
Sbjct: 1   GRTALHKAAISGRLELVKYLLEK-GVDINRTDEDGNTALHIAAENGNLEVLKLLL 54

Length = 54

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

 Score = 54.9 bits (133), Expect = 5e-10
 Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST- 69
          +++G+LP      EL+K+FS++G +    +   K TG SKG+ FV F++ E    V  T 
Sbjct: 2  VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETM 61

Query: 70 DSHVLEGSRLSIQ 82
          ++++L    L  +
Sbjct: 62 NNYLLFERLLKCK 74

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

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

 Score = 60.2 bits (146), Expect = 6e-10
 Identities = 27/111 (24%), Positives = 55/111 (49%), Gaps = 12/111 (10%)

Query: 1   MSNSIR------QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGF 54
           +    R      +   ++V NL  +V+ ++L++ F+++G+I +A+VM D + G S+GF F
Sbjct: 165 IKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGS-GRSRGFAF 223

Query: 55  VTFQNKE----AVDKVFSTD-SHVLEGSRLSIQPSDSHNRMAENMEDRFNQ 100
           V F+  E    AV+++         EG +L +  +         +  +F +
Sbjct: 224 VNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEE 274

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

 Score = 54.4 bits (131), Expect = 7e-10
 Identities = 23/51 (45%), Positives = 32/51 (62%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          I++G+LP      ELKK+FS++G + N  V   K TG SK +GF+ F N E
Sbjct: 2  IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPE 52

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

 Score = 54.2 bits (131), Expect = 8e-10
 Identities = 18/39 (46%), Positives = 27/39 (69%)

Query: 23 NELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
           +L++ FS YG I    V++D+ TG S+GFGFV F++ E
Sbjct: 14 RDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVE 52

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

 Score = 54.3 bits (131), Expect = 8e-10
 Identities = 23/51 (45%), Positives = 33/51 (64%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          IFVG+L   +    L+  F+ +G+I +A V+ D  TG SKG+GFV+F  KE
Sbjct: 2  IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKE 52

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

 Score = 54.2 bits (131), Expect = 9e-10
 Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 3/60 (5%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKN---TGLSKGFGFVTFQNKEAVDKV 66
          ++++GNL   ++   L K FS+YG+I     +F K+    G  +G+ FVTF+ KE  +K 
Sbjct: 1  RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

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

 Score = 59.1 bits (143), Expect = 1e-09
 Identities = 26/66 (39%), Positives = 40/66 (60%), Gaps = 1/66 (1%)

Query: 4   SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAV 63
              Q   ++V NL  TV+  +L++ FSE G+I +A VM D+  G+S+GFGFV F N E  
Sbjct: 281 MKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEA 339

Query: 64  DKVFST 69
           ++  + 
Sbjct: 340 NRAVTE 345

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|241116 cd12672, RRM_DAZL, RNA recognition motif in vertebrate deleted in azoospermia-like (DAZL) proteins

 Score = 54.1 bits (130), Expect = 1e-09
 Identities = 25/77 (32%), Positives = 46/77 (59%), Gaps = 4/77 (5%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          N +FVG +   +   E++ FF++YG +    ++ D+ TG+SKG+GFV+F +   V K+  
Sbjct: 6  NTVFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDDVDVQKI-- 62

Query: 69 TDSHV-LEGSRLSIQPS 84
           +S +   G +L + P+
Sbjct: 63 VESQINFHGKKLKLGPA 79

This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 82

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

 Score = 54.3 bits (130), Expect = 1e-09
 Identities = 25/77 (32%), Positives = 43/77 (55%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+FVG +      + L+ +F EYG+I    ++ D+ +G  +GFGFVTF + + VDK+   
Sbjct: 2  KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQ 61

Query: 70 DSHVLEGSRLSIQPSDS 86
            H + G    ++ + S
Sbjct: 62 KYHTINGHNAEVRKALS 78

This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 18/51 (35%), Positives = 32/51 (62%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          ++VGNL + ++ ++L+  F  +G+I    +  D  TG SKG+GF+ F + E
Sbjct: 1  LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAE 51

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

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 16/51 (31%), Positives = 31/51 (60%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          + VGNLP   +  + ++  S +G +    +++ ++TG SKG+GFV + +K 
Sbjct: 2  LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKA 52

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

 Score = 53.7 bits (129), Expect = 1e-09
 Identities = 23/68 (33%), Positives = 39/68 (57%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          IFVG+L   V+   L   FS +    +A VM+D  +G S+G+GFV+F++++  +   +  
Sbjct: 2  IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 71 SHVLEGSR 78
          +    GSR
Sbjct: 62 NGKWLGSR 69

This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 75

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

 Score = 53.7 bits (130), Expect = 1e-09
 Identities = 19/49 (38%), Positives = 27/49 (55%)

Query: 13 VGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          V NL      ++L++ F  +G I    +  DK TG S+GF FVTF  +E
Sbjct: 4  VTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTRE 52

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

 Score = 53.5 bits (129), Expect = 1e-09
 Identities = 24/72 (33%), Positives = 39/72 (54%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          +FVGNLP+  +  +L   F   G   +  ++ DK TG SKG  FV F   EA+ K     
Sbjct: 3  LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62

Query: 71 SHVLEGSRLSIQ 82
            +L+G +++++
Sbjct: 63 HTLLKGRKINVE 74

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

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

 Score = 53.5 bits (129), Expect = 1e-09
 Identities = 24/71 (33%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          +++GNL W ++ +++++FF    +I +  +  DK TG  KGFG V F ++E++D     D
Sbjct: 2  VYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALKLD 60

Query: 71 SHVLEGSRLSI 81
            VL G  + I
Sbjct: 61 GTVLCGRPIRI 71

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 53.5 bits (129), Expect = 2e-09
 Identities = 21/56 (37%), Positives = 31/56 (55%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
          ++V  LP   +H  LK  FS+YG ++  S+   K+TG  KGF F+ F+  E   K 
Sbjct: 2  VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKA 57

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

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

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 3/77 (3%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQI--MNASVMFDKNTG-LSKGFGFVTFQNKEAVDKV 66
          +I+V NL + +  ++L+  FS++G++  +      D+  G L+ GF FVTF++  + +  
Sbjct: 2  EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENA 61

Query: 67 FSTDSHVLEGSRLSIQP 83
             +   L G ++S+  
Sbjct: 62 LQLNGTELGGRKISVSL 78

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

 Score = 53.1 bits (128), Expect = 2e-09
 Identities = 23/71 (32%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 13 VGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK-EAVDKVFSTDS 71
          V NL +  + ++L++ F +YG++ +  +  D+ T  S+GF FV F +K +A D + + D 
Sbjct: 3  VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 72 HVLEGSRLSIQ 82
            L+G  L +Q
Sbjct: 63 KELDGRELRVQ 73

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

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

 Score = 53.5 bits (128), Expect = 2e-09
 Identities = 25/73 (34%), Positives = 39/73 (53%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          KIFVG +        L+ +F +YG+I    VM D+ +G  +GF FVTF + + VDK+   
Sbjct: 2  KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQ 61

Query: 70 DSHVLEGSRLSIQ 82
            H + G    ++
Sbjct: 62 KYHTINGHNCEVK 74

This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 53.1 bits (128), Expect = 2e-09
 Identities = 27/72 (37%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFST 69
          IFV NLP     + L + FS +G + N  V+ D  T   KG+GFVT  N +EA   + S 
Sbjct: 4  IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 70 DSHVLEGSRLSI 81
          + + L G  L +
Sbjct: 64 NGYRLGGRVLQV 75

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

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

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 23/50 (46%), Positives = 32/50 (64%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN 59
          +IFVG+L   V+   L + FS+Y     A V+ DK TG SKG+GFV+F +
Sbjct: 8  RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSD 57

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

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

 Score = 52.9 bits (127), Expect = 2e-09
 Identities = 28/75 (37%), Positives = 43/75 (57%), Gaps = 7/75 (9%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTF----QNKEAVDKV 66
          +FV NL ++V+  +L  FFS+   I +A V+ D  TG S+G+GFVTF      +EA+ K+
Sbjct: 2  LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 67 FSTDSHVLEGSRLSI 81
           +     L G  L +
Sbjct: 62 KNK---KLHGRILRL 73

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 53.2 bits (127), Expect = 2e-09
 Identities = 19/50 (38%), Positives = 36/50 (72%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
          ++V  LP T++  EL++ FS+YG+I+ + ++ D+ TG+S+G GF+ F  +
Sbjct: 5  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKR 54

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

 Score = 52.6 bits (127), Expect = 3e-09
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 5/73 (6%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          +FV  L   V   +L +FFS+ G++ +  ++ D+N+  SKG  +V F ++E+V       
Sbjct: 2  VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALG-- 59

Query: 71 SHVLEGSRLSIQP 83
             L G RL  QP
Sbjct: 60 ---LTGQRLLGQP 69

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|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 52.9 bits (127), Expect = 4e-09
 Identities = 20/55 (36%), Positives = 34/55 (61%), Gaps = 2/55 (3%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGL--SKGFGFVTFQNKEA 62
          K+FVG +P + S  +L++ F +YG +   +V+ D++     SKG  FVTF  ++A
Sbjct: 3  KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKA 57

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 84

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

 Score = 52.3 bits (126), Expect = 4e-09
 Identities = 25/70 (35%), Positives = 46/70 (65%), Gaps = 1/70 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE-AVDKVFST 69
          ++V NLP+++++N+L K FS+YG+++  +++ DK T  SKG  F+ F ++E A   V + 
Sbjct: 4  VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 70 DSHVLEGSRL 79
          ++  L G  L
Sbjct: 64 NNKELFGRTL 73

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

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

 Score = 52.3 bits (126), Expect = 4e-09
 Identities = 18/75 (24%), Positives = 42/75 (56%), Gaps = 2/75 (2%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS- 68
          ++ V NLP  +  ++L+K F  +G I +  + + K+ G  + FGFV ++ +E   K    
Sbjct: 2  RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKD-GKFRKFGFVGYKTEEEAQKALKH 60

Query: 69 TDSHVLEGSRLSIQP 83
           ++  ++ S+++++ 
Sbjct: 61 FNNSFIDTSKITVEI 75

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

 Score = 52.0 bits (125), Expect = 4e-09
 Identities = 20/57 (35%), Positives = 34/57 (59%), Gaps = 2/57 (3%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           ++ V N+P+     +L++ F ++G I++  ++F  N   SKGFGFVTF N    D+
Sbjct: 1  KRLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIF--NERGSKGFGFVTFANSADADR 55

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

 Score = 52.3 bits (125), Expect = 6e-09
 Identities = 23/68 (33%), Positives = 43/68 (63%), Gaps = 1/68 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK-EAVDKVFST 69
          +++  LP T++  +++  FS +G+I+N+ V+ D+ TGLS+G  F+ F  + EA + + S 
Sbjct: 3  LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITSF 62

Query: 70 DSHVLEGS 77
          + H   GS
Sbjct: 63 NGHKPPGS 70

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

 Score = 51.9 bits (124), Expect = 6e-09
 Identities = 19/50 (38%), Positives = 36/50 (72%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
          ++V  LP T+S  E+++ FS+YG+I+ + ++ D+ TG+S+G GF+ F  +
Sbjct: 4  LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRFDKR 53

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

 Score = 51.8 bits (125), Expect = 8e-09
 Identities = 17/54 (31%), Positives = 28/54 (51%)

Query: 12 FVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          +VG+L   V+   L + FS  G +++  V  D  T  S G+ +V FQN    ++
Sbjct: 3  YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAER 56

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

 Score = 56.1 bits (135), Expect = 8e-09
 Identities = 26/64 (40%), Positives = 43/64 (67%), Gaps = 1/64 (1%)

Query: 2   SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
           S+SI+  N ++V  LP T++ +EL+  FS +GQI+ + ++ D  TGLSKG GF+ F  ++
Sbjct: 84  SDSIKGAN-LYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRD 142

Query: 62  AVDK 65
             D+
Sbjct: 143 EADR 146

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

 Score = 51.3 bits (123), Expect = 8e-09
 Identities = 20/71 (28%), Positives = 32/71 (45%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          +FVGNL +  + +EL+  F   G+I    +M  +++G  KGF FV F+  E         
Sbjct: 1  LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60

Query: 71 SHVLEGSRLSI 81
                 R+  
Sbjct: 61 HLNGRALRVEY 71

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|205076 pfam12796, Ank_2, Ankyrin repeats (3 copies)

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 22/59 (37%), Positives = 37/59 (62%), Gaps = 3/59 (5%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTD 320
           A+ G L++ VK L +    ++N  D++G   LH A   G+L++V+ L+E  GAD+N+ D
Sbjct: 36  ARNGNLEI-VKLLLE-HGADVNAKDKDGNTALHLAARNGNLEIVKLLLEH-GADINLKD 91

Length = 91

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

 Score = 51.5 bits (124), Expect = 1e-08
 Identities = 21/58 (36%), Positives = 40/58 (68%), Gaps = 4/58 (6%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE----AVD 64
          I++G LP+ ++  ++   FS+YG+I++ +++ DK TG SKGF F+ ++++     AVD
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVD 69

This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well. . Length = 89

>gnl|CDD|206028 pfam13857, Ank_5, Ankyrin repeats (many copies)

 Score = 50.4 bits (121), Expect = 1e-08
 Identities = 23/57 (40%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 274 LTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA 330
           L +    ++N  D NG   LH A   G L++VQ L++  G D+N+ DSDG   LD A
Sbjct: 1   LLEHGPIDLNATDGNGNTPLHLAAKYGALELVQWLLKP-GVDLNLRDSDGLTALDLA 56

Length = 56

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

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 19/56 (33%), Positives = 34/56 (60%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVD 64
          NKIF+G LP  +S +++K+    +G++   +++ D  TGLSKG+ F  + +    D
Sbjct: 1  NKIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTD 56

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

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

 Score = 50.8 bits (122), Expect = 1e-08
 Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 13 VGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DS 71
          V  LP  ++  EL+  F   G I +  ++ D+ TG S G+GFV + ++    K  +T + 
Sbjct: 5  VNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNG 64

Query: 72 HVLEGSRLSI 81
            +   RL +
Sbjct: 65 FEIRNKRLKV 74

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|240695 cd12249, RRM1_hnRNPR_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 50.6 bits (122), Expect = 1e-08
 Identities = 21/55 (38%), Positives = 33/55 (60%), Gaps = 1/55 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          +FVG +P  +  +EL   F + G I    +M D + GL++G+ FVT+ NKEA  +
Sbjct: 4  VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFS-GLNRGYAFVTYTNKEAAQR 57

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

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

 Score = 50.8 bits (122), Expect = 1e-08
 Identities = 22/56 (39%), Positives = 32/56 (57%), Gaps = 1/56 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNA-SVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          +F+GNL   V    L   FS +G I+    +M D +TG SKGF F+++ + EA D 
Sbjct: 4  LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDA 59

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

>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins

 Score = 50.7 bits (121), Expect = 2e-08
 Identities = 27/75 (36%), Positives = 43/75 (57%), Gaps = 4/75 (5%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          +++FVGNLP  V  +ELK+FF +YG ++   +    + G    FGFV F + E V K+ S
Sbjct: 4  HQLFVGNLPHDVDKSELKEFFQQYGNVVELRI---NSGGKLPNFGFVVFDDSEPVQKILS 60

Query: 69 TDSHVLEGS-RLSIQ 82
              +  G  RL+++
Sbjct: 61 NRPIMFRGDVRLNVE 75

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

 Score = 50.8 bits (121), Expect = 2e-08
 Identities = 24/75 (32%), Positives = 42/75 (56%)

Query: 8  LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
          + KIFVG L    +  +++++F E+G+I    +  D  T   +GF F+TF+ ++ V KV 
Sbjct: 4  VKKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVL 63

Query: 68 STDSHVLEGSRLSIQ 82
              H + GS+  I+
Sbjct: 64 EKKFHNVSGSKCEIK 78

This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. . Length = 80

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

 Score = 50.4 bits (120), Expect = 2e-08
 Identities = 22/73 (30%), Positives = 40/73 (54%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+FVG L    +  ++K++F  +G+I N  +  D  T   +GF FVT+ ++E V K+  +
Sbjct: 1  KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60

Query: 70 DSHVLEGSRLSIQ 82
            H +   +  I+
Sbjct: 61 RYHQIGSGKCEIK 73

This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. . Length = 75

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

 Score = 50.3 bits (120), Expect = 2e-08
 Identities = 18/56 (32%), Positives = 36/56 (64%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          K+FVG++P T++  E++  F E+G ++  +++ DK TG  +G  FV +  ++  D+
Sbjct: 1  KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADR 56

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

 Score = 50.2 bits (121), Expect = 2e-08
 Identities = 22/55 (40%), Positives = 34/55 (61%), Gaps = 1/55 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          IF+ NL  ++ +  L   FS +G I++  V  D+N G SKG+GFV F+ +EA  +
Sbjct: 5  IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDEN-GGSKGYGFVHFETEEAAVR 58

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

 Score = 49.7 bits (119), Expect = 3e-08
 Identities = 28/77 (36%), Positives = 40/77 (51%), Gaps = 5/77 (6%)

Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
              +FV       S  +L  +FS +G +MN  V+ DK+ G+   +  V F +KE VDKV
Sbjct: 1  AERSVFVSGFKRGTSEEQLMDYFSAFGPVMN--VIMDKDKGV---YAIVEFDSKEGVDKV 55

Query: 67 FSTDSHVLEGSRLSIQP 83
           S   H L G RL ++P
Sbjct: 56 LSEPQHTLNGHRLRVRP 72

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

>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating protein-binding protein 2 (G3BP2) and similar proteins

 Score = 50.0 bits (119), Expect = 3e-08
 Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          +++FVGNLP  +  +ELK+FF  +G ++   +      G    FGFV F + E V ++  
Sbjct: 6  HQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQRILG 65

Query: 69 TDSHVLEGS-RLSIQ 82
              +  G  RL+++
Sbjct: 66 AKPIMFRGEVRLNVE 80

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

 Score = 49.1 bits (118), Expect = 4e-08
 Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 9/74 (12%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+FVGNLP   +  EL+  F +YG +    V+        K +GFV  + +E  +     
Sbjct: 1  KLFVGNLPDATTSEELRALFEKYGTVTECDVV--------KNYGFVHMEEEEDAEDAIKA 52

Query: 70 -DSHVLEGSRLSIQ 82
           + +   G R++++
Sbjct: 53 LNGYEFMGKRINVE 66

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

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

 Score = 49.7 bits (119), Expect = 5e-08
 Identities = 19/73 (26%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFST 69
          ++V N+      ++L++ F +YG I++  +  D  T   +GF +V F++ ++A D ++  
Sbjct: 3  LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 70 DSHVLEGSRLSIQ 82
          D     G  + IQ
Sbjct: 63 DRTRFLGREIEIQ 75

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

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

 Score = 49.5 bits (118), Expect = 5e-08
 Identities = 19/73 (26%), Positives = 39/73 (53%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          ++VGN+ +  +  EL+  FS  G I   +++ DK +G  KG+ ++ F  +++V+   + D
Sbjct: 2  VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVALD 61

Query: 71 SHVLEGSRLSIQP 83
               G  + + P
Sbjct: 62 ESSFRGRVIKVLP 74

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

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

 Score = 48.9 bits (117), Expect = 5e-08
 Identities = 21/76 (27%), Positives = 42/76 (55%), Gaps = 9/76 (11%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFS 68
          ++++G LP+     ++++FF  YG+I        +   L  GFGFV F++ ++A D V+ 
Sbjct: 1  RVYIGRLPYRARERDVERFFKGYGRI--------REINLKNGFGFVEFEDPRDADDAVYE 52

Query: 69 TDSHVLEGSRLSIQPS 84
           +   L G R+ ++ +
Sbjct: 53 LNGKELCGERVIVEHA 68

This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|241052 cd12608, RRM1_CoAA, RNA recognition motif 1 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 48.7 bits (116), Expect = 6e-08
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 9/76 (11%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK-VFS 68
          KIFVGN+    S  EL+  F  YG +++ +VM        + F FV  + + A D+ +  
Sbjct: 2  KIFVGNVDEDTSQEELRALFEAYGAVLSCAVM--------RQFAFVHLRGEAAADRAIEE 53

Query: 69 TDSHVLEGSRLSIQPS 84
           +   L G +L ++ S
Sbjct: 54 LNGRELHGRKLVVEHS 69

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

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

 Score = 49.1 bits (118), Expect = 7e-08
 Identities = 25/80 (31%), Positives = 39/80 (48%), Gaps = 6/80 (7%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASV-----MFDKNTGLSKGFGFVTFQNKEAVDK 65
          +FV NL +  +   LKK F + G + + ++            LS G+GFV F++KEA  K
Sbjct: 3  LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 66 VFSTDSH-VLEGSRLSIQPS 84
                  VL+G  L ++ S
Sbjct: 63 ALKRLQGTVLDGHALELKLS 82

This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 82

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

 Score = 53.1 bits (127), Expect = 7e-08
 Identities = 29/89 (32%), Positives = 53/89 (59%), Gaps = 4/89 (4%)

Query: 4   SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAV 63
           SI+  N ++V NLP T++ ++L   F +YGQI+  +++ DK TG  +G  FV F  +E  
Sbjct: 190 SIKDTN-LYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEA 248

Query: 64  DKVFSTDSHVL-EGSR--LSIQPSDSHNR 89
            +  S  ++V+ EG    L+++ ++ H +
Sbjct: 249 QEAISALNNVIPEGGSQPLTVRLAEEHGK 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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 53.4 bits (128), Expect = 7e-08
 Identities = 25/84 (29%), Positives = 44/84 (52%), Gaps = 1/84 (1%)

Query: 11  IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
           +FV  L       +L +FFS+ G++ +   + D+N+  SKG  +V F + E+V K  +  
Sbjct: 92  VFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALT 151

Query: 71  SHVLEGSRLSIQPSDSH-NRMAEN 93
             +L G  + +Q S +  NR A+ 
Sbjct: 152 GQMLLGRPIIVQSSQAEKNRAAKA 175

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

 Score = 48.9 bits (116), Expect = 8e-08
 Identities = 22/50 (44%), Positives = 35/50 (70%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
          +FVG+L   ++  ++K  F+ +G+I +A V+ D  TG SKG+GFV+F NK
Sbjct: 4  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNK 53

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|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 = 8e-08
 Identities = 19/56 (33%), Positives = 34/56 (60%), Gaps = 1/56 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          +I V NLP  V+ + L++ F   G++ +  VM  ++ G S+ FGFV F+++E   +
Sbjct: 2  RIIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRD-GKSRRFGFVGFKSEEDAQQ 56

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

 Score = 49.2 bits (118), Expect = 9e-08
 Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF-ST 69
          +FVG L    +   L++ FS YG I    ++ D  TG SKG+ FV ++++    + +   
Sbjct: 6  LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 70 DSHVLEGSRL 79
             V++GS +
Sbjct: 66 HKLVIDGSEI 75

This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. Length = 93

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

 Score = 52.6 bits (126), Expect = 1e-07
 Identities = 23/61 (37%), Positives = 38/61 (62%), Gaps = 4/61 (6%)

Query: 10  KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTF----QNKEAVDK 65
           K++VGNL + ++  EL++ F  +G I +  +  D  TG SKGFGF+ F    + KEA++ 
Sbjct: 188 KLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEV 247

Query: 66  V 66
           +
Sbjct: 248 M 248

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|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 = 48.0 bits (115), Expect = 1e-07
 Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 6/52 (11%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
          ++VGNLP  ++  EL++ FS +G I    V  D      KG+ FV F   EA
Sbjct: 3  VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEA 48

This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 73

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

 Score = 47.8 bits (114), Expect = 1e-07
 Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 4/74 (5%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFS 68
          +I+VGNLP  +   +++  F +YG I    +   KN      F FV F++ ++A D V  
Sbjct: 1  RIYVGNLPGDIRERDIEDLFYKYGPIKAIDL---KNRRRGPPFAFVEFEDPRDAEDAVRG 57

Query: 69 TDSHVLEGSRLSIQ 82
           D +  +G RL ++
Sbjct: 58 RDGYDFDGYRLRVE 71

This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. . Length = 72

>gnl|CDD|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 47.9 bits (114), Expect = 1e-07
 Identities = 20/73 (27%), Positives = 40/73 (54%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          ++VGN+ +  +  EL+  F   G +   +++ DK +G  KGF ++ F +KE+V    + D
Sbjct: 2  VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALALD 61

Query: 71 SHVLEGSRLSIQP 83
            +  G ++ + P
Sbjct: 62 ESLFRGRQIKVMP 74

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

>gnl|CDD|240927 cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 48.1 bits (114), Expect = 2e-07
 Identities = 23/56 (41%), Positives = 34/56 (60%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          +IFVG +P  +  +EL   F + G I +  +M D  TGL++G+ FVTF  KEA  +
Sbjct: 3  EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQE 58

This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. Length = 79

>gnl|CDD|200936 pfam00023, Ank, Ankyrin repeat

 Score = 46.4 bits (111), Expect = 2e-07
 Identities = 17/33 (51%), Positives = 21/33 (63%), Gaps = 1/33 (3%)

Query: 288 NGLNCLHWACDRGHLKVVQHLIEKCGADVNVTD 320
           +G   LH A   GHL+VV+ L+E  GADVN  D
Sbjct: 1   DGNTPLHLAARNGHLEVVKLLLEA-GADVNARD 32

Ankyrins are multifunctional adaptors that link specific proteins to the membrane-associated, spectrin- actin cytoskeleton. This repeat-domain is a 'membrane-binding' domain of up to 24 repeated units, and it mediates most of the protein's binding activities. Repeats 13-24 are especially active, with known sites of interaction for the Na/K ATPase, Cl/HCO(3) anion exchanger, voltage-gated sodium channel, clathrin heavy chain and L1 family cell adhesion molecules. The ANK repeats are found to form a contiguous spiral stack such that ion transporters like the anion exchanger associate in a large central cavity formed by the ANK repeat spiral, while clathrin and cell adhesion molecules associate with specific regions outside this cavity. Length = 33

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

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 21/79 (26%), Positives = 45/79 (56%), Gaps = 2/79 (2%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK-EAVDKVF 67
          +K+FV  LP++V+  EL+K F ++G + +  ++ +++ G  KG  +V ++N+  A   V 
Sbjct: 3  HKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRS-GKPKGLAYVEYENESSASQAVL 61

Query: 68 STDSHVLEGSRLSIQPSDS 86
            D   ++   +S+  S+ 
Sbjct: 62 KMDGTEIKEKTISVAISNP 80

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

 Score = 47.7 bits (113), Expect = 2e-07
 Identities = 19/49 (38%), Positives = 31/49 (63%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN 59
          +F+ +LP   +  +L + F  +G +++A V  DK T LSK FGFV++ N
Sbjct: 7  LFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDN 55

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 17/61 (27%), Positives = 37/61 (60%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          N+I+V ++   +S +++K  F  +G+I + S+  D  TG  KG+GF+ ++N ++     +
Sbjct: 1  NRIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIA 60

Query: 69 T 69
          +
Sbjct: 61 S 61

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

 Score = 46.9 bits (112), Expect = 3e-07
 Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          ++ V NLP+  +  +LKK FS +G +   ++   K  G  KGF FV F +K   +K
Sbjct: 1  RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIP-RKPDGKKKGFAFVQFTSKADAEK 55

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

 Score = 47.0 bits (111), Expect = 4e-07
 Identities = 22/50 (44%), Positives = 36/50 (72%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
          +FVG+L   ++ +++K  F+ +G+I +A V+ D  TG SKG+GFV+F NK
Sbjct: 4  VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNK 53

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

 Score = 47.1 bits (112), Expect = 4e-07
 Identities = 19/53 (35%), Positives = 33/53 (62%), Gaps = 1/53 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
          K+FVG L    + N+++  F+ +G I   +V+ D+N G S+G  FVTF +++ 
Sbjct: 3  KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQN-GQSRGCAFVTFASRQC 54

This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 81

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

 Score = 47.3 bits (113), Expect = 4e-07
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 11 IFVGNLPWT-VSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV-FS 68
          +FV  LP T    + L+K FS+ G+     +      G  +GF FV +   E  ++   +
Sbjct: 5  LFVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIA-PNGQPRGFAFVEYATAEDAEEAQQA 63

Query: 69 TDSHVLEGSRLSI 81
           + H L+GS + +
Sbjct: 64 LNGHSLQGSPIRV 76

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

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 46.9 bits (112), Expect = 4e-07
 Identities = 25/88 (28%), Positives = 37/88 (42%), Gaps = 21/88 (23%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMF-----------DKNTGLSKGF------- 52
          +FVGNLP T    +LKK F ++G I   SV F            K   + K F       
Sbjct: 3  VFVGNLPLTTKKKDLKKLFKQFGPI--ESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNV 60

Query: 53 -GFVTFQNKEAVDKVFSTDSHVLEGSRL 79
            +V F+ +E+ +K    +    EG  +
Sbjct: 61 NAYVVFKEEESAEKALKLNGTEFEGHHI 88

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

>gnl|CDD|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 46.6 bits (111), Expect = 4e-07
 Identities = 20/72 (27%), Positives = 41/72 (56%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          ++VG +P+  + +E++ +FS  G+I    +M   +TG  +G  F+TF+ +EA  +  + D
Sbjct: 1  VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALALD 60

Query: 71 SHVLEGSRLSIQ 82
             + G  L ++
Sbjct: 61 GEDMGGRFLKVE 72

This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 46.9 bits (112), Expect = 5e-07
 Identities = 16/51 (31%), Positives = 31/51 (60%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          +FV  L +  + ++L++ F EYG I    ++ DK TG  +G+ F+ F+++ 
Sbjct: 4  LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHER 54

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

 Score = 46.2 bits (110), Expect = 5e-07
 Identities = 22/50 (44%), Positives = 34/50 (68%), Gaps = 1/50 (2%)

Query: 8  LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTF 57
          L ++FV  +P + +  +L++ F E+G I   S++ DKNTG SKGFG+V F
Sbjct: 1  LTRLFV-VIPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKF 49

This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 74

>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 46.4 bits (110), Expect = 6e-07
 Identities = 19/49 (38%), Positives = 29/49 (59%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN 59
          +F+ +LP      EL + F  +G +++A V  D+ T  SK FGFV+F N
Sbjct: 7  LFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDN 55

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

 Score = 46.3 bits (110), Expect = 7e-07
 Identities = 24/67 (35%), Positives = 38/67 (56%), Gaps = 4/67 (5%)

Query: 13 VGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSH 72
          V  LP  ++ +E++  FS  G+I +  ++ DK TG S G+GFV + + E  +K  +T   
Sbjct: 6  VNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINT--- 62

Query: 73 VLEGSRL 79
           L G RL
Sbjct: 63 -LNGLRL 68

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

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

 Score = 49.8 bits (119), Expect = 1e-06
 Identities = 22/55 (40%), Positives = 34/55 (61%), Gaps = 1/55 (1%)

Query: 11  IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           IFV NL  +V +  L   FS++G I++  V  D+N G S+G+GFV F+ +E+   
Sbjct: 91  IFVKNLDKSVDNKALFDTFSKFGNILSCKVATDEN-GKSRGYGFVHFEKEESAKA 144

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

 Score = 45.3 bits (108), Expect = 1e-06
 Identities = 25/76 (32%), Positives = 42/76 (55%), Gaps = 6/76 (7%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFS 68
          K++VGNL    +  EL+  F +YG +   SV   +N     GF FV F++ ++A D V +
Sbjct: 1  KVYVGNLGPRATKRELEDEFEKYGPL--RSVWVARN---PPGFAFVEFEDPRDAEDAVRA 55

Query: 69 TDSHVLEGSRLSIQPS 84
           D   + G+R+ ++ S
Sbjct: 56 LDGRRICGNRVRVELS 71

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

>gnl|CDD|241015 cd12571, RRM6_RBM19, RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 45.5 bits (108), Expect = 1e-06
 Identities = 27/79 (34%), Positives = 42/79 (53%), Gaps = 7/79 (8%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKN---TGLSKGFGFVTFQNKEAVDK 65
          +KI V N+P+  +  EL++ FS +G++   +V   K    TG  +GFGFV F  K+   +
Sbjct: 1  SKILVRNIPFEATVKELRELFSTFGEL--KTVRLPKKMTGTGSHRGFGFVDFITKQDAKR 58

Query: 66 VFST--DSHVLEGSRLSIQ 82
           F     S  L G RL ++
Sbjct: 59 AFKALCHSTHLYGRRLVLE 77

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

 Score = 45.5 bits (108), Expect = 1e-06
 Identities = 19/46 (41%), Positives = 27/46 (58%)

Query: 16 LPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          LP T++  E +  F   G + N  ++ DK TG S GFGFV +Q+ E
Sbjct: 8  LPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAE 53

This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. . Length = 81

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

 Score = 45.2 bits (107), Expect = 1e-06
 Identities = 29/77 (37%), Positives = 46/77 (59%), Gaps = 8/77 (10%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASV--MFDKNTGLSKGFGFVTFQN-KEAVDKV 66
          KI V NLP+  +  +++  FS YGQ+ +  V   FD++    +GF FV F   KEA++ +
Sbjct: 2  KILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQSA---RGFAFVEFSTAKEALNAM 58

Query: 67 FS-TDSHVLEGSRLSIQ 82
           +  D+H+L G RL +Q
Sbjct: 59 NALKDTHLL-GRRLVLQ 74

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|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 9 (SRSF9)

 Score = 45.2 bits (107), Expect = 1e-06
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 4/74 (5%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFS 68
          +I+VGNLP  V   +L+  F +YG+I +  +   KN      F FV F++ ++A D VF 
Sbjct: 1  RIYVGNLPSDVREKDLEDLFYKYGRIRDIEL---KNRRGLVPFAFVRFEDPRDAEDAVFG 57

Query: 69 TDSHVLEGSRLSIQ 82
           + +     RL ++
Sbjct: 58 RNGYDFGQCRLRVE 71

This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. . Length = 72

>gnl|CDD|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 45.3 bits (107), Expect = 1e-06
 Identities = 19/53 (35%), Positives = 32/53 (60%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
          ++FVG +P  +  +EL   F + G I +  +M D  +G ++G+ F+TF  KEA
Sbjct: 3  EVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEA 55

This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains. . Length = 79

>gnl|CDD|241090 cd12646, RRM_SRSF7, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 7 (SRSF7)

 Score = 45.0 bits (106), Expect = 2e-06
 Identities = 28/81 (34%), Positives = 43/81 (53%), Gaps = 6/81 (7%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFS 68
          K++VGNL       EL++ FS YG +   +V   +N     GF FV F++ ++A D V  
Sbjct: 1  KVYVGNLGTGAGKGELERAFSYYGPLR--TVWIARN---PPGFAFVEFEDPRDAEDAVRG 55

Query: 69 TDSHVLEGSRLSIQPSDSHNR 89
           D  V+ GSR+ ++ S    R
Sbjct: 56 LDGKVICGSRVRVELSTGMPR 76

This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 77

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

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 17/55 (30%), Positives = 31/55 (56%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          + VG L   V+ + LK+ FS YG + +  +  D+   L +G+ +V F++ E  +K
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEK 55

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

>gnl|CDD|241086 cd12642, RRM_TRA2A, RNA recognition motif in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins

 Score = 45.0 bits (106), Expect = 2e-06
 Identities = 22/68 (32%), Positives = 40/68 (58%), Gaps = 7/68 (10%)

Query: 21 SHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQ----NKEAVDKVFSTDSHVLEG 76
          +  +L++ FS YG +   +V++D+ TG S+GF FV F+    +KEA++     +   L+G
Sbjct: 12 TERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEH---ANGMELDG 68

Query: 77 SRLSIQPS 84
           R+ +  S
Sbjct: 69 RRIRVDYS 76

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

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

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 28/75 (37%), Positives = 41/75 (54%), Gaps = 12/75 (16%)

Query: 10 KIFVGNLPWT--VSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK-V 66
          ++FVGNL  T  VS  +L++ FS+YG+I+  S        L KG+GFV F N+E     V
Sbjct: 2  RVFVGNLN-TDKVSKEDLEEIFSKYGKILGIS--------LHKGYGFVQFDNEEDARAAV 52

Query: 67 FSTDSHVLEGSRLSI 81
             +   + G +L I
Sbjct: 53 AGENGREIAGQKLDI 67

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

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 2/74 (2%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+ V NL + VS +++K+ F+E+G +  A+V +D++ G S G   V F+ +    K    
Sbjct: 2  KLLVSNLDFGVSDDDIKELFAEFGALKKAAVHYDRS-GRSLGTADVVFERRADALKAMKQ 60

Query: 70 DSHV-LEGSRLSIQ 82
           + V L+G  + IQ
Sbjct: 61 YNGVPLDGRPMKIQ 74

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

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 22/74 (29%), Positives = 43/74 (58%), Gaps = 2/74 (2%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA-VDKVFST 69
          +FVG L  +V+ ++L++ FS +G + +  ++  K+ G  +GF ++  +  EA + K  ST
Sbjct: 2  LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 70 DSHV-LEGSRLSIQ 82
           +    +GS L I+
Sbjct: 62 LNGTKWKGSVLKIE 75

This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. Length = 78

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

 Score = 44.6 bits (105), Expect = 3e-06
 Identities = 21/73 (28%), Positives = 39/73 (53%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          KIFVG L       +++++F  +G++ +  +  D  T   +GF F+TF+ +E V K+   
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 70 DSHVLEGSRLSIQ 82
            H +  S+  I+
Sbjct: 61 KYHNVGLSKCEIK 73

This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 75

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

 Score = 44.4 bits (105), Expect = 3e-06
 Identities = 20/48 (41%), Positives = 30/48 (62%), Gaps = 1/48 (2%)

Query: 11 IFVGNLPWTVSHNELKKFF-SEYGQIMNASVMFDKNTGLSKGFGFVTF 57
          IFVG+L   V+ ++L   F S +    +A +M D  TG+S+G+GFV F
Sbjct: 4  IFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRF 51

This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 80

>gnl|CDD|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 44.0 bits (104), Expect = 3e-06
 Identities = 19/73 (26%), Positives = 39/73 (53%), Gaps = 4/73 (5%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFST 69
          ++VGNLP  +   E++  F +YG I++  +          G+ F+ F++ ++A D +   
Sbjct: 2  VYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPPR---PPGYAFIEFEDARDAEDAIRGR 58

Query: 70 DSHVLEGSRLSIQ 82
          D +  +G RL ++
Sbjct: 59 DGYDFDGQRLRVE 71

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

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

 Score = 44.2 bits (105), Expect = 3e-06
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 3/73 (4%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          IFVG L   V+  EL + FS +G+I+   V   K    +  F F+ F+ ++A  +   ++
Sbjct: 6  IFVGQLSPDVTKEELNERFSRHGKILE--VNLIKRANHTNAFAFIKFEREQAAARAVESE 63

Query: 71 SH-VLEGSRLSIQ 82
          +H +L+   + +Q
Sbjct: 64 NHSMLKNKTMHVQ 76

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

 Score = 44.3 bits (104), Expect = 4e-06
 Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 4/69 (5%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          + V  LP  ++ +EL+  FS  G++ +A ++ DK  G S G+GFV + N +  ++  +T 
Sbjct: 4  LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINT- 62

Query: 71 SHVLEGSRL 79
             L G RL
Sbjct: 63 ---LNGLRL 68

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

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 16/51 (31%), Positives = 23/51 (45%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          ++VG L   V    L   F  +G I +  +  D  T   +GF FV F+  E
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPE 51

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

 Score = 43.5 bits (103), Expect = 5e-06
 Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF-ST 69
          ++V  L  T    +LK+ FS+YG+++ A ++ +  +  ++ FGFVT  + E   K     
Sbjct: 2  LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCIQHL 61

Query: 70 DSHVLEGSRLSIQ 82
              L G  +S++
Sbjct: 62 HRTELHGRVISVE 74

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

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

 Score = 43.8 bits (104), Expect = 5e-06
 Identities = 16/59 (27%), Positives = 33/59 (55%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          +++G+L   +    +   F+E G++ +  ++ +K TG S G+GFV F   EA ++   +
Sbjct: 2  LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

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

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

 Score = 43.4 bits (102), Expect = 5e-06
 Identities = 22/74 (29%), Positives = 40/74 (54%), Gaps = 9/74 (12%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFS 68
          ++F+G L       ++++FF  YG+I        ++  L +GFGFV F + ++A D V+ 
Sbjct: 1  RVFIGRLNPAAREKDVERFFKGYGRI--------RDIDLKRGFGFVEFDDPRDADDAVYE 52

Query: 69 TDSHVLEGSRLSIQ 82
           D   L   R++I+
Sbjct: 53 LDGKELCNERVTIE 66

This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. . Length = 70

>gnl|CDD|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 43.5 bits (103), Expect = 6e-06
 Identities = 20/62 (32%), Positives = 32/62 (51%)

Query: 23 NELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ 82
            L + FS  G+I   S+  D+ TG SKGF ++ F++ + V+K    D   L G  L + 
Sbjct: 18 RSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKALELDGSDLGGGNLVVD 77

Query: 83 PS 84
           +
Sbjct: 78 EA 79

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 43.9 bits (103), Expect = 6e-06
 Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 1/79 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF-ST 69
          +F+ +LP      +L + F  +G +++A V  DK T LSK FGFV++ N  +      + 
Sbjct: 10 LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAM 69

Query: 70 DSHVLEGSRLSIQPSDSHN 88
          +   +   RL +Q   S N
Sbjct: 70 NGFQIGMKRLKVQLKRSKN 88

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|240719 cd12273, RRM1_NEFsp, RNA recognition motif 1 in vertebrate putative RNA exonuclease NEF-sp

 Score = 43.2 bits (102), Expect = 7e-06
 Identities = 13/73 (17%), Positives = 34/73 (46%), Gaps = 5/73 (6%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK-VFST 69
          ++ G  P +   +++K+ F   G +   +++            F+TF+N EA    + + 
Sbjct: 2  VYAGPFPTSFCLSDVKRLFETCGPVRKVTMLSRTVQ----PHAFITFENLEAAQLAIETL 57

Query: 70 DSHVLEGSRLSIQ 82
          +   ++G+ + +Q
Sbjct: 58 NGASVDGNCIKVQ 70

This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. . Length = 71

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

 Score = 43.0 bits (102), Expect = 7e-06
 Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 6/57 (10%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           ++FVGNLP  ++  E K+ FS+YG++  + V  +K     KGFGF+    +   +K
Sbjct: 2  CRLFVGNLPNDITEEEFKELFSKYGEV--SEVFLNKE----KGFGFIRLDTRTNAEK 52

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|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 43.1 bits (102), Expect = 8e-06
 Identities = 21/52 (40%), Positives = 32/52 (61%), Gaps = 2/52 (3%)

Query: 11 IFVGNLPWTVSHNELKKFFSE-YGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          +FVG+L   V   +L +FFS+ Y     A V+ D+N G S+G+GFV F ++ 
Sbjct: 4  LFVGDLTPDVDDYQLYEFFSKRYPSCKGAKVVLDQN-GNSRGYGFVRFSDES 54

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

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

 Score = 43.1 bits (102), Expect = 8e-06
 Identities = 22/57 (38%), Positives = 33/57 (57%), Gaps = 2/57 (3%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK-EAVDKV 66
          IFV NL + V   +LK+ F   G+++ A +  DK  G S+G G V F++  EAV  +
Sbjct: 1  IFVANLDYKVGWKKLKEVFKLAGKVVRADIKEDKE-GKSRGMGVVQFEHPIEAVQAI 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|241031 cd12587, RRM1_PSF, RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 42.6 bits (100), Expect = 9e-06
 Identities = 19/51 (37%), Positives = 32/51 (62%), Gaps = 6/51 (11%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
          ++FVGNLP  ++ +E KK F++YG+     V  +K     KGFGF+  +++
Sbjct: 3  RLFVGNLPADITEDEFKKLFAKYGE--PGEVFINK----GKGFGFIKLESR 47

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

 Score = 42.6 bits (101), Expect = 9e-06
 Identities = 18/55 (32%), Positives = 31/55 (56%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          +++  LP   +  +L+K    +G+I++   + DK T   KG+GFV F + EA  K
Sbjct: 3  VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALK 57

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

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

 Score = 46.8 bits (111), Expect = 1e-05
 Identities = 16/56 (28%), Positives = 34/56 (60%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVD 64
           ++I++GNLP  +  +++K+    +G +   +++ D  TGLSKG+ F  +++    D
Sbjct: 296 DRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTD 351

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

 Score = 42.9 bits (100), Expect = 1e-05
 Identities = 22/65 (33%), Positives = 36/65 (55%), Gaps = 2/65 (3%)

Query: 7  QLNK--IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVD 64
          QL+K  +++  LP   +  +L K    YG+I++   + DKNT   KG+GFV F +  A  
Sbjct: 1  QLSKTNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQ 60

Query: 65 KVFST 69
          K  ++
Sbjct: 61 KAVAS 65

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

>gnl|CDD|223738 COG0666, Arp, FOG: Ankyrin repeat [General function prediction only]

 Score = 45.6 bits (107), Expect = 1e-05
 Identities = 28/115 (24%), Positives = 46/115 (40%), Gaps = 10/115 (8%)

Query: 242 SSMINDESQL--DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDR 299
             +I D      D + +     A     D +VK L      ++N  D +G   LH A   
Sbjct: 58  LKLIVDRHLAARDLDGRLPLHSAASKGDDKIVKLLLAS-GADVNAKDADGDTPLHLAALN 116

Query: 300 GHLK-----VVQHLIEK--CGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
           G+       V + L+E        N+ D DG+  L +A      D++E L+ +G+
Sbjct: 117 GNPPEGNIEVAKLLLEAGADLDVNNLRDEDGNTPLHWAALNGDADIVELLLEAGA 171

Length = 235

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

 Score = 42.2 bits (99), Expect = 1e-05
 Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 8/63 (12%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+FVGNLP   +  E++  F +YG+++   ++        K +GFV   +K A D+    
Sbjct: 2  KLFVGNLPPEATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIRN 53

Query: 70 DSH 72
            H
Sbjct: 54 LHH 56

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

 Score = 42.2 bits (99), Expect = 1e-05
 Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 9/76 (11%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVD--KV 66
          +++FVGNLP  ++  E++K F +YG+     +   K+    KGFGF+  + +   +  K 
Sbjct: 2  SRLFVGNLPPDITEEEMRKLFEKYGKA--GEIFIHKD----KGFGFIRLETRTLAEIAKA 55

Query: 67 FSTDSHVLEGSRLSIQ 82
             D+  L G +L ++
Sbjct: 56 -ELDNMPLRGKQLRVR 70

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

>gnl|CDD|241037 cd12593, RRM_RBM11, RNA recognition motif in vertebrate RNA-binding protein 11 (RBM11)

 Score = 42.3 bits (99), Expect = 1e-05
 Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          +FVGNL   V    L + F + G +   ++  DK  G  K FGFV F++ E+V    +  
Sbjct: 4  LFVGNLECRVREEILYELFLQAGPLTKVTICKDKE-GKPKSFGFVCFKHSESVPYAIA-- 60

Query: 71 SHVLEGSRLSIQPSDSH 87
            +L G RL  +P   H
Sbjct: 61 --LLNGIRLYGRPIKVH 75

This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. . Length = 75

>gnl|CDD|205076 pfam12796, Ank_2, Ankyrin repeats (3 copies)

 Score = 42.6 bits (101), Expect = 2e-05
 Identities = 20/54 (37%), Positives = 33/54 (61%), Gaps = 3/54 (5%)

Query: 293 LHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           LH A   G+L++V+ L+EK GADVN+ D+  D  L  A    + ++++ L+  G
Sbjct: 1   LHLAAKNGNLELVKLLLEK-GADVNLGDT--DTALHLAARNGNLEIVKLLLEHG 51

Length = 91

>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 = 41.9 bits (99), Expect = 2e-05
 Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 6/52 (11%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
          +FVG L   V+ +EL+  F  +G+I+   +         KG GFV F ++ A
Sbjct: 4  VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPP------GKGCGFVQFVHRAA 49

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

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 14/60 (23%), Positives = 31/60 (51%), Gaps = 5/60 (8%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTF----QNKEAVDK 65
          ++ V NL + V+  +L++ F   G++    + +D+ +G S+G   V F      + A+ +
Sbjct: 2  RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQ 60

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|241040 cd12596, RRM1_SRSF6, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 6 (SRSF6)

 Score = 41.8 bits (98), Expect = 2e-05
 Identities = 19/74 (25%), Positives = 41/74 (55%), Gaps = 9/74 (12%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFS 68
          ++++G L + V   ++++FF  YG+++           L  G+GFV F++ ++A D V+ 
Sbjct: 1  RVYIGRLSYHVREKDIQRFFGGYGKLLEID--------LKNGYGFVEFEDSRDADDAVYE 52

Query: 69 TDSHVLEGSRLSIQ 82
           +   L G R+ ++
Sbjct: 53 LNGKDLCGERVIVE 66

This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. . Length = 70

>gnl|CDD|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 41.8 bits (98), Expect = 2e-05
 Identities = 19/55 (34%), Positives = 31/55 (56%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          +FVGNL +      L + F + G I    ++ D  T + KGF +V F+++ AV+K
Sbjct: 2  VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEK 56

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

>gnl|CDD|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 = 42.0 bits (99), Expect = 2e-05
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 2/74 (2%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          I VG +  ++S ++LK+FFS  G++    +  D     S  F FV F + E+     +  
Sbjct: 3  IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGD--RQHSARFAFVEFADAESALSALNLS 60

Query: 71 SHVLEGSRLSIQPS 84
            +L G  L + PS
Sbjct: 61 GTLLGGHPLRVSPS 74

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

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

 Score = 42.0 bits (98), Expect = 2e-05
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          + V  LP  ++  ELK  F   G+I +  ++ DK TG S G+GFV + + +  +K  +T 
Sbjct: 7  LIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT- 65

Query: 71 SHVLEGSRLSIQ 82
             L G RL  +
Sbjct: 66 ---LNGLRLQTK 74

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|222984 PHA03100, PHA03100, ankyrin repeat protein; Provisional

 Score = 45.4 bits (108), Expect = 2e-05
 Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 278 KDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTD 337
               IN  D  G   LH+A    + + V++L++  GA+ N+ +  GD  L  A    + +
Sbjct: 181 YGVPINIKDVYGFTPLHYAVYNNNPEFVKYLLDL-GANPNLVNKYGDTPLHIAILNNNKE 239

Query: 338 LIEYLVNSG 346
           + + L+N+G
Sbjct: 240 IFKLLLNNG 248

Length = 422

>gnl|CDD|240930 cd12486, RRM1_ACF, RNA recognition motif 1 found in vertebrate APOBEC-1 complementation factor (ACF)

 Score = 41.5 bits (97), Expect = 3e-05
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 2/71 (2%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK-EAVDKVFS 68
          +IF+G LP  +  +EL     + G+I    +M D N G ++G+ FVTF NK EA + +  
Sbjct: 3  EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMDFN-GNNRGYAFVTFSNKQEAKNAIKQ 61

Query: 69 TDSHVLEGSRL 79
           +++ +   RL
Sbjct: 62 LNNYEIRNGRL 72

This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, 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. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. . Length = 78

>gnl|CDD|197603 smart00248, ANK, ankyrin repeats

 Score = 40.3 bits (95), Expect = 3e-05
 Identities = 14/31 (45%), Positives = 22/31 (70%), Gaps = 1/31 (3%)

Query: 288 NGLNCLHWACDRGHLKVVQHLIEKCGADVNV 318
           +G   LH A + G+L+VV+ L++K GAD+N 
Sbjct: 1   DGRTPLHLAAENGNLEVVKLLLDK-GADINA 30

Ankyrin repeats are about 33 amino acids long and occur in at least four consecutive copies. They are involved in protein-protein interactions. The core of the repeat seems to be an helix-loop-helix structure. Length = 30

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

 Score = 41.9 bits (98), Expect = 3e-05
 Identities = 15/41 (36%), Positives = 29/41 (70%)

Query: 21 SHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          +  +L++ FS+YG I + S+++D+ +  S+GF FV F+N +
Sbjct: 22 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 62

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

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

 Score = 41.8 bits (98), Expect = 3e-05
 Identities = 22/83 (26%), Positives = 43/83 (51%), Gaps = 3/83 (3%)

Query: 9  NKIFVGNLPWTVSHNE-LKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
           K+ + NLPW++     LKK F  YG++  A++   +   L  GF FVT + ++  +   
Sbjct: 1  PKLIIRNLPWSIKKPVKLKKIFGRYGKVREATIPRKRGGKLC-GFAFVTMKKRKNAEIAL 59

Query: 68 -STDSHVLEGSRLSIQPSDSHNR 89
           +T+   ++G  +++  +   NR
Sbjct: 60 ENTNGLEIDGRPVAVDWAVQKNR 82

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|205784 pfam13606, Ank_3, Ankyrin repeat

 Score = 39.9 bits (94), Expect = 3e-05
 Identities = 13/31 (41%), Positives = 20/31 (64%), Gaps = 1/31 (3%)

Query: 288 NGLNCLHWACDRGHLKVVQHLIEKCGADVNV 318
           +G   LH A   G+L++V+ L+E  GAD+N 
Sbjct: 1   DGNTPLHLAARNGNLELVKLLLEH-GADINA 30

Ankyrins are multifunctional adaptors that link specific proteins to the membrane-associated, spectrin- actin cytoskeleton. This repeat-domain is a 'membrane-binding' domain of up to 24 repeated units, and it mediates most of the protein's binding activities. Length = 30

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

 Score = 41.3 bits (97), Expect = 3e-05
 Identities = 15/53 (28%), Positives = 32/53 (60%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
          +++VG++ + +  + +++ FS +G I +  + +D  T   KGF FV ++  EA
Sbjct: 2  RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEA 54

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

>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 41.2 bits (97), Expect = 3e-05
 Identities = 18/73 (24%), Positives = 41/73 (56%), Gaps = 6/73 (8%)

Query: 12 FVGNLPWTVSHNELKKFFSEYGQIMNASVMF---DKNTGLSKGFGFVTFQNKEAVDKVFS 68
          ++GNLP+ V+  ++K+FF     +  +SV       + G  +GFG+  F++++++ +  S
Sbjct: 5  YLGNLPYDVTEEDIKEFFRG---LNVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALS 61

Query: 69 TDSHVLEGSRLSI 81
           +   L+  R+ +
Sbjct: 62 LNDESLKNRRIRV 74

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 40.7 bits (95), Expect = 4e-05
 Identities = 20/81 (24%), Positives = 41/81 (50%), Gaps = 9/81 (11%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFS 68
          ++++G L +     ++++FF  YG+I+           L  G+GFV F + ++A D V+ 
Sbjct: 1  RVYIGRLSYQARERDVERFFKGYGKILEVD--------LKNGYGFVEFDDLRDADDAVYE 52

Query: 69 TDSHVLEGSRLSIQPSDSHNR 89
           +   L G R+ ++ +    R
Sbjct: 53 LNGKDLCGERVIVEHARGPRR 73

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

>gnl|CDD|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 40.8 bits (96), Expect = 5e-05
 Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 1/51 (1%)

Query: 8  LNKIFVGNLPWTVSHNELKKFFSEYG-QIMNASVMFDKNTGLSKGFGFVTF 57
           N I +  LP +V+  +++     +G +  +  +M  K TG S+GF FV F
Sbjct: 2  NNTIMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFVEF 52

This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 81

>gnl|CDD|241089 cd12645, RRM_SRSF3, RNA recognition motif in vertebrate serine/arginine-rich splicing factor 3 (SRSF3)

 Score = 41.2 bits (96), Expect = 5e-05
 Identities = 27/81 (33%), Positives = 42/81 (51%), Gaps = 6/81 (7%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFS 68
          K++VGNL    +  EL++ F  YG +   SV   +N     GF FV F++ ++A D V  
Sbjct: 6  KVYVGNLGNNGNKTELERAFGYYGPLR--SVWVARN---PPGFAFVEFEDPRDAADAVRE 60

Query: 69 TDSHVLEGSRLSIQPSDSHNR 89
           D   L G R+ ++ S+   R
Sbjct: 61 LDGRTLCGCRVRVELSNGEKR 81

This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation and tumor induction and maintenance. SRSF3 can shuttle between the nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 81

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

 Score = 41.1 bits (97), Expect = 5e-05
 Identities = 19/59 (32%), Positives = 33/59 (55%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
          N +FV  L    +  +L+  FS +G+I +  V+ DK TG S  + F+ F+ KE  ++ +
Sbjct: 4  NVLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAY 62

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

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

 Score = 40.8 bits (95), Expect = 5e-05
 Identities = 22/56 (39%), Positives = 35/56 (62%), Gaps = 2/56 (3%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          +IFV NLP+ ++  +LK+ FS+ G +M A +  +   G SKG G V F + E+ +K
Sbjct: 1  QIFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKME--NGKSKGCGTVRFDSPESAEK 54

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

 Score = 43.8 bits (103), Expect = 7e-05
 Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 1/72 (1%)

Query: 11  IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFST 69
           IFV NL        L + F  +G + N  ++ D  T   KG+GFV+  N  EA   + S 
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 70  DSHVLEGSRLSI 81
           + + L    L +
Sbjct: 332 NGYTLGNRVLQV 343

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

>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 40.4 bits (95), Expect = 7e-05
 Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 3/76 (3%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMF--DKNTGLSKGFGFVTFQNKEAVDKVFS 68
          ++VGNL W  +  +L+   +E G +   S+ F   K  G SKGF +V F ++ A   V  
Sbjct: 1  LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 69 -TDSHVLEGSRLSIQP 83
            +     G +  +  
Sbjct: 61 KLEGREFNGKKCVVTY 76

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

>gnl|CDD|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 = 40.3 bits (95), Expect = 7e-05
 Identities = 18/76 (23%), Positives = 44/76 (57%), Gaps = 3/76 (3%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSE-YGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKV 66
          +++ V NLP +++  ELK+ FS+  G+I +  ++  ++ G S+   F+ ++  +EA    
Sbjct: 1  SRLIVKNLPASLTEAELKEHFSKHGGEITDVKLLRTED-GKSRRIAFIGYKTEEEAQKAK 59

Query: 67 FSTDSHVLEGSRLSIQ 82
             ++  +  S++S++
Sbjct: 60 DYFNNTYINTSKISVE 75

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

 Score = 40.5 bits (94), Expect = 7e-05
 Identities = 29/81 (35%), Positives = 41/81 (50%), Gaps = 5/81 (6%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFST 69
          IFV NL      + L + F  +G + N  V+ D NT   KGFGFVT  N  EA   + S 
Sbjct: 6  IFVYNLAPDADESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASL 65

Query: 70 DSHVLEGSR---LSIQPSDSH 87
          + + L G R   +S + + +H
Sbjct: 66 NGYRL-GDRVLQVSFKTNKTH 85

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

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

 Score = 43.8 bits (103), Expect = 8e-05
 Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 4/69 (5%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          + V  LP T++  E++  F+  G+I +  ++ DK TG S G+GFV +   E  +K  ++ 
Sbjct: 6  LIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNS- 64

Query: 71 SHVLEGSRL 79
             L G RL
Sbjct: 65 ---LNGLRL 70

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

 Score = 40.0 bits (93), Expect = 9e-05
 Identities = 24/57 (42%), Positives = 35/57 (61%), Gaps = 2/57 (3%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTF-QNKEAVDKV 66
          +FV NL + V   +LK+ FS  G ++ A ++ DK+ G S+G G VTF Q  EAV  +
Sbjct: 3  VFVANLDYKVGWKKLKEVFSMAGMVVRADILEDKD-GKSRGIGTVTFEQPIEAVQAI 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|240898 cd12452, RRM_ARP_like, RNA recognition motif in yeast asparagine-rich protein (ARP) and similar proteins

 Score = 40.5 bits (95), Expect = 9e-05
 Identities = 19/87 (21%), Positives = 37/87 (42%), Gaps = 14/87 (16%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYG----------QIMNASVMFDKNTGLSKGFGFVTFQNK 60
          +++ NLP   +  EL+ +F++YG               + +  K++      GF  FQ+ 
Sbjct: 3  LYISNLPPDTTQLELESWFTQYGVRPVAFWTLKTPDEDAYVSSKDS----ISGFAVFQSH 58

Query: 61 EAVDKVFSTDSHVLEGSRLSIQPSDSH 87
          E   +  + +   L    + +QPS S 
Sbjct: 59 EEAMEALALNGRCLGERAIEVQPSSSR 85

This subfamily corresponds to the RRM of ARP, also termed NRP1, encoded by Saccharomyces cerevisiae YDL167C. Although its exact biological function remains unclear, ARP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), two Ran-binding protein zinc fingers (zf-RanBP), and an asparagine-rich region. It may possess RNA-binding and zinc ion binding activities. Additional research had indicated that ARP may function as a factor involved in the stress response. . Length = 88

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

 Score = 40.6 bits (94), Expect = 9e-05
 Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 7  QLNK--IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVD 64
          QL+K  +++  LP   +  +L K    YG+I++   + DK T   KG+GFV F +  A  
Sbjct: 4  QLSKTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQ 63

Query: 65 KVFS 68
          K  S
Sbjct: 64 KAVS 67

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

>gnl|CDD|240917 cd12473, RRM2_MSSP1, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 40.5 bits (94), Expect = 9e-05
 Identities = 16/58 (27%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          +++ NLP ++   EL+     +GQ+++  ++ D ++G S+G GF   ++ E  + V S
Sbjct: 3  LYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIS 59

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

 Score = 40.1 bits (93), Expect = 9e-05
 Identities = 20/59 (33%), Positives = 31/59 (52%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          + V  LP  ++  E K  F   G+I +  ++ DK TG S G+GFV + +    DK  +T
Sbjct: 6  LIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINT 64

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|222277 pfam13637, Ank_4, Ankyrin repeats (many copies)

 Score = 38.8 bits (91), Expect = 1e-04
 Identities = 20/48 (41%), Positives = 32/48 (66%), Gaps = 2/48 (4%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLI 309
           A  G+L+ LVK L + K  +IN+ DE+G   LH A + G+L+V++ L+
Sbjct: 9   AISGRLE-LVKYLLE-KGVDINRTDEDGNTALHIAAENGNLEVLKLLL 54

Length = 54

>gnl|CDD|223738 COG0666, Arp, FOG: Ankyrin repeat [General function prediction only]

 Score = 42.5 bits (99), Expect = 1e-04
 Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 6/81 (7%)

Query: 272 KQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA- 330
             L  + D ++   D +G   LH A  +G  K+V+ L+   GADVN  D+DGD  L  A 
Sbjct: 56  LLLKLIVDRHLAARDLDGRLPLHSAASKGDDKIVKLLLAS-GADVNAKDADGDTPLHLAA 114

Query: 331 ----KAIEHTDLIEYLVNSGS 347
                   + ++ + L+ +G+
Sbjct: 115 LNGNPPEGNIEVAKLLLEAGA 135

Length = 235

>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 40.0 bits (93), Expect = 1e-04
 Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 13 VGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          V NLP  VS+  L++ FS +GQ+  A V+ D + G   G G V F  K +  K
Sbjct: 4  VKNLPQFVSNELLEEAFSMFGQVERAVVIVD-DRGRPTGKGIVEFAGKPSARK 55

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|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 43.5 bits (102), Expect = 1e-04
 Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 1/53 (1%)

Query: 10  KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
           ++FVG +P  +  +EL   F + G I    +M D + G ++G+ FVTF  KE 
Sbjct: 60  EVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFS-GQNRGYAFVTFCGKEE 111

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. Length = 578

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

 Score = 39.9 bits (93), Expect = 1e-04
 Identities = 18/53 (33%), Positives = 30/53 (56%)

Query: 13 VGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          V NLP + +  E ++    YG I    +++ + TG SKG+GFV +  K++  K
Sbjct: 4  VTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASK 56

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 14/51 (27%), Positives = 27/51 (52%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          IFV  +       ++   F+E+G+I N  +  D+ TG  KG+  + ++ K+
Sbjct: 9  IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKK 59

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|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 40.3 bits (95), Expect = 1e-04
 Identities = 20/62 (32%), Positives = 27/62 (43%), Gaps = 15/62 (24%)

Query: 15 NLPWTVSHNELKKFFSEY---------GQIMNASVMFDK------NTGLSKGFGFVTFQN 59
          NLP +V   +LK+ F +           +I    +M D         G SKG+GFV F N
Sbjct: 7  NLPKSVDEKKLKELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFTN 66

Query: 60 KE 61
           E
Sbjct: 67 HE 68

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

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

 Score = 39.0 bits (92), Expect = 1e-04
 Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 6/61 (9%)

Query: 25 LKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP 83
          L K FS +G +    ++  K      GF FV F  +EA +K     +  +  G  L +  
Sbjct: 1  LYKLFSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

Query: 84 S 84
          S
Sbjct: 56 S 56

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

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

 Score = 39.7 bits (92), Expect = 2e-04
 Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 1/82 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          +F   L   +   +L++FFS  G++ +  ++ D+N+  SKG  +V F +  +V       
Sbjct: 4  VFCMQLAARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAIGLT 63

Query: 71 SHVLEGSRLSIQPSDSH-NRMA 91
             + G  + +Q S +  NR A
Sbjct: 64 GQRVLGVPIIVQASQAEKNRAA 85

This subgroup corresponds to the RRM1 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

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

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 4/72 (5%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          + V  LP  ++  E +  F   G+I +  ++ DK TG S G+GFV + + +  +K  +T 
Sbjct: 5  LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT- 63

Query: 71 SHVLEGSRLSIQ 82
             L G RL  +
Sbjct: 64 ---LNGLRLQTK 72

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|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 39.4 bits (92), Expect = 2e-04
 Identities = 26/80 (32%), Positives = 36/80 (45%), Gaps = 6/80 (7%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFD---KNTG--LSKGFGFVTFQNKEAVDK 65
          +FV NL ++ ++  L   F      + A V      K  G  LS GFGFV F+ KE    
Sbjct: 3  LFVKNLNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQA 62

Query: 66 VFST-DSHVLEGSRLSIQPS 84
               D  VL+G  L ++ S
Sbjct: 63 ALKAMDGFVLDGHTLVVKFS 82

This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 84

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

 Score = 42.7 bits (100), Expect = 2e-04
 Identities = 13/64 (20%), Positives = 34/64 (53%)

Query: 6   RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           ++ N+I+V ++   +S  ++K  F  +G+I+   +         KG+GF+ + N ++  +
Sbjct: 202 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSE 261

Query: 66  VFST 69
             ++
Sbjct: 262 AIAS 265

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

>gnl|CDD|240919 cd12475, RRM2_RBMS3, RNA recognition motif 2 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 15/56 (26%), Positives = 32/56 (57%), Gaps = 1/56 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
          +++ NLP ++   EL+     +G +++  ++ D N G+S+G GF   ++ E  + V
Sbjct: 4  LYISNLPVSMDEQELENMLKPFGHVISTRILRDAN-GVSRGVGFARMESTEKCEVV 58

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

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 16/51 (31%), Positives = 32/51 (62%), Gaps = 6/51 (11%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
          ++FVGNLP  ++  + KK F +YG+   + V  +++    +GFGF+  +++
Sbjct: 3  RLFVGNLPTDITEEDFKKLFEKYGE--PSEVFINRD----RGFGFIRLESR 47

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

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 25/69 (36%), Positives = 32/69 (46%), Gaps = 4/69 (5%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          IF+ NL        L + F  +G + N  V+ D NT   KGFGFVT  N E      ++ 
Sbjct: 4  IFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIAS- 62

Query: 71 SHVLEGSRL 79
             L G RL
Sbjct: 63 ---LNGYRL 68

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

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

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 5/69 (7%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          +FVGNL   V+   L + F + G +    +  D N G  K F FVTF+++ +V   ++  
Sbjct: 4  LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVP--YAIQ 60

Query: 71 SHVLEGSRL 79
            +L G RL
Sbjct: 61 --LLNGIRL 67

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|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 9/76 (11%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKG--FGFVTFQNK-EAVDKV 66
          +I+VGNLP  +   +++  F +YG I +  +   KN    +G  F FV F++  +A D V
Sbjct: 1  RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDL---KN---RRGPPFAFVEFEDPRDAEDAV 54

Query: 67 FSTDSHVLEGSRLSIQ 82
          +  D +  +G RL ++
Sbjct: 55 YGRDGYDYDGYRLRVE 70

This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 1/48 (2%)

Query: 13 VGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
          V NL   VS+  L++ FS++G++  A V+ D + G S G G V F  K
Sbjct: 4  VKNLSPFVSNELLEQAFSQFGEVERAVVIVD-DRGRSTGEGIVEFSRK 50

This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 80

>gnl|CDD|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 15/56 (26%), Positives = 32/56 (57%), Gaps = 3/56 (5%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
          I+VG +P   + +EL++ F  +G+I   ++ F ++ G +  +GFVT++      + 
Sbjct: 5  IYVGKIPIDTTRSELRQRFQPFGEIEEITLHF-RDDGDN--YGFVTYRYACDAFRA 57

This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 89

>gnl|CDD|240918 cd12474, RRM2_MSSP2, RNA recognition motif 2 found in vertebrate single-stranded DNA-binding protein MSSP-2

 Score = 38.9 bits (90), Expect = 3e-04
 Identities = 14/58 (24%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          +++ NLP ++   EL+     +GQ+++  ++ D + G S+G GF   ++ E  + + +
Sbjct: 3  LYISNLPLSMDEQELESMLKPFGQVISTRILRDAS-GTSRGVGFARMESTEKCEAIIT 59

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|140343 PTZ00322, PTZ00322, 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional

 Score = 42.2 bits (99), Expect = 3e-04
 Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 1/60 (1%)

Query: 283 NQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYL 342
           N  D +G   LH AC  GH++VV+ L+E  GAD  + D DG   L+ A+     ++++ L
Sbjct: 109 NCRDYDGRTPLHIACANGHVQVVRVLLE-FGADPTLLDKDGKTPLELAEENGFREVVQLL 167

Length = 664

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

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 12 FVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDS 71
          FVGNLP+     +L   F +   + +  ++ DK T   KGF +V F++ E++ +    D 
Sbjct: 5  FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALEYDG 63

Query: 72 HVLEGSRLSI 81
           + +   L +
Sbjct: 64 ALFDDRSLRV 73

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

>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)

 Score = 38.9 bits (90), Expect = 3e-04
 Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 1/82 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          +F   L   +   +L+ FFS  G++ +  ++ D+N+  SKG  +V F   ++V       
Sbjct: 4  VFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLT 63

Query: 71 SHVLEGSRLSIQPSDSH-NRMA 91
             L G  + +Q S +  NR+A
Sbjct: 64 GQRLLGVPIIVQASQAEKNRLA 85

This subgroup corresponds to the RRM1 of RBM23, also termed RNA-binding region-containing protein 4, or splicing factor SF2, which may function as a pre-mRNA splicing factor. It shows high sequence homology to RNA-binding protein 39 (RBM39 or HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In contrast to RBM39, RBM23 contains only two RRMs. . Length = 85

>gnl|CDD|241053 cd12609, RRM2_CoAA, RNA recognition motif 2 in vertebrate RRM-containing coactivator activator/modulator (CoAA)

 Score = 38.3 bits (89), Expect = 4e-04
 Identities = 19/74 (25%), Positives = 41/74 (55%), Gaps = 9/74 (12%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK-EAVDKVFS 68
          KIFVGN+  T + +EL+  F E+G+++    +        K + FV  + + EA+  + +
Sbjct: 2  KIFVGNVSATCTSDELRGLFEEFGRVVECDKV--------KDYAFVHMEREEEALAAIEA 53

Query: 69 TDSHVLEGSRLSIQ 82
           +   ++G R++++
Sbjct: 54 LNGKEVKGRRINVE 67

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

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

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 8/62 (12%)

Query: 9  NKI-FVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN----KEAV 63
          N+I +V NLP+ +S  EL   F +YG I    +   K T   +G  FV +++    K A 
Sbjct: 2  NRILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNAC 58

Query: 64 DK 65
          D 
Sbjct: 59 DH 60

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

 Score = 38.5 bits (89), Expect = 4e-04
 Identities = 17/51 (33%), Positives = 30/51 (58%), Gaps = 1/51 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
          K+F+G +    + N+++  FS +GQI    ++   + GLS+G  FVTF  +
Sbjct: 3  KLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGPD-GLSRGCAFVTFTTR 52

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

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 15/59 (25%), Positives = 32/59 (54%), Gaps = 1/59 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          +++ NLP  +   +L+     YGQ+++  ++ D   G S+G GF   +++E  + + S 
Sbjct: 3  LYISNLPLHMDEQDLETMLKPYGQVISTRILRDSK-GQSRGVGFARMESREKCEDIISK 60

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

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 9/72 (12%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE-AVDKVFST 69
          ++V NLP + +  +L++ FSEYG++     + D        + FV F+ ++ AV  +   
Sbjct: 4  LYVRNLPLSTTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEM 55

Query: 70 DSHVLEGSRLSI 81
          +   LEGS + +
Sbjct: 56 NGKELEGSPIEV 67

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

>gnl|CDD|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 = 37.9 bits (89), Expect = 5e-04
 Identities = 12/67 (17%), Positives = 30/67 (44%), Gaps = 2/67 (2%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYG-QIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          + +  LP++ +  +++ FFS          +++D + G   G  +V F + E   +    
Sbjct: 2  VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDD-GRPTGEAYVEFASPEDARRALRK 60

Query: 70 DSHVLEG 76
           ++ + G
Sbjct: 61 HNNKMGG 67

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

 Score = 38.0 bits (89), Expect = 5e-04
 Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 3/61 (4%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVD---KVF 67
          ++VGNL   V+   L + F + G ++N  +  D+ T   +G+GFV F ++E  D   K+ 
Sbjct: 1  VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 68 S 68
          +
Sbjct: 61 N 61

This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. . Length = 74

>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 38.0 bits (89), Expect = 5e-04
 Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 10/61 (16%)

Query: 6  RQLNKIFV-GNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVD 64
          R+ N ++V G     ++   LKK FS +G I+N S+  +KN       GFVTF+  E+ D
Sbjct: 2  RKGNTLYVHGY---GLTEEILKKAFSPFGNIINISMEKEKNC------GFVTFEKMESAD 52

Query: 65 K 65
          +
Sbjct: 53 R 53

This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. . Length = 75

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

 Score = 37.9 bits (89), Expect = 5e-04
 Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 9/77 (11%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE---AVDKVF 67
          + + NLP  V+ ++L    S +G++ N  ++  KN         V   + E   ++   +
Sbjct: 2  LHLRNLPPDVTESDLIALVSPFGKVTNVLLLRGKNQ------ALVEMDSVESAKSMVDYY 55

Query: 68 STDSHVLEGSRLSIQPS 84
           T   ++ G R+ IQ S
Sbjct: 56 LTVPALIRGRRVYIQYS 72

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

>gnl|CDD|241047 cd12603, RRM_hnRNPC, RNA recognition motif in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2)

 Score = 38.1 bits (88), Expect = 5e-04
 Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 10/75 (13%)

Query: 9  NKIFVGNL-PWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKV 66
          +++F+GNL    V  ++++  FS+YG+I+  SV         KGF FV + N + A   V
Sbjct: 2  SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAV 53

Query: 67 FSTDSHVLEGSRLSI 81
             D  ++ G  L I
Sbjct: 54 AGEDGRMIAGQVLDI 68

This subgroup corresponds to the RRM of heterogeneous nuclear ribonucleoprotein C (hnRNP) proteins C1 and C2, 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 hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. hnRNP C proteins contain two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes the variable region, the basic region and the KSG box rich in repeated Lys-Ser-Gly sequences, the leucine zipper, and the acidic region. The RRM is capable of binding poly(U). The KSG box may bind to RNA. The leucine zipper may be involved in dimer formation. The acidic and hydrophilic C-teminus harbors a putative nucleoside triphosphate (NTP)-binding fold and a protein kinase phosphorylation site. . Length = 71

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

 Score = 38.2 bits (88), Expect = 5e-04
 Identities = 29/81 (35%), Positives = 39/81 (48%), Gaps = 5/81 (6%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFST 69
          IFV NL      + L + F  +G + N  V+ D  T   KGFGFVT  N  EA   + S 
Sbjct: 4  IFVYNLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASL 63

Query: 70 DSHVLEGSR---LSIQPSDSH 87
          + + L G R   +S + S  H
Sbjct: 64 NGYRL-GDRVLQVSFKTSKQH 83

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

>gnl|CDD|241197 cd12753, RRM1_RBM10, RNA recognition motif 1 in vertebrate RNA-binding protein 10 (RBM10)

 Score = 38.1 bits (88), Expect = 6e-04
 Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 3/80 (3%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYG-QIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
          N I +  LP   +  +++    E+G Q     +M +K++G S+GF FV F + +   +  
Sbjct: 3  NIIMLRMLPQNATETDIRGQLQEHGIQPREVRLMRNKSSGQSRGFAFVEFNHLQDATRWM 62

Query: 68 STDSHVLE--GSRLSIQPSD 85
            + H L   G ++S+  SD
Sbjct: 63 EANQHSLMILGQKVSMHYSD 82

This subgroup corresponds to the RRM1 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. . Length = 85

>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 37.6 bits (87), Expect = 6e-04
 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK-EAVDKVFS 68
          ++FVG +P  V  +EL   F   G+I    +M D + G ++G+ FV +  K EA   V  
Sbjct: 3  EVFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDFD-GKNRGYAFVMYTQKHEAKRAVRE 61

Query: 69 TDSHVLEGSRL 79
           +++ +   RL
Sbjct: 62 LNNYEIRPGRL 72

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

 Score = 38.1 bits (88), Expect = 6e-04
 Identities = 25/69 (36%), Positives = 33/69 (47%), Gaps = 4/69 (5%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          IFV NL      + L + F  +G + N  V+ D NT   KGFGFVT  N +      ++ 
Sbjct: 6  IFVYNLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIAS- 64

Query: 71 SHVLEGSRL 79
             L G RL
Sbjct: 65 ---LNGYRL 70

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

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

 Score = 37.5 bits (87), Expect = 7e-04
 Identities = 18/52 (34%), Positives = 31/52 (59%), Gaps = 1/52 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          K+FVG L    +  E+++ FS YG++ +  +M D+    S+G  FV + +KE
Sbjct: 1  KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMK-QSRGCAFVKYSSKE 51

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

>gnl|CDD|241048 cd12604, RRM_RALY, RNA recognition motif in vertebrate RNA-binding protein Raly

 Score = 37.3 bits (86), Expect = 8e-04
 Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 10/75 (13%)

Query: 9  NKIFVGNL-PWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKV 66
          +++F+GNL    V  ++++  FS+YG+++  SV         KG+ FV + N + A   V
Sbjct: 2  SRVFIGNLNTAVVKKSDVETIFSKYGRVVGCSV--------HKGYAFVQYSNERHARGAV 53

Query: 67 FSTDSHVLEGSRLSI 81
             +  VL G  L I
Sbjct: 54 IGENGRVLAGQTLDI 68

This subgroup corresponds to the RRM of Raly, also termed autoantigen p542, or heterogeneous nuclear ribonucleoprotein C-like 2, or hnRNP core protein C-like 2, or hnRNP associated with lethal yellow protein homolog, an RNA-binding protein that may play a critical role in embryonic development. It is encoded by Raly, a ubiquitously expressed gene of unknown function. Raly shows a high degree of identity with the 5' sequences of p542 gene encoding autoantigen, which can cross-react with EBNA-1 of the Epstein Barr virus. Raly contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes a unique glycine/serine-rich stretch. . Length = 76

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

 Score = 37.3 bits (86), Expect = 9e-04
 Identities = 25/57 (43%), Positives = 33/57 (57%), Gaps = 2/57 (3%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTF-QNKEAVDKV 66
          IFV NL + V   +LK+ FS  G +  A +  DK+ G S+G G VTF Q  EAV  +
Sbjct: 3  IFVANLDFKVGWKKLKEVFSIAGTVKRADIKEDKD-GKSRGMGTVTFEQPIEAVQAI 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|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 18/54 (33%), Positives = 32/54 (59%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAV 63
           +FVGN+P  VS + ++K   + G++++   + D +TG  K FGF  F++ E  
Sbjct: 2  TVFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGA 55

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

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

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 8/73 (10%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          ++VG L   V+  +L+  F ++G+I + +V+  +         FVTF  +EA +K     
Sbjct: 4  LYVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQC------AFVTFTTREAAEKAAERL 57

Query: 71 SH--VLEGSRLSI 81
           +  ++ G RL +
Sbjct: 58 FNKLIINGRRLKL 70

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

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

 Score = 36.7 bits (86), Expect = 0.002
 Identities = 14/56 (25%), Positives = 29/56 (51%), Gaps = 7/56 (12%)

Query: 11 IFVGNLPWTVSHNELKK----FFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
          +++ NL   +  +ELK+     FS++G +++        T   +G  FV F++ E+
Sbjct: 2  LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASK---TLKMRGQAFVVFKDVES 54

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|240849 cd12403, RRM1_NCL, RNA recognition motif 1 in vertebrate nucleolin

 Score = 36.7 bits (85), Expect = 0.002
 Identities = 22/55 (40%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          +FVGNL      +ELK   SE+    N +V  D   G SK FG+V F++ E ++K
Sbjct: 3  LFVGNLNPNKDFDELKTAISEFFSKKNLAVQ-DVRIGSSKKFGYVDFESAEDLEK 56

This subfamily corresponds to the RRM1 of ubiquitously expressed protein nucleolin, also termed protein C23. Nucleolin is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. RRM1, together with RRM2, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 75

>gnl|CDD|240812 cd12366, RRM1_RBM45, RNA recognition motif 1 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 14/38 (36%), Positives = 25/38 (65%)

Query: 20 VSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTF 57
          V+ ++L++ F+ +G+I +  V+ DK T  SKG  +V F
Sbjct: 14 VTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKF 51

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

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 20/56 (35%), Positives = 32/56 (57%), Gaps = 2/56 (3%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          +IFV NLP+  +   LK  F+E G ++ A +  +   G SKG G V F++ E  ++
Sbjct: 1  QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVRFESPEVAER 54

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|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 36.4 bits (84), Expect = 0.002
 Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 1/52 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          ++FVG +P  +  +EL   F   G+I    +M +  +G ++G+ FV +  KE
Sbjct: 3  EVFVGKIPRDMYEDELVPLFERAGKIYEFRLMME-FSGENRGYAFVMYTTKE 53

This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), 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, RBM46 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|240890 cd12444, RRM1_CPEBs, RNA recognition motif 1 in cytoplasmic polyadenylation element-binding protein CPEB-1, CPEB-2, CPEB-3, CPEB-4 and similar protiens

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 9/24 (37%), Positives = 15/24 (62%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYG 33
          K+FVG LPW ++  ++   F  +G
Sbjct: 2  KVFVGGLPWDITEADILNSFRRFG 25

This subfamily corresponds to the RRM1 of the CPEB family of proteins that bind to defined groups of mRNAs and act as either translational repressors or activators to regulate their translation. CPEB proteins are well conserved in both, vertebrates and invertebrates. Based on sequence similarity, RNA-binding specificity, and functional regulation of translation, the CPEB proteins have been classified into two subfamilies. The first subfamily includes CPEB-1 and related proteins. CPEB-1 is an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. Otherwise, it may function as a translational inhibitor when dephosphorylated and bind to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm. The second subfamily includes CPEB-2, CPEB-3, CPEB-4, and related protiens. Due to high sequence similarity, members in this subfamily may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. CPEB-2 impedes target RNA translation at elongation; it directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All CPEB proteins are nucleus-cytoplasm shuttling proteins. They contain an N-terminal unstructured region, followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. CPEB-2, -3, and -4 have conserved nuclear export signals that are not present in CPEB-1. . Length = 112

>gnl|CDD|241003 cd12559, RRM_SRSF10, RNA recognition motif in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFST 69
          +FV N+       +L++ F  YG I++  V  D  T   +GF +V F++ ++A D + + 
Sbjct: 3  LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62

Query: 70 DSHVLEGSRLSIQ 82
          D   + G ++ IQ
Sbjct: 63 DRKWICGRQIEIQ 75

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

>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN 59
          +FVGNL  T++  EL++ F  YG + +  +      G    + FV F N
Sbjct: 5  LFVGNLEITITEEELRRAFERYGVVEDVDIKRPPR-GQGNAYAFVKFLN 52

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

 Score = 35.9 bits (82), Expect = 0.002
 Identities = 17/58 (29%), Positives = 31/58 (53%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          ++V  L  T    +LK  FS+YG+++ A V+ +  +  ++ +GFVT    E   K  +
Sbjct: 4  LWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCIN 61

This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1. Length = 76

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

 Score = 35.9 bits (82), Expect = 0.003
 Identities = 17/58 (29%), Positives = 29/58 (50%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          +++  L    +  +L K    YG+I++   + DK T   KG+GFV F +  A  K  +
Sbjct: 4  LYIRGLHPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 61

This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 75

>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 15/56 (26%), Positives = 31/56 (55%)

Query: 13 VGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          + NLP T +  + ++    +G +    +++ + TG SKG+GFV +  K++  +  S
Sbjct: 4  IANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKS 59

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|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 35.9 bits (83), Expect = 0.003
 Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 2/74 (2%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          ++V ++   V+  +L   FS  GQ+++  V  D N+ L   F F+ F ++E      S  
Sbjct: 5  VYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLR--FAFIEFTDEEGARAALSLS 62

Query: 71 SHVLEGSRLSIQPS 84
            +L    + + PS
Sbjct: 63 GTMLGFYPVRVLPS 76

This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 80

>gnl|CDD|240713 cd12267, RRM_YRA1_MLO3, RNA recognition motif in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 16/61 (26%), Positives = 31/61 (50%), Gaps = 2/61 (3%)

Query: 10 KIFVGNLPWTVSHNELKKFF-SEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          K+ V NLP  V+  +++++F S+ G I    + +++  G S G   +TF+      K + 
Sbjct: 1  KVIVSNLPKDVTEAQIREYFVSQIGPIKRVLLSYNEG-GKSTGIANITFKRAGDATKAYD 59

Query: 69 T 69
           
Sbjct: 60 K 60

This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p. . Length = 77

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

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 23/87 (26%), Positives = 39/87 (44%), Gaps = 16/87 (18%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          +++GNLP + S  EL++   ++G I    ++ +KN        FV F +     KV +T 
Sbjct: 6  VYIGNLPESYSEEELREDLEKFGPIDQIKIVKEKN------IAFVHFLSIANAIKVVTT- 58

Query: 71 SHVLEGSRLSIQPSDSHNRMAENMEDR 97
                  L  +P D  +R     +DR
Sbjct: 59 --------LPCEP-DYASRRIFYGKDR 76

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|241051 cd12607, RRM2_RBM4, RNA recognition motif 2 in vertebrate RNA-binding protein 4 (RBM4)

 Score = 35.4 bits (81), Expect = 0.004
 Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 9/74 (12%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQ-NKEAVDKVFS 68
          K+ VGN+  + ++ EL+  F EYG ++   ++        K + FV  +  ++AV+ +  
Sbjct: 2  KLHVGNISSSCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRG 53

Query: 69 TDSHVLEGSRLSIQ 82
           D+   +G R+ +Q
Sbjct: 54 LDNTEFQGKRMHVQ 67

This subgroup corresponds to the RRM2 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|240802 cd12356, RRM_PPARGC1B, RNA recognition motif in peroxisome proliferator-activated receptor gamma coactivator 1-beta (PGC-1-beta) and similar proteins

 Score = 35.2 bits (81), Expect = 0.004
 Identities = 18/51 (35%), Positives = 32/51 (62%), Gaps = 3/51 (5%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          I++ NL  ++S  ELKK F  +G+I    V+  K+ G  + +GF+T+++ E
Sbjct: 5  IYIRNLSSSMSSTELKKRFEVFGEIEECKVLI-KSRG--EKYGFITYRHSE 52

This subfamily corresponds to the RRM of PGC-1beta, also termed PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or PGC-1-related estrogen receptor alpha coactivator, which is one of the members of PGC-1 transcriptional coactivators family, including PGC-1alpha and PGC-1-related coactivator (PRC). PGC-1beta plays a nonredundant role in controlling mitochondrial oxidative energy metabolism and affects both, insulin sensitivity and mitochondrial biogenesis, and functions in a number of oxidative tissues. It is involved in maintaining baseline mitochondrial function and cardiac contractile function following pressure overload hypertrophy by preserving glucose metabolism and preventing oxidative stress. PGC-1beta induces hypertriglyceridemia in response to dietary fats through activating hepatic lipogenesis and lipoprotein secretion. It can stimulate apolipoprotein C3 (APOC3) expression, further mediating hypolipidemic effect of nicotinic acid. PGC-1beta also drives nuclear respiratory factor 1 (NRF-1) target gene expression and NRF-1 and estrogen related receptor alpha (ERRalpha)-dependent mitochondrial biogenesis. The modulation of the expression of PGC-1beta can trigger ERRalpha-induced adipogenesis. PGC-1beta is also a potent regulator inducing angiogenesis in skeletal muscle. The transcriptional activity of PGC-1beta can be increased through binding to host cell factor (HCF), a cellular protein involved in herpes simplex virus (HSV) infection and cell cycle regulation. PGC-1beta is a multi-domain protein containing an N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, two glutamic/aspartic acid-rich acidic domains, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha, PGC-1beta lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. . Length = 79

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	347
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.89
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.86
PTZ00458	90	acyl CoA binding protein; Provisional	99.86
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.85
KOG4412|consensus	226		99.84
KOG4412|consensus	226		99.83
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.83
cd00435	85	ACBP Acyl CoA binding protein (ACBP) binds thiol e	99.82
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.81
KOG0131|consensus	203		99.8
KOG0145|consensus	360		99.79
KOG0817|consensus	142		99.79
KOG0148|consensus	321		99.78
KOG0144|consensus	510		99.77
KOG0117|consensus	506		99.76
PF00887	87	ACBP: Acyl CoA binding protein; InterPro: IPR00058	99.76
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.75
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.73
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.73
COG4281	87	ACB Acyl-CoA-binding protein [Lipid metabolism]	99.73
PHA02743	166	Viral ankyrin protein; Provisional	99.72
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.71
PF12796	89	Ank_2: Ankyrin repeats (3 copies); InterPro: IPR02	99.71
KOG0149|consensus	247		99.7
KOG0509|consensus	600		99.69
KOG0508|consensus	615		99.68
KOG0512|consensus	228		99.68
PHA02736	154	Viral ankyrin protein; Provisional	99.68
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.68
PHA02791	284	ankyrin-like protein; Provisional	99.67
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.67
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.67
PHA02741	169	hypothetical protein; Provisional	99.67
KOG0195|consensus	448		99.66
PHA02741	169	hypothetical protein; Provisional	99.65
KOG0124|consensus	544		99.65
KOG0512|consensus	228		99.65
PHA02791	284	ankyrin-like protein; Provisional	99.64
KOG0127|consensus	678		99.64
KOG4214|consensus	117		99.64
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.63
KOG0127|consensus	678		99.63
PHA02875	413	ankyrin repeat protein; Provisional	99.63
PHA02795	437	ankyrin-like protein; Provisional	99.62
PHA02878	477	ankyrin repeat protein; Provisional	99.62
PHA02874	434	ankyrin repeat protein; Provisional	99.61
PHA02859	209	ankyrin repeat protein; Provisional	99.61
PHA02884	300	ankyrin repeat protein; Provisional	99.61
PHA02859	209	ankyrin repeat protein; Provisional	99.61
KOG0117|consensus	506		99.61
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.6
KOG0509|consensus	600		99.6
PLN03192	823	Voltage-dependent potassium channel; Provisional	99.6
PHA02743	166	Viral ankyrin protein; Provisional	99.59
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.59
KOG4205|consensus	311		99.59
KOG0502|consensus	296		99.59
KOG0105|consensus	241		99.58
PF13637	54	Ank_4: Ankyrin repeats (many copies); PDB: 3B95_A	99.58
PHA02875	413	ankyrin repeat protein; Provisional	99.58
PHA03095	471	ankyrin-like protein; Provisional	99.57
PHA02798	489	ankyrin-like protein; Provisional	99.57
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.56
KOG0515|consensus	752		99.56
PF13857	56	Ank_5: Ankyrin repeats (many copies); PDB: 1SW6_A	99.56
KOG0123|consensus	369		99.56
PHA03095	471	ankyrin-like protein; Provisional	99.56
KOG0110|consensus	725		99.56
PLN03120	260	nucleic acid binding protein; Provisional	99.55
KOG0145|consensus	360		99.55
KOG0121|consensus	153		99.55
PHA02946	446	ankyin-like protein; Provisional	99.55
KOG0125|consensus	376		99.55
KOG0109|consensus	346		99.54
PHA03100	480	ankyrin repeat protein; Provisional	99.54
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.54
PHA02946	446	ankyin-like protein; Provisional	99.54
PHA03100	480	ankyrin repeat protein; Provisional	99.53
KOG0123|consensus	369		99.53
PHA02878	477	ankyrin repeat protein; Provisional	99.52
KOG0122|consensus	270		99.52
PHA02884	300	ankyrin repeat protein; Provisional	99.52
KOG0510|consensus	929		99.51
PHA02874	434	ankyrin repeat protein; Provisional	99.51
KOG4177|consensus	1143		99.51
PHA02716	764	CPXV016; CPX019; EVM010; Provisional	99.5
KOG0113|consensus	335		99.49
PHA02736	154	Viral ankyrin protein; Provisional	99.49
PHA02989	494	ankyrin repeat protein; Provisional	99.49
KOG0126|consensus	219		99.48
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.48
PHA02716	764	CPXV016; CPX019; EVM010; Provisional	99.48
PLN03213	759	repressor of silencing 3; Provisional	99.48
KOG0510|consensus	929		99.47
KOG0514|consensus	452		99.47
PLN03121	243	nucleic acid binding protein; Provisional	99.47
PHA02876	682	ankyrin repeat protein; Provisional	99.46
PLN03192	823	Voltage-dependent potassium channel; Provisional	99.46
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.46
KOG0514|consensus	452		99.45
KOG4207|consensus	256		99.45
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.45
KOG4177|consensus	1143		99.44
PHA02917	661	ankyrin-like protein; Provisional	99.43
PHA02876	682	ankyrin repeat protein; Provisional	99.42
KOG0505|consensus	527		99.42
KOG0508|consensus	615		99.42
PHA02917	661	ankyrin-like protein; Provisional	99.41
PTZ00322	664	6-phosphofructo-2-kinase/fructose-2,6-biphosphatas	99.41
PHA02798	489	ankyrin-like protein; Provisional	99.41
PHA02989	494	ankyrin repeat protein; Provisional	99.41
PHA02795	437	ankyrin-like protein; Provisional	99.41
KOG0107|consensus	195		99.4
KOG0147|consensus	549		99.38
PHA02730	672	ankyrin-like protein; Provisional	99.38
PHA02730	672	ankyrin-like protein; Provisional	99.38
smart00362	72	RRM_2 RNA recognition motif.	99.38
KOG4206|consensus	221		99.37
KOG0505|consensus	527		99.36
cd00204	126	ANK ankyrin repeats; ankyrin repeats mediate prote	99.36
KOG0111|consensus	298		99.35
KOG0114|consensus	124		99.35
smart00360	71	RRM RNA recognition motif.	99.34
KOG1710|consensus	396		99.33
KOG0507|consensus	854		99.32
KOG0148|consensus	321		99.28
PHA02792	631	ankyrin-like protein; Provisional	99.28
KOG0195|consensus	448		99.28
COG0666	235	Arp FOG: Ankyrin repeat [General function predicti	99.27
KOG1710|consensus	396		99.27
KOG0108|consensus	435		99.27
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.26
PF13637	54	Ank_4: Ankyrin repeats (many copies); PDB: 3B95_A	99.26
KOG0130|consensus	170		99.25
PF12796	89	Ank_2: Ankyrin repeats (3 copies); InterPro: IPR02	99.24
KOG4211|consensus	510		99.24
KOG0144|consensus	510		99.23
COG0666	235	Arp FOG: Ankyrin repeat [General function predicti	99.23
PHA02792	631	ankyrin-like protein; Provisional	99.22
TIGR00870	743	trp transient-receptor-potential calcium channel p	99.2
KOG0502|consensus	296		99.2
KOG0515|consensus	752		99.18
KOG4212|consensus	608		99.17
cd00204	126	ANK ankyrin repeats; ankyrin repeats mediate prote	99.16
KOG4214|consensus	117		99.16
TIGR00870	743	trp transient-receptor-potential calcium channel p	99.14
smart00361	70	RRM_1 RNA recognition motif.	99.09
KOG0506|consensus	622		99.07
KOG4205|consensus	311		99.05
KOG3676|consensus	782		99.04
KOG1457|consensus	284		99.02
KOG0131|consensus	203		99.01
KOG0147|consensus	549		98.99
KOG0705|consensus	749		98.99
KOG0507|consensus	854		98.98
KOG0153|consensus	377		98.98
KOG0146|consensus	371		98.97
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.96
KOG0818|consensus	669		98.95
PF13606	30	Ank_3: Ankyrin repeat	98.93
PF00023	33	Ank: Ankyrin repeat Hereditary spherocytosis; Inte	98.9
KOG4208|consensus	214		98.9
PF13857	56	Ank_5: Ankyrin repeats (many copies); PDB: 1SW6_A	98.86
KOG3676|consensus	782		98.86
KOG0106|consensus	216		98.85
KOG0124|consensus	544		98.85
KOG0415|consensus	479		98.84
KOG0783|consensus	1267		98.83
KOG0146|consensus	371		98.83
KOG0109|consensus	346		98.82
PTZ00322	664	6-phosphofructo-2-kinase/fructose-2,6-biphosphatas	98.8
KOG4661|consensus	940		98.76
KOG0116|consensus	419		98.76
PF13606	30	Ank_3: Ankyrin repeat	98.75
KOG0110|consensus	725		98.72
KOG4454|consensus	267		98.71
KOG0522|consensus	560		98.71
KOG4369|consensus	2131		98.68
KOG4212|consensus	608		98.67
KOG1548|consensus	382		98.66
KOG0783|consensus	1267		98.61
KOG4209|consensus	231		98.59
PF00023	33	Ank: Ankyrin repeat Hereditary spherocytosis; Inte	98.56
KOG0226|consensus	290		98.56
KOG0132|consensus	894		98.55
KOG0129|consensus	520		98.53
KOG0533|consensus	243		98.52
KOG4369|consensus	2131		98.36
KOG2384|consensus	223		98.36
KOG0511|consensus	516		98.34
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.34
KOG0782|consensus	1004		98.32
KOG0782|consensus	1004		98.31
KOG0520|consensus	975		98.3
KOG0151|consensus	877		98.28
KOG0120|consensus	500		98.25
KOG4660|consensus	549		98.22
KOG1190|consensus	492		98.22
KOG0521|consensus	785		98.18
KOG0128|consensus	881		98.14
KOG1365|consensus	508		98.14
KOG3609|consensus	822		98.1
KOG0520|consensus	975		97.92
KOG4210|consensus	285		97.9
KOG1190|consensus	492		97.88
KOG0129|consensus	520		97.87
KOG4211|consensus	510		97.87
KOG1995|consensus	351		97.87
KOG0521|consensus	785		97.73
KOG4210|consensus	285		97.72
KOG0511|consensus	516		97.66
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.59
KOG0112|consensus	975		97.59
KOG0705|consensus	749		97.58
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.54
KOG0120|consensus	500		97.49
KOG1365|consensus	508		97.49
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.45
KOG0506|consensus	622		97.44
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.4
KOG2193|consensus	584		97.35
KOG1457|consensus	284		97.3
KOG3878|consensus	469		97.29
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.25
KOG4849|consensus	498		97.22
KOG0818|consensus	669		97.2
smart00248	30	ANK ankyrin repeats. Ankyrin repeats are about 33	97.17
KOG4676|consensus	479		97.12
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	97.06
KOG0522|consensus	560		97.05
smart00248	30	ANK ankyrin repeats. Ankyrin repeats are about 33	97.04
KOG3152|consensus	278		97.02
KOG4206|consensus	221		96.9
KOG0106|consensus	216		96.87
KOG0149|consensus	247		96.81
KOG2505|consensus	591		96.73
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	96.72
KOG4307|consensus	944		96.68
KOG0121|consensus	153		96.25
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.19
KOG2384|consensus	223		96.17
KOG0126|consensus	219		96.11
KOG1456|consensus	494		96.11
KOG0122|consensus	270		96.11
KOG0105|consensus	241		96.1
KOG0128|consensus	881		96.1
KOG1855|consensus	484		96.04
KOG2314|consensus	698		96.01
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.89
KOG0114|consensus	124		95.87
KOG1456|consensus	494		95.58
KOG0115|consensus	275		95.42
KOG0112|consensus	975		95.4
KOG1548|consensus	382		95.39
KOG3609|consensus	822		95.16
PLN03213	759	repressor of silencing 3; Provisional	95.11
PLN03120	260	nucleic acid binding protein; Provisional	95.1
KOG2068|consensus	327		95.09
KOG0125|consensus	376		95.01
KOG4307|consensus	944		94.93
KOG1996|consensus	378		94.8
smart00362	72	RRM_2 RNA recognition motif.	94.69
KOG0113|consensus	335		94.29
KOG0107|consensus	195		94.27
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.19
PF06128	284	Shigella_OspC: Shigella flexneri OspC protein; Int	94.16
KOG0226|consensus	290		94.14
PLN03121	243	nucleic acid binding protein; Provisional	94.12
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	94.04
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	93.86
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	93.06
COG0724	306	RNA-binding proteins (RRM domain) [General functio	92.92
smart00360	71	RRM RNA recognition motif.	92.92
KOG2135|consensus	526		92.65
KOG0130|consensus	170		92.6
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	92.0
KOG4285|consensus	350		91.89
KOG2202|consensus	260		91.6
KOG4207|consensus	256		89.98
PF11929	76	DUF3447: Domain of unknown function (DUF3447); Int	89.94
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	89.78
KOG0108|consensus	435		88.48
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	88.25
KOG0533|consensus	243		88.2
KOG0151|consensus	877		87.75
KOG2416|consensus	718		87.21
KOG2505|consensus	591		85.83
PF03158	192	DUF249: Multigene family 530 protein; InterPro: IP	82.4
KOG0116|consensus	419		82.12
KOG2591|consensus	684		80.55

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.89  E-value=3.7e-23  Score=187.66  Aligned_cols=148  Identities=20%  Similarity=0.287  Sum_probs=124.1

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~   83 (347)
                      ....++|||+|||+++|+++|+++|++||.|.+|+|++|+.|++++|||||+|.+.++|.+|++ +++..+.+++|+|.+
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~  183 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSY  183 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeec
Confidence            3456899999999999999999999999999999999999999999999999999999999997 499999999999998


Q ss_pred             CCcccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHH
Q psy630           84 SDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAM  163 (347)
Q Consensus        84 ~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~  163 (347)
                      +.+...       .....++||+|||..+++++|+++|+.||.|....+..++.     .++.|..||.+  ..+.++|.
T Consensus       184 a~p~~~-------~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~-----tg~~kG~aFV~--F~~~e~A~  249 (346)
T TIGR01659       184 ARPGGE-------SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKL-----TGTPRGVAFVR--FNKREEAQ  249 (346)
T ss_pred             cccccc-------ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCC-----CCccceEEEEE--ECCHHHHH
Confidence            865432       12346799999999999999999999999998777765542     34455555554  45577777


Q ss_pred             HHH
Q psy630          164 SKY  166 (347)
Q Consensus       164 ~~y  166 (347)
                      ++.
T Consensus       250 ~Ai  252 (346)
T TIGR01659       250 EAI  252 (346)
T ss_pred             HHH
Confidence            663

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=99.86  E-value=9.6e-22  Score=187.59  Aligned_cols=154  Identities=15%  Similarity=0.311  Sum_probs=122.7

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      ....++|||||||+++++++|+++|++||.|.+|+|++|+.||+++|||||+|.+.++|++|+.. |+..+.||.|+|.+
T Consensus       104 ~~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~r  183 (612)
T TIGR01645       104 LAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  183 (612)
T ss_pred             hcCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecc
Confidence            45678999999999999999999999999999999999999999999999999999999999985 99999999999987


Q ss_pred             CCcccccchhh----hhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCH
Q psy630           84 SDSHNRMAENM----EDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAK  159 (347)
Q Consensus        84 ~~~~~~~~~~~----~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~  159 (347)
                      ...........    ...-...++||+||+..+++++|+++|+.||.+....+..++.     .++.|+.+|..+.  +.
T Consensus       184 p~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~-----tgksKGfGFVeFe--~~  256 (612)
T TIGR01645       184 PSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPT-----GRGHKGYGFIEYN--NL  256 (612)
T ss_pred             cccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCC-----CCCcCCeEEEEEC--CH
Confidence            55432111000    0011236899999999999999999999999998777665432     2455666665543  45


Q ss_pred             HHHHHH
Q psy630          160 SEAMSK  165 (347)
Q Consensus       160 ~eA~~~  165 (347)
                      ++|.++
T Consensus       257 e~A~kA  262 (612)
T TIGR01645       257 QSQSEA  262 (612)
T ss_pred             HHHHHH
Confidence            666554

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.

>PTZ00458 acyl CoA binding protein; Provisional

Probab=99.86  E-value=6.1e-22  Score=141.85  Aligned_cols=84  Identities=33%  Similarity=0.742  Sum_probs=79.9

Q ss_pred             hcccccccccCCcc--cccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhh
Q psy630           97 RFNQACDYLPSLVK--KLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVD  174 (347)
Q Consensus        97 ~f~~~~~~v~~l~~--~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~l~  174 (347)
                      .|..+..+|++++.  .++.+++++||++|+|+|+|+|+.++||++++++|+||+||.++++|++++||++||++++++.
T Consensus         4 ~F~~A~~~v~~~~~~~~~s~d~~L~lYalyKQAt~G~c~~~~P~~~d~~~raKw~AW~~l~~ms~~eA~~~YI~l~~~l~   83 (90)
T PTZ00458          4 LFEECVSFINSLPKTVNLSVEIKLDLYKYYKQSTVGNCNIKEPSMFKYQDRKKYEAWKSIENLNREDAKKRYVEIVTELF   83 (90)
T ss_pred             HHHHHHHHHHhCCCCCCCCHHHHHHHHHHHhhhccCCCCCCCCCcccHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Confidence            48888889999887  6999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCChh
Q psy630          175 AGWEDK  180 (347)
Q Consensus       175 ~~~~~~  180 (347)
                      |+|+..
T Consensus        84 ~~w~~~   89 (90)
T PTZ00458         84 PNWEKG   89 (90)
T ss_pred             hccccC
Confidence            999864

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.85  E-value=1.4e-21  Score=180.78  Aligned_cols=146  Identities=21%  Similarity=0.332  Sum_probs=121.5

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      ..++|||+|||+++++++|+++|++||+|.+|+|++++.+|+++|||||+|.+.++|++|+.. ++..+.|+.|.|.++.
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            367899999999999999999999999999999999999999999999999999999999985 9999999999999886


Q ss_pred             cccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           86 SHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        86 ~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      +...       ....+++||+|||..+++++|..+|+.||.+....+..++.     .+..|+.+|..  .-+.++|.++
T Consensus        82 ~~~~-------~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~-----~~~~~g~~fv~--f~~~~~A~~a  147 (352)
T TIGR01661        82 PSSD-------SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNV-----TGLSKGVGFIR--FDKRDEADRA  147 (352)
T ss_pred             cccc-------ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCC-----CCCcCcEEEEE--ECCHHHHHHH
Confidence            6432       22356899999999999999999999999998766655432     22344444443  4467777766


Q ss_pred             H
Q psy630          166 Y  166 (347)
Q Consensus       166 y  166 (347)
                      .
T Consensus       148 i  148 (352)
T TIGR01661       148 I  148 (352)
T ss_pred             H
Confidence            3

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

>KOG4412|consensus

Probab=99.84  E-value=1.2e-21  Score=154.57  Aligned_cols=126  Identities=26%  Similarity=0.411  Sum_probs=106.9

Q ss_pred             cccccCCCccccCCCCCccceeeccc-----CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHH
Q psy630          221 DESQESGSKENEGQTKGWVNVSSMIN-----DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHW  295 (347)
Q Consensus       221 ~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~  295 (347)
                      .++++.-....-.++-|...++..+.     .++..|+.|++|||.|++.+..++++.|+...++++|..+..|+|||||
T Consensus        33 r~dqD~Rt~LHwa~S~g~~eiv~fLlsq~nv~~ddkDdaGWtPlhia~s~g~~evVk~Ll~r~~advna~tn~G~T~LHy  112 (226)
T KOG4412|consen   33 RDDQDGRTPLHWACSFGHVEIVYFLLSQPNVKPDDKDDAGWTPLHIAASNGNDEVVKELLNRSGADVNATTNGGQTCLHY  112 (226)
T ss_pred             cccccCCceeeeeeecCchhHHHHHHhcCCCCCCCccccCCchhhhhhhcCcHHHHHHHhcCCCCCcceecCCCcceehh
Confidence            33444445555556666554444433     3677799999999999999999999988885699999999999999999


Q ss_pred             HHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          296 ACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       296 A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |+..|+.+|+++||+ .|+.|+.+|..|.||||-|+..|.++++++|+..||
T Consensus       113 AagK~r~eIaqlLle-~ga~i~~kD~~~qtplHRAAavGklkvie~Li~~~a  163 (226)
T KOG4412|consen  113 AAGKGRLEIAQLLLE-KGALIRIKDKQGQTPLHRAAAVGKLKVIEYLISQGA  163 (226)
T ss_pred             hhcCChhhHHHHHHh-cCCCCcccccccCchhHHHHhccchhhHHHHHhcCC
Confidence            999999999999999 799999999999999999999999999999999986

>KOG4412|consensus

Probab=99.83  E-value=7.1e-21  Score=150.31  Aligned_cols=99  Identities=29%  Similarity=0.310  Sum_probs=90.8

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      ++|.....|.|+||+|+..+..++.++|+. +|+.++.+|..|.||||-|+.-|.+.++++|+. .|+.+|.+|..|+||
T Consensus        98 dvna~tn~G~T~LHyAagK~r~eIaqlLle-~ga~i~~kD~~~qtplHRAAavGklkvie~Li~-~~a~~n~qDk~G~Tp  175 (226)
T KOG4412|consen   98 DVNATTNGGQTCLHYAAGKGRLEIAQLLLE-KGALIRIKDKQGQTPLHRAAAVGKLKVIEYLIS-QGAPLNTQDKYGFTP  175 (226)
T ss_pred             CcceecCCCcceehhhhcCChhhHHHHHHh-cCCCCcccccccCchhHHHHhccchhhHHHHHh-cCCCCCcccccCccH
Confidence            567778899999999998888889999999 789999999999999999999999999999998 699999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||.|..-||.++..+|+++||
T Consensus       176 L~~al~e~~~d~a~lLV~~gA  196 (226)
T KOG4412|consen  176 LHHALAEGHPDVAVLLVRAGA  196 (226)
T ss_pred             HHHHHhccCchHHHHHHHhcc
Confidence            999988889999999999987

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.83  E-value=1.3e-20  Score=180.32  Aligned_cols=155  Identities=23%  Similarity=0.283  Sum_probs=124.8

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccC
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP   83 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~   83 (347)
                      .....++|||+|||+.+++++|+++|++||.|..|+++.++.+|+++|||||+|.+.++|.+|+.+++..+.|++|.|..
T Consensus        85 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        85 AERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQS  164 (457)
T ss_pred             cccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEee
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCcccccchh----hh-hhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCC
Q psy630           84 SDSHNRMAEN----ME-DRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMA  158 (347)
Q Consensus        84 ~~~~~~~~~~----~~-~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~  158 (347)
                      +.........    .. ..-...++||+|||..+++++|.++|+.||.|....+..+..     .|+.|+.||..  ..+
T Consensus       165 ~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~-----~g~~~g~afV~--f~~  237 (457)
T TIGR01622       165 SQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPE-----TGRSKGFGFIQ--FHD  237 (457)
T ss_pred             cchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCC-----CCccceEEEEE--ECC
Confidence            6543322111    00 011246899999999999999999999999998776665432     24555556655  445


Q ss_pred             HHHHHHH
Q psy630          159 KSEAMSK  165 (347)
Q Consensus       159 ~~eA~~~  165 (347)
                      .++|..+
T Consensus       238 ~e~A~~A  244 (457)
T TIGR01622       238 AEEAKEA  244 (457)
T ss_pred             HHHHHHH
Confidence            6777666

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.

>cd00435 ACBP Acyl CoA binding protein (ACBP) binds thiol esters of long fatty acids and coenzyme A in a one-to-one binding mode with high specificity and affinity

Probab=99.82  E-value=1.2e-20  Score=135.10  Aligned_cols=82  Identities=39%  Similarity=0.752  Sum_probs=79.2

Q ss_pred             hhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhhc
Q psy630           96 DRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDA  175 (347)
Q Consensus        96 ~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~l~~  175 (347)
                      ..|..+..+|+.++..++.+++++||++|+|+++|+|+.++||+++++++.||+||.++++|+++|||+.||++++++.|
T Consensus         3 ~~F~~A~~~v~~~~~~~~~~~~L~lYalyKQAt~G~~~~~~P~~~d~~~~~K~~AW~~l~~ms~~eA~~~YV~~~~~l~~   82 (85)
T cd00435           3 EEFEAAAEKVKKLKTKPSNEEKLQLYSLYKQATVGDCNTERPGMFDLKGRAKWDAWNSLKGMSKEDAMKAYIAKVEELIA   82 (85)
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHhccCCCCCCCCCcccHhhHHHHHHHHHcCCCCHHHHHHHHHHHHHHHhh
Confidence            46888899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cC
Q psy630          176 GW  177 (347)
Q Consensus       176 ~~  177 (347)
                      +|
T Consensus        83 ~~   84 (85)
T cd00435          83 KY   84 (85)
T ss_pred             cc
Confidence            87

Acyl-CoAs are important intermediates in fatty lipid synthesis and fatty acid degradation and play a role in regulation of intermediary metabolism and gene regulation. The suggested role of ACBP is to act as a intracellular acyl-CoA transporter and pool former. ACBPs are present in a large group of eukaryotic species and several tissue-specific isoforms have been detected.

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

Probab=99.81  E-value=5e-20  Score=180.44  Aligned_cols=143  Identities=22%  Similarity=0.351  Sum_probs=117.4

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCccc
Q psy630           10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDSHN   88 (347)
Q Consensus        10 ~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~~~   88 (347)
                      +|||||||+++|+++|+++|++||.|.+|+|++|+.|++++|||||+|.+.++|.+|+.. ++..+.|+.|+|.++....
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~   81 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDP   81 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccc
Confidence            699999999999999999999999999999999999999999999999999999999985 9999999999998875432


Q ss_pred             ccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           89 RMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        89 ~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..     ......++||+|||.++++++|.++|+.||.|....+..+..      |+.|+.||..  ..+.++|.++
T Consensus        82 ~~-----~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~------g~skg~afV~--F~~~e~A~~A  145 (562)
T TIGR01628        82 SL-----RRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDEN------GKSRGYGFVH--FEKEESAKAA  145 (562)
T ss_pred             cc-----cccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCC------CCcccEEEEE--ECCHHHHHHH
Confidence            21     122345799999999999999999999999998766655432      3344444444  3345555554

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0131|consensus

Probab=99.80  E-value=9.5e-20  Score=143.52  Aligned_cols=121  Identities=21%  Similarity=0.328  Sum_probs=109.0

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI   81 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v   81 (347)
                      .+.++..+||||||+..++++.|.++|-+.|+|..+++++|+.+...+||||++|.++++|+-|++. |...+.||+|+|
T Consensus         4 ~~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv   83 (203)
T KOG0131|consen    4 IERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRV   83 (203)
T ss_pred             cccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEE
Confidence            3456778999999999999999999999999999999999999999999999999999999999995 999999999999


Q ss_pred             cCCCcccccchhhhhhcccccccccCCcccccchhhHHHHhhccccce
Q psy630           82 QPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATV  129 (347)
Q Consensus        82 ~~~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~  129 (347)
                      ..+.....      ..-..+++||+||.+.+++..|.+.|+.||++..
T Consensus        84 ~kas~~~~------nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~  125 (203)
T KOG0131|consen   84 NKASAHQK------NLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLIS  125 (203)
T ss_pred             Eecccccc------cccccccccccccCcchhHHHHHHHHHhcccccc
Confidence            98873322      1234489999999999999999999999999865

>KOG0145|consensus

Probab=99.79  E-value=1.5e-19  Score=149.84  Aligned_cols=146  Identities=20%  Similarity=0.354  Sum_probs=124.6

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      ..++|.|.-||..+|+++++.+|...|+|.+|++++|+.+|.|-||+||.|-++++|++|+.. ||..+..+.|+|.++.
T Consensus        40 skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyAR  119 (360)
T KOG0145|consen   40 SKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYAR  119 (360)
T ss_pred             ccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEecc
Confidence            446899999999999999999999999999999999999999999999999999999999985 9999999999999998


Q ss_pred             cccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           86 SHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        86 ~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      +...       ....+++||.+||..++..++.++|++||.|..-++..+.-     .|-+|+.+|..+  =.+.||.++
T Consensus       120 PSs~-------~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqv-----tg~srGVgFiRF--DKr~EAe~A  185 (360)
T KOG0145|consen  120 PSSD-------SIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQV-----TGLSRGVGFIRF--DKRIEAEEA  185 (360)
T ss_pred             CChh-------hhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcc-----cceecceeEEEe--cchhHHHHH
Confidence            7543       45678999999999999999999999999998777766642     344555555443  235667666


Q ss_pred             H
Q psy630          166 Y  166 (347)
Q Consensus       166 y  166 (347)
                      .
T Consensus       186 I  186 (360)
T KOG0145|consen  186 I  186 (360)
T ss_pred             H
Confidence            3

>KOG0817|consensus

Probab=99.79  E-value=1e-19  Score=140.95  Aligned_cols=87  Identities=44%  Similarity=0.768  Sum_probs=83.1

Q ss_pred             hhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhh
Q psy630           95 EDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVD  174 (347)
Q Consensus        95 ~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~l~  174 (347)
                      ...|..+.-.|++|+..++.++++.||++|+|+++|+|++++||+++++||+||+||+.+++|+.++||++||+++.+|.
T Consensus         6 ~~~Fe~a~~~~~~l~~~p~~ee~L~lYglyKQAt~G~~~~~kPg~~d~~~k~Kw~AW~~l~~~s~~eA~~~Yv~~~~~l~   85 (142)
T KOG0817|consen    6 EAKFEAAAEAVKNLKKKPSNEELLKLYGLYKQATVGDCNTPKPGFFDEEGKAKWQAWNSLGGMSKEEAMEAYVEKVEELI   85 (142)
T ss_pred             HHHHHHHHHHHHhcccCCCHHHHHHHHHHHHhhccCCCCCCCCchhhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHH
Confidence            45688888889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCChhh
Q psy630          175 AGWEDKE  181 (347)
Q Consensus       175 ~~~~~~~  181 (347)
                      +.|....
T Consensus        86 ~~~~~~~   92 (142)
T KOG0817|consen   86 PKYGAEA   92 (142)
T ss_pred             HHhhccc
Confidence            9999874

>KOG0148|consensus

Probab=99.78  E-value=3.7e-19  Score=148.46  Aligned_cols=128  Identities=22%  Similarity=0.428  Sum_probs=112.0

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCcc
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDSH   87 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~~   87 (347)
                      -.+||+.|.+.++.+.|++.|.+||+|.+++|++|..|++|+||+||-|-+.++|+.||.. ||.=|.+|.|+-.|+..+
T Consensus        63 fhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRK  142 (321)
T KOG0148|consen   63 FHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRK  142 (321)
T ss_pred             eeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccC
Confidence            3799999999999999999999999999999999999999999999999999999999985 999999999999998776


Q ss_pred             cccch----hhhhhcc-----cccccccCCcccccchhhHHHHhhccccceecccCCC
Q psy630           88 NRMAE----NMEDRFN-----QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDK  136 (347)
Q Consensus        88 ~~~~~----~~~~~f~-----~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~  136 (347)
                      .....    ..++.|+     .+++||+|++..++++.+++.|+.||+|.+.++..++
T Consensus       143 p~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q  200 (321)
T KOG0148|consen  143 PSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ  200 (321)
T ss_pred             ccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEeccc
Confidence            53211    1122232     3789999999999999999999999999988776553

>KOG0144|consensus

Probab=99.77  E-value=3.3e-19  Score=157.62  Aligned_cols=125  Identities=22%  Similarity=0.416  Sum_probs=108.0

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc--CCCccCC--ccccc
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST--DSHVLEG--SRLSI   81 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~--~~~~~~g--~~l~v   81 (347)
                      .+.-++|||.+|..++|.+|+++|++||.|.+|.|++|+.|+.++|||||.|.+.++|.+|+..  |-+++.|  .+|.|
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            4455899999999999999999999999999999999999999999999999999999999985  8888887  46677


Q ss_pred             cCCCcccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCC
Q psy630           82 QPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDK  136 (347)
Q Consensus        82 ~~~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~  136 (347)
                      ++++...++.      ....++||+.|+...++.+++++|++||.|....+..+.
T Consensus       112 k~Ad~E~er~------~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~  160 (510)
T KOG0144|consen  112 KYADGERERI------VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP  160 (510)
T ss_pred             cccchhhhcc------ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecc
Confidence            7887655432      345678999999999999999999999999865555443

>KOG0117|consensus

Probab=99.76  E-value=7.8e-19  Score=155.99  Aligned_cols=169  Identities=18%  Similarity=0.311  Sum_probs=125.3

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCcc-CCccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVL-EGSRLSI   81 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~-~g~~l~v   81 (347)
                      .+...+-||||.||.++.|++|.-+|++.|+|-++++|+|+.+|.+||||||+|.+.+.|+.|++. |.+.| .|+.|.|
T Consensus        79 ~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igv  158 (506)
T KOG0117|consen   79 PPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGV  158 (506)
T ss_pred             CCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEE
Confidence            345678999999999999999999999999999999999999999999999999999999999986 77766 6999998


Q ss_pred             cCCCcccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCC-------------------------
Q psy630           82 QPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDK-------------------------  136 (347)
Q Consensus        82 ~~~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~-------------------------  136 (347)
                      +.+..             .+++||+|+|...+.+++++-+...+.-.+--+..+.                         
T Consensus       159 c~Sva-------------n~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aR  225 (506)
T KOG0117|consen  159 CVSVA-------------NCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMAR  225 (506)
T ss_pred             EEeee-------------cceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHH
Confidence            86644             3568999999999999999998887665432222222                         


Q ss_pred             ----CCccchhHHHHHHHHHHcCCCCHHHHHHHH-HHHHHHhhccCChhhhhhh
Q psy630          137 ----PSWYNMEAKSKYNAWNSLGQMAKSEAMSKY-IALLKEVDAGWEDKEQEEI  185 (347)
Q Consensus       137 ----p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y-i~~~~~l~~~~~~~~~~~~  185 (347)
                          |+.+.+.|..-...|..-+.-..+|+|.+. +.+|++|+.+..++.++..
T Consensus       226 rKl~~g~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~  279 (506)
T KOG0117|consen  226 RKLMPGKIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKL  279 (506)
T ss_pred             hhccCCceeecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHH
Confidence                233444444444455554444455555554 5555555555555544443

>PF00887 ACBP: Acyl CoA binding protein; InterPro: IPR000582 Acyl-CoA-binding protein (ACBP) is a small (10 Kd) protein that binds medium- and long-chain acyl-CoA esters with very high affinity and may function as an intracellular carrier of acyl-CoA esters []

Probab=99.76  E-value=2.2e-19  Score=130.41  Aligned_cols=84  Identities=39%  Similarity=0.816  Sum_probs=75.5

Q ss_pred             hhhcccccccccCCcc--cccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHH
Q psy630           95 EDRFNQACDYLPSLVK--KLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKE  172 (347)
Q Consensus        95 ~~~f~~~~~~v~~l~~--~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~  172 (347)
                      +..|..+..+|++++.  .++.++.+.||++|+|+++|+|..++|+++++.++.||+||.++++||++|||+.||+++++
T Consensus         2 e~~F~~A~~~v~~~~~~~~~~~~~~L~LYalyKQAt~Gd~~~~~P~~~d~~~~~K~~AW~~l~gms~~eA~~~Yi~~v~~   81 (87)
T PF00887_consen    2 EEEFEAAVEFVSNLPKKSQLSNDDKLELYALYKQATHGDCDTPRPGFFDIEGRAKWDAWKALKGMSKEEAMREYIELVEE   81 (87)
T ss_dssp             HHHHHHHHHHHHHSSSCSTS-HHHHHHHHHHHHHHHTSS--S-CTTTTCHHHHHHHHHHHTTTTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccccCCCCHHHHHHHHHHHHHHHhCCCcCCCCcchhHHHHHHHHHHHHccCCCHHHHHHHHHHHHHH
Confidence            4568888999999999  99999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccCC
Q psy630          173 VDAGWE  178 (347)
Q Consensus       173 l~~~~~  178 (347)
                      +.++|.
T Consensus        82 ~~~~~~   87 (87)
T PF00887_consen   82 LIPKYE   87 (87)
T ss_dssp             HHHHH-
T ss_pred             HHHhcC
Confidence            998873

ACBP is also known as diazepam binding inhibitor (DBI) or endozepine (EP) because of its ability to displace diazepam from the benzodiazepine (BZD) recognition site located on the GABA type A receptor. It is therefore possible that this protein also acts as a neuropeptide to modulate the action of the GABA receptor []. ACBP is a highly conserved protein of about 90 residues that is found in all four eukaryotic kingdoms, Animalia, Plantae, Fungi and Protista, and in some eubacterial species []. Although ACBP occurs as a completely independent protein, intact ACB domains have been identified in a number of large, multifunctional proteins in a variety of eukaryotic species. These include large membrane-associated proteins with N-terminal ACB domains, multifunctional enzymes with both ACB and peroxisomal enoyl-CoA Delta(3), Delta(2)-enoyl-CoA isomerase domains, and proteins with both an ACB domain and ankyrin repeats (IPR002110 from INTERPRO) []. The ACB domain consists of four alpha-helices arranged in a bowl shape with a highly exposed acyl-CoA-binding site. The ligand is bound through specific interactions with residues on the protein, most notably several conserved positive charges that interact with the phosphate group on the adenosine-3'phosphate moiety, and the acyl chain is sandwiched between the hydrophobic surfaces of CoA and the protein []. Other proteins containing an ACB domain include: Endozepine-like peptide (ELP) (gene DBIL5) from mouse []. ELP is a testis-specific ACBP homologue that may be involved in the energy metabolism of the mature sperm. MA-DBI, a transmembrane protein of unknown function which has been found in mammals. MA-DBI contains a N-terminal ACB domain. DRS-1 [], a human protein of unknown function that contains a N-terminal ACB domain and a C-terminal enoyl-CoA isomerase/hydratase domain. ; GO: 0000062 fatty-acyl-CoA binding; PDB: 2CB8_A 2FJ9_A 2LBB_A 1ST7_A 3EPY_B 2FDQ_C 1NTI_A 1HB8_A 1ACA_A 1NVL_A ....

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.75  E-value=4.6e-18  Score=157.34  Aligned_cols=171  Identities=20%  Similarity=0.357  Sum_probs=127.9

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCC--ccccccC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEG--SRLSIQP   83 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g--~~l~v~~   83 (347)
                      ..++|||+|||+++++++|+++|++||.|..++++.+..++.++|||||+|.+.++|..|+.. ++..+.|  +++.|.+
T Consensus        88 ~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~~  167 (352)
T TIGR01661        88 KGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKF  167 (352)
T ss_pred             ccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            456899999999999999999999999999999999988899999999999999999999975 8888877  4566766


Q ss_pred             CCcccccch--------------hhh------------------------------------------------------
Q psy630           84 SDSHNRMAE--------------NME------------------------------------------------------   95 (347)
Q Consensus        84 ~~~~~~~~~--------------~~~------------------------------------------------------   95 (347)
                      +........              ...                                                      
T Consensus       168 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (352)
T TIGR01661       168 ANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASPP  247 (352)
T ss_pred             CCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCCc
Confidence            543220000              000                                                      


Q ss_pred             --h---------------hcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCC
Q psy630           96 --D---------------RFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMA  158 (347)
Q Consensus        96 --~---------------~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~  158 (347)
                        .               .-...++||+|||..+++++|.++|+.||.|....+..++.     .++.|+.|+..  ..+
T Consensus       248 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~-----t~~skG~aFV~--F~~  320 (352)
T TIGR01661       248 ATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLT-----TNQCKGYGFVS--MTN  320 (352)
T ss_pred             cccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCC-----CCCccceEEEE--ECC
Confidence              0               00012599999999999999999999999999888776542     45666666665  566


Q ss_pred             HHHHHHHHHHHHHHhhccCChhhhhhhhcccc
Q psy630          159 KSEAMSKYIALLKEVDAGWEDKEQEEINWDWK  190 (347)
Q Consensus       159 ~~eA~~~yi~~~~~l~~~~~~~~~~~~~~~~~  190 (347)
                      .++|+++    ++.|...+...  +.+..+|+
T Consensus       321 ~~~A~~A----i~~lnG~~~~g--r~i~V~~~  346 (352)
T TIGR01661       321 YDEAAMA----ILSLNGYTLGN--RVLQVSFK  346 (352)
T ss_pred             HHHHHHH----HHHhCCCEECC--eEEEEEEc
Confidence            8888765    55555554443  23444444

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

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.73  E-value=1.1e-17  Score=159.69  Aligned_cols=109  Identities=22%  Similarity=0.396  Sum_probs=96.8

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccC-Ccccccc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLE-GSRLSIQ   82 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~-g~~l~v~   82 (347)
                      +...++|||+|||+++++++|+++|++||.|.+++|++| .+|+++|||||+|.+.++|++|++. |+..+. |+.+.|.
T Consensus        55 p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~  133 (578)
T TIGR01648        55 PGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVC  133 (578)
T ss_pred             CCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccc
Confidence            455689999999999999999999999999999999999 6899999999999999999999986 887774 7877776


Q ss_pred             CCCcccccchhhhhhcccccccccCCcccccchhhHHHHhhcccc
Q psy630           83 PSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQA  127 (347)
Q Consensus        83 ~~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v  127 (347)
                      .+.             ...++||+|||..+++++|++.|+.++..
T Consensus       134 ~S~-------------~~~rLFVgNLP~~~TeeeL~eeFskv~eg  165 (578)
T TIGR01648       134 ISV-------------DNCRLFVGGIPKNKKREEILEEFSKVTEG  165 (578)
T ss_pred             ccc-------------cCceeEeecCCcchhhHHHHHHhhcccCC
Confidence            543             24579999999999999999999998753

Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

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

Probab=99.73  E-value=7.5e-18  Score=165.11  Aligned_cols=152  Identities=20%  Similarity=0.385  Sum_probs=124.0

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccC----Ccccc
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLE----GSRLS   80 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~----g~~l~   80 (347)
                      ...++|||+|||+++|+++|+++|++||.|.++.++++. +|.++|||||+|.+.++|.+|++. ++..+.    |+.+.
T Consensus       176 ~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~-~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~  254 (562)
T TIGR01628       176 KKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLY  254 (562)
T ss_pred             cCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeE
Confidence            345789999999999999999999999999999999986 699999999999999999999985 999999    99999


Q ss_pred             ccCCCcccccchhhhh-----------hcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHH
Q psy630           81 IQPSDSHNRMAENMED-----------RFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYN  149 (347)
Q Consensus        81 v~~~~~~~~~~~~~~~-----------~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~  149 (347)
                      |.++..+..+......           .....++||+||+..+++++|+++|+.||.|+...+..+.      .|+.|+.
T Consensus       255 v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d~------~g~~~g~  328 (562)
T TIGR01628       255 VGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE------KGVSRGF  328 (562)
T ss_pred             eecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEECC------CCCcCCe
Confidence            9988776654322222           2334679999999999999999999999999987776653      3344544


Q ss_pred             HHHHcCCCCHHHHHHHH
Q psy630          150 AWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       150 aw~~~~~~~~~eA~~~y  166 (347)
                      +|..  ..+.++|.++.
T Consensus       329 gfV~--f~~~~~A~~A~  343 (562)
T TIGR01628       329 GFVC--FSNPEEANRAV  343 (562)
T ss_pred             EEEE--eCCHHHHHHHH
Confidence            4443  44677777774

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>COG4281 ACB Acyl-CoA-binding protein [Lipid metabolism]

Probab=99.73  E-value=3.6e-18  Score=113.62  Aligned_cols=82  Identities=37%  Similarity=0.667  Sum_probs=76.9

Q ss_pred             hhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhhc
Q psy630           96 DRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDA  175 (347)
Q Consensus        96 ~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~l~~  175 (347)
                      ..|.++..-|..|+..++.++|+++|++|+|.++|+....+||+|+++|+.||+||..+++.|.++|.++||.+|++|..
T Consensus         4 ~~Feqa~~dV~~L~~kP~~d~LLkLYAL~KQ~s~GD~~~ekPG~~d~~gr~K~eAW~~LKGksqedA~qeYialVeeLka   83 (87)
T COG4281           4 TRFEQAQTDVKELSEKPSNDELLKLYALFKQGSVGDNDGEKPGFFDIVGRYKYEAWAGLKGKSQEDARQEYIALVEELKA   83 (87)
T ss_pred             hHHHHHHHHHHHhccCCCcHHHHHHHHHHHhccccccCCCCCCccccccchhHHHHhhccCccHHHHHHHHHHHHHHHHh
Confidence            45777777899999999999999999999999999999999999999999999999999999999999999999999976


Q ss_pred             cC
Q psy630          176 GW  177 (347)
Q Consensus       176 ~~  177 (347)
                      ++
T Consensus        84 k~   85 (87)
T COG4281          84 KY   85 (87)
T ss_pred             hc
Confidence            54

>PHA02743 Viral ankyrin protein; Provisional

Probab=99.72  E-value=3.2e-17  Score=134.94  Aligned_cols=99  Identities=14%  Similarity=0.193  Sum_probs=88.5

Q ss_pred             CcccCCCCCcHHHHHHcCChHH---HHHHHhhcCCCCccccC-CCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCC
Q psy630          248 ESQLDDNEKNIYEWAKEGKLDM---LVKQLTKLKDFNINQLD-ENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDG  323 (347)
Q Consensus       248 ~~~~~~~~~~~l~~a~~~~~~~---~~~lL~~~~~~~~~~~d-~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g  323 (347)
                      .+..+..|+|+||+|+..+...   ++++|+. .|+++|.+| ..|.||||+|+.+++.+++++|+.+.|++++.+|..|
T Consensus        50 ~~~~d~~g~t~Lh~Aa~~g~~~~~~~i~~Ll~-~Gadin~~d~~~g~TpLh~A~~~g~~~iv~~Ll~~~gad~~~~d~~g  128 (166)
T PHA02743         50 LHRYDHHGRQCTHMVAWYDRANAVMKIELLVN-MGADINARELGTGNTLLHIAASTKNYELAEWLCRQLGVNLGAINYQH  128 (166)
T ss_pred             hhccCCCCCcHHHHHHHhCccCHHHHHHHHHH-cCCCCCCCCCCCCCcHHHHHHHhCCHHHHHHHHhccCCCccCcCCCC
Confidence            4556788999999999876643   3678887 799999998 5899999999999999999999943699999999999


Q ss_pred             CcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          324 DYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       324 ~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      .||||+|+..++.+++++|+++||
T Consensus       129 ~tpL~~A~~~~~~~iv~~Ll~~ga  152 (166)
T PHA02743        129 ETAYHIAYKMRDRRMMEILRANGA  152 (166)
T ss_pred             CCHHHHHHHcCCHHHHHHHHHcCC
Confidence            999999999999999999999987

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

Probab=99.71  E-value=4.7e-17  Score=129.68  Aligned_cols=83  Identities=31%  Similarity=0.715  Sum_probs=77.5

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ...++|||+|||+++++++|+++|++||.|..+.|+.++.|++++|||||+|.+.++|+.|++. ++..+.|+.|+|.++
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a  111 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPA  111 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeC
Confidence            4467899999999999999999999999999999999999999999999999999999999984 999999999999988


Q ss_pred             Cccc
Q psy630           85 DSHN   88 (347)
Q Consensus        85 ~~~~   88 (347)
                      .++.
T Consensus       112 ~~~~  115 (144)
T PLN03134        112 NDRP  115 (144)
T ss_pred             CcCC
Confidence            6644

>PF12796 Ank_2: Ankyrin repeats (3 copies); InterPro: IPR020683 This entry represents the ankyrin repeat-containing domain

Probab=99.71  E-value=7.7e-17  Score=118.48  Aligned_cols=83  Identities=31%  Similarity=0.531  Sum_probs=74.5

Q ss_pred             HHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCCHHH
Q psy630          259 YEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDL  338 (347)
Q Consensus       259 l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~~~  338 (347)
                      ||.|+..+...++++|.. .+.+++.    |.||||+||..|+.+++++|++ .|++++.+|..|+||||+|+..|+.++
T Consensus         1 L~~A~~~~~~~~~~~ll~-~~~~~~~----~~~~l~~A~~~~~~~~~~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~   74 (89)
T PF12796_consen    1 LHIAAQNGNLEILKFLLE-KGADINL----GNTALHYAAENGNLEIVKLLLE-NGADINSQDKNGNTALHYAAENGNLEI   74 (89)
T ss_dssp             HHHHHHTTTHHHHHHHHH-TTSTTTS----SSBHHHHHHHTTTHHHHHHHHH-TTTCTT-BSTTSSBHHHHHHHTTHHHH
T ss_pred             CHHHHHcCCHHHHHHHHH-CcCCCCC----CCCHHHHHHHcCCHHHHHHHHH-hcccccccCCCCCCHHHHHHHcCCHHH
Confidence            567777777778888888 6777766    8999999999999999999999 799999999999999999999999999


Q ss_pred             HHHHHhCCC
Q psy630          339 IEYLVNSGS  347 (347)
Q Consensus       339 v~~Ll~~GA  347 (347)
                      +++|+++|+
T Consensus        75 ~~~Ll~~g~   83 (89)
T PF12796_consen   75 VKLLLEHGA   83 (89)
T ss_dssp             HHHHHHTTT
T ss_pred             HHHHHHcCC
Confidence            999999986

These domains contain multiple repeats of a beta(2)-alpha(2) motif. The ankyrin repeat is one of the most common protein-protein interaction motifs in nature. Ankyrin repeats are tandemly repeated modules of about 33 amino acids. They occur in a large number of functionally diverse proteins mainly from eukaryotes. The few known examples from prokaryotes and viruses may be the result of horizontal gene transfers []. The repeat has been found in proteins of diverse function such as transcriptional initiators, cell-cycle regulators, cytoskeletal, ion transporters and signal transducers. The ankyrin fold appears to be defined by its structure rather than its function since there is no specific sequence or structure which is universally recognised by it. The conserved fold of the ankyrin repeat unit is known from several crystal and solution structures [, , , ]. Each repeat folds into a helix-loop-helix structure with a beta-hairpin/loop region projecting out from the helices at a 90o angle. The repeats stack together to form an L-shaped structure [, ].; PDB: 3AAA_C 3F6Q_A 2KBX_A 3IXE_A 3TWR_D 3TWV_A 3TWT_B 3TWQ_A 3TWS_A 3TWX_B ....

>KOG0149|consensus

Probab=99.70  E-value=3.9e-17  Score=134.27  Aligned_cols=80  Identities=36%  Similarity=0.759  Sum_probs=75.2

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCCc
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~~   86 (347)
                      ..++||||+|+|.++.+.|+++|++||+|++..|+.|+.||+|+||+||+|++.++|.+|++....+|+||+..+..+.-
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLASL   90 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchhhh
Confidence            44699999999999999999999999999999999999999999999999999999999999977889999988887654

>KOG0509|consensus

Probab=99.69  E-value=6.6e-17  Score=150.68  Aligned_cols=99  Identities=28%  Similarity=0.480  Sum_probs=68.1

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccC-CCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLD-ENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d-~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      +.+..|.+|.++||||+.++...++++|+. +|+++|..+ .-|.|||||||.+||..+|.+|++ +|||++.+|.+|.|
T Consensus        70 ~v~~~D~~g~tlLHWAAiNNrl~v~r~li~-~gadvn~~gG~l~stPLHWAar~G~~~vv~lLlq-hGAdpt~~D~~G~~  147 (600)
T KOG0509|consen   70 SVNNPDREGVTLLHWAAINNRLDVARYLIS-HGADVNAIGGVLGSTPLHWAARNGHISVVDLLLQ-HGADPTLKDKQGLT  147 (600)
T ss_pred             CCCCCCcCCccceeHHHHcCcHHHHHHHHH-cCCCccccCCCCCCCcchHHHHcCcHHHHHHHHH-cCCCCceecCCCCc
Confidence            455566667777777777777667777666 677777665 456677777777777777777776 57777777777777


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|++.|+..+|.|||.+||
T Consensus       148 ~lHla~~~~~~~~vayll~~~~  169 (600)
T KOG0509|consen  148 PLHLAAQFGHTALVAYLLSKGA  169 (600)
T ss_pred             HHHHHHHhCchHHHHHHHHhcc
Confidence            7777777777777777766653

>KOG0508|consensus

Probab=99.68  E-value=3.6e-17  Score=146.87  Aligned_cols=101  Identities=24%  Similarity=0.333  Sum_probs=95.5

Q ss_pred             ccCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCC
Q psy630          245 INDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGD  324 (347)
Q Consensus       245 ~~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~  324 (347)
                      ..++|.......|||.+||..++.+++++|.+ ++++++..|..|.|+||+||.+||.+|+++|++ .|||+|.++..|+
T Consensus       107 ga~VN~tT~TNStPLraACfDG~leivKyLvE-~gad~~IanrhGhTcLmIa~ykGh~~I~qyLle-~gADvn~ks~kGN  184 (615)
T KOG0508|consen  107 GASVNDTTRTNSTPLRAACFDGHLEIVKYLVE-HGADPEIANRHGHTCLMIACYKGHVDIAQYLLE-QGADVNAKSYKGN  184 (615)
T ss_pred             cCccccccccCCccHHHHHhcchhHHHHHHHH-cCCCCcccccCCCeeEEeeeccCchHHHHHHHH-hCCCcchhcccCc
Confidence            34577777788899999999999999999998 899999999999999999999999999999999 6999999999999


Q ss_pred             cHHHHHHHcCCHHHHHHHHhCCC
Q psy630          325 YGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       325 TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |+||.|+..|+.+++++||.+||
T Consensus       185 TALH~caEsG~vdivq~Ll~~ga  207 (615)
T KOG0508|consen  185 TALHDCAESGSVDIVQLLLKHGA  207 (615)
T ss_pred             hHHHhhhhcccHHHHHHHHhCCc
Confidence            99999999999999999999986

>KOG0512|consensus

Probab=99.68  E-value=1e-16  Score=125.94  Aligned_cols=96  Identities=23%  Similarity=0.245  Sum_probs=84.0

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      -.|..|.++.|+||.|+..++..+++.|+. .|++++.+...||||||-||.+.+.+++.+||+ +|+|||++....+||
T Consensus        89 ~vNtrD~D~YTpLHRAaYn~h~div~~ll~-~gAn~~a~T~~GWTPLhSAckWnN~~va~~LLq-hgaDVnA~t~g~ltp  166 (228)
T KOG0512|consen   89 HVNTRDEDEYTPLHRAAYNGHLDIVHELLL-SGANKEAKTNEGWTPLHSACKWNNFEVAGRLLQ-HGADVNAQTKGLLTP  166 (228)
T ss_pred             cccccccccccHHHHHHhcCchHHHHHHHH-ccCCcccccccCccchhhhhcccchhHHHHHHh-ccCcccccccccchh
Confidence            368889999999999999999999988888 799999999999999999999999999999998 799999999999999


Q ss_pred             HHHHHHcCCHH-HHHHHHh
Q psy630          327 LDYAKAIEHTD-LIEYLVN  344 (347)
Q Consensus       327 Lh~A~~~~~~~-~v~~Ll~  344 (347)
                      ||+||.+.+.. .+.+||.
T Consensus       167 Lhlaa~~rn~r~t~~~Ll~  185 (228)
T KOG0512|consen  167 LHLAAGNRNSRDTLELLLH  185 (228)
T ss_pred             hHHhhcccchHHHHHHHhh
Confidence            99999877644 4556654

>PHA02736 Viral ankyrin protein; Provisional

Probab=99.68  E-value=1e-16  Score=130.44  Aligned_cols=97  Identities=14%  Similarity=0.124  Sum_probs=86.8

Q ss_pred             ccCCCCCcHHHHHHcCChH---HHHHHHhhcCCCCccccCC-CCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          250 QLDDNEKNIYEWAKEGKLD---MLVKQLTKLKDFNINQLDE-NGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       250 ~~~~~~~~~l~~a~~~~~~---~~~~lL~~~~~~~~~~~d~-~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      ..+..|.|+||+|+..+..   +++++|+. .|++++.++. .|.||||+|+..++.+++++|+.+.|++++.+|..|.|
T Consensus        50 ~~d~~g~t~Lh~a~~~~~~~~~e~v~~Ll~-~gadin~~~~~~g~T~Lh~A~~~~~~~i~~~Ll~~~g~d~n~~~~~g~t  128 (154)
T PHA02736         50 EYNRHGKQCVHIVSNPDKADPQEKLKLLME-WGADINGKERVFGNTPLHIAVYTQNYELATWLCNQPGVNMEILNYAFKT  128 (154)
T ss_pred             HhcCCCCEEEEeecccCchhHHHHHHHHHH-cCCCccccCCCCCCcHHHHHHHhCCHHHHHHHHhCCCCCCccccCCCCC
Confidence            3467899999999887764   45677777 7999999984 99999999999999999999997359999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|+..|+.+++++|+++||
T Consensus       129 pL~~A~~~~~~~i~~~Ll~~ga  150 (154)
T PHA02736        129 PYYVACERHDAKMMNILRAKGA  150 (154)
T ss_pred             HHHHHHHcCCHHHHHHHHHcCC
Confidence            9999999999999999999997

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.68  E-value=2.7e-16  Score=150.69  Aligned_cols=122  Identities=14%  Similarity=0.142  Sum_probs=99.8

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc---CCCccCCccccccCC
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST---DSHVLEGSRLSIQPS   84 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~---~~~~~~g~~l~v~~~   84 (347)
                      .+.|||+|||+++++++|+++|++||.|.+|.++++      +|||||+|.+.++|+.|+..   ++..+.|++|.|.++
T Consensus         2 s~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s   75 (481)
T TIGR01649         2 SPVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYS   75 (481)
T ss_pred             ccEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEec
Confidence            578999999999999999999999999999999853      57999999999999999973   789999999999988


Q ss_pred             Cccc-ccchhh----hhhcccccccccCCcccccchhhHHHHhhccccceecccCC
Q psy630           85 DSHN-RMAENM----EDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus        85 ~~~~-~~~~~~----~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                      ..+. .+....    ...-....++|.||+..+++++|.++|+.||.|....+..+
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~  131 (481)
T TIGR01649        76 TSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTK  131 (481)
T ss_pred             CCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEec
Confidence            6542 111100    00011246899999999999999999999999987766443

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).

>PHA02791 ankyrin-like protein; Provisional

Probab=99.67  E-value=3.3e-16  Score=139.04  Aligned_cols=91  Identities=16%  Similarity=0.205  Sum_probs=84.1

Q ss_pred             CCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCC-cHHHHHHH
Q psy630          254 NEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGD-YGLDYAKA  332 (347)
Q Consensus       254 ~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~-TpLh~A~~  332 (347)
                      .+.||||+|+..+..+++++|+. .|++++.+|..|+||||+||..|+.+++++|+. +|++++.++..|+ ||||+|+.
T Consensus        60 d~~TpLh~Aa~~g~~eiV~lLL~-~Gadvn~~d~~G~TpLh~Aa~~g~~eivk~Ll~-~gadin~~~~~g~~TpL~~Aa~  137 (284)
T PHA02791         60 ENEFPLHQAATLEDTKIVKILLF-SGMDDSQFDDKGNTALYYAVDSGNMQTVKLFVK-KNWRLMFYGKTGWKTSFYHAVM  137 (284)
T ss_pred             CCCCHHHHHHHCCCHHHHHHHHH-CCCCCCCCCCCCCCHHHHHHHcCCHHHHHHHHH-CCCCcCccCCCCCcHHHHHHHH
Confidence            46899999999889999999988 799999999999999999999999999999998 7999999998885 89999999


Q ss_pred             cCCHHHHHHHHhCC
Q psy630          333 IEHTDLIEYLVNSG  346 (347)
Q Consensus       333 ~~~~~~v~~Ll~~G  346 (347)
                      .|+.++|++|+++|
T Consensus       138 ~g~~eivk~LL~~~  151 (284)
T PHA02791        138 LNDVSIVSYFLSEI  151 (284)
T ss_pred             cCCHHHHHHHHhcC
Confidence            99999999999876

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.67  E-value=1.6e-16  Score=154.26  Aligned_cols=166  Identities=16%  Similarity=0.239  Sum_probs=117.8

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ...++|||+|||+.+++++|+++|++||.|..+.+++++.+|.++|||||+|.+.+.|..|+.. ++..+.|+.|.|.++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            3457999999999999999999999999999999999999999999999999999999999974 999999999999877


Q ss_pred             Ccccccch---------------hhhh------hcccccccccCCccc--c--------cchhhHHHHhhccccceeccc
Q psy630           85 DSHNRMAE---------------NMED------RFNQACDYLPSLVKK--L--------DSSTLLKFYALYKQATVGQCN  133 (347)
Q Consensus        85 ~~~~~~~~---------------~~~~------~f~~~~~~v~~l~~~--~--------~~e~l~~~f~~fg~v~~g~~~  133 (347)
                      ........               ....      .....++++.|+...  +        ..++|.++|+.||.|....+.
T Consensus       373 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~  452 (509)
T TIGR01642       373 CVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIP  452 (509)
T ss_pred             ccCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEee
Confidence            54221100               0000      012345677777532  1        125789999999999976665


Q ss_pred             CCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhhccCCh
Q psy630          134 IDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWED  179 (347)
Q Consensus       134 ~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~l~~~~~~  179 (347)
                      .+.+..-  .+..++.+|  +...+.++|.++    +..|...|..
T Consensus       453 ~~~~~~~--~~~~~G~~f--V~F~~~e~A~~A----~~~lnGr~~~  490 (509)
T TIGR01642       453 RPNGDRN--STPGVGKVF--LEYADVRSAEKA----MEGMNGRKFN  490 (509)
T ss_pred             ccCcCCC--cCCCcceEE--EEECCHHHHHHH----HHHcCCCEEC
Confidence            4322111  111223333  345567888777    4455554443

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.67  E-value=1.2e-16  Score=155.19  Aligned_cols=148  Identities=17%  Similarity=0.212  Sum_probs=107.1

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhcc------------CCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEY------------GQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSH   72 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~------------G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~   72 (347)
                      ....++|||||||+.+|+++|+++|.++            +.|..+.+      +..+|||||+|.+.++|..|+.+++.
T Consensus       172 ~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al~l~g~  245 (509)
T TIGR01642       172 TRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAMALDSI  245 (509)
T ss_pred             CccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhhcCCCe
Confidence            4567899999999999999999999875            23333333      45679999999999999999988999


Q ss_pred             ccCCccccccCCCcccccc--------hh--------------hhhhcccccccccCCcccccchhhHHHHhhcccccee
Q psy630           73 VLEGSRLSIQPSDSHNRMA--------EN--------------MEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVG  130 (347)
Q Consensus        73 ~~~g~~l~v~~~~~~~~~~--------~~--------------~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g  130 (347)
                      .+.|+.|.|.+........        ..              ....-...+|||+|||..+++++|.++|+.||.+...
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            9999999997543322000        00              0001123589999999999999999999999998866


Q ss_pred             cccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          131 QCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       131 ~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      .+..+..     .|..|+.||..+  .+.++|..+
T Consensus       326 ~~~~~~~-----~g~~~g~afv~f--~~~~~a~~A  353 (509)
T TIGR01642       326 NLIKDIA-----TGLSKGYAFCEY--KDPSVTDVA  353 (509)
T ss_pred             EEEecCC-----CCCcCeEEEEEE--CCHHHHHHH
Confidence            5544321     344555566554  445566555

Members of this subfamily are found in plants, metazoa and fungi.

>PHA02741 hypothetical protein; Provisional

Probab=99.67  E-value=3.7e-16  Score=129.08  Aligned_cols=100  Identities=19%  Similarity=0.228  Sum_probs=89.6

Q ss_pred             CCcccCCCCCcHHHHHHcCCh----HHHHHHHhhcCCCCccccCC-CCchHHHHHHHcCCHHHHHHHHhhcCCCccccCC
Q psy630          247 DESQLDDNEKNIYEWAKEGKL----DMLVKQLTKLKDFNINQLDE-NGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS  321 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~----~~~~~lL~~~~~~~~~~~d~-~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~  321 (347)
                      +.+..+..|.|+||+|+..+.    ..++++|.. .++++|.++. .|+||||+|+..++.+++++||...|++++.+|.
T Consensus        52 ~in~~d~~g~T~Lh~A~~~g~~~~~~~ii~~Ll~-~gadin~~~~~~g~TpLh~A~~~~~~~iv~~Ll~~~g~~~~~~n~  130 (169)
T PHA02741         52 ALNATDDAGQMCIHIAAEKHEAQLAAEIIDHLIE-LGADINAQEMLEGDTALHLAAHRRDHDLAEWLCCQPGIDLHFCNA  130 (169)
T ss_pred             hhhccCCCCCcHHHHHHHcCChHHHHHHHHHHHH-cCCCCCCCCcCCCCCHHHHHHHcCCHHHHHHHHhCCCCCCCcCCC
Confidence            456677889999999998776    467888888 7999999985 9999999999999999999999635999999999


Q ss_pred             CCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          322 DGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       322 ~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      .|+||||+|+..++.+++++|++.+|
T Consensus       131 ~g~tpL~~A~~~~~~~iv~~L~~~~~  156 (169)
T PHA02741        131 DNKSPFELAIDNEDVAMMQILREIVA  156 (169)
T ss_pred             CCCCHHHHHHHCCCHHHHHHHHHHHH
Confidence            99999999999999999999998754

>KOG0195|consensus

Probab=99.66  E-value=1.9e-16  Score=134.17  Aligned_cols=99  Identities=27%  Similarity=0.357  Sum_probs=93.7

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      |.|.-|+-|.++||+|+.+++..++++|+. .|+.+|..+....||||+|+.+||-++|+.||+ ..+|+|+.+..|+||
T Consensus        26 dln~gddhgfsplhwaakegh~aivemll~-rgarvn~tnmgddtplhlaaahghrdivqkll~-~kadvnavnehgntp  103 (448)
T KOG0195|consen   26 DLNVGDDHGFSPLHWAAKEGHVAIVEMLLS-RGARVNSTNMGDDTPLHLAAAHGHRDIVQKLLS-RKADVNAVNEHGNTP  103 (448)
T ss_pred             ccccccccCcchhhhhhhcccHHHHHHHHh-cccccccccCCCCcchhhhhhcccHHHHHHHHH-HhcccchhhccCCCc
Confidence            456667889999999999999999999999 899999999999999999999999999999999 699999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||||.-|...+++-|+..||
T Consensus       104 lhyacfwgydqiaedli~~ga  124 (448)
T KOG0195|consen  104 LHYACFWGYDQIAEDLISCGA  124 (448)
T ss_pred             hhhhhhhcHHHHHHHHHhccc
Confidence            999999999999999999997

>PHA02741 hypothetical protein; Provisional

Probab=99.65  E-value=7.2e-16  Score=127.38  Aligned_cols=98  Identities=27%  Similarity=0.467  Sum_probs=85.5

Q ss_pred             cccCCCCCcHHHHHHcCChHHHHHHHhhc-----CCCCccccCCCCchHHHHHHHcCC----HHHHHHHHhhcCCCcccc
Q psy630          249 SQLDDNEKNIYEWAKEGKLDMLVKQLTKL-----KDFNINQLDENGLNCLHWACDRGH----LKVVQHLIEKCGADVNVT  319 (347)
Q Consensus       249 ~~~~~~~~~~l~~a~~~~~~~~~~lL~~~-----~~~~~~~~d~~g~tpLh~A~~~g~----~~~v~~Ll~~~ga~i~~~  319 (347)
                      +..+..|.++||+|+..+..+++++|...     .+++++.+|..|+||||+|+..|+    .+++++|+. +|+++|.+
T Consensus        15 ~~~~~~g~t~Lh~Aa~~g~~~~v~~l~~~~~~~~~ga~in~~d~~g~T~Lh~A~~~g~~~~~~~ii~~Ll~-~gadin~~   93 (169)
T PHA02741         15 AEKNSEGENFFHEAARCGCFDIIARFTPFIRGDCHAAALNATDDAGQMCIHIAAEKHEAQLAAEIIDHLIE-LGADINAQ   93 (169)
T ss_pred             hccccCCCCHHHHHHHcCCHHHHHHHHHHhccchhhhhhhccCCCCCcHHHHHHHcCChHHHHHHHHHHHH-cCCCCCCC
Confidence            34567899999999988888888876431     367899999999999999999999    588999999 79999999


Q ss_pred             CC-CCCcHHHHHHHcCCHHHHHHHHh-CCC
Q psy630          320 DS-DGDYGLDYAKAIEHTDLIEYLVN-SGS  347 (347)
Q Consensus       320 d~-~g~TpLh~A~~~~~~~~v~~Ll~-~GA  347 (347)
                      +. .|+||||+|+..++.+++++|+. .|+
T Consensus        94 ~~~~g~TpLh~A~~~~~~~iv~~Ll~~~g~  123 (169)
T PHA02741         94 EMLEGDTALHLAAHRRDHDLAEWLCCQPGI  123 (169)
T ss_pred             CcCCCCCHHHHHHHcCCHHHHHHHHhCCCC
Confidence            86 89999999999999999999997 464

>KOG0124|consensus

Probab=99.65  E-value=8.6e-17  Score=139.55  Aligned_cols=123  Identities=18%  Similarity=0.446  Sum_probs=108.1

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCc
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~   86 (347)
                      +++||||.+.+...++.|+..|..||+|.+|.+..|+.|++.+|||||+|+-++.|+.|++. |+..++||.|+|.+.+.
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsN  192 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSN  192 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCC
Confidence            57899999999999999999999999999999999999999999999999999999999996 99999999999998766


Q ss_pred             ccccc------hhhhhhcccccccccCCcccccchhhHHHHhhccccceecc
Q psy630           87 HNRMA------ENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQC  132 (347)
Q Consensus        87 ~~~~~------~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~  132 (347)
                      ...-.      ++....|  .++||..+.+++++++++..|..||.+.....
T Consensus       193 mpQAQpiID~vqeeAk~f--nRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~L  242 (544)
T KOG0124|consen  193 MPQAQPIIDMVQEEAKKF--NRIYVASVHPDLSETDIKSVFEAFGEIVKCQL  242 (544)
T ss_pred             CcccchHHHHHHHHHHhh--heEEeeecCCCccHHHHHHHHHhhcceeeEEe
Confidence            44321      2222334  57899999999999999999999999984333

>KOG0512|consensus

Probab=99.65  E-value=3.6e-16  Score=122.92  Aligned_cols=89  Identities=25%  Similarity=0.330  Sum_probs=79.8

Q ss_pred             cHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCCH
Q psy630          257 NIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHT  336 (347)
Q Consensus       257 ~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~  336 (347)
                      .++-+|..+.+..+..+|.. ..-.+|.+|.+|.||||-|+.+||++||..|+. .||+++++...||||||.||.-++.
T Consensus        66 l~lwaae~nrl~eV~~lL~e-~an~vNtrD~D~YTpLHRAaYn~h~div~~ll~-~gAn~~a~T~~GWTPLhSAckWnN~  143 (228)
T KOG0512|consen   66 LLLWAAEKNRLTEVQRLLSE-KANHVNTRDEDEYTPLHRAAYNGHLDIVHELLL-SGANKEAKTNEGWTPLHSACKWNNF  143 (228)
T ss_pred             HHHHHHhhccHHHHHHHHHh-ccccccccccccccHHHHHHhcCchHHHHHHHH-ccCCcccccccCccchhhhhcccch
Confidence            44555666777777777766 677799999999999999999999999999998 7999999999999999999999999


Q ss_pred             HHHHHHHhCCC
Q psy630          337 DLIEYLVNSGS  347 (347)
Q Consensus       337 ~~v~~Ll~~GA  347 (347)
                      +++-.||++||
T Consensus       144 ~va~~LLqhga  154 (228)
T KOG0512|consen  144 EVAGRLLQHGA  154 (228)
T ss_pred             hHHHHHHhccC
Confidence            99999999997

>PHA02791 ankyrin-like protein; Provisional

Probab=99.64  E-value=1.2e-15  Score=135.57  Aligned_cols=98  Identities=17%  Similarity=0.163  Sum_probs=87.8

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCc-hHHHHHHHcCCHHHHHHHHhhcCCCccccC-CCC
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGL-NCLHWACDRGHLKVVQHLIEKCGADVNVTD-SDG  323 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~-tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d-~~g  323 (347)
                      .+.+..+..|.|+||+|+..+..+++++|+. .+++++.++..|+ ||||+|+..|+.+++++||+ .+.+.  .| ..|
T Consensus        85 advn~~d~~G~TpLh~Aa~~g~~eivk~Ll~-~gadin~~~~~g~~TpL~~Aa~~g~~eivk~LL~-~~~~~--~d~~~g  160 (284)
T PHA02791         85 MDDSQFDDKGNTALYYAVDSGNMQTVKLFVK-KNWRLMFYGKTGWKTSFYHAVMLNDVSIVSYFLS-EIPST--FDLAIL  160 (284)
T ss_pred             CCCCCCCCCCCCHHHHHHHcCCHHHHHHHHH-CCCCcCccCCCCCcHHHHHHHHcCCHHHHHHHHh-cCCcc--cccccC
Confidence            4577788999999999999999999999999 8999999998885 99999999999999999998 56543  23 358


Q ss_pred             CcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          324 DYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       324 ~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      .||||+|+..|+.+++++||++||
T Consensus       161 ~TpLh~Aa~~g~~eiv~lLL~~gA  184 (284)
T PHA02791        161 LSCIHITIKNGHVDMMILLLDYMT  184 (284)
T ss_pred             ccHHHHHHHcCCHHHHHHHHHCCC
Confidence            999999999999999999999997

>KOG0127|consensus

Probab=99.64  E-value=4.9e-16  Score=141.43  Aligned_cols=126  Identities=24%  Similarity=0.406  Sum_probs=108.7

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCcc
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDSH   87 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~~   87 (347)
                      .||||++||++++.++|.++|+.+|+|..+.++.++.++.++||+||+|.-.+++++|+.. ++..|.|+.|.|..+..+
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            6899999999999999999999999999999999999999999999999999999999987 999999999999987664


Q ss_pred             cccc-----------------hhhhh--hcccccccccCCcccccchhhHHHHhhccccceecccC
Q psy630           88 NRMA-----------------ENMED--RFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNI  134 (347)
Q Consensus        88 ~~~~-----------------~~~~~--~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~  134 (347)
                      .+..                 .+...  ......+.|+|||..+.+.+|..+|+.||.|....++.
T Consensus        86 ~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~  151 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPR  151 (678)
T ss_pred             ccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEccc
Confidence            4321                 00111  11246789999999999999999999999998766664

>KOG4214|consensus

Probab=99.64  E-value=5.6e-16  Score=109.05  Aligned_cols=82  Identities=29%  Similarity=0.483  Sum_probs=74.0

Q ss_pred             HHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCCHHHHHH
Q psy630          262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEY  341 (347)
Q Consensus       262 a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~~~v~~  341 (347)
                      ...|..+++.+....  +.++|..- .|++|||||+..|.++++.+|+. .||+|+.+|..|-|||..|+..||.+||++
T Consensus        10 vkNG~~DeVk~~v~~--g~nVn~~~-ggR~plhyAAD~GQl~ilefli~-iGA~i~~kDKygITPLLsAvwEGH~~cVkl   85 (117)
T KOG4214|consen   10 VKNGEIDEVKQSVNE--GLNVNEIY-GGRTPLHYAADYGQLSILEFLIS-IGANIQDKDKYGITPLLSAVWEGHRDCVKL   85 (117)
T ss_pred             hccCcHHHHHHHHHc--cccHHHHh-CCcccchHhhhcchHHHHHHHHH-hccccCCccccCCcHHHHHHHHhhHHHHHH
Confidence            345667777777776  78887764 89999999999999999999999 699999999999999999999999999999


Q ss_pred             HHhCCC
Q psy630          342 LVNSGS  347 (347)
Q Consensus       342 Ll~~GA  347 (347)
                      ||++||
T Consensus        86 LL~~GA   91 (117)
T KOG4214|consen   86 LLQNGA   91 (117)
T ss_pred             HHHcCc
Confidence            999997

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.63  E-value=1e-15  Score=146.70  Aligned_cols=146  Identities=16%  Similarity=0.160  Sum_probs=107.9

Q ss_pred             CCCeEEEeCCCC-CCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            7 QLNKIFVGNLPW-TVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         7 ~~~~l~V~nLp~-~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ..++|||+|||+ .+|+++|+++|+.||.|..|+|++++     +|||||+|.+.++|..|+.. |+..+.|++|.|.++
T Consensus       274 ~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s  348 (481)
T TIGR01649       274 PGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPS  348 (481)
T ss_pred             CCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            557999999998 69999999999999999999999863     59999999999999999985 999999999999876


Q ss_pred             Ccccccc-----------------hhhhhh-------------cccccccccCCcccccchhhHHHHhhccc--cceecc
Q psy630           85 DSHNRMA-----------------ENMEDR-------------FNQACDYLPSLVKKLDSSTLLKFYALYKQ--ATVGQC  132 (347)
Q Consensus        85 ~~~~~~~-----------------~~~~~~-------------f~~~~~~v~~l~~~~~~e~l~~~f~~fg~--v~~g~~  132 (347)
                      .......                 ......             ....++||+|||..+++++|+++|+.||.  ++...+
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            4321100                 000000             12357999999999999999999999998  443333


Q ss_pred             cCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          133 NIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       133 ~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ...+.+       .+..|+  ++..+.++|.++.
T Consensus       429 ~~~~~~-------~~~~gf--VeF~~~e~A~~Al  453 (481)
T TIGR01649       429 FPKDNE-------RSKMGL--LEWESVEDAVEAL  453 (481)
T ss_pred             ecCCCC-------cceeEE--EEcCCHHHHHHHH
Confidence            222211       122233  3345677777763

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=99.63  E-value=3.1e-16  Score=142.72  Aligned_cols=153  Identities=18%  Similarity=0.328  Sum_probs=120.1

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCcc
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDSH   87 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~~   87 (347)
                      -+|.|+|||+.+...+|+.+|+.||.|..|.|++.+. |+-+|||||.|....+|..|++. |++.|.||+|.|.||-++
T Consensus       118 ~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~d-gklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~K  196 (678)
T KOG0127|consen  118 WRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKD-GKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDK  196 (678)
T ss_pred             ceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCC-CCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeeccc
Confidence            4699999999999999999999999999999998776 55569999999999999999996 999999999999987653


Q ss_pred             cccc------------------------------------------hhhhh-----------------------------
Q psy630           88 NRMA------------------------------------------ENMED-----------------------------   96 (347)
Q Consensus        88 ~~~~------------------------------------------~~~~~-----------------------------   96 (347)
                      ....                                          +..+.                             
T Consensus       197 d~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~  276 (678)
T KOG0127|consen  197 DTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKES  276 (678)
T ss_pred             ccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccCcc
Confidence            3100                                          00000                             


Q ss_pred             ------------hcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHH
Q psy630           97 ------------RFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMS  164 (347)
Q Consensus        97 ------------~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~  164 (347)
                                  .-...++||+|||.++++++|.+.|+.||.+....+-..+.     .+++|+-||..+..   +.|.+
T Consensus       277 ~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~-----T~~skGtAFv~Fkt---~~~~~  348 (678)
T KOG0127|consen  277 DKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKD-----TGHSKGTAFVKFKT---QIAAQ  348 (678)
T ss_pred             cchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccC-----CCCcccceEEEecc---HHHHH
Confidence                        00015789999999999999999999999998877766543     77888888886543   33334


Q ss_pred             HHHHHH
Q psy630          165 KYIALL  170 (347)
Q Consensus       165 ~yi~~~  170 (347)
                      ..|+.+
T Consensus       349 ~ci~~A  354 (678)
T KOG0127|consen  349 NCIEAA  354 (678)
T ss_pred             HHHHhc
Confidence            444443

>PHA02875 ankyrin repeat protein; Provisional

Probab=99.63  E-value=1.6e-15  Score=143.49  Aligned_cols=100  Identities=17%  Similarity=0.210  Sum_probs=79.0

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCC-C
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDG-D  324 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g-~  324 (347)
                      .+++..+..|.||||+|+..+..+++++|+. .+++++.+|..|.||||+|+..|+.+++++|++ .|++++..+..| .
T Consensus       126 ad~~~~~~~g~tpLh~A~~~~~~~~v~~Ll~-~g~~~~~~d~~g~TpL~~A~~~g~~eiv~~Ll~-~ga~~n~~~~~~~~  203 (413)
T PHA02875        126 ADPDIPNTDKFSPLHLAVMMGDIKGIELLID-HKACLDIEDCCGCTPLIIAMAKGDIAICKMLLD-SGANIDYFGKNGCV  203 (413)
T ss_pred             CCCCCCCCCCCCHHHHHHHcCCHHHHHHHHh-cCCCCCCCCCCCCCHHHHHHHcCCHHHHHHHHh-CCCCCCcCCCCCCc
Confidence            3566677778888888887777777777777 678888888888888888888888888888887 688888877766 4


Q ss_pred             cHHHHHHHcCCHHHHHHHHhCCC
Q psy630          325 YGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       325 TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||||+|+..|+.+++++|+++||
T Consensus       204 t~l~~A~~~~~~~iv~~Ll~~ga  226 (413)
T PHA02875        204 AALCYAIENNKIDIVRLFIKRGA  226 (413)
T ss_pred             hHHHHHHHcCCHHHHHHHHHCCc
Confidence            77888888888888888888876

>PHA02795 ankyrin-like protein; Provisional

Probab=99.62  E-value=1.7e-15  Score=139.94  Aligned_cols=92  Identities=28%  Similarity=0.222  Sum_probs=86.9

Q ss_pred             CCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHc
Q psy630          254 NEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAI  333 (347)
Q Consensus       254 ~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~  333 (347)
                      .+.+++|.|..++..+++++|.. +|+++|.+|..|.||||+|+..|+.+++++|++ +|+++|.+|..|.||||+|+..
T Consensus       187 ~~~t~l~~a~~~~~~eIve~LIs-~GADIN~kD~~G~TpLh~Aa~~g~~eiVelLL~-~GAdIN~~d~~G~TpLh~Aa~~  264 (437)
T PHA02795        187 IQYTRGFLVDEPTVLEIYKLCIP-YIEDINQLDAGGRTLLYRAIYAGYIDLVSWLLE-NGANVNAVMSNGYTCLDVAVDR  264 (437)
T ss_pred             hccchhHHHHhcCHHHHHHHHHh-CcCCcCcCCCCCCCHHHHHHHcCCHHHHHHHHH-CCCCCCCcCCCCCCHHHHHHHc
Confidence            46689999999999999999999 899999999999999999999999999999999 7999999999999999999998


Q ss_pred             C--------CHHHHHHHHhCCC
Q psy630          334 E--------HTDLIEYLVNSGS  347 (347)
Q Consensus       334 ~--------~~~~v~~Ll~~GA  347 (347)
                      |        +.+++++|+++||
T Consensus       265 g~~~~~~~~~~eIvelLL~~ga  286 (437)
T PHA02795        265 GSVIARRETHLKILEILLREPL  286 (437)
T ss_pred             CCcccccccHHHHHHHHHhCCC
Confidence            8        4699999999986

>PHA02878 ankyrin repeat protein; Provisional

Probab=99.62  E-value=2e-15  Score=145.22  Aligned_cols=99  Identities=24%  Similarity=0.307  Sum_probs=67.6

Q ss_pred             CCcccCCC-CCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          247 DESQLDDN-EKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       247 ~~~~~~~~-~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      +.+..+.. |.||||+|+..+..+++++|+. .|++++.+|..|.||||+|+..++.+++++|++ .|++++.+|..|.|
T Consensus       159 din~~~~~~g~tpLh~A~~~~~~~iv~~Ll~-~gad~n~~d~~g~tpLh~A~~~~~~~iv~~Ll~-~ga~in~~d~~g~T  236 (477)
T PHA02878        159 DINMKDRHKGNTALHYATENKDQRLTELLLS-YGANVNIPDKTNNSPLHHAVKHYNKPIVHILLE-NGASTDARDKCGNT  236 (477)
T ss_pred             CCCccCCCCCCCHHHHHHhCCCHHHHHHHHH-CCCCCCCcCCCCCCHHHHHHHhCCHHHHHHHHH-cCCCCCCCCCCCCC
Confidence            44555555 6677777776666666666666 667777777777777777777777777777776 57777777777777


Q ss_pred             HHHHHHHc-CCHHHHHHHHhCCC
Q psy630          326 GLDYAKAI-EHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~-~~~~~v~~Ll~~GA  347 (347)
                      |||+|+.. ++.+++++|+++||
T Consensus       237 pLh~A~~~~~~~~iv~~Ll~~ga  259 (477)
T PHA02878        237 PLHISVGYCKDYDILKLLLEHGV  259 (477)
T ss_pred             HHHHHHHhcCCHHHHHHHHHcCC
Confidence            77777653 56677777777664

>PHA02874 ankyrin repeat protein; Provisional

Probab=99.61  E-value=2.8e-15  Score=142.57  Aligned_cols=100  Identities=25%  Similarity=0.304  Sum_probs=90.9

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      .+.+..+..|.|+||+|+..+..+++++|++ .|++++.+|..|.||||+|+..++.+++++|++ .|++++.+|..|.|
T Consensus       115 ~d~n~~~~~g~T~Lh~A~~~~~~~~v~~Ll~-~gad~n~~d~~g~tpLh~A~~~~~~~iv~~Ll~-~g~~~n~~~~~g~t  192 (434)
T PHA02874        115 IDVNIKDAELKTFLHYAIKKGDLESIKMLFE-YGADVNIEDDNGCYPIHIAIKHNFFDIIKLLLE-KGAYANVKDNNGES  192 (434)
T ss_pred             CCCCCCCCCCccHHHHHHHCCCHHHHHHHHh-CCCCCCCcCCCCCCHHHHHHHCCcHHHHHHHHH-CCCCCCCCCCCCCC
Confidence            3566677889999999999888889999888 799999999999999999999999999999998 79999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|+..|+.+++++|+++||
T Consensus       193 pL~~A~~~g~~~iv~~Ll~~g~  214 (434)
T PHA02874        193 PLHNAAEYGDYACIKLLIDHGN  214 (434)
T ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Confidence            9999999999999999999885

>PHA02859 ankyrin repeat protein; Provisional

Probab=99.61  E-value=4.1e-15  Score=127.04  Aligned_cols=100  Identities=21%  Similarity=0.191  Sum_probs=85.9

Q ss_pred             cCCcccC-CCCCcHHHHHHcC---ChHHHHHHHhhcCCCCccccCCCCchHHHHHHH--cCCHHHHHHHHhhcCCCcccc
Q psy630          246 NDESQLD-DNEKNIYEWAKEG---KLDMLVKQLTKLKDFNINQLDENGLNCLHWACD--RGHLKVVQHLIEKCGADVNVT  319 (347)
Q Consensus       246 ~~~~~~~-~~~~~~l~~a~~~---~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~--~g~~~~v~~Ll~~~ga~i~~~  319 (347)
                      .+.+..+ ..+.|+||.|+..   ...+++++|++ .|+++|.+|..|.||||+|+.  .++.+++++|++ +|++++.+
T Consensus        77 advn~~~~~~g~TpLh~a~~~~~~~~~eiv~~Ll~-~gadin~~d~~G~TpLh~a~~~~~~~~~iv~~Li~-~gadin~~  154 (209)
T PHA02859         77 ADVNFKTRDNNLSALHHYLSFNKNVEPEILKILID-SGSSITEEDEDGKNLLHMYMCNFNVRINVIKLLID-SGVSFLNK  154 (209)
T ss_pred             CCCCccCCCCCCCHHHHHHHhCccccHHHHHHHHH-CCCCCCCcCCCCCCHHHHHHHhccCCHHHHHHHHH-cCCCcccc
Confidence            3566665 4789999986542   35788898888 899999999999999999876  468999999999 79999999


Q ss_pred             CCCCCcHHHH-HHHcCCHHHHHHHHhCCC
Q psy630          320 DSDGDYGLDY-AKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       320 d~~g~TpLh~-A~~~~~~~~v~~Ll~~GA  347 (347)
                      |..|.||||. |+..++.+++++|+++||
T Consensus       155 d~~g~t~Lh~~a~~~~~~~iv~~Ll~~Ga  183 (209)
T PHA02859        155 DFDNNNILYSYILFHSDKKIFDFLTSLGI  183 (209)
T ss_pred             cCCCCcHHHHHHHhcCCHHHHHHHHHcCC
Confidence            9999999995 567889999999999986

>PHA02884 ankyrin repeat protein; Provisional

Probab=99.61  E-value=4.2e-15  Score=132.16  Aligned_cols=89  Identities=20%  Similarity=0.119  Sum_probs=48.4

Q ss_pred             cHHHHHHcCChHHHHHHHhhcCCCCccccC----CCCchHHHHHHHcCCHHHHHHHHhhcCCCcccc-CCCCCcHHHHHH
Q psy630          257 NIYEWAKEGKLDMLVKQLTKLKDFNINQLD----ENGLNCLHWACDRGHLKVVQHLIEKCGADVNVT-DSDGDYGLDYAK  331 (347)
Q Consensus       257 ~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d----~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~-d~~g~TpLh~A~  331 (347)
                      ++|++|+..+..+++++|++ .|+++|.++    ..|.||||+|+..++.+++++|++ +||++|.+ +..|.||||+|+
T Consensus        35 ~lL~~A~~~~~~eivk~LL~-~GAdiN~~~~~sd~~g~TpLh~Aa~~~~~eivklLL~-~GADVN~~~~~~g~TpLh~Aa  112 (300)
T PHA02884         35 NILYSSIKFHYTDIIDAILK-LGADPEAPFPLSENSKTNPLIYAIDCDNDDAAKLLIR-YGADVNRYAEEAKITPLYISV  112 (300)
T ss_pred             HHHHHHHHcCCHHHHHHHHH-CCCCccccCcccCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCcCcccCCCCCCHHHHHH
Confidence            44455555555555555555 455555542    355555555555555555555555 45555554 234555555555


Q ss_pred             HcCCHHHHHHHHhCCC
Q psy630          332 AIEHTDLIEYLVNSGS  347 (347)
Q Consensus       332 ~~~~~~~v~~Ll~~GA  347 (347)
                      ..++.+++++|+.+||
T Consensus       113 ~~~~~eivklLL~~GA  128 (300)
T PHA02884        113 LHGCLKCLEILLSYGA  128 (300)
T ss_pred             HcCCHHHHHHHHHCCC
Confidence            5555555555555554

>PHA02859 ankyrin repeat protein; Provisional

Probab=99.61  E-value=5.4e-15  Score=126.33  Aligned_cols=98  Identities=20%  Similarity=0.228  Sum_probs=85.4

Q ss_pred             CcccCCCCCcHHHHHHcCC--hHHHHHHHhhcCCCCccccC-CCCchHHHHHHHc---CCHHHHHHHHhhcCCCccccCC
Q psy630          248 ESQLDDNEKNIYEWAKEGK--LDMLVKQLTKLKDFNINQLD-ENGLNCLHWACDR---GHLKVVQHLIEKCGADVNVTDS  321 (347)
Q Consensus       248 ~~~~~~~~~~~l~~a~~~~--~~~~~~lL~~~~~~~~~~~d-~~g~tpLh~A~~~---g~~~~v~~Ll~~~ga~i~~~d~  321 (347)
                      .+..+..|.||||+|+..+  ..+++++|++ .|+++|.++ ..|+||||+|+..   ++.+++++|++ +|+++|.+|.
T Consensus        44 ~n~~~~~g~TpLh~a~~~~~~~~eiv~~Ll~-~gadvn~~~~~~g~TpLh~a~~~~~~~~~eiv~~Ll~-~gadin~~d~  121 (209)
T PHA02859         44 VNDCNDLYETPIFSCLEKDKVNVEILKFLIE-NGADVNFKTRDNNLSALHHYLSFNKNVEPEILKILID-SGSSITEEDE  121 (209)
T ss_pred             hhccCccCCCHHHHHHHcCCCCHHHHHHHHH-CCCCCCccCCCCCCCHHHHHHHhCccccHHHHHHHHH-CCCCCCCcCC
Confidence            3456778999999998643  6788999998 899999997 4899999998764   47999999999 7999999999


Q ss_pred             CCCcHHHHHHH--cCCHHHHHHHHhCCC
Q psy630          322 DGDYGLDYAKA--IEHTDLIEYLVNSGS  347 (347)
Q Consensus       322 ~g~TpLh~A~~--~~~~~~v~~Ll~~GA  347 (347)
                      .|.||||+|+.  .++.+++++|+++||
T Consensus       122 ~G~TpLh~a~~~~~~~~~iv~~Li~~ga  149 (209)
T PHA02859        122 DGKNLLHMYMCNFNVRINVIKLLIDSGV  149 (209)
T ss_pred             CCCCHHHHHHHhccCCHHHHHHHHHcCC
Confidence            99999999986  468999999999986

>KOG0117|consensus

Probab=99.61  E-value=2.2e-15  Score=134.29  Aligned_cols=124  Identities=16%  Similarity=0.269  Sum_probs=100.3

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCe-eEEEEeeeC-CCCCceeEEEEEEcCHHHHHHHHhc---CCCccCCcccc
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQI-MNASVMFDK-NTGLSKGFGFVTFQNKEAVDKVFST---DSHVLEGSRLS   80 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i-~~~~i~~~~-~t~~~~g~afV~f~~~~~a~~a~~~---~~~~~~g~~l~   80 (347)
                      ...++|||||||.+.++++|.+.|++.++- ..|-+..++ +..++||||||+|.+...|..|.+.   ....+.|+.+.
T Consensus       162 van~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~klwgn~~t  241 (506)
T KOG0117|consen  162 VANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIKLWGNAIT  241 (506)
T ss_pred             eecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCceeecCCcce
Confidence            356799999999999999999999998764 445444333 3467999999999999999888863   56678899999


Q ss_pred             ccCCCcccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceec
Q psy630           81 IQPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQ  131 (347)
Q Consensus        81 v~~~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~  131 (347)
                      |.||.+..........  .-..+||+||+..+|+|.|+++|+.||.++.+.
T Consensus       242 VdWAep~~e~ded~ms--~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVk  290 (506)
T KOG0117|consen  242 VDWAEPEEEPDEDTMS--KVKVLYVRNLMESTTEETLKKLFNEFGKVERVK  290 (506)
T ss_pred             eeccCcccCCChhhhh--heeeeeeeccchhhhHHHHHHHHHhccceEEee
Confidence            9999997765443322  236789999999999999999999999987433

>PF00076 RRM_1: RNA recognition motif

Probab=99.60  E-value=4.3e-15  Score=103.78  Aligned_cols=69  Identities=36%  Similarity=0.764  Sum_probs=65.1

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCcccc
Q psy630           11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLS   80 (347)
Q Consensus        11 l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~   80 (347)
                      |||+|||+++++++|+++|++||.|..+.++.+ .++.++|||||+|.+.++|++|+. +++..+.|+.|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999998 579999999999999999999999 499999998874

(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 ....

>KOG0509|consensus

Probab=99.60  E-value=2.4e-15  Score=140.40  Aligned_cols=100  Identities=24%  Similarity=0.325  Sum_probs=88.0

Q ss_pred             cCCcccC-CCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCC
Q psy630          246 NDESQLD-DNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGD  324 (347)
Q Consensus       246 ~~~~~~~-~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~  324 (347)
                      .++|... ..+.||||||+..++..++.+|++ +|++++.+|.+|.||||+||..||..++.+||. .|+++|.+|.+|+
T Consensus       102 advn~~gG~l~stPLHWAar~G~~~vv~lLlq-hGAdpt~~D~~G~~~lHla~~~~~~~~vayll~-~~~d~d~~D~~gr  179 (600)
T KOG0509|consen  102 ADVNAIGGVLGSTPLHWAARNGHISVVDLLLQ-HGADPTLKDKQGLTPLHLAAQFGHTALVAYLLS-KGADIDLRDNNGR  179 (600)
T ss_pred             CCccccCCCCCCCcchHHHHcCcHHHHHHHHH-cCCCCceecCCCCcHHHHHHHhCchHHHHHHHH-hcccCCCcCCCCC
Confidence            3567666 567899999999999999999999 899999999999999999999999999999998 5999999999999


Q ss_pred             cHHHHHHHcCCHHHHHHHHhCCC
Q psy630          325 YGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       325 TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||||||+..|+...+..||..||
T Consensus       180 TpLmwAaykg~~~~v~~LL~f~a  202 (600)
T KOG0509|consen  180 TPLMWAAYKGFALFVRRLLKFGA  202 (600)
T ss_pred             CHHHHHHHhcccHHHHHHHHhcc
Confidence            99999999998887888888775

>PLN03192 Voltage-dependent potassium channel; Provisional

Probab=99.60  E-value=4.4e-15  Score=151.37  Aligned_cols=103  Identities=25%  Similarity=0.314  Sum_probs=90.8

Q ss_pred             ecccCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCC---------------------
Q psy630          243 SMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGH---------------------  301 (347)
Q Consensus       243 ~~~~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~---------------------  301 (347)
                      ....+.+..|..|.|+||.|+..++.+++++|++ .|+++|.+|..|.||||+|+..||                     
T Consensus       546 ~~G~d~n~~d~~G~TpLh~Aa~~g~~~~v~~Ll~-~gadin~~d~~G~TpL~~A~~~g~~~iv~~L~~~~~~~~~~~~~~  624 (823)
T PLN03192        546 KAKLDPDIGDSKGRTPLHIAASKGYEDCVLVLLK-HACNVHIRDANGNTALWNAISAKHHKIFRILYHFASISDPHAAGD  624 (823)
T ss_pred             HCCCCCCCCCCCCCCHHHHHHHcChHHHHHHHHh-cCCCCCCcCCCCCCHHHHHHHhCCHHHHHHHHhcCcccCcccCch
Confidence            3445688889999999999999999999999999 899999999999999886655554                     


Q ss_pred             ----------HHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          302 ----------LKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       302 ----------~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                                .+++++|++ +|+++|.+|..|+||||+|+..|+.+++++|+++||
T Consensus       625 ~L~~Aa~~g~~~~v~~Ll~-~Gadin~~d~~G~TpLh~A~~~g~~~iv~~Ll~~GA  679 (823)
T PLN03192        625 LLCTAAKRNDLTAMKELLK-QGLNVDSEDHQGATALQVAMAEDHVDMVRLLIMNGA  679 (823)
T ss_pred             HHHHHHHhCCHHHHHHHHH-CCCCCCCCCCCCCCHHHHHHHCCcHHHHHHHHHcCC
Confidence                      555666777 799999999999999999999999999999999997

>PHA02743 Viral ankyrin protein; Provisional

Probab=99.59  E-value=4e-15  Score=122.44  Aligned_cols=97  Identities=21%  Similarity=0.414  Sum_probs=77.9

Q ss_pred             cccCCCCC-cHHHHHHcCChHHHH---HHHhhcCCCCccccCCCCchHHHHHHHcCCHHH---HHHHHhhcCCCccccC-
Q psy630          249 SQLDDNEK-NIYEWAKEGKLDMLV---KQLTKLKDFNINQLDENGLNCLHWACDRGHLKV---VQHLIEKCGADVNVTD-  320 (347)
Q Consensus       249 ~~~~~~~~-~~l~~a~~~~~~~~~---~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~---v~~Ll~~~ga~i~~~d-  320 (347)
                      +..+..+. +++++|+.|+...+.   ++|.. .+..++.+|..|+||||+||.+|+.++   +++|+. .|+++|.+| 
T Consensus        14 ~~~~~~~~~~l~~a~~~g~~~~l~~~~~~l~~-~g~~~~~~d~~g~t~Lh~Aa~~g~~~~~~~i~~Ll~-~Gadin~~d~   91 (166)
T PHA02743         14 VEIDEDEQNTFLRICRTGNIYELMEVAPFISG-DGHLLHRYDHHGRQCTHMVAWYDRANAVMKIELLVN-MGADINAREL   91 (166)
T ss_pred             hhhccCCCcHHHHHHHcCCHHHHHHHHHHHhh-cchhhhccCCCCCcHHHHHHHhCccCHHHHHHHHHH-cCCCCCCCCC
Confidence            33444444 555566777775444   45555 688899999999999999999988654   789998 799999998 


Q ss_pred             CCCCcHHHHHHHcCCHHHHHHHHh-CCC
Q psy630          321 SDGDYGLDYAKAIEHTDLIEYLVN-SGS  347 (347)
Q Consensus       321 ~~g~TpLh~A~~~~~~~~v~~Ll~-~GA  347 (347)
                      ..|.||||+|+..++.+++++|+. .||
T Consensus        92 ~~g~TpLh~A~~~g~~~iv~~Ll~~~ga  119 (166)
T PHA02743         92 GTGNTLLHIAASTKNYELAEWLCRQLGV  119 (166)
T ss_pred             CCCCcHHHHHHHhCCHHHHHHHHhccCC
Confidence            589999999999999999999995 675

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.59  E-value=4.3e-15  Score=142.13  Aligned_cols=143  Identities=15%  Similarity=0.248  Sum_probs=106.5

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCC-eeEEEE-eeeCCCCCceeEEEEEEcCHHHHHHHHhc---CCCccCCccccc
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQ-IMNASV-MFDKNTGLSKGFGFVTFQNKEAVDKVFST---DSHVLEGSRLSI   81 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~-i~~~~i-~~~~~t~~~~g~afV~f~~~~~a~~a~~~---~~~~~~g~~l~v   81 (347)
                      +.++|||+|||+++++++|.+.|++++. +..+.+ .....+++++|||||+|.+.++|..|++.   ....+.|+.|.|
T Consensus       137 ~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~V  216 (578)
T TIGR01648       137 DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAV  216 (578)
T ss_pred             cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEE
Confidence            4678999999999999999999999864 333333 33344578899999999999999999974   345688999999


Q ss_pred             cCCCcccccchhhhhhcccccccccCCcccccchhhHHHHhhc--cccceecccCCCCCccchhHHHHHHHHHHcCCCCH
Q psy630           82 QPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALY--KQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAK  159 (347)
Q Consensus        82 ~~~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~f--g~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~  159 (347)
                      .++.+........  .-...+|||+||+..+++++|+++|+.|  |.|....+.  +           ..||  +...+.
T Consensus       217 dwA~p~~~~d~~~--~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--r-----------gfAF--VeF~s~  279 (578)
T TIGR01648       217 DWAEPEEEVDEDV--MAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--R-----------DYAF--VHFEDR  279 (578)
T ss_pred             Eeecccccccccc--cccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--c-----------CeEE--EEeCCH
Confidence            9987754322111  1223689999999999999999999999  888754322  1           1233  345567


Q ss_pred             HHHHHHH
Q psy630          160 SEAMSKY  166 (347)
Q Consensus       160 ~eA~~~y  166 (347)
                      ++|.++.
T Consensus       280 e~A~kAi  286 (578)
T TIGR01648       280 EDAVKAM  286 (578)
T ss_pred             HHHHHHH
Confidence            8887763

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.

>KOG4205|consensus

Probab=99.59  E-value=2.2e-15  Score=133.09  Aligned_cols=129  Identities=25%  Similarity=0.494  Sum_probs=112.1

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSD   85 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~   85 (347)
                      .+.+++||++|+++++++.|+++|.+||.|..|.+++|+.+++++||+||+|.+.+....++....+.+.|+.|.+.++-
T Consensus         4 ~~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    4 GESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAV   83 (311)
T ss_pred             cCCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceecc
Confidence            47789999999999999999999999999999999999999999999999999999999999888899999999999988


Q ss_pred             cccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCC
Q psy630           86 SHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus        86 ~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                      ++....... ......++||+.+|..+++++++++|..||.|....+..+
T Consensus        84 ~r~~~~~~~-~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d  132 (311)
T KOG4205|consen   84 SREDQTKVG-RHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYD  132 (311)
T ss_pred             Ccccccccc-cccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeec
Confidence            765432221 1113468999999999999999999999997776555554

>KOG0502|consensus

Probab=99.59  E-value=1.8e-15  Score=123.43  Aligned_cols=99  Identities=26%  Similarity=0.267  Sum_probs=94.7

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      ..|..|..|.|+|.||+..++..++++|++ .|++++...+...|+|.+|+..|..+||++||. .+.|||.-|.+|-||
T Consensus       152 ~VN~~De~GfTpLiWAaa~G~i~vV~fLL~-~GAdp~~lgk~resALsLAt~ggytdiV~lLL~-r~vdVNvyDwNGgTp  229 (296)
T KOG0502|consen  152 KVNACDEFGFTPLIWAAAKGHIPVVQFLLN-SGADPDALGKYRESALSLATRGGYTDIVELLLT-REVDVNVYDWNGGTP  229 (296)
T ss_pred             cccCccccCchHhHHHHhcCchHHHHHHHH-cCCChhhhhhhhhhhHhHHhcCChHHHHHHHHh-cCCCcceeccCCCce
Confidence            468899999999999999999999999999 899999999999999999999999999999999 699999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |-||++.||.+||+.||..||
T Consensus       230 LlyAvrgnhvkcve~Ll~sGA  250 (296)
T KOG0502|consen  230 LLYAVRGNHVKCVESLLNSGA  250 (296)
T ss_pred             eeeeecCChHHHHHHHHhcCC
Confidence            999999999999999999997

>KOG0105|consensus

Probab=99.58  E-value=4.7e-15  Score=117.29  Aligned_cols=135  Identities=18%  Similarity=0.234  Sum_probs=107.9

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      .+..++|||+|||.++.+.+|+++|-+||.|..|.+...   ....+||||+|++..+|+.|+.- ++-.++|..|+|.+
T Consensus         3 gr~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEf   79 (241)
T KOG0105|consen    3 GRNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEF   79 (241)
T ss_pred             CcccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEe
Confidence            466789999999999999999999999999999987432   34568999999999999999986 99999999999997


Q ss_pred             CCcccccc-------------------hhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccch
Q psy630           84 SDSHNRMA-------------------ENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNM  142 (347)
Q Consensus        84 ~~~~~~~~-------------------~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~  142 (347)
                      +.......                   .-....-....+.|.+||+..++.+|++.+..-|.|...++..+-.|..++
T Consensus        80 prggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rDg~GvV~~  157 (241)
T KOG0105|consen   80 PRGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRDGVGVVEY  157 (241)
T ss_pred             ccCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecccceeeee
Confidence            75532100                   000111223578899999999999999999999999888887776555433

>PF13637 Ank_4: Ankyrin repeats (many copies); PDB: 3B95_A 3B7B_A 3F6Q_A 2KBX_A 3IXE_A 2DWZ_C 2DVW_A 3AJI_A 1S70_B 2HE0_A

Probab=99.58  E-value=3.8e-15  Score=98.37  Aligned_cols=54  Identities=41%  Similarity=0.760  Sum_probs=46.4

Q ss_pred             CchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCCHHHHHHHH
Q psy630          289 GLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLV  343 (347)
Q Consensus       289 g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~~~v~~Ll  343 (347)
                      |+||||+||..|+.+++++|++ .|+++|.+|.+|+||||+|+..|+.+++++||
T Consensus         1 g~t~lh~A~~~g~~~~~~~Ll~-~~~din~~d~~g~t~lh~A~~~g~~~~~~~Ll   54 (54)
T PF13637_consen    1 GRTPLHWAARSGNLEIVKLLLE-HGADINAQDEDGRTPLHYAAKNGNIDIVKFLL   54 (54)
T ss_dssp             SSBHHHHHHHTT-HHHHHHHHH-TTSGTT-B-TTS--HHHHHHHTT-HHHHHHHH
T ss_pred             CChHHHHHHHhCCHHHHHHHHH-CCCCCCCCCCCCCCHHHHHHHccCHHHHHHHC
Confidence            7899999999999999999999 69999999999999999999999999999996

...

>PHA02875 ankyrin repeat protein; Provisional

Probab=99.58  E-value=1.2e-14  Score=137.56  Aligned_cols=95  Identities=21%  Similarity=0.186  Sum_probs=90.1

Q ss_pred             cCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHH
Q psy630          251 LDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA  330 (347)
Q Consensus       251 ~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A  330 (347)
                      .+..|.||||+|+..+..+++++|++ .|++++.++..|.||||+|+..|+.+++++|++ +|++++.+|..|.||||+|
T Consensus        98 ~~~~g~tpL~~A~~~~~~~iv~~Ll~-~gad~~~~~~~g~tpLh~A~~~~~~~~v~~Ll~-~g~~~~~~d~~g~TpL~~A  175 (413)
T PHA02875         98 FYKDGMTPLHLATILKKLDIMKLLIA-RGADPDIPNTDKFSPLHLAVMMGDIKGIELLID-HKACLDIEDCCGCTPLIIA  175 (413)
T ss_pred             ccCCCCCHHHHHHHhCCHHHHHHHHh-CCCCCCCCCCCCCCHHHHHHHcCCHHHHHHHHh-cCCCCCCCCCCCCCHHHHH
Confidence            34568899999999999999999999 899999999999999999999999999999999 7999999999999999999


Q ss_pred             HHcCCHHHHHHHHhCCC
Q psy630          331 KAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       331 ~~~~~~~~v~~Ll~~GA  347 (347)
                      +..|+.+++++|+++||
T Consensus       176 ~~~g~~eiv~~Ll~~ga  192 (413)
T PHA02875        176 MAKGDIAICKMLLDSGA  192 (413)
T ss_pred             HHcCCHHHHHHHHhCCC
Confidence            99999999999999997

>PHA03095 ankyrin-like protein; Provisional

Probab=99.57  E-value=1e-14  Score=140.24  Aligned_cols=101  Identities=22%  Similarity=0.206  Sum_probs=90.8

Q ss_pred             ccCCcccCCCCCcHHHHHHcCChH--HHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCC
Q psy630          245 INDESQLDDNEKNIYEWAKEGKLD--MLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSD  322 (347)
Q Consensus       245 ~~~~~~~~~~~~~~l~~a~~~~~~--~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~  322 (347)
                      ..+++..+..|.||||+|+..+..  .++.+|.. .++++|.+|..|+||||+|+..|+.+++++||+ .|++++.+|..
T Consensus       212 g~~~~~~d~~g~tpLh~Aa~~~~~~~~~v~~ll~-~g~din~~d~~g~TpLh~A~~~~~~~~v~~LL~-~gad~n~~~~~  289 (471)
T PHA03095        212 GCDPAATDMLGNTPLHSMATGSSCKRSLVLPLLI-AGISINARNRYGQTPLHYAAVFNNPRACRRLIA-LGADINAVSSD  289 (471)
T ss_pred             CCCCcccCCCCCCHHHHHHhcCCchHHHHHHHHH-cCCCCCCcCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCcccCCC
Confidence            346788899999999999877653  45566666 699999999999999999999999999999999 79999999999


Q ss_pred             CCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          323 GDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       323 g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |.||||+|+..|+.+++++||++|+
T Consensus       290 g~tpl~~A~~~~~~~~v~~LL~~~~  314 (471)
T PHA03095        290 GNTPLSLMVRNNNGRAVRAALAKNP  314 (471)
T ss_pred             CCCHHHHHHHhCCHHHHHHHHHhCC
Confidence            9999999999999999999999875

>PHA02798 ankyrin-like protein; Provisional

Probab=99.57  E-value=1.1e-14  Score=140.58  Aligned_cols=102  Identities=24%  Similarity=0.297  Sum_probs=83.3

Q ss_pred             cccCCcccCCCCCcHHHHHHcC-----ChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcC---CHHHHHHHHhhcCCC
Q psy630          244 MINDESQLDDNEKNIYEWAKEG-----KLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRG---HLKVVQHLIEKCGAD  315 (347)
Q Consensus       244 ~~~~~~~~~~~~~~~l~~a~~~-----~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g---~~~~v~~Ll~~~ga~  315 (347)
                      ...+++..+..|.||||.++.+     +...++++|++ .|+++|.+|..|+||||+|+.++   +.+++++|++ .|++
T Consensus        60 ~Gadvn~~d~~g~TpL~~~~~n~~~~~~~~~iv~~Ll~-~GadiN~~d~~G~TpLh~a~~~~~~~~~~iv~~Ll~-~Gad  137 (489)
T PHA02798         60 LGANVNGLDNEYSTPLCTILSNIKDYKHMLDIVKILIE-NGADINKKNSDGETPLYCLLSNGYINNLEILLFMIE-NGAD  137 (489)
T ss_pred             CCCCCCCCCCCCCChHHHHHHhHHhHHhHHHHHHHHHH-CCCCCCCCCCCcCcHHHHHHHcCCcChHHHHHHHHH-cCCC
Confidence            3346777778888888887653     45678888888 78888888888899999888875   6788888888 6899


Q ss_pred             ccccCCCCCcHHHHHHHcCC---HHHHHHHHhCCC
Q psy630          316 VNVTDSDGDYGLDYAKAIEH---TDLIEYLVNSGS  347 (347)
Q Consensus       316 i~~~d~~g~TpLh~A~~~~~---~~~v~~Ll~~GA  347 (347)
                      ++.+|..|.||||+|+..++   .+++++|+++||
T Consensus       138 vn~~d~~g~tpL~~a~~~~~~~~~~vv~~Ll~~ga  172 (489)
T PHA02798        138 TTLLDKDGFTMLQVYLQSNHHIDIEIIKLLLEKGV  172 (489)
T ss_pred             ccccCCCCCcHHHHHHHcCCcchHHHHHHHHHhCC
Confidence            98888889999998888887   888888888885

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.56  E-value=3.5e-14  Score=136.03  Aligned_cols=78  Identities=29%  Similarity=0.640  Sum_probs=74.1

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      .++|||+|||+.+++++|+++|++||.|..|.+++++.+|+++|||||+|.+.++|.+|+.. ++..+.|++|.|.++.
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            57999999999999999999999999999999999999999999999999999999999984 9999999999999854

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.

>KOG0515|consensus

Probab=99.56  E-value=8.3e-15  Score=133.24  Aligned_cols=87  Identities=34%  Similarity=0.507  Sum_probs=78.7

Q ss_pred             HHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCCHH
Q psy630          258 IYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTD  337 (347)
Q Consensus       258 ~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~~  337 (347)
                      +|.+|..|.++.+.+.+-+  --|+...+..|.|+||-|+..||.+||+|||. +|++||+.|++||||||.|+.|++..
T Consensus       554 LLDaaLeGEldlVq~~i~e--v~DpSqpNdEGITaLHNAiCaghyeIVkFLi~-~ganVNa~DSdGWTPLHCAASCNnv~  630 (752)
T KOG0515|consen  554 LLDAALEGELDLVQRIIYE--VTDPSQPNDEGITALHNAICAGHYEIVKFLIE-FGANVNAADSDGWTPLHCAASCNNVP  630 (752)
T ss_pred             HHhhhhcchHHHHHHHHHh--hcCCCCCCccchhHHhhhhhcchhHHHHHHHh-cCCcccCccCCCCchhhhhhhcCchH
Confidence            5567778888766666655  56788899999999999999999999999999 89999999999999999999999999


Q ss_pred             HHHHHHhCCC
Q psy630          338 LIEYLVNSGS  347 (347)
Q Consensus       338 ~v~~Ll~~GA  347 (347)
                      +++.|++.||
T Consensus       631 ~ckqLVe~Ga  640 (752)
T KOG0515|consen  631 MCKQLVESGA  640 (752)
T ss_pred             HHHHHHhccc
Confidence            9999999997

>PF13857 Ank_5: Ankyrin repeats (many copies); PDB: 1SW6_A 3EHR_B 3EHQ_A

Probab=99.56  E-value=3.5e-15  Score=99.12  Aligned_cols=51  Identities=43%  Similarity=0.677  Sum_probs=33.8

Q ss_pred             CCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHH
Q psy630          279 DFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA  330 (347)
Q Consensus       279 ~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A  330 (347)
                      ..+++.+|..|.||||+||..|+.+++++||+ .|++++.+|..|+||||+|
T Consensus         6 ~~~~n~~d~~G~T~LH~A~~~g~~~~v~~Ll~-~g~d~~~~d~~G~Tpl~~A   56 (56)
T PF13857_consen    6 PADVNAQDKYGNTPLHWAARYGHSEVVRLLLQ-NGADPNAKDKDGQTPLHYA   56 (56)
T ss_dssp             T--TT---TTS--HHHHHHHHT-HHHHHHHHH-CT--TT---TTS--HHHH-
T ss_pred             cCCCcCcCCCCCcHHHHHHHcCcHHHHHHHHH-CcCCCCCCcCCCCCHHHhC
Confidence            48999999999999999999999999999997 8999999999999999997

>KOG0123|consensus

Probab=99.56  E-value=6.8e-15  Score=134.56  Aligned_cols=129  Identities=22%  Similarity=0.335  Sum_probs=111.8

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCcc
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDSH   87 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~~   87 (347)
                      ..||||   +++|+..|.+.|+++|+++++++.+|. |  +-|||||.|.++.+|.+|+.. |...+.|++++|.++...
T Consensus         2 ~sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd   75 (369)
T KOG0123|consen    2 ASLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD   75 (369)
T ss_pred             CceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC
Confidence            468999   999999999999999999999999998 6  999999999999999999986 999999999999998765


Q ss_pred             cccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           88 NRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        88 ~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...            +||.||++.++...|.++|+.||+|.+.++.++..|       +|+. |..  .-+.++|.++
T Consensus        76 ~~~------------~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g-------~kg~-FV~--f~~e~~a~~a  131 (369)
T KOG0123|consen   76 PSL------------VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG-------SKGY-FVQ--FESEESAKKA  131 (369)
T ss_pred             Cce------------eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC-------ceee-EEE--eCCHHHHHHH
Confidence            542            899999999999999999999999999888888776       4554 443  3345555444

>PHA03095 ankyrin-like protein; Provisional

Probab=99.56  E-value=1.6e-14  Score=138.97  Aligned_cols=99  Identities=23%  Similarity=0.193  Sum_probs=58.7

Q ss_pred             CCcccCCCCCcHHHHHHcCC-hHHHHHHHhhcCCCCccccCCCCchHHHHHH--HcCCHHHHHHHHhhcCCCccccCCCC
Q psy630          247 DESQLDDNEKNIYEWAKEGK-LDMLVKQLTKLKDFNINQLDENGLNCLHWAC--DRGHLKVVQHLIEKCGADVNVTDSDG  323 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~-~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~--~~g~~~~v~~Ll~~~ga~i~~~d~~g  323 (347)
                      +.+..+..|.||||+|+..+ ...++++|.+ .|++++.+|..|.||||+|+  .+++.+++++|++ .|++++.+|..|
T Consensus        75 din~~~~~g~TpLh~A~~~~~~~~iv~lLl~-~ga~in~~~~~g~tpLh~a~~~~~~~~~iv~~Ll~-~gad~~~~d~~g  152 (471)
T PHA03095         75 DVNAPERCGFTPLHLYLYNATTLDVIKLLIK-AGADVNAKDKVGRTPLHVYLSGFNINPKVIRLLLR-KGADVNALDLYG  152 (471)
T ss_pred             CCCCCCCCCCCHHHHHHHcCCcHHHHHHHHH-cCCCCCCCCCCCCCHHHHHhhCCcCCHHHHHHHHH-cCCCCCccCCCC
Confidence            45555556666666655555 3556666665 56666666666666666666  3445566666665 466666666666


Q ss_pred             CcHHHHHHHcC--CHHHHHHHHhCCC
Q psy630          324 DYGLDYAKAIE--HTDLIEYLVNSGS  347 (347)
Q Consensus       324 ~TpLh~A~~~~--~~~~v~~Ll~~GA  347 (347)
                      .||||+|+..+  +.+++++|+++||
T Consensus       153 ~tpL~~a~~~~~~~~~iv~~Ll~~g~  178 (471)
T PHA03095        153 MTPLAVLLKSRNANVELLRLLIDAGA  178 (471)
T ss_pred             CCHHHHHHHcCCCCHHHHHHHHHcCC
Confidence            66666665544  4556666666654

>KOG0110|consensus

Probab=99.56  E-value=7.2e-15  Score=138.01  Aligned_cols=155  Identities=20%  Similarity=0.332  Sum_probs=117.6

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCC---CCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNT---GLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t---~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ++|||.||++++|.+.+..+|..+|.|.++.|..-+.-   -.|.|||||+|.+.++|+.|++. +|+.++|+.|.|+.+
T Consensus       516 t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S  595 (725)
T KOG0110|consen  516 TKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKIS  595 (725)
T ss_pred             hhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEec
Confidence            44999999999999999999999999999998765431   23569999999999999999996 999999999999887


Q ss_pred             Cccccc--chhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHH
Q psy630           85 DSHNRM--AENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEA  162 (347)
Q Consensus        85 ~~~~~~--~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA  162 (347)
                      ..+..-  .......-....|.|+|+|..++-.+++++|+.||++...  +.|+-   -..+..++.+|  +..+++.||
T Consensus       596 ~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksv--RlPKK---~~k~a~rGF~F--v~f~t~~ea  668 (725)
T KOG0110|consen  596 ENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSV--RLPKK---IGKGAHRGFGF--VDFLTPREA  668 (725)
T ss_pred             cCccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeee--ccchh---hcchhhcccee--eeccCcHHH
Confidence            722110  0111111124589999999999999999999999999854  44432   01222233344  458899999


Q ss_pred             HHHHHHHH
Q psy630          163 MSKYIALL  170 (347)
Q Consensus       163 ~~~yi~~~  170 (347)
                      .+++-.+.
T Consensus       669 ~nA~~al~  676 (725)
T KOG0110|consen  669 KNAFDALG  676 (725)
T ss_pred             HHHHHhhc
Confidence            99985554

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.55  E-value=1.6e-14  Score=123.05  Aligned_cols=77  Identities=17%  Similarity=0.381  Sum_probs=71.7

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCCcc
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDSH   87 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~~~   87 (347)
                      .++|||+|||+.+++++|+++|+.||.|..|.|++++.   ++|||||+|.+.++|..|+.+++..+.|+.|.|.++...
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEeccCC
Confidence            57999999999999999999999999999999998863   579999999999999999988999999999999987654

>KOG0145|consensus

Probab=99.55  E-value=7.4e-15  Score=122.20  Aligned_cols=145  Identities=21%  Similarity=0.426  Sum_probs=112.8

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCC--cccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEG--SRLS   80 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g--~~l~   80 (347)
                      +.-...+|||++||..+|..+|+.+|++||.|...+|+.|..||.++|++||.|+.+.+|+.|+.. ||..-.|  .+|.
T Consensus       123 ~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepIt  202 (360)
T KOG0145|consen  123 DSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPIT  202 (360)
T ss_pred             hhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeE
Confidence            334456899999999999999999999999999999999999999999999999999999999985 8888766  4788


Q ss_pred             ccCCCcccccc--------------------hhh---------------hhhcc---------------------ccccc
Q psy630           81 IQPSDSHNRMA--------------------ENM---------------EDRFN---------------------QACDY  104 (347)
Q Consensus        81 v~~~~~~~~~~--------------------~~~---------------~~~f~---------------------~~~~~  104 (347)
                      |+++.......                    ...               ...|.                     .-++|
T Consensus       203 VKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciF  282 (360)
T KOG0145|consen  203 VKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCIF  282 (360)
T ss_pred             EEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCeeEEE
Confidence            87765532110                    000               00111                     13789


Q ss_pred             ccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHH
Q psy630          105 LPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNS  153 (347)
Q Consensus       105 v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~  153 (347)
                      |=||.++.++.-|.++|++||-|+..++..+-.     ..+.|+.+|..
T Consensus       283 vYNLspd~de~~LWQlFgpFGAv~nVKvirD~t-----tnkCKGfgFVt  326 (360)
T KOG0145|consen  283 VYNLSPDADESILWQLFGPFGAVTNVKVIRDFT-----TNKCKGFGFVT  326 (360)
T ss_pred             EEecCCCchHhHHHHHhCcccceeeEEEEecCC-----cccccceeEEE
Confidence            999999999999999999999999888766532     23445555554

>KOG0121|consensus

Probab=99.55  E-value=8.2e-15  Score=109.01  Aligned_cols=82  Identities=20%  Similarity=0.414  Sum_probs=76.3

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      ..+..++||||||++.++|++|.++|+++|.|..|.+-.|+.+..+.|||||+|.+.++|..|++. +++.++.++|+|.
T Consensus        32 a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D  111 (153)
T KOG0121|consen   32 ALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRID  111 (153)
T ss_pred             HHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeee
Confidence            346778999999999999999999999999999999989999899999999999999999999997 9999999999997


Q ss_pred             CCC
Q psy630           83 PSD   85 (347)
Q Consensus        83 ~~~   85 (347)
                      +--
T Consensus       112 ~D~  114 (153)
T KOG0121|consen  112 WDA  114 (153)
T ss_pred             ccc
Confidence            653

>PHA02946 ankyin-like protein; Provisional

Probab=99.55  E-value=3e-14  Score=135.28  Aligned_cols=102  Identities=17%  Similarity=0.155  Sum_probs=88.9

Q ss_pred             ecccCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCC--HHHHHHHHhhcCCCccc-c
Q psy630          243 SMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGH--LKVVQHLIEKCGADVNV-T  319 (347)
Q Consensus       243 ~~~~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~--~~~v~~Ll~~~ga~i~~-~  319 (347)
                      +...+++..+..|.||||+|+..+..+++++|+. .|+++|.+|..|+||||+|+..++  .+++++|++ .|+++|. .
T Consensus        60 ~~Gadvn~~d~~G~TpLh~Aa~~g~~eiv~lLL~-~GAdin~~d~~g~TpLh~A~~~~~~~~e~v~lLl~-~Gadin~~~  137 (446)
T PHA02946         60 HRGYSPNETDDDGNYPLHIASKINNNRIVAMLLT-HGADPNACDKQHKTPLYYLSGTDDEVIERINLLVQ-YGAKINNSV  137 (446)
T ss_pred             HCcCCCCccCCCCCCHHHHHHHcCCHHHHHHHHH-CcCCCCCCCCCCCCHHHHHHHcCCchHHHHHHHHH-cCCCccccc
Confidence            3445688889999999999999999999999998 799999999999999999987664  788999998 7999995 6


Q ss_pred             CCCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          320 DSDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       320 d~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |..|.|||| ||..++.+++++|+++||
T Consensus       138 d~~g~tpL~-aa~~~~~~vv~~Ll~~ga  164 (446)
T PHA02946        138 DEEGCGPLL-ACTDPSERVFKKIMSIGF  164 (446)
T ss_pred             CCCCCcHHH-HHHCCChHHHHHHHhccc
Confidence            889999997 666789999999999886

>KOG0125|consensus

Probab=99.55  E-value=8.1e-15  Score=125.87  Aligned_cols=85  Identities=26%  Similarity=0.604  Sum_probs=77.1

Q ss_pred             CccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccc
Q psy630            2 SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLS   80 (347)
Q Consensus         2 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~   80 (347)
                      +++....++|+|+|||+...+.||+.+|++||.|.+|.|+.+.  .-||||+||+|++.++|++|.+. +|.++.||+|.
T Consensus        90 s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIE  167 (376)
T KOG0125|consen   90 SSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIE  167 (376)
T ss_pred             CCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEE
Confidence            4556677899999999999999999999999999999999875  45899999999999999999986 99999999999


Q ss_pred             ccCCCccc
Q psy630           81 IQPSDSHN   88 (347)
Q Consensus        81 v~~~~~~~   88 (347)
                      |..+..+-
T Consensus       168 Vn~ATarV  175 (376)
T KOG0125|consen  168 VNNATARV  175 (376)
T ss_pred             Eeccchhh
Confidence            99887753

>KOG0109|consensus

Probab=99.54  E-value=7.7e-15  Score=124.06  Aligned_cols=108  Identities=20%  Similarity=0.438  Sum_probs=97.1

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccCCCcc
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQPSDSH   87 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~~~~~   87 (347)
                      -+|||||||..+++.+|+.+|++||+|++|.|+++        ||||..++...+..|+. +++-.++|..|.|.-+.++
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            36999999999999999999999999999999865        99999999999999999 5999999999999888776


Q ss_pred             cccchhhhhhcccccccccCCcccccchhhHHHHhhccccceeccc
Q psy630           88 NRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCN  133 (347)
Q Consensus        88 ~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~  133 (347)
                      +.         ...+++|+|+.+..+..+++..|..||.+.+-++.
T Consensus        75 sk---------~stkl~vgNis~tctn~ElRa~fe~ygpviecdiv  111 (346)
T KOG0109|consen   75 SK---------ASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIV  111 (346)
T ss_pred             CC---------CccccccCCCCccccCHHHhhhhcccCCceeeeee
Confidence            43         34678999999999999999999999999865543

>PHA03100 ankyrin repeat protein; Provisional

Probab=99.54  E-value=2.6e-14  Score=137.74  Aligned_cols=100  Identities=25%  Similarity=0.364  Sum_probs=94.1

Q ss_pred             cCCcccCCCCCcHHHHHH--cCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcC--CHHHHHHHHhhcCCCccccCC
Q psy630          246 NDESQLDDNEKNIYEWAK--EGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRG--HLKVVQHLIEKCGADVNVTDS  321 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~--~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g--~~~~v~~Ll~~~ga~i~~~d~  321 (347)
                      .+.+..+..|.||||+|+  ..+..+++++|++ .|++++..+..|.||||+|+..+  +.+++++|++ .|++++.+|.
T Consensus        97 a~i~~~d~~g~tpL~~A~~~~~~~~~iv~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~~iv~~Ll~-~g~din~~d~  174 (480)
T PHA03100         97 ANVNAPDNNGITPLLYAISKKSNSYSIVEYLLD-NGANVNIKNSDGENLLHLYLESNKIDLKILKLLID-KGVDINAKNR  174 (480)
T ss_pred             CCCCCCCCCCCchhhHHHhcccChHHHHHHHHH-cCCCCCccCCCCCcHHHHHHHcCCChHHHHHHHHH-CCCCcccccC
Confidence            345667888999999999  9999999999999 89999999999999999999999  9999999999 7999999999


Q ss_pred             CCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          322 DGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       322 ~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      .|.||||+|+..|+.+++++|+++||
T Consensus       175 ~g~tpL~~A~~~~~~~iv~~Ll~~ga  200 (480)
T PHA03100        175 YGYTPLHIAVEKGNIDVIKFLLDNGA  200 (480)
T ss_pred             CCCCHHHHHHHhCCHHHHHHHHHcCC
Confidence            99999999999999999999999986

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.54  E-value=3.2e-14  Score=99.46  Aligned_cols=69  Identities=28%  Similarity=0.705  Sum_probs=63.2

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccc
Q psy630           11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLS   80 (347)
Q Consensus        11 l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~   80 (347)
                      |||+|||+++++++|+++|+.||.|..+++..++. +.++|+|||+|.+.++|..|+.. ++..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999987 99999999999999999999997 77999998763

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 ....

>PHA02946 ankyin-like protein; Provisional

Probab=99.54  E-value=3.5e-14  Score=134.80  Aligned_cols=99  Identities=18%  Similarity=0.285  Sum_probs=83.7

Q ss_pred             cCCcccCCCCCcHHHHHHcCC--hHHHHHHHhhcCCCCccc-cCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCC
Q psy630          246 NDESQLDDNEKNIYEWAKEGK--LDMLVKQLTKLKDFNINQ-LDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSD  322 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~--~~~~~~lL~~~~~~~~~~-~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~  322 (347)
                      .+++..|..|.||||+|+..+  ..+++++|+. .|++++. .|..|.|||| ||..++.+++++|++ .|++++.+|..
T Consensus        96 Adin~~d~~g~TpLh~A~~~~~~~~e~v~lLl~-~Gadin~~~d~~g~tpL~-aa~~~~~~vv~~Ll~-~gad~~~~d~~  172 (446)
T PHA02946         96 ADPNACDKQHKTPLYYLSGTDDEVIERINLLVQ-YGAKINNSVDEEGCGPLL-ACTDPSERVFKKIMS-IGFEARIVDKF  172 (446)
T ss_pred             CCCCCCCCCCCCHHHHHHHcCCchHHHHHHHHH-cCCCcccccCCCCCcHHH-HHHCCChHHHHHHHh-ccccccccCCC
Confidence            467888899999999887654  3567888888 7999985 6889999997 666789999999998 79999999999


Q ss_pred             CCcHHHHHHHcCC--HHHHHHHHhCCC
Q psy630          323 GDYGLDYAKAIEH--TDLIEYLVNSGS  347 (347)
Q Consensus       323 g~TpLh~A~~~~~--~~~v~~Ll~~GA  347 (347)
                      |+||||+|+..++  .+++++|+++||
T Consensus       173 G~t~Lh~A~~~~~~~~~~v~~Ll~~Ga  199 (446)
T PHA02946        173 GKNHIHRHLMSDNPKASTISWMMKLGI  199 (446)
T ss_pred             CCCHHHHHHHhcCCCHHHHHHHHHcCC
Confidence            9999999887554  689999999986

>PHA03100 ankyrin repeat protein; Provisional

Probab=99.53  E-value=3.5e-14  Score=136.92  Aligned_cols=99  Identities=24%  Similarity=0.255  Sum_probs=91.3

Q ss_pred             CCcccCCCC------CcHHHHHHcCCh--HHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccc
Q psy630          247 DESQLDDNE------KNIYEWAKEGKL--DMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNV  318 (347)
Q Consensus       247 ~~~~~~~~~------~~~l~~a~~~~~--~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~  318 (347)
                      +.+..+..+      .+++|.|+..+.  ..++++|+. .|+++|.+|..|.||||+|+..|+.+++++|++ .|++++.
T Consensus       201 ~~~~~~~~~~~~~~~~t~l~~a~~~~~~~~~iv~~Ll~-~g~din~~d~~g~TpL~~A~~~~~~~iv~~Ll~-~gad~n~  278 (480)
T PHA03100        201 DINAGDIETLLFTIFETPLHIAACYNEITLEVVNYLLS-YGVPINIKDVYGFTPLHYAVYNNNPEFVKYLLD-LGANPNL  278 (480)
T ss_pred             CccCCCCCCCcHHHHHhHHHHHHHhCcCcHHHHHHHHH-cCCCCCCCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCc
Confidence            455555566      899999998888  889999999 799999999999999999999999999999999 7999999


Q ss_pred             cCCCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          319 TDSDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       319 ~d~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      +|..|.||||+|+..++.+++++|+++||
T Consensus       279 ~d~~g~tpl~~A~~~~~~~iv~~Ll~~g~  307 (480)
T PHA03100        279 VNKYGDTPLHIAILNNNKEIFKLLLNNGP  307 (480)
T ss_pred             cCCCCCcHHHHHHHhCCHHHHHHHHhcCC
Confidence            99999999999999999999999999996

>KOG0123|consensus

Probab=99.53  E-value=2.1e-14  Score=131.40  Aligned_cols=130  Identities=23%  Similarity=0.415  Sum_probs=112.0

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ++...|||.||+++++...|.++|+.||.|++|++.++.. | ++|| ||.|.+.++|.+|+.. ||..+.|++|.|...
T Consensus        74 rd~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~  150 (369)
T KOG0123|consen   74 RDPSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLF  150 (369)
T ss_pred             cCCceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeec
Confidence            3445599999999999999999999999999999999975 6 9999 9999999999999997 999999999999988


Q ss_pred             Ccccccchhhhh-hcccccccccCCcccccchhhHHHHhhccccceecccCCCCC
Q psy630           85 DSHNRMAENMED-RFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPS  138 (347)
Q Consensus        85 ~~~~~~~~~~~~-~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~  138 (347)
                      ..+..+..+... .-....++|.+.+.+.+++.+..+|+.||.++...+..+..+
T Consensus       151 ~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g  205 (369)
T KOG0123|consen  151 ERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIG  205 (369)
T ss_pred             cchhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCC
Confidence            887665544333 222367899999999999999999999999998888776543

>PHA02878 ankyrin repeat protein; Provisional

Probab=99.52  E-value=4.7e-14  Score=135.77  Aligned_cols=99  Identities=19%  Similarity=0.210  Sum_probs=87.3

Q ss_pred             ccCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHc-CCHHHHHHHHhhcCCCccccCC-C
Q psy630          245 INDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDR-GHLKVVQHLIEKCGADVNVTDS-D  322 (347)
Q Consensus       245 ~~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~-g~~~~v~~Ll~~~ga~i~~~d~-~  322 (347)
                      ..+.+..+..|.||||.|+..+...++++|+. .|++++.+|..|.||||+|+.. ++.+++++|++ +|+++|.++. .
T Consensus       191 gad~n~~d~~g~tpLh~A~~~~~~~iv~~Ll~-~ga~in~~d~~g~TpLh~A~~~~~~~~iv~~Ll~-~gadvn~~~~~~  268 (477)
T PHA02878        191 GANVNIPDKTNNSPLHHAVKHYNKPIVHILLE-NGASTDARDKCGNTPLHISVGYCKDYDILKLLLE-HGVDVNAKSYIL  268 (477)
T ss_pred             CCCCCCcCCCCCCHHHHHHHhCCHHHHHHHHH-cCCCCCCCCCCCCCHHHHHHHhcCCHHHHHHHHH-cCCCCCccCCCC
Confidence            34677788889999999998888889999998 8999999999999999999975 68999999998 6999999886 7


Q ss_pred             CCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          323 GDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       323 g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |.||||+|  .++.+++++|+++||
T Consensus       269 g~TpLh~A--~~~~~~v~~Ll~~ga  291 (477)
T PHA02878        269 GLTALHSS--IKSERKLKLLLEYGA  291 (477)
T ss_pred             CCCHHHHH--ccCHHHHHHHHHCCC
Confidence            99999999  567899999999987

>KOG0122|consensus

Probab=99.52  E-value=3.5e-14  Score=117.35  Aligned_cols=82  Identities=27%  Similarity=0.458  Sum_probs=77.3

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      .+..+|-|.|||.++++.+|+++|.+||.|..+.+.+|+.||.++|||||.|.+.+.|.+|+.. ||.-++.-.|+|.++
T Consensus       187 ~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEws  266 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWS  266 (270)
T ss_pred             CccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEec
Confidence            4567899999999999999999999999999999999999999999999999999999999985 999999999999998


Q ss_pred             Ccc
Q psy630           85 DSH   87 (347)
Q Consensus        85 ~~~   87 (347)
                      .|+
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            764

>PHA02884 ankyrin repeat protein; Provisional

Probab=99.52  E-value=6.8e-14  Score=124.45  Aligned_cols=88  Identities=23%  Similarity=0.247  Sum_probs=78.6

Q ss_pred             CCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccC-CCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHH
Q psy630          252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLD-ENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA  330 (347)
Q Consensus       252 ~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d-~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A  330 (347)
                      +..|.||||+|+..+..+++++|+. .|+++|.++ ..|.||||+|+..++.+++++|+. +|++++.+|..|.||||+|
T Consensus        67 d~~g~TpLh~Aa~~~~~eivklLL~-~GADVN~~~~~~g~TpLh~Aa~~~~~eivklLL~-~GAdin~kd~~G~TpL~~A  144 (300)
T PHA02884         67 ENSKTNPLIYAIDCDNDDAAKLLIR-YGADVNRYAEEAKITPLYISVLHGCLKCLEILLS-YGADINIQTNDMVTPIELA  144 (300)
T ss_pred             CCCCCCHHHHHHHcCCHHHHHHHHH-cCCCcCcccCCCCCCHHHHHHHcCCHHHHHHHHH-CCCCCCCCCCCCCCHHHHH
Confidence            3578999999999999999999999 899999964 589999999999999999999999 7999999999999999999


Q ss_pred             HHcCCHHHHHH
Q psy630          331 KAIEHTDLIEY  341 (347)
Q Consensus       331 ~~~~~~~~v~~  341 (347)
                      +..++..++.+
T Consensus       145 ~~~~~~~~~~~  155 (300)
T PHA02884        145 LMICNNFLAFM  155 (300)
T ss_pred             HHhCChhHHHH
Confidence            98665554433

>KOG0510|consensus

Probab=99.51  E-value=3.6e-14  Score=135.46  Aligned_cols=127  Identities=24%  Similarity=0.278  Sum_probs=99.3

Q ss_pred             ccccccCCCccccCCCCCcc----ceeecccCCcccCCCCCcHHHHHHcCCh-HHHHHHHhhcCCCCccccCCCCchHHH
Q psy630          220 WDESQESGSKENEGQTKGWV----NVSSMINDESQLDDNEKNIYEWAKEGKL-DMLVKQLTKLKDFNINQLDENGLNCLH  294 (347)
Q Consensus       220 ~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~l~~a~~~~~-~~~~~lL~~~~~~~~~~~d~~g~tpLh  294 (347)
                      .+++...-.+......+|..    .+.....+.+....++.+|||.|+.++. ..+.++|.......+|..|-.|+||||
T Consensus       267 ~~~d~dg~tpLH~a~r~G~~~svd~Ll~~Ga~I~~kn~d~~spLH~AA~yg~~ntv~rLL~~~~~rllne~D~~g~tpLH  346 (929)
T KOG0510|consen  267 NDEDNDGCTPLHYAARQGGPESVDNLLGFGASINSKNKDEESPLHFAAIYGRINTVERLLQESDTRLLNESDLHGMTPLH  346 (929)
T ss_pred             hcccccCCchHHHHHHcCChhHHHHHHHcCCcccccCCCCCCchHHHHHcccHHHHHHHHhCcCccccccccccCCCchh
Confidence            44444445555556666653    2334445778888889999998776655 455555553455678999999999999


Q ss_pred             HHHHcCCHHHHHHHHhhcCCCcc---ccCCCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          295 WACDRGHLKVVQHLIEKCGADVN---VTDSDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       295 ~A~~~g~~~~v~~Ll~~~ga~i~---~~d~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      +|+..||..++++||+ .||+.+   ..|.+|.||||.|+..|+..+|++|+.+||
T Consensus       347 laa~~gH~~v~qlLl~-~GA~~~~~~e~D~dg~TaLH~Aa~~g~~~av~~Li~~Ga  401 (929)
T KOG0510|consen  347 LAAKSGHDRVVQLLLN-KGALFLNMSEADSDGNTALHLAAKYGNTSAVQKLISHGA  401 (929)
T ss_pred             hhhhcCHHHHHHHHHh-cChhhhcccccccCCchhhhHHHHhccHHHHHHHHHcCC
Confidence            9999999999999999 699988   459999999999999999999999999997

>PHA02874 ankyrin repeat protein; Provisional

Probab=99.51  E-value=9e-14  Score=132.28  Aligned_cols=100  Identities=26%  Similarity=0.367  Sum_probs=89.3

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhc----------------------CCCCccccCCCCchHHHHHHHcCCHHH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKL----------------------KDFNINQLDENGLNCLHWACDRGHLKV  304 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~----------------------~~~~~~~~d~~g~tpLh~A~~~g~~~~  304 (347)
                      +.+..+..+.+++|.|+..+..+++++|...                      .|++++.+|..|.||||+|+..|+.++
T Consensus        60 ~~n~~~~~~~t~L~~A~~~~~~~iv~~Ll~~g~~~~~~~~~~~~~~~i~~ll~~g~d~n~~~~~g~T~Lh~A~~~~~~~~  139 (434)
T PHA02874         60 DINHINTKIPHPLLTAIKIGAHDIIKLLIDNGVDTSILPIPCIEKDMIKTILDCGIDVNIKDAELKTFLHYAIKKGDLES  139 (434)
T ss_pred             CCCCCCCCCCCHHHHHHHcCCHHHHHHHHHCCCCCCcchhccCCHHHHHHHHHCcCCCCCCCCCCccHHHHHHHCCCHHH
Confidence            4566777889999999988888888888761                      245677889999999999999999999


Q ss_pred             HHHHHhhcCCCccccCCCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          305 VQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       305 v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      +++|++ .|++++.+|..|.||||+|+..|+.+++++|+++||
T Consensus       140 v~~Ll~-~gad~n~~d~~g~tpLh~A~~~~~~~iv~~Ll~~g~  181 (434)
T PHA02874        140 IKMLFE-YGADVNIEDDNGCYPIHIAIKHNFFDIIKLLLEKGA  181 (434)
T ss_pred             HHHHHh-CCCCCCCcCCCCCCHHHHHHHCCcHHHHHHHHHCCC
Confidence            999999 799999999999999999999999999999999986

>KOG4177|consensus

Probab=99.51  E-value=3.5e-14  Score=142.89  Aligned_cols=99  Identities=24%  Similarity=0.221  Sum_probs=92.7

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      .++..+..+.||||.|+..+...++++|++ +|++++.+|+.|+||||.||..|+.+|+.+|++ +||++|..|.+|.||
T Consensus       532 ~v~~~~~r~~TpLh~A~~~g~v~~VkfLLe-~gAdv~ak~~~G~TPLH~Aa~~G~~~i~~LLlk-~GA~vna~d~~g~Tp  609 (1143)
T KOG4177|consen  532 NVDLRTGRGYTPLHVAVHYGNVDLVKFLLE-HGADVNAKDKLGYTPLHQAAQQGHNDIAELLLK-HGASVNAADLDGFTP  609 (1143)
T ss_pred             ceehhcccccchHHHHHhcCCchHHHHhhh-CCccccccCCCCCChhhHHHHcChHHHHHHHHH-cCCCCCcccccCcch
Confidence            356677888999999999999999999999 899999999999999999999999999999999 799999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+..|+++++++|+..|+
T Consensus       610 L~iA~~lg~~~~~k~l~~~~~  630 (1143)
T KOG4177|consen  610 LHIAVRLGYLSVVKLLKVVTA  630 (1143)
T ss_pred             hHHHHHhcccchhhHHHhccC
Confidence            999999999999999998775

>PHA02716 CPXV016; CPX019; EVM010; Provisional

Probab=99.50  E-value=7.9e-14  Score=137.48  Aligned_cols=101  Identities=15%  Similarity=0.085  Sum_probs=88.0

Q ss_pred             ccCCcccCCCCCcHHHHHHcCCh--HHHHHHHhhcCCCCccccCCCCchHHHHH--------------------------
Q psy630          245 INDESQLDDNEKNIYEWAKEGKL--DMLVKQLTKLKDFNINQLDENGLNCLHWA--------------------------  296 (347)
Q Consensus       245 ~~~~~~~~~~~~~~l~~a~~~~~--~~~~~lL~~~~~~~~~~~d~~g~tpLh~A--------------------------  296 (347)
                      ..+++..+..|.||||+|+..+.  .+++++|++ .|+++|.+|..|+||||+|                          
T Consensus       202 GADVN~kD~~G~TPLH~Aa~~g~~~~eIVklLLe-~GADVN~kD~~G~TPLh~Ai~~a~n~~~EIvkiLie~~d~n~~~~  280 (764)
T PHA02716        202 GVNVNLQNNHLITPLHTYLITGNVCASVIKKIIE-LGGDMDMKCVNGMSPIMTYIINIDNINPEITNIYIESLDGNKVKN  280 (764)
T ss_pred             CCCCCCCCCCCCCHHHHHHHcCCCCHHHHHHHHH-cCCCCCCCCCCCCCHHHHHHHhhhccCHHHHHHHHHhcccccccc
Confidence            34677888899999999987763  478999988 8999999999999999975                          


Q ss_pred             -----------HHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHH--cCCHHHHHHHHhCCC
Q psy630          297 -----------CDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKA--IEHTDLIEYLVNSGS  347 (347)
Q Consensus       297 -----------~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~--~~~~~~v~~Ll~~GA  347 (347)
                                 +..|+.+++++|++ .|++++.+|..|+||||+|+.  .++.+++++|+++||
T Consensus       281 ~~~~L~~~i~AA~~g~leiVklLLe-~GAdIN~kD~~G~TPLH~Aaa~~~~~~eIVklLLe~GA  343 (764)
T PHA02716        281 IPMILHSYITLARNIDISVVYSFLQ-PGVKLHYKDSAGRTCLHQYILRHNISTDIIKLLHEYGN  343 (764)
T ss_pred             chhhhHHHHHHHHcCCHHHHHHHHh-CCCceeccCCCCCCHHHHHHHHhCCCchHHHHHHHcCC
Confidence                       44578899999999 799999999999999999864  468899999999997

>KOG0113|consensus

Probab=99.49  E-value=6.5e-14  Score=118.95  Aligned_cols=79  Identities=25%  Similarity=0.566  Sum_probs=74.1

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ..-+||||+.|+++++|..|+..|+.||+|..|+|++++.||+++|||||+|....+..+|.+. +|.+|+|+.|.|..-
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            3458999999999999999999999999999999999999999999999999999999999986 999999999988643

>PHA02736 Viral ankyrin protein; Provisional

Probab=99.49  E-value=3e-14  Score=115.91  Aligned_cols=96  Identities=22%  Similarity=0.330  Sum_probs=75.7

Q ss_pred             cccCCCCCcHHHHHHcCChHHHHHHHhh------cCCCCccccCCCCchHHHHHHHcCCHH---HHHHHHhhcCCCcccc
Q psy630          249 SQLDDNEKNIYEWAKEGKLDMLVKQLTK------LKDFNINQLDENGLNCLHWACDRGHLK---VVQHLIEKCGADVNVT  319 (347)
Q Consensus       249 ~~~~~~~~~~l~~a~~~~~~~~~~lL~~------~~~~~~~~~d~~g~tpLh~A~~~g~~~---~v~~Ll~~~ga~i~~~  319 (347)
                      +..+..|.|+||+|+..+.  ++.++..      ..+..++.+|..|+||||+||..|+.+   ++++|+. .|+++|.+
T Consensus        11 ~~~d~~g~tpLh~A~~~g~--~~~l~~~~~~~~~~~~~~~~~~d~~g~t~Lh~a~~~~~~~~~e~v~~Ll~-~gadin~~   87 (154)
T PHA02736         11 SEPDIEGENILHYLCRNGG--VTDLLAFKNAISDENRYLVLEYNRHGKQCVHIVSNPDKADPQEKLKLLME-WGADINGK   87 (154)
T ss_pred             HhcCCCCCCHHHHHHHhCC--HHHHHHHHHHhcchhHHHHHHhcCCCCEEEEeecccCchhHHHHHHHHHH-cCCCcccc
Confidence            4456789999999887765  2333321      011224557899999999999999874   6889998 79999999


Q ss_pred             CC-CCCcHHHHHHHcCCHHHHHHHHhC-CC
Q psy630          320 DS-DGDYGLDYAKAIEHTDLIEYLVNS-GS  347 (347)
Q Consensus       320 d~-~g~TpLh~A~~~~~~~~v~~Ll~~-GA  347 (347)
                      +. .|+||||+|+..++.+++++|+.+ |+
T Consensus        88 ~~~~g~T~Lh~A~~~~~~~i~~~Ll~~~g~  117 (154)
T PHA02736         88 ERVFGNTPLHIAVYTQNYELATWLCNQPGV  117 (154)
T ss_pred             CCCCCCcHHHHHHHhCCHHHHHHHHhCCCC
Confidence            85 899999999999999999999974 64

>PHA02989 ankyrin repeat protein; Provisional

Probab=99.49  E-value=1.4e-13  Score=133.09  Aligned_cols=98  Identities=18%  Similarity=0.258  Sum_probs=86.3

Q ss_pred             cCCcccCCCCCcHHHHHHcCC------hHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCcccc
Q psy630          246 NDESQLDDNEKNIYEWAKEGK------LDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVT  319 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~------~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~  319 (347)
                      .+.+..+..+.+++|.+..++      ...++.+|..  ++++|.+|..|+||||+|+..|+.+++++||+ .|+++|.+
T Consensus       209 a~vn~~~~~~~t~l~~~~~~~~~~~~~~~~il~~l~~--~advn~~d~~G~TpL~~Aa~~~~~~~v~~LL~-~Gadin~~  285 (494)
T PHA02989        209 VNIETNNNGSESVLESFLDNNKILSKKEFKVLNFILK--YIKINKKDKKGFNPLLISAKVDNYEAFNYLLK-LGDDIYNV  285 (494)
T ss_pred             CCccccCCccccHHHHHHHhchhhcccchHHHHHHHh--CCCCCCCCCCCCCHHHHHHHhcCHHHHHHHHH-cCCCcccc
Confidence            356667778899998765543      3567777776  69999999999999999999999999999999 79999999


Q ss_pred             CCCCCcHHHHHHHcCCHHHHHHHHhCC
Q psy630          320 DSDGDYGLDYAKAIEHTDLIEYLVNSG  346 (347)
Q Consensus       320 d~~g~TpLh~A~~~~~~~~v~~Ll~~G  346 (347)
                      |..|.||||+|+..|+.+++++||+.+
T Consensus       286 d~~G~TpL~~A~~~~~~~iv~~LL~~~  312 (494)
T PHA02989        286 SKDGDTVLTYAIKHGNIDMLNRILQLK  312 (494)
T ss_pred             CCCCCCHHHHHHHcCCHHHHHHHHhcC
Confidence            999999999999999999999999876

>KOG0126|consensus

Probab=99.48  E-value=4.4e-15  Score=117.19  Aligned_cols=83  Identities=23%  Similarity=0.542  Sum_probs=75.7

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      .+..-|||||||++.|+.+|-.+|++||.|+.|.+++|+.||+|+||||+.|.+..+...|+.. ||..+.||.|+|...
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            4566899999999999999999999999999999999999999999999999999888888875 999999999999865


Q ss_pred             Cccc
Q psy630           85 DSHN   88 (347)
Q Consensus        85 ~~~~   88 (347)
                      ....
T Consensus       113 ~~Yk  116 (219)
T KOG0126|consen  113 SNYK  116 (219)
T ss_pred             cccc
Confidence            5543

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

Probab=99.48  E-value=9.8e-14  Score=133.09  Aligned_cols=81  Identities=20%  Similarity=0.436  Sum_probs=76.3

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      ..++|||+|||+++++++|+++|+.||.|.+++|++++.+|+++|||||+|.+.++|.+|+.. |+..++|+.|+|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            457999999999999999999999999999999999999999999999999999999999985 9999999999999876


Q ss_pred             cc
Q psy630           86 SH   87 (347)
Q Consensus        86 ~~   87 (347)
                      +.
T Consensus       283 ~p  284 (612)
T TIGR01645       283 TP  284 (612)
T ss_pred             CC
Confidence            53

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>PHA02716 CPXV016; CPX019; EVM010; Provisional

Probab=99.48  E-value=1.8e-13  Score=135.06  Aligned_cols=84  Identities=15%  Similarity=0.099  Sum_probs=72.5

Q ss_pred             cCCccc-CCCCCcHHHHHHc--CChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCC--HHHHHHHHhhcCCCccccC
Q psy630          246 NDESQL-DDNEKNIYEWAKE--GKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGH--LKVVQHLIEKCGADVNVTD  320 (347)
Q Consensus       246 ~~~~~~-~~~~~~~l~~a~~--~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~--~~~v~~Ll~~~ga~i~~~d  320 (347)
                      .+.+.. +..|.||||+|+.  .+..+++++|++ .|+++|.+|..|.||||+|+..|+  .+++++||+ +||++|.+|
T Consensus       167 ADIN~~~d~~G~TpLH~A~~n~~~~~eIVklLLe-~GADVN~kD~~G~TPLH~Aa~~g~~~~eIVklLLe-~GADVN~kD  244 (764)
T PHA02716        167 VNLNYVCKKTGYGILHAYLGNMYVDIDILEWLCN-NGVNVNLQNNHLITPLHTYLITGNVCASVIKKIIE-LGGDMDMKC  244 (764)
T ss_pred             CCcccccCCCCCcHHHHHHHhccCCHHHHHHHHH-cCCCCCCCCCCCCCHHHHHHHcCCCCHHHHHHHHH-cCCCCCCCC
Confidence            455666 7889999998753  234678888888 799999999999999999999995  489999999 799999999


Q ss_pred             CCCCcHHHHHH
Q psy630          321 SDGDYGLDYAK  331 (347)
Q Consensus       321 ~~g~TpLh~A~  331 (347)
                      ..|+||||+|+
T Consensus       245 ~~G~TPLh~Ai  255 (764)
T PHA02716        245 VNGMSPIMTYI  255 (764)
T ss_pred             CCCCCHHHHHH
Confidence            99999999763

>PLN03213 repressor of silencing 3; Provisional

Probab=99.48  E-value=5.8e-14  Score=126.62  Aligned_cols=77  Identities=27%  Similarity=0.555  Sum_probs=70.2

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCH--HHHHHHHhc-CCCccCCccccccC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK--EAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~--~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      ...+||||||++++++++|+..|..||.|..|.|+  +.||  ||||||+|...  .++.+|+.. |+..+.|+.|+|..
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            44689999999999999999999999999999999  4467  99999999987  689999985 99999999999999


Q ss_pred             CCcc
Q psy630           84 SDSH   87 (347)
Q Consensus        84 ~~~~   87 (347)
                      |.+.
T Consensus        85 AKP~   88 (759)
T PLN03213         85 AKEH   88 (759)
T ss_pred             ccHH
Confidence            9774

>KOG0510|consensus

Probab=99.47  E-value=1e-13  Score=132.36  Aligned_cols=99  Identities=21%  Similarity=0.244  Sum_probs=91.6

Q ss_pred             CcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHh-hcCCCccccCCCCCcH
Q psy630          248 ESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIE-KCGADVNVTDSDGDYG  326 (347)
Q Consensus       248 ~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~-~~ga~i~~~d~~g~Tp  326 (347)
                      .+..|.+|.||||+|+..+....+..|+. .|++++.++.++.||||.||.+|++.+|+-||+ ..-..+|..|..|.||
T Consensus       266 v~~~d~dg~tpLH~a~r~G~~~svd~Ll~-~Ga~I~~kn~d~~spLH~AA~yg~~ntv~rLL~~~~~rllne~D~~g~tp  344 (929)
T KOG0510|consen  266 VNDEDNDGCTPLHYAARQGGPESVDNLLG-FGASINSKNKDEESPLHFAAIYGRINTVERLLQESDTRLLNESDLHGMTP  344 (929)
T ss_pred             hhcccccCCchHHHHHHcCChhHHHHHHH-cCCcccccCCCCCCchHHHHHcccHHHHHHHHhCcCccccccccccCCCc
Confidence            46678999999999999999999999998 899999999999999999999999999999997 3335788899999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||.|+..||..++++||++||
T Consensus       345 LHlaa~~gH~~v~qlLl~~GA  365 (929)
T KOG0510|consen  345 LHLAAKSGHDRVVQLLLNKGA  365 (929)
T ss_pred             hhhhhhcCHHHHHHHHHhcCh
Confidence            999999999999999999997

>KOG0514|consensus

Probab=99.47  E-value=6.6e-14  Score=122.38  Aligned_cols=145  Identities=21%  Similarity=0.294  Sum_probs=97.1

Q ss_pred             hhHHHHHHHhhhcccccchhhhhhhcccccccCCCccccCCCCCccceeecccC-----CcccCCCCCcHHHHHHc----
Q psy630          194 KAMSKYIALLNEVDASWEDKEQEEINWDESQESGSKENEGQTKGWVNVSSMIND-----ESQLDDNEKNIYEWAKE----  264 (347)
Q Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~l~~a~~----  264 (347)
                      .....+.+.|+.+++..-+=    .-.-.+.+.....+-..+-+..+|++.+.|     .++++..|.|++..++.    
T Consensus       240 e~V~~~l~~f~als~~lL~y----vVNlaDsNGNTALHYsVSHaNF~VV~~LLDSgvC~VD~qNrAGYtpiMLaALA~lk  315 (452)
T KOG0514|consen  240 EQVEDYLAYFEALSPPLLEY----VVNLADSNGNTALHYAVSHANFDVVSILLDSGVCDVDQQNRAGYTPVMLAALAKLK  315 (452)
T ss_pred             HHHHHHHHHHHhcChHHHHH----HhhhhcCCCCeeeeeeecccchHHHHHHhccCcccccccccccccHHHHHHHHhhc
Confidence            44567778887776643210    001111222223333334444455555443     56667778887776542    


Q ss_pred             -CChHHHHHHHhhcCCCCccccC-CCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCCHHHHHHH
Q psy630          265 -GKLDMLVKQLTKLKDFNINQLD-ENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYL  342 (347)
Q Consensus       265 -~~~~~~~~lL~~~~~~~~~~~d-~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~~~v~~L  342 (347)
                       .....++.-|..  -.++|++- ..|+|+|++|+.+|+.++|+.||. ||||||.+|.+|.|+|+.||..||.+||++|
T Consensus       316 ~~~d~~vV~~LF~--mgnVNaKAsQ~gQTALMLAVSHGr~d~vk~LLa-cgAdVNiQDdDGSTALMCA~EHGhkEivklL  392 (452)
T KOG0514|consen  316 QPADRTVVERLFK--MGDVNAKASQHGQTALMLAVSHGRVDMVKALLA-CGADVNIQDDDGSTALMCAAEHGHKEIVKLL  392 (452)
T ss_pred             chhhHHHHHHHHh--ccCcchhhhhhcchhhhhhhhcCcHHHHHHHHH-ccCCCccccCCccHHHhhhhhhChHHHHHHH
Confidence             223344444544  34667764 479999999999999999999999 8999999999999999999999999999999


Q ss_pred             HhC
Q psy630          343 VNS  345 (347)
Q Consensus       343 l~~  345 (347)
                      |..
T Consensus       393 LA~  395 (452)
T KOG0514|consen  393 LAV  395 (452)
T ss_pred             hcc
Confidence            864

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.47  E-value=2.2e-13  Score=114.28  Aligned_cols=78  Identities=18%  Similarity=0.203  Sum_probs=71.4

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCCc
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~~   86 (347)
                      ...+|||+||++.+|+++|+++|+.||+|..|+|+++.   ..+|||||+|.++++++.|+.++|..|.+++|.|.+...
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~~   80 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQ   80 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCcc
Confidence            45799999999999999999999999999999999884   455899999999999999999999999999999987665


Q ss_pred             c
Q psy630           87 H   87 (347)
Q Consensus        87 ~   87 (347)
                      .
T Consensus        81 y   81 (243)
T PLN03121         81 Y   81 (243)
T ss_pred             c
Confidence            3

>PHA02876 ankyrin repeat protein; Provisional

Probab=99.46  E-value=2.6e-13  Score=136.28  Aligned_cols=100  Identities=25%  Similarity=0.307  Sum_probs=80.8

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCC-HHHHHHHHhhcCCCccccCCCCC
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGH-LKVVQHLIEKCGADVNVTDSDGD  324 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~-~~~v~~Ll~~~ga~i~~~d~~g~  324 (347)
                      .+.+..+..|.||||+|+..+...++++|++ .|++++..+..|.||||+|+..++ ..++++|++ .|+++|.+|..|+
T Consensus       366 adin~~d~~G~TpLh~Aa~~~~~~iv~~Ll~-~gad~~~~~~~g~T~Lh~A~~~~~~~~~vk~Ll~-~gadin~~d~~G~  443 (682)
T PHA02876        366 ANVNARDYCDKTPIHYAAVRNNVVIINTLLD-YGADIEALSQKIGTALHFALCGTNPYMSVKTLID-RGANVNSKNKDLS  443 (682)
T ss_pred             CCCccCCCCCCCHHHHHHHcCCHHHHHHHHH-CCCCccccCCCCCchHHHHHHcCCHHHHHHHHHh-CCCCCCcCCCCCC
Confidence            3566677788888888887777778888877 778888888888888888876555 456788888 6899999999999


Q ss_pred             cHHHHHHHcC-CHHHHHHHHhCCC
Q psy630          325 YGLDYAKAIE-HTDLIEYLVNSGS  347 (347)
Q Consensus       325 TpLh~A~~~~-~~~~v~~Ll~~GA  347 (347)
                      ||||+|+..| +.+++++|+++||
T Consensus       444 TpLh~Aa~~~~~~~iv~lLl~~Ga  467 (682)
T PHA02876        444 TPLHYACKKNCKLDVIEMLLDNGA  467 (682)
T ss_pred             hHHHHHHHhCCcHHHHHHHHHCCC
Confidence            9999999876 6899999999886

>PLN03192 Voltage-dependent potassium channel; Provisional

Probab=99.46  E-value=2.3e-13  Score=138.80  Aligned_cols=90  Identities=21%  Similarity=0.249  Sum_probs=76.1

Q ss_pred             CcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCC
Q psy630          256 KNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEH  335 (347)
Q Consensus       256 ~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~  335 (347)
                      .+.++.|+..+...+++.|+. .|+++|..|..|+||||+||.+|+.+++++|++ +|+++|.+|.+|+||||+|+..|+
T Consensus       526 ~~~L~~Aa~~g~~~~l~~Ll~-~G~d~n~~d~~G~TpLh~Aa~~g~~~~v~~Ll~-~gadin~~d~~G~TpL~~A~~~g~  603 (823)
T PLN03192        526 ASNLLTVASTGNAALLEELLK-AKLDPDIGDSKGRTPLHIAASKGYEDCVLVLLK-HACNVHIRDANGNTALWNAISAKH  603 (823)
T ss_pred             hhHHHHHHHcCCHHHHHHHHH-CCCCCCCCCCCCCCHHHHHHHcChHHHHHHHHh-cCCCCCCcCCCCCCHHHHHHHhCC
Confidence            344444444455556666666 699999999999999999999999999999999 799999999999999999999999


Q ss_pred             HHHHHHHHhCCC
Q psy630          336 TDLIEYLVNSGS  347 (347)
Q Consensus       336 ~~~v~~Ll~~GA  347 (347)
                      .+++++|++.|+
T Consensus       604 ~~iv~~L~~~~~  615 (823)
T PLN03192        604 HKIFRILYHFAS  615 (823)
T ss_pred             HHHHHHHHhcCc
Confidence            888888877653

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.46  E-value=2.3e-13  Score=123.84  Aligned_cols=82  Identities=30%  Similarity=0.645  Sum_probs=74.6

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCC--ccccccC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEG--SRLSIQP   83 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g--~~l~v~~   83 (347)
                      ..++|||+|||+++|+++|+++|++||.|..++|++++.+++++|||||+|.+.++|++|++. ++..+.|  ++|.|.+
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            456899999999999999999999999999999999999999999999999999999999985 9988876  6888887


Q ss_pred             CCccc
Q psy630           84 SDSHN   88 (347)
Q Consensus        84 ~~~~~   88 (347)
                      +....
T Consensus       272 a~~~~  276 (346)
T TIGR01659       272 AEEHG  276 (346)
T ss_pred             CCccc
Confidence            76543

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).

>KOG0514|consensus

Probab=99.45  E-value=1.9e-13  Score=119.51  Aligned_cols=92  Identities=24%  Similarity=0.317  Sum_probs=86.8

Q ss_pred             CCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHH
Q psy630          252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAK  331 (347)
Q Consensus       252 ~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~  331 (347)
                      ..-|.|+|..|...+..++++.|+. .|+++|.+|.+|.|+|++||.+||.+|+++||...++|+...|.+|.|+|.+|.
T Consensus       337 sQ~gQTALMLAVSHGr~d~vk~LLa-cgAdVNiQDdDGSTALMCA~EHGhkEivklLLA~p~cd~sLtD~DgSTAl~IAl  415 (452)
T KOG0514|consen  337 SQHGQTALMLAVSHGRVDMVKALLA-CGADVNIQDDDGSTALMCAAEHGHKEIVKLLLAVPSCDISLTDVDGSTALSIAL  415 (452)
T ss_pred             hhhcchhhhhhhhcCcHHHHHHHHH-ccCCCccccCCccHHHhhhhhhChHHHHHHHhccCcccceeecCCCchhhhhHH
Confidence            4568999999999999999999999 999999999999999999999999999999999889999999999999999999


Q ss_pred             HcCCHHHHHHHHh
Q psy630          332 AIEHTDLIEYLVN  344 (347)
Q Consensus       332 ~~~~~~~v~~Ll~  344 (347)
                      ..||.+|.-+|..
T Consensus       416 eagh~eIa~mlYa  428 (452)
T KOG0514|consen  416 EAGHREIAVMLYA  428 (452)
T ss_pred             hcCchHHHHHHHH
Confidence            9999999888754

>KOG4207|consensus

Probab=99.45  E-value=9.7e-14  Score=111.85  Aligned_cols=85  Identities=27%  Similarity=0.552  Sum_probs=80.3

Q ss_pred             CccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccc
Q psy630            2 SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLS   80 (347)
Q Consensus         2 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~   80 (347)
                      .++++.+.+|-|-||.+.++-++|+.+|++||.|-.|.|++|+.|+.++|||||.|....+|+.|+.. +|.+++|+.|.
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelr   86 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELR   86 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceee
Confidence            35778899999999999999999999999999999999999999999999999999999999999986 99999999999


Q ss_pred             ccCCCc
Q psy630           81 IQPSDS   86 (347)
Q Consensus        81 v~~~~~   86 (347)
                      |+.|..
T Consensus        87 Vq~ary   92 (256)
T KOG4207|consen   87 VQMARY   92 (256)
T ss_pred             ehhhhc
Confidence            997754

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.45  E-value=6.4e-13  Score=118.38  Aligned_cols=128  Identities=24%  Similarity=0.452  Sum_probs=105.8

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCc
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~   86 (347)
                      .++|||+|||+++++++|+++|.+||.|..+.+..++.+|.++|||||+|.+.+.+..|+.. ++..+.|+.|.|.++..
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            58999999999999999999999999999999999998999999999999999999999986 99999999999998542


Q ss_pred             ----ccccch-------------hhhhhcccccccccCCcccccchhhHHHHhhccccceecccCC
Q psy630           87 ----HNRMAE-------------NMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus        87 ----~~~~~~-------------~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                          +.....             ...........++.+++.......+...|..+|.+....+...
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  260 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPS  260 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCC
Confidence                221110             0011122356788899999999999999999999865444443

>KOG4177|consensus

Probab=99.44  E-value=1.8e-13  Score=137.93  Aligned_cols=94  Identities=28%  Similarity=0.349  Sum_probs=85.5

Q ss_pred             CCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHH
Q psy630          252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAK  331 (347)
Q Consensus       252 ~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~  331 (347)
                      ...+.+++|.+..-+...+.+.+.. .|++++.++..|.||||.||..|+..+|++||+ +|+++++++..|+||||.||
T Consensus       504 ~~~~l~~lhla~~~~~v~~~~~l~~-~ga~v~~~~~r~~TpLh~A~~~g~v~~VkfLLe-~gAdv~ak~~~G~TPLH~Aa  581 (1143)
T KOG4177|consen  504 AKKGLTPLHLAADEDTVKVAKILLE-HGANVDLRTGRGYTPLHVAVHYGNVDLVKFLLE-HGADVNAKDKLGYTPLHQAA  581 (1143)
T ss_pred             chhccchhhhhhhhhhHHHHHHHhh-cCCceehhcccccchHHHHHhcCCchHHHHhhh-CCccccccCCCCCChhhHHH
Confidence            3556778888777777777777777 799999999999999999999999999999999 79999999999999999999


Q ss_pred             HcCCHHHHHHHHhCCC
Q psy630          332 AIEHTDLIEYLVNSGS  347 (347)
Q Consensus       332 ~~~~~~~v~~Ll~~GA  347 (347)
                      ..|+.+|+.+|+++||
T Consensus       582 ~~G~~~i~~LLlk~GA  597 (1143)
T KOG4177|consen  582 QQGHNDIAELLLKHGA  597 (1143)
T ss_pred             HcChHHHHHHHHHcCC
Confidence            9999999999999997

>PHA02917 ankyrin-like protein; Provisional

Probab=99.43  E-value=5.3e-13  Score=131.87  Aligned_cols=101  Identities=21%  Similarity=0.207  Sum_probs=86.0

Q ss_pred             cccCCcccCCCCCcHHHHH--HcCChHHHHHHHhhcCCCCccccCC---CC-----------chHHHHHHH---------
Q psy630          244 MINDESQLDDNEKNIYEWA--KEGKLDMLVKQLTKLKDFNINQLDE---NG-----------LNCLHWACD---------  298 (347)
Q Consensus       244 ~~~~~~~~~~~~~~~l~~a--~~~~~~~~~~lL~~~~~~~~~~~d~---~g-----------~tpLh~A~~---------  298 (347)
                      ...+++..|..|.|+||.+  +..++.+++++|++ .|+++|..|.   .|           .||||+|+.         
T Consensus       125 ~Gadin~~d~~g~T~L~~~~a~~~~~~eivklLi~-~Ga~vn~~d~~~~~g~~~~~~~~~~~~t~L~~a~~~~~~~~~~~  203 (661)
T PHA02917        125 HGFDLSVKCENHRSVIENYVMTDDPVPEIIDLFIE-NGCSVLYEDEDDEYGYAYDDYQPRNCGTVLHLYIISHLYSESDT  203 (661)
T ss_pred             cCCCCCccCCCCccHHHHHHHccCCCHHHHHHHHH-cCCCccccccccccccccccccccccccHHHHHHhhcccccccc
Confidence            4457888889999999843  45778899999999 8999987653   34           599999986         


Q ss_pred             --cCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCCH--HHHHHHHhCCC
Q psy630          299 --RGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHT--DLIEYLVNSGS  347 (347)
Q Consensus       299 --~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~--~~v~~Ll~~GA  347 (347)
                        +++.+++++|++ +|+++|.+|..|.||||+|+..|+.  ++|++|++ ||
T Consensus       204 ~~~~~~eiv~~Li~-~Gadvn~~d~~G~TpLh~A~~~g~~~~eivk~Li~-g~  254 (661)
T PHA02917        204 RAYVRPEVVKCLIN-HGIKPSSIDKNYCTALQYYIKSSHIDIDIVKLLMK-GI  254 (661)
T ss_pred             cccCcHHHHHHHHH-CCCCcccCCCCCCcHHHHHHHcCCCcHHHHHHHHh-CC
Confidence              568999999999 7999999999999999999999985  79999985 64

>PHA02876 ankyrin repeat protein; Provisional

Probab=99.42  E-value=8.1e-13  Score=132.70  Aligned_cols=99  Identities=19%  Similarity=0.230  Sum_probs=53.6

Q ss_pred             CCcccCCCCCcHHHHHHc-CChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          247 DESQLDDNEKNIYEWAKE-GKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~-~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      +.+..+..|.|+||+|+. ++...++.+|.. .|+++|.+|..|.||||+|+..|+.+++++|++ +|++++..+..|.|
T Consensus       333 din~~d~~g~TpLh~A~~~~~~~~iv~lLl~-~gadin~~d~~G~TpLh~Aa~~~~~~iv~~Ll~-~gad~~~~~~~g~T  410 (682)
T PHA02876        333 DVNAADRLYITPLHQASTLDRNKDIVITLLE-LGANVNARDYCDKTPIHYAAVRNNVVIINTLLD-YGADIEALSQKIGT  410 (682)
T ss_pred             CCCCcccCCCcHHHHHHHhCCcHHHHHHHHH-cCCCCccCCCCCCCHHHHHHHcCCHHHHHHHHH-CCCCccccCCCCCc
Confidence            344445555555555543 334445555554 455555555555555555555555555555555 45555555555555


Q ss_pred             HHHHHHHcCC-HHHHHHHHhCCC
Q psy630          326 GLDYAKAIEH-TDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~-~~~v~~Ll~~GA  347 (347)
                      |||+|+..++ ..++++|+++||
T Consensus       411 ~Lh~A~~~~~~~~~vk~Ll~~ga  433 (682)
T PHA02876        411 ALHFALCGTNPYMSVKTLIDRGA  433 (682)
T ss_pred             hHHHHHHcCCHHHHHHHHHhCCC
Confidence            5555554433 344555555554

>KOG0505|consensus

Probab=99.42  E-value=2.4e-13  Score=124.65  Aligned_cols=36  Identities=36%  Similarity=0.417  Sum_probs=21.7

Q ss_pred             cCCCccccCCCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          312 CGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       312 ~ga~i~~~d~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      +|.+++.+|.+||||||.|+.-|..+++++|+++||
T Consensus       220 ag~~~~~~D~dgWtPlHAAA~Wg~~~~~elL~~~ga  255 (527)
T KOG0505|consen  220 AGYSVNIKDYDGWTPLHAAAHWGQEDACELLVEHGA  255 (527)
T ss_pred             hccCcccccccCCCcccHHHHhhhHhHHHHHHHhhc
Confidence            455566666666666666666666666666666554

>KOG0508|consensus

Probab=99.42  E-value=2.4e-13  Score=122.59  Aligned_cols=93  Identities=27%  Similarity=0.331  Sum_probs=87.3

Q ss_pred             CCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHH
Q psy630          253 DNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKA  332 (347)
Q Consensus       253 ~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~  332 (347)
                      -.|.++|-+|...++.+++++|+. .++++|.......|||-.||.-||++++++|++ +|+|++..|..|.|.||+||.
T Consensus        82 IegappLWaAsaAGHl~vVk~L~~-~ga~VN~tT~TNStPLraACfDG~leivKyLvE-~gad~~IanrhGhTcLmIa~y  159 (615)
T KOG0508|consen   82 IEGAPPLWAASAAGHLEVVKLLLR-RGASVNDTTRTNSTPLRAACFDGHLEIVKYLVE-HGADPEIANRHGHTCLMIACY  159 (615)
T ss_pred             cCCCchhhHHhccCcHHHHHHHHH-hcCccccccccCCccHHHHHhcchhHHHHHHHH-cCCCCcccccCCCeeEEeeec
Confidence            467788888888888889999999 789999999999999999999999999999998 799999999999999999999


Q ss_pred             cCCHHHHHHHHhCCC
Q psy630          333 IEHTDLIEYLVNSGS  347 (347)
Q Consensus       333 ~~~~~~v~~Ll~~GA  347 (347)
                      .||.+|+++|++.||
T Consensus       160 kGh~~I~qyLle~gA  174 (615)
T KOG0508|consen  160 KGHVDIAQYLLEQGA  174 (615)
T ss_pred             cCchHHHHHHHHhCC
Confidence            999999999999997

>PHA02917 ankyrin-like protein; Provisional

Probab=99.41  E-value=1.3e-12  Score=129.17  Aligned_cols=98  Identities=19%  Similarity=0.202  Sum_probs=85.8

Q ss_pred             CcccCCCCCcHHHHHHcCC-----------------------hHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHH
Q psy630          248 ESQLDDNEKNIYEWAKEGK-----------------------LDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKV  304 (347)
Q Consensus       248 ~~~~~~~~~~~l~~a~~~~-----------------------~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~  304 (347)
                      ....+..|.||||.|+.+.                       ...++++|+. +|+++|.+|..|+||||+|+..++.++
T Consensus       389 ~~~~~~~G~TpL~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~Ll~-~GAdIN~kd~~G~TpLh~Aa~~~~~~~  467 (661)
T PHA02917        389 AVNHLDDGEIPIGHLCKSNYGCYNFYTYTYKKGLCDMSYACPILSTINICLP-YLKDINMIDKRGETLLHKAVRYNKQSL  467 (661)
T ss_pred             ccccCCCCCChhHHHHHhcccchhhhhhhhhhccchhhhhhhhHHHHHHHHH-CCCCCCCCCCCCcCHHHHHHHcCCHHH
Confidence            3444567999999876432                       2346688888 899999999999999999999999999


Q ss_pred             HHHHHhhcCCCccccCCCCCcHHHHHHH-cCCHHHHHHHHhCCC
Q psy630          305 VQHLIEKCGADVNVTDSDGDYGLDYAKA-IEHTDLIEYLVNSGS  347 (347)
Q Consensus       305 v~~Ll~~~ga~i~~~d~~g~TpLh~A~~-~~~~~~v~~Ll~~GA  347 (347)
                      +++|++ +|+++|.+|..|.||||+|+. .++.+++++|+.+||
T Consensus       468 v~~Ll~-~GAdin~~d~~G~T~L~~A~~~~~~~~iv~~LL~~ga  510 (661)
T PHA02917        468 VSLLLE-SGSDVNIRSNNGYTCIAIAINESRNIELLKMLLCHKP  510 (661)
T ss_pred             HHHHHH-CcCCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHcCC
Confidence            999999 799999999999999999996 789999999999986

>PTZ00322 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional

Probab=99.41  E-value=9.3e-13  Score=130.82  Aligned_cols=85  Identities=29%  Similarity=0.425  Sum_probs=76.9

Q ss_pred             HHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCCHH
Q psy630          258 IYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTD  337 (347)
Q Consensus       258 ~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~~  337 (347)
                      ++++|..|+.. ++++|+. .|+++|.+|..|+||||+||.+|+.+++++||+ +|++++.+|..|.||||+|+..|+.+
T Consensus        86 L~~aa~~G~~~-~vk~LL~-~Gadin~~d~~G~TpLh~Aa~~g~~eiv~~LL~-~Gadvn~~d~~G~TpLh~A~~~g~~~  162 (664)
T PTZ00322         86 LCQLAASGDAV-GARILLT-GGADPNCRDYDGRTPLHIACANGHVQVVRVLLE-FGADPTLLDKDGKTPLELAEENGFRE  162 (664)
T ss_pred             HHHHHHcCCHH-HHHHHHH-CCCCCCCcCCCCCcHHHHHHHCCCHHHHHHHHH-CCCCCCCCCCCCCCHHHHHHHCCcHH
Confidence            55666666665 5666666 699999999999999999999999999999999 79999999999999999999999999


Q ss_pred             HHHHHHhC
Q psy630          338 LIEYLVNS  345 (347)
Q Consensus       338 ~v~~Ll~~  345 (347)
                      ++++|+.+
T Consensus       163 iv~~Ll~~  170 (664)
T PTZ00322        163 VVQLLSRH  170 (664)
T ss_pred             HHHHHHhC
Confidence            99999988

>PHA02798 ankyrin-like protein; Provisional

Probab=99.41  E-value=1.1e-12  Score=126.63  Aligned_cols=101  Identities=15%  Similarity=0.216  Sum_probs=89.9

Q ss_pred             ccCCcccCCCCCcHHHHHHcCC---hHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCC---HHHHHHHHhhcCCCccc
Q psy630          245 INDESQLDDNEKNIYEWAKEGK---LDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGH---LKVVQHLIEKCGADVNV  318 (347)
Q Consensus       245 ~~~~~~~~~~~~~~l~~a~~~~---~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~---~~~v~~Ll~~~ga~i~~  318 (347)
                      ..+.+..+..|.||||+|+.++   ..+++++|++ .|++++.+|..|.||||+|+..++   .+++++|++ .|++++.
T Consensus        99 GadiN~~d~~G~TpLh~a~~~~~~~~~~iv~~Ll~-~Gadvn~~d~~g~tpL~~a~~~~~~~~~~vv~~Ll~-~gadin~  176 (489)
T PHA02798         99 GADINKKNSDGETPLYCLLSNGYINNLEILLFMIE-NGADTTLLDKDGFTMLQVYLQSNHHIDIEIIKLLLE-KGVDINT  176 (489)
T ss_pred             CCCCCCCCCCcCcHHHHHHHcCCcChHHHHHHHHH-cCCCccccCCCCCcHHHHHHHcCCcchHHHHHHHHH-hCCCccc
Confidence            3467888899999999998764   6788898888 899999999999999999999998   999999999 6999999


Q ss_pred             cC-CCCCcHHHHHHHc----CCHHHHHHHHhCCC
Q psy630          319 TD-SDGDYGLDYAKAI----EHTDLIEYLVNSGS  347 (347)
Q Consensus       319 ~d-~~g~TpLh~A~~~----~~~~~v~~Ll~~GA  347 (347)
                      ++ ..|.||||.++..    ++.+++++|+++||
T Consensus       177 ~~~~~~~t~Lh~~~~~~~~~~~~~ivk~Li~~Ga  210 (489)
T PHA02798        177 HNNKEKYDTLHCYFKYNIDRIDADILKLFVDNGF  210 (489)
T ss_pred             ccCcCCCcHHHHHHHhccccCCHHHHHHHHHCCC
Confidence            85 5799999998764    47999999999996

>PHA02989 ankyrin repeat protein; Provisional

Probab=99.41  E-value=9.9e-13  Score=127.14  Aligned_cols=102  Identities=18%  Similarity=0.156  Sum_probs=87.4

Q ss_pred             cccCCcccCCCCCcHHHHHHcC---ChHHHHHHHhhcCCCCc-cccCCCCchHHHHHHHc--CCHHHHHHHHhhcCCCcc
Q psy630          244 MINDESQLDDNEKNIYEWAKEG---KLDMLVKQLTKLKDFNI-NQLDENGLNCLHWACDR--GHLKVVQHLIEKCGADVN  317 (347)
Q Consensus       244 ~~~~~~~~~~~~~~~l~~a~~~---~~~~~~~lL~~~~~~~~-~~~d~~g~tpLh~A~~~--g~~~~v~~Ll~~~ga~i~  317 (347)
                      ...+.+..+..|.||||.|...   +..+++++|++ .|+++ +.+|..|+||||+|+..  ++.+++++|++ +|++++
T Consensus        97 ~Gadin~~d~~g~tpL~~a~~~~~~~~~eiv~~Ll~-~Gadin~~~d~~g~tpLh~a~~~~~~~~~iv~~Ll~-~Gadi~  174 (494)
T PHA02989         97 FGADINLKTFNGVSPIVCFIYNSNINNCDMLRFLLS-KGINVNDVKNSRGYNLLHMYLESFSVKKDVIKILLS-FGVNLF  174 (494)
T ss_pred             CCCCCCCCCCCCCcHHHHHHHhcccCcHHHHHHHHH-CCCCcccccCCCCCCHHHHHHHhccCCHHHHHHHHH-cCCCcc
Confidence            3446778888999999976543   46778999998 89999 78999999999998754  68999999999 799999


Q ss_pred             c-cCCCCCcHHHHHHHcC----CHHHHHHHHhCCC
Q psy630          318 V-TDSDGDYGLDYAKAIE----HTDLIEYLVNSGS  347 (347)
Q Consensus       318 ~-~d~~g~TpLh~A~~~~----~~~~v~~Ll~~GA  347 (347)
                      . .+..|.||||+|+..+    +.+++++|+++||
T Consensus       175 ~~~~~~g~tpL~~a~~~~~~~~~~~iv~~Ll~~Ga  209 (494)
T PHA02989        175 EKTSLYGLTPMNIYLRNDIDVISIKVIKYLIKKGV  209 (494)
T ss_pred             ccccccCCChHHHHHhcccccccHHHHHHHHhCCC
Confidence            9 6889999999998764    8999999999997

>PHA02795 ankyrin-like protein; Provisional

Probab=99.41  E-value=9.6e-13  Score=121.87  Aligned_cols=92  Identities=17%  Similarity=0.089  Sum_probs=81.3

Q ss_pred             CCCcHHHHHHcCChHHHHHHHhhcCCCCcc-cc-----CCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHH
Q psy630          254 NEKNIYEWAKEGKLDMLVKQLTKLKDFNIN-QL-----DENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGL  327 (347)
Q Consensus       254 ~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~-~~-----d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpL  327 (347)
                      .+.+++|.|+..+..+++++|+. .|++.+ ..     +..|.|++|.|+.+++.+++++|+. +||++|.+|..|.|||
T Consensus       148 ~~~t~lh~A~~~~~~eIVk~Lls-~Ga~~~n~~~~~l~~~~~~t~l~~a~~~~~~eIve~LIs-~GADIN~kD~~G~TpL  225 (437)
T PHA02795        148 ECLNAYFRGICKKESSVVEFILN-CGIPDENDVKLDLYKIIQYTRGFLVDEPTVLEIYKLCIP-YIEDINQLDAGGRTLL  225 (437)
T ss_pred             CCCCHHHHHHHcCcHHHHHHHHh-cCCcccccccchhhhhhccchhHHHHhcCHHHHHHHHHh-CcCCcCcCCCCCCCHH
Confidence            34789999999888999999999 676432 22     1347899999999999999999999 7999999999999999


Q ss_pred             HHHHHcCCHHHHHHHHhCCC
Q psy630          328 DYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       328 h~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |+|+..|+.+++++|+++||
T Consensus       226 h~Aa~~g~~eiVelLL~~GA  245 (437)
T PHA02795        226 YRAIYAGYIDLVSWLLENGA  245 (437)
T ss_pred             HHHHHcCCHHHHHHHHHCCC
Confidence            99999999999999999997

>KOG0107|consensus

Probab=99.40  E-value=5.6e-13  Score=104.87  Aligned_cols=77  Identities=29%  Similarity=0.502  Sum_probs=69.7

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      -.++||||||+..+++.+|+..|..||.+..|.|.+++     .|||||+|++..+|+.|+.. +|..|.|..++|..+.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            46899999999999999999999999999999997654     69999999999999999985 9999999999998776


Q ss_pred             ccc
Q psy630           86 SHN   88 (347)
Q Consensus        86 ~~~   88 (347)
                      ...
T Consensus        84 G~~   86 (195)
T KOG0107|consen   84 GRP   86 (195)
T ss_pred             CCc
Confidence            544

>KOG0147|consensus

Probab=99.38  E-value=7.2e-14  Score=127.99  Aligned_cols=159  Identities=20%  Similarity=0.281  Sum_probs=129.2

Q ss_pred             CCccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCcccc
Q psy630            1 MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLS   80 (347)
Q Consensus         1 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~   80 (347)
                      +++..++.|++|+-.|+...+..+|.++|+.+|.|..|+++.|+.++.++|.|||+|.+.+++..|+.+.|..+.|.+|.
T Consensus       172 l~~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~  251 (549)
T KOG0147|consen  172 LSPEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVI  251 (549)
T ss_pred             CCchHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeE
Confidence            35566788999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCcccccchhhhhhccc-------ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHH
Q psy630           81 IQPSDSHNRMAENMEDRFNQ-------ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNS  153 (347)
Q Consensus        81 v~~~~~~~~~~~~~~~~f~~-------~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~  153 (347)
                      |+.....+.+.......+..       ..+||+||...+++++++..|..||.|.......+.-     .|+.|+.++-+
T Consensus       252 vq~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~-----tG~skgfGfi~  326 (549)
T KOG0147|consen  252 VQLSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSE-----TGRSKGFGFIT  326 (549)
T ss_pred             ecccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccc-----cccccCcceEE
Confidence            99887755544333333321       2379999999999999999999999999877766531     45555555544


Q ss_pred             cCCCCHHHHHHHH
Q psy630          154 LGQMAKSEAMSKY  166 (347)
Q Consensus       154 ~~~~~~~eA~~~y  166 (347)
                        .-..+.|+++.
T Consensus       327 --f~~~~~ar~a~  337 (549)
T KOG0147|consen  327 --FVNKEDARKAL  337 (549)
T ss_pred             --EecHHHHHHHH
Confidence              33456666553

>PHA02730 ankyrin-like protein; Provisional

Probab=99.38  E-value=2.1e-12  Score=125.29  Aligned_cols=99  Identities=19%  Similarity=0.228  Sum_probs=85.2

Q ss_pred             CCcccCCCCCcHHHH---HHcCC---------hHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCC
Q psy630          247 DESQLDDNEKNIYEW---AKEGK---------LDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGA  314 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~---a~~~~---------~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga  314 (347)
                      +.+..+..|.|+||.   +...+         ...++++|+. .|+++|.+|..|.||||+|+..++.+++++|++ +||
T Consensus       409 dIN~kd~~G~T~Lh~~i~a~~~n~~~~~~e~~~~~ivk~LIs-~GADINakD~~G~TPLh~Aa~~~~~eive~LI~-~GA  486 (672)
T PHA02730        409 AINHVSNNGRLCMYGLILSRFNNCGYHCYETILIDVFDILSK-YMDDIDMIDNENKTLLYYAVDVNNIQFARRLLE-YGA  486 (672)
T ss_pred             cccccccCCCchHhHHHHHHhccccccccchhHHHHHHHHHh-cccchhccCCCCCCHHHHHHHhCCHHHHHHHHH-CCC
Confidence            456677889999984   33221         2246888988 899999999999999999999999999999999 799


Q ss_pred             CccccCC-CCCcHHHHHHH--cCCHHHHHHHHhCCC
Q psy630          315 DVNVTDS-DGDYGLDYAKA--IEHTDLIEYLVNSGS  347 (347)
Q Consensus       315 ~i~~~d~-~g~TpLh~A~~--~~~~~~v~~Ll~~GA  347 (347)
                      ++|.+|. .|.||||+|+.  .++.+++++|+++||
T Consensus       487 dIN~~d~~~g~TaL~~Aa~~~~~~~eIv~~LLs~ga  522 (672)
T PHA02730        487 SVNTTSRSIINTAIQKSSYRRENKTKLVDLLLSYHP  522 (672)
T ss_pred             CCCCCCCcCCcCHHHHHHHhhcCcHHHHHHHHHcCC
Confidence            9999997 69999999997  478999999999996

>PHA02730 ankyrin-like protein; Provisional

Probab=99.38  E-value=2e-12  Score=125.47  Aligned_cols=94  Identities=19%  Similarity=0.192  Sum_probs=83.7

Q ss_pred             ccCCCCCcHHHHHHcCC---hHHHHHHHhhcCCCCccccCCCCchHHHHHHHcC--CHHHHHHHHhhcCC--CccccCCC
Q psy630          250 QLDDNEKNIYEWAKEGK---LDMLVKQLTKLKDFNINQLDENGLNCLHWACDRG--HLKVVQHLIEKCGA--DVNVTDSD  322 (347)
Q Consensus       250 ~~~~~~~~~l~~a~~~~---~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g--~~~~v~~Ll~~~ga--~i~~~d~~  322 (347)
                      ..|..|.|+||+|+..+   +.+++++|+. .|++++.+|..|+||||+|+..+  +.+++++|++ +|+  +++..+.-
T Consensus        36 ~kd~~G~TaLh~A~~~~~~~~~eivklLLs-~GAdin~kD~~G~TPLh~Aa~~~~~~~eIv~~Ll~-~~~~~~~~~~~~~  113 (672)
T PHA02730         36 HIDRRGNNALHCYVSNKCDTDIKIVRLLLS-RGVERLCRNNEGLTPLGVYSKRKYVKSQIVHLLIS-SYSNASNELTSNI  113 (672)
T ss_pred             hcCCCCCcHHHHHHHcCCcCcHHHHHHHHh-CCCCCcccCCCCCChHHHHHHcCCCcHHHHHHHHh-cCCCCCccccccc
Confidence            56778999999998876   4789999998 89999999999999999999976  7999999998 765  55888888


Q ss_pred             CCcHHHHHHH--cCCHHHHHHHHhC
Q psy630          323 GDYGLDYAKA--IEHTDLIEYLVNS  345 (347)
Q Consensus       323 g~TpLh~A~~--~~~~~~v~~Ll~~  345 (347)
                      +.+|||.++.  .++.+++++|+..
T Consensus       114 ~d~~l~~y~~s~n~~~~~vk~Li~~  138 (672)
T PHA02730        114 NDFDLYSYMSSDNIDLRLLKYLIVD  138 (672)
T ss_pred             CCchHHHHHHhcCCcHHHHHHHHHh
Confidence            9999999999  8999999999963

>smart00362 RRM_2 RNA recognition motif

Probab=99.38  E-value=2.1e-12  Score=89.95  Aligned_cols=71  Identities=38%  Similarity=0.709  Sum_probs=65.2

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630           10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus        10 ~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      +|||+|||+.++.++|+++|++||.+..+.+..++  +.++|+|||+|.+.+.|+.|+.. ++..+.|+.+.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            58999999999999999999999999999998776  77899999999999999999985 8899999888763

>KOG4206|consensus

Probab=99.37  E-value=4.2e-12  Score=104.58  Aligned_cols=133  Identities=19%  Similarity=0.318  Sum_probs=104.9

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHH----HHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKK----FFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSR   78 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~----~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~   78 (347)
                      +.+...||||.||+..+..++|++    +|++||.|..|...+   |.+.+|-|||.|.+.+.|..|+.. +|..+.|++
T Consensus         5 ~~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~   81 (221)
T KOG4206|consen    5 SVNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKP   81 (221)
T ss_pred             ccCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCch
Confidence            445556999999999999999987    999999999988753   688999999999999999999986 999999999


Q ss_pred             ccccCCCcccccchh-------------------------hhh------------------hcccccccccCCcccccch
Q psy630           79 LSIQPSDSHNRMAEN-------------------------MED------------------RFNQACDYLPSLVKKLDSS  115 (347)
Q Consensus        79 l~v~~~~~~~~~~~~-------------------------~~~------------------~f~~~~~~v~~l~~~~~~e  115 (347)
                      ++|++|..+..-...                         ...                  .-....+|+.|+|...+.+
T Consensus        82 mriqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e  161 (221)
T KOG4206|consen   82 MRIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESE  161 (221)
T ss_pred             hheecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHH
Confidence            999998775421110                         000                  1122467899999999999


Q ss_pred             hhHHHHhhccccceecccCCCCCc
Q psy630          116 TLLKFYALYKQATVGQCNIDKPSW  139 (347)
Q Consensus       116 ~l~~~f~~fg~v~~g~~~~~~p~~  139 (347)
                      .+..+|..|.--.....-..++++
T Consensus       162 ~l~~lf~qf~g~keir~i~~~~~i  185 (221)
T KOG4206|consen  162 MLSDLFEQFPGFKEIRLIPPRSGI  185 (221)
T ss_pred             HHHHHHhhCcccceeEeccCCCce
Confidence            999999988877655555555543

>KOG0505|consensus

Probab=99.36  E-value=9.1e-13  Score=120.83  Aligned_cols=92  Identities=30%  Similarity=0.487  Sum_probs=85.0

Q ss_pred             CCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHH
Q psy630          253 DNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKA  332 (347)
Q Consensus       253 ~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~  332 (347)
                      ...-.++.+++.++...+..+|..  +++++..+.+|.|+||-+|.-.+.+||.+|++ +|++||.+|..||||||.|+.
T Consensus        39 ~~sa~~l~A~~~~d~~ev~~ll~~--ga~~~~~n~DglTalhq~~id~~~e~v~~l~e-~ga~Vn~~d~e~wtPlhaaas  115 (527)
T KOG0505|consen   39 EDSAVFLEACSRGDLEEVRKLLNR--GASPNLCNVDGLTALHQACIDDNLEMVKFLVE-NGANVNAQDNEGWTPLHAAAS  115 (527)
T ss_pred             CchHHHHhccccccHHHHHHHhcc--CCCccccCCccchhHHHHHhcccHHHHHHHHH-hcCCccccccccCCcchhhcc
Confidence            445567778889999998888876  78889999999999999999999999999999 799999999999999999999


Q ss_pred             cCCHHHHHHHHhCCC
Q psy630          333 IEHTDLIEYLVNSGS  347 (347)
Q Consensus       333 ~~~~~~v~~Ll~~GA  347 (347)
                      +||..++++|+++||
T Consensus       116 cg~~~i~~~li~~gA  130 (527)
T KOG0505|consen  116 CGYLNIVEYLIQHGA  130 (527)
T ss_pred             cccHHHHHHHHHhhh
Confidence            999999999999997

>cd00204 ANK ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins

Probab=99.36  E-value=1e-11  Score=96.35  Aligned_cols=93  Identities=32%  Similarity=0.483  Sum_probs=68.2

Q ss_pred             CCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHH
Q psy630          252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAK  331 (347)
Q Consensus       252 ~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~  331 (347)
                      +..|.+++|+|+..+...+++.|.. .+.+.+..+..|.||||+|+..+..+++++|+. .|++++..+..|.||+|+|+
T Consensus         4 ~~~g~t~l~~a~~~~~~~~i~~li~-~~~~~~~~~~~g~~~l~~a~~~~~~~~~~~ll~-~~~~~~~~~~~~~~~l~~a~   81 (126)
T cd00204           4 DEDGRTPLHLAASNGHLEVVKLLLE-NGADVNAKDNDGRTPLHLAAKNGHLEIVKLLLE-KGADVNARDKDGNTPLHLAA   81 (126)
T ss_pred             CcCCCCHHHHHHHcCcHHHHHHHHH-cCCCCCccCCCCCcHHHHHHHcCCHHHHHHHHH-cCCCccccCCCCCCHHHHHH
Confidence            3556777777777776677777776 566666777777777777777777777777777 57777777777777777777


Q ss_pred             HcCCHHHHHHHHhCC
Q psy630          332 AIEHTDLIEYLVNSG  346 (347)
Q Consensus       332 ~~~~~~~v~~Ll~~G  346 (347)
                      ..++.+++++|+++|
T Consensus        82 ~~~~~~~~~~L~~~~   96 (126)
T cd00204          82 RNGNLDVVKLLLKHG   96 (126)
T ss_pred             HcCcHHHHHHHHHcC
Confidence            777777777777654

The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.

>KOG0111|consensus

Probab=99.35  E-value=4.1e-13  Score=109.21  Aligned_cols=84  Identities=23%  Similarity=0.441  Sum_probs=79.5

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      ..+.|+||||+|...+++.-|...|-+||.|..|+++.|..+++.||||||+|...++|.+|+.. |...+.||.|+|.+
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~   86 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNL   86 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEee
Confidence            45678999999999999999999999999999999999999999999999999999999999985 99999999999999


Q ss_pred             CCccc
Q psy630           84 SDSHN   88 (347)
Q Consensus        84 ~~~~~   88 (347)
                      +.|..
T Consensus        87 AkP~k   91 (298)
T KOG0111|consen   87 AKPEK   91 (298)
T ss_pred             cCCcc
Confidence            98854

>KOG0114|consensus

Probab=99.35  E-value=2.8e-12  Score=92.02  Aligned_cols=82  Identities=17%  Similarity=0.340  Sum_probs=72.2

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      ++...+-|||+|||+++|.++..++|.+||.|..|+|-..+   .-+|.|||.|.+..+|.+|+.. +|..+.++.+.|.
T Consensus        14 ppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k---~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vl   90 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK---ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVL   90 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc---CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEE
Confidence            35567889999999999999999999999999999995443   4579999999999999999985 9999999999998


Q ss_pred             CCCccc
Q psy630           83 PSDSHN   88 (347)
Q Consensus        83 ~~~~~~   88 (347)
                      +.++..
T Consensus        91 yyq~~~   96 (124)
T KOG0114|consen   91 YYQPED   96 (124)
T ss_pred             ecCHHH
Confidence            877643

>smart00360 RRM RNA recognition motif

Probab=99.34  E-value=4.5e-12  Score=87.93  Aligned_cols=70  Identities=40%  Similarity=0.756  Sum_probs=64.7

Q ss_pred             EeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630           13 VGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus        13 V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      |+|||..+++++|+++|++||.|..+.+..++.++.++|+|||+|.+.++|..|+.. ++..+.|+.+.|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            689999999999999999999999999999887899999999999999999999985 8888999888763

>KOG1710|consensus

Probab=99.33  E-value=4.4e-12  Score=107.74  Aligned_cols=111  Identities=18%  Similarity=0.208  Sum_probs=91.3

Q ss_pred             ccCCCCCccceeecccCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccc-cCCCCchHHHHHHHcCCHHHHHHHH
Q psy630          231 NEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQ-LDENGLNCLHWACDRGHLKVVQHLI  309 (347)
Q Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~-~d~~g~tpLh~A~~~g~~~~v~~Ll  309 (347)
                      .....++...+.+.....+.+|+.|+++|..|+..+..+++++|++ .|+|+|. ++..+.||||+||..|+.+++++|+
T Consensus        21 ~Kndt~~a~~LLs~vr~vn~~D~sGMs~LahAaykGnl~~v~lll~-~gaDvN~~qhg~~YTpLmFAALSGn~dvcrlll   99 (396)
T KOG1710|consen   21 DKNDTEAALALLSTVRQVNQRDPSGMSVLAHAAYKGNLTLVELLLE-LGADVNDKQHGTLYTPLMFAALSGNQDVCRLLL   99 (396)
T ss_pred             ccCcHHHHHHHHHHhhhhhccCCCcccHHHHHHhcCcHHHHHHHHH-hCCCcCcccccccccHHHHHHHcCCchHHHHHH
Confidence            3445555555655556688899999998877776666668888888 7999987 4667899999999999999999999


Q ss_pred             hhcCCCccccCCCCCcHHHHHHHcCCHHHHHHHH
Q psy630          310 EKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLV  343 (347)
Q Consensus       310 ~~~ga~i~~~d~~g~TpLh~A~~~~~~~~v~~Ll  343 (347)
                      + .|+.....++-|+|+-.+|+..|+.+||.++-
T Consensus       100 d-aGa~~~~vNsvgrTAaqmAAFVG~H~CV~iIN  132 (396)
T KOG1710|consen  100 D-AGARMYLVNSVGRTAAQMAAFVGHHECVAIIN  132 (396)
T ss_pred             h-ccCccccccchhhhHHHHHHHhcchHHHHHHh
Confidence            9 89999999999999999999999999987653

>KOG0507|consensus

Probab=99.32  E-value=1.6e-12  Score=123.52  Aligned_cols=100  Identities=19%  Similarity=0.239  Sum_probs=92.0

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      ...+..|..|.|++|.|+..+...+.++|++ +.+-++..|..|.+|||+|+++|+.+++++||. .+..+|+.+..|.|
T Consensus        40 ds~n~qd~~gfTalhha~Lng~~~is~llle-~ea~ldl~d~kg~~plhlaaw~g~~e~vkmll~-q~d~~na~~~e~~t  117 (854)
T KOG0507|consen   40 DSHNLQDYSGFTLLHHAVLNGQNQISKLLLD-YEALLDLCDTKGILPLHLAAWNGNLEIVKMLLL-QTDILNAVNIENET  117 (854)
T ss_pred             ccccccCccchhHHHHHHhcCchHHHHHHhc-chhhhhhhhccCcceEEehhhcCcchHHHHHHh-cccCCCcccccCcC
Confidence            3467778899999999999999999999998 788888999999999999999999999999998 68999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||.|++.||.+++.|||++||
T Consensus       118 plhlaaqhgh~dvv~~Ll~~~a  139 (854)
T KOG0507|consen  118 PLHLAAQHGHLEVVFYLLKKNA  139 (854)
T ss_pred             ccchhhhhcchHHHHHHHhcCC
Confidence            9999999999999999999986

>KOG0148|consensus

Probab=99.28  E-value=8.5e-12  Score=104.78  Aligned_cols=77  Identities=23%  Similarity=0.452  Sum_probs=70.3

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      +..+.++|||||++..+|++++++.|++||+|.+|++.+++      ||+||.|.+.|+|..||.. |+..+.|+.+++.
T Consensus       160 ssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q------GYaFVrF~tkEaAahAIv~mNntei~G~~VkCs  233 (321)
T KOG0148|consen  160 SSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ------GYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCS  233 (321)
T ss_pred             CCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEeccc------ceEEEEecchhhHHHHHHHhcCceeCceEEEEe
Confidence            34667899999999999999999999999999999998774      8999999999999999986 9999999999998


Q ss_pred             CCCc
Q psy630           83 PSDS   86 (347)
Q Consensus        83 ~~~~   86 (347)
                      |-..
T Consensus       234 WGKe  237 (321)
T KOG0148|consen  234 WGKE  237 (321)
T ss_pred             cccc
Confidence            7654

>PHA02792 ankyrin-like protein; Provisional

Probab=99.28  E-value=9.8e-12  Score=119.50  Aligned_cols=100  Identities=20%  Similarity=0.187  Sum_probs=80.6

Q ss_pred             cCCcccCCC--CCcHHHHHHcCChHH---HHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccC
Q psy630          246 NDESQLDDN--EKNIYEWAKEGKLDM---LVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTD  320 (347)
Q Consensus       246 ~~~~~~~~~--~~~~l~~a~~~~~~~---~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d  320 (347)
                      .+.+..+..  +.+++|+|+.+....   ++++|.. .|+++|.+|..|.||||+|+..++.+++++|++ +|+++|.+|
T Consensus       363 ADIN~kD~~g~~~TpLh~A~~n~~~~v~~IlklLIs-~GADIN~kD~~G~TPLh~Aa~~~n~eivelLLs-~GADIN~kD  440 (631)
T PHA02792        363 NVVVEDDDNIINIMPLFPTLSIHESDVLSILKLCKP-YIDDINKIDKHGRSILYYCIESHSVSLVEWLID-NGADINITT  440 (631)
T ss_pred             CchhhhcCCCCChhHHHHHHHhccHhHHHHHHHHHh-cCCccccccccCcchHHHHHHcCCHHHHHHHHH-CCCCCCCcC
Confidence            355556555  458888887766553   4666677 799999999999999999999999999999999 799999999


Q ss_pred             CCCCcHHHHHHH--c-C-------CHHHHHHHHhCCC
Q psy630          321 SDGDYGLDYAKA--I-E-------HTDLIEYLVNSGS  347 (347)
Q Consensus       321 ~~g~TpLh~A~~--~-~-------~~~~v~~Ll~~GA  347 (347)
                      ..|.||||+|+.  . +       ..+++++||++|.
T Consensus       441 ~~G~TpL~~A~~~~~~~~~~i~~~~~~il~lLLs~~p  477 (631)
T PHA02792        441 KYGSTCIGICVILAHACIPEIAELYIKILEIILSKLP  477 (631)
T ss_pred             CCCCCHHHHHHHHHhcccHHHHHHHHHHHHHHHhcCC
Confidence            999999999976  2 2       2556888888763

>KOG0195|consensus

Probab=99.28  E-value=1.6e-12  Score=110.57  Aligned_cols=88  Identities=32%  Similarity=0.579  Sum_probs=79.8

Q ss_pred             cHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCCH
Q psy630          257 NIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHT  336 (347)
Q Consensus       257 ~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~  336 (347)
                      .++++|++|+...+.-.|.. ...+.|.-|.+|.+||||||..||..+++.||. -|+.+|..+....||||+|+..||.
T Consensus         3 dif~wcregna~qvrlwld~-tehdln~gddhgfsplhwaakegh~aivemll~-rgarvn~tnmgddtplhlaaahghr   80 (448)
T KOG0195|consen    3 DIFGWCREGNAFQVRLWLDD-TEHDLNVGDDHGFSPLHWAAKEGHVAIVEMLLS-RGARVNSTNMGDDTPLHLAAAHGHR   80 (448)
T ss_pred             hhhhhhhcCCeEEEEEEecC-cccccccccccCcchhhhhhhcccHHHHHHHHh-cccccccccCCCCcchhhhhhcccH
Confidence            47889999998866555655 788999999999999999999999999999999 5999999999999999999999999


Q ss_pred             HHHHHHHhCC
Q psy630          337 DLIEYLVNSG  346 (347)
Q Consensus       337 ~~v~~Ll~~G  346 (347)
                      ++|..||+.-
T Consensus        81 divqkll~~k   90 (448)
T KOG0195|consen   81 DIVQKLLSRK   90 (448)
T ss_pred             HHHHHHHHHh
Confidence            9999999764

>COG0666 Arp FOG: Ankyrin repeat [General function prediction only]

Probab=99.27  E-value=3e-11  Score=103.78  Aligned_cols=97  Identities=29%  Similarity=0.326  Sum_probs=60.0

Q ss_pred             CCcccCCCCCcHHHHHHcCCh-----HHHHHHHhhcCCC---CccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccc
Q psy630          247 DESQLDDNEKNIYEWAKEGKL-----DMLVKQLTKLKDF---NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNV  318 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~-----~~~~~lL~~~~~~---~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~  318 (347)
                      +++..+..|.|++|.|...+.     ..++++|+. .++   ..+.+|..|.||||+|+..|+.+++.+|+. .|++++.
T Consensus        98 ~~~~~~~~g~t~l~~a~~~~~~~~~~~~~~~~ll~-~g~~~~~~~~~~~~g~tpl~~A~~~~~~~~~~~ll~-~~~~~~~  175 (235)
T COG0666          98 DVNAKDADGDTPLHLAALNGNPPEGNIEVAKLLLE-AGADLDVNNLRDEDGNTPLHWAALNGDADIVELLLE-AGADPNS  175 (235)
T ss_pred             CcccccCCCCcHHHHHHhcCCcccchHHHHHHHHH-cCCCCCCccccCCCCCchhHHHHHcCchHHHHHHHh-cCCCCcc
Confidence            445566666666666666555     555666555 444   444446666666666666666666666666 5666666


Q ss_pred             cCCCCCcHHHHHHHcCCHHHHHHHHhC
Q psy630          319 TDSDGDYGLDYAKAIEHTDLIEYLVNS  345 (347)
Q Consensus       319 ~d~~g~TpLh~A~~~~~~~~v~~Ll~~  345 (347)
                      .+..|.|+||+|+..++.+++..|+..
T Consensus       176 ~~~~g~t~l~~a~~~~~~~~~~~l~~~  202 (235)
T COG0666         176 RNSYGVTALDPAAKNGRIELVKLLLDK  202 (235)
T ss_pred             cccCCCcchhhhcccchHHHHHHHHhc
Confidence            666666666666666666666666554

>KOG1710|consensus

Probab=99.27  E-value=4.6e-12  Score=107.66  Aligned_cols=95  Identities=27%  Similarity=0.369  Sum_probs=85.3

Q ss_pred             ccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCcccc-CCCCCcHHH
Q psy630          250 QLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVT-DSDGDYGLD  328 (347)
Q Consensus       250 ~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~-d~~g~TpLh  328 (347)
                      ++|.....+|.+...++......+|..  -.++|.+|..|+|||..|+..|+.++|++||+ .|+|||.. +..+.||||
T Consensus         8 qld~~~~~Lle~i~Kndt~~a~~LLs~--vr~vn~~D~sGMs~LahAaykGnl~~v~lll~-~gaDvN~~qhg~~YTpLm   84 (396)
T KOG1710|consen    8 QLDAPKSPLLEAIDKNDTEAALALLST--VRQVNQRDPSGMSVLAHAAYKGNLTLVELLLE-LGADVNDKQHGTLYTPLM   84 (396)
T ss_pred             cccchhhHHHHHHccCcHHHHHHHHHH--hhhhhccCCCcccHHHHHHhcCcHHHHHHHHH-hCCCcCcccccccccHHH
Confidence            345666788888899999988888766  55689999999999999999999999999999 79999986 667999999


Q ss_pred             HHHHcCCHHHHHHHHhCCC
Q psy630          329 YAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       329 ~A~~~~~~~~v~~Ll~~GA  347 (347)
                      +|+..|+.++.++||+.||
T Consensus        85 FAALSGn~dvcrllldaGa  103 (396)
T KOG1710|consen   85 FAALSGNQDVCRLLLDAGA  103 (396)
T ss_pred             HHHHcCCchHHHHHHhccC
Confidence            9999999999999999997

>KOG0108|consensus

Probab=99.27  E-value=8.5e-12  Score=115.24  Aligned_cols=81  Identities=27%  Similarity=0.654  Sum_probs=77.4

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCcc
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDSH   87 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~~   87 (347)
                      +.|||||+|+++++++|..+|+..|.|.+++++.|+.||+++||||++|.+.+.+.+|++. |+..+.||+|+|.++...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            8899999999999999999999999999999999999999999999999999999999996 999999999999998775


Q ss_pred             cc
Q psy630           88 NR   89 (347)
Q Consensus        88 ~~   89 (347)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            44

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.26  E-value=3.7e-11  Score=84.05  Aligned_cols=72  Identities=36%  Similarity=0.738  Sum_probs=65.7

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630           10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus        10 ~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      +|+|+|||+.+++++|+++|+.+|.|..+.+..++.+ .++|+|||+|.+.++|..|+.. ++..+.|+.+.|.
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~   73 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVE   73 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEe
Confidence            4899999999999999999999999999999987753 7789999999999999999986 8888999988775

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).

>PF13637 Ank_4: Ankyrin repeats (many copies); PDB: 3B95_A 3B7B_A 3F6Q_A 2KBX_A 3IXE_A 2DWZ_C 2DVW_A 3AJI_A 1S70_B 2HE0_A

Probab=99.26  E-value=1.9e-11  Score=80.54  Aligned_cols=54  Identities=30%  Similarity=0.503  Sum_probs=45.2

Q ss_pred             CCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHH
Q psy630          255 EKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLI  309 (347)
Q Consensus       255 ~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll  309 (347)
                      |+|++|+|+..+..+++++|.+ .+.++|.+|..|+||||+|+.+|+.+++++||
T Consensus         1 g~t~lh~A~~~g~~~~~~~Ll~-~~~din~~d~~g~t~lh~A~~~g~~~~~~~Ll   54 (54)
T PF13637_consen    1 GRTPLHWAARSGNLEIVKLLLE-HGADINAQDEDGRTPLHYAAKNGNIDIVKFLL   54 (54)
T ss_dssp             SSBHHHHHHHTT-HHHHHHHHH-TTSGTT-B-TTS--HHHHHHHTT-HHHHHHHH
T ss_pred             CChHHHHHHHhCCHHHHHHHHH-CCCCCCCCCCCCCCHHHHHHHccCHHHHHHHC
Confidence            5799999999999999999998 69999999999999999999999999999986

...

>KOG0130|consensus

Probab=99.25  E-value=8.6e-12  Score=93.83  Aligned_cols=77  Identities=22%  Similarity=0.432  Sum_probs=73.2

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCc
Q psy630           10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDS   86 (347)
Q Consensus        10 ~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~   86 (347)
                      -|||.++-...+++++.+.|..||+|..+.+..|+.||..+|||.|+|.+.+.|++|+.. |+..+.|+.+.|.|+-.
T Consensus        74 Ii~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv  151 (170)
T KOG0130|consen   74 IIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFV  151 (170)
T ss_pred             EEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEe
Confidence            589999999999999999999999999999999999999999999999999999999986 99999999999987643

>PF12796 Ank_2: Ankyrin repeats (3 copies); InterPro: IPR020683 This entry represents the ankyrin repeat-containing domain

Probab=99.24  E-value=2.2e-11  Score=89.25  Aligned_cols=64  Identities=36%  Similarity=0.561  Sum_probs=58.1

Q ss_pred             CCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccC
Q psy630          255 EKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTD  320 (347)
Q Consensus       255 ~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d  320 (347)
                      +.+++|+|+..+..+++++|.+ .+++++.+|..|+||||+|+.+|+.+++++|++ +|++++.+|
T Consensus        26 ~~~~l~~A~~~~~~~~~~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~n   89 (89)
T PF12796_consen   26 GNTALHYAAENGNLEIVKLLLE-NGADINSQDKNGNTALHYAAENGNLEIVKLLLE-HGADVNIRN   89 (89)
T ss_dssp             SSBHHHHHHHTTTHHHHHHHHH-TTTCTT-BSTTSSBHHHHHHHTTHHHHHHHHHH-TTT-TTSS-
T ss_pred             CCCHHHHHHHcCCHHHHHHHHH-hcccccccCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCCcC
Confidence            7789999999999999999999 899999999999999999999999999999999 699999875

These domains contain multiple repeats of a beta(2)-alpha(2) motif. The ankyrin repeat is one of the most common protein-protein interaction motifs in nature. Ankyrin repeats are tandemly repeated modules of about 33 amino acids. They occur in a large number of functionally diverse proteins mainly from eukaryotes. The few known examples from prokaryotes and viruses may be the result of horizontal gene transfers []. The repeat has been found in proteins of diverse function such as transcriptional initiators, cell-cycle regulators, cytoskeletal, ion transporters and signal transducers. The ankyrin fold appears to be defined by its structure rather than its function since there is no specific sequence or structure which is universally recognised by it. The conserved fold of the ankyrin repeat unit is known from several crystal and solution structures [, , , ]. Each repeat folds into a helix-loop-helix structure with a beta-hairpin/loop region projecting out from the helices at a 90o angle. The repeats stack together to form an L-shaped structure [, ].; PDB: 3AAA_C 3F6Q_A 2KBX_A 3IXE_A 3TWR_D 3TWV_A 3TWT_B 3TWQ_A 3TWS_A 3TWX_B ....

>KOG4211|consensus

Probab=99.24  E-value=1.6e-11  Score=111.41  Aligned_cols=161  Identities=17%  Similarity=0.245  Sum_probs=116.6

Q ss_pred             CccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccc
Q psy630            2 SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSI   81 (347)
Q Consensus         2 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v   81 (347)
                      ++......-|-+++|||++|+++|++||+.++ |..+.+.+  .+|++.|-|||+|.+.+++++|++.+...+..|.|.|
T Consensus         4 ~~e~~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEV   80 (510)
T KOG4211|consen    4 ENEGSTAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPR--RNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEV   80 (510)
T ss_pred             ccCCCcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEec--cCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEE
Confidence            44455566777889999999999999999997 77765554  4699999999999999999999999999999999999


Q ss_pred             cCCCccccc--chhh--hhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCC
Q psy630           82 QPSDSHNRM--AENM--EDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQM  157 (347)
Q Consensus        82 ~~~~~~~~~--~~~~--~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~  157 (347)
                      -.+.+....  ....  ...-..-.|.+++||..+++++|.+||+..-.++.+...+     .+..+|.-.+|++++..+
T Consensus        81 f~~~~~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~-----~d~rgR~tGEAfVqF~sq  155 (510)
T KOG4211|consen   81 FTAGGAEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLP-----MDQRGRPTGEAFVQFESQ  155 (510)
T ss_pred             EccCCccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeee-----ccCCCCcccceEEEecCH
Confidence            876543210  0000  0112335778999999999999999999877766533222     234667777888886654


Q ss_pred             -CHHHHHHHHHHHH
Q psy630          158 -AKSEAMSKYIALL  170 (347)
Q Consensus       158 -~~~eA~~~yi~~~  170 (347)
                       ..+.|+.+..+.+
T Consensus       156 e~ae~Al~rhre~i  169 (510)
T KOG4211|consen  156 ESAEIALGRHRENI  169 (510)
T ss_pred             HHHHHHHHHHHHhh
Confidence             3344444443333

>KOG0144|consensus

Probab=99.23  E-value=6.8e-12  Score=111.77  Aligned_cols=84  Identities=30%  Similarity=0.568  Sum_probs=74.3

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CC-CccCC--cccccc
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DS-HVLEG--SRLSIQ   82 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~-~~~~g--~~l~v~   82 (347)
                      +.++||||-|++.+||.+++++|++||.|.+|+|+++.. +.+||||||.|.+.+-|..|++. |+ ..+.|  .+|.|+
T Consensus       123 ~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~-~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVk  201 (510)
T KOG0144|consen  123 EERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPD-GLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVK  201 (510)
T ss_pred             cchhhhhhhccccccHHHHHHHHHhhCccchhhheeccc-ccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEE
Confidence            467899999999999999999999999999999999985 99999999999999999999985 54 34544  689999


Q ss_pred             CCCcccccc
Q psy630           83 PSDSHNRMA   91 (347)
Q Consensus        83 ~~~~~~~~~   91 (347)
                      ++++++.+.
T Consensus       202 FADtqkdk~  210 (510)
T KOG0144|consen  202 FADTQKDKD  210 (510)
T ss_pred             ecccCCCch
Confidence            999877643

>COG0666 Arp FOG: Ankyrin repeat [General function prediction only]

Probab=99.23  E-value=4.5e-11  Score=102.69  Aligned_cols=97  Identities=29%  Similarity=0.382  Sum_probs=85.3

Q ss_pred             cccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCC-----HHHHHHHHhhcCC---CccccC
Q psy630          249 SQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGH-----LKVVQHLIEKCGA---DVNVTD  320 (347)
Q Consensus       249 ~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~-----~~~v~~Ll~~~ga---~i~~~d  320 (347)
                      ...+....++++.++......++.++.. .+++++.+|..|.||||+|+.+++     .+++++||+ .|+   +.+.+|
T Consensus        67 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~-~~~~~~~~~~~g~t~l~~a~~~~~~~~~~~~~~~~ll~-~g~~~~~~~~~~  144 (235)
T COG0666          67 AARDLDGRLPLHSAASKGDDKIVKLLLA-SGADVNAKDADGDTPLHLAALNGNPPEGNIEVAKLLLE-AGADLDVNNLRD  144 (235)
T ss_pred             ccCCccccCHHHHHHHcCcHHHHHHHHH-cCCCcccccCCCCcHHHHHHhcCCcccchHHHHHHHHH-cCCCCCCccccC
Confidence            3344567788888887777777777777 799999999999999999999999     999999999 799   666679


Q ss_pred             CCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          321 SDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       321 ~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ..|+||||+|+..|+.+++.+|++.||
T Consensus       145 ~~g~tpl~~A~~~~~~~~~~~ll~~~~  171 (235)
T COG0666         145 EDGNTPLHWAALNGDADIVELLLEAGA  171 (235)
T ss_pred             CCCCchhHHHHHcCchHHHHHHHhcCC
Confidence            999999999999999999999999875

>PHA02792 ankyrin-like protein; Provisional

Probab=99.22  E-value=5e-11  Score=114.67  Aligned_cols=90  Identities=19%  Similarity=0.173  Sum_probs=76.1

Q ss_pred             CcHHHHHHcCChHHHHHHHhhcCCCCccccCCCC--chHHHHHHHcCCH---HHHHHHHhhcCCCccccCCCCCcHHHHH
Q psy630          256 KNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENG--LNCLHWACDRGHL---KVVQHLIEKCGADVNVTDSDGDYGLDYA  330 (347)
Q Consensus       256 ~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g--~tpLh~A~~~g~~---~~v~~Ll~~~ga~i~~~d~~g~TpLh~A  330 (347)
                      ...++.|+..+..+++++|.. .|++++.+|..|  .||||+|+.....   +++++|++ +||++|.+|..|+||||+|
T Consensus       340 ~n~~~~Aa~~gn~eIVelLIs-~GADIN~kD~~g~~~TpLh~A~~n~~~~v~~IlklLIs-~GADIN~kD~~G~TPLh~A  417 (631)
T PHA02792        340 INKYFQKFDNRDPKVVEYILK-NGNVVVEDDDNIINIMPLFPTLSIHESDVLSILKLCKP-YIDDINKIDKHGRSILYYC  417 (631)
T ss_pred             chHHHHHHHcCCHHHHHHHHH-cCCchhhhcCCCCChhHHHHHHHhccHhHHHHHHHHHh-cCCccccccccCcchHHHH
Confidence            344555565666668888888 799999998875  6999998876654   46888898 7999999999999999999


Q ss_pred             HHcCCHHHHHHHHhCCC
Q psy630          331 KAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       331 ~~~~~~~~v~~Ll~~GA  347 (347)
                      +..++.+++++|+++||
T Consensus       418 a~~~n~eivelLLs~GA  434 (631)
T PHA02792        418 IESHSVSLVEWLIDNGA  434 (631)
T ss_pred             HHcCCHHHHHHHHHCCC
Confidence            99999999999999997

>TIGR00870 trp transient-receptor-potential calcium channel protein

Probab=99.20  E-value=6.7e-11  Score=119.95  Aligned_cols=105  Identities=18%  Similarity=0.231  Sum_probs=77.4

Q ss_pred             eeecccCCcccCCCCCcHHHHHHcCChHH---HHHHHhhcCCCC------ccc----cCCCCchHHHHHHHcCCHHHHHH
Q psy630          241 VSSMINDESQLDDNEKNIYEWAKEGKLDM---LVKQLTKLKDFN------INQ----LDENGLNCLHWACDRGHLKVVQH  307 (347)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~l~~a~~~~~~~---~~~lL~~~~~~~------~~~----~d~~g~tpLh~A~~~g~~~~v~~  307 (347)
                      +...+.+....+..|.|+||+|+.++...   +..++.. .+..      ++.    .+..|.||||+||.+|+.+++++
T Consensus        68 iv~lLl~~g~~~~~G~T~Lh~A~~~~~~~v~~ll~~l~~-~~~~~~~~~~~~~~~~~~~~~G~TpLhlAa~~~~~eiVkl  146 (743)
T TIGR00870        68 LTELLLNLSCRGAVGDTLLHAISLEYVDAVEAILLHLLA-AFRKSGPLELANDQYTSEFTPGITALHLAAHRQNYEIVKL  146 (743)
T ss_pred             HHHHHHhCCCCCCcChHHHHHHHhccHHHHHHHHHHHhh-cccccCchhhhccccccccCCCCcHHHHHHHhCCHHHHHH
Confidence            33333333335678899999998855443   3333333 1211      111    23469999999999999999999


Q ss_pred             HHhhcCCCccccC--------------CCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          308 LIEKCGADVNVTD--------------SDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       308 Ll~~~ga~i~~~d--------------~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+ .|++++.++              ..|.||||+|+..|+.+++++|+++||
T Consensus       147 LL~-~GAdv~~~~~~~~~~~~~~~~~~~~g~tpL~~Aa~~~~~~iv~lLl~~ga  199 (743)
T TIGR00870       147 LLE-RGASVPARACGDFFVKSQGVDSFYHGESPLNAAACLGSPSIVALLSEDPA  199 (743)
T ss_pred             HHh-CCCCCCcCcCCchhhcCCCCCcccccccHHHHHHHhCCHHHHHHHhcCCc
Confidence            999 799999764              258999999999999999999999986

after chronic exposure to capsaicin. (McCleskey and Gold, 1999).

>KOG0502|consensus

Probab=99.20  E-value=1.7e-11  Score=100.47  Aligned_cols=95  Identities=26%  Similarity=0.416  Sum_probs=87.1

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      ++..+.....++|..|+.|+...++++|+. .+.++|..|.+|-|||.||+..+|.+||+.||. .||+++..+..|.++
T Consensus       185 dp~~lgk~resALsLAt~ggytdiV~lLL~-r~vdVNvyDwNGgTpLlyAvrgnhvkcve~Ll~-sGAd~t~e~dsGy~~  262 (296)
T KOG0502|consen  185 DPDALGKYRESALSLATRGGYTDIVELLLT-REVDVNVYDWNGGTPLLYAVRGNHVKCVESLLN-SGADVTQEDDSGYWI  262 (296)
T ss_pred             ChhhhhhhhhhhHhHHhcCChHHHHHHHHh-cCCCcceeccCCCceeeeeecCChHHHHHHHHh-cCCCcccccccCCcH
Confidence            566666777899999999999999999999 899999999999999999999999999999999 799999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHh
Q psy630          327 LDYAKAIEHTDLIEYLVN  344 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~  344 (347)
                      +..|+..|+. +|+..++
T Consensus       263 mdlAValGyr-~Vqqvie  279 (296)
T KOG0502|consen  263 MDLAVALGYR-IVQQVIE  279 (296)
T ss_pred             HHHHHHhhhH-HHHHHHH
Confidence            9999999987 6665554

>KOG0515|consensus

Probab=99.18  E-value=3.4e-11  Score=110.06  Aligned_cols=96  Identities=25%  Similarity=0.247  Sum_probs=84.5

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccC-CCCC
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTD-SDGD  324 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d-~~g~  324 (347)
                      .|+.+.++.|-|+||-|..+++..|+++|++ .|+++|..|.+||||||+||.++++.+|+.|++ +|+.|-+.. +++.
T Consensus       574 ~DpSqpNdEGITaLHNAiCaghyeIVkFLi~-~ganVNa~DSdGWTPLHCAASCNnv~~ckqLVe-~GaavfAsTlSDme  651 (752)
T KOG0515|consen  574 TDPSQPNDEGITALHNAICAGHYEIVKFLIE-FGANVNAADSDGWTPLHCAASCNNVPMCKQLVE-SGAAVFASTLSDME  651 (752)
T ss_pred             cCCCCCCccchhHHhhhhhcchhHHHHHHHh-cCCcccCccCCCCchhhhhhhcCchHHHHHHHh-ccceEEeeeccccc
Confidence            3677888999999999999999999999999 899999999999999999999999999999999 799887764 4788


Q ss_pred             cHHHHH--HHcCCHHHHHHHH
Q psy630          325 YGLDYA--KAIEHTDLIEYLV  343 (347)
Q Consensus       325 TpLh~A--~~~~~~~~v~~Ll  343 (347)
                      ||..-+  ...|...|..||.
T Consensus       652 Ta~eKCee~eeGY~~CsqyL~  672 (752)
T KOG0515|consen  652 TAAEKCEEMEEGYDQCSQYLY  672 (752)
T ss_pred             chhhhcchhhhhHHHHHHHHH
Confidence            988766  3457788888874

>KOG4212|consensus

Probab=99.17  E-value=7.7e-11  Score=105.22  Aligned_cols=130  Identities=15%  Similarity=0.219  Sum_probs=103.1

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHh-ccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFS-EYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~-~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      ....|.+||.|||+++..++|+++|. +.|+|..|.+..|. +|+++|||.|+|++++.+++|++. |.+.+.||+|.|+
T Consensus        41 ~~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vK  119 (608)
T KOG4212|consen   41 AARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVK  119 (608)
T ss_pred             ccccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEe
Confidence            34567799999999999999999995 68999999999997 599999999999999999999996 9999999999997


Q ss_pred             CCCcccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCC
Q psy630           83 PSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDK  136 (347)
Q Consensus        83 ~~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~  136 (347)
                      .-.... +.+.....-.....|++++..+.-...+...++--|....++...+.
T Consensus       120 Ed~d~q-~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~  172 (608)
T KOG4212|consen  120 EDHDEQ-RDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDD  172 (608)
T ss_pred             ccCchh-hhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccc
Confidence            543311 11111111223567888898888888888888877777666666653

>cd00204 ANK ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins

Probab=99.16  E-value=2.8e-10  Score=88.12  Aligned_cols=93  Identities=31%  Similarity=0.441  Sum_probs=84.8

Q ss_pred             cccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHH
Q psy630          249 SQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLD  328 (347)
Q Consensus       249 ~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh  328 (347)
                      +..+..|.+++|.|+..+...++++|.. .+..++..+..|.||+|+|+..++.+++++|+. .|.+++..+..|.||||
T Consensus        34 ~~~~~~g~~~l~~a~~~~~~~~~~~ll~-~~~~~~~~~~~~~~~l~~a~~~~~~~~~~~L~~-~~~~~~~~~~~~~~~l~  111 (126)
T cd00204          34 NAKDNDGRTPLHLAAKNGHLEIVKLLLE-KGADVNARDKDGNTPLHLAARNGNLDVVKLLLK-HGADVNARDKDGRTPLH  111 (126)
T ss_pred             CccCCCCCcHHHHHHHcCCHHHHHHHHH-cCCCccccCCCCCCHHHHHHHcCcHHHHHHHHH-cCCCCcccCCCCCCHHH
Confidence            5667788899999888888888998888 678888899999999999999999999999999 69999999999999999


Q ss_pred             HHHHcCCHHHHHHHH
Q psy630          329 YAKAIEHTDLIEYLV  343 (347)
Q Consensus       329 ~A~~~~~~~~v~~Ll  343 (347)
                      +|...++.+++++|+
T Consensus       112 ~~~~~~~~~~~~~Ll  126 (126)
T cd00204         112 LAAKNGHLEVVKLLL  126 (126)
T ss_pred             HHHhcCCHHHHHHhC
Confidence            999999999999885

The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other types of domains. The structural repeat unit contains two antiparallel helices and a beta-hairpin, repeats are stacked in a superhelical arrangement; this alignment contains 4 consecutive repeats.

>KOG4214|consensus

Probab=99.16  E-value=1.3e-10  Score=82.12  Aligned_cols=76  Identities=22%  Similarity=0.248  Sum_probs=69.0

Q ss_pred             CCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHH
Q psy630          253 DNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA  330 (347)
Q Consensus       253 ~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A  330 (347)
                      ..+++|+|+|+..+...+.++|.. .|++++.+|++|.|||.-|++.||.+||++||+ .||+-..+.-+|.+.+..+
T Consensus        32 ~ggR~plhyAAD~GQl~ilefli~-iGA~i~~kDKygITPLLsAvwEGH~~cVklLL~-~GAdrt~~~PdG~~~~eat  107 (117)
T KOG4214|consen   32 YGGRTPLHYAADYGQLSILEFLIS-IGANIQDKDKYGITPLLSAVWEGHRDCVKLLLQ-NGADRTIHAPDGTALIEAT  107 (117)
T ss_pred             hCCcccchHhhhcchHHHHHHHHH-hccccCCccccCCcHHHHHHHHhhHHHHHHHHH-cCcccceeCCCchhHHhhc
Confidence            378999999999999999999998 899999999999999999999999999999999 7999888888887766543

>TIGR00870 trp transient-receptor-potential calcium channel protein

Probab=99.14  E-value=7.9e-11  Score=119.46  Aligned_cols=80  Identities=21%  Similarity=0.103  Sum_probs=73.8

Q ss_pred             CCCCcHHHHHHcCChHHHHHHHhhcCCCCccccC--------------CCCchHHHHHHHcCCHHHHHHHHhhcCCCccc
Q psy630          253 DNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLD--------------ENGLNCLHWACDRGHLKVVQHLIEKCGADVNV  318 (347)
Q Consensus       253 ~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d--------------~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~  318 (347)
                      ..|.||||.|+..++.+++++|++ .|++++.++              ..|.||||+|+..|+.+++++|++ +|+|+|.
T Consensus       126 ~~G~TpLhlAa~~~~~eiVklLL~-~GAdv~~~~~~~~~~~~~~~~~~~~g~tpL~~Aa~~~~~~iv~lLl~-~gadin~  203 (743)
T TIGR00870       126 TPGITALHLAAHRQNYEIVKLLLE-RGASVPARACGDFFVKSQGVDSFYHGESPLNAAACLGSPSIVALLSE-DPADILT  203 (743)
T ss_pred             CCCCcHHHHHHHhCCHHHHHHHHh-CCCCCCcCcCCchhhcCCCCCcccccccHHHHHHHhCCHHHHHHHhc-CCcchhh
Confidence            568999999999999999999999 899998653              358999999999999999999999 7999999


Q ss_pred             cCCCCCcHHHHHHHcC
Q psy630          319 TDSDGDYGLDYAKAIE  334 (347)
Q Consensus       319 ~d~~g~TpLh~A~~~~  334 (347)
                      +|..|+||||+|+..+
T Consensus       204 ~d~~g~T~Lh~A~~~~  219 (743)
T TIGR00870       204 ADSLGNTLLHLLVMEN  219 (743)
T ss_pred             HhhhhhHHHHHHHhhh
Confidence            9999999999999987

after chronic exposure to capsaicin. (McCleskey and Gold, 1999).

>smart00361 RRM_1 RNA recognition motif

Probab=99.09  E-value=3.2e-10  Score=78.94  Aligned_cols=60  Identities=15%  Similarity=0.411  Sum_probs=53.6

Q ss_pred             HHHHHHHHh----ccCCeeEEE-EeeeCCC--CCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccc
Q psy630           22 HNELKKFFS----EYGQIMNAS-VMFDKNT--GLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI   81 (347)
Q Consensus        22 ~~~l~~~f~----~~G~i~~~~-i~~~~~t--~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v   81 (347)
                      +++|+++|+    +||.|.++. ++.++.+  +.++|||||+|.+.++|.+|+.. |+..+.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            567888888    999999995 7777767  89999999999999999999985 999999998875

>KOG0506|consensus

Probab=99.07  E-value=1.2e-10  Score=105.14  Aligned_cols=88  Identities=28%  Similarity=0.436  Sum_probs=83.3

Q ss_pred             CcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCC
Q psy630          256 KNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEH  335 (347)
Q Consensus       256 ~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~  335 (347)
                      ..++++|..|++..+.+++++  +.+++.+|.+.+|+||.||..||.+++++||+.++.+++.+|..|+|||.-|...+|
T Consensus       508 i~~~~aa~~GD~~alrRf~l~--g~D~~~~DyD~RTaLHvAAaEG~v~v~kfl~~~~kv~~~~kDRw~rtPlDdA~~F~h  585 (622)
T KOG0506|consen  508 INVMYAAKNGDLSALRRFALQ--GMDLETKDYDDRTALHVAAAEGHVEVVKFLLNACKVDPDPKDRWGRTPLDDAKHFKH  585 (622)
T ss_pred             hhhhhhhhcCCHHHHHHHHHh--cccccccccccchhheeecccCceeHHHHHHHHHcCCCChhhccCCCcchHhHhcCc
Confidence            357788999999999999999  999999999999999999999999999999998999999999999999999999999


Q ss_pred             HHHHHHHHhC
Q psy630          336 TDLIEYLVNS  345 (347)
Q Consensus       336 ~~~v~~Ll~~  345 (347)
                      .+++++|-+.
T Consensus       586 ~~v~k~L~~~  595 (622)
T KOG0506|consen  586 KEVVKLLEEA  595 (622)
T ss_pred             HHHHHHHHHH
Confidence            9999999653

>KOG4205|consensus

Probab=99.05  E-value=2.2e-10  Score=101.57  Aligned_cols=120  Identities=27%  Similarity=0.490  Sum_probs=93.2

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCCc
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~~   86 (347)
                      ..++|||++||+++++.+++++|.+||.|..+.++.|..+.+++||+||.|.+.+++++++....+.|+|+.+.|.+|.+
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~~f~~~~gk~vevkrA~p  175 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQKFHDFNGKKVEVKRAIP  175 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecccceeeecCceeeEeeccc
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccccchhhhhhcccccccccCCcccccchhhHHHHhhccccc
Q psy630           87 HNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQAT  128 (347)
Q Consensus        87 ~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~  128 (347)
                      +..........  .......++....+.-.+..+|..|+++.
T Consensus       176 k~~~~~~~~~~--~~~~~~~~~g~~~~~~~l~~~~~g~~~~~  215 (311)
T KOG4205|consen  176 KEVMQSTKSSV--STRGKGNNLGNGRTGFFLKKYFKGYGPVG  215 (311)
T ss_pred             hhhcccccccc--ccccccccccccccccccchhccccCccc
Confidence            76532110000  01111123333344445666677777664

>KOG3676|consensus

Probab=99.04  E-value=4.5e-10  Score=108.22  Aligned_cols=94  Identities=21%  Similarity=0.236  Sum_probs=79.7

Q ss_pred             CCCCCcHHHHHHcCChHHHHHHHhhcCCCCcccc--------CC---------------CCchHHHHHHHcCCHHHHHHH
Q psy630          252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQL--------DE---------------NGLNCLHWACDRGHLKVVQHL  308 (347)
Q Consensus       252 ~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~--------d~---------------~g~tpLh~A~~~g~~~~v~~L  308 (347)
                      ...|.++||.|.......++.+|+. .|+|++++        +.               .|..||-+||..++.+|+++|
T Consensus       181 eY~GqSaLHiAIv~~~~~~V~lLl~-~gADV~aRa~G~FF~~~dqk~~rk~T~Y~G~~YfGEyPLSfAAC~nq~eivrlL  259 (782)
T KOG3676|consen  181 EYYGQSALHIAIVNRDAELVRLLLA-AGADVHARACGAFFCPDDQKASRKSTNYTGYFYFGEYPLSFAACTNQPEIVRLL  259 (782)
T ss_pred             hhcCcchHHHHHHhccHHHHHHHHH-cCCchhhHhhccccCcccccccccccCCcceeeeccCchHHHHHcCCHHHHHHH
Confidence            3568899999999888889999888 78888742        11               256799999999999999999


Q ss_pred             HhhcCCCccccCCCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          309 IEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       309 l~~~ga~i~~~d~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ++ +|||++++|..|+|.||..+..-..++-.++|++||
T Consensus       260 l~-~gAd~~aqDS~GNTVLH~lVi~~~~~My~~~L~~ga  297 (782)
T KOG3676|consen  260 LA-HGADPNAQDSNGNTVLHMLVIHFVTEMYDLALELGA  297 (782)
T ss_pred             Hh-cCCCCCccccCCChHHHHHHHHHHHHHHHHHHhcCC
Confidence            98 699999999999999999999888888889998886

>KOG1457|consensus

Probab=99.02  E-value=1.7e-09  Score=88.59  Aligned_cols=83  Identities=20%  Similarity=0.359  Sum_probs=63.9

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEee-eCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccC---Ccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMF-DKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLE---GSR   78 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~-~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~---g~~   78 (347)
                      .+...|||||++||-++.-.+|..+|..|-.-..+.+.. ++...-.+-+|||+|.+...|..|+.. ||..|+   +..
T Consensus        30 ~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~st  109 (284)
T KOG1457|consen   30 EPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGST  109 (284)
T ss_pred             cccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCce
Confidence            455689999999999999999999999885555555432 222122358999999999999999986 999996   566


Q ss_pred             ccccCCCc
Q psy630           79 LSIQPSDS   86 (347)
Q Consensus        79 l~v~~~~~   86 (347)
                      |+|..+.+
T Consensus       110 LhiElAKS  117 (284)
T KOG1457|consen  110 LHIELAKS  117 (284)
T ss_pred             eEeeehhc
Confidence            77765543

>KOG0131|consensus

Probab=99.01  E-value=3.3e-10  Score=89.99  Aligned_cols=84  Identities=27%  Similarity=0.478  Sum_probs=75.4

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeE-EEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMN-ASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~-~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      .....++||+||.+.+++..|.+.|+.||.+.. -.|+++..||.++|||||.|.+.+.+.+|+.. |+..+..++++|.
T Consensus        93 l~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~  172 (203)
T KOG0131|consen   93 LDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVS  172 (203)
T ss_pred             ccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEE
Confidence            344568999999999999999999999998865 48999999999999999999999999999986 9999999999998


Q ss_pred             CCCccc
Q psy630           83 PSDSHN   88 (347)
Q Consensus        83 ~~~~~~   88 (347)
                      ++..+.
T Consensus       173 ya~k~~  178 (203)
T KOG0131|consen  173 YAFKKD  178 (203)
T ss_pred             EEEecC
Confidence            775543

>KOG0147|consensus

Probab=98.99  E-value=4.8e-10  Score=103.25  Aligned_cols=81  Identities=32%  Similarity=0.638  Sum_probs=74.2

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      +.++||||||-+.+++.+|+..|+.||.|..|.+++|..||.++||+|++|.+.+.|.+|++. ||..+-|+.|+|....
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            344599999999999999999999999999999999999999999999999999999999885 9999999999987554


Q ss_pred             cc
Q psy630           86 SH   87 (347)
Q Consensus        86 ~~   87 (347)
                      .+
T Consensus       357 ~r  358 (549)
T KOG0147|consen  357 ER  358 (549)
T ss_pred             ee
Confidence            43

>KOG0705|consensus

Probab=98.99  E-value=9e-10  Score=101.83  Aligned_cols=95  Identities=23%  Similarity=0.330  Sum_probs=81.4

Q ss_pred             CCCCCcHHHHHHcCChHHHHHHHhhcCCCCccc--cCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHH
Q psy630          252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQ--LDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDY  329 (347)
Q Consensus       252 ~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~--~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~  329 (347)
                      .+-|..++.+....|+..+.-||.......+|.  .+.+|+|+||+||..|++.+.++|+. +|+|+.++|..|+|||.|
T Consensus       622 ~~lgqqLl~A~~~~Dl~t~~lLLAhg~~~e~~~t~~~~~grt~LHLa~~~gnVvl~QLLiW-yg~dv~~rda~g~t~l~y  700 (749)
T KOG0705|consen  622 EPLGQQLLRAVAAEDLQTAILLLAHGSREEVNETCGEGDGRTALHLAARKGNVVLAQLLIW-YGVDVMARDAHGRTALFY  700 (749)
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHhccCchhhhccccCCCCcchhhhhhhhcchhHHHHHHH-hCccceecccCCchhhhh
Confidence            356778888888888887776666533344544  45678999999999999999999998 899999999999999999


Q ss_pred             HHHcCCHHHHHHHHhCCC
Q psy630          330 AKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       330 A~~~~~~~~v~~Ll~~GA  347 (347)
                      |-+.|.-+|+.+||++|.
T Consensus       701 ar~a~sqec~d~llq~gc  718 (749)
T KOG0705|consen  701 ARQAGSQECIDVLLQYGC  718 (749)
T ss_pred             HhhcccHHHHHHHHHcCC
Confidence            999999999999999984

>KOG0507|consensus

Probab=98.98  E-value=2.9e-10  Score=108.36  Aligned_cols=110  Identities=22%  Similarity=0.217  Sum_probs=92.8

Q ss_pred             CCCCccceeecccC----CcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHH
Q psy630          234 QTKGWVNVSSMIND----ESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLI  309 (347)
Q Consensus       234 ~~~~~~~~~~~~~~----~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll  309 (347)
                      +-.|...++..+.+    ....+..|.+++|+|+..+..+++++|+. .+..+|.....|.||||.|+++||.+++.+||
T Consensus        57 ~Lng~~~is~llle~ea~ldl~d~kg~~plhlaaw~g~~e~vkmll~-q~d~~na~~~e~~tplhlaaqhgh~dvv~~Ll  135 (854)
T KOG0507|consen   57 VLNGQNQISKLLLDYEALLDLCDTKGILPLHLAAWNGNLEIVKMLLL-QTDILNAVNIENETPLHLAAQHGHLEVVFYLL  135 (854)
T ss_pred             HhcCchHHHHHHhcchhhhhhhhccCcceEEehhhcCcchHHHHHHh-cccCCCcccccCcCccchhhhhcchHHHHHHH
Confidence            33444444444443    23456788999999988888888888777 57889999999999999999999999999999


Q ss_pred             hhcCCCccccCCCCCcHHHHHHHcCCHHHHHHHHhC
Q psy630          310 EKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNS  345 (347)
Q Consensus       310 ~~~ga~i~~~d~~g~TpLh~A~~~~~~~~v~~Ll~~  345 (347)
                      + +|+|+-..|.++.|+|.+|++.|..++|.+|++.
T Consensus       136 ~-~~adp~i~nns~~t~ldlA~qfgr~~Vvq~ll~~  170 (854)
T KOG0507|consen  136 K-KNADPFIRNNSKETVLDLASRFGRAEVVQMLLQK  170 (854)
T ss_pred             h-cCCCccccCcccccHHHHHHHhhhhHHHHHHhhh
Confidence            9 7999999999999999999999999999999874

>KOG0153|consensus

Probab=98.98  E-value=8.4e-10  Score=96.14  Aligned_cols=75  Identities=28%  Similarity=0.539  Sum_probs=68.2

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc--CCCccCCccccccC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST--DSHVLEGSRLSIQP   83 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~--~~~~~~g~~l~v~~   83 (347)
                      ...++|||++|-..+++.+|+++|.+||+|.++++...+      ++|||+|.+..+|+.|.+.  +..+++|+.|.|.|
T Consensus       226 ~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~W  299 (377)
T KOG0153|consen  226 TSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKW  299 (377)
T ss_pred             cceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcceeeecceEEEEEe
Confidence            445799999999999999999999999999999987643      6999999999999999975  99999999999999


Q ss_pred             CCc
Q psy630           84 SDS   86 (347)
Q Consensus        84 ~~~   86 (347)
                      ..+
T Consensus       300 g~~  302 (377)
T KOG0153|consen  300 GRP  302 (377)
T ss_pred             CCC
Confidence            887

>KOG0146|consensus

Probab=98.97  E-value=9.6e-10  Score=92.38  Aligned_cols=84  Identities=27%  Similarity=0.482  Sum_probs=78.9

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      .+.++|||=.||....+.+|-.+|-.||.|.+.++..|+.|..|++|+||.|++..+++.||.. ||..|+-++|+|+..
T Consensus       283 PeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLK  362 (371)
T KOG0146|consen  283 PEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLK  362 (371)
T ss_pred             CCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhc
Confidence            4678999999999999999999999999999999999999999999999999999999999985 999999999999988


Q ss_pred             Ccccc
Q psy630           85 DSHNR   89 (347)
Q Consensus        85 ~~~~~   89 (347)
                      .++..
T Consensus       363 RPkda  367 (371)
T KOG0146|consen  363 RPKDA  367 (371)
T ss_pred             Ccccc
Confidence            77653

>PF13893 RRM_5: RNA recognition motif

Probab=98.96  E-value=8.9e-10  Score=73.08  Aligned_cols=55  Identities=27%  Similarity=0.578  Sum_probs=48.0

Q ss_pred             HHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630           25 LKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus        25 l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      |+++|++||.|..+.+..++     +++|||+|.+.++|..|+.. |+..+.|++|+|.++
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999987543     58999999999999999985 999999999998753

(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 ....

>KOG0818|consensus

Probab=98.95  E-value=2.6e-09  Score=97.14  Aligned_cols=85  Identities=28%  Similarity=0.375  Sum_probs=76.6

Q ss_pred             cHHHHHHcCChHHHHHHHhhcCCCCccccCC-CCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCC
Q psy630          257 NIYEWAKEGKLDMLVKQLTKLKDFNINQLDE-NGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEH  335 (347)
Q Consensus       257 ~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~-~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~  335 (347)
                      .++..++.++...+.++|..  |+++|..+. .|.||||.|+..|+..-+++|+- +|||+++.|..|.||+.+|-..||
T Consensus       136 QLhasvRt~nlet~LRll~l--GA~~N~~hpekg~TpLHvAAk~Gq~~Q~ElL~v-YGAD~~a~d~~GmtP~~~AR~~gH  212 (669)
T KOG0818|consen  136 QLHSSVRTGNLETCLRLLSL--GAQANFFHPEKGNTPLHVAAKAGQILQAELLAV-YGADPGAQDSSGMTPVDYARQGGH  212 (669)
T ss_pred             HHHHHhhcccHHHHHHHHHc--ccccCCCCcccCCchhHHHHhccchhhhhHHhh-ccCCCCCCCCCCCcHHHHHHhcCc
Confidence            45556778888999998888  999999875 69999999999999999999997 899999999999999999999999


Q ss_pred             HHHHHHHHh
Q psy630          336 TDLIEYLVN  344 (347)
Q Consensus       336 ~~~v~~Ll~  344 (347)
                      .+++.-|++
T Consensus       213 ~~laeRl~e  221 (669)
T KOG0818|consen  213 HELAERLVE  221 (669)
T ss_pred             hHHHHHHHH
Confidence            999887765

>PF13606 Ank_3: Ankyrin repeat

Probab=98.93  E-value=1.2e-09  Score=62.03  Aligned_cols=30  Identities=47%  Similarity=0.728  Sum_probs=26.5

Q ss_pred             CCchHHHHHHHcCCHHHHHHHHhhcCCCccc
Q psy630          288 NGLNCLHWACDRGHLKVVQHLIEKCGADVNV  318 (347)
Q Consensus       288 ~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~  318 (347)
                      +|+||||+||..|+.+++++||+ +|+|||.
T Consensus         1 ~G~T~Lh~A~~~g~~e~v~~Ll~-~gadvn~   30 (30)
T PF13606_consen    1 NGNTPLHLAASNGNIEIVKYLLE-HGADVNA   30 (30)
T ss_pred             CCCCHHHHHHHhCCHHHHHHHHH-cCCCCCC
Confidence            58899999999999999999998 6999874

>PF00023 Ank: Ankyrin repeat Hereditary spherocytosis; InterPro: IPR002110 The ankyrin repeat is one of the most common protein-protein interaction motifs in nature

Probab=98.90  E-value=2.1e-09  Score=62.80  Aligned_cols=33  Identities=42%  Similarity=0.763  Sum_probs=30.6

Q ss_pred             CCchHHHHHHHcCCHHHHHHHHhhcCCCccccCC
Q psy630          288 NGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS  321 (347)
Q Consensus       288 ~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~  321 (347)
                      +|.||||+||..|+.+++++||+ +|++++.+|.
T Consensus         1 dG~TpLh~A~~~~~~~~v~~Ll~-~ga~~~~~d~   33 (33)
T PF00023_consen    1 DGNTPLHYAAQRGHPDIVKLLLK-HGADINARDN   33 (33)
T ss_dssp             TSBBHHHHHHHTTCHHHHHHHHH-TTSCTTCBCT
T ss_pred             CcccHHHHHHHHHHHHHHHHHHH-CcCCCCCCCC
Confidence            58999999999999999999999 7999999874

Ankyrin repeats are tandemly repeated modules of about 33 amino acids. They occur in a large number of functionally diverse proteins mainly from eukaryotes. The few known examples from prokaryotes and viruses may be the result of horizontal gene transfers []. The repeat has been found in proteins of diverse function such as transcriptional initiators, cell-cycle regulators, cytoskeletal, ion transporters and signal transducers. The ankyrin fold appears to be defined by its structure rather than its function since there is no specific sequence or structure which is universally recognised by it. The conserved fold of the ankyrin repeat unit is known from several crystal and solution structures [, , , ]. Each repeat folds into a helix-loop-helix structure with a beta-hairpin/loop region projecting out from the helices at a 90o angle. The repeats stack together to form an L-shaped structure [, ].; GO: 0005515 protein binding; PDB: 1D9S_A 1NFI_F 1IKN_D 1WDY_A 1OT8_C 1QYM_A 1TR4_A 1UOH_A 1N11_A 1K1A_A ....

>KOG4208|consensus

Probab=98.90  E-value=2.6e-09  Score=86.79  Aligned_cols=78  Identities=22%  Similarity=0.422  Sum_probs=69.6

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhcc-CCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccCCCc
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEY-GQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~-G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~~~~   86 (347)
                      .-+||+.+|.-+.+.++..+|.+| |.+..+++.|++.||.|+|||||+|.+.+.|.-|-+ +|...+.|+.|.+..-.+
T Consensus        50 g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmpp  129 (214)
T KOG4208|consen   50 GVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPP  129 (214)
T ss_pred             cceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCc
Confidence            458999999999999999999988 788888999999999999999999999999999887 488888899888776544

>PF13857 Ank_5: Ankyrin repeats (many copies); PDB: 1SW6_A 3EHR_B 3EHQ_A

Probab=98.86  E-value=2.5e-09  Score=70.83  Aligned_cols=50  Identities=24%  Similarity=0.328  Sum_probs=32.1

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHH
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWA  296 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A  296 (347)
                      .+.+..|..|.|+||+|+..+..+++++|++ .+++++.+|..|+||||+|
T Consensus         7 ~~~n~~d~~G~T~LH~A~~~g~~~~v~~Ll~-~g~d~~~~d~~G~Tpl~~A   56 (56)
T PF13857_consen    7 ADVNAQDKYGNTPLHWAARYGHSEVVRLLLQ-NGADPNAKDKDGQTPLHYA   56 (56)
T ss_dssp             --TT---TTS--HHHHHHHHT-HHHHHHHHH-CT--TT---TTS--HHHH-
T ss_pred             CCCcCcCCCCCcHHHHHHHcCcHHHHHHHHH-CcCCCCCCcCCCCCHHHhC
Confidence            4567888999999999999999999999996 9999999999999999997

>KOG3676|consensus

Probab=98.86  E-value=6.8e-09  Score=100.26  Aligned_cols=90  Identities=18%  Similarity=0.190  Sum_probs=83.8

Q ss_pred             CCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCC--ccccCCCCCcHHHHHH
Q psy630          254 NEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGAD--VNVTDSDGDYGLDYAK  331 (347)
Q Consensus       254 ~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~--i~~~d~~g~TpLh~A~  331 (347)
                      -|..||..|+.-+.++++++|++ .++|++.+|..|+|.||..+.+...++..++|. +|++  ...+|.+|.|||.+|+
T Consensus       239 fGEyPLSfAAC~nq~eivrlLl~-~gAd~~aqDS~GNTVLH~lVi~~~~~My~~~L~-~ga~~l~~v~N~qgLTPLtLAa  316 (782)
T KOG3676|consen  239 FGEYPLSFAACTNQPEIVRLLLA-HGADPNAQDSNGNTVLHMLVIHFVTEMYDLALE-LGANALEHVRNNQGLTPLTLAA  316 (782)
T ss_pred             eccCchHHHHHcCCHHHHHHHHh-cCCCCCccccCCChHHHHHHHHHHHHHHHHHHh-cCCCccccccccCCCChHHHHH
Confidence            46788888888888889999999 899999999999999999999999999999999 7999  9999999999999999


Q ss_pred             HcCCHHHHHHHHhC
Q psy630          332 AIEHTDLIEYLVNS  345 (347)
Q Consensus       332 ~~~~~~~v~~Ll~~  345 (347)
                      ..|..++.+++++.
T Consensus       317 klGk~emf~~ile~  330 (782)
T KOG3676|consen  317 KLGKKEMFQHILER  330 (782)
T ss_pred             HhhhHHHHHHHHHh
Confidence            99999999998875

>KOG0106|consensus

Probab=98.85  E-value=3e-09  Score=88.71  Aligned_cols=116  Identities=22%  Similarity=0.419  Sum_probs=92.5

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCcc
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDSH   87 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~~   87 (347)
                      .++|||+||+.+.+.+++.+|..||.+..+.+.        .||+||+|.+..+|..|+.. ++..+.|..+.|.++...
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            579999999999999999999999999888763        47999999999999999985 999999988888877642


Q ss_pred             ccc-------------chhhhhhcccccccccCCcccccchhhHHHHhhccccceecc
Q psy630           88 NRM-------------AENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQC  132 (347)
Q Consensus        88 ~~~-------------~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~  132 (347)
                      ...             ............+.|.++.....+.+|.+.|..||++++...
T Consensus        74 ~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~  131 (216)
T KOG0106|consen   74 RRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA  131 (216)
T ss_pred             ccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh
Confidence            110             001111223456778888888999999999999999975544

>KOG0124|consensus

Probab=98.85  E-value=4.1e-09  Score=92.33  Aligned_cols=83  Identities=19%  Similarity=0.439  Sum_probs=75.4

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      +.+...+|||..+-++.++++|+..|+.||+|..|++.+++.++..+||+|++|.+..+...|+.. |-..++|+.|+|.
T Consensus       206 eAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVG  285 (544)
T KOG0124|consen  206 EAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVG  285 (544)
T ss_pred             HHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecc
Confidence            345667999999999999999999999999999999999998888999999999999999999974 9999999999998


Q ss_pred             CCCc
Q psy630           83 PSDS   86 (347)
Q Consensus        83 ~~~~   86 (347)
                      .+-.
T Consensus       286 k~vT  289 (544)
T KOG0124|consen  286 KCVT  289 (544)
T ss_pred             cccC
Confidence            6544

>KOG0415|consensus

Probab=98.84  E-value=3.9e-09  Score=92.08  Aligned_cols=82  Identities=28%  Similarity=0.523  Sum_probs=75.3

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~~~   85 (347)
                      +-+-|||=.|.|-+|+++|+-+|+.||.|.+|.|++|+.||.+-.||||+|.+.++.++|.- ++...|.++.|.|.+++
T Consensus       238 PeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQ  317 (479)
T KOG0415|consen  238 PENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQ  317 (479)
T ss_pred             CcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhh
Confidence            44679999999999999999999999999999999999999999999999999999999985 58889999999998876


Q ss_pred             ccc
Q psy630           86 SHN   88 (347)
Q Consensus        86 ~~~   88 (347)
                      +-.
T Consensus       318 SVs  320 (479)
T KOG0415|consen  318 SVS  320 (479)
T ss_pred             hhh
Confidence            643

>KOG0783|consensus

Probab=98.83  E-value=1.5e-09  Score=104.29  Aligned_cols=85  Identities=19%  Similarity=0.279  Sum_probs=72.8

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCC-CCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCC
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDE-NGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGD  324 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~-~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~  324 (347)
                      +-.+..|..|++++|.+...+...+++.|++ +|++++.+|. .|+||||-|...|+++++.+||. +|+.+..+|.+|.
T Consensus        43 n~anikD~~GR~alH~~~S~~k~~~l~wLlq-hGidv~vqD~ESG~taLHRaiyyG~idca~lLL~-~g~SL~i~Dkegl  120 (1267)
T KOG0783|consen   43 NLANIKDRYGRTALHIAVSENKNSFLRWLLQ-HGIDVFVQDEESGYTALHRAIYYGNIDCASLLLS-KGRSLRIKDKEGL  120 (1267)
T ss_pred             hhhhHHHhhccceeeeeeccchhHHHHHHHh-cCceeeeccccccchHhhHhhhhchHHHHHHHHh-cCCceEEecccCC
Confidence            3467788889999998888888888888888 6899988886 68999999999999999999998 6999999999999


Q ss_pred             cHHHHHHH
Q psy630          325 YGLDYAKA  332 (347)
Q Consensus       325 TpLh~A~~  332 (347)
                      .||..-++
T Consensus       121 splq~~~r  128 (1267)
T KOG0783|consen  121 SPLQFLSR  128 (1267)
T ss_pred             CHHHHHhh
Confidence            99888766

>KOG0146|consensus

Probab=98.83  E-value=3.5e-09  Score=89.02  Aligned_cols=83  Identities=27%  Similarity=0.502  Sum_probs=71.2

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-C-CCccCC--cccccc
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-D-SHVLEG--SRLSIQ   82 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~-~~~~~g--~~l~v~   82 (347)
                      +.|+||||-|.+.-.|++++.+|..||.|.+|.+.+... |.++|||||.|.+.-+|+.||.. + ...+.|  ..|.|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~d-g~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPD-GNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCC-CCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            678999999999999999999999999999999999875 99999999999999999999974 3 334444  467778


Q ss_pred             CCCccccc
Q psy630           83 PSDSHNRM   90 (347)
Q Consensus        83 ~~~~~~~~   90 (347)
                      +++..++|
T Consensus        97 ~ADTdkER  104 (371)
T KOG0146|consen   97 FADTDKER  104 (371)
T ss_pred             eccchHHH
Confidence            87765543

>KOG0109|consensus

Probab=98.82  E-value=3.7e-09  Score=90.04  Aligned_cols=77  Identities=27%  Similarity=0.509  Sum_probs=69.3

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      ....++|+||||.+.++.++|+..|++||+|.+|.|++        +|+||.|...+.|..|++. ++.+|.|+++.|+.
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk--------dy~fvh~d~~eda~~air~l~~~~~~gk~m~vq~  146 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK--------DYAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQL  146 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeeec--------ceeEEEEeeccchHHHHhcccccccccceeeeee
Confidence            34667999999999999999999999999999999975        5999999999999999975 99999999999998


Q ss_pred             CCcccc
Q psy630           84 SDSHNR   89 (347)
Q Consensus        84 ~~~~~~   89 (347)
                      +.++-+
T Consensus       147 stsrlr  152 (346)
T KOG0109|consen  147 STSRLR  152 (346)
T ss_pred             eccccc
Confidence            766543

>PTZ00322 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional

Probab=98.80  E-value=9.7e-09  Score=102.34  Aligned_cols=85  Identities=21%  Similarity=0.122  Sum_probs=77.5

Q ss_pred             ccCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhc-------CCCcc
Q psy630          245 INDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKC-------GADVN  317 (347)
Q Consensus       245 ~~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~-------ga~i~  317 (347)
                      ..+.+..|..|.|+||+|+..++..++++|+. .|++++.+|..|.||||+|+..|+.+++++|+. +       |++++
T Consensus       105 Gadin~~d~~G~TpLh~Aa~~g~~eiv~~LL~-~Gadvn~~d~~G~TpLh~A~~~g~~~iv~~Ll~-~~~~~~~~ga~~~  182 (664)
T PTZ00322        105 GADPNCRDYDGRTPLHIACANGHVQVVRVLLE-FGADPTLLDKDGKTPLELAEENGFREVVQLLSR-HSQCHFELGANAK  182 (664)
T ss_pred             CCCCCCcCCCCCcHHHHHHHCCCHHHHHHHHH-CCCCCCCCCCCCCCHHHHHHHCCcHHHHHHHHh-CCCcccccCCCCC
Confidence            34677888999999999999999999999999 799999999999999999999999999999998 7       89999


Q ss_pred             ccCCCCCcHHHHHH
Q psy630          318 VTDSDGDYGLDYAK  331 (347)
Q Consensus       318 ~~d~~g~TpLh~A~  331 (347)
                      ..+..|.+|+..+.
T Consensus       183 ~~~~~g~~~~~~~~  196 (664)
T PTZ00322        183 PDSFTGKPPSLEDS  196 (664)
T ss_pred             ccccCCCCccchhh
Confidence            99998988876554

>KOG4661|consensus

Probab=98.76  E-value=1.3e-08  Score=94.00  Aligned_cols=80  Identities=24%  Similarity=0.449  Sum_probs=74.1

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      -.|+|||++|+..+...+|+.+|++||.|+..+++++..+.-.++|+||+..+.+.|.+||.. +.+.++|+.|.|..+.
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            357999999999999999999999999999999999987777899999999999999999985 9999999999998765


Q ss_pred             c
Q psy630           86 S   86 (347)
Q Consensus        86 ~   86 (347)
                      .
T Consensus       484 N  484 (940)
T KOG4661|consen  484 N  484 (940)
T ss_pred             c
Confidence            5

>KOG0116|consensus

Probab=98.76  E-value=1.6e-08  Score=93.25  Aligned_cols=81  Identities=27%  Similarity=0.480  Sum_probs=70.1

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSD   85 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~   85 (347)
                      ....+|||+|||++++..+|+++|++||.|....|......++..+||||+|.+..+++.|+..+...++|+++.|....
T Consensus       286 ~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  286 ADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEKR  365 (419)
T ss_pred             ecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEecc
Confidence            34456999999999999999999999999999888765433555599999999999999999999999999999997554


Q ss_pred             c
Q psy630           86 S   86 (347)
Q Consensus        86 ~   86 (347)
                      +
T Consensus       366 ~  366 (419)
T KOG0116|consen  366 P  366 (419)
T ss_pred             c
Confidence            4

>PF13606 Ank_3: Ankyrin repeat

Probab=98.75  E-value=1e-08  Score=58.21  Aligned_cols=26  Identities=23%  Similarity=0.562  Sum_probs=24.9

Q ss_pred             CCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          322 DGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       322 ~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      +|+||||+||..|+.+++++||++||
T Consensus         1 ~G~T~Lh~A~~~g~~e~v~~Ll~~ga   26 (30)
T PF13606_consen    1 NGNTPLHLAASNGNIEIVKYLLEHGA   26 (30)
T ss_pred             CCCCHHHHHHHhCCHHHHHHHHHcCC
Confidence            58999999999999999999999996

>KOG0110|consensus

Probab=98.72  E-value=1.1e-08  Score=97.09  Aligned_cols=82  Identities=30%  Similarity=0.561  Sum_probs=74.5

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCc
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~   86 (347)
                      .++|+|+|||+..+-.+++++|..||.+.+|+|+.-...+.++|||||+|-++.+|..|+.. ..+-+.||.|.++|+..
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~  692 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKS  692 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhcc
Confidence            57999999999999999999999999999999998755677899999999999999999975 78889999999999987


Q ss_pred             ccc
Q psy630           87 HNR   89 (347)
Q Consensus        87 ~~~   89 (347)
                      ...
T Consensus       693 d~~  695 (725)
T KOG0110|consen  693 DNT  695 (725)
T ss_pred             chH
Confidence            543

>KOG4454|consensus

Probab=98.71  E-value=7.1e-09  Score=84.82  Aligned_cols=116  Identities=16%  Similarity=0.193  Sum_probs=92.0

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI   81 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v   81 (347)
                      .+++..++|||+|+...++++.|.++|-+.|+|..|.|+.++. ++.+ ||||.|.++.+..-|+.+ ||..+.++.+.|
T Consensus         4 aaae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~   81 (267)
T KOG4454|consen    4 AAAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQR   81 (267)
T ss_pred             CCcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccchhhc
Confidence            3567789999999999999999999999999999999988875 6666 999999999999999997 999999999888


Q ss_pred             cCCCcccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCC
Q psy630           82 QPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDK  136 (347)
Q Consensus        82 ~~~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~  136 (347)
                      ++-.....           +     -+...++.+.+...|+.-+.+.-+.+....
T Consensus        82 ~~r~G~sh-----------a-----pld~r~~~ei~~~v~s~a~p~~~~R~~~~~  120 (267)
T KOG4454|consen   82 TLRCGNSH-----------A-----PLDERVTEEILYEVFSQAGPIEGVRIPTDN  120 (267)
T ss_pred             ccccCCCc-----------c-----hhhhhcchhhheeeecccCCCCCccccccc
Confidence            75433211           1     133446667777777777777666655543

>KOG0522|consensus

Probab=98.71  E-value=4.2e-08  Score=90.47  Aligned_cols=87  Identities=25%  Similarity=0.375  Sum_probs=72.4

Q ss_pred             cHHHHHH-cCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCC
Q psy630          257 NIYEWAK-EGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEH  335 (347)
Q Consensus       257 ~~l~~a~-~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~  335 (347)
                      .++|++. ..+...+.+.|.......++..|..|.||||+|+..||...++.|+. +||++..+|..||+|||-|+..|+
T Consensus        22 ~~lh~~~~~~~~~sl~~el~~~~~~~id~~D~~g~TpLhlAV~Lg~~~~a~~Ll~-a~Adv~~kN~~gWs~L~EAv~~g~  100 (560)
T KOG0522|consen   22 KPLHWAVVTTDSDSLEQELLAKVSLVIDRRDPPGRTPLHLAVRLGHVEAARILLS-AGADVSIKNNEGWSPLHEAVSTGN  100 (560)
T ss_pred             cccchhhhccchhhHHHHHhhhhhceeccccCCCCccHHHHHHhcCHHHHHHHHh-cCCCccccccccccHHHHHHHcCC
Confidence            3455554 45555666655553567789999999999999999999999999999 799999999999999999999999


Q ss_pred             HHHHHHHHh
Q psy630          336 TDLIEYLVN  344 (347)
Q Consensus       336 ~~~v~~Ll~  344 (347)
                      ..++..+|.
T Consensus       101 ~q~i~~vlr  109 (560)
T KOG0522|consen  101 EQIITEVLR  109 (560)
T ss_pred             HHHHHHHHH
Confidence            988776654

>KOG4369|consensus

Probab=98.68  E-value=8.4e-09  Score=102.05  Aligned_cols=92  Identities=33%  Similarity=0.362  Sum_probs=76.1

Q ss_pred             CCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCcccc-CCCCCcHHHHHHH
Q psy630          254 NEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVT-DSDGDYGLDYAKA  332 (347)
Q Consensus       254 ~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~-d~~g~TpLh~A~~  332 (347)
                      .-.+.|..||.|++.+++++|+. .|+++..+|..|.+||.+|+-.||..+|..||+ +.++|.++ |..+.|+|.+||.
T Consensus       756 n~~t~LT~acaggh~e~vellv~-rganiehrdkkgf~plImaatagh~tvV~~llk-~ha~veaQsdrtkdt~lSlacs  833 (2131)
T KOG4369|consen  756 NIKTNLTSACAGGHREEVELLVV-RGANIEHRDKKGFVPLIMAATAGHITVVQDLLK-AHADVEAQSDRTKDTMLSLACS  833 (2131)
T ss_pred             cccccccccccCccHHHHHHHHH-hcccccccccccchhhhhhcccCchHHHHHHHh-hhhhhhhhcccccCceEEEecC
Confidence            34577888888888888888887 688888888888888888888888888888887 68888876 6678888888888


Q ss_pred             cCCHHHHHHHHhCCC
Q psy630          333 IEHTDLIEYLVNSGS  347 (347)
Q Consensus       333 ~~~~~~v~~Ll~~GA  347 (347)
                      .|++++|++||.+||
T Consensus       834 ggr~~vvelLl~~ga  848 (2131)
T KOG4369|consen  834 GGRTRVVELLLNAGA  848 (2131)
T ss_pred             CCcchHHHHHHHhhc
Confidence            888888888888876

>KOG4212|consensus

Probab=98.67  E-value=2.8e-08  Score=89.10  Aligned_cols=74  Identities=27%  Similarity=0.503  Sum_probs=67.3

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      .++.++|||+|||+++|.+.|++-|..||.|..+.|+.   .|+++|  .|.|.+++.|++|+.. ++..+.||.|.|.+
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y  607 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTY  607 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeee
Confidence            46678899999999999999999999999999999964   378887  8999999999999997 99999999999865

>KOG1548|consensus

Probab=98.66  E-value=5.8e-08  Score=84.81  Aligned_cols=164  Identities=17%  Similarity=0.255  Sum_probs=112.6

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeE--------EEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCcc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMN--------ASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVL   74 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~--------~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~   74 (347)
                      .+...+.|||+|||.++|.+++.++|++||.|..        |++.++.. |+.+|=|.+.|-..+++..|+.. ++..+
T Consensus       130 ~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~-G~lKGDaLc~y~K~ESVeLA~~ilDe~~~  208 (382)
T KOG1548|consen  130 EPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDEL  208 (382)
T ss_pred             ccccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCcccc
Confidence            3455677999999999999999999999997743        78888875 99999999999999999999996 99999


Q ss_pred             CCccccccCCCcccc-----------------cchhh--------------hhhcccccccccCCcc--c--cc------
Q psy630           75 EGSRLSIQPSDSHNR-----------------MAENM--------------EDRFNQACDYLPSLVK--K--LD------  113 (347)
Q Consensus        75 ~g~~l~v~~~~~~~~-----------------~~~~~--------------~~~f~~~~~~v~~l~~--~--~~------  113 (347)
                      .|+.|+|++|.-...                 +....              ...-..+++.++|+-.  .  -+      
T Consensus       209 rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~d  288 (382)
T KOG1548|consen  209 RGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLND  288 (382)
T ss_pred             cCcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHH
Confidence            999999997654210                 00000              0001125677777632  1  12      


Q ss_pred             -chhhHHHHhhccccceecccCCCC-CccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhhccCChhhhhh
Q psy630          114 -SSTLLKFYALYKQATVGQCNIDKP-SWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEE  184 (347)
Q Consensus       114 -~e~l~~~f~~fg~v~~g~~~~~~p-~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~l~~~~~~~~~~~  184 (347)
                       .++|++-...||++....+.-..| |...+            ..-+.++|..-    ++-|...|.+.++-.
T Consensus       289 lkedl~eec~K~G~v~~vvv~d~hPdGvvtV------------~f~n~eeA~~c----iq~m~GR~fdgRql~  345 (382)
T KOG1548|consen  289 LKEDLTEECEKFGQVRKVVVYDRHPDGVVTV------------SFRNNEEADQC----IQTMDGRWFDGRQLT  345 (382)
T ss_pred             HHHHHHHHHHHhCCcceEEEeccCCCceeEE------------EeCChHHHHHH----HHHhcCeeecceEEE
Confidence             245667789999998766654444 32222            12234455432    566677888765433

>KOG0783|consensus

Probab=98.61  E-value=3e-08  Score=95.63  Aligned_cols=77  Identities=26%  Similarity=0.238  Sum_probs=68.5

Q ss_pred             HHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCC-CCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          270 LVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS-DGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       270 ~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~-~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      +.-++....+--+|.+|..|+|+||+|+..+..+++++||+ +|++++.+|. .|+||||-|...|+.+|+-+||.+|+
T Consensus        33 lk~F~~k~c~n~anikD~~GR~alH~~~S~~k~~~l~wLlq-hGidv~vqD~ESG~taLHRaiyyG~idca~lLL~~g~  110 (1267)
T KOG0783|consen   33 LKGFSEKSCQNLANIKDRYGRTALHIAVSENKNSFLRWLLQ-HGIDVFVQDEESGYTALHRAIYYGNIDCASLLLSKGR  110 (1267)
T ss_pred             HHHHHHHhhhhhhhHHHhhccceeeeeeccchhHHHHHHHh-cCceeeeccccccchHhhHhhhhchHHHHHHHHhcCC
Confidence            45555554444578999999999999999999999999999 6999999998 59999999999999999999999985

>KOG4209|consensus

Probab=98.59  E-value=5.9e-08  Score=83.06  Aligned_cols=81  Identities=25%  Similarity=0.466  Sum_probs=75.2

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSD   85 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~   85 (347)
                      -+.+.+||||+.+.+|-+++..+|+.||.|..+.++.++.+|.++||+||+|.+.+.+..++.+++..+.|+.+.|.+..
T Consensus        99 ~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt~~r  178 (231)
T KOG4209|consen   99 VDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVTLKR  178 (231)
T ss_pred             cCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceeeeee
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999987654


Q ss_pred             c
Q psy630           86 S   86 (347)
Q Consensus        86 ~   86 (347)
                      .
T Consensus       179 ~  179 (231)
T KOG4209|consen  179 T  179 (231)
T ss_pred             e
Confidence            3

>PF00023 Ank: Ankyrin repeat Hereditary spherocytosis; InterPro: IPR002110 The ankyrin repeat is one of the most common protein-protein interaction motifs in nature

Probab=98.56  E-value=7.7e-08  Score=56.10  Aligned_cols=26  Identities=35%  Similarity=0.677  Sum_probs=24.9

Q ss_pred             CCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          322 DGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       322 ~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      +|.||||+|+..|+.+++++||++||
T Consensus         1 dG~TpLh~A~~~~~~~~v~~Ll~~ga   26 (33)
T PF00023_consen    1 DGNTPLHYAAQRGHPDIVKLLLKHGA   26 (33)
T ss_dssp             TSBBHHHHHHHTTCHHHHHHHHHTTS
T ss_pred             CcccHHHHHHHHHHHHHHHHHHHCcC
Confidence            58999999999999999999999997

Ankyrin repeats are tandemly repeated modules of about 33 amino acids. They occur in a large number of functionally diverse proteins mainly from eukaryotes. The few known examples from prokaryotes and viruses may be the result of horizontal gene transfers []. The repeat has been found in proteins of diverse function such as transcriptional initiators, cell-cycle regulators, cytoskeletal, ion transporters and signal transducers. The ankyrin fold appears to be defined by its structure rather than its function since there is no specific sequence or structure which is universally recognised by it. The conserved fold of the ankyrin repeat unit is known from several crystal and solution structures [, , , ]. Each repeat folds into a helix-loop-helix structure with a beta-hairpin/loop region projecting out from the helices at a 90o angle. The repeats stack together to form an L-shaped structure [, ].; GO: 0005515 protein binding; PDB: 1D9S_A 1NFI_F 1IKN_D 1WDY_A 1OT8_C 1QYM_A 1TR4_A 1UOH_A 1N11_A 1K1A_A ....

>KOG0226|consensus

Probab=98.56  E-value=6.3e-08  Score=81.13  Aligned_cols=86  Identities=24%  Similarity=0.424  Sum_probs=77.2

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI   81 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v   81 (347)
                      +-+.+.-+||.|.|..+++++-|-..|.+|-.-...++++++.||+++||+||-|.+..++.+|+.. +|..++.++|..
T Consensus       185 ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpikl  264 (290)
T KOG0226|consen  185 EWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKL  264 (290)
T ss_pred             cCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHh
Confidence            4456677899999999999999999999998878889999999999999999999999999999985 999999999998


Q ss_pred             cCCCccc
Q psy630           82 QPSDSHN   88 (347)
Q Consensus        82 ~~~~~~~   88 (347)
                      ..+..+.
T Consensus       265 RkS~wke  271 (290)
T KOG0226|consen  265 RKSEWKE  271 (290)
T ss_pred             hhhhHHh
Confidence            7665554

>KOG0132|consensus

Probab=98.55  E-value=1e-07  Score=91.27  Aligned_cols=77  Identities=17%  Similarity=0.406  Sum_probs=69.6

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCc
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~   86 (347)
                      .||||||+||..+++.+|..+|+.||.|.+|.++..      +|||||......+|.+|+.. +...+.++.|+|.|+..
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            479999999999999999999999999999988654      58999999999999999985 88889999999999987


Q ss_pred             cccc
Q psy630           87 HNRM   90 (347)
Q Consensus        87 ~~~~   90 (347)
                      +.-+
T Consensus       495 ~G~k  498 (894)
T KOG0132|consen  495 KGPK  498 (894)
T ss_pred             CCcc
Confidence            6643

>KOG0129|consensus

Probab=98.53  E-value=2.6e-07  Score=85.00  Aligned_cols=130  Identities=18%  Similarity=0.334  Sum_probs=86.7

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCC---CCcee---EEEEEEcCHHHHHHHHhcCCCccCCcc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNT---GLSKG---FGFVTFQNKEAVDKVFSTDSHVLEGSR   78 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t---~~~~g---~afV~f~~~~~a~~a~~~~~~~~~g~~   78 (347)
                      +.-.++||||+||++++|+.|...|..||.+ .|.++...+.   --++|   |+|+.|+++.++..-+...-..-.+..
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~y  334 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGNYY  334 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccceE
Confidence            3446799999999999999999999999976 4555532111   12466   999999998887766643111111111


Q ss_pred             ccccCCCcccc-------------cch-hhhhhcccccccccCCcccccchhhHHHHh-hccccceecccCC
Q psy630           79 LSIQPSDSHNR-------------MAE-NMEDRFNQACDYLPSLVKKLDSSTLLKFYA-LYKQATVGQCNID  135 (347)
Q Consensus        79 l~v~~~~~~~~-------------~~~-~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~-~fg~v~~g~~~~~  135 (347)
                      +.|.-..-+..             ... .....-...++||++||-.++.++|..+|. .||.|..+-|.++
T Consensus       335 f~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD  406 (520)
T KOG0129|consen  335 FKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTD  406 (520)
T ss_pred             EEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccC
Confidence            22211111000             000 111222457999999999999999999999 9999999888887

>KOG0533|consensus

Probab=98.52  E-value=2.6e-07  Score=78.95  Aligned_cols=80  Identities=28%  Similarity=0.546  Sum_probs=71.6

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      ...+|+|.|||+.+++++|+++|..||.+..+-+-.++ .|.+.|.|-|.|...++|.+|++. ++..++|+++.+....
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~  160 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIIS  160 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEec
Confidence            34689999999999999999999999988888888887 599999999999999999999985 8899999999887665


Q ss_pred             cc
Q psy630           86 SH   87 (347)
Q Consensus        86 ~~   87 (347)
                      +.
T Consensus       161 ~~  162 (243)
T KOG0533|consen  161 SP  162 (243)
T ss_pred             Cc
Confidence            53

>KOG4369|consensus

Probab=98.36  E-value=1.9e-07  Score=92.74  Aligned_cols=99  Identities=23%  Similarity=0.255  Sum_probs=72.8

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCcccc-CCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQL-DENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~-d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      .+...|..|.+++..|+-+++..+++.|+. ..+++..+ |..+.|+|.+||..|+.++|.+||. +|++-..++-...|
T Consensus       782 niehrdkkgf~plImaatagh~tvV~~llk-~ha~veaQsdrtkdt~lSlacsggr~~vvelLl~-~gankehrnvsDyt  859 (2131)
T KOG4369|consen  782 NIEHRDKKGFVPLIMAATAGHITVVQDLLK-AHADVEAQSDRTKDTMLSLACSGGRTRVVELLLN-AGANKEHRNVSDYT  859 (2131)
T ss_pred             cccccccccchhhhhhcccCchHHHHHHHh-hhhhhhhhcccccCceEEEecCCCcchHHHHHHH-hhccccccchhhcC
Confidence            456667777777777777777777777776 56666653 6677777777777777777777777 57777777777777


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||.+|...|..++|.+||.+|+
T Consensus       860 Plsla~Sggy~~iI~~llS~Gs  881 (2131)
T KOG4369|consen  860 PLSLARSGGYTKIIHALLSSGS  881 (2131)
T ss_pred             chhhhcCcchHHHHHHHhhccc
Confidence            7777777777777777777774

>KOG2384|consensus

Probab=98.36  E-value=8.9e-07  Score=71.41  Aligned_cols=66  Identities=27%  Similarity=0.238  Sum_probs=61.6

Q ss_pred             CCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcC-CCccccCCCCCcHHHHHHHcCCHHHHHHHHhC
Q psy630          279 DFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCG-ADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNS  345 (347)
Q Consensus       279 ~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~g-a~i~~~d~~g~TpLh~A~~~~~~~~v~~Ll~~  345 (347)
                      +.++|.+|..|||||+.|+..|..+.+.+|+. .| +.|...|..|.+++.+|-..|+.+++..|.++
T Consensus         2 e~~in~rD~fgWTalmcaa~eg~~eavsyllg-rg~a~vgv~d~ssldaaqlaek~g~~~fvh~lfe~   68 (223)
T KOG2384|consen    2 EGNINARDAFGWTALMCAAMEGSNEAVSYLLG-RGVAFVGVTDESSLDAAQLAEKGGAQAFVHSLFEN   68 (223)
T ss_pred             CCCccchhhhcchHHHHHhhhcchhHHHHHhc-cCcccccccccccchHHHHHHhcChHHHHHHHHHH
Confidence            46799999999999999999999999999999 59 89999999999999999999999999988764

>KOG0511|consensus

Probab=98.34  E-value=8.7e-07  Score=78.62  Aligned_cols=73  Identities=27%  Similarity=0.315  Sum_probs=56.9

Q ss_pred             CcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHH
Q psy630          256 KNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKA  332 (347)
Q Consensus       256 ~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~  332 (347)
                      ..++.+|+.|+.+.+..++.  .|.++|..|....+||.+|+..||.++|++||+ +||-...-..+|.-. ||++.
T Consensus        38 ~elceacR~GD~d~v~~LVe--tgvnVN~vD~fD~spL~lAsLcGHe~vvklLLe-nGAiC~rdtf~G~RC-~YgaL  110 (516)
T KOG0511|consen   38 GELCEACRAGDVDRVRYLVE--TGVNVNAVDRFDSSPLYLASLCGHEDVVKLLLE-NGAICSRDTFDGDRC-HYGAL  110 (516)
T ss_pred             HHHHHHhhcccHHHHHHHHH--hCCCcchhhcccccHHHHHHHcCcHHHHHHHHH-cCCcccccccCcchh-hhhhh
Confidence            35666777777776555554  599999999999999999999999999999998 798777666677644 44444

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.34  E-value=3.7e-06  Score=61.53  Aligned_cols=67  Identities=16%  Similarity=0.315  Sum_probs=58.2

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhc--cCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccC
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSE--YGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLE   75 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~--~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~   75 (347)
                      +||-|+|||...|.++|.+.+..  .|..-.+.++.|..++.+.|||||.|.+.+.+.+-... +|..+.
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~   71 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWP   71 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccc
Confidence            68999999999999999988864  36777889999999999999999999999999888775 766664

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG0782|consensus

Probab=98.32  E-value=2.3e-06  Score=79.67  Aligned_cols=92  Identities=25%  Similarity=0.306  Sum_probs=53.1

Q ss_pred             CCCCCcHHHHHHcCChHHHHHHHhhcCCC-CccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHH
Q psy630          252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDF-NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA  330 (347)
Q Consensus       252 ~~~~~~~l~~a~~~~~~~~~~lL~~~~~~-~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A  330 (347)
                      +.+..++||+|+..+..+++++|+++.+. .++..|..|.|+||-|+..++-.++.+|++ .||.+...|..|.||-.-|
T Consensus       896 ~~~~~sllh~a~~tg~~eivkyildh~p~elld~~de~get~lhkaa~~~~r~vc~~lvd-agasl~ktd~kg~tp~era  974 (1004)
T KOG0782|consen  896 GPDHCSLLHYAAKTGNGEIVKYILDHGPSELLDMADETGETALHKAACQRNRAVCQLLVD-AGASLRKTDSKGKTPQERA  974 (1004)
T ss_pred             CcchhhHHHHHHhcCChHHHHHHHhcCCHHHHHHHhhhhhHHHHHHHHhcchHHHHHHHh-cchhheecccCCCChHHHH
Confidence            34445566666655555566655553222 234455566666666666666666666665 5666666666666666666


Q ss_pred             HHcCCHHHHHHHHh
Q psy630          331 KAIEHTDLIEYLVN  344 (347)
Q Consensus       331 ~~~~~~~~v~~Ll~  344 (347)
                      -..|..+++.||-.
T Consensus       975 qqa~d~dlaayle~  988 (1004)
T KOG0782|consen  975 QQAGDPDLAAYLES  988 (1004)
T ss_pred             HhcCCchHHHHHhh
Confidence            66666666665543

>KOG0782|consensus

Probab=98.31  E-value=1.1e-06  Score=81.60  Aligned_cols=92  Identities=17%  Similarity=0.277  Sum_probs=80.0

Q ss_pred             CCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCC--ccccCCCCCcHHHHH
Q psy630          253 DNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGAD--VNVTDSDGDYGLDYA  330 (347)
Q Consensus       253 ~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~--i~~~d~~g~TpLh~A  330 (347)
                      ..+.++|.++..+++-.+.+.-..  |.++-.++.+..|.||+|+..|+-+||++||+ +|-.  ++..|..|.|+||-|
T Consensus       865 piseeil~av~~~D~~klqE~h~~--gg~ll~~~~~~~sllh~a~~tg~~eivkyild-h~p~elld~~de~get~lhka  941 (1004)
T KOG0782|consen  865 PISEEILRAVLSSDLMKLQETHLN--GGSLLIQGPDHCSLLHYAAKTGNGEIVKYILD-HGPSELLDMADETGETALHKA  941 (1004)
T ss_pred             CccHHHHHHHHhccHHHHHHHHhc--CCceEeeCcchhhHHHHHHhcCChHHHHHHHh-cCCHHHHHHHhhhhhHHHHHH
Confidence            345678999999998877777666  66777888999999999999999999999999 5653  566788999999999


Q ss_pred             HHcCCHHHHHHHHhCCC
Q psy630          331 KAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       331 ~~~~~~~~v~~Ll~~GA  347 (347)
                      +..++..++.+|++.||
T Consensus       942 a~~~~r~vc~~lvdaga  958 (1004)
T KOG0782|consen  942 ACQRNRAVCQLLVDAGA  958 (1004)
T ss_pred             HHhcchHHHHHHHhcch
Confidence            99999999999999997

>KOG0520|consensus

Probab=98.30  E-value=3.7e-07  Score=90.74  Aligned_cols=96  Identities=17%  Similarity=0.241  Sum_probs=66.1

Q ss_pred             cCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHH
Q psy630          251 LDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA  330 (347)
Q Consensus       251 ~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A  330 (347)
                      ..-.+++++|.++......+++.+.+..+......|.+|.-.+|+ |..++.+.+-+|+.-+|..++.+|..||||||||
T Consensus       570 ~~~r~~lllhL~a~~lyawLie~~~e~~~~~~~eld~d~qgV~hf-ca~lg~ewA~ll~~~~~~ai~i~D~~G~tpL~wA  648 (975)
T KOG0520|consen  570 VNFRDMLLLHLLAELLYAWLIEKVIEWAGSGDLELDRDGQGVIHF-CAALGYEWAFLPISADGVAIDIRDRNGWTPLHWA  648 (975)
T ss_pred             CCCcchHHHHHHHHHhHHHHHHHHhcccccCchhhcccCCChhhH-hhhcCCceeEEEEeecccccccccCCCCcccchH
Confidence            345667777777777777777777763355555566666666666 5556666665555446777777888888888888


Q ss_pred             HHcCCHHHHHHHHhCCC
Q psy630          331 KAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       331 ~~~~~~~~v~~Ll~~GA  347 (347)
                      +..|+..++..|++.||
T Consensus       649 a~~G~e~l~a~l~~lga  665 (975)
T KOG0520|consen  649 AFRGREKLVASLIELGA  665 (975)
T ss_pred             hhcCHHHHHHHHHHhcc
Confidence            88888777777776664

>KOG0151|consensus

Probab=98.28  E-value=1.1e-06  Score=83.70  Aligned_cols=82  Identities=20%  Similarity=0.410  Sum_probs=70.8

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeC---CCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDK---NTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLS   80 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~---~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~   80 (347)
                      ...++++||+||++.++++.|...|..||+|.+++|+..+   .....+-|+||-|-+..++++|++. ++..+.++.++
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K  250 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMK  250 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeee
Confidence            3457899999999999999999999999999999998554   2244568999999999999999986 99999999988


Q ss_pred             ccCCCc
Q psy630           81 IQPSDS   86 (347)
Q Consensus        81 v~~~~~   86 (347)
                      +.|..+
T Consensus       251 ~gWgk~  256 (877)
T KOG0151|consen  251 LGWGKA  256 (877)
T ss_pred             eccccc
Confidence            887633

>KOG0120|consensus

Probab=98.25  E-value=1.9e-06  Score=80.72  Aligned_cols=84  Identities=26%  Similarity=0.471  Sum_probs=77.0

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      +....++||++||...++.+++++...||.+....++.+..+|.++||||-+|.+......|+.. ||..+.++.+.|+.
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~  365 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQR  365 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeeh
Confidence            34456899999999999999999999999999999999999999999999999999999999985 99999999999998


Q ss_pred             CCccc
Q psy630           84 SDSHN   88 (347)
Q Consensus        84 ~~~~~   88 (347)
                      +....
T Consensus       366 A~~g~  370 (500)
T KOG0120|consen  366 AIVGA  370 (500)
T ss_pred             hhccc
Confidence            76644

>KOG4660|consensus

Probab=98.22  E-value=1.1e-06  Score=81.64  Aligned_cols=72  Identities=25%  Similarity=0.446  Sum_probs=63.8

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLS   80 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~   80 (347)
                      +.-..++|+|-|||.++++++|+..|+.||+|..|+.     |-..+|.+||+|.+...|++|++. ++..+.|+.+.
T Consensus        71 ~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   71 KDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             ccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            3456789999999999999999999999999999765     445579999999999999999986 99999998887

>KOG1190|consensus

Probab=98.22  E-value=5.1e-06  Score=74.38  Aligned_cols=116  Identities=16%  Similarity=0.275  Sum_probs=91.4

Q ss_pred             CCeEEEeCCCCC-CCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630            8 LNKIFVGNLPWT-VSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus         8 ~~~l~V~nLp~~-~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      ...|-|.||... +|.+-|.-+|..||.|..|+|..++.     --|.|.+.+...|+.|+.. +|+.+.|++|+|.++.
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            457888998765 79999999999999999999998763     5799999999999999986 9999999999998653


Q ss_pred             ccc------c-----------------cchhhhh----hc-ccccccccCCcccccchhhHHHHhhccccc
Q psy630           86 SHN------R-----------------MAENMED----RF-NQACDYLPSLVKKLDSSTLLKFYALYKQAT  128 (347)
Q Consensus        86 ~~~------~-----------------~~~~~~~----~f-~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~  128 (347)
                      -..      .                 ..++...    .| ..+++++.|+|+.+++|+++.+|..-|-..
T Consensus       372 H~~vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~v  442 (492)
T KOG1190|consen  372 HTNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQV  442 (492)
T ss_pred             CccccCCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcCCceE
Confidence            211      0                 0000011    11 236889999999999999999999877653

>KOG0521|consensus

Probab=98.18  E-value=1.7e-06  Score=86.47  Aligned_cols=89  Identities=28%  Similarity=0.312  Sum_probs=81.1

Q ss_pred             CCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHH
Q psy630          253 DNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKA  332 (347)
Q Consensus       253 ~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~  332 (347)
                      ..|.+++|.|+..+...++++|++ .++++|..|..|+||||.+...|+...+..|++ .|++.++.+.+|.+||++|..
T Consensus       654 ~~~~s~lh~a~~~~~~~~~e~ll~-~ga~vn~~d~~g~~plh~~~~~g~~~~~~~ll~-~~a~~~a~~~~~~~~l~~a~~  731 (785)
T KOG0521|consen  654 CIGCSLLHVAVGTGDSGAVELLLQ-NGADVNALDSKGRTPLHHATASGHTSIACLLLK-RGADPNAFDPDGKLPLDIAME  731 (785)
T ss_pred             hcccchhhhhhccchHHHHHHHHh-cCCcchhhhccCCCcchhhhhhcccchhhhhcc-ccccccccCccCcchhhHHhh
Confidence            456899999999999999999999 899999999999999999999999999999999 699999999999999999988


Q ss_pred             cCCHHHHHHHH
Q psy630          333 IEHTDLIEYLV  343 (347)
Q Consensus       333 ~~~~~~v~~Ll  343 (347)
                      ..+.+++-+|.
T Consensus       732 ~~~~d~~~l~~  742 (785)
T KOG0521|consen  732 AANADIVLLLR  742 (785)
T ss_pred             hccccHHHHHh
Confidence            88877776653

>KOG0128|consensus

Probab=98.14  E-value=7.2e-08  Score=93.35  Aligned_cols=124  Identities=22%  Similarity=0.203  Sum_probs=97.7

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccC
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP   83 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~   83 (347)
                      +.++..++||+||++.+.+.+|...|..+|.+..+++..-...++.+|+|||+|...+.+.+|+.++...+-|       
T Consensus       663 ~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g-------  735 (881)
T KOG0128|consen  663 EIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG-------  735 (881)
T ss_pred             HHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh-------
Confidence            3455678999999999999999999999998888777645556889999999999999999999874444433       


Q ss_pred             CCcccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCC
Q psy630           84 SDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQ  156 (347)
Q Consensus        84 ~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~  156 (347)
                                      ...++|+|.|...+.+.++.++..+|.++.....+.+      -|+.|+.|...+.+
T Consensus       736 ----------------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r------~gkpkg~a~v~y~~  786 (881)
T KOG0128|consen  736 ----------------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR------AGKPKGKARVDYNT  786 (881)
T ss_pred             ----------------hhhhheeCCCCCCchHHHHhhccccCCccccchhhhh------ccccccceeccCCC
Confidence                            2356799999999999999999999999865544433      44555555555443

>KOG1365|consensus

Probab=98.14  E-value=4e-06  Score=74.39  Aligned_cols=142  Identities=13%  Similarity=0.192  Sum_probs=98.3

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhcc----CCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCC
Q psy630           10 KIFVGNLPWTVSHNELKKFFSEY----GQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSD   85 (347)
Q Consensus        10 ~l~V~nLp~~~t~~~l~~~f~~~----G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~   85 (347)
                      -|-.++||+++++.++.+||.+-    |....|-+++.+ .|+..|-|||.|..++.|+.|+..+...++-|.|.+-++.
T Consensus       163 ivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElFRST  241 (508)
T KOG1365|consen  163 IVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELFRST  241 (508)
T ss_pred             EEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHHHHh
Confidence            46678999999999999999632    344556666654 4999999999999999999999987777777777665433


Q ss_pred             cccc-------c--------ch---------hhhhhcccccccccCCcccccchhhHHHHhhccccceecccCC-CCCcc
Q psy630           86 SHNR-------M--------AE---------NMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNID-KPSWY  140 (347)
Q Consensus        86 ~~~~-------~--------~~---------~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~-~p~~~  140 (347)
                      ...-       .        ..         .....-...++.+++||...+-|+++.|++.|-.-.    ..- -....
T Consensus       242 aaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i----~f~gVHmv~  317 (508)
T KOG1365|consen  242 AAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDI----RFQGVHMVL  317 (508)
T ss_pred             HHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhc----ccceeEEEE
Confidence            2110       0        00         000111245788999999999999999999886432    110 01123


Q ss_pred             chhHHHHHHHHHHcCC
Q psy630          141 NMEAKSKYNAWNSLGQ  156 (347)
Q Consensus       141 ~~~~~~K~~aw~~~~~  156 (347)
                      +..||..++||.++.+
T Consensus       318 N~qGrPSGeAFIqm~n  333 (508)
T KOG1365|consen  318 NGQGRPSGEAFIQMRN  333 (508)
T ss_pred             cCCCCcChhhhhhhhh
Confidence            4567778888887544

>KOG3609|consensus

Probab=98.10  E-value=6.5e-06  Score=80.51  Aligned_cols=95  Identities=21%  Similarity=0.266  Sum_probs=69.6

Q ss_pred             CCCCCcHHHHHHcCChHHHHHHHhhcCC--CCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCc-------------
Q psy630          252 DDNEKNIYEWAKEGKLDMLVKQLTKLKD--FNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADV-------------  316 (347)
Q Consensus       252 ~~~~~~~l~~a~~~~~~~~~~lL~~~~~--~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i-------------  316 (347)
                      ...+...+.++-.|+...+.+.|.....  .++|+.|.-|+++||+|..+.+.+++++|++ ++..+             
T Consensus        23 ~~~e~~fL~a~E~gd~~~V~k~l~~~~~~~lninc~d~lGr~al~iai~nenle~~eLLl~-~~~~~gdALL~aI~~~~v  101 (822)
T KOG3609|consen   23 NEGEKGFLLAHENGDVPLVAKALEYKAVSKLNINCRDPLGRLALHIAIDNENLELQELLLD-TSSEEGDALLLAIAVGSV  101 (822)
T ss_pred             chhhHHHHHHHHcCChHHHHHHHHhccccccchhccChHhhhceecccccccHHHHHHHhc-CccccchHHHHHHHHHHH
Confidence            3455667777777777777777766433  5677788888888888888888888888877 33111             


Q ss_pred             -----c------------------ccCCCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          317 -----N------------------VTDSDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       317 -----~------------------~~d~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                           .                  ..-.-+-|||.+||..+++||+++||++||
T Consensus       102 ~~VE~ll~~~~~~~~~~~~~d~~~~~ft~ditPliLAAh~NnyEil~~Ll~kg~  155 (822)
T KOG3609|consen  102 PLVELLLVHFVDAPYLERSGDANSPHFTPDITPLMLAAHLNNFEILQCLLTRGH  155 (822)
T ss_pred             HHHHHHHhcccccchhccccccCcccCCCCccHHHHHHHhcchHHHHHHHHcCC
Confidence                 0                  111246799999999999999999999986

>KOG0520|consensus

Probab=97.92  E-value=5.1e-06  Score=82.86  Aligned_cols=95  Identities=28%  Similarity=0.446  Sum_probs=79.6

Q ss_pred             CcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCcccc------CC
Q psy630          248 ESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVT------DS  321 (347)
Q Consensus       248 ~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~------d~  321 (347)
                      ....|.++...+|.|+.++....+.++.- .+..++.+|..||||||||+.+||..++..|+. .|++.+..      .-
T Consensus       601 ~~eld~d~qgV~hfca~lg~ewA~ll~~~-~~~ai~i~D~~G~tpL~wAa~~G~e~l~a~l~~-lga~~~~~tdps~~~p  678 (975)
T KOG0520|consen  601 DLELDRDGQGVIHFCAALGYEWAFLPISA-DGVAIDIRDRNGWTPLHWAAFRGREKLVASLIE-LGADPGAVTDPSPETP  678 (975)
T ss_pred             chhhcccCCChhhHhhhcCCceeEEEEee-cccccccccCCCCcccchHhhcCHHHHHHHHHH-hccccccccCCCCCCC
Confidence            45567788888999888888876665555 789999999999999999999999999999998 68876653      23


Q ss_pred             CCCcHHHHHHHcCCHHHHHHHHh
Q psy630          322 DGDYGLDYAKAIEHTDLIEYLVN  344 (347)
Q Consensus       322 ~g~TpLh~A~~~~~~~~v~~Ll~  344 (347)
                      .|.|+-.+|...|+..+..+|-+
T Consensus       679 ~g~ta~~la~s~g~~gia~~lse  701 (975)
T KOG0520|consen  679 GGKTAADLARANGHKGIAGYLSE  701 (975)
T ss_pred             CCCchhhhhhcccccchHHHHhh
Confidence            69999999999999998888754

>KOG4210|consensus

Probab=97.90  E-value=1.8e-05  Score=70.18  Aligned_cols=142  Identities=20%  Similarity=0.145  Sum_probs=104.9

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCC-CccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDS-HVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~~~   85 (347)
                      ...+.|+|++...+.+.+...++..+|...............++|++++.|...+.+..++...+ ....++.+..-...
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            46789999999999999899999999988888887777788999999999999999999998744 35555544433322


Q ss_pred             cccccchh---hhhhccccccc-ccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHH
Q psy630           86 SHNRMAEN---MEDRFNQACDY-LPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNS  153 (347)
Q Consensus        86 ~~~~~~~~---~~~~f~~~~~~-v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~  153 (347)
                      ....+...   ........++| |.+++..++.++|+..|..+|.++..++...++     .+..|..|...
T Consensus       167 ~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~-----s~~~kg~a~~~  233 (285)
T KOG4210|consen  167 RRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEE-----SGDSKGFAYVD  233 (285)
T ss_pred             cccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCC-----ccchhhhhhhh
Confidence            22211111   11223335566 999999999999999999999999877776654     44555555554

>KOG1190|consensus

Probab=97.88  E-value=1.1e-05  Score=72.23  Aligned_cols=117  Identities=16%  Similarity=0.276  Sum_probs=84.0

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc---CCCccCCcccccc
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST---DSHVLEGSRLSIQ   82 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~---~~~~~~g~~l~v~   82 (347)
                      ...+-|.++|||++++|.++-.++.+||.|..+.+.+.+    +  .||++|.+.++|...+..   -...+.|+++.|+
T Consensus        26 ~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGk----n--QAflem~d~~sAvtmv~~y~~~~p~lr~~~~yiq   99 (492)
T KOG1190|consen   26 EPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGK----N--QAFLEMADEESAVTMVNYYTSVTPVLRGQPIYIQ   99 (492)
T ss_pred             CCcceeEeccCCccccHHHHHHhcccccceeeeeeeccc----h--hhhhhhcchhhhhheeecccccCccccCcceeeh
Confidence            356789999999999999999999999999998886543    3  799999999988774432   3344678888887


Q ss_pred             CCCccc---------ccch--------------hhhh-hcc---------cccccccCCcccccchhhHHHHhhccccc
Q psy630           83 PSDSHN---------RMAE--------------NMED-RFN---------QACDYLPSLVKKLDSSTLLKFYALYKQAT  128 (347)
Q Consensus        83 ~~~~~~---------~~~~--------------~~~~-~f~---------~~~~~v~~l~~~~~~e~l~~~f~~fg~v~  128 (347)
                      ++.-..         .+.+              +... .+.         --.+.|.++-..++-+-|.++|+.||-|.
T Consensus       100 ~sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~Vl  178 (492)
T KOG1190|consen  100 YSNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGFVL  178 (492)
T ss_pred             hhhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcceeE
Confidence            642211         0000              0000 000         12456778888899999999999999886

>KOG0129|consensus

Probab=97.87  E-value=4.4e-05  Score=70.68  Aligned_cols=83  Identities=29%  Similarity=0.443  Sum_probs=68.5

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHh-ccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccC----Cc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFS-EYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLE----GS   77 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~-~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~----g~   77 (347)
                      ..++..+|||||+||.-++.++|-.+|+ -||.|..+.|-+|++-++++|-|=|+|.+..+..+||...-..+.    .+
T Consensus       365 q~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsarFvql~h~d~~K  444 (520)
T KOG0129|consen  365 QPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISARFVQLDHTDIDK  444 (520)
T ss_pred             cccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhhheEEEeccccce
Confidence            3467789999999999999999999998 699999999999988899999999999999999999975333332    23


Q ss_pred             cccccCCC
Q psy630           78 RLSIQPSD   85 (347)
Q Consensus        78 ~l~v~~~~   85 (347)
                      ++.|.+.-
T Consensus       445 RVEIkPYv  452 (520)
T KOG0129|consen  445 RVEIKPYV  452 (520)
T ss_pred             eeeeccee
Confidence            45555443

>KOG4211|consensus

Probab=97.87  E-value=2.6e-05  Score=71.64  Aligned_cols=76  Identities=14%  Similarity=0.339  Sum_probs=62.2

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeE-EEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMN-ASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP   83 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~-~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~   83 (347)
                      ....|-+++||+.||+++|.+||+-.-.+.. +.++.++. +++.|-|||.|.+.+.|+.|+..+...|.-|.|.|-+
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~r-gR~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIEvF~  178 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQR-GRPTGEAFVQFESQESAEIALGRHRENIGHRYIEVFR  178 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCC-CCcccceEEEecCHHHHHHHHHHHHHhhccceEEeeh
Confidence            4456888999999999999999987654444 55666664 8899999999999999999998877778777777653

>KOG1995|consensus

Probab=97.87  E-value=1.8e-05  Score=70.03  Aligned_cols=83  Identities=23%  Similarity=0.356  Sum_probs=73.6

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCee--------EEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIM--------NASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEG   76 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~--------~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g   76 (347)
                      ...-+|||-+||..+++.++.++|.++|.|.        .|.|.+++.|++++|-|.|.|.+...|+.|+.- ++..+.|
T Consensus        64 s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~g  143 (351)
T KOG1995|consen   64 SDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCG  143 (351)
T ss_pred             cccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccC
Confidence            4456899999999999999999999999774        367889999999999999999999999999985 9999999


Q ss_pred             ccccccCCCccc
Q psy630           77 SRLSIQPSDSHN   88 (347)
Q Consensus        77 ~~l~v~~~~~~~   88 (347)
                      ..|+|..+..+.
T Consensus       144 n~ikvs~a~~r~  155 (351)
T KOG1995|consen  144 NTIKVSLAERRT  155 (351)
T ss_pred             CCchhhhhhhcc
Confidence            999998776543

>KOG0521|consensus

Probab=97.73  E-value=2.1e-05  Score=78.87  Aligned_cols=68  Identities=34%  Similarity=0.342  Sum_probs=61.4

Q ss_pred             CCCccccC--CCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          279 DFNINQLD--ENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       279 ~~~~~~~d--~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      +.++|..+  ..|.|+||.|+..+..-++++||+ +|+++|..|..|+||||.+...|+...+..|+++||
T Consensus       644 ~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~-~ga~vn~~d~~g~~plh~~~~~g~~~~~~~ll~~~a  713 (785)
T KOG0521|consen  644 GCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQ-NGADVNALDSKGRTPLHHATASGHTSIACLLLKRGA  713 (785)
T ss_pred             hhhhccchhhhcccchhhhhhccchHHHHHHHHh-cCCcchhhhccCCCcchhhhhhcccchhhhhccccc
Confidence            55555533  468999999999999999999999 899999999999999999999999999999999987

>KOG4210|consensus

Probab=97.72  E-value=2.7e-05  Score=69.12  Aligned_cols=81  Identities=25%  Similarity=0.530  Sum_probs=72.2

Q ss_pred             CCeEE-EeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCCc
Q psy630            8 LNKIF-VGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         8 ~~~l~-V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~~   86 (347)
                      ..++| |++|++.+++++|+.+|..+|.|..++++.++.++.++|||||.|........++..+...+.|+++.+....+
T Consensus       184 s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  263 (285)
T KOG4210|consen  184 SDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALNDQTRSIGGRPLRLEEDEP  263 (285)
T ss_pred             cccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhcccCcccCcccccccCCC
Confidence            34566 99999999999999999999999999999999999999999999999998888887667778889999887766


Q ss_pred             cc
Q psy630           87 HN   88 (347)
Q Consensus        87 ~~   88 (347)
                      ..
T Consensus       264 ~~  265 (285)
T KOG4210|consen  264 RP  265 (285)
T ss_pred             Cc
Confidence            54

>KOG0511|consensus

Probab=97.66  E-value=0.00014  Score=65.05  Aligned_cols=57  Identities=30%  Similarity=0.451  Sum_probs=54.4

Q ss_pred             chHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          290 LNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       290 ~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      .--|-.||..|..+.++.|++ .|.+||++|.-...||.+|+.+||.++|++||++||
T Consensus        37 f~elceacR~GD~d~v~~LVe-tgvnVN~vD~fD~spL~lAsLcGHe~vvklLLenGA   93 (516)
T KOG0511|consen   37 FGELCEACRAGDVDRVRYLVE-TGVNVNAVDRFDSSPLYLASLCGHEDVVKLLLENGA   93 (516)
T ss_pred             hHHHHHHhhcccHHHHHHHHH-hCCCcchhhcccccHHHHHHHcCcHHHHHHHHHcCC
Confidence            446889999999999999999 799999999999999999999999999999999998

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.59  E-value=0.00024  Score=49.65  Aligned_cols=67  Identities=21%  Similarity=0.415  Sum_probs=44.2

Q ss_pred             eEEEeCCCCCCCHHHHH----HHHhccC-CeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630           10 KIFVGNLPWTVSHNELK----KFFSEYG-QIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus        10 ~l~V~nLp~~~t~~~l~----~~f~~~G-~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      .|||.|||-+..-..++    .++..+| .|.+|.          .+.|+|.|.+.+.|.+|.+. ++..+.|+.|.|.+
T Consensus         4 ~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~   73 (90)
T PF11608_consen    4 LLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSF   73 (90)
T ss_dssp             EEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEES
T ss_pred             EEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEE
Confidence            58999999999887665    5555665 555541          36899999999999999985 99999999999988


Q ss_pred             CCc
Q psy630           84 SDS   86 (347)
Q Consensus        84 ~~~   86 (347)
                      ...
T Consensus        74 ~~~   76 (90)
T PF11608_consen   74 SPK   76 (90)
T ss_dssp             S--
T ss_pred             cCC
Confidence            744

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>KOG0112|consensus

Probab=97.59  E-value=3.3e-05  Score=75.80  Aligned_cols=126  Identities=13%  Similarity=0.174  Sum_probs=95.1

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      +...+++||+|||+..+++.+|+..|..+|.|.+|.|-+.+. +.-..|+||.|.+...+-.|... .+..|..-.+.+.
T Consensus       368 D~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~-~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~g  446 (975)
T KOG0112|consen  368 DFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI-KTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIG  446 (975)
T ss_pred             chhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC-CcccchhhhhhhccccCcccchhhcCCccccCccccc
Confidence            345678999999999999999999999999999999866532 44557999999998887777753 4444443344554


Q ss_pred             CCCcccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCc
Q psy630           83 PSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSW  139 (347)
Q Consensus        83 ~~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~  139 (347)
                      +..++..         ....++++++....+...+...|..||.|...++.--.|.+
T Consensus       447 lG~~kst---------~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq~ya  494 (975)
T KOG0112|consen  447 LGQPKST---------PTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQPYA  494 (975)
T ss_pred             ccccccc---------cceeeccCCCCCCChHHHHHHHhhccCcceeeecccCCcce
Confidence            4433221         23456799999999999999999999999876666555543

>KOG0705|consensus

Probab=97.58  E-value=0.00013  Score=68.55  Aligned_cols=66  Identities=15%  Similarity=0.198  Sum_probs=58.8

Q ss_pred             cccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCc
Q psy630          249 SQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADV  316 (347)
Q Consensus       249 ~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i  316 (347)
                      ..-+.+|+|+||.|+.-++..+.+||.= +|+++-.+|.+|+|+|.||-..|.-+|+..||. +|+..
T Consensus       655 t~~~~~grt~LHLa~~~gnVvl~QLLiW-yg~dv~~rda~g~t~l~yar~a~sqec~d~llq-~gcp~  720 (749)
T KOG0705|consen  655 TCGEGDGRTALHLAARKGNVVLAQLLIW-YGVDVMARDAHGRTALFYARQAGSQECIDVLLQ-YGCPD  720 (749)
T ss_pred             cccCCCCcchhhhhhhhcchhHHHHHHH-hCccceecccCCchhhhhHhhcccHHHHHHHHH-cCCCc
Confidence            3456778999999998888888888885 899999999999999999999999999999998 78754

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.54  E-value=0.00016  Score=63.39  Aligned_cols=80  Identities=23%  Similarity=0.387  Sum_probs=61.9

Q ss_pred             CCeEEEeCCCCCCCHHHH------HHHHhccCCeeEEEEeeeCCCCCc-ee--EEEEEEcCHHHHHHHHhc-CCCccCCc
Q psy630            8 LNKIFVGNLPWTVSHNEL------KKFFSEYGQIMNASVMFDKNTGLS-KG--FGFVTFQNKEAVDKVFST-DSHVLEGS   77 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l------~~~f~~~G~i~~~~i~~~~~t~~~-~g--~afV~f~~~~~a~~a~~~-~~~~~~g~   77 (347)
                      ..-+||-+||+.+..++.      .++|.+||.|..|.|-+...+-.+ .+  -.||+|.+.++|.+|+.. +|..++||
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            345899999999988873      699999999998877543211111 12  249999999999999987 99999999


Q ss_pred             cccccCCCcc
Q psy630           78 RLSIQPSDSH   87 (347)
Q Consensus        78 ~l~v~~~~~~   87 (347)
                      .|+..+...+
T Consensus       194 ~lkatYGTTK  203 (480)
T COG5175         194 VLKATYGTTK  203 (480)
T ss_pred             eEeeecCchH
Confidence            9988765543

>KOG0120|consensus

Probab=97.49  E-value=0.00011  Score=69.21  Aligned_cols=142  Identities=18%  Similarity=0.299  Sum_probs=100.2

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhcc-----------C-CeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEY-----------G-QIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSH   72 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~-----------G-~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~   72 (347)
                      -.+.+++||+++|+.++++....+|..-           | .+..+.+-.      .+.|||++|.+.+.|..++..++.
T Consensus       172 t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~------~~nfa~ie~~s~~~at~~~~~~~~  245 (500)
T KOG0120|consen  172 TRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNL------EKNFAFIEFRSISEATEAMALDGI  245 (500)
T ss_pred             hhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecc------cccceeEEecCCCchhhhhcccch
Confidence            3466889999999999999999999753           2 255555533      357999999999999999999999


Q ss_pred             ccCCccccccCCCcccccc-h---------------hhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCC
Q psy630           73 VLEGSRLSIQPSDSHNRMA-E---------------NMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDK  136 (347)
Q Consensus        73 ~~~g~~l~v~~~~~~~~~~-~---------------~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~  136 (347)
                      .+.|+++.+.......... .               .....-....+||++||..+++.+++++...||....-.+..+.
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            9999998886443322110 0               00111123678999999999999999999999988654444443


Q ss_pred             CCccchhHHHHHHHHHHcCCC
Q psy630          137 PSWYNMEAKSKYNAWNSLGQM  157 (347)
Q Consensus       137 p~~~~~~~~~K~~aw~~~~~~  157 (347)
                      +     .|-.|..|+-+..+-
T Consensus       326 ~-----~g~skg~af~ey~dp  341 (500)
T KOG0120|consen  326 A-----TGNSKGFAFCEYCDP  341 (500)
T ss_pred             c-----cccccceeeeeeeCC
Confidence            3     244555555554443

>KOG1365|consensus

Probab=97.49  E-value=0.00015  Score=64.60  Aligned_cols=145  Identities=16%  Similarity=0.261  Sum_probs=95.5

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCCc
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~~   86 (347)
                      +..-+-.++||+..++.++-.+|+-......-+.+.....|...|.+.|.|.+.+.-+.|++.+.+.+.++.+.|-.+..
T Consensus        59 ~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryievYka~g  138 (508)
T KOG1365|consen   59 DNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYIEVYKATG  138 (508)
T ss_pred             cceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHhhhhhccCCceeeeccCc
Confidence            34455678999999999999999743222111222222346667999999999999999999988889999999877655


Q ss_pred             cccc-----chhhhhhc----ccccccccCCcccccchhhHHHHhhccccc---eecccCCCCCccchhHHHHHHHHHHc
Q psy630           87 HNRM-----AENMEDRF----NQACDYLPSLVKKLDSSTLLKFYALYKQAT---VGQCNIDKPSWYNMEAKSKYNAWNSL  154 (347)
Q Consensus        87 ~~~~-----~~~~~~~f----~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~---~g~~~~~~p~~~~~~~~~K~~aw~~~  154 (347)
                      ..-.     .......|    +.-.+.+++||.+.++.++.+||+.--.++   ++-..+.+|     -||..++||.-+
T Consensus       139 e~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-----dgrpTGdAFvlf  213 (508)
T KOG1365|consen  139 EEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-----DGRPTGDAFVLF  213 (508)
T ss_pred             hhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-----CCCcccceEEEe
Confidence            3211     00111111    234567889999999999999997433332   233333343     456677777765


Q ss_pred             CC
Q psy630          155 GQ  156 (347)
Q Consensus       155 ~~  156 (347)
                      ..
T Consensus       214 a~  215 (508)
T KOG1365|consen  214 AC  215 (508)
T ss_pred             cC
Confidence            44

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=97.45  E-value=0.00028  Score=52.89  Aligned_cols=54  Identities=22%  Similarity=0.376  Sum_probs=35.8

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc
Q psy630           10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST   69 (347)
Q Consensus        10 ~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~   69 (347)
                      -|+|.+++..++.++|++.|++||.|..|.+.+.      -.-|||.|.+.+.|+.|+..
T Consensus         3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G------~~~g~VRf~~~~~A~~a~~~   56 (105)
T PF08777_consen    3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRG------DTEGYVRFKTPEAAQKALEK   56 (105)
T ss_dssp             EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHH
T ss_pred             EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCC------CCEEEEEECCcchHHHHHHH
Confidence            4788899999999999999999999999888543      24799999999999999974

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0506|consensus

Probab=97.44  E-value=9.6e-05  Score=67.79  Aligned_cols=60  Identities=22%  Similarity=0.408  Sum_probs=52.8

Q ss_pred             cCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCCHHHHHHHHhC
Q psy630          285 LDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNS  345 (347)
Q Consensus       285 ~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~~~v~~Ll~~  345 (347)
                      ++..+.-++++|+..|.+..++-+.- .|.|++.+|++.+|+||+|+..|+.+++++||+.
T Consensus       502 ~~~~~~i~~~~aa~~GD~~alrRf~l-~g~D~~~~DyD~RTaLHvAAaEG~v~v~kfl~~~  561 (622)
T KOG0506|consen  502 RENDTVINVMYAAKNGDLSALRRFAL-QGMDLETKDYDDRTALHVAAAEGHVEVVKFLLNA  561 (622)
T ss_pred             ccccchhhhhhhhhcCCHHHHHHHHH-hcccccccccccchhheeecccCceeHHHHHHHH
Confidence            34567789999999999988866655 5999999999999999999999999999999874

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.40  E-value=0.00057  Score=44.27  Aligned_cols=52  Identities=17%  Similarity=0.424  Sum_probs=42.9

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHH
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF   67 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~   67 (347)
                      +.|-|.+.|++..+. +..+|.+||+|..+.+.      ...-+.||.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~------~~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVP------ESTNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcC------CCCcEEEEEECCHHHHHhhC
Confidence            578899999888755 55699999999998875      23458999999999999985

>KOG2193|consensus

Probab=97.35  E-value=0.00019  Score=64.85  Aligned_cols=106  Identities=20%  Similarity=0.315  Sum_probs=82.0

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc--CCCccCCccccccCCCc
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST--DSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~--~~~~~~g~~l~v~~~~~   86 (347)
                      .++|++||.+.++-.+|..+|...---.+-.++.      ..||+||.+.+...+.+|++.  ....+.|+.+.|...-+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            5699999999999999999996531111111111      248999999999999999985  44557899998877766


Q ss_pred             ccccchhhhhhcccccccccCCcccccchhhHHHHhhccccce
Q psy630           87 HNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATV  129 (347)
Q Consensus        87 ~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~  129 (347)
                      +..++         ..+-++|+|+.+-++.+..|.+.||.+..
T Consensus        76 kkqrs---------rk~Qirnippql~wevld~Ll~qyg~ve~  109 (584)
T KOG2193|consen   76 KKQRS---------RKIQIRNIPPQLQWEVLDSLLAQYGTVEN  109 (584)
T ss_pred             HHHHh---------hhhhHhcCCHHHHHHHHHHHHhccCCHhH
Confidence            55432         34779999999999999999999998864

>KOG1457|consensus

Probab=97.30  E-value=0.00025  Score=58.79  Aligned_cols=62  Identities=19%  Similarity=0.360  Sum_probs=48.9

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCcc
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVL   74 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~   74 (347)
                      .+|||.||.+.+|+++|+.+|+.|-.....+|. .+   ....+|||+|.+.+.|..|+.. +|..+
T Consensus       211 stlfianl~~~~~ed~l~~~~~~~~gf~~l~~~-~~---~g~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  211 STLFIANLGPNCTEDELKQLLSRYPGFHILKIR-AR---GGMPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             hhHhhhccCCCCCHHHHHHHHHhCCCceEEEEe-cC---CCcceEeecHHHHHHHHHHHHHhhccee
Confidence            489999999999999999999999765555552 22   2346899999999999999864 55443

>KOG3878|consensus

Probab=97.29  E-value=0.00029  Score=61.64  Aligned_cols=70  Identities=24%  Similarity=0.450  Sum_probs=63.2

Q ss_pred             ccccchhhHHHHhhccccceecccCCC---CCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhhccCCh
Q psy630          110 KKLDSSTLLKFYALYKQATVGQCNIDK---PSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWED  179 (347)
Q Consensus       110 ~~~~~e~l~~~f~~fg~v~~g~~~~~~---p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~l~~~~~~  179 (347)
                      ..++-++.++|.++-+|+..|++++++   -|++++.|+-+-.+|..++.|++++||..||.++..+.+-+..
T Consensus        51 ~h~~YEd~lKLial~kQv~~Gp~n~d~~p~~G~lDv~GnDr~~~W~~LG~~sre~AM~~FV~Lldr~C~~F~~  123 (469)
T KOG3878|consen   51 IHLSYEDNLKLIALKKQVALGPFNTDRAPALGVLDVIGNDRQQHWQLLGEISREQAMEGFVDLLDRMCSAFRP  123 (469)
T ss_pred             cCCChhhhhhhhhhHhhhhcCCCCcccCcccceeecccChHHHHHHHHhcccHHHHHHHHHHHHHhcchhhhh
Confidence            457888999999999999999999754   3899999999999999999999999999999999998887665

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.25  E-value=0.0012  Score=48.68  Aligned_cols=77  Identities=17%  Similarity=0.343  Sum_probs=51.4

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEE-EeeeC------CCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccc
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNAS-VMFDK------NTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRL   79 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~-i~~~~------~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l   79 (347)
                      ..+.|.|=+.|+.. ...+-++|++||.|.+.. +.++.      ........-.|+|.++.+|.+|+..||..+.|..+
T Consensus         5 ~~~wVtVFGfp~~~-~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~m   83 (100)
T PF05172_consen    5 SETWVTVFGFPPSA-SNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSLM   83 (100)
T ss_dssp             GCCEEEEE---GGG-HHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCEE
T ss_pred             CCeEEEEEccCHHH-HHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcEE
Confidence            45668888999995 456788999999998764 11110      00123468999999999999999999999998644


Q ss_pred             -cccCC
Q psy630           80 -SIQPS   84 (347)
Q Consensus        80 -~v~~~   84 (347)
                       -|.+.
T Consensus        84 vGV~~~   89 (100)
T PF05172_consen   84 VGVKPC   89 (100)
T ss_dssp             EEEEE-
T ss_pred             EEEEEc
Confidence             45555

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.

>KOG4849|consensus

Probab=97.22  E-value=0.00026  Score=62.35  Aligned_cols=75  Identities=21%  Similarity=0.452  Sum_probs=64.2

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccC--CeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630           10 KIFVGNLPWTVSHNELKKFFSEYG--QIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus        10 ~l~V~nLp~~~t~~~l~~~f~~~G--~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      -+|||||-|.+|+++|-+.+..-|  .+.++++..++..|.|+|||.|...+..+.++.++. ....++|+.-.|...
T Consensus        82 ~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~~  159 (498)
T KOG4849|consen   82 CCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLSY  159 (498)
T ss_pred             EEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeecc
Confidence            589999999999999988887665  466778888888999999999999999999999986 788888887666543

>KOG0818|consensus

Probab=97.20  E-value=0.00065  Score=62.80  Aligned_cols=67  Identities=15%  Similarity=0.209  Sum_probs=54.0

Q ss_pred             ecccCCcccC-CCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHh
Q psy630          243 SMINDESQLD-DNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIE  310 (347)
Q Consensus       243 ~~~~~~~~~~-~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~  310 (347)
                      +...+.|-.+ +.|.|+||.|+..+...-+++|.- +|++++..|..|+||+.+|-..||-++..-|++
T Consensus       154 ~lGA~~N~~hpekg~TpLHvAAk~Gq~~Q~ElL~v-YGAD~~a~d~~GmtP~~~AR~~gH~~laeRl~e  221 (669)
T KOG0818|consen  154 SLGAQANFFHPEKGNTPLHVAAKAGQILQAELLAV-YGADPGAQDSSGMTPVDYARQGGHHELAERLVE  221 (669)
T ss_pred             HcccccCCCCcccCCchhHHHHhccchhhhhHHhh-ccCCCCCCCCCCCcHHHHHHhcCchHHHHHHHH
Confidence            3344555443 457899999888777777788877 899999999999999999999999988776665

>smart00248 ANK ankyrin repeats

Probab=97.17  E-value=0.00068  Score=36.84  Aligned_cols=28  Identities=46%  Similarity=0.758  Sum_probs=21.1

Q ss_pred             CchHHHHHHHcCCHHHHHHHHhhcCCCcc
Q psy630          289 GLNCLHWACDRGHLKVVQHLIEKCGADVN  317 (347)
Q Consensus       289 g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~  317 (347)
                      |.||||+|+..++.+++++|++ .|.+++
T Consensus         2 ~~~~l~~~~~~~~~~~~~~ll~-~~~~~~   29 (30)
T smart00248        2 GRTPLHLAAENGNLEVVKLLLD-KGADIN   29 (30)
T ss_pred             CCCHHHHHHHcCCHHHHHHHHH-cCCCCC
Confidence            6778888888888888888887 566654

Ankyrin repeats are about 33 amino acids long and occur in at least four consecutive copies. They are involved in protein-protein interactions. The core of the repeat seems to be an helix-loop-helix structure.

>KOG4676|consensus

Probab=97.12  E-value=0.00058  Score=61.19  Aligned_cols=125  Identities=12%  Similarity=0.171  Sum_probs=87.7

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCC---CCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKN---TGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~---t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      ..-|-|.||.+.+|.++++.+|.-.|.|..+.++-...   -......|||-|.+...+..|-.+-.++|-++.|.|.++
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~   86 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPY   86 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEec
Confidence            34789999999999999999999999999998865321   123467899999999988888777566676776666543


Q ss_pred             Ccccccch------------------------------------------hhh-----hhc--ccccccccCCcccccch
Q psy630           85 DSHNRMAE------------------------------------------NME-----DRF--NQACDYLPSLVKKLDSS  115 (347)
Q Consensus        85 ~~~~~~~~------------------------------------------~~~-----~~f--~~~~~~v~~l~~~~~~e  115 (347)
                      ........                                          .+.     ..+  ...+++|.+|+..+...
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            32111000                                          000     000  01357888888888888


Q ss_pred             hhHHHHhhccccceecc
Q psy630          116 TLLKFYALYKQATVGQC  132 (347)
Q Consensus       116 ~l~~~f~~fg~v~~g~~  132 (347)
                      ++.++|..||.+....+
T Consensus       167 e~~e~f~r~Gev~ya~~  183 (479)
T KOG4676|consen  167 ESGESFERKGEVSYAHT  183 (479)
T ss_pred             hhhhhhhhcchhhhhhh
Confidence            88999999888865433

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

Probab=97.06  E-value=0.00013  Score=58.29  Aligned_cols=61  Identities=11%  Similarity=0.124  Sum_probs=46.3

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|..||..  ..+.++|..++
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~-----tg~~kGfaFV~--F~~~e~A~~Al   93 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRE-----TGRSRGFGFVN--FNDEGAATAAI   93 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCC-----CCCcceEEEEE--ECCHHHHHHHH
Confidence            446899999999999999999999999998777665432     34556666655  44567777764

>KOG0522|consensus

Probab=97.05  E-value=0.0015  Score=61.17  Aligned_cols=62  Identities=13%  Similarity=0.153  Sum_probs=47.6

Q ss_pred             cccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhh
Q psy630          249 SQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEK  311 (347)
Q Consensus       249 ~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~  311 (347)
                      +..|..|.|+||.|..-++.....+|+. .++++..+++.||+|||-|+..|+..++..+|.+
T Consensus        49 d~~D~~g~TpLhlAV~Lg~~~~a~~Ll~-a~Adv~~kN~~gWs~L~EAv~~g~~q~i~~vlr~  110 (560)
T KOG0522|consen   49 DRRDPPGRTPLHLAVRLGHVEAARILLS-AGADVSIKNNEGWSPLHEAVSTGNEQIITEVLRH  110 (560)
T ss_pred             ccccCCCCccHHHHHHhcCHHHHHHHHh-cCCCccccccccccHHHHHHHcCCHHHHHHHHHH
Confidence            3345566777777665555545555655 5999999999999999999999999988888763

>smart00248 ANK ankyrin repeats

Probab=97.04  E-value=0.00099  Score=36.14  Aligned_cols=26  Identities=23%  Similarity=0.447  Sum_probs=23.8

Q ss_pred             CCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          322 DGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       322 ~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      .|.||||+|+..++.+++++|+++|+
T Consensus         1 ~~~~~l~~~~~~~~~~~~~~ll~~~~   26 (30)
T smart00248        1 DGRTPLHLAAENGNLEVVKLLLDKGA   26 (30)
T ss_pred             CCCCHHHHHHHcCCHHHHHHHHHcCC
Confidence            47899999999999999999999874

Ankyrin repeats are about 33 amino acids long and occur in at least four consecutive copies. They are involved in protein-protein interactions. The core of the repeat seems to be an helix-loop-helix structure.

>KOG3152|consensus

Probab=97.02  E-value=0.00058  Score=57.88  Aligned_cols=72  Identities=17%  Similarity=0.390  Sum_probs=58.6

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCC--------CCceeE----EEEEEcCHHHHHHHHhc-CCCc
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNT--------GLSKGF----GFVTFQNKEAVDKVFST-DSHV   73 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t--------~~~~g~----afV~f~~~~~a~~a~~~-~~~~   73 (347)
                      .+.-||+++|||.+.-.-|+++|++||.|-.|.+-....+        |.++++    |.|+|.+...|..+... |+..
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            4568999999999999999999999999999988655444        333333    66999999999888775 9898


Q ss_pred             cCCcc
Q psy630           74 LEGSR   78 (347)
Q Consensus        74 ~~g~~   78 (347)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            88874

>KOG4206|consensus

Probab=96.90  E-value=0.0035  Score=52.36  Aligned_cols=75  Identities=15%  Similarity=0.295  Sum_probs=60.5

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccC-Ccccccc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLE-GSRLSIQ   82 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~-g~~l~v~   82 (347)
                      ......+|+.|||..++.+.+..+|.+|..-..++++..+     ++.|||+|.+...+..|... ++..+. ...+.|.
T Consensus       143 ~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~  217 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQIT  217 (221)
T ss_pred             CCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEec
Confidence            3455689999999999999999999999999999987654     48999999998888888864 655554 5556665


Q ss_pred             CC
Q psy630           83 PS   84 (347)
Q Consensus        83 ~~   84 (347)
                      ++
T Consensus       218 ~a  219 (221)
T KOG4206|consen  218 FA  219 (221)
T ss_pred             cc
Confidence            54

>KOG0106|consensus

Probab=96.87  E-value=0.00071  Score=56.87  Aligned_cols=72  Identities=28%  Similarity=0.537  Sum_probs=61.2

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ...+.++|.|++..+.+++|.++|.++|.+....+        ..+++||+|...+++..|+.. ++..+.|+.|.+...
T Consensus        97 ~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen   97 RTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             cccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeeeccc
Confidence            34568899999999999999999999999854433        357899999999999999986 999999999998544


Q ss_pred             C
Q psy630           85 D   85 (347)
Q Consensus        85 ~   85 (347)
                      .
T Consensus       169 ~  169 (216)
T KOG0106|consen  169 S  169 (216)
T ss_pred             C
Confidence            3

>KOG0149|consensus

Probab=96.81  E-value=0.00036  Score=58.44  Aligned_cols=69  Identities=13%  Similarity=0.175  Sum_probs=53.4

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhhccCChh
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWEDK  180 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~l~~~~~~~  180 (347)
                      .+|||++|+.....+.|+++|..||+|.+.-+..++.     .||+|+.+|..+++  .+-|.++    +++-.|-.+..
T Consensus        13 TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~-----t~rskGyGfVTf~d--~~aa~rA----c~dp~piIdGR   81 (247)
T KOG0149|consen   13 TKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKN-----TGRSKGYGFVTFRD--AEAATRA----CKDPNPIIDGR   81 (247)
T ss_pred             EEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccC-----CccccceeeEEeec--HHHHHHH----hcCCCCccccc
Confidence            6899999999999999999999999999988888875     78889888876544  4444444    44444444443

>KOG2505|consensus

Probab=96.73  E-value=0.0046  Score=57.49  Aligned_cols=67  Identities=22%  Similarity=0.227  Sum_probs=53.4

Q ss_pred             HcCChHHHHHHHhhcCCCCccc------cCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHH
Q psy630          263 KEGKLDMLVKQLTKLKDFNINQ------LDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAK  331 (347)
Q Consensus       263 ~~~~~~~~~~lL~~~~~~~~~~------~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~  331 (347)
                      ..+..+..++.|.. .+...|.      .+....|+||+|+..|...+|.+||. .|+|+-.+|..|.||..++.
T Consensus       399 kk~~~p~~ie~lke-n~lsgnf~~~pe~~~~ltsT~LH~aa~qg~~k~v~~~Le-eg~Dp~~kd~~Grtpy~ls~  471 (591)
T KOG2505|consen  399 KKKPEPDSIEALKE-NLLSGNFDVTPEANDYLTSTFLHYAAAQGARKCVKYFLE-EGCDPSTKDGAGRTPYSLSA  471 (591)
T ss_pred             hccCchhHHHHHHh-cCCcccccccccccccccchHHHHHHhcchHHHHHHHHH-hcCCchhcccCCCCcccccc
Confidence            44555666666666 4544433      34557899999999999999999999 79999999999999999876

>PF00076 RRM_1: RNA recognition motif

Probab=96.72  E-value=0.0008  Score=46.04  Aligned_cols=55  Identities=15%  Similarity=0.143  Sum_probs=38.8

Q ss_pred             ccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          103 DYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       103 ~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      +||+|||..+++++|+++|+.||.+....+.....+.      .+..||..  ..+.++|+.+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~------~~~~a~V~--F~~~~~a~~a   55 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGK------SKGYAFVE--FESEEDAEKA   55 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSS------EEEEEEEE--ESSHHHHHHH
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccccccc------ccceEEEE--EcCHHHHHHH
Confidence            5899999999999999999999999876666542222      22223333  4456666665

(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 ....

>KOG4307|consensus

Probab=96.68  E-value=0.004  Score=59.98  Aligned_cols=74  Identities=19%  Similarity=0.401  Sum_probs=60.8

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      +-|-+.|+|++++-++|.+||..|-.+-.-.+++..+.|...|-|.|-|++.++|.+|... ++..|..|.+.+.
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~  942 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLR  942 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEE
Confidence            3678899999999999999999997765433334445699999999999999999999975 8888888877653

>KOG0121|consensus

Probab=96.25  E-value=0.0018  Score=49.06  Aligned_cols=82  Identities=10%  Similarity=0.092  Sum_probs=53.5

Q ss_pred             hhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHH
Q psy630           93 NMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKE  172 (347)
Q Consensus        93 ~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~  172 (347)
                      .+...-...++||+||...+++|++.+||++.|.|....+-.++.-       ...-.|--++..++++|..+    ++-
T Consensus        29 ~~~a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~k-------ktpCGFCFVeyy~~~dA~~A----lry   97 (153)
T KOG0121|consen   29 QLEALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFK-------KTPCGFCFVEYYSRDDAEDA----LRY   97 (153)
T ss_pred             HHHHHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCC-------cCccceEEEEEecchhHHHH----HHH
Confidence            3444456689999999999999999999999999987666555421       01112223445577777665    444


Q ss_pred             hhccCChhhhhhh
Q psy630          173 VDAGWEDKEQEEI  185 (347)
Q Consensus       173 l~~~~~~~~~~~~  185 (347)
                      +...-.++++..+
T Consensus        98 isgtrLddr~ir~  110 (153)
T KOG0121|consen   98 ISGTRLDDRPIRI  110 (153)
T ss_pred             hccCcccccceee
Confidence            4455555544433

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.19  E-value=0.01  Score=46.57  Aligned_cols=55  Identities=25%  Similarity=0.398  Sum_probs=45.1

Q ss_pred             HHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCCc
Q psy630           24 ELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDS   86 (347)
Q Consensus        24 ~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~~   86 (347)
                      +|.+.|..||.+.-+++..+        .-.|+|.+-.+|.+|+.++|..+.|+.|.|+...+
T Consensus        52 ~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals~dg~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALSLDGIQVNGRTLKIRLKTP  106 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHHGCCSEETTEEEEEEE---
T ss_pred             HHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHccCCcEECCEEEEEEeCCc
Confidence            56788889999988888643        47899999999999999999999999999987765

; PDB: 1UFW_A 2DNR_A.

>KOG2384|consensus

Probab=96.17  E-value=0.014  Score=47.65  Aligned_cols=73  Identities=16%  Similarity=0.080  Sum_probs=58.5

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCC-CCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCC
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKD-FNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS  321 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~-~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~  321 (347)
                      ++|..|..|+|++..|+..+.-+++.+|+. .| +.+...|..|.+++.+|-..|+.+++..|.+ +-.+-...++
T Consensus         4 ~in~rD~fgWTalmcaa~eg~~eavsyllg-rg~a~vgv~d~ssldaaqlaek~g~~~fvh~lfe-~~~ets~p~n   77 (223)
T KOG2384|consen    4 NINARDAFGWTALMCAAMEGSNEAVSYLLG-RGVAFVGVTDESSLDAAQLAEKGGAQAFVHSLFE-NDRETSHPMN   77 (223)
T ss_pred             CccchhhhcchHHHHHhhhcchhHHHHHhc-cCcccccccccccchHHHHHHhcChHHHHHHHHH-HhccCCCccc
Confidence            567788999999987766566667777777 56 8999999999999999999999999999988 4444444433

>KOG0126|consensus

Probab=96.11  E-value=0.00046  Score=55.44  Aligned_cols=53  Identities=23%  Similarity=0.197  Sum_probs=42.4

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCC
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQ  156 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~  156 (347)
                      ..|-|||++||..+++.+++-+|+.||.+.......++.     +|++|+.||...++
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~-----TGKSKGFaFLcYED   86 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKK-----TGKSKGFAFLCYED   86 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCC-----CCcccceEEEEecC
Confidence            358899999999999999999999999998555555543     77888877765444

>KOG1456|consensus

Probab=96.11  E-value=0.034  Score=49.89  Aligned_cols=113  Identities=15%  Similarity=0.146  Sum_probs=82.8

Q ss_pred             CCeEEEeCCCCC-CCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630            8 LNKIFVGNLPWT-VSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus         8 ~~~l~V~nLp~~-~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      ..-+.|-+|... ++-+.|..+|=.||.|..|++++-+     .|.|.|+..+..+.++|+.. |+..+-|.+|.|..+.
T Consensus       287 g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~Sk  361 (494)
T KOG1456|consen  287 GCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSK  361 (494)
T ss_pred             CcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEEeecc
Confidence            345677788776 5667889999999999999999765     48999999999999999985 7777788888776442


Q ss_pred             ccc-----------------ccchhhh-------------hhcccccccccCCcccccchhhHHHHhhcc
Q psy630           86 SHN-----------------RMAENME-------------DRFNQACDYLPSLVKKLDSSTLLKFYALYK  125 (347)
Q Consensus        86 ~~~-----------------~~~~~~~-------------~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg  125 (347)
                      ...                 ..+....             -.+....++.-|.|..++++.+..++..-.
T Consensus       362 Q~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~  431 (494)
T KOG1456|consen  362 QNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKD  431 (494)
T ss_pred             ccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcC
Confidence            210                 0001111             112335667778899999999998887544

>KOG0122|consensus

Probab=96.11  E-value=0.0014  Score=55.21  Aligned_cols=60  Identities=17%  Similarity=0.144  Sum_probs=49.8

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..+++.|.||+.++++++|.+||..||.++..-+-.++.     .|.+|+.||..  ..++++|.++
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~-----TG~~kGFAFVt--F~sRddA~rA  247 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKE-----TGLSKGFAFVT--FESRDDAARA  247 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccc-----cCcccceEEEE--EecHHHHHHH
Confidence            568899999999999999999999999998655555554     77888888876  4568888877

>KOG0105|consensus

Probab=96.10  E-value=0.023  Score=45.97  Aligned_cols=57  Identities=30%  Similarity=0.418  Sum_probs=50.7

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST   69 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~   69 (347)
                      ....+|.|++||++-+.++|+++..+.|.|....+.+|       |++.|+|...++.+.|+..
T Consensus       113 rSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~  169 (241)
T KOG0105|consen  113 RSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRK  169 (241)
T ss_pred             ccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHh
Confidence            34457999999999999999999999999999988776       4899999999999999974

>KOG0128|consensus

Probab=96.10  E-value=0.0036  Score=61.69  Aligned_cols=77  Identities=17%  Similarity=0.258  Sum_probs=64.5

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCc
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~   86 (347)
                      ..+||+|.|+..|.++++.+++.+|.+.+.+++..+. |+++|.|||.|.+..++.+++.. +...+.-+.+.|+.+.+
T Consensus       737 ~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~-gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  737 ISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRA-GKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhheeCCCCCCchHHHHhhccccCCccccchhhhhc-cccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            4689999999999999999999999999999888774 99999999999999998888865 55555555556655444

>KOG1855|consensus

Probab=96.04  E-value=0.0059  Score=55.62  Aligned_cols=63  Identities=25%  Similarity=0.354  Sum_probs=53.9

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeee---CCC--CC--------ceeEEEEEEcCHHHHHHHHhc
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFD---KNT--GL--------SKGFGFVTFQNKEAVDKVFST   69 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~---~~t--~~--------~~g~afV~f~~~~~a~~a~~~   69 (347)
                      +.++|.+-|||.+-.-+-|.++|..+|.|..|+|...   +..  +.        .+-+|+|+|...+.|.+|.++
T Consensus       230 ~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~  305 (484)
T KOG1855|consen  230 PSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAREL  305 (484)
T ss_pred             ccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHh
Confidence            6789999999999988999999999999999999765   222  21        256899999999999999986

>KOG2314|consensus

Probab=96.01  E-value=0.0099  Score=56.05  Aligned_cols=75  Identities=23%  Similarity=0.356  Sum_probs=58.4

Q ss_pred             CCCeEEEeCCCCCCCH--H----HHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccC-Ccc
Q psy630            7 QLNKIFVGNLPWTVSH--N----ELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLE-GSR   78 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~--~----~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~-g~~   78 (347)
                      -..-|+|-|+|---..  +    -|..+|+++|++....++.+.. |..+||.|++|.+...|+.|++. ||+.++ .+.
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~-ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE-GGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc-CCeeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            3456888888864322  2    2468899999999999998887 44999999999999999999985 888875 445


Q ss_pred             cccc
Q psy630           79 LSIQ   82 (347)
Q Consensus        79 l~v~   82 (347)
                      ..|.
T Consensus       136 f~v~  139 (698)
T KOG2314|consen  136 FFVR  139 (698)
T ss_pred             EEee
Confidence            5554

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=95.89  E-value=0.048  Score=38.32  Aligned_cols=56  Identities=23%  Similarity=0.386  Sum_probs=39.7

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST   69 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~   69 (347)
                      |....-.||+ .|......+|.++|+.||.| .|.++-|.       -|||.....+.+..++..
T Consensus         6 P~RdHVFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l~~r~~~~~v~~~   61 (87)
T PF08675_consen    6 PSRDHVFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVALHNRDQAKVVMNT   61 (87)
T ss_dssp             -SGCCEEEEE---TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEECCCHHHHHHHHH
T ss_pred             CCcceEEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEeecHHHHHHHHHH
Confidence            3344445565 99999999999999999987 55555543       599999999999888764

; 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.

>KOG0114|consensus

Probab=95.87  E-value=0.0046  Score=45.09  Aligned_cols=36  Identities=14%  Similarity=0.181  Sum_probs=30.3

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCC
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                      ...+||+|||.+++.++..++|+.||.|.-.++...
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~   53 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNT   53 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecCc
Confidence            356799999999999999999999999976555443

>KOG1456|consensus

Probab=95.58  E-value=0.034  Score=49.91  Aligned_cols=118  Identities=14%  Similarity=0.103  Sum_probs=86.0

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc---CCCccCCcccccc
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST---DSHVLEGSRLSIQ   82 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~---~~~~~~g~~l~v~   82 (347)
                      ...--|.|++|-..+++.+|-+.++.||.|..+..+..      +..|.|+|++.+.|..++.+   +...+.|+...+.
T Consensus        29 ~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~------~r~alvefedi~~akn~Vnfaa~n~i~i~gq~Al~N  102 (494)
T KOG1456|consen   29 NPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPH------KRQALVEFEDIEGAKNCVNFAADNQIYIAGQQALFN  102 (494)
T ss_pred             CCCceEEEeccccccchhHHHHHHhcCCceEEEEeccc------cceeeeeeccccchhhheehhccCcccccCchhhcc
Confidence            34457899999999999999999999999998877543      34799999999999999975   7777888888777


Q ss_pred             CCCccc-ccchhhhhhcccccc--cccCCcccccchhhHHHHhhcccccee
Q psy630           83 PSDSHN-RMAENMEDRFNQACD--YLPSLVKKLDSSTLLKFYALYKQATVG  130 (347)
Q Consensus        83 ~~~~~~-~~~~~~~~~f~~~~~--~v~~l~~~~~~e~l~~~f~~fg~v~~g  130 (347)
                      ++.+.. +|.. .+..-....+  -|-|--..++-+-|..+....|+|...
T Consensus       103 yStsq~i~R~g-~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRI  152 (494)
T KOG1456|consen  103 YSTSQCIERPG-DESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRI  152 (494)
T ss_pred             cchhhhhccCC-CCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEE
Confidence            774432 2111 1111111222  233444678999999999999998743

>KOG0115|consensus

Probab=95.42  E-value=0.018  Score=49.13  Aligned_cols=74  Identities=24%  Similarity=0.371  Sum_probs=59.0

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-C----CCccCCccccccC
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-D----SHVLEGSRLSIQP   83 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~----~~~~~g~~l~v~~   83 (347)
                      ..|||.||+.-+..+.+.+-|+.||+|....++.|- .+++.+-++|.|...-.+.+|... +    +....+++..|.+
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~-r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP  110 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEP  110 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCCh
Confidence            469999999999999999999999999887777664 488999999999999888888865 2    2223455555544

>KOG0112|consensus

Probab=95.40  E-value=0.024  Score=56.50  Aligned_cols=78  Identities=14%  Similarity=0.240  Sum_probs=64.5

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCC--cccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEG--SRLS   80 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g--~~l~   80 (347)
                      .....+.+||++|++.+....|...|..||.|..|.+-      +...||||.|.+...++.|+.. .+..++|  +.++
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~------hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~r  524 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYR------HGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLR  524 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecc------cCCcceeeecccCccchhhHHHHhcCcCCCCCcccc
Confidence            34567899999999999999999999999999987763      2346999999999999999985 7888765  6677


Q ss_pred             ccCCCcc
Q psy630           81 IQPSDSH   87 (347)
Q Consensus        81 v~~~~~~   87 (347)
                      |.++...
T Consensus       525 vdla~~~  531 (975)
T KOG0112|consen  525 VDLASPP  531 (975)
T ss_pred             cccccCC
Confidence            7766553

>KOG1548|consensus

Probab=95.39  E-value=0.035  Score=49.42  Aligned_cols=78  Identities=23%  Similarity=0.365  Sum_probs=59.4

Q ss_pred             ccCCCeEEEeCC--CC--CCC-------HHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCC
Q psy630            5 IRQLNKIFVGNL--PW--TVS-------HNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSH   72 (347)
Q Consensus         5 ~~~~~~l~V~nL--p~--~~t-------~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~   72 (347)
                      .+..++|.++|+  |.  ..+       .++|.+-.++||.|.+|.|.-    ..+.|.+-|.|.+.+.|..|+.. +|-
T Consensus       262 ~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d----~hPdGvvtV~f~n~eeA~~ciq~m~GR  337 (382)
T KOG1548|consen  262 ARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYD----RHPDGVVTVSFRNNEEADQCIQTMDGR  337 (382)
T ss_pred             ccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEec----cCCCceeEEEeCChHHHHHHHHHhcCe
Confidence            455678999987  11  122       234566678999999998752    34679999999999999999996 999


Q ss_pred             ccCCccccccCCCc
Q psy630           73 VLEGSRLSIQPSDS   86 (347)
Q Consensus        73 ~~~g~~l~v~~~~~   86 (347)
                      .|.||.|.-.....
T Consensus       338 ~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  338 WFDGRQLTASIWDG  351 (382)
T ss_pred             eecceEEEEEEeCC
Confidence            99999987665443

>KOG3609|consensus

Probab=95.16  E-value=0.02  Score=56.80  Aligned_cols=63  Identities=14%  Similarity=0.111  Sum_probs=41.1

Q ss_pred             CCcHHHHHHcCChHHHHHHHhhcCCC--------C-ccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCcccc
Q psy630          255 EKNIYEWAKEGKLDMLVKQLTKLKDF--------N-INQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVT  319 (347)
Q Consensus       255 ~~~~l~~a~~~~~~~~~~lL~~~~~~--------~-~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~  319 (347)
                      |..+|++.+.+-.. ++++++.+...        + ....-..+.|||.+||..++.+|+++||++ |+.+...
T Consensus        89 gdALL~aI~~~~v~-~VE~ll~~~~~~~~~~~~~d~~~~~ft~ditPliLAAh~NnyEil~~Ll~k-g~~i~~P  160 (822)
T KOG3609|consen   89 GDALLLAIAVGSVP-LVELLLVHFVDAPYLERSGDANSPHFTPDITPLMLAAHLNNFEILQCLLTR-GHCIPIP  160 (822)
T ss_pred             chHHHHHHHHHHHH-HHHHHHhcccccchhccccccCcccCCCCccHHHHHHHhcchHHHHHHHHc-CCCCCCC
Confidence            55555655555444 44444441111        0 112334588999999999999999999994 9987654

>PLN03213 repressor of silencing 3; Provisional

Probab=95.11  E-value=0.0092  Score=55.34  Aligned_cols=34  Identities=12%  Similarity=0.060  Sum_probs=30.9

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceeccc
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCN  133 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~  133 (347)
                      ..+|||+||...+++++|..+|+.||.|....+.
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp   43 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV   43 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe
Confidence            4689999999999999999999999999876665

>PLN03120 nucleic acid binding protein; Provisional

Probab=95.10  E-value=0.013  Score=50.77  Aligned_cols=37  Identities=5%  Similarity=0.084  Sum_probs=32.6

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCC
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDK  136 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~  136 (347)
                      ..++||+||++.+++++|+++|+.||.|....+..++
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~   40 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSEN   40 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecC
Confidence            3579999999999999999999999999987776554

>KOG2068|consensus

Probab=95.09  E-value=0.01  Score=52.59  Aligned_cols=80  Identities=20%  Similarity=0.405  Sum_probs=62.4

Q ss_pred             CeEEEeCCCCCCCHHHH---HHHHhccCCeeEEEEeeeCC--CCC-ceeEEEEEEcCHHHHHHHHhc-CCCccCCccccc
Q psy630            9 NKIFVGNLPWTVSHNEL---KKFFSEYGQIMNASVMFDKN--TGL-SKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI   81 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l---~~~f~~~G~i~~~~i~~~~~--t~~-~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v   81 (347)
                      +-+||-+||....++.+   .++|.+||.|..|.+.++..  .+. ...-++|+|...++|..|+.. ++.++.|+.++.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            45788899998876655   37899999999998877652  111 122389999999999999998 999999999887


Q ss_pred             cCCCccc
Q psy630           82 QPSDSHN   88 (347)
Q Consensus        82 ~~~~~~~   88 (347)
                      .+...+-
T Consensus       158 ~~gttky  164 (327)
T KOG2068|consen  158 SLGTTKY  164 (327)
T ss_pred             hhCCCcc
Confidence            7766544

>KOG0125|consensus

Probab=95.01  E-value=0.018  Score=50.87  Aligned_cols=78  Identities=8%  Similarity=0.053  Sum_probs=52.8

Q ss_pred             hhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhh
Q psy630           95 EDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVD  174 (347)
Q Consensus        95 ~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~l~  174 (347)
                      ...+..++++|+|+|...-+-||+.+|..||.|..+.|.+..=       -+|+..|+.++  +.++|.++    .++|.
T Consensus        91 ~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNER-------GSKGFGFVTme--n~~dadRA----Ra~LH  157 (376)
T KOG0125|consen   91 SSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNER-------GSKGFGFVTME--NPADADRA----RAELH  157 (376)
T ss_pred             CCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccC-------CCCccceEEec--ChhhHHHH----HHHhh
Confidence            3456778999999999999999999999999998777765421       14555555543  46666665    34444


Q ss_pred             ccCChhhhhhh
Q psy630          175 AGWEDKEQEEI  185 (347)
Q Consensus       175 ~~~~~~~~~~~  185 (347)
                      ...-+-+..++
T Consensus       158 gt~VEGRkIEV  168 (376)
T KOG0125|consen  158 GTVVEGRKIEV  168 (376)
T ss_pred             cceeeceEEEE
Confidence            44444433333

>KOG4307|consensus

Probab=94.93  E-value=0.029  Score=54.36  Aligned_cols=120  Identities=11%  Similarity=0.076  Sum_probs=84.0

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCCc
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~~   86 (347)
                      +...+-+++.++.....+++++|.-. .|-.+.|..+...+...|.++|+|.....++.|+..|...+-.|.+.|.++..
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            34556678999999999999999532 24455666666545558999999999999999999888888888887765433


Q ss_pred             ccccchh-----------------------------hhhhc---ccccccccCCcccccchhhHHHHhhcccc
Q psy630           87 HNRMAEN-----------------------------MEDRF---NQACDYLPSLVKKLDSSTLLKFYALYKQA  127 (347)
Q Consensus        87 ~~~~~~~-----------------------------~~~~f---~~~~~~v~~l~~~~~~e~l~~~f~~fg~v  127 (347)
                      ......+                             ....|   ...++||..||..++..++.++|..--.|
T Consensus       389 ~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~V  461 (944)
T KOG4307|consen  389 LGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAV  461 (944)
T ss_pred             cccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhh
Confidence            2110000                             00001   12578999999999998888877754444

>KOG1996|consensus

Probab=94.80  E-value=0.079  Score=46.10  Aligned_cols=62  Identities=19%  Similarity=0.187  Sum_probs=49.0

Q ss_pred             HHHHHHHhccCCeeEEEEeeeCCCCCcee-EEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630           23 NELKKFFSEYGQIMNASVMFDKNTGLSKG-FGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus        23 ~~l~~~f~~~G~i~~~~i~~~~~t~~~~g-~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      +++++.+++||.|..|.|...+..-.... -.||+|...++|.+|+.. ||-.|+||.+.-.+.
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fy  364 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFY  364 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheec
Confidence            46678889999999998877654333332 379999999999999985 999999998876654

>smart00362 RRM_2 RNA recognition motif

Probab=94.69  E-value=0.011  Score=39.96  Aligned_cols=34  Identities=9%  Similarity=0.158  Sum_probs=28.9

Q ss_pred             cccccCCcccccchhhHHHHhhccccceecccCC
Q psy630          102 CDYLPSLVKKLDSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus       102 ~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                      +++|+++|..++.++++++|..||.+....+...
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~   34 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKD   34 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecC
Confidence            4789999999999999999999999876555443

>KOG0113|consensus

Probab=94.29  E-value=0.013  Score=50.98  Aligned_cols=62  Identities=18%  Similarity=0.114  Sum_probs=50.4

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIAL  169 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~  169 (347)
                      .++||+.|+.++++.+|...|..||.|.-..+..++     ..|++|+.||.+  ++...+.+.+|-+.
T Consensus       102 ~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~-----vTgkskGYAFIe--ye~erdm~~AYK~a  163 (335)
T KOG0113|consen  102 KTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDK-----VTGKSKGYAFIE--YEHERDMKAAYKDA  163 (335)
T ss_pred             ceeeeeeccccccHHHHHHHHHhcCcceeEEEeeec-----ccCCccceEEEE--eccHHHHHHHHHhc
Confidence            789999999999999999999999999865555443     578888888876  55577778888553

>KOG0107|consensus

Probab=94.27  E-value=0.022  Score=45.76  Aligned_cols=40  Identities=13%  Similarity=0.176  Sum_probs=33.9

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCc
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSW  139 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~  139 (347)
                      .+.+||+||+..+++.+|...|..||.+...=+....||+
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGf   49 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGF   49 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCc
Confidence            5789999999999999999999999999765555555654

>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=94.19  E-value=0.055  Score=44.64  Aligned_cols=73  Identities=18%  Similarity=0.217  Sum_probs=42.0

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhc-cCCe---eEEEEeeeCCCCC--ceeEEEEEEcCHHHHHHHHhc-CCCccCCc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSE-YGQI---MNASVMFDKNTGL--SKGFGFVTFQNKEAVDKVFST-DSHVLEGS   77 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~-~G~i---~~~~i~~~~~t~~--~~g~afV~f~~~~~a~~a~~~-~~~~~~g~   77 (347)
                      .....+|.|++|||.+|++++.+.+.. ++.-   ..+.-.....+.+  ...-|||.|.+.+.+..-... +|+.|.+.
T Consensus         4 ~~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~   83 (176)
T PF03467_consen    4 EKEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDS   83 (176)
T ss_dssp             -----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-T
T ss_pred             cccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECC
Confidence            345669999999999999988886665 5544   3333112221111  235699999999987777664 77766443

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.

>PF06128 Shigella_OspC: Shigella flexneri OspC protein; InterPro: IPR010366 This family consists of the Shigella flexneri specific protein OspC

Probab=94.16  E-value=0.25  Score=41.71  Aligned_cols=89  Identities=22%  Similarity=0.312  Sum_probs=61.5

Q ss_pred             CcHHHHHHcCChHHHHHHHhhcCCCCccccCCC----CchHHHHHH--HcCCHHHHHHHHhhcC-CCcccc---CCCCCc
Q psy630          256 KNIYEWAKEGKLDMLVKQLTKLKDFNINQLDEN----GLNCLHWAC--DRGHLKVVQHLIEKCG-ADVNVT---DSDGDY  325 (347)
Q Consensus       256 ~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~----g~tpLh~A~--~~g~~~~v~~Ll~~~g-a~i~~~---d~~g~T  325 (347)
                      .+++-.+....-..+..+|+.  ......+|--    +.--+-|+-  ......+++..|. .| +++|.+   -+.|.|
T Consensus       180 ~~Am~~si~~~K~dva~~lls--~f~ft~~dv~~~~~~~ydieY~LS~h~a~~kvL~~Fi~-~Glv~vN~~F~~~NSGdt  256 (284)
T PF06128_consen  180 HQAMWLSIGNAKEDVALYLLS--KFNFTKQDVASMEKELYDIEYLLSEHSASYKVLEYFIN-RGLVDVNKKFQKVNSGDT  256 (284)
T ss_pred             HHHHHHHhcccHHHHHHHHHh--hcceecchhhhcCcchhhHHHHHhhcCCcHHHHHHHHh-ccccccchhhhccCCcch
Confidence            355555666666777777776  4444444432    222333332  3345677888887 46 677774   678999


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      -|.-|...++.+++.+||++||
T Consensus       257 MLDNA~Ky~~~emi~~Llk~GA  278 (284)
T PF06128_consen  257 MLDNAMKYKNSEMIAFLLKYGA  278 (284)
T ss_pred             HHHhHHhcCcHHHHHHHHHcCc
Confidence            9999999999999999999998

The function of this family is unknown but it is thought that Osp proteins may be involved in postinvasion events related to virulence. Since bacterial pathogens adapt to multiple environments during the course of infecting a host, it has been proposed that Shigella evolved a mechanism to take advantage of a unique intracellular cue, which is mediated through MxiE, to express proteins when the organism reaches the eukaryotic cytosol [].

>KOG0226|consensus

Probab=94.14  E-value=0.035  Score=47.30  Aligned_cols=163  Identities=16%  Similarity=0.205  Sum_probs=106.9

Q ss_pred             CeEEEeCCCCCCCHHH-H--HHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            9 NKIFVGNLPWTVSHNE-L--KKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~-l--~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      -..|++++-.++..+- +  ...|+-|-......+.+++. +.-++++|+.|.......++-.. +++.+.-+++++...
T Consensus        97 f~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p-~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~g  175 (290)
T KOG0226|consen   97 FRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRP-QPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAG  175 (290)
T ss_pred             ccccccccccccCCCCCCcchhhhccchhhhhhhhhhcCC-CccCcccccCcchhhhhhhhccccccccccCcceeeccc
Confidence            4567777777766554 3  56677666666666776654 67789999999988877777655 666666555665544


Q ss_pred             CcccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHH
Q psy630           85 DSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMS  164 (347)
Q Consensus        85 ~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~  164 (347)
                      ..-.... ..+-.-....||.+.|-.+++++.+-..|.+|..-.-..+..++     -.|++|+..|..+.+  ..+   
T Consensus       176 tswedPs-l~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdk-----RTgKSkgygfVSf~~--pad---  244 (290)
T KOG0226|consen  176 TSWEDPS-LAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDK-----RTGKSKGYGFVSFRD--PAD---  244 (290)
T ss_pred             cccCCcc-cccCccccceeecccccccccHHHHHHHHHhccchhhccccccc-----cccccccceeeeecC--HHH---
Confidence            4322211 11111233589999999999999999999999877655554432     367777776666443  443   


Q ss_pred             HHHHHHHHhhccCChhhhhh
Q psy630          165 KYIALLKEVDAGWEDKEQEE  184 (347)
Q Consensus       165 ~yi~~~~~l~~~~~~~~~~~  184 (347)
                       |+..++++.+.+-..++.-
T Consensus       245 -~~rAmrem~gkyVgsrpik  263 (290)
T KOG0226|consen  245 -YVRAMREMNGKYVGSRPIK  263 (290)
T ss_pred             -HHHHHHhhcccccccchhH
Confidence             4555777777777665443

>PLN03121 nucleic acid binding protein; Provisional

Probab=94.12  E-value=0.031  Score=47.77  Aligned_cols=35  Identities=9%  Similarity=0.034  Sum_probs=31.5

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCC
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                      .++||+||++.+++++|++||+.||.|....+..+
T Consensus         6 ~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D   40 (243)
T PLN03121          6 YTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS   40 (243)
T ss_pred             eEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC
Confidence            57899999999999999999999999997776654

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=94.04  E-value=0.4  Score=31.91  Aligned_cols=52  Identities=19%  Similarity=0.381  Sum_probs=42.2

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhcc---CCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEY---GQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS   68 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~---G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~   68 (347)
                      .+|+|+++. +++.++++.+|..|   .....|.++-|.       -|-|.|.+.+.|.+|+.
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~   60 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALV   60 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHH
Confidence            479999985 47778899999988   235588888775       37899999999999985

>PF14259 RRM_6: RNA recognition motif (a

Probab=93.86  E-value=0.029  Score=38.30  Aligned_cols=56  Identities=14%  Similarity=0.192  Sum_probs=36.5

Q ss_pred             ccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          103 DYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       103 ~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      +||+|||+.+++++|.++|+.||.+....+...+.+      +.+..||..+  -+.++|.+.+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~------~~~~~a~v~f--~~~~~a~~al   56 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDG------QSRGFAFVEF--SSEEDAKRAL   56 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTS------SEEEEEEEEE--SSHHHHHHHH
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeecc------ccCCEEEEEe--CCHHHHHHHH
Confidence            589999999999999999999998865555444322      2233455543  3566666653

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 ....

>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=93.06  E-value=0.039  Score=37.36  Aligned_cols=34  Identities=9%  Similarity=0.167  Sum_probs=28.6

Q ss_pred             cccccCCcccccchhhHHHHhhccccceecccCC
Q psy630          102 CDYLPSLVKKLDSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus       102 ~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                      +++|++||..+++++++++|+.||.+....+...
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~   34 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRD   34 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeC
Confidence            3689999999999999999999998876555543

This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=92.92  E-value=0.032  Score=48.96  Aligned_cols=59  Identities=12%  Similarity=0.116  Sum_probs=43.9

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|.++|..||.+....+..++     ..++.|+.|+..+  .+.++|..+
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~-----~~~~~~g~~~v~f--~~~~~~~~a  173 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDR-----ETGKSRGFAFVEF--ESEESAEKA  173 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeecc-----ccCccCceEEEEe--cCHHHHHHH
Confidence            5899999999999999999999999999776666654     3455555555543  334555544

>smart00360 RRM RNA recognition motif

Probab=92.92  E-value=0.03  Score=37.57  Aligned_cols=54  Identities=17%  Similarity=0.150  Sum_probs=36.5

Q ss_pred             ccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          105 LPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       105 v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      |+++|..+++++++++|+.||.+....+...+.     .++.++.|+..  ..+.++|..+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~-----~~~~~~~a~v~--f~~~~~a~~a   54 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKD-----TGKSKGFAFVE--FESEEDAEKA   54 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCC-----CCCCCceEEEE--eCCHHHHHHH
Confidence            578999999999999999999887665554432     22333444443  3456666655

>KOG2135|consensus

Probab=92.65  E-value=0.05  Score=50.44  Aligned_cols=70  Identities=19%  Similarity=0.357  Sum_probs=56.9

Q ss_pred             EEeCCCCCC-CHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCCcc
Q psy630           12 FVGNLPWTV-SHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDSH   87 (347)
Q Consensus        12 ~V~nLp~~~-t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~~~   87 (347)
                      -+.-.|+.. +-.+|..+|.+||.|..|++-      .+.--|.|+|.+...|-.|....+.+|+||.|+|.|..+.
T Consensus       376 ~lek~~~glnt~a~ln~hfA~fG~i~n~qv~------~~~~~a~vTF~t~aeag~a~~s~~avlnnr~iKl~whnps  446 (526)
T KOG2135|consen  376 ALEKSPFGLNTIADLNPHFAQFGEIENIQVD------YSSLHAVVTFKTRAEAGEAYASHGAVLNNRFIKLFWHNPS  446 (526)
T ss_pred             hhhccCCCCchHhhhhhhhhhcCcccccccc------CchhhheeeeeccccccchhccccceecCceeEEEEecCC
Confidence            334445554 567899999999999999873      3345799999999999888888999999999999987664

>KOG0130|consensus

Probab=92.60  E-value=0.046  Score=41.96  Aligned_cols=61  Identities=13%  Similarity=0.063  Sum_probs=45.3

Q ss_pred             cccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           98 FNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        98 f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...-.+||.++.+..+++++.+.|+-||.|...-++.++-     .|..|+.|..+  +...++|..+
T Consensus        70 VEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRR-----tGy~KGYaLvE--Yet~keAq~A  130 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRR-----TGYVKGYALVE--YETLKEAQAA  130 (170)
T ss_pred             eeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccc-----cccccceeeee--hHhHHHHHHH
Confidence            3445789999999999999999999999999877777653     44456555554  4445555555

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=92.00  E-value=0.61  Score=36.40  Aligned_cols=74  Identities=18%  Similarity=0.213  Sum_probs=51.9

Q ss_pred             ccCCCeEEEeCCCCCC-CHHHH---HHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCcccc
Q psy630            5 IRQLNKIFVGNLPWTV-SHNEL---KKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLS   80 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~-t~~~l---~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~   80 (347)
                      ...+.+|.|+=|..++ ..+++   -..++.||+|.+|...     |  +.-|.|+|.+..+|=.|+..-.....|..+.
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-----G--rqsavVvF~d~~SAC~Av~Af~s~~pgtm~q  155 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-----G--RQSAVVVFKDITSACKAVSAFQSRAPGTMFQ  155 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-----C--CceEEEEehhhHHHHHHHHhhcCCCCCceEE
Confidence            3456788898776665 23344   4556789999998763     3  4579999999999999998633456666666


Q ss_pred             ccCCC
Q psy630           81 IQPSD   85 (347)
Q Consensus        81 v~~~~   85 (347)
                      ..+-.
T Consensus       156 CsWqq  160 (166)
T PF15023_consen  156 CSWQQ  160 (166)
T ss_pred             eeccc
Confidence            65543

>KOG4285|consensus

Probab=91.89  E-value=0.55  Score=41.26  Aligned_cols=71  Identities=13%  Similarity=0.309  Sum_probs=53.6

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCc-cccccCCCc
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGS-RLSIQPSDS   86 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~-~l~v~~~~~   86 (347)
                      ..|-|=++|+.-+.- |-.+|++||.|+.....      ...-+-+|.|.+.-.|++|+..+|..|+|. .|-|.++..
T Consensus       198 ~WVTVfGFppg~~s~-vL~~F~~cG~Vvkhv~~------~ngNwMhirYssr~~A~KALskng~ii~g~vmiGVkpCtD  269 (350)
T KOG4285|consen  198 TWVTVFGFPPGQVSI-VLNLFSRCGEVVKHVTP------SNGNWMHIRYSSRTHAQKALSKNGTIIDGDVMIGVKPCTD  269 (350)
T ss_pred             ceEEEeccCccchhH-HHHHHHhhCeeeeeecC------CCCceEEEEecchhHHHHhhhhcCeeeccceEEeeeecCC
Confidence            445555888876544 66789999999887653      334589999999999999999999999875 345666544

>KOG2202|consensus

Probab=91.60  E-value=0.081  Score=45.28  Aligned_cols=60  Identities=17%  Similarity=0.275  Sum_probs=46.1

Q ss_pred             HHHHHHh-ccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630           24 ELKKFFS-EYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus        24 ~l~~~f~-~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ++...|+ +||+|.++.|-.+. ...-.|=+||.|...++|++|+.. |+--+.|++|...+.
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            3344444 89999998765543 234568899999999999999986 999999999876654

>KOG4207|consensus

Probab=89.98  E-value=0.093  Score=43.43  Aligned_cols=60  Identities=12%  Similarity=0.173  Sum_probs=40.1

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCC-CHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQM-AKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~-~~~eA~~~  165 (347)
                      ..+-|-||...++.++|..+|.+||.|.  ++.+|+.   ......++.||..+.+. ..++|+.+
T Consensus        14 ~SLkVdNLTyRTspd~LrrvFekYG~vg--DVyIPrd---r~Tr~sRgFaFVrf~~k~daedA~da   74 (256)
T KOG4207|consen   14 TSLKVDNLTYRTSPDDLRRVFEKYGRVG--DVYIPRD---RYTRQSRGFAFVRFHDKRDAEDALDA   74 (256)
T ss_pred             eeEEecceeccCCHHHHHHHHHHhCccc--ceecccc---cccccccceeEEEeeecchHHHHHHh
Confidence            4677999999999999999999999986  5555442   12344455566555443 23344443

>PF11929 DUF3447: Domain of unknown function (DUF3447); InterPro: IPR020683 This entry represents the ankyrin repeat-containing domain

Probab=89.94  E-value=0.74  Score=32.11  Aligned_cols=47  Identities=23%  Similarity=0.335  Sum_probs=31.7

Q ss_pred             cHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhh
Q psy630          257 NIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEK  311 (347)
Q Consensus       257 ~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~  311 (347)
                      ..+..|..|+..++.+.+.+ .+ .++      ...|..|+..-+.+++.+|++.
T Consensus         8 ~tl~~Ai~GGN~eII~~c~~-~~-~~~------~~~l~~AI~~H~n~i~~~l~~~   54 (76)
T PF11929_consen    8 KTLEYAIIGGNFEIINICLK-KN-KPD------NDCLEYAIKSHNNEIADWLIEN   54 (76)
T ss_pred             HHHHHHHhCCCHHHHHHHHH-Hh-ccH------HHHHHHHHHHhhHHHHHHHHHh
Confidence            45567777777777777665 11 111      4568888888888888888874

These domains contain multiple repeats of a beta(2)-alpha(2) motif. The ankyrin repeat is one of the most common protein-protein interaction motifs in nature. Ankyrin repeats are tandemly repeated modules of about 33 amino acids. They occur in a large number of functionally diverse proteins mainly from eukaryotes. The few known examples from prokaryotes and viruses may be the result of horizontal gene transfers []. The repeat has been found in proteins of diverse function such as transcriptional initiators, cell-cycle regulators, cytoskeletal, ion transporters and signal transducers. The ankyrin fold appears to be defined by its structure rather than its function since there is no specific sequence or structure which is universally recognised by it. The conserved fold of the ankyrin repeat unit is known from several crystal and solution structures [, , , ]. Each repeat folds into a helix-loop-helix structure with a beta-hairpin/loop region projecting out from the helices at a 90o angle. The repeats stack together to form an L-shaped structure [, ].

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=89.78  E-value=4  Score=30.73  Aligned_cols=65  Identities=12%  Similarity=0.260  Sum_probs=44.3

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhcc-CCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCC
Q psy630           10 KIFVGNLPWTVSHNELKKFFSEY-GQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEG   76 (347)
Q Consensus        10 ~l~V~nLp~~~t~~~l~~~f~~~-G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g   76 (347)
                      .+.+...|..++.++|..+.+.+ ..|..++|+++.  ..++-.+.+.|.+...|..-... ||..|+.
T Consensus        15 ~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   15 LCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             EEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            34444444445555665555554 457788888864  34667799999999999988875 8887753

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG0108|consensus

Probab=88.48  E-value=0.14  Score=48.21  Aligned_cols=92  Identities=11%  Similarity=0.161  Sum_probs=61.3

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhhccCChh
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWEDK  180 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~l~~~~~~~  180 (347)
                      ..+||+|+|+++++++|..+|+..|.|..-+...++.     .|+.|+.+|.++++  .++|..+    ++.|..  .+-
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~-----tG~~~G~~f~~~~~--~~~~~~a----~~~lNg--~~~   85 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRE-----TGKPKGFGFCEFTD--EETAERA----IRNLNG--AEF   85 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeeccccc-----CCCcCceeeEecCc--hhhHHHH----HHhcCC--ccc
Confidence            5789999999999999999999999999877777765     66777777777655  3444443    233321  111


Q ss_pred             hhhhhhccccchhhhHHHHHHHhhh
Q psy630          181 EQEEINWDWKPNQKAMSKYIALLNE  205 (347)
Q Consensus       181 ~~~~~~~~~~~~~~~~~~~~~~~~~  205 (347)
                      ..+.++.+|+...+...+...+.+.
T Consensus        86 ~gr~l~v~~~~~~~~~~~~~~~~~~  110 (435)
T KOG0108|consen   86 NGRKLRVNYASNRKNAERSLASHNA  110 (435)
T ss_pred             CCceEEeecccccchhHHHHhhccc
Confidence            2234566676665655444444433

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=88.25  E-value=0.15  Score=36.64  Aligned_cols=70  Identities=11%  Similarity=0.190  Sum_probs=45.9

Q ss_pred             EEEEEcCHHHHHHHHhc--CCCccCCcccccc--CCCcccccchhhhhhcccccccccCCcccccchhhHHHHh
Q psy630           53 GFVTFQNKEAVDKVFST--DSHVLEGSRLSIQ--PSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYA  122 (347)
Q Consensus        53 afV~f~~~~~a~~a~~~--~~~~~~g~~l~v~--~~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~  122 (347)
                      |.|+|.+..-|+..+..  ....+++..+.|.  +.....-..-+........++.|.++|..++++.+++...
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~Le   74 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKLE   74 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEEEEEEcccCCEEEEeCCCCCCChhhheeeEE
Confidence            67999999999999986  4444555555443  3222221111222233457889999999999999887554

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG0533|consensus

Probab=88.20  E-value=0.22  Score=43.06  Aligned_cols=39  Identities=10%  Similarity=0.097  Sum_probs=34.6

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCc
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSW  139 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~  139 (347)
                      ..++|.|||..+.+++|++||..|+++.-+.++.++.|.
T Consensus        84 ~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~  122 (243)
T KOG0533|consen   84 TKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGR  122 (243)
T ss_pred             ceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCC
Confidence            578999999999999999999999988888888877553

>KOG0151|consensus

Probab=87.75  E-value=0.28  Score=47.98  Aligned_cols=62  Identities=11%  Similarity=0.145  Sum_probs=46.0

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      .++||+|+++.++++.|+..|+.||++...++..++...-  ..+.+-.+|++  .|++.+|.++.
T Consensus       175 TNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeE--k~r~r~cgfva--fmnR~D~era~  236 (877)
T KOG0151|consen  175 TNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEE--KRRERNCGFVA--FMNRADAERAL  236 (877)
T ss_pred             cceeeecCCccccHHHHHHHhcccCcccceeeecccchhh--hccccccceee--ehhhhhHHHHH
Confidence            6899999999999999999999999999989888765211  11222234443  67777776663

>KOG2416|consensus

Probab=87.21  E-value=0.37  Score=46.18  Aligned_cols=73  Identities=14%  Similarity=0.153  Sum_probs=54.1

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHh-ccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCcc---CCccccc
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFS-EYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVL---EGSRLSI   81 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~-~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~---~g~~l~v   81 (347)
                      ..+-|||.||-.-+|.-+|+.++. ..|.|....|      .+-+..|||.|.+.+.|...... ++..+   +++.|.+
T Consensus       443 ~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm------DkIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~a  516 (718)
T KOG2416|consen  443 PSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM------DKIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIA  516 (718)
T ss_pred             ccceEeeecccccchHHHHHHHHhhccCchHHHHH------HHhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEe
Confidence            346799999999999999999998 5666666633      23357899999999988877764 65554   3556665


Q ss_pred             cCCC
Q psy630           82 QPSD   85 (347)
Q Consensus        82 ~~~~   85 (347)
                      .+..
T Consensus       517 df~~  520 (718)
T KOG2416|consen  517 DFVR  520 (718)
T ss_pred             eecc
Confidence            5543

>KOG2505|consensus

Probab=85.83  E-value=0.64  Score=43.77  Aligned_cols=48  Identities=13%  Similarity=0.066  Sum_probs=39.0

Q ss_pred             cccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHH
Q psy630          249 SQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWAC  297 (347)
Q Consensus       249 ~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~  297 (347)
                      ...+.-..|+||+|+..+...++..++. .++|+..+|..|+||..+++
T Consensus       424 e~~~~ltsT~LH~aa~qg~~k~v~~~Le-eg~Dp~~kd~~Grtpy~ls~  471 (591)
T KOG2505|consen  424 EANDYLTSTFLHYAAAQGARKCVKYFLE-EGCDPSTKDGAGRTPYSLSA  471 (591)
T ss_pred             cccccccchHHHHHHhcchHHHHHHHHH-hcCCchhcccCCCCcccccc
Confidence            3344557799999988777777777777 57999999999999999987

>PF03158 DUF249: Multigene family 530 protein; InterPro: IPR004858 This entry represents multigene family 530 proteins from African swine fever virus (ASFV) viruses

Probab=82.40  E-value=3  Score=34.30  Aligned_cols=47  Identities=23%  Similarity=0.450  Sum_probs=41.8

Q ss_pred             hHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCCHHHHHHHHh
Q psy630          291 NCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVN  344 (347)
Q Consensus       291 tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~~~v~~Ll~  344 (347)
                      .-|.+|+..|-+..+-..|+ +|.+++.      +.|..|+..+|..++.+++.
T Consensus       145 ~hl~~a~~kgll~F~letlk-ygg~~~~------~vls~Av~ynhRkIL~yfi~  191 (192)
T PF03158_consen  145 QHLEKAAAKGLLPFVLETLK-YGGNVDI------IVLSQAVKYNHRKILDYFIR  191 (192)
T ss_pred             HHHHHHHHCCCHHHHHHHHH-cCCcccH------HHHHHHHHhhHHHHHHHhhc
Confidence            35789999999999999998 7999875      79999999999999999875

These proteins may be involved in promoting survival of infected macrophages [].

>KOG0116|consensus

Probab=82.12  E-value=0.77  Score=43.11  Aligned_cols=37  Identities=11%  Similarity=0.227  Sum_probs=32.9

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCC
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKP  137 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p  137 (347)
                      ..|||+|||.+++..+|.++|..||.|+.+.+....|
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~  325 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSP  325 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEecc
Confidence            4689999999999999999999999999888777553

>KOG2591|consensus

Probab=80.55  E-value=4.2  Score=39.03  Aligned_cols=66  Identities=12%  Similarity=0.345  Sum_probs=52.5

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHh--ccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc---CCCccCCcccc
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFS--EYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST---DSHVLEGSRLS   80 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~--~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~---~~~~~~g~~l~   80 (347)
                      .+-|.++-||..+..++++.+|+  .+-++.+|.+-.+..       =||+|.+..+|+.|.+.   ..+.|.|++|.
T Consensus       175 RcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n-------WyITfesd~DAQqAykylreevk~fqgKpIm  245 (684)
T KOG2591|consen  175 RCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN-------WYITFESDTDAQQAYKYLREEVKTFQGKPIM  245 (684)
T ss_pred             eeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc-------eEEEeecchhHHHHHHHHHHHHHhhcCcchh
Confidence            45678899999999999999996  467788888765542       58999999999988863   56667787764

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	347
2cop_A	109	Solution Structure Of Rsgi Ruh-040, An Acbp Domain		2e-15
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		2e-13
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		2e-11
3flv_A	119	The Crystal Structure Of Human Acyl-Coenzymea Bindi		3e-11
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		6e-11
2wh5_A	106	Crystal Structure Of Human Acyl-Coa Binding Domain		7e-11
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		7e-11
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		8e-11
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		3e-10
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		6e-10
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		1e-09
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		2e-09
2cqu_A	116	Solution Structure Of Rsgi Ruh-045, A Human Acyl-Co		2e-09
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		2e-09
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		3e-09
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		3e-09
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		4e-09
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-09
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		5e-09
4hqd_A	169	Crystal Structure Of Engineered Protein. Northeast		8e-09
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		9e-09
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		1e-08
1hbk_A	89	Acyl-Coa Binding Protein From Plasmodium Falciparum		2e-08
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		3e-08
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		4e-08
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		5e-08
2fdq_A	86	Crystal Structure Of Acbp From Armadillo Harderian		5e-08
1hb6_A	86	Structure Of Bovine Acyl-Coa Binding Protein In Ort		5e-08
2lbb_A	96	Solution Structure Of Acyl Coa Binding Protein From		5e-08
1st7_A	86	Solution Structure Of Acyl Coenzyme A Binding Prote		6e-08
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		6e-08
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		6e-08
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		8e-08
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		9e-08
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		9e-08
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		9e-08
2fj9_A	86	High Resolution Crystal Structure Of The Unliganded		1e-07
2xzt_G	136	Caspase-3 In Complex With Darpin-3.4_i78s Length =		1e-07
2cb8_A	87	High Resolution Crystal Structure Of Liganded Human		1e-07
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		1e-07
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		1e-07
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		2e-07
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		2e-07
2xeh_A	157	Structural Determinants For Improved Thermal Stabil		2e-07
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		3e-07
2xee_A	157	Structural Determinants For Improved Thermal Stabil		3e-07
3zuv_B	136	Crystal Structure Of A Designed Selected Ankyrin Re		3e-07
2qyj_A	166	Crystal Structure Of A Designed Full Consensus Anky		3e-07
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		3e-07
4dui_A	169	Darpin D1 Binding To Tubulin Beta Chain (not In Com		3e-07
3nog_D	169	Designed Ankyrin Repeat Protein (Darpin) Binders To		4e-07
4gpm_A	169	Crystal Structure Of Engineered Protein. Northeast		4e-07
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		4e-07
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		5e-07
4drx_E	169	Gtp-Tubulin In Complex With A Darpin Length = 169		5e-07
3epy_A	89	Crystal Structure Of Human Acyl-Coa Binding Domain		6e-07
1sxl_A	97	Resonance Assignments And Solution Structure Of The		6e-07
3fp5_A	106	Crystal Structure Of Acbp From Moniliophthora Perni		7e-07
3b7b_A	237	Euhmt1 (Glp) Ankyrin Repeat Domain (Structure 1) Le		8e-07
4hb5_A	169	Crystal Structure Of Engineered Protein. Northeast		9e-07
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		1e-06
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		2e-06
1n0r_A	126	4ank: A Designed Ankyrin Repeat Protein With Four I		2e-06
3noc_D	169	Designed Ankyrin Repeat Protein (Darpin) Binders To		2e-06
2dgq_A	108	Solution Structure Of The N-Terminal Rna Binding Do		2e-06
2dgp_A	106	Solution Structure Of The N-Terminal Rna Binding Do		2e-06
3ucg_A	89	Crystal Structure Of A Rna Binding Domain Of Hypoth		2e-06
3b4d_A	96	Crystal Structure Of Human Pabpn1 Rrm Length = 96		2e-06
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		2e-06
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		3e-06
2v4h_C	136	Nemo Cc2-Lz Domain - 1d5 Darpin Complex Length = 13		3e-06
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		3e-06
2cph_A	107	Solution Structure Of The C-Terminal Rna Recognitio		4e-06
1n0q_A	93	3ank: A Designed Ankyrin Repeat Protein With Three		4e-06
3q9u_C	158	In Silico And In Vitro Co-Evolution Of A High Affin		4e-06
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		6e-06
1mj0_A	166	Sank E3_5: An Artificial Ankyrin Repeat Protein Len		7e-06
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		1e-05
4atz_D	154	Ad5 Knob In Complex With A Designed Ankyrin Repeat		1e-05
3f6q_A	179	Crystal Structure Of Integrin-Linked Kinase Ankyrin		1e-05
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		2e-05
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		2e-05
2kbx_A	171	Solution Structure Of Ilk-Pinch Complex Length = 17		2e-05
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		3e-05
4gmr_A	169	Crystal Structure Of Engineered Protein. Northeast		3e-05
3ehq_A	222	Crystal Structure Of Human Osteoclast Stimulating F		3e-05
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		3e-05
1wtb_A	79	Complex Structure Of The C-Terminal Rna-Binding Dom		4e-05
3zu7_B	169	Crystal Structure Of A Designed Selected Ankyrin Re		5e-05
2j8s_D	169	Drug Export Pathway Of Multidrug Exporter Acrb Reve		5e-05
2khc_A	118	Bruno Rrm3+ Length = 118		6e-05
2p2c_P	169	Inhibition Of Caspase-2 By A Designed Ankyrin Repea		6e-05
2xnr_A	97	Structural Insights Into Cis Element Recognition Of		8e-05
2xnq_A	97	Structural Insights Into Cis Element Recognition Of		9e-05
3nnh_A	88	Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuug		1e-04
3sde_B	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		1e-04
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		1e-04
1mx4_A	168	Structure Of P18ink4c (F82q) Length = 168		1e-04
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		1e-04
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		1e-04
1iqt_A	75	Solution Structure Of The C-Terminal Rna-Binding Do		1e-04
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		1e-04
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		1e-04
4f6r_D	169	Tubulin:stathmin-Like Domain Complex Length = 169		2e-04
2l41_A	77	Nab3 Rrm - Ucuu Complex Length = 77		2e-04
2kvi_A	96	Structure Of Nab3 Rrm Length = 96		2e-04
2cpz_A	115	Solution Structure Of Rna Binding Domain 3 In Cug T		2e-04
1mx6_A	168	Structure Of P18ink4c (F92n) Length = 168		2e-04
1ycs_B	239	P53-53bp2 Complex Length = 239		2e-04
4a63_B	239	Crystal Structure Of The P73-Aspp2 Complex At 2.6a		2e-04
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		2e-04
2cpf_A	98	Solution Structure Of The Penultimate Rna Recogniti		2e-04
2i38_A	150	Solution Structure Of The Rrm Of Srp20 Length = 150		2e-04
2e5g_A	94	Solution Structure Of Rna Binding Domain In Rna Bin		2e-04
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		2e-04
2i2y_A	150	Solution Structure Of The Rrm Of Srp20 Bound To The		2e-04
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		2e-04
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		2e-04
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		3e-04
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		3e-04
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		3e-04
3v30_A	172	Crystal Structure Of The Peptide Bound Complex Of T		3e-04
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		3e-04
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		3e-04
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		3e-04
1ihb_A	162	Crystal Structure Of P18-Ink4c(Ink6) Length = 162		4e-04
1bu9_A	168	Solution Structure Of P18-Ink4c, 21 Structures Leng		4e-04
1mx2_A	168	Structure Of F71n Mutant Of P18ink4c Length = 168		4e-04
3uxg_A	172	Crystal Structure Of Rfxank Length = 172		4e-04
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		4e-04
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		4e-04
2cpj_A	99	Solution Structure Of The N-Terminal Rna Recognitio		4e-04
2dnq_A	90	Solution Structure Of Rna Binding Domain 1 In Rna-B		4e-04
1x4a_A	109	Solution Structure Of Rrm Domain In Splicing Factor		5e-04
4grg_A	135	Crystal Structure Of Ige Complexed With E2_79, An A		5e-04
3eu9_A	240	The Ankyrin Repeat Domain Of Huntingtin Interacting		5e-04
1s70_B	299	Complex Between Protein Ser/thr Phosphatase-1 (delt		5e-04
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		5e-04
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		6e-04
2do0_A	114	Solution Structure Of The Rna Binding Domain Of Het		6e-04
2hvz_A	101	Solution Structure Of The Rrm Domain Of Sr Rich Fac		6e-04
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		6e-04
2dgt_A	92	Solution Structure Of The Second Rna Binding Domain		8e-04
3v2o_A	183	Crystal Structure Of The Peptide Bound Complex Of T		8e-04

>pdb|2COP|A Chain A, Solution Structure Of Rsgi Ruh-040, An Acbp Domain From Human Cdna Length = 109

Iteration: 1
 Score = 79.7 bits (195), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 36/92 (39%), Positives = 56/92 (60%)
Query: 93  NMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWN 152
            + + F +A  +L  L++      LL  YA YKQ  VG CN  KPS+++ E K K+ AW 
Sbjct: 7   GLAELFEKAAAHLQGLIQVASREQLLYLYARYKQVKVGNCNTPKPSFFDFEGKQKWEAWK 66
Query: 153 SLGQMAKSEAMSKYIALLKEVDAGWEDKEQEE 184
           +LG  + S+AM +YIA++K++D GW  +  E+
Sbjct: 67  ALGDSSPSQAMQEYIAVVKKLDPGWNPQIPEK 98

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 72.8 bits (177), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 28/77 (36%), Positives = 49/77 (63%)
Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
          ++ K+FVG L W+ +   L+ +FS+YG++++  +M DK T  S+GFGFV F++   V  V
Sbjct: 15 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV 74
Query: 67 FSTDSHVLEGSRLSIQP 83
           ++  H L+G  +  +P
Sbjct: 75 LASRPHTLDGRNIDPKP 91

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 29/60 (48%), Positives = 44/60 (73%)
Query: 7   QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
           +  KIFVG +   V   E ++FFS++G I++A +M DK+TG S+GFGFVT+ + +AVD+V
Sbjct: 86  KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRV 145

>pdb|3FLV|A Chain A, The Crystal Structure Of Human Acyl-Coenzymea Binding Domain Containing 5 Length = 119

Iteration: 1
 Score = 65.9 bits (159), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 32/83 (38%), Positives = 50/83 (60%), Gaps = 4/83 (4%)
Query: 95  EDRFNQACDYLPSLVK----KLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNA 150
           E RF  A   + SL K    +  +  +LKFY+ YKQAT G C + +P +++   + K++A
Sbjct: 25  ETRFEAAVKVIQSLPKNGSFQPTNEMMLKFYSFYKQATEGPCKLSRPGFWDPIGRYKWDA 84
Query: 151 WNSLGQMAKSEAMSKYIALLKEV 173
           W+SLG M K EAM  Y+  +K++
Sbjct: 85  WSSLGDMTKEEAMIAYVEEMKKI 107

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 65.1 bits (157), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 30/83 (36%), Positives = 48/83 (57%), Gaps = 2/83 (2%)
Query: 10  KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           K+F+G L W  +   L+++F ++G++    VM D  T  S+GFGFVTF ++  VDKV + 
Sbjct: 27  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 70  DSHVLEGSRLSIQPSDSHNRMAE 92
             H L+    +I P  +  R A+
Sbjct: 87  SRHELDSK--TIDPKVAFPRRAQ 107

>pdb|2WH5|A Chain A, Crystal Structure Of Human Acyl-Coa Binding Domain 4 Complexed With Stearoyl-Coa Length = 106

Iteration: 1
 Score = 64.7 bits (156), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 27/57 (47%), Positives = 43/57 (75%)
Query: 117 LLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEV 173
           +L+FY+ YKQAT+G C + +P +++   + K++AWNSLG+M++ EAMS YI  +K V
Sbjct: 35  MLRFYSYYKQATMGPCLVPRPGFWDPIGRYKWDAWNSLGKMSREEAMSAYITEMKLV 91

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 64.7 bits (156), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 27/66 (40%), Positives = 43/66 (65%)
Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          +F+G L W  +  +LK +FS++G++++ ++  D  TG S+GFGFV F+  E+VDKV    
Sbjct: 2  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 71 SHVLEG 76
           H L G
Sbjct: 62 EHKLNG 67

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 64.7 bits (156), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 27/67 (40%), Positives = 45/67 (67%)
Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K FVG L W  S  +LK +F+++G++++ ++  D NTG S+GFGF+ F++  +V+KV   
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 70 DSHVLEG 76
            H L+G
Sbjct: 73 KEHRLDG 79

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 62.8 bits (151), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 26/66 (39%), Positives = 41/66 (62%)
Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+F+G L W  +   L+++F ++G++    VM D  T  S+GFGFVTF ++  VDKV + 
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 70 DSHVLE 75
            H L+
Sbjct: 62 SRHELD 67

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 61.6 bits (148), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 45/74 (60%)
Query: 8  LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
            KIFVG LP+  +   L+K+F  +G I  A V+ D+ TG S+G+GFVT  ++ A ++  
Sbjct: 17 FTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERAC 76
Query: 68 STDSHVLEGSRLSI 81
             + +++G + ++
Sbjct: 77 KDPNPIIDGRKANV 90

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 60.8 bits (146), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 25/81 (30%), Positives = 49/81 (60%), Gaps = 3/81 (3%)
Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          NKIFVG +P      EL+++F ++G +    +++D      +GFGF+TF+++++VD+  +
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN 70
Query: 69 TDSHVLEGSRLSI---QPSDS 86
             H + G ++ +   +P DS
Sbjct: 71 MHFHDIMGKKVEVKRAEPRDS 91

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 59.7 bits (143), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 46/84 (54%)
Query: 8   LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
           + KIFVG +      + L+ +F +YG+I    +M D+ +G  +GF FVTF + ++VDK+ 
Sbjct: 97  VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
Query: 68  STDSHVLEGSRLSIQPSDSHNRMA 91
               H + G    ++ + S   MA
Sbjct: 157 IQKYHTVNGHNCEVRKALSKQEMA 180

>pdb|2CQU|A Chain A, Solution Structure Of Rsgi Ruh-045, A Human Acyl-Coa Binding Protein Length = 116

Iteration: 1
 Score = 59.7 bits (143), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 32/85 (37%), Positives = 47/85 (55%), Gaps = 1/85 (1%)
Query: 84  SDSHNRMAENMEDR-FNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNM 142
           S   NR A     + F  + + +  L K   +   LK YALYKQAT G CN+ KP  +++
Sbjct: 5   SSGMNRTAMRASQKDFENSMNQVKLLKKDPGNEVKLKLYALYKQATEGPCNMPKPGVFDL 64
Query: 143 EAKSKYNAWNSLGQMAKSEAMSKYI 167
             K+K++AWN+LG + K  A   Y+
Sbjct: 65  INKAKWDAWNALGSLPKEAARQNYV 89

>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 = 59.7 bits (143), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 46/84 (54%)
Query: 8   LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
           + KIFVG +      + L+ +F +YG+I    +M D+ +G  +GF FVTF + ++VDK+ 
Sbjct: 103 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 162
Query: 68  STDSHVLEGSRLSIQPSDSHNRMA 91
               H + G    ++ + S   MA
Sbjct: 163 IQKYHTVNGHNCEVRKALSKQEMA 186

>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 = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 46/84 (54%)
Query: 8   LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
           + KIFVG +      + L+ +F +YG+I    +M D+ +G  +GF FVTF + ++VDK+ 
Sbjct: 105 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164
Query: 68  STDSHVLEGSRLSIQPSDSHNRMA 91
               H + G    ++ + S   MA
Sbjct: 165 IQKYHTVNGHNCEVRKALSKQEMA 188

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 46/84 (54%)
Query: 8   LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
           + KIFVG +      + L+ +F +YG+I    +M D+ +G  +GF FVTF + ++VDK+ 
Sbjct: 104 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
Query: 68  STDSHVLEGSRLSIQPSDSHNRMA 91
               H + G    ++ + S   MA
Sbjct: 164 IQKYHTVNGHNCEVRKALSKQEMA 187

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 58.9 bits (141), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 46/83 (55%), Gaps = 2/83 (2%)
Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
          QL K+F+G L +  +   L+  F ++G + +  VM D NT  S+GFGFVT+   E VD  
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71
Query: 67 FSTDSHVLEGSRLSIQPSDSHNR 89
           +   H ++G    ++P  + +R
Sbjct: 72 MNARPHKVDGR--VVEPKRAVSR 92

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 58.9 bits (141), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 46/83 (55%), Gaps = 2/83 (2%)
Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
          QL K+F+G L +  +   L+  F ++G + +  VM D NT  S+GFGFVT+   E VD  
Sbjct: 10 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 69
Query: 67 FSTDSHVLEGSRLSIQPSDSHNR 89
           +   H ++G    ++P  + +R
Sbjct: 70 MNARPHKVDGR--VVEPKRAVSR 90

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 58.5 bits (140), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 41/59 (69%), Gaps = 1/59 (1%)
Query: 2   SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
           S SIR  N ++V  LP T+S  E+++ FS+YG+I+ + ++ D+ TG+S+G GF+ F  +
Sbjct: 85  SASIRDAN-LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKR 142

>pdb|4HQD|A Chain A, Crystal Structure Of Engineered Protein. Northeast Structural Genomics Consortium Target Or265. Length = 169

Iteration: 1
 Score = 57.8 bits (138), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 36/98 (36%), Positives = 54/98 (55%), Gaps = 9/98 (9%)
Query: 253 DNEKNIYEWAKEGKLDMLVKQLTKL---KDFNINQLDENGLNCLHWACDRGHLKVVQHLI 309
           D    ++  AKEG      K++ KL   K  ++N  D +G   LH+A   GH ++V+ LI
Sbjct: 36  DGRTPLHYAAKEGH-----KEIVKLLISKGADVNAKDSDGRTPLHYAAKEGHKEIVKLLI 90
Query: 310 EKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
            K GADVN  DSDG   L YA    H ++++ L++ G+
Sbjct: 91  SK-GADVNAKDSDGRTPLHYAAKEGHKEIVKLLISKGA 127

>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 = 57.8 bits (138), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 27/88 (30%), Positives = 49/88 (55%), Gaps = 1/88 (1%)
Query: 6  RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE-AVD 64
          R L  +FVGN+P+  +  +LK  FSE G +++  +++D+ TG  KG+GF  +Q++E A+ 
Sbjct: 6  RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65
Query: 65 KVFSTDSHVLEGSRLSIQPSDSHNRMAE 92
           + + +     G  L +  + S     E
Sbjct: 66 AMRNLNGREFSGRALRVDNAASEKNKEE 93

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 57.8 bits (138), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 41/59 (69%), Gaps = 1/59 (1%)
Query: 2   SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
           S SIR  N ++V  LP T++  EL++ FS+YG+I+ + ++ D+ TG+S+G GF+ F  +
Sbjct: 83  SASIRDAN-LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKR 140

>pdb|1HBK|A Chain A, Acyl-Coa Binding Protein From Plasmodium Falciparum Length = 89

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 26/89 (29%), Positives = 48/89 (53%), Gaps = 2/89 (2%)
Query: 93  NMEDRFNQACDYLPSLVKKLDSSTLLKF--YALYKQATVGQCNIDKPSWYNMEAKSKYNA 150
           +M   F +   ++  L + ++    LK   Y  YKQ+T+G CNI +PS +    + KY A
Sbjct: 1   HMAQVFEECVSFINGLPRTINLPNELKLDLYKYYKQSTIGNCNIKEPSAHKYIDRKKYEA 60
Query: 151 WNSLGQMAKSEAMSKYIALLKEVDAGWED 179
           W S+  + + +A  +Y+ ++ E+   W+D
Sbjct: 61  WKSVENLNREDAQKRYVDIVSEIFPYWQD 89

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 56.2 bits (134), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 25/62 (40%), Positives = 41/62 (66%)
Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          IFVG L    +  ++K +F ++G++ +A +MFDK T   +GFGFVTF++++ V+KV    
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 71 SH 72
           H
Sbjct: 62 FH 63

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 55.8 bits (133), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 22/70 (31%), Positives = 40/70 (57%)
Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
          Q  K+F+G L +  +   L+ ++ ++G++ +  VM D  +  S+GFGFVTF +   VD  
Sbjct: 26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 85
Query: 67 FSTDSHVLEG 76
           +   H ++G
Sbjct: 86 MAARPHSIDG 95

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 55.5 bits (132), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 29/91 (31%), Positives = 50/91 (54%), Gaps = 7/91 (7%)
Query: 5   IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK-EAV 63
           +  +  + V NL +  S + L++ F +YG++ +  +  D+ T  S+GF FV F +K +A 
Sbjct: 67  VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126
Query: 64  DKVFSTDSHVLEGSRLSIQ------PSDSHN 88
           D + + D  VL+G  L +Q      P DSH+
Sbjct: 127 DAMDAMDGAVLDGRELRVQMARYGRPPDSHH 157

>pdb|2FDQ|A Chain A, Crystal Structure Of Acbp From Armadillo Harderian Gland Length = 86

Iteration: 1
 Score = 55.5 bits (132), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 46/76 (60%)
Query: 98  FNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQM 157
           F++A + + +L  K     +L  Y+ YKQATVG  N ++P   + + K+K++AWN L   
Sbjct: 5   FDKAAEEVKNLKTKPADDEMLFIYSHYKQATVGDINTERPGMLDFKGKAKWDAWNQLKGT 64
Query: 158 AKSEAMSKYIALLKEV 173
           +K +AM  YI  ++E+
Sbjct: 65  SKEDAMKSYIDKVEEL 80

>pdb|1HB6|A Chain A, Structure Of Bovine Acyl-Coa Binding Protein In Orthorhombic Crystal Form Length = 86

Iteration: 1
 Score = 55.1 bits (131), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 45/76 (59%)
Query: 98  FNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQM 157
           F++A + +  L  K     +L  Y+ YKQATVG  N ++P   + + K+K++AWN L   
Sbjct: 5   FDKAAEEVKHLKTKPADEEMLFIYSHYKQATVGDINTERPGMLDFKGKAKWDAWNELKGT 64
Query: 158 AKSEAMSKYIALLKEV 173
           +K +AM  YI  ++E+
Sbjct: 65  SKEDAMKAYIDKVEEL 80

>pdb|2LBB|A Chain A, Solution Structure Of Acyl Coa Binding Protein From Babesia Bovis T2bo Length = 96

Iteration: 1
 Score = 55.1 bits (131), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 31/85 (36%), Positives = 44/85 (51%), Gaps = 1/85 (1%)
Query: 96  DRFNQACDYLPSLVKKLDSST-LLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSL 154
           D F+ A  Y+ +    + S+   L FY  YKQATVG CN  KP    ++ K K+ AWN+L
Sbjct: 12  DDFDAAVKYVSNTTTMMASNDDKLCFYKYYKQATVGDCNKPKPGMLQLQEKYKWEAWNAL 71
Query: 155 GQMAKSEAMSKYIALLKEVDAGWED 179
             M+   A   Y+ LL  +   W +
Sbjct: 72  RGMSTESAKEAYVKLLDTLAPSWRN 96

>pdb|1ST7|A Chain A, Solution Structure Of Acyl Coenzyme A Binding Protein From Yeast Length = 86

Iteration: 1
 Score = 55.1 bits (131), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 50/78 (64%), Gaps = 3/78 (3%)
Query: 100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAK 159
           +A + LP+   K  +  LL+ YALYKQATVG  + +KP  +NM+ + K+ AW +L   ++
Sbjct: 10  KAVNELPT---KPSTDELLELYALYKQATVGDNDKEKPGIFNMKDRYKWEAWENLKGKSQ 66
Query: 160 SEAMSKYIALLKEVDAGW 177
            +A  +YIAL+ ++ A +
Sbjct: 67  EDAEKEYIALVDQLIAKY 84

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 55.1 bits (131), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 43/68 (63%), Gaps = 1/68 (1%)
Query: 11  IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK-EAVDKVFST 69
           +++  LP T++  +++  FS +G+I+N+ V+ D+ TGLS+G  F+ F  + EA + + S 
Sbjct: 91  LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 70  DSHVLEGS 77
           + H   GS
Sbjct: 151 NGHKPPGS 158

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 55.1 bits (131), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 43/68 (63%), Gaps = 1/68 (1%)
Query: 11  IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK-EAVDKVFST 69
           +++  LP T++  +++  FS +G+I+N+ V+ D+ TGLS+G  F+ F  + EA + + S 
Sbjct: 91  LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 70  DSHVLEGS 77
           + H   GS
Sbjct: 151 NGHKPPGS 158

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 54.7 bits (130), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 27/76 (35%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 1  MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
          +  ++++ + + V  LPW  +  +LK++FS +G+++   V  D  TG SKGFGFV F   
Sbjct: 8  VKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEY 67
Query: 61 EAVDKVFSTDSHVLEG 76
          E   KV S   H+++G
Sbjct: 68 ETQVKVMS-QRHMIDG 82

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 25/76 (32%), Positives = 44/76 (57%), Gaps = 2/76 (2%)
Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          N +FVG +   +   E++ FF+ YG +    ++ D+ TG+SKG+GFV+F N   V K+  
Sbjct: 11 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 69
Query: 69 TDSHVLEGSRLSIQPS 84
          +  +   G +L + P+
Sbjct: 70 SQIN-FHGKKLKLGPA 84

>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Mvh Rna, Uguuc Length = 87

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 25/76 (32%), Positives = 44/76 (57%), Gaps = 2/76 (2%)
Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          N +FVG +   +   E++ FF+ YG +    ++ D+ TG+SKG+GFV+F N   V K+  
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68
Query: 69 TDSHVLEGSRLSIQPS 84
          +  +   G +L + P+
Sbjct: 69 SQIN-FHGKKLKLGPA 83

>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like In Complex With Rna, Uuguucuu Length = 102

Iteration: 1
 Score = 54.3 bits (129), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 25/76 (32%), Positives = 44/76 (57%), Gaps = 2/76 (2%)
Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          N +FVG +   +   E++ FF+ YG +    ++ D+ TG+SKG+GFV+F N   V K+  
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68
Query: 69 TDSHVLEGSRLSIQPS 84
          +  +   G +L + P+
Sbjct: 69 SQIN-FHGKKLKLGPA 83

>pdb|2FJ9|A Chain A, High Resolution Crystal Structure Of The Unliganded Human Acbp Length = 86

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 42/76 (55%)
Query: 98  FNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQM 157
           F +A + +  L  K     +L  Y  YKQATVG  N ++P   +   K+K++AWN L   
Sbjct: 5   FEKAAEEVRHLKTKPSDEEMLFIYGHYKQATVGDINTERPGMLDFTGKAKWDAWNELKGT 64
Query: 158 AKSEAMSKYIALLKEV 173
           +K +AM  YI  ++E+
Sbjct: 65  SKEDAMKAYINKVEEL 80

>pdb|2XZT|G Chain G, Caspase-3 In Complex With Darpin-3.4_i78s Length = 136

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/67 (40%), Positives = 43/67 (64%), Gaps = 1/67 (1%)
Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           ++N +D+ G+  LH A  RGHL++V+ L+ K GADVN +DS G   L  A  + H +++E
Sbjct: 39  DVNAMDDAGVTPLHLAAKRGHLEIVEVLL-KHGADVNASDSWGRTPLHLAATVGHLEIVE 97
Query: 341 YLVNSGS 347
            L+  G+
Sbjct: 98  VLLEYGA 104

>pdb|2CB8|A Chain A, High Resolution Crystal Structure Of Liganded Human L-Acbp Length = 87

Iteration: 1
 Score = 54.3 bits (129), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 42/76 (55%)
Query: 98  FNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQM 157
           F +A + +  L  K     +L  Y  YKQATVG  N ++P   +   K+K++AWN L   
Sbjct: 6   FEKAAEEVRHLKTKPSDEEMLFIYGHYKQATVGDINTERPGMLDFTGKAKWDAWNELKGT 65
Query: 158 AKSEAMSKYIALLKEV 173
           +K +AM  YI  ++E+
Sbjct: 66  SKEDAMKAYINKVEEL 81

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 29/88 (32%), Positives = 49/88 (55%), Gaps = 7/88 (7%)
Query: 8   LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK-EAVDKV 66
           +  + V NL +  S + L++ F +YG++ +  +  D+ T  S+GF FV F +K +A D +
Sbjct: 47  MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 106
Query: 67  FSTDSHVLEGSRLSIQ------PSDSHN 88
            + D  VL+G  L +Q      P DSH+
Sbjct: 107 DAMDGAVLDGRELRVQMARYGRPPDSHH 134

>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 = 53.5 bits (127), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 20/52 (38%), Positives = 40/52 (76%)
Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
          ++V NLP+++++N+L + FS+YG+++  ++M DK+T  SKG  F+ F +K++
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDS 70

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 53.5 bits (127), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 19/50 (38%), Positives = 36/50 (72%)
Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
          ++V  LP T+S  E+++ FS+YG+I+ + ++ D+ TG+S+G GF+ F  +
Sbjct: 4  LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKR 53

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 24/66 (36%), Positives = 44/66 (66%), Gaps = 3/66 (4%)
Query: 8  LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK---EAVD 64
          +  I+VGNL ++ +  ++K+ FS++G++ N  +++D+ T   KGFGFV  Q +   EA+ 
Sbjct: 1  MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIA 60
Query: 65 KVFSTD 70
          K+ +TD
Sbjct: 61 KLDNTD 66

>pdb|2XEH|A Chain A, Structural Determinants For Improved Thermal Stability Of Designed Ankyrin Repeat Proteins With A Redesigned C- Capping Module. Length = 157

Iteration: 1
 Score = 53.1 bits (126), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 34/95 (35%), Positives = 54/95 (56%), Gaps = 3/95 (3%)
Query: 253 DNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKC 312
           D    ++  A+EG L++ V+ L K    ++N  D++G   LH A   GHL++V+ L+ K 
Sbjct: 34  DGYTPLHLAAREGHLEI-VEVLLK-AGADVNAKDKDGYTPLHLAAREGHLEIVEVLL-KA 90
Query: 313 GADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
           GADVN  D DG   L  A    H +++E L+ +G+
Sbjct: 91  GADVNAKDKDGYTPLHLAAREGHLEIVEVLLKAGA 125

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 30/83 (36%), Positives = 50/83 (60%), Gaps = 3/83 (3%)
Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFS 68
          K+FVG L +  +   L++ FS+YGQI    V+ D+ T  S+GFGFVTF+N  +A D + +
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 69 TDSHVLEGSRLSIQPS--DSHNR 89
           +   ++G ++ +  +   S NR
Sbjct: 74 MNGKSVDGRQIRVDQAGKSSDNR 96

>pdb|2XEE|A Chain A, Structural Determinants For Improved Thermal Stability Of Designed Ankyrin Repeat Proteins With A Redesigned C- Capping Module. Length = 157

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 33/90 (36%), Positives = 53/90 (58%), Gaps = 3/90 (3%)
Query: 258 IYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVN 317
           ++  A+EG L++ V+ L K    ++N  D++G   LH A   GHL++V+ L+ K GADVN
Sbjct: 39  LHLAAREGHLEI-VEVLLK-AGADVNAKDKDGYTPLHLAAREGHLEIVEVLL-KAGADVN 95
Query: 318 VTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
             D DG   L  A    H +++E L+ +G+
Sbjct: 96  AKDKDGYTPLHLAAREGHLEIVEVLLKAGA 125

>pdb|3ZUV|B Chain B, Crystal Structure Of A Designed Selected Ankyrin Repeat Protein In Complex With The Phosphorylated Map Kinase Erk2 Length = 136

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 33/92 (35%), Positives = 52/92 (56%), Gaps = 3/92 (3%)
Query: 256 KNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGAD 315
           K + E A+ G+ D +  ++      ++N LDE+GL  LH A   GHL++V+ L+ K GAD
Sbjct: 16  KKLLEAARAGQDDEV--RILMANGADVNALDEDGLTPLHLAAQLGHLEIVEVLL-KYGAD 72
Query: 316 VNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
           VN  D+ G   L  A    H +++E L+  G+
Sbjct: 73  VNAEDNFGITPLHLAAIRGHLEIVEVLLKHGA 104

>pdb|2QYJ|A Chain A, Crystal Structure Of A Designed Full Consensus Ankyrin Length = 166

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 34/95 (35%), Positives = 54/95 (56%), Gaps = 3/95 (3%)
Query: 253 DNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKC 312
           D    ++  A+EG L+ +V+ L K    ++N  D++G   LH A   GHL++V+ L+ K 
Sbjct: 46  DGYTPLHLAAREGHLE-IVEVLLK-AGADVNAKDKDGYTPLHLAAREGHLEIVEVLL-KA 102
Query: 313 GADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
           GADVN  D DG   L  A    H +++E L+ +G+
Sbjct: 103 GADVNAKDKDGYTPLHLAAREGHLEIVEVLLKAGA 137

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 29/76 (38%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS- 68
          ++FV NL +T S  +L+K FS YG +       D  T   KGF FVTF   E   K ++ 
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 69 TDSHVLEGSRLSIQPS 84
           D  V +G  L + PS
Sbjct: 70 VDGQVFQGRMLHVLPS 85

>pdb|4DUI|A Chain A, Darpin D1 Binding To Tubulin Beta Chain (not In Complex) Length = 169

Iteration: 1
 Score = 52.8 bits (125), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 33/95 (34%), Positives = 51/95 (53%), Gaps = 3/95 (3%)
Query: 253 DNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKC 312
           D  K + E A+ G+ D +  ++      ++N  D +GL  LH A   GHL++V+ L+ K 
Sbjct: 13  DLGKKLLEAARAGQDDEV--RILMANGADVNATDASGLTPLHLAATYGHLEIVEVLL-KH 69
Query: 313 GADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
           GADVN  D  G   L  A  I H +++E L+  G+
Sbjct: 70  GADVNAIDIXGSTPLHLAALIGHLEIVEVLLKHGA 104

>pdb|3NOG|D Chain D, Designed Ankyrin Repeat Protein (Darpin) Binders To Acrb: Plasticity Of The Interface Length = 169

Iteration: 1
 Score = 52.4 bits (124), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 29/67 (43%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           ++N  D  G+  LH A DRGHL+VV+ L+ K GADVN  D +G   L  A  I H +++E
Sbjct: 72  DVNADDSLGVTPLHLAADRGHLEVVEVLL-KNGADVNANDHNGFTPLHLAANIGHLEIVE 130
Query: 341 YLVNSGS 347
            L+  G+
Sbjct: 131 VLLKHGA 137

>pdb|4GPM|A Chain A, Crystal Structure Of Engineered Protein. Northeast Structural Genomics Consortium Target Or264. Length = 169

Iteration: 1
 Score = 52.4 bits (124), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 35/92 (38%), Positives = 52/92 (56%), Gaps = 3/92 (3%)
Query: 256 KNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGAD 315
           K + E A+ G  D  VK L +    ++N  D +G   LH A + GH +VV+ LI K GAD
Sbjct: 6   KRLIEAAENGNKDR-VKDLIE-NGADVNASDSDGRTPLHHAAENGHKEVVKLLISK-GAD 62
Query: 316 VNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
           VN  DSDG   L +A    H ++++ L++ G+
Sbjct: 63  VNAKDSDGRTPLHHAAENGHKEVVKLLISKGA 94

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 52.4 bits (124), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 4/74 (5%)
Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          +++VG+L + ++ + L+  F  +G+I +  +M D  TG SKG+GF+TF + E   K    
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 70 DSHVLEGSRLSIQP 83
              L G  L+ +P
Sbjct: 88 ----LNGFELAGRP 97

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 52.0 bits (123), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 53/89 (59%), Gaps = 4/89 (4%)
Query: 4   SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAV 63
           SI+  N ++V NLP T++ ++L   F +YG I+  +++ DK TG  +G  FV +  +E  
Sbjct: 97  SIKDTN-LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 155
Query: 64  DKVFSTDSHVLE--GSR-LSIQPSDSHNR 89
            +  S  ++V+   GS+ LS++ ++ H +
Sbjct: 156 QEAISALNNVIPEGGSQPLSVRLAEEHGK 184

>pdb|4DRX|E Chain E, Gtp-Tubulin In Complex With A Darpin Length = 169

Iteration: 1
 Score = 52.0 bits (123), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 33/95 (34%), Positives = 51/95 (53%), Gaps = 3/95 (3%)
Query: 253 DNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKC 312
           D  K + E A+ G+ D +  ++      ++N  D +GL  LH A   GHL++V+ L+ K 
Sbjct: 13  DLGKKLLEAARAGQDDEV--RILMANGADVNATDASGLTPLHLAATYGHLEIVEVLL-KH 69
Query: 313 GADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
           GADVN  D  G   L  A  I H +++E L+  G+
Sbjct: 70  GADVNAIDIMGSTPLHLAALIGHLEIVEVLLKHGA 104

>pdb|3EPY|A Chain A, Crystal Structure Of Human Acyl-Coa Binding Domain 7 Complexed With Palmitoyl-Coa Length = 89

Iteration: 1
 Score = 51.6 bits (122), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 43/76 (56%)
Query: 98  FNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQM 157
           F++A + +  L  + D   L + Y LYKQA VG  NI  P   +++ K+K+ AWN    +
Sbjct: 8   FDRAAEDVRKLKARPDDGELKELYGLYKQAIVGDINIACPGMLDLKGKAKWEAWNLKKGL 67
Query: 158 AKSEAMSKYIALLKEV 173
           +  +A S YI+  KE+
Sbjct: 68  STEDATSAYISKAKEL 83

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 51.6 bits (122), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 28/89 (31%), Positives = 52/89 (58%), Gaps = 4/89 (4%)
Query: 4  SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAV 63
          SI+  N ++V NLP T++ ++L   F +YG I+  +++ DK TG  +G  FV +  +E  
Sbjct: 10 SIKDTN-LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 68
Query: 64 DKVFSTDSHVL-EGSR--LSIQPSDSHNR 89
           +  S  ++V+ EG    LS++ ++ H +
Sbjct: 69 QEAISALNNVIPEGGSQPLSVRLAEEHGK 97

>pdb|3FP5|A Chain A, Crystal Structure Of Acbp From Moniliophthora Perniciosa Length = 106

Iteration: 1
 Score = 51.2 bits (121), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 44/81 (54%), Gaps = 4/81 (4%)
Query: 97  RFNQACDYLPSLVK----KLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWN 152
           +F++A + + SL K    K      L FY  +KQATVG  NI +P   +   K+K++AW 
Sbjct: 7   KFDKAVEIVQSLPKDGPIKPTQDEQLYFYKYFKQATVGDVNISRPGLMDFTGKAKWDAWK 66
Query: 153 SLGQMAKSEAMSKYIALLKEV 173
           S+   +K  A  KY+  L E+
Sbjct: 67  SVEGTSKEVAYQKYVEKLLEI 87

>pdb|3B7B|A Chain A, Euhmt1 (Glp) Ankyrin Repeat Domain (Structure 1) Length = 237

Iteration: 1
 Score = 51.2 bits (121), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 39/131 (29%), Positives = 62/131 (47%), Gaps = 7/131 (5%)
Query: 222 ESQESGSKENEGQTKGWVNVSSMI-----NDESQLDDNEKNIYEWAKEGKLDMLVKQLTK 276
           E Q   S  +     G V++  M+     N ++  +D    + E A+   L+  VK L K
Sbjct: 7   EHQNKRSPLHAAAEAGHVDICHMLVQAGANIDTCSEDQRTPLMEAAENNHLEA-VKYLIK 65
Query: 277 LKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHT 336
                ++  D  G  CLH A  +GH +VVQ+L+     DVN  D  G   + +A   +H 
Sbjct: 66  AGAL-VDPKDAEGSTCLHLAAKKGHYEVVQYLLSNGQMDVNCQDDGGWTPMIWATEYKHV 124
Query: 337 DLIEYLVNSGS 347
           DL++ L++ GS
Sbjct: 125 DLVKLLLSKGS 135

>pdb|4HB5|A Chain A, Crystal Structure Of Engineered Protein. Northeast Structural Genomics Consortium Target Or267. Length = 169

Iteration: 1
 Score = 51.2 bits (121), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 32/92 (34%), Positives = 50/92 (54%), Gaps = 3/92 (3%)
Query: 256 KNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGAD 315
           K + E A+ G  D +   L    D N +  D +G   LH+A + GH ++V+ L+ K GAD
Sbjct: 6   KRLIEAAENGNKDRVKDLLENGADPNAS--DSDGRTPLHYAAENGHKEIVKLLLSK-GAD 62
Query: 316 VNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
            N  DSDG   L YA    H ++++ L++ G+
Sbjct: 63  PNAKDSDGRTPLHYAAENGHKEIVKLLLSKGA 94

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 50.8 bits (120), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 24/73 (32%), Positives = 42/73 (57%), Gaps = 4/73 (5%)
Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          ++VG+L + ++ + L+  F  +G+I N  +M D +TG SKG+GF+TF + E   +     
Sbjct: 8  LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ- 66
Query: 71 SHVLEGSRLSIQP 83
             L G  L+ +P
Sbjct: 67 ---LNGFELAGRP 76

>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 = 50.4 bits (119), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 23/76 (30%), Positives = 45/76 (59%), Gaps = 3/76 (3%)
Query: 7   QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
           Q  ++ V N+P+     +L++ F ++G+I++  ++F++    SKGFGFVTF+N    D+ 
Sbjct: 28  QPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRA 85
Query: 67  FST-DSHVLEGSRLSI 81
                  V+EG ++ +
Sbjct: 86  REKLHGTVVEGRKIEV 101

>pdb|1N0R|A Chain A, 4ank: A Designed Ankyrin Repeat Protein With Four Identical Consensus Repeats Length = 126

Iteration: 1
 Score = 50.4 bits (119), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/90 (35%), Positives = 52/90 (57%), Gaps = 3/90 (3%)
Query: 258 IYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVN 317
           ++  A+ G L++ VK L +    ++N  D+NG   LH A   GHL+VV+ L+E  GADVN
Sbjct: 6   LHLAARNGHLEV-VKLLLE-AGADVNAKDKNGRTPLHLAARNGHLEVVKLLLE-AGADVN 62
Query: 318 VTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
             D +G   L  A    H ++++ L+ +G+
Sbjct: 63  AKDKNGRTPLHLAARNGHLEVVKLLLEAGA 92

>pdb|3NOC|D Chain D, Designed Ankyrin Repeat Protein (Darpin) Binders To Acrb: Plasticity Of The Interface Length = 169

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/67 (40%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           ++N  D  G+  LH A  RGHL++V+ L+ K GADVN +DS G   L  A    H +++E
Sbjct: 72  DVNAKDSLGVTPLHLAARRGHLEIVEVLL-KNGADVNASDSHGFTPLHLAAKRGHLEIVE 130
Query: 341 YLVNSGS 347
            L+ +G+
Sbjct: 131 VLLKNGA 137

>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Bruno-Like 6 Rna-Binding Protein Length = 108

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/84 (34%), Positives = 45/84 (53%), Gaps = 4/84 (4%)
Query: 10  KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           K+FVG +P  +   +LK  F E+G+I   +V+ D+ TGL KG  F+T+  +++  K  S 
Sbjct: 17  KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 70  --DSHVLEGSRLSIQ--PSDSHNR 89
             +   L G    IQ  P+ S  R
Sbjct: 77  LHEQKTLPGMNRPIQVKPAASEGR 100

>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 = 50.1 bits (118), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 4/80 (5%)
Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+F+G +P  +   +LK  F E+G+I   +V+ D+ TG+ KG  F+T+  +E+  K  S 
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 70 --DSHVLEGSRLSIQ--PSD 85
            +   L G    IQ  P+D
Sbjct: 75 LHEQKTLPGMNRPIQVKPAD 94

>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens At 1.95 A Resolution Length = 89

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 21/77 (27%), Positives = 42/77 (54%)
Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          I+VGN+ +  +  EL+  F   G +   +++ DK +G  KGF ++ F +KE+V    + D
Sbjct: 9  IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 68
Query: 71 SHVLEGSRLSIQPSDSH 87
            +  G ++ + P  ++
Sbjct: 69 ESLFRGRQIKVIPKRTN 85

>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm Length = 96

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 21/77 (27%), Positives = 42/77 (54%)
Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          I+VGN+ +  +  EL+  F   G +   +++ DK +G  KGF ++ F +KE+V    + D
Sbjct: 8  IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALD 67
Query: 71 SHVLEGSRLSIQPSDSH 87
            +  G ++ + P  ++
Sbjct: 68 ESLFRGRQIKVIPKRTN 84

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 22/73 (30%), Positives = 44/73 (60%), Gaps = 3/73 (4%)
Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          ++ V N+P+     +L++ F ++G+I++  ++F++    SKGFGFVTF+N    D+    
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREK 74
Query: 70 -DSHVLEGSRLSI 81
              V+EG ++ +
Sbjct: 75 LHGTVVEGRKIEV 87

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 42/72 (58%), Gaps = 1/72 (1%)
Query: 4   SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAV 63
           SI+  N ++V NLP T++ ++L   F +YG I+  +++ DK TG  +G  FV +  +E  
Sbjct: 86  SIKDTN-LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 144
Query: 64  DKVFSTDSHVLE 75
            +  S  ++V+ 
Sbjct: 145 QEAISALNNVIP 156

>pdb|2V4H|C Chain C, Nemo Cc2-Lz Domain - 1d5 Darpin Complex Length = 136

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 33/92 (35%), Positives = 48/92 (52%), Gaps = 3/92 (3%)
Query: 256 KNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGAD 315
           K + E A+ G+ D +   +    D N N  D  G   LH A D  HL++V+ L+ K GAD
Sbjct: 16  KKLLEAARAGQDDEVRILMANGADVNAN--DRKGNTPLHLAADYDHLEIVEVLL-KHGAD 72
Query: 316 VNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
           VN  D+DG   L  A    H +++E L+  G+
Sbjct: 73  VNAHDNDGSTPLHLAALFGHLEIVEVLLKHGA 104

>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of Xenopus Laevis Epabp2 Length = 124

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 20/73 (27%), Positives = 39/73 (53%)
Query: 11  IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
           ++VGN+ +  +  +L+  FS  G I   +++ DK +G  KG+ ++ F  + +VD   + D
Sbjct: 39  VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMD 98
Query: 71  SHVLEGSRLSIQP 83
             V  G  + + P
Sbjct: 99  ETVFRGRTIKVLP 111

>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 107

Iteration: 1
 Score = 49.3 bits (116), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 29/83 (34%), Positives = 46/83 (55%), Gaps = 7/83 (8%)
Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKN---TGLSKGFGFVTFQNKEAVDK 65
          +KI V N+P+  +  E+++ FS +G++   +V   K    TG  +GFGFV F  K+   K
Sbjct: 16 SKILVRNIPFQANQREIRELFSTFGEL--KTVRLPKKMTGTGAHRGFGFVDFITKQDAKK 73
Query: 66 VFSTDSHV--LEGSRLSIQPSDS 86
           F+   H   L G RL ++ +DS
Sbjct: 74 AFNALCHSTHLYGRRLVLEWADS 96

>pdb|1N0Q|A Chain A, 3ank: A Designed Ankyrin Repeat Protein With Three Identical Consensus Repeats Length = 93

Iteration: 1
 Score = 48.9 bits (115), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 31/86 (36%), Positives = 48/86 (55%), Gaps = 3/86 (3%)
Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
           A+ G L+++   L    D  +N  D+NG   LH A   GHL+VV+ L+E  GADVN  D 
Sbjct: 10  ARNGHLEVVKLLLEAGAD--VNAKDKNGRTPLHLAARNGHLEVVKLLLE-AGADVNAKDK 66
Query: 322 DGDYGLDYAKAIEHTDLIEYLVNSGS 347
           +G   L  A    H ++++ L+ +G+
Sbjct: 67  NGRTPLHLAARNGHLEVVKLLLEAGA 92

>pdb|3Q9U|C Chain C, In Silico And In Vitro Co-Evolution Of A High Affinity Complementary Protein-Protein Interface Length = 158

Iteration: 1
 Score = 48.9 bits (115), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 33/95 (34%), Positives = 51/95 (53%), Gaps = 3/95 (3%)
Query: 253 DNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKC 312
           D  K + E A  G+ D +  ++      ++N  D+NGL  LH A   G L++V+ L+ K 
Sbjct: 5   DLGKKLLEAAAAGQDDEV--RILMANGADVNATDDNGLTPLHLAAANGQLEIVEVLL-KN 61
Query: 313 GADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
           GADVN +DS G   L  A    H +++E L+  G+
Sbjct: 62  GADVNASDSAGITPLHLAAYDGHLEIVEVLLKHGA 96

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 48.5 bits (114), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 22/50 (44%), Positives = 35/50 (70%)
Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
          +FVG+L   ++  ++K  F+ +G+I +A V+ D  TG SKG+GFV+F NK
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNK 67

>pdb|1MJ0|A Chain A, Sank E3_5: An Artificial Ankyrin Repeat Protein Length = 166

Iteration: 1
 Score = 48.1 bits (113), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 32/96 (33%), Positives = 50/96 (52%), Gaps = 3/96 (3%)
Query: 252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEK 311
           +D    ++  A  G L+++   L    D N + L   G+  LH A   GHL++V+ L+ K
Sbjct: 45  NDGYTPLHLAASNGHLEIVEVLLKNGADVNASDL--TGITPLHLAAATGHLEIVEVLL-K 101
Query: 312 CGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
            GADVN  D+DG   L  A    H +++E L+  G+
Sbjct: 102 HGADVNAYDNDGHTPLHLAAKYGHLEIVEVLLKHGA 137

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 34/94 (36%), Positives = 50/94 (53%), Gaps = 8/94 (8%)
Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDK--NTGLSKGFGFVTFQNKEAVDKVF 67
          K FVG +P T S  +L++ F +YG +   +V+ D+  N   SKG  FVTF  ++A  +  
Sbjct: 5  KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 68 ST--DSHVLEGSRLSIQ--PSDSHNRMAENMEDR 97
          +   +  VL G    IQ  P+DS    A  +EDR
Sbjct: 65 NALHNXKVLPGXHHPIQXKPADSEKNNA--VEDR 96

>pdb|4ATZ|D Chain D, Ad5 Knob In Complex With A Designed Ankyrin Repeat Protein Length = 154

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 30/95 (31%), Positives = 51/95 (53%), Gaps = 3/95 (3%)
Query: 253 DNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKC 312
           D  K + E A+ G+ D +  ++      + N  D  G   LH A   GHL++V+ L+ + 
Sbjct: 1   DLGKKLLEAARAGQDDEV--RILMANGADANAYDHYGRTPLHMAAAVGHLEIVEVLL-RN 57
Query: 313 GADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
           GADVN  D++G   L  A ++ H +++E L+  G+
Sbjct: 58  GADVNAVDTNGTTPLHLAASLGHLEIVEVLLKYGA 92

>pdb|3F6Q|A Chain A, Crystal Structure Of Integrin-Linked Kinase Ankyrin Repeat Domain In Complex With Pinch1 Lim1 Domain Length = 179

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/63 (38%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           ++NQ D++G + LHWAC  G   VV+ LI + GA +NV +   D  L  A +  H D+++
Sbjct: 31  DLNQGDDHGFSPLHWACREGRSAVVEMLIMR-GARINVMNRGDDTPLHLAASHGHRDIVQ 89
Query: 341 YLV 343
            L+
Sbjct: 90  KLL 92

>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 = 47.0 bits (110), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 34/94 (36%), Positives = 51/94 (54%), Gaps = 8/94 (8%)
Query: 10  KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDK--NTGLSKGFGFVTFQNKEAVDKVF 67
           K+FVG +P T S  +L++ F +YG +   +V+ D+  N   SKG  FVTF  ++A  +  
Sbjct: 17  KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 68  ST--DSHVLEGSRLSIQ--PSDSHNRMAENMEDR 97
           +   +  VL G    IQ  P+DS    A  +EDR
Sbjct: 77  NALHNMKVLPGMHHPIQMKPADSEKNNA--VEDR 108

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 34/94 (36%), Positives = 51/94 (54%), Gaps = 8/94 (8%)
Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDK--NTGLSKGFGFVTFQNKEAVDKVF 67
          K+FVG +P T S  +L++ F +YG +   +V+ D+  N   SKG  FVTF  ++A  +  
Sbjct: 5  KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 68 ST--DSHVLEGSRLSIQ--PSDSHNRMAENMEDR 97
          +   +  VL G    IQ  P+DS    A  +EDR
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEKNNA--VEDR 96

>pdb|2KBX|A Chain A, Solution Structure Of Ilk-Pinch Complex Length = 171

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/63 (38%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           ++NQ D++G + LHWAC  G   VV+ LI + GA +NV +   D  L  A +  H D+++
Sbjct: 26  DLNQGDDHGFSPLHWACREGRSAVVEMLIMR-GARINVMNRGDDTPLHLAASHGHRDIVQ 84
Query: 341 YLV 343
            L+
Sbjct: 85  KLL 87

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 46.2 bits (108), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 22/50 (44%), Positives = 35/50 (70%)
Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
          +FVG+L   ++  ++K  F+ +G+I +A V+ D  TG SKG+GFV+F NK
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNK 67

>pdb|4GMR|A Chain A, Crystal Structure Of Engineered Protein. Northeast Structural Genomics Consortium Target Or266. Length = 169

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 32/92 (34%), Positives = 50/92 (54%), Gaps = 3/92 (3%)
Query: 256 KNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGAD 315
           K + E A+ G  D  VK L +    ++N  D +G   LH A + GH +VV+ L+ + GAD
Sbjct: 6   KRLIEAAENGNKDR-VKDLLE-NGADVNASDSDGKTPLHLAAENGHKEVVKLLLSQ-GAD 62
Query: 316 VNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
            N  DSDG   L  A    H ++++ L++ G+
Sbjct: 63  PNAKDSDGKTPLHLAAENGHKEVVKLLLSQGA 94

>pdb|3EHQ|A Chain A, Crystal Structure Of Human Osteoclast Stimulating Factor Length = 222

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 33/118 (27%), Positives = 60/118 (50%), Gaps = 6/118 (5%)
Query: 232 EGQTKGWVNV--SSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENG 289
           +G +KG   +  S+ + ++++  DN   ++E AK G L  L + L       +N LD+ G
Sbjct: 51  KGTSKGRTGLIPSNYVAEQAESIDNP--LHEAAKRGNLSWLRECLDN--RVGVNGLDKAG 106
Query: 290 LNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
              L+WAC  GH  +V+ L  +   ++N  +  GD  L  A    + D+++ L+  G+
Sbjct: 107 STALYWACHGGHKDIVEXLFTQPNIELNQQNKLGDTALHAAAWKGYADIVQLLLAKGA 164

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 19/61 (31%), Positives = 34/61 (55%)
Query: 8   LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
           L  + V  +P TV   +L++ F  YG I +  ++ D+ T  S+G+GFV FQ+  +  +  
Sbjct: 42  LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
Query: 68  S 68
           +
Sbjct: 102 A 102

>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of Hnrnp D (Auf1) With Telomere Dna Length = 79

Iteration: 1
 Score = 45.8 bits (107), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 21/75 (28%), Positives = 40/75 (53%)
Query: 8  LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
          + KIFVG L       +++++F  +G++ +  +  D  T   +GF F+TF+ +E V K+ 
Sbjct: 1  VKKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60
Query: 68 STDSHVLEGSRLSIQ 82
              H +  S+  I+
Sbjct: 61 EKKYHNVGLSKCEIK 75

>pdb|3ZU7|B Chain B, Crystal Structure Of A Designed Selected Ankyrin Repeat Protein In Complex With The Map Kinase Erk2 Length = 169

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 26/67 (38%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           ++N  D +G   LH A D GHL++V+ L+ K GADVN  D+ G   L  A    H +++E
Sbjct: 72  DVNARDTDGWTPLHLAADNGHLEIVEVLL-KYGADVNAQDAYGLTPLHLAADRGHLEIVE 130
Query: 341 YLVNSGS 347
            L+  G+
Sbjct: 131 VLLKHGA 137

>pdb|2J8S|D Chain D, Drug Export Pathway Of Multidrug Exporter Acrb Revealed By Darpin Inhibitors Length = 169

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 26/62 (41%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           ++N  D+NG+  LH A +RGHL++V+ L+ K GADVN  D  G    D +    + DL E
Sbjct: 105 DVNAKDDNGITPLHLAANRGHLEIVEVLL-KYGADVNAQDKFGKTAFDISINNGNEDLAE 163
Query: 341 YL 342
            L
Sbjct: 164 IL 165

>pdb|2KHC|A Chain A, Bruno Rrm3+ Length = 118

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 20/52 (38%), Positives = 32/52 (61%)
Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
          +F+ +LP   +  +L   F  +G +++A V  DK T LSK FGFV+F N ++
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDS 94

>pdb|2P2C|P Chain P, Inhibition Of Caspase-2 By A Designed Ankyrin Repeat Protein (Darpin) Length = 169

Iteration: 1
 Score = 45.1 bits (105), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 33/90 (36%), Positives = 50/90 (55%), Gaps = 3/90 (3%)
Query: 258 IYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVN 317
           ++  AK G L++ V+ L K    ++N  D  G   LH A D GHL++V+ L+ K GADVN
Sbjct: 51  LHLAAKTGHLEI-VEVLLKYG-ADVNAWDNYGATPLHLAADNGHLEIVEVLL-KHGADVN 107
Query: 318 VTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
             D +G   L  A    H +++E L+  G+
Sbjct: 108 AKDYEGFTPLHLAAYDGHLEIVEVLLKYGA 137

>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non- Polyadenylated Rnas By The Nab3-Rrm Length = 97

Iteration: 1
 Score = 44.7 bits (104), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 28/83 (33%), Positives = 45/83 (54%), Gaps = 10/83 (12%)
Query: 9  NKIFVGNLPW-TVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
          +++F+GNLP   VS  +L + FS YG IM  ++   KN      FGF+ F N ++V    
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KN-----AFGFIQFDNPQSVRDAI 74
Query: 68 STDSHVLE-GSRLSIQPSDSHNR 89
            +S  +  G +L ++ S S+ R
Sbjct: 75 ECESQEMNFGKKLILEVSSSNAR 97

>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non- Polyadenylated Rnas By The Nab3-Rrm Length = 97

Iteration: 1
 Score = 44.3 bits (103), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 28/83 (33%), Positives = 45/83 (54%), Gaps = 10/83 (12%)
Query: 9  NKIFVGNLPW-TVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
          +++F+GNLP   VS  +L + FS YG IM  ++   KN      FGF+ F N ++V    
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KN-----AFGFIQFDNPQSVRDAI 74
Query: 68 STDSHVLE-GSRLSIQPSDSHNR 89
            +S  +  G +L ++ S S+ R
Sbjct: 75 EXESQEMNFGKKLILEVSSSNAR 97

>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna Length = 88

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 30/83 (36%), Positives = 46/83 (55%), Gaps = 6/83 (7%)
Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDK--NTGLSKGFGFVTFQNKEAVDKVF 67
          K+FVG +P T S  +L++ F +YG +   +V+ D+  N   SKG  FVTF  ++A  +  
Sbjct: 5  KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 68 ST--DSHVLEGSRLSIQ--PSDS 86
          +   +  VL G    IQ  P+DS
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADS 87

>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 43/78 (55%), Gaps = 9/78 (11%)
Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA--VD 64
          Q +++FVGNLP  ++  E++K F +YG+     V   K+    KGFGF+  + +    + 
Sbjct: 21 QRSRLFVGNLPPDITEEEMRKLFEKYGK--AGEVFIHKD----KGFGFIRLETRTLAEIA 74
Query: 65 KVFSTDSHVLEGSRLSIQ 82
          KV   D+  L G +L ++
Sbjct: 75 KV-ELDNMPLRGKQLRVR 91

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 33/52 (63%)
Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
          +++G++P+  +  ++    S  G ++N  +MFD  TG SKG+ F+ F++ E+
Sbjct: 7  VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLES 58

>pdb|1MX4|A Chain A, Structure Of P18ink4c (F82q) Length = 168

Iteration: 1
 Score = 44.3 bits (103), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/90 (30%), Positives = 45/90 (50%), Gaps = 2/90 (2%)
Query: 258 IYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVN 317
           I++ A+ G+LD L   L    D NI   D  G   LH A   GHL+VV+ L++   ++V 
Sbjct: 74  IHDAARAGQLDTLQTLLEFQADVNIE--DNEGNLPLHLAAKEGHLRVVEFLVKHTASNVG 131
Query: 318 VTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
             +  GD   D A+     +++  +  +G+
Sbjct: 132 HRNHKGDTACDLARLYGRNEVVSLMQANGA 161

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 33/52 (63%)
Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
          +++G++P+  +  ++    S  G ++N  +MFD  TG SKG+ F+ F++ E+
Sbjct: 5  VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLES 56

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 33/52 (63%)
Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
          +++G++P+  +  ++    S  G ++N  +MFD  TG SKG+ F+ F++ E+
Sbjct: 6  VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLES 57

>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1) Length = 75

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 20/72 (27%), Positives = 38/72 (52%)
Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          IFVG L       +++++F  +G++ +  +  D  T   +GF F+TF+ +E V K+    
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 71 SHVLEGSRLSIQ 82
           H +  S+  I+
Sbjct: 62 YHNVGLSKCEIK 73

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 46/82 (56%), Gaps = 1/82 (1%)
Query: 1   MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
           ++   R  N+I+V ++   +S +++K  F  +G+I +A++  D  TG  KG+GF+ ++  
Sbjct: 118 LAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKA 177
Query: 61  EAV-DKVFSTDSHVLEGSRLSI 81
           ++  D V S +   L G  L +
Sbjct: 178 QSSQDAVSSMNLFDLGGQYLRV 199

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/62 (38%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
          Q+  ++V NL   +    L+K FS +G I +A VM +   G SKGFGFV F + E   K 
Sbjct: 14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG--GRSKGFGFVCFSSPEEATKA 71
Query: 67 FS 68
           +
Sbjct: 72 VT 73

>pdb|4F6R|D Chain D, Tubulin:stathmin-Like Domain Complex Length = 169

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 33/96 (34%), Positives = 53/96 (55%), Gaps = 3/96 (3%)
Query: 252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEK 311
           D  +  ++  A +G L+ +V+ L K    ++N  D+ G   LH A   GHL++V+ L+ K
Sbjct: 45  DSGKTPLHLAAIKGHLE-IVEVLLK-HGADVNAADKMGDTPLHLAALYGHLEIVEVLL-K 101
Query: 312 CGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
            GADVN TD+ G   L  A    H +++E L+  G+
Sbjct: 102 NGADVNATDTYGFTPLHLAADAGHLEIVEVLLKYGA 137

>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex Length = 77

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/83 (33%), Positives = 45/83 (54%), Gaps = 10/83 (12%)
Query: 9  NKIFVGNLPW-TVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
          +++F+GNLP   VS  +L + FS YG IM  ++   KN      FGF+ F N ++V    
Sbjct: 3  SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KN-----AFGFIQFDNPQSVRDAI 54
Query: 68 STDSHVLE-GSRLSIQPSDSHNR 89
            +S  +  G +L ++ S S+ R
Sbjct: 55 ECESQEMNFGKKLILEVSSSNAR 77

>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm Length = 96

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/83 (33%), Positives = 45/83 (54%), Gaps = 10/83 (12%)
Query: 9  NKIFVGNLPW-TVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
          +++F+GNLP   VS  +L + FS YG IM  ++   KN      FGF+ F N ++V    
Sbjct: 11 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI---KN-----AFGFIQFDNPQSVRDAI 62
Query: 68 STDSHVLE-GSRLSIQPSDSHNR 89
            +S  +  G +L ++ S S+ R
Sbjct: 63 ECESQEMNFGKKLILEVSSSNAR 85

>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet Repeat Rna-Binding Protein 1 Length = 115

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 11  IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK-EAVDKVFST 69
           +F+ +LP      +L + F  +G +++A V  DK T LSK FGFV++ N   A   + S 
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87
Query: 70  DSHVLEGSRLSIQPSDSHN 88
           +   +   RL +Q   S N
Sbjct: 88  NGFQIGMKRLKVQLKRSKN 106

>pdb|1MX6|A Chain A, Structure Of P18ink4c (F92n) Length = 168

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 2/90 (2%)
Query: 258 IYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVN 317
           I++ A+ G LD L   L    D NI   D  G   LH A   GHL+VV+ L++   ++V 
Sbjct: 74  IHDAARAGFLDTLQTLLENQADVNIE--DNEGNLPLHLAAKEGHLRVVEFLVKHTASNVG 131
Query: 318 VTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
             +  GD   D A+     +++  +  +G+
Sbjct: 132 HRNHKGDTACDLARLYGRNEVVSLMQANGA 161

>pdb|1YCS|B Chain B, P53-53bp2 Complex Length = 239

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/84 (29%), Positives = 49/84 (58%), Gaps = 3/84 (3%)
Query: 264 EGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDG 323
           EG+ D++ + + ++ D ++   ++ G+  LH A   GH ++V+ L++  G +VN  DSDG
Sbjct: 47  EGEFDLVQRIIYEVDDPSLP--NDEGITALHNAVCAGHTEIVKFLVQF-GVNVNAADSDG 103
Query: 324 DYGLDYAKAIEHTDLIEYLVNSGS 347
              L  A +  +  + ++LV SG+
Sbjct: 104 WTPLHCAASCNNVQVCKFLVESGA 127

>pdb|4A63|B Chain B, Crystal Structure Of The P73-Aspp2 Complex At 2.6a Resolution Length = 239

Iteration: 1
 Score = 43.5 bits (101), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/84 (29%), Positives = 49/84 (58%), Gaps = 3/84 (3%)
Query: 264 EGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDG 323
           EG+ D++ + + ++ D ++   ++ G+  LH A   GH ++V+ L++  G +VN  DSDG
Sbjct: 47  EGEFDLVQRIIYEVDDPSLP--NDEGITALHNAVCAGHTEIVKFLVQF-GVNVNAADSDG 103
Query: 324 DYGLDYAKAIEHTDLIEYLVNSGS 347
              L  A +  +  + ++LV SG+
Sbjct: 104 WTPLHCAASCNNVQVCKFLVESGA 127

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/65 (32%), Positives = 40/65 (61%), Gaps = 7/65 (10%)
Query: 21 SHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN----KEAVDKVFSTDSHVLEG 76
          +  +L++ FS+YG I + S+++D+ +  S+GF FV F+N    KEA ++    +   L+G
Sbjct: 25 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME---LDG 81
Query: 77 SRLSI 81
           R+ +
Sbjct: 82 RRIRV 86

>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 98

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/85 (29%), Positives = 43/85 (50%), Gaps = 4/85 (4%)
Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTG---LSKGFGFVTFQNKEAVDKVF 67
          +F+ NL ++ +   LK  FS+ G I + ++   KN     LS GFGFV ++  E   K  
Sbjct: 8  LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 67
Query: 68 ST-DSHVLEGSRLSIQPSDSHNRMA 91
               H ++G +L ++ S+   + A
Sbjct: 68 KQLQGHTVDGHKLEVRISERATKPA 92

>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20 Length = 150

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/81 (33%), Positives = 42/81 (51%), Gaps = 6/81 (7%)
Query: 10  KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFS 68
           K++VGNL    +  EL++ F  YG +   SV   +N     GF FV F++ ++A D V  
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLR--SVWVARN---PPGFAFVEFEDPRDAADAVRD 129
Query: 69  TDSHVLEGSRLSIQPSDSHNR 89
            D   L G R+ ++ S+   R
Sbjct: 130 LDGRTLCGCRVRVELSNGEKR 150

>pdb|2E5G|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 21 Length = 94

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 8  LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
          L  +FV   P  V   +L ++F  +G +  ASV+ DK+ G+   F  V   +  A + V 
Sbjct: 8  LRSVFVSGFPRGVDSAQLSEYFLAFGPV--ASVVMDKDKGV---FAIVEMGDVGAREAVL 62
Query: 68 STDSHVLEGSRLSIQPSD 85
          S   H L G RL ++P +
Sbjct: 63 SQSQHSLGGHRLRVRPRE 80

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 45/82 (54%), Gaps = 1/82 (1%)
Query: 1   MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
           ++   R  N+I+V ++   +S +++K  F  +G+I + ++  D  TG  KG+GF+ ++  
Sbjct: 102 LAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKA 161
Query: 61  EAV-DKVFSTDSHVLEGSRLSI 81
           ++  D V S +   L G  L +
Sbjct: 162 QSSQDAVSSXNLFDLGGQYLRV 183

>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna Cauc Length = 150

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/81 (33%), Positives = 42/81 (51%), Gaps = 6/81 (7%)
Query: 10  KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFS 68
           K++VGNL    +  EL++ F  YG +   SV   +N     GF FV F++ ++A D V  
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLR--SVWVARN---PPGFAFVEFEDPRDAADAVRE 129
Query: 69  TDSHVLEGSRLSIQPSDSHNR 89
            D   L G R+ ++ S+   R
Sbjct: 130 LDGRTLCGCRVRVELSNGEKR 150

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/68 (33%), Positives = 39/68 (57%), Gaps = 2/68 (2%)
Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          IF+ NL  ++ +  L   FS +G I++  V+ D+N   SKG+GFV F+ +EA ++     
Sbjct: 8  IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKM 65
Query: 71 SHVLEGSR 78
          + +L   R
Sbjct: 66 NGMLLNDR 73

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/70 (31%), Positives = 41/70 (58%), Gaps = 7/70 (10%)
Query: 21 SHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN----KEAVDKVFSTDSHVLEG 76
          +  +L++ FS+YG I + S+++D+ +  S+GF FV F+N    KEA ++    +   L+G
Sbjct: 28 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME---LDG 84
Query: 77 SRLSIQPSDS 86
           R+ +    S
Sbjct: 85 RRIRVSGPSS 94

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 21/65 (32%), Positives = 40/65 (61%), Gaps = 7/65 (10%)
Query: 21 SHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN----KEAVDKVFSTDSHVLEG 76
          +  +L++ FS+YG I + S+++D+ +  S+GF FV F+N    KEA ++    +   L+G
Sbjct: 28 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGME---LDG 84
Query: 77 SRLSI 81
           R+ +
Sbjct: 85 RRIRV 89

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 45/82 (54%), Gaps = 1/82 (1%)
Query: 1   MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
           ++   R  N+I+V ++   +S +++K  F  +G+I + ++  D  TG  KG+GF+ ++  
Sbjct: 103 LAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKA 162
Query: 61  EAV-DKVFSTDSHVLEGSRLSI 81
           ++  D V S +   L G  L +
Sbjct: 163 QSSQDAVSSMNLFDLGGQYLRV 184

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 40/64 (62%), Gaps = 4/64 (6%)
Query: 4   SIRQ--LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
           S+R+  +  IF+ NL  ++ +  L   FS +G I++  V+ D+N   SKG+GFV F+ +E
Sbjct: 97  SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQE 154
Query: 62  AVDK 65
           A ++
Sbjct: 155 AAER 158

>pdb|3V30|A Chain A, Crystal Structure Of The Peptide Bound Complex Of The Ankyrin Repeat Domains Of Human Rfxank Length = 172

Iteration: 1
 Score = 42.7 bits (99), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 28/87 (32%), Positives = 48/87 (55%), Gaps = 2/87 (2%)
Query: 257 NIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADV 316
           +I++ A +G+LD L + L K  D  +N+ DE G   L WA   G ++ V+ L+E  GAD 
Sbjct: 5   SIHQLAAQGELDQLKEHLRK-GDNLVNKPDERGFTPLIWASAFGEIETVRFLLE-WGADP 62
Query: 317 NVTDSDGDYGLDYAKAIEHTDLIEYLV 343
           ++   + +  L  A    +TD++  L+
Sbjct: 63  HILAKERESALSLASTGGYTDIVGLLL 89

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 42/73 (57%), Gaps = 7/73 (9%)
Query: 13  VGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN----KEAVDKVFS 68
           V  L    +  +L++ FS+YG I + S+++D+ +  S+GF FV F+N    KEA ++   
Sbjct: 51  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 69  TDSHVLEGSRLSI 81
            +   L+G R+ +
Sbjct: 111 ME---LDGRRIRV 120

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 40/64 (62%), Gaps = 4/64 (6%)
Query: 4   SIRQ--LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
           S+R+  +  IF+ NL  ++ +  L   FS +G I++  V+ D+N   SKG+GFV F+ +E
Sbjct: 92  SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQE 149
Query: 62  AVDK 65
           A ++
Sbjct: 150 AAER 153

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          + V  LP  ++ +EL+  FS  G++ +A ++ DK  G S G+GFV +   +  ++  +T 
Sbjct: 7  LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT- 65
Query: 71 SHVLEGSRL 79
             L G RL
Sbjct: 66 ---LNGLRL 71

>pdb|1IHB|A Chain A, Crystal Structure Of P18-Ink4c(Ink6) Length = 162

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 2/90 (2%)
Query: 258 IYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVN 317
           I++ A+ G LD L   L    D NI   D  G   LH A   GHL+VV+ L++   ++V 
Sbjct: 74  IHDAARAGFLDTLQTLLEFQADVNIE--DNEGNLPLHLAAKEGHLRVVEFLVKHTASNVG 131
Query: 318 VTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
             +  GD   D A+     +++  +  +G+
Sbjct: 132 HRNHKGDTACDLARLYGRNEVVSLMQANGA 161

>pdb|1BU9|A Chain A, Solution Structure Of P18-Ink4c, 21 Structures Length = 168

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 2/90 (2%)
Query: 258 IYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVN 317
           I++ A+ G LD L   L    D NI   D  G   LH A   GHL+VV+ L++   ++V 
Sbjct: 74  IHDAARAGFLDTLQTLLEFQADVNIE--DNEGNLPLHLAAKEGHLRVVEFLVKHTASNVG 131
Query: 318 VTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
             +  GD   D A+     +++  +  +G+
Sbjct: 132 HRNHKGDTACDLARLYGRNEVVSLMQANGA 161

>pdb|1MX2|A Chain A, Structure Of F71n Mutant Of P18ink4c Length = 168

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 2/90 (2%)
Query: 258 IYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVN 317
           I++ A+ G LD L   L    D NI   D  G   LH A   GHL+VV+ L++   ++V 
Sbjct: 74  IHDAARAGFLDTLQTLLEFQADVNIE--DNEGNLPLHLAAKEGHLRVVEFLVKHTASNVG 131
Query: 318 VTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
             +  GD   D A+     +++  +  +G+
Sbjct: 132 HRNHKGDTACDLARLYGRNEVVSLMQANGA 161

>pdb|3UXG|A Chain A, Crystal Structure Of Rfxank Length = 172

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 28/87 (32%), Positives = 48/87 (55%), Gaps = 2/87 (2%)
Query: 257 NIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADV 316
           +I++ A +G+LD L + L K  D  +N+ DE G   L WA   G ++ V+ L+E  GAD 
Sbjct: 5   SIHQLAAQGELDQLKEHLRK-GDNLVNKPDERGFTPLIWASAFGEIETVRFLLE-WGADP 62
Query: 317 NVTDSDGDYGLDYAKAIEHTDLIEYLV 343
           ++   + +  L  A    +TD++  L+
Sbjct: 63  HILAKERESALSLASTGGYTDIVGLLL 89

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 11  IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK-EAVDKVFST 69
           +FVG+L   V    L+  F ++   ++  VM+D  TG S+G+GFV+F ++ +A + + S 
Sbjct: 90  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 70  DSHVLEGSRLSI 81
               L G  L I
Sbjct: 150 QGQDLNGRPLRI 161

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 23/71 (32%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 8  LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
          +  IF+ NL  ++ +  L   FS +G I++  V+ D+N   SKG+GFV F+ +EA ++  
Sbjct: 11 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAI 68
Query: 68 STDSHVLEGSR 78
             + +L   R
Sbjct: 69 EKMNGMLLNDR 79

>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif Of Nono Length = 99

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 9/81 (11%)
Query: 4  SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK--E 61
          +  Q +++FVGNLP  ++  E++K F +YG+     +  D      KGFGF+  + +   
Sbjct: 11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLA 64
Query: 62 AVDKVFSTDSHVLEGSRLSIQ 82
           + KV   D+  L G +L ++
Sbjct: 65 EIAKV-ELDNMPLRGKQLRVR 84

>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding Protein 30 Length = 90

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/76 (26%), Positives = 41/76 (53%), Gaps = 9/76 (11%)
Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAV-DKVFS 68
          K+F+GNLP   +  E++  F +YG+++   ++        K +GFV  ++K A  D + +
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRN 61
Query: 69 TDSHVLEGSRLSIQPS 84
             + L G  ++++ S
Sbjct: 62 LHHYKLHGVNINVEAS 77

>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2 Length = 109

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 23/74 (31%), Positives = 41/74 (55%), Gaps = 4/74 (5%)
Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFS 68
          +I+VGNLP  +   +++  F +YG I +  +   KN      F FV F++ ++A D V+ 
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVEFEDPRDAEDAVYG 80
Query: 69 TDSHVLEGSRLSIQ 82
           D +  +G RL ++
Sbjct: 81 RDGYDYDGYRLRVE 94

>pdb|4GRG|A Chain A, Crystal Structure Of Ige Complexed With E2_79, An Anti-Ige Inhibitor Length = 135

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 34/95 (35%), Positives = 51/95 (53%), Gaps = 3/95 (3%)
Query: 253 DNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKC 312
           D  K + E A+ G+ D  V+ LT     ++N  D  G   LH A   GHL++V+ L+ K 
Sbjct: 13  DLGKKLLEAARAGQDDE-VRILTA-NGADVNANDYWGHTPLHLAAMLGHLEIVEVLL-KN 69
Query: 313 GADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
           GADVN T + G   L  A   +H +++E L+  G+
Sbjct: 70  GADVNATGNTGRTPLHLAAWADHLEIVEVLLKHGA 104

>pdb|3EU9|A Chain A, The Ankyrin Repeat Domain Of Huntingtin Interacting Protein 14 Length = 240

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 1/54 (1%)
Query: 293 LHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           LHWA  +GHL +V  L+ K GAD ++ D +G   +  A    HT ++ YL+  G
Sbjct: 80  LHWATRQGHLSMVVQLM-KYGADPSLIDGEGCSCIHLAAQFGHTSIVAYLIAKG 132

>pdb|1S70|B Chain B, Complex Between Protein Ser/thr Phosphatase-1 (delta) And The Myosin Phosphatase Targeting Subunit 1 (mypt1) Length = 299

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 26/83 (31%), Positives = 47/83 (56%), Gaps = 3/83 (3%)
Query: 265 GKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGD 324
           G  + +++ L +  D N   +D  GL  LH AC   ++ +V+ L+E  GA++N  D++G 
Sbjct: 51  GDTEEVLRLLERGADINYANVD--GLTALHQACIDDNVDMVKFLVEN-GANINQPDNEGW 107
Query: 325 YGLDYAKAIEHTDLIEYLVNSGS 347
             L  A +  + D+ EYL++ G+
Sbjct: 108 IPLHAAASCGYLDIAEYLISQGA 130

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/59 (33%), Positives = 31/59 (52%)
Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          + V  LP  ++ +E K  F   G I +  ++ DK TG S G+GFV + +    DK  +T
Sbjct: 7  LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINT 65

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 1/72 (1%)
Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK-EAVDKVFST 69
          +FVG+L   V    L+  F ++   ++  VM+D  TG S+G+GFV+F ++ +A + + S 
Sbjct: 4  LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 70 DSHVLEGSRLSI 81
              L G  L I
Sbjct: 64 QGQDLNGRPLRI 75

>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of Heterogeneous Nuclear Ribonucleoprotein M Length = 114

Iteration: 1
 Score = 42.0 bits (97), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 32/97 (32%), Positives = 49/97 (50%), Gaps = 13/97 (13%)
Query: 11  IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTF-QNKEAVDKVFST 69
           +FV NL + V   +LK+ FS  G ++ A ++ DK+ G S+G G VTF Q+ EAV  +   
Sbjct: 18  VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAI--- 73
Query: 70  DSHVLEGSRLSIQPSDSHNRMAENMEDRFNQACDYLP 106
              +  G  L  +P      M   M++R     D+ P
Sbjct: 74  --SMFNGQLLFDRP------MHVKMDERALPKGDFFP 102

>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8 Length = 101

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 28/81 (34%), Positives = 43/81 (53%), Gaps = 6/81 (7%)
Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFS 68
          K++VGNL       EL++ FS YG +   +V   +N     GF FV F++ ++A D V  
Sbjct: 2  KVYVGNLGTGAGKGELERAFSYYGPLR--TVWIARN---PPGFAFVEFEDPRDAEDAVRG 56
Query: 69 TDSHVLEGSRLSIQPSDSHNR 89
           D  V+ GSR+ ++ S    R
Sbjct: 57 LDGKVICGSRVRVELSTGMPR 77

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 13 VGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFSTDS 71
          V NL +  S + L++ F +YG++ +  +  + +T   +GF FV F + ++A D   + D 
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 72 HVLEGSRLSIQ 82
            L+G  L +Q
Sbjct: 78 AELDGRELRVQ 88

>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In Rna- Binding Protein 30 Length = 92

Iteration: 1
 Score = 41.2 bits (95), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 9/83 (10%)
Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE-AVDKVFS 68
          K+ VGN+  T ++ EL+  F EYG ++   ++        K + FV  +  E AV+ +  
Sbjct: 12 KLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRG 63
Query: 69 TDSHVLEGSRLSIQPSDSHNRMA 91
           D+   +G R+ +Q S S  R A
Sbjct: 64 LDNTEFQGKRMHVQLSTSRLRTA 86

>pdb|3V2O|A Chain A, Crystal Structure Of The Peptide Bound Complex Of The Ankyrin Repeat Domains Of Human Ankra2 Length = 183

Iteration: 1
 Score = 41.2 bits (95), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 27/94 (28%), Positives = 50/94 (53%), Gaps = 5/94 (5%)
Query: 254 NEKNIYEWAKEGKLDMLVKQLTKLKDFN-INQLDENGLNCLHWACDRGHLKVVQHLIEKC 312
           N  ++++ A +G++  L    T+++  N IN  DE G   L WA   G + VV+ L++  
Sbjct: 19  NSLSVHQLAAQGEMLYLA---TRIEQENVINHTDEEGFTPLMWAAAHGQIAVVEFLLQN- 74
Query: 313 GADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           GAD  +     +  L  A +  +TD+++ L++ G
Sbjct: 75  GADPQLLGKGRESALSLACSKGYTDIVKMLLDCG 108

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	347
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	8e-29
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	2e-28
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	5e-28
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	6e-28
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	5e-25
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	6e-28
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-26
2cqu_A	116	Peroxisomal D3,D2-enoyl-COA isomerase; acyl-COA bi	9e-28
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	3e-27
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	3e-27
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	7e-27
2cop_A	109	Acyl-coenzyme A binding domain containing 6; acyl	1e-26
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	2e-26
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-26
1hbk_A	89	ACBP, acyl-COA binding protein; fatty acid metabol	3e-26
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	3e-26
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	9e-26
2lbb_A	96	Acyl COA binding protein; protein binding, structu	1e-25
2cb8_A	87	Acyl-COA-binding protein; acyl-coenzyme A binding	1e-25
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	1e-25
1st7_A	86	ACBP, acyl-COA-binding protein; four helix bundle,	2e-25
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-24
3epy_A	89	Acyl-COA-binding domain-containing protein 7; acyl	3e-24
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-23
3fp5_A	106	Acyl-COA binding protein; ACBP, cacao disease, fat	2e-23
3flv_A	119	Acyl-COA-binding domain-containing protein 5; lipi	3e-23
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	3e-23
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	4e-23
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	6e-23
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	6e-23
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-18
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	9e-23
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-22
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-21
2wh5_A	106	Acyl-COA-binding domain-containing protein 4; alte	2e-22
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	3e-22
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-22
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-22
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	4e-22
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	5e-22
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-18
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	5e-22
1x4e_A	85	RNA binding motif, single-stranded interacting pro	8e-22
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-21
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-21
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	3e-21
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-21
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	4e-21
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	4e-21
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-21
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-18
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-21
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-16
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	6e-21
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	6e-21
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-18
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	6e-21
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	6e-21
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	7e-21
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	8e-21
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	9e-21
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-20
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-20
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-20
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-20
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-20
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-20
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	3e-20
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-20
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-14
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	4e-20
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	5e-20
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	6e-20
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	6e-20
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	7e-20
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	9e-20
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-19
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-19
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	3e-19
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	3e-19
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	4e-19
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	6e-14
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	5e-19
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	5e-19
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-18
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	7e-19
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	7e-19
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	7e-19
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-18
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-18
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-18
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-18
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-18
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-18
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-18
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-18
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-18
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	3e-18
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-18
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-15
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-11
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	5e-18
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	5e-18
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	6e-18
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	6e-18
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	6e-18
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-17
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-17
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-17
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-17
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-17
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	3e-17
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	4e-17
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	4e-17
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	4e-17
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	5e-17
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	5e-17
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	5e-17
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	6e-17
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	7e-17
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	7e-17
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	9e-17
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	1e-16
3ehr_A	222	Osteoclast-stimulating factor 1; beta barrel, heli	1e-16
3ehr_A	222	Osteoclast-stimulating factor 1; beta barrel, heli	4e-15
3ehr_A	222	Osteoclast-stimulating factor 1; beta barrel, heli	1e-11
3ehr_A	222	Osteoclast-stimulating factor 1; beta barrel, heli	1e-08
3ehr_A	222	Osteoclast-stimulating factor 1; beta barrel, heli	2e-07
3ehr_A	222	Osteoclast-stimulating factor 1; beta barrel, heli	3e-06
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	9e-16
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	3e-16
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-16
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-14
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	5e-16
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	5e-16
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	7e-16
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	8e-16
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-15
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	1e-15
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-15
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-15
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-15
2div_A	99	TRNA selenocysteine associated protein; structural	2e-15
3f6q_A	179	Integrin-linked protein kinase; ILK, integrin-link	2e-15
3f6q_A	179	Integrin-linked protein kinase; ILK, integrin-link	1e-14
3f6q_A	179	Integrin-linked protein kinase; ILK, integrin-link	2e-13
3f6q_A	179	Integrin-linked protein kinase; ILK, integrin-link	5e-10
3f6q_A	179	Integrin-linked protein kinase; ILK, integrin-link	1e-07
1n11_A	437	Ankyrin; clathrin, BAND 3, anion exchanger, struct	3e-15
1n11_A	437	Ankyrin; clathrin, BAND 3, anion exchanger, struct	5e-14
1n11_A	437	Ankyrin; clathrin, BAND 3, anion exchanger, struct	1e-13
1n11_A	437	Ankyrin; clathrin, BAND 3, anion exchanger, struct	1e-13
1n11_A	437	Ankyrin; clathrin, BAND 3, anion exchanger, struct	1e-13
1n11_A	437	Ankyrin; clathrin, BAND 3, anion exchanger, struct	1e-12
1n11_A	437	Ankyrin; clathrin, BAND 3, anion exchanger, struct	1e-12
1n11_A	437	Ankyrin; clathrin, BAND 3, anion exchanger, struct	3e-12
1n11_A	437	Ankyrin; clathrin, BAND 3, anion exchanger, struct	9e-08
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-15
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-15
3v30_A	172	DNA-binding protein rfxank; structural genomics co	4e-15
3v30_A	172	DNA-binding protein rfxank; structural genomics co	3e-14
3v30_A	172	DNA-binding protein rfxank; structural genomics co	1e-11
3v30_A	172	DNA-binding protein rfxank; structural genomics co	1e-07
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	4e-15
3v31_A	167	Ankyrin repeat family A protein 2; structural geno	4e-15
3v31_A	167	Ankyrin repeat family A protein 2; structural geno	2e-14
3v31_A	167	Ankyrin repeat family A protein 2; structural geno	2e-09
2fo1_E	373	LIN-12 protein; beta-barrel, protein-DNA complex,	4e-15
2fo1_E	373	LIN-12 protein; beta-barrel, protein-DNA complex,	2e-10
2fo1_E	373	LIN-12 protein; beta-barrel, protein-DNA complex,	3e-10
2fo1_E	373	LIN-12 protein; beta-barrel, protein-DNA complex,	5e-10
2fo1_E	373	LIN-12 protein; beta-barrel, protein-DNA complex,	1e-09
2fo1_E	373	LIN-12 protein; beta-barrel, protein-DNA complex,	3e-08
2fo1_E	373	LIN-12 protein; beta-barrel, protein-DNA complex,	1e-05
1n0r_A	126	4ANK, 4 ankyrin repeats; structural protein; 1.50A	6e-15
1n0r_A	126	4ANK, 4 ankyrin repeats; structural protein; 1.50A	7e-13
1n0r_A	126	4ANK, 4 ankyrin repeats; structural protein; 1.50A	3e-10
1n0r_A	126	4ANK, 4 ankyrin repeats; structural protein; 1.50A	3e-07
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	6e-15
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	1e-14
3aaa_C	123	Myotrophin, protein V-1; actin capping protein, ba	1e-14
3aaa_C	123	Myotrophin, protein V-1; actin capping protein, ba	1e-13
3aaa_C	123	Myotrophin, protein V-1; actin capping protein, ba	9e-11
3c5r_A	137	BARD-1, BRCA1-associated ring domain protein 1; an	2e-14
3c5r_A	137	BARD-1, BRCA1-associated ring domain protein 1; an	3e-13
3c5r_A	137	BARD-1, BRCA1-associated ring domain protein 1; an	6e-12
1wdy_A	285	2-5A-dependent ribonuclease; hydrolase, RNA-bindin	2e-14
1wdy_A	285	2-5A-dependent ribonuclease; hydrolase, RNA-bindin	1e-11
1wdy_A	285	2-5A-dependent ribonuclease; hydrolase, RNA-bindin	8e-11
1wdy_A	285	2-5A-dependent ribonuclease; hydrolase, RNA-bindin	1e-09
1wdy_A	285	2-5A-dependent ribonuclease; hydrolase, RNA-bindin	3e-08
3hra_A	201	Ankyrin repeat family protein; structural protein;	2e-14
3hra_A	201	Ankyrin repeat family protein; structural protein;	1e-12
3hra_A	201	Ankyrin repeat family protein; structural protein;	2e-12
3hra_A	201	Ankyrin repeat family protein; structural protein;	9e-12
3hra_A	201	Ankyrin repeat family protein; structural protein;	5e-04
1d9s_A	136	Cyclin-dependent kinase 4 inhibitor B; helix-turn-	2e-14
1d9s_A	136	Cyclin-dependent kinase 4 inhibitor B; helix-turn-	4e-13
1d9s_A	136	Cyclin-dependent kinase 4 inhibitor B; helix-turn-	9e-08
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-14
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	3e-14
2vge_A	229	RELA-associated inhibitor; iaspp, nucleus, apoptos	3e-14
2vge_A	229	RELA-associated inhibitor; iaspp, nucleus, apoptos	6e-08
3ljn_A	364	Hypothetical protein; ankyrin, structural genomics	5e-14
3ljn_A	364	Hypothetical protein; ankyrin, structural genomics	2e-13
3ljn_A	364	Hypothetical protein; ankyrin, structural genomics	3e-12
3ljn_A	364	Hypothetical protein; ankyrin, structural genomics	9e-10
3ljn_A	364	Hypothetical protein; ankyrin, structural genomics	2e-09
3ljn_A	364	Hypothetical protein; ankyrin, structural genomics	7e-07
2dzn_A	228	Probable 26S proteasome regulatory subunit P28; an	7e-14
2dzn_A	228	Probable 26S proteasome regulatory subunit P28; an	7e-13
2dzn_A	228	Probable 26S proteasome regulatory subunit P28; an	5e-12
2dzn_A	228	Probable 26S proteasome regulatory subunit P28; an	3e-11
2dzn_A	228	Probable 26S proteasome regulatory subunit P28; an	6e-08
3b7b_A	237	Euchromatic histone-lysine N-methyltransferase 1;	9e-14
3b7b_A	237	Euchromatic histone-lysine N-methyltransferase 1;	7e-13
3b7b_A	237	Euchromatic histone-lysine N-methyltransferase 1;	2e-12
3b7b_A	237	Euchromatic histone-lysine N-methyltransferase 1;	1e-11
3b7b_A	237	Euchromatic histone-lysine N-methyltransferase 1;	1e-06
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	1e-13
2y1l_E	169	Darpin-8.4; hydrolase-inhibitor complex, DEVD darp	1e-13
2y1l_E	169	Darpin-8.4; hydrolase-inhibitor complex, DEVD darp	5e-12
2y1l_E	169	Darpin-8.4; hydrolase-inhibitor complex, DEVD darp	4e-09
2y1l_E	169	Darpin-8.4; hydrolase-inhibitor complex, DEVD darp	3e-05
1ihb_A	162	P18-INK4C(INK6), cyclin-dependent kinase 6 inhibit	2e-13
1ihb_A	162	P18-INK4C(INK6), cyclin-dependent kinase 6 inhibit	2e-13
1ihb_A	162	P18-INK4C(INK6), cyclin-dependent kinase 6 inhibit	5e-10
1ihb_A	162	P18-INK4C(INK6), cyclin-dependent kinase 6 inhibit	6e-09
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	2e-13
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-13
1bi7_B	156	P16INK4A, MTS1, multiple tumor suppressor; cyclin	2e-13
1bi7_B	156	P16INK4A, MTS1, multiple tumor suppressor; cyclin	7e-12
1bi7_B	156	P16INK4A, MTS1, multiple tumor suppressor; cyclin	1e-11
1bi7_B	156	P16INK4A, MTS1, multiple tumor suppressor; cyclin	3e-09
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	2e-13
1k1a_A	241	B-cell lymphoma 3-encoded protein; BCL-3, NF-kappa	2e-13
1k1a_A	241	B-cell lymphoma 3-encoded protein; BCL-3, NF-kappa	6e-12
1k1a_A	241	B-cell lymphoma 3-encoded protein; BCL-3, NF-kappa	8e-12
1k1a_A	241	B-cell lymphoma 3-encoded protein; BCL-3, NF-kappa	3e-11
1k1a_A	241	B-cell lymphoma 3-encoded protein; BCL-3, NF-kappa	2e-10
1k1a_A	241	B-cell lymphoma 3-encoded protein; BCL-3, NF-kappa	2e-09
1n0q_A	93	3ANK, 3 ankyrin repeats; structural protein; 1.26A	3e-13
1n0q_A	93	3ANK, 3 ankyrin repeats; structural protein; 1.26A	2e-11
1n0q_A	93	3ANK, 3 ankyrin repeats; structural protein; 1.26A	9e-08
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	3e-13
1awc_B	153	Protein (GA binding protein beta 1); complex (tran	4e-13
1awc_B	153	Protein (GA binding protein beta 1); complex (tran	1e-10
1awc_B	153	Protein (GA binding protein beta 1); complex (tran	4e-09
1awc_B	153	Protein (GA binding protein beta 1); complex (tran	5e-06
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	4e-13
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	5e-13
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	6e-13
1ycs_B	239	53BP2, P53BP2; ankyrin repeats, SH3, tumor suppres	6e-13
1ycs_B	239	53BP2, P53BP2; ankyrin repeats, SH3, tumor suppres	1e-10
1ycs_B	239	53BP2, P53BP2; ankyrin repeats, SH3, tumor suppres	1e-09
1ycs_B	239	53BP2, P53BP2; ankyrin repeats, SH3, tumor suppres	4e-08
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	6e-13
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	6e-13
2l6b_A	115	NR1C; ankyrin, consensus, repeat protein, ising mo	8e-13
2l6b_A	115	NR1C; ankyrin, consensus, repeat protein, ising mo	4e-11
2l6b_A	115	NR1C; ankyrin, consensus, repeat protein, ising mo	8e-11
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	9e-13
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	9e-13
3eu9_A	240	Huntingtin-interacting protein 14; epigenetics, an	1e-12
3eu9_A	240	Huntingtin-interacting protein 14; epigenetics, an	4e-12
3eu9_A	240	Huntingtin-interacting protein 14; epigenetics, an	1e-11
3eu9_A	240	Huntingtin-interacting protein 14; epigenetics, an	3e-11
3eu9_A	240	Huntingtin-interacting protein 14; epigenetics, an	9e-10
3eu9_A	240	Huntingtin-interacting protein 14; epigenetics, an	8e-05
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-12
1bd8_A	156	P19INK4D CDK4/6 inhibitor; tumor suppressor, ankyr	1e-12
1bd8_A	156	P19INK4D CDK4/6 inhibitor; tumor suppressor, ankyr	2e-12
1bd8_A	156	P19INK4D CDK4/6 inhibitor; tumor suppressor, ankyr	1e-11
1bd8_A	156	P19INK4D CDK4/6 inhibitor; tumor suppressor, ankyr	1e-10
2rfm_A	192	Putative ankyrin repeat protein TV1425; ANK repeat	1e-12
2rfm_A	192	Putative ankyrin repeat protein TV1425; ANK repeat	2e-11
2rfm_A	192	Putative ankyrin repeat protein TV1425; ANK repeat	5e-11
2rfm_A	192	Putative ankyrin repeat protein TV1425; ANK repeat	2e-04
1yyh_A	253	HN1;, notch 1, ankyrin domain; ankyrin repeats, ce	2e-12
1yyh_A	253	HN1;, notch 1, ankyrin domain; ankyrin repeats, ce	3e-11
1yyh_A	253	HN1;, notch 1, ankyrin domain; ankyrin repeats, ce	1e-10
1yyh_A	253	HN1;, notch 1, ankyrin domain; ankyrin repeats, ce	3e-06
1yyh_A	253	HN1;, notch 1, ankyrin domain; ankyrin repeats, ce	9e-06
3twr_A	165	Tankyrase-2; ankyrin repeat, protein-protein inter	2e-12
3twr_A	165	Tankyrase-2; ankyrin repeat, protein-protein inter	3e-12
3twr_A	165	Tankyrase-2; ankyrin repeat, protein-protein inter	4e-12
3twr_A	165	Tankyrase-2; ankyrin repeat, protein-protein inter	3e-08
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	3e-12
2f8y_A	223	Notch homolog 1, translocation-associated (drosoph	3e-12
2f8y_A	223	Notch homolog 1, translocation-associated (drosoph	3e-11
2f8y_A	223	Notch homolog 1, translocation-associated (drosoph	6e-11
2f8y_A	223	Notch homolog 1, translocation-associated (drosoph	8e-06
2jab_A	136	H10-2-G3; HER2, darpin, ankyrin repeat protein, me	4e-12
2jab_A	136	H10-2-G3; HER2, darpin, ankyrin repeat protein, me	5e-11
2jab_A	136	H10-2-G3; HER2, darpin, ankyrin repeat protein, me	4e-08
2jab_A	136	H10-2-G3; HER2, darpin, ankyrin repeat protein, me	2e-04
2zgd_A	110	3 repeat synthetic ankyrin; ankyrin repeat, hydrox	5e-12
2zgd_A	110	3 repeat synthetic ankyrin; ankyrin repeat, hydrox	3e-10
2zgd_A	110	3 repeat synthetic ankyrin; ankyrin repeat, hydrox	4e-05
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-12
2xai_A	261	ASB-9, ankyrin repeat and SOCS box protein 9; tran	6e-12
2xai_A	261	ASB-9, ankyrin repeat and SOCS box protein 9; tran	1e-11
2xai_A	261	ASB-9, ankyrin repeat and SOCS box protein 9; tran	4e-11
2xai_A	261	ASB-9, ankyrin repeat and SOCS box protein 9; tran	1e-10
2xai_A	261	ASB-9, ankyrin repeat and SOCS box protein 9; tran	9e-09
2xai_A	261	ASB-9, ankyrin repeat and SOCS box protein 9; tran	2e-08
2xai_A	261	ASB-9, ankyrin repeat and SOCS box protein 9; tran	4e-04
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	6e-12
3deo_A	183	Signal recognition particle 43 kDa protein; chloro	8e-12
3deo_A	183	Signal recognition particle 43 kDa protein; chloro	2e-11
3deo_A	183	Signal recognition particle 43 kDa protein; chloro	6e-08
3deo_A	183	Signal recognition particle 43 kDa protein; chloro	2e-05
1ikn_D	236	Protein (I-kappa-B-alpha), protein (NF-kappa-B P50	1e-11
1ikn_D	236	Protein (I-kappa-B-alpha), protein (NF-kappa-B P50	7e-11
1ikn_D	236	Protein (I-kappa-B-alpha), protein (NF-kappa-B P50	4e-09
1ikn_D	236	Protein (I-kappa-B-alpha), protein (NF-kappa-B P50	5e-09
1ikn_D	236	Protein (I-kappa-B-alpha), protein (NF-kappa-B P50	8e-09
1ikn_D	236	Protein (I-kappa-B-alpha), protein (NF-kappa-B P50	9e-06
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-11
1s70_B	299	130 kDa myosin-binding subunit of smooth muscle my	2e-11
1s70_B	299	130 kDa myosin-binding subunit of smooth muscle my	8e-11
1s70_B	299	130 kDa myosin-binding subunit of smooth muscle my	3e-10
1s70_B	299	130 kDa myosin-binding subunit of smooth muscle my	2e-08
1s70_B	299	130 kDa myosin-binding subunit of smooth muscle my	8e-06
3utm_A	351	Tankyrase-1; tankyrase, TNKS, ankryin repeat clust	2e-11
3utm_A	351	Tankyrase-1; tankyrase, TNKS, ankryin repeat clust	1e-10
3utm_A	351	Tankyrase-1; tankyrase, TNKS, ankryin repeat clust	1e-10
3utm_A	351	Tankyrase-1; tankyrase, TNKS, ankryin repeat clust	2e-08
3utm_A	351	Tankyrase-1; tankyrase, TNKS, ankryin repeat clust	6e-08
3utm_A	351	Tankyrase-1; tankyrase, TNKS, ankryin repeat clust	3e-06
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-11
3t8k_A	186	Uncharacterized protein; structural genomics, PSI-	2e-11
3t8k_A	186	Uncharacterized protein; structural genomics, PSI-	3e-08
3t8k_A	186	Uncharacterized protein; structural genomics, PSI-	3e-08
3t8k_A	186	Uncharacterized protein; structural genomics, PSI-	1e-07
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-11
2aja_A	376	Ankyrin repeat family protein; NESG, Q5ZSV0, struc	2e-11
2aja_A	376	Ankyrin repeat family protein; NESG, Q5ZSV0, struc	5e-10
2aja_A	376	Ankyrin repeat family protein; NESG, Q5ZSV0, struc	2e-06
2aja_A	376	Ankyrin repeat family protein; NESG, Q5ZSV0, struc	3e-04
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-11
3d9h_A	285	CDNA FLJ77766, highly similar to HOMO sapiens anky	2e-11
3d9h_A	285	CDNA FLJ77766, highly similar to HOMO sapiens anky	5e-11
3d9h_A	285	CDNA FLJ77766, highly similar to HOMO sapiens anky	3e-10
3d9h_A	285	CDNA FLJ77766, highly similar to HOMO sapiens anky	1e-09
3d9h_A	285	CDNA FLJ77766, highly similar to HOMO sapiens anky	5e-09
3d9h_A	285	CDNA FLJ77766, highly similar to HOMO sapiens anky	2e-04
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-07
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-11
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	4e-11
3kea_A	285	K1L; tropism, ANK repeat, viral protein; 2.30A {Va	4e-11
3kea_A	285	K1L; tropism, ANK repeat, viral protein; 2.30A {Va	4e-11
3kea_A	285	K1L; tropism, ANK repeat, viral protein; 2.30A {Va	5e-10
3kea_A	285	K1L; tropism, ANK repeat, viral protein; 2.30A {Va	2e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	9e-06
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	5e-11
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	6e-11
3ui2_A	244	Signal recognition particle 43 kDa protein, chlor;	7e-11
3ui2_A	244	Signal recognition particle 43 kDa protein, chlor;	8e-11
3ui2_A	244	Signal recognition particle 43 kDa protein, chlor;	2e-07
3ui2_A	244	Signal recognition particle 43 kDa protein, chlor;	1e-06
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	8e-11
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-10
1oy3_D	282	Transcription factor inhibitor I-kappa-B-beta; pro	2e-10
1oy3_D	282	Transcription factor inhibitor I-kappa-B-beta; pro	2e-10
1oy3_D	282	Transcription factor inhibitor I-kappa-B-beta; pro	1e-09
1oy3_D	282	Transcription factor inhibitor I-kappa-B-beta; pro	3e-09
1oy3_D	282	Transcription factor inhibitor I-kappa-B-beta; pro	5e-08
1oy3_D	282	Transcription factor inhibitor I-kappa-B-beta; pro	4e-07
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-10
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-10
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	3e-10
1x5p_A	97	Negative elongation factor E; structure genomics,	5e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	9e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-09
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	9e-10
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	9e-10
2etb_A	256	Transient receptor potential cation channel subfam	1e-09
2etb_A	256	Transient receptor potential cation channel subfam	2e-07
2etb_A	256	Transient receptor potential cation channel subfam	1e-06
2etb_A	256	Transient receptor potential cation channel subfam	1e-06
2etb_A	256	Transient receptor potential cation channel subfam	2e-05
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-09
1sw6_A	327	Regulatory protein SWI6; transcription regulation,	1e-09
1sw6_A	327	Regulatory protein SWI6; transcription regulation,	4e-09
1sw6_A	327	Regulatory protein SWI6; transcription regulation,	6e-05
3aji_A	231	26S proteasome non-ATPase regulatory subunit 10; g	1e-09
3aji_A	231	26S proteasome non-ATPase regulatory subunit 10; g	4e-08
3aji_A	231	26S proteasome non-ATPase regulatory subunit 10; g	3e-07
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	5e-09
2pnn_A	273	Transient receptor potential cation channel subfa	2e-09
2pnn_A	273	Transient receptor potential cation channel subfa	3e-05
2pnn_A	273	Transient receptor potential cation channel subfa	3e-05
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-09
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	6e-09
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	7e-09
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-08
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-08
2rfa_A	232	Transient receptor potential cation channel subfa	3e-08
2rfa_A	232	Transient receptor potential cation channel subfa	4e-07
2rfa_A	232	Transient receptor potential cation channel subfa	1e-05
2rfa_A	232	Transient receptor potential cation channel subfa	1e-05
2rfa_A	232	Transient receptor potential cation channel subfa	2e-05
2b0o_E	301	UPLC1; arfgap, structural genomics, structural gen	5e-08
1dcq_A	278	PYK2-associated protein beta; zinc-binding module,	1e-07
1dcq_A	278	PYK2-associated protein beta; zinc-binding module,	1e-04
3jxi_A	260	Vanilloid receptor-related osmotically activated p	2e-07
3jxi_A	260	Vanilloid receptor-related osmotically activated p	6e-05
3jxi_A	260	Vanilloid receptor-related osmotically activated p	9e-05
3jue_A	368	Arfgap with coiled-coil, ANK repeat and PH domain	2e-07
3jue_A	368	Arfgap with coiled-coil, ANK repeat and PH domain	2e-05
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	3e-07
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	5e-07
1qzv_F	154	Plant photosystem I: subunit PSAF; photosynthesis,	5e-05
3lvq_E	497	ARF-GAP with SH3 domain, ANK repeat and PH domain	2e-04
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	3e-04
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	5e-04

>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 =  106 bits (266), Expect = 8e-29
 Identities = 23/75 (30%), Positives = 45/75 (60%)

Query: 2  SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
           +S  + NKIFVG +P      EL+++F ++G +    +++D      +GFGF+TF++++
Sbjct: 4  GSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQ 63

Query: 62 AVDKVFSTDSHVLEG 76
          +VD+  +   H + G
Sbjct: 64 SVDQAVNMHFHDIMG 78

>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 =  105 bits (265), Expect = 2e-28
 Identities = 25/70 (35%), Positives = 42/70 (60%)

Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
             KIFVG LP+  +   L+K+F  +G I  A V+ D+ TG S+G+GFVT  ++ A ++ 
Sbjct: 16 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75

Query: 67 FSTDSHVLEG 76
              + +++G
Sbjct: 76 CKDPNPIIDG 85

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score =  103 bits (259), Expect = 5e-28
 Identities = 26/67 (38%), Positives = 43/67 (64%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          KIFVG L    +  ++K +F ++G++ +A +MFDK T   +GFGFVTF++++ V+KV   
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 70 DSHVLEG 76
            H +  
Sbjct: 61 HFHEINN 67

>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 =  106 bits (266), Expect = 6e-28
 Identities = 30/73 (41%), Positives = 47/73 (64%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
            KIFVG +   V   E ++FFS++G I++A +M DK+TG S+GFGFVT+ + +AVD+V  
Sbjct: 88  GKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ 147

Query: 69  TDSHVLEGSRLSI 81
                 +  ++ I
Sbjct: 148 NKFIDFKDRKIEI 160

>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 = 98.4 bits (246), Expect = 5e-25
 Identities = 25/71 (35%), Positives = 46/71 (64%), Gaps = 1/71 (1%)

Query: 6  RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          ++  K+F+G L W  + + L+++F +YG + +  +M D  TG S+GFGF++F+   +VD+
Sbjct: 1  KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60

Query: 66 VFSTDSHVLEG 76
          V     H+L+G
Sbjct: 61 VVK-TQHILDG 70

>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 =  106 bits (268), Expect = 6e-28
 Identities = 25/92 (27%), Positives = 43/92 (46%), Gaps = 3/92 (3%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
            KIFVG +      + L+ +F +YG+I    +M D+ +G  +GF FVTF + ++VDK+  
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 164

Query: 69  TDSHVLEGSRLSI---QPSDSHNRMAENMEDR 97
              H + G    +            + +   R
Sbjct: 165 QKYHTVNGHNCEVRKALSKQEMASASSSQRGR 196

>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 =  102 bits (256), Expect = 3e-26
 Identities = 27/80 (33%), Positives = 44/80 (55%)

Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
          QL K+F+G L +  +   L+  F ++G + +  VM D NT  S+GFGFVT+   E VD  
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 71

Query: 67 FSTDSHVLEGSRLSIQPSDS 86
           +   H ++G  +  + + S
Sbjct: 72 MNARPHKVDGRVVEPKRAVS 91

>2cqu_A Peroxisomal D3,D2-enoyl-COA isomerase; acyl-COA binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 116

 Score =  103 bits (259), Expect = 9e-28
 Identities = 34/98 (34%), Positives = 52/98 (53%)

Query: 95  EDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSL 154
           +  F  + + +  L K   +   LK YALYKQAT G CN+ KP  +++  K+K++AWN+L
Sbjct: 17  QKDFENSMNQVKLLKKDPGNEVKLKLYALYKQATEGPCNMPKPGVFDLINKAKWDAWNAL 76

Query: 155 GQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPN 192
           G + K  A   Y+ L+  +    E   Q E   D  P+
Sbjct: 77  GSLPKEAARQNYVDLVSSLSPSLESSSQVEPGTDSGPS 114

>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 =  102 bits (257), Expect = 3e-27
 Identities = 22/73 (30%), Positives = 41/73 (56%)

Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
          Q  K+F+G L +  +   L+ ++ ++G++ +  VM D  +  S+GFGFVTF +   VD  
Sbjct: 26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 85

Query: 67 FSTDSHVLEGSRL 79
           +   H ++G  +
Sbjct: 86 MAARPHSIDGRVV 98

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score =  101 bits (253), Expect = 3e-27
 Identities = 20/69 (28%), Positives = 37/69 (53%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          KIFVG L       +++++F  +G++ +  +  D  T   +GF F+TF+ +E V K+   
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 70 DSHVLEGSR 78
            H +  S+
Sbjct: 61 KYHNVGLSK 69

>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 =  101 bits (254), Expect = 7e-27
 Identities = 26/70 (37%), Positives = 41/70 (58%)

Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
             K+F+G L W  +   L+++F ++G++    VM D  T  S+GFGFVTF ++  VDKV
Sbjct: 24 SGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 83

Query: 67 FSTDSHVLEG 76
           +   H L+ 
Sbjct: 84 LAQSRHELDS 93

>2cop_A Acyl-coenzyme A binding domain containing 6; acyl COA binding protein, COA binding protein, lipid binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 109

 Score =  101 bits (252), Expect = 1e-26
 Identities = 36/96 (37%), Positives = 57/96 (59%)

Query: 89  RMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKY 148
             +  + + F +A  +L  L++      LL  YA YKQ  VG CN  KPS+++ E K K+
Sbjct: 3   SGSSGLAELFEKAAAHLQGLIQVASREQLLYLYARYKQVKVGNCNTPKPSFFDFEGKQKW 62

Query: 149 NAWNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEE 184
            AW +LG  + S+AM +YIA++K++D GW  +  E+
Sbjct: 63  EAWKALGDSSPSQAMQEYIAVVKKLDPGWNPQIPEK 98

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 99.5 bits (249), Expect = 2e-26
 Identities = 26/67 (38%), Positives = 41/67 (61%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+F+G L W  +   L+++F ++G++    VM D  T  S+GFGFVTF ++  VDKV + 
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 70 DSHVLEG 76
            H L+ 
Sbjct: 62 SRHELDS 68

>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 =  100 bits (250), Expect = 2e-26
 Identities = 27/70 (38%), Positives = 46/70 (65%)

Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
          ++ K+FVG L W+ +   L+ +FS+YG++++  +M DK T  S+GFGFV F++   V  V
Sbjct: 15 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV 74

Query: 67 FSTDSHVLEG 76
           ++  H L+G
Sbjct: 75 LASRPHTLDG 84

>1hbk_A ACBP, acyl-COA binding protein; fatty acid metabolism; HET: COA MYR; 2.0A {Plasmodium falciparum} SCOP: a.11.1.1 Length = 89

 Score = 99.2 bits (247), Expect = 3e-26
 Identities = 26/89 (29%), Positives = 47/89 (52%), Gaps = 2/89 (2%)

Query: 93  NMEDRFNQACDYLPSLVK--KLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNA 150
           +M   F +   ++  L +   L +   L  Y  YKQ+T+G CNI +PS +    + KY A
Sbjct: 1   HMAQVFEECVSFINGLPRTINLPNELKLDLYKYYKQSTIGNCNIKEPSAHKYIDRKKYEA 60

Query: 151 WNSLGQMAKSEAMSKYIALLKEVDAGWED 179
           W S+  + + +A  +Y+ ++ E+   W+D
Sbjct: 61  WKSVENLNREDAQKRYVDIVSEIFPYWQD 89

>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 = 99.6 bits (249), Expect = 3e-26
 Identities = 27/76 (35%), Positives = 45/76 (59%), Gaps = 1/76 (1%)

Query: 1  MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
          +  ++++ + + V  LPW  +  +LK++FS +G+++   V  D  TG SKGFGFV F   
Sbjct: 8  VKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEY 67

Query: 61 EAVDKVFSTDSHVLEG 76
          E   KV S   H+++G
Sbjct: 68 ETQVKVMS-QRHMIDG 82

>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 = 97.6 bits (244), Expect = 9e-26
 Identities = 27/70 (38%), Positives = 46/70 (65%)

Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
             K+FVG L W  S  +LK +F+++G++++ ++  D NTG S+GFGF+ F++  +V+KV
Sbjct: 10 DAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKV 69

Query: 67 FSTDSHVLEG 76
               H L+G
Sbjct: 70 LDQKEHRLDG 79

>2lbb_A Acyl COA binding protein; protein binding, structural genomi seattle structural genomics center for infectious disease,; NMR {Babesia bovis} Length = 96

 Score = 97.7 bits (243), Expect = 1e-25
 Identities = 32/96 (33%), Positives = 46/96 (47%), Gaps = 4/96 (4%)

Query: 85  DSHNRMAENMEDRFNQACDYLPSLVKK-LDSSTLLKFYALYKQATVGQCNIDKPSWYNME 143
             H+ M+    D F+ A  Y+ +       +   L FY  YKQATVG CN  KP    ++
Sbjct: 4   HHHHHMSA---DDFDAAVKYVSNTTTMMASNDDKLCFYKYYKQATVGDCNKPKPGMLQLQ 60

Query: 144 AKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWED 179
            K K+ AWN+L  M+   A   Y+ LL  +   W +
Sbjct: 61  EKYKWEAWNALRGMSTESAKEAYVKLLDTLAPSWRN 96

>2cb8_A Acyl-COA-binding protein; acyl-coenzyme A binding protein, fatty acid, acetylation, alternative splicing, lipid-binding, transport; HET: MYA; 1.4A {Homo sapiens} PDB: 2fj9_A 1aca_A* 1hb6_A 1hb8_A 1nti_A 1nvl_A* 2abd_A 2fdq_A Length = 87

 Score = 97.6 bits (243), Expect = 1e-25
 Identities = 27/83 (32%), Positives = 44/83 (53%)

Query: 95  EDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSL 154
           +  F +A + +  L  K     +L  Y  YKQATVG  N ++P   +   K+K++AWN L
Sbjct: 3   QAEFEKAAEEVRHLKTKPSDEEMLFIYGHYKQATVGDINTERPGMLDFTGKAKWDAWNEL 62

Query: 155 GQMAKSEAMSKYIALLKEVDAGW 177
              +K +AM  YI  ++E+   +
Sbjct: 63  KGTSKEDAMKAYINKVEELKKKY 85

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 98.2 bits (245), Expect = 1e-25
 Identities = 22/89 (24%), Positives = 41/89 (46%), Gaps = 1/89 (1%)

Query: 6   RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           R    +F   L   +   +L+ FFS  G++ +  ++ D+N+  SKG  +V F   ++V  
Sbjct: 23  RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPL 82

Query: 66  VFSTDSHVLEGSRLSIQPSDS-HNRMAEN 93
                   L G  + +Q S +  NR++  
Sbjct: 83  AIGLTGQRLLGVPIIVQASQAEKNRLSGP 111

>1st7_A ACBP, acyl-COA-binding protein; four helix bundle, transport protein; NMR {Saccharomyces cerevisiae} Length = 86

 Score = 96.9 bits (241), Expect = 2e-25
 Identities = 29/84 (34%), Positives = 49/84 (58%)

Query: 94  MEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNS 153
           +   F +    +  L  K  +  LL+ YALYKQATVG  + +KP  +NM+ + K+ AW +
Sbjct: 1   VSQLFEEKAKAVNELPTKPSTDELLELYALYKQATVGDNDKEKPGIFNMKDRYKWEAWEN 60

Query: 154 LGQMAKSEAMSKYIALLKEVDAGW 177
           L   ++ +A  +YIAL+ ++ A +
Sbjct: 61  LKGKSQEDAEKEYIALVDQLIAKY 84

>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 = 94.2 bits (235), Expect = 3e-24
 Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 2/73 (2%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          N +FVG +   +   E++ FF+ YG +    ++ D+ TG+SKG+GFV+F N   V K+  
Sbjct: 10 NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68

Query: 69 TDSHVLEGSRLSI 81
                 G +L +
Sbjct: 69 -SQINFHGKKLKL 80

>3epy_A Acyl-COA-binding domain-containing protein 7; acyl-COA binding protein, fatty acid, lipid metabolism, structural genomics; HET: COA PLM; 2.00A {Homo sapiens} Length = 89

 Score = 93.8 bits (233), Expect = 3e-24
 Identities = 27/84 (32%), Positives = 46/84 (54%)

Query: 94  MEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNS 153
           ++  F++A + +  L  + D   L + Y LYKQA VG  NI  P   +++ K+K+ AWN 
Sbjct: 4   LQADFDRAAEDVRKLKARPDDGELKELYGLYKQAIVGDINIACPGMLDLKGKAKWEAWNL 63

Query: 154 LGQMAKSEAMSKYIALLKEVDAGW 177
              ++  +A S YI+  KE+   +
Sbjct: 64  KKGLSTEDATSAYISKAKELIEKY 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 = 93.2 bits (232), Expect = 1e-23
 Identities = 19/82 (23%), Positives = 35/82 (42%)

Query: 1  MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
          + + + +   +F+ NL +      L +   ++G +    V+   +T  SKG  F  F  +
Sbjct: 8  LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQ 67

Query: 61 EAVDKVFSTDSHVLEGSRLSIQ 82
          EA  K  +  S   EG  L + 
Sbjct: 68 EAAQKCLAAASLEAEGGGLKLD 89

>3fp5_A Acyl-COA binding protein; ACBP, cacao disease, fatty acid metabolism, lipid binding protein; HET: MES; 1.61A {Moniliophthora perniciosa} Length = 106

 Score = 91.9 bits (228), Expect = 2e-23
 Identities = 30/94 (31%), Positives = 50/94 (53%), Gaps = 4/94 (4%)

Query: 95  EDRFNQACDYLPSLVK----KLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNA 150
           + +F++A + + SL K    K      L FY  +KQATVG  NI +P   +   K+K++A
Sbjct: 5   KAKFDKAVEIVQSLPKDGPIKPTQDEQLYFYKYFKQATVGDVNISRPGLMDFTGKAKWDA 64

Query: 151 WNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEE 184
           W S+   +K  A  KY+  L E+    + +E ++
Sbjct: 65  WKSVEGTSKEVAYQKYVEKLLEILKKADTEESKK 98

>3flv_A Acyl-COA-binding domain-containing protein 5; lipid binding, structural genomics, struct genomics consortium, SGC, lipid-binding, membrane; HET: STE COA; 1.70A {Homo sapiens} Length = 119

 Score = 92.4 bits (229), Expect = 3e-23
 Identities = 35/108 (32%), Positives = 54/108 (50%), Gaps = 7/108 (6%)

Query: 84  SDSHNRMAENM---EDRFNQACDYLPSLVK----KLDSSTLLKFYALYKQATVGQCNIDK 136
            D            E RF  A   + SL K    +  +  +LKFY+ YKQAT G C + +
Sbjct: 11  VDLGTENLYFQSMHETRFEAAVKVIQSLPKNGSFQPTNEMMLKFYSFYKQATEGPCKLSR 70

Query: 137 PSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEE 184
           P +++   + K++AW+SLG M K EAM  Y+  +K++       E+ E
Sbjct: 71  PGFWDPIGRYKWDAWSSLGDMTKEEAMIAYVEEMKKIIETMPMTEKVE 118

>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 = 91.0 bits (227), Expect = 3e-23
 Identities = 21/74 (28%), Positives = 40/74 (54%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           I+VGN+ +  +  EL+  F   G +   +++ DK +G  KGF ++ F +KE+V    + 
Sbjct: 8  SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLAL 67

Query: 70 DSHVLEGSRLSIQP 83
          D  +  G ++ + P
Sbjct: 68 DESLFRGRQIKVIP 81

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 90.8 bits (226), Expect = 4e-23
 Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 5/74 (6%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           +FV   P  V   +L ++F  +G +  ASV+ DK+ G    F  V   +  A + V S 
Sbjct: 10 SVFVSGFPRGVDSAQLSEYFLAFGPV--ASVVMDKDKG---VFAIVEMGDVGAREAVLSQ 64

Query: 70 DSHVLEGSRLSIQP 83
            H L G RL ++P
Sbjct: 65 SQHSLGGHRLRVRP 78

>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 = 90.8 bits (226), Expect = 6e-23
 Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 4/85 (4%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
           K+FVG L +  +   L++ FS+YGQI    V+ D+ T  S+GFGFVTF+N +       
Sbjct: 13 GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72

Query: 69 T-DSHVLEGSRLSI---QPSDSHNR 89
            +   ++G ++ +     S  +  
Sbjct: 73 AMNGKSVDGRQIRVDQAGKSSDNRS 97

>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 = 92.7 bits (231), Expect = 6e-23
 Identities = 19/75 (25%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
           +K+F+G LP  ++ +++K+  + +G +   +++ D  TGLSKG+ F  + +    D+  +
Sbjct: 95  HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 154

Query: 69  T-DSHVLEGSRLSIQ 82
             +   L   +L +Q
Sbjct: 155 GLNGMQLGDKKLLVQ 169

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 80.0 bits (198), Expect = 3e-18
 Identities = 16/96 (16%), Positives = 40/96 (41%), Gaps = 11/96 (11%)

Query: 5  IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMN-----ASVMFDKNTGLSKGFGFVTFQN 59
          +    +++VGN+P+ ++   +  FF+   ++        + +        K F F+ F++
Sbjct: 1  LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 60

Query: 60 KEAVDKVFSTDSHVLEGSRLSI------QPSDSHNR 89
           +   +  + D  + +G  L I      QP    ++
Sbjct: 61 VDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHK 96

>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 = 90.9 bits (226), Expect = 9e-23
 Identities = 20/75 (26%), Positives = 39/75 (52%)

Query: 10  KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
            ++VGN+ +  +  +L+  FS  G I   +++ DK +G  KG+ ++ F  + +VD   + 
Sbjct: 38  SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAM 97

Query: 70  DSHVLEGSRLSIQPS 84
           D  V  G  + + P 
Sbjct: 98  DETVFRGRTIKVLPK 112

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 92.8 bits (231), Expect = 2e-22
 Identities = 18/69 (26%), Positives = 40/69 (57%)

Query: 1   MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
           ++   R  N+I+V ++   +S +++K  F  +G+I +A++  D  TG  KG+GF+ ++  
Sbjct: 118 LAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKA 177

Query: 61  EAVDKVFST 69
           ++     S+
Sbjct: 178 QSSQDAVSS 186

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 89.7 bits (223), Expect = 3e-21
 Identities = 18/101 (17%), Positives = 49/101 (48%), Gaps = 1/101 (0%)

Query: 2   SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
             ++  +++++VG++ + +  + +++ F+ +G I +  + +D  T   KGF FV ++  E
Sbjct: 22  QGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPE 81

Query: 62  AVDKVFST-DSHVLEGSRLSIQPSDSHNRMAENMEDRFNQA 101
           A        +S +L G  + +    +  +    ++    +A
Sbjct: 82  AAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEA 122

>2wh5_A Acyl-COA-binding domain-containing protein 4; alternative splicing, fatty acid metabolism, lipid transport, lipid binding protein; HET: STE ST9 COA; 2.60A {Homo sapiens} Length = 106

 Score = 89.3 bits (221), Expect = 2e-22
 Identities = 32/99 (32%), Positives = 54/99 (54%), Gaps = 4/99 (4%)

Query: 90  MAENMEDRFNQACDYLPSLVK----KLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAK 145
              + + +F  A   + +L K    +     +L+FY+ YKQAT+G C + +P +++   +
Sbjct: 4   PEPDCQKQFQAAVSVIQNLPKNGSYRPSYEEMLRFYSYYKQATMGPCLVPRPGFWDPIGR 63

Query: 146 SKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEE 184
            K++AWNSLG+M++ EAMS YI  +K V     D     
Sbjct: 64  YKWDAWNSLGKMSREEAMSAYITEMKLVAQKVIDTVPLG 102

>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 = 88.9 bits (221), Expect = 3e-22
 Identities = 29/84 (34%), Positives = 47/84 (55%), Gaps = 4/84 (4%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+F+G +P  +   +LK  F E+G+I   +V+ D+ TG+ KG  F+T+  +E+  K  S 
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74

Query: 70 --DSHVLEGSRLSIQ--PSDSHNR 89
            +   L G    IQ  P+DS +R
Sbjct: 75 LHEQKTLPGMNRPIQVKPADSESR 98

>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 = 88.8 bits (221), Expect = 3e-22
 Identities = 29/77 (37%), Positives = 39/77 (50%), Gaps = 1/77 (1%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
           ++FV NL +T S  +L+K FS YG +       D  T   KGF FVTF   E   K ++
Sbjct: 9  GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 69 T-DSHVLEGSRLSIQPS 84
            D  V +G  L + PS
Sbjct: 69 EVDGQVFQGRMLHVLPS 85

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 88.4 bits (220), Expect = 4e-22
 Identities = 20/57 (35%), Positives = 41/57 (71%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          + ++V NLP+++++N+L + FS+YG+++  ++M DK+T  SKG  F+ F +K++   
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73

>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 = 87.9 bits (219), Expect = 4e-22
 Identities = 18/57 (31%), Positives = 32/57 (56%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
            +FVG+L   V    L+  F ++   ++  VM+D  TG S+G+GFV+F +++    
Sbjct: 2  FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 58

>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 = 90.3 bits (225), Expect = 5e-22
 Identities = 20/69 (28%), Positives = 41/69 (59%), Gaps = 1/69 (1%)

Query: 10  KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
            ++V  LP T++  EL++ FS+YG+I+ + ++ D+ TG+S+G GF+ F  +   ++    
Sbjct: 90  NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 149

Query: 70  -DSHVLEGS 77
            +     G+
Sbjct: 150 LNGQKPSGA 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 = 80.3 bits (199), Expect = 2e-18
 Identities = 19/81 (23%), Positives = 39/81 (48%), Gaps = 1/81 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           + V  LP  ++  E +  F   G+I +  ++ DK TG S G+GFV + + +  +K  +T
Sbjct: 4  NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 70 -DSHVLEGSRLSIQPSDSHNR 89
           +   L+   + +  +   + 
Sbjct: 64 LNGLRLQTKTIKVSYARPSSA 84

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 89.4 bits (222), Expect = 5e-22
 Identities = 27/92 (29%), Positives = 48/92 (52%), Gaps = 7/92 (7%)

Query: 4   SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAV 63
            +  +  + V NL +  S + L++ F +YG++ +  +  D+ T  S+GF FV F +K   
Sbjct: 43  DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 102

Query: 64  DK-VFSTDSHVLEGSRLSIQ------PSDSHN 88
           +  + + D  VL+G  L +Q      P DSH+
Sbjct: 103 EDAMDAMDGAVLDGRELRVQMARYGRPPDSHH 134

>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 = 87.2 bits (217), Expect = 8e-22
 Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 1/71 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           +++  L    +  +L K    YG+I++   + DK T   KG+GFV F +  A  K  + 
Sbjct: 7  GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66

Query: 70 -DSHVLEGSRL 79
            +  ++    
Sbjct: 67 LKASGVQAQMA 77

>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 = 86.9 bits (216), Expect = 1e-21
 Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 9/84 (10%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          + +FVG     ++ +EL++FFS+YG +M+  +         + F FVTF + +    +  
Sbjct: 6  SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG 60

Query: 69 TDSHVLEGSRLSI---QPSDSHNR 89
           D  +++G  + I   +P  + N 
Sbjct: 61 ED-LIIKGISVHISNAEPKHNSNS 83

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 86.5 bits (215), Expect = 2e-21
 Identities = 20/57 (35%), Positives = 37/57 (64%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          + ++VG+L + ++ + L+  F  +G+I N  +M D +TG SKG+GF+TF + E   +
Sbjct: 6  SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62

>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 = 86.2 bits (214), Expect = 3e-21
 Identities = 22/60 (36%), Positives = 38/60 (63%)

Query: 6  RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          R L  +FVGN+P+  +  +LK  FSE G +++  +++D+ TG  KG+GF  +Q++E    
Sbjct: 6  RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65

>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 = 85.7 bits (213), Expect = 3e-21
 Identities = 21/56 (37%), Positives = 34/56 (60%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           +FVG+L   ++   +   F+ +G+I +A V+ D  TG SKG+GFV+F NK   + 
Sbjct: 8  HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 63

>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 = 85.7 bits (213), Expect = 4e-21
 Identities = 17/57 (29%), Positives = 33/57 (57%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
            + V  L    +  +L++ FS+YG I + S+++D+ +  S+GF FV F+N +   +
Sbjct: 16 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKE 72

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 85.8 bits (213), Expect = 4e-21
 Identities = 16/79 (20%), Positives = 42/79 (53%), Gaps = 2/79 (2%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK-VF 67
          +K+F+  LP++ +  EL++    +G + +  ++ ++  G  KG  +V ++N+    + V 
Sbjct: 18 HKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVM 76

Query: 68 STDSHVLEGSRLSIQPSDS 86
            D   ++ + + +  S+S
Sbjct: 77 KMDGMTIKENIIKVAISNS 95

>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 = 88.5 bits (220), Expect = 5e-21
 Identities = 19/75 (25%), Positives = 42/75 (56%), Gaps = 1/75 (1%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
           +K+F+G LP  ++ +++K+  + +G +   +++ D  TGLSKG+ F  + +    D+  +
Sbjct: 115 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 174

Query: 69  T-DSHVLEGSRLSIQ 82
             +   L   +L +Q
Sbjct: 175 GLNGMQLGDKKLLVQ 189

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 80.8 bits (200), Expect = 2e-18
 Identities = 16/110 (14%), Positives = 44/110 (40%), Gaps = 5/110 (4%)

Query: 7   QLNKIFVGNLPWTVSHNELKKFFSEYGQIMN-----ASVMFDKNTGLSKGFGFVTFQNKE 61
              +++VGN+P+ ++   +  FF+   ++        + +        K F F+ F++ +
Sbjct: 3   MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 62

Query: 62  AVDKVFSTDSHVLEGSRLSIQPSDSHNRMAENMEDRFNQACDYLPSLVKK 111
              +  + D  + +G  L I+    +  +    E+        + ++V  
Sbjct: 63  ETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPD 112

>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 = 87.7 bits (218), Expect = 5e-21
 Identities = 22/91 (24%), Positives = 42/91 (46%), Gaps = 3/91 (3%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
             +F+GNL    S  ELK   SE     + +V+ D  TG ++ FG+V F++ E ++K   
Sbjct: 14  FNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKALE 72

Query: 69  TDSHVLEGSRLSIQPSDSHNRMAENMEDRFN 99
                + G+ + ++      R ++ +     
Sbjct: 73  LTGLKVFGNEIKLEKPKG--RDSKKVRAART 101

>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 = 75.7 bits (187), Expect = 1e-16
 Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 6/77 (7%)

Query: 6   RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           R    +   NL + ++ +ELK+ F +  +I           G SKG  ++ F+++   +K
Sbjct: 97  RAARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEK 151

Query: 66  VFST-DSHVLEGSRLSI 81
                    ++G  +S+
Sbjct: 152 NLEEKQGAEIDGRSVSL 168

>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 = 84.9 bits (211), Expect = 6e-21
 Identities = 21/72 (29%), Positives = 42/72 (58%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           I+VGNL ++ +  ++K+ FS++G++ N  +++D+ T   KGFGFV  Q +   + +   
Sbjct: 3  NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKL 62

Query: 70 DSHVLEGSRLSI 81
          D+    G  + +
Sbjct: 63 DNTDFMGRTIRV 74

>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 = 87.2 bits (217), Expect = 6e-21
 Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 1/70 (1%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
             ++V NLP T++ ++L   F +YG I+  +++ DK TG  +G  FV +  +E   +  S
Sbjct: 90  TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149

Query: 69  T-DSHVLEGS 77
             ++ + EG 
Sbjct: 150 ALNNVIPEGG 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 = 80.3 bits (199), Expect = 2e-18
 Identities = 19/81 (23%), Positives = 31/81 (38%), Gaps = 1/81 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           + V  LP  ++  EL   F   G I    +M D  TG S G+ FV F ++    +    
Sbjct: 5  NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64

Query: 70 -DSHVLEGSRLSIQPSDSHNR 89
           +   +   RL +  +     
Sbjct: 65 LNGITVRNKRLKVSYARPGGE 85

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 86.3 bits (214), Expect = 6e-21
 Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
             + V  L    +  +L++ FS+YG I + S+++D+ +  S+GF FV F+N +   +   
Sbjct: 47  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 106

Query: 69  T-DSHVLEGSRLSIQ 82
             +   L+G R+ + 
Sbjct: 107 RANGMELDGRRIRVD 121

>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 = 86.3 bits (214), Expect = 6e-21
 Identities = 18/57 (31%), Positives = 32/57 (56%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
            + V  +P TV   +L++ F  YG I +  ++ D+ T  S+G+GFV FQ+  +  +
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQ 99

>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 = 85.5 bits (212), Expect = 7e-21
 Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 2/69 (2%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
           K+F+G L    +   LK  F ++G I    ++ D+ T  S+GF F+TF+N         
Sbjct: 8  GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAK 66

Query: 69 T-DSHVLEG 76
            +   L G
Sbjct: 67 DMNGKSLHG 75

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 85.4 bits (212), Expect = 8e-21
 Identities = 23/93 (24%), Positives = 44/93 (47%), Gaps = 9/93 (9%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK-VF 67
           + +FV NL + V   +LK+ FS  G ++ A ++ DK+ G S+G G VTF+      + + 
Sbjct: 16  STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAIS 74

Query: 68  STDSHVLEGSRLSIQPSDSHNRMAENMEDRFNQ 100
             +  +L    + +       +M E    + + 
Sbjct: 75  MFNGQLLFDRPMHV-------KMDERALPKGDF 100

>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 = 85.1 bits (211), Expect = 9e-21
 Identities = 22/56 (39%), Positives = 36/56 (64%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           +FVG+L   ++  ++K  F+ +G+I +A V+ D  TG SKG+GFV+F NK   + 
Sbjct: 17 HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 72

>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 = 84.2 bits (209), Expect = 1e-20
 Identities = 16/57 (28%), Positives = 23/57 (40%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
            ++VG L   V    L   F  +G I +  +  D  T   +GF FV F+  E    
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 69

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 84.7 bits (210), Expect = 1e-20
 Identities = 20/56 (35%), Positives = 32/56 (57%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           +F+ +LP   +  +L   F  +G +++A V  DK T LSK FGFV+F N ++   
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQV 97

>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 = 83.7 bits (208), Expect = 2e-20
 Identities = 18/65 (27%), Positives = 27/65 (41%), Gaps = 3/65 (4%)

Query: 1  MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
          M+ + R    ++VG L   V    L   F  +G I +  +  D  T   +GF FV F+  
Sbjct: 3  MATTKR---VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 59

Query: 61 EAVDK 65
          E    
Sbjct: 60 EDAAA 64

>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 = 84.2 bits (209), Expect = 2e-20
 Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 4  SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK-EA 62
           +  +  + V NL +  S + L++ F +YG++ +  +  + +T   +GF FV F ++ +A
Sbjct: 9  DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDA 68

Query: 63 VDKVFSTDSHVLEGSRLSIQ 82
           D   + D   L+G  L +Q
Sbjct: 69 QDAEAAMDGAELDGRELRVQ 88

>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 = 83.0 bits (206), Expect = 3e-20
 Identities = 18/76 (23%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 6  RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
             +K+FVG     ++  EL++FF +YG++++  +         + F FVTF + +    
Sbjct: 9  HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS 63

Query: 66 VFSTDSHVLEGSRLSI 81
          +   D  +++G  + I
Sbjct: 64 LCGED-LIIKGISVHI 78

>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 = 83.9 bits (208), Expect = 3e-20
 Identities = 19/57 (33%), Positives = 31/57 (54%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
            +F+ +LP      +L + F  +G +++A V  DK T LSK FGFV++ N  +   
Sbjct: 26 ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQA 82

>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 = 83.4 bits (207), Expect = 3e-20
 Identities = 19/57 (33%), Positives = 28/57 (49%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
            I V NL       +L++ F  +G I    +  DK TG SKGF F++F  +E   +
Sbjct: 16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 72

>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 = 85.3 bits (212), Expect = 3e-20
 Identities = 18/56 (32%), Positives = 32/56 (57%)

Query: 10  KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
            +FVG+L   V    L+  F ++   ++  VM+D  TG S+G+GFV+F +++    
Sbjct: 89  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 144

>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 = 69.1 bits (170), Expect = 2e-14
 Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          ++VGNL   ++ + LK++F   G I N  +M DK    +  + FV +      +    T
Sbjct: 3  LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQT 60

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 83.2 bits (206), Expect = 4e-20
 Identities = 13/90 (14%), Positives = 27/90 (30%), Gaps = 4/90 (4%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
           ++    L   V    LK    +YG++    ++    T    G   V F +     +   
Sbjct: 7  KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 69 T-DSHVLEGSRLSIQ---PSDSHNRMAENM 94
                + G+ +  Q         +  E +
Sbjct: 67 NLHLTSVMGNIIHAQLDIKGQQRMKYYELI 96

>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 = 84.9 bits (210), Expect = 5e-20
 Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 1/80 (1%)

Query: 4   SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAV 63
            +  +  + V NL +  S + L++ F +YG++ +  +  D+ T  S+GF FV F +K   
Sbjct: 66  DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 125

Query: 64  DK-VFSTDSHVLEGSRLSIQ 82
           +  + + D  VL+G  L +Q
Sbjct: 126 EDAMDAMDGAVLDGRELRVQ 145

>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 = 82.7 bits (205), Expect = 6e-20
 Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 4/80 (5%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTG---LSKGFGFVTFQNKEAVDK 65
          + +F+ NL ++ +   LK  FS+ G I + ++   KN     LS GFGFV ++  E   K
Sbjct: 6  SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 66 VFST-DSHVLEGSRLSIQPS 84
                 H ++G +L ++ S
Sbjct: 66 ALKQLQGHTVDGHKLEVRIS 85

>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 = 82.7 bits (205), Expect = 6e-20
 Identities = 20/56 (35%), Positives = 36/56 (64%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          +++VG+L + ++ + L+  F  +G+I +  +M D  TG SKG+GF+TF + E   K
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKK 83

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 84.2 bits (208), Expect = 7e-20
 Identities = 18/95 (18%), Positives = 40/95 (42%), Gaps = 3/95 (3%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYG--QIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
             ++VG+  W  +  +L +     G   ++      ++  G SKG+  V   ++ +V K+
Sbjct: 56  AAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKL 115

Query: 67  FST-DSHVLEGSRLSIQPSDSHNRMAENMEDRFNQ 100
                  VL G ++ ++P+   N      + R  +
Sbjct: 116 LELLPGKVLNGEKVDVRPATRQNLSQFEAQARKRE 150

>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 = 81.9 bits (203), Expect = 9e-20
 Identities = 16/56 (28%), Positives = 33/56 (58%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           +++G++P+  +  ++    S  G ++N  +MFD  TG SKG+ F+ F++ E+   
Sbjct: 4  VVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 59

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 82.9 bits (205), Expect = 1e-19
 Identities = 16/57 (28%), Positives = 23/57 (40%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
             ++VG L   V    L   F  +G I +  +  D  T   +GF FV F+  E    
Sbjct: 64  RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 120

>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 = 81.6 bits (202), Expect = 2e-19
 Identities = 19/57 (33%), Positives = 37/57 (64%), Gaps = 2/57 (3%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           ++ V N+P+     +L++ F ++G+I++  ++F++    SKGFGFVTF+N    D+
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADR 70

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 80.8 bits (200), Expect = 3e-19
 Identities = 19/57 (33%), Positives = 37/57 (64%), Gaps = 2/57 (3%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           ++ V N+P+     +L++ F ++G+I++  ++F++    SKGFGFVTF+N    D+
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADR 84

>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 = 80.3 bits (199), Expect = 3e-19
 Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKN-TGLSKGFGFVTFQNKEAVDK 65
           K+ +G L   V+ + + + FS YG+I    +  ++    LSKG+ +V F+N +  +K
Sbjct: 5  TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEK 62

>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 = 84.7 bits (210), Expect = 4e-19
 Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 1/61 (1%)

Query: 6   RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
                + V NL   VS+  L++ FS++G +  A V+ D + G + G GFV F  K    K
Sbjct: 94  THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARK 152

Query: 66  V 66
            
Sbjct: 153 A 153

>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 = 70.1 bits (172), Expect = 6e-14
 Identities = 20/76 (26%), Positives = 37/76 (48%), Gaps = 7/76 (9%)

Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
          Q  ++FVGNLP  ++  + K+ F  YG+     +  D      +GFGF+  +++   +  
Sbjct: 21 QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIA 74

Query: 67 FST-DSHVLEGSRLSI 81
           +  D  +L+   L I
Sbjct: 75 KAELDGTILKSRPLRI 90

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 80.0 bits (198), Expect = 5e-19
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           +F+GNL    S  ELK   SE     + +V+ D  TG ++ FG+V F++ E ++K    
Sbjct: 19 NLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLEKALEL 77

Query: 70 DSHVLEGSRLSIQPS 84
              + G+ + ++  
Sbjct: 78 TGLKVFGNEIKLEKP 92

>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 = 82.3 bits (204), Expect = 5e-19
 Identities = 30/90 (33%), Positives = 47/90 (52%), Gaps = 6/90 (6%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGL--SKGFGFVTFQNKEAVDKVF 67
          K+FVG +P T S  +L++ F +YG +   +V+ D++     SKG  FVTF  ++A  +  
Sbjct: 5  KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64

Query: 68 ST--DSHVLEGSRLSIQ--PSDSHNRMAEN 93
          +   +  VL G    IQ  P+DS    A  
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEKNNAVE 94

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 80.7 bits (200), Expect = 2e-18
 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 3/70 (4%)

Query: 10  KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           K+F+G +    + N+++  FS +GQI    ++     GLS+G  FVTF  +         
Sbjct: 97  KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKA 155

Query: 70  --DSHVLEGS 77
              +  +EG 
Sbjct: 156 MHQAQTMEGC 165

>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 = 80.0 bits (198), Expect = 7e-19
 Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 3/81 (3%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDK-NTGLSKGFGFVTFQNKEAVDKVF 67
          +KI V N+P+  +  E+++ FS +G++    +      TG  +GFGFV F  K+   K F
Sbjct: 16 SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75

Query: 68 S--TDSHVLEGSRLSIQPSDS 86
          +    S  L G RL ++ +DS
Sbjct: 76 NALCHSTHLYGRRLVLEWADS 96

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 79.6 bits (197), Expect = 7e-19
 Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
             +VGNLP+     ++   F +   I +  ++ DK+T   KGF +V F   +++ +  +
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 74

Query: 69 TDSHVLEGSRLSI 81
           D  +L    L +
Sbjct: 75 YDGALLGDRSLRV 87

>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 = 79.6 bits (197), Expect = 7e-19
 Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 1/57 (1%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           K+ V NL + VS  ++++ F+E+G +  A+V +D+ +G S G   V F+ K    K
Sbjct: 30 GKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALK 85

>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 = 80.1 bits (198), Expect = 1e-18
 Identities = 14/57 (24%), Positives = 27/57 (47%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
            +FV  +    +  ++   F+EYG+I N  +  D+ TG  KG+  V ++  +    
Sbjct: 23 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQA 79

>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 = 79.2 bits (196), Expect = 1e-18
 Identities = 20/59 (33%), Positives = 32/59 (54%)

Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          Q   ++VG L   VS   L + F + G ++N  +  D+ TG  +G+GFV F ++E  D 
Sbjct: 14 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72

>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 = 78.8 bits (195), Expect = 2e-18
 Identities = 24/59 (40%), Positives = 33/59 (55%), Gaps = 2/59 (3%)

Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          Q+  ++V NL   +    L+K FS +G I +A VM +   G SKGFGFV F + E   K
Sbjct: 14 QVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATK 70

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 78.8 bits (195), Expect = 2e-18
 Identities = 14/54 (25%), Positives = 27/54 (50%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
            +FV  +    +  ++   F+EYG+I N  +  D+ TG  KG+  V ++  + 
Sbjct: 24 WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 77

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 78.8 bits (195), Expect = 2e-18
 Identities = 14/56 (25%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           +++ NLP ++   EL+     +GQ+++  ++ D  +G S+G GF   ++ E  + 
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEA 81

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 78.4 bits (194), Expect = 2e-18
 Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 2/57 (3%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           +IFV NLP+  +   LK  F+E G ++ A +  +   G SKG G V F++ E  ++
Sbjct: 9  CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAER 63

>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 = 78.0 bits (193), Expect = 2e-18
 Identities = 25/90 (27%), Positives = 44/90 (48%), Gaps = 9/90 (10%)

Query: 1  MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
            +S +   K+ VGN+  T ++ EL+  F EYG ++   ++        K + FV  +  
Sbjct: 3  SGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERA 54

Query: 61 E-AVDKVFSTDSHVLEGSRLSIQPSDSHNR 89
          E AV+ +   D+   +G R+ +Q S S  R
Sbjct: 55 EDAVEAIRGLDNTEFQGKRMHVQLSTSRLR 84

>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 = 79.0 bits (195), Expect = 2e-18
 Identities = 18/57 (31%), Positives = 33/57 (57%), Gaps = 1/57 (1%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           K+ V NL + VS  ++++ F+E+G +  A+V +D+ +G S G   V F+ +    K
Sbjct: 36 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALK 91

>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 = 77.7 bits (192), Expect = 3e-18
 Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 6  RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
               +FVGNL   V    L + F + G +   ++  D+  G  K FGFV F++ E+V  
Sbjct: 14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSY 72

>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 = 77.6 bits (192), Expect = 3e-18
 Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMN-ASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           IF+GNL   +    L   FS +G I+    +M D +TG SKG+ F+ F + +A D 
Sbjct: 7  GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63

>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 = 82.3 bits (204), Expect = 4e-18
 Identities = 18/90 (20%), Positives = 40/90 (44%), Gaps = 1/90 (1%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
             + V NLP +++  + ++    +G +    +++ + TG SKG+GF  +  K++  +  S
Sbjct: 96  ALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKS 155

Query: 69  T-DSHVLEGSRLSIQPSDSHNRMAENMEDR 97
                 L    L +  +D+       +  R
Sbjct: 156 DLLGKPLGPRTLYVHWTDAGQLTPALLHSR 185

>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 = 72.7 bits (179), Expect = 8e-15
 Identities = 15/80 (18%), Positives = 29/80 (36%), Gaps = 3/80 (3%)

Query: 2   SNSIRQLNKIFVGNLPWTVSHNE-LKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
           + ++     + V  LP   +  + L +  S         +   +  G  KGF  + ++  
Sbjct: 178 TPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETA 236

Query: 61  EAVDK-VFSTDSHVLEGSRL 79
           E  ++     D   L GS L
Sbjct: 237 EMAEEAQQQADGLSLGGSHL 256

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 62.7 bits (153), Expect = 2e-11
 Identities = 20/86 (23%), Positives = 31/86 (36%), Gaps = 8/86 (9%)

Query: 6  RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          R   KI +  LP  V++ E+    S+Y        +        KG  FVT  N E  + 
Sbjct: 20 RNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEA 72

Query: 66 VFST-DSHVLEGSRLSIQPSDSHNRM 90
            +      L    LS+Q   +   +
Sbjct: 73 AINAFHQSRLRERELSVQLQPTDALL 98

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 77.3 bits (191), Expect = 5e-18
 Identities = 18/87 (20%), Positives = 30/87 (34%), Gaps = 9/87 (10%)

Query: 6  RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNAS--------VMFDKNTGLSKGFGFVTF 57
             N IFV  L   V+   +  +F + G I            +  D+ TG  KG   V+F
Sbjct: 11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 70

Query: 58 QNKEAVDKVFST-DSHVLEGSRLSIQP 83
           +  +        D     G+ + +  
Sbjct: 71 DDPPSAKAAIDWFDGKEFSGNPIKVSF 97

>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 = 76.9 bits (190), Expect = 5e-18
 Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 2/58 (3%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYG--QIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           +++GNL W  +  +L +     G   I+      ++  G SKGF  V   ++ +  K
Sbjct: 3  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKK 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 = 80.9 bits (199), Expect = 6e-18
 Identities = 19/96 (19%), Positives = 35/96 (36%), Gaps = 3/96 (3%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYG--QIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
             +++GNL W  +  +L +     G   I+      ++  G SKGF  V   ++ +  K+
Sbjct: 69  IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKL 128

Query: 67  FST-DSHVLEGSRLSIQPSDSHNRMAENMEDRFNQA 101
                   L G    + P +        M+ R    
Sbjct: 129 MDLLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQ 164

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 77.3 bits (191), Expect = 6e-18
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 6/76 (7%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFS 68
          K++VGNL       EL++ FS YG +    +  +       GF FV F++ ++A D V  
Sbjct: 2  KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56

Query: 69 TDSHVLEGSRLSIQPS 84
           D  V+ GSR+ ++ S
Sbjct: 57 LDGKVICGSRVRVELS 72

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 79.5 bits (196), Expect = 6e-18
 Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 9/93 (9%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
            K+ V NL + VS  ++++ F+E+G +  A+V +D+ +G S G   V F+ +    K   
Sbjct: 89  AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMK 147

Query: 69  T-DSHVLEGSRLSIQPSDSHNRMAENMEDRFNQ 100
                 L+G  + IQ       +  +  D  + 
Sbjct: 148 QYKGVPLDGRPMDIQ-------LVASQIDLEHH 173

>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 = 76.9 bits (190), Expect = 1e-17
 Identities = 15/56 (26%), Positives = 30/56 (53%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           +FV ++      +E+++ F +YG+I N  +  D+ TG SKG+  V ++  +    
Sbjct: 28 ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 83

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 76.1 bits (188), Expect = 1e-17
 Identities = 21/89 (23%), Positives = 47/89 (52%), Gaps = 9/89 (10%)

Query: 2  SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          S+    + K+F+GNLP   +  E++  F +YG+++   ++        K +GFV  ++K 
Sbjct: 2  SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKT 53

Query: 62 -AVDKVFSTDSHVLEGSRLSIQPSDSHNR 89
           A D + +   + L G  ++++ S + ++
Sbjct: 54 AAEDAIRNLHHYKLHGVNINVEASKNKSK 82

>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 = 76.9 bits (190), Expect = 1e-17
 Identities = 25/109 (22%), Positives = 51/109 (46%), Gaps = 6/109 (5%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK-VF 67
             IF+ NL  ++ +  L   FS +G I++  V+ D+N   SKG+GFV F+ +EA ++ + 
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIE 63

Query: 68  STDSHVLEGSRLSIQPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSST 116
             +  +L   ++ +          E   +   +A ++    +K     +
Sbjct: 64  KMNGMLLNDRKVFVGR---FKSRKEREAELGARAKEFTNVYIKNFGPGS 109

>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 = 75.7 bits (187), Expect = 1e-17
 Identities = 20/89 (22%), Positives = 39/89 (43%), Gaps = 9/89 (10%)

Query: 2  SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          S S     KIFVGN+    +  EL+  F   G+++   V+        K + FV  + + 
Sbjct: 3  SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEA 54

Query: 62 -AVDKVFSTDSHVLEGSRLSIQPSDSHNR 89
           A   +   +   ++G R++++ S    +
Sbjct: 55 DAKAAIAQLNGKEVKGKRINVELSTKGQK 83

>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 = 75.4 bits (186), Expect = 3e-17
 Identities = 21/85 (24%), Positives = 39/85 (45%), Gaps = 4/85 (4%)

Query: 1  MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
             +     +I+VGNLP  +   +++  F +YG I +  +   +       F FV F++ 
Sbjct: 15 RGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG---GPPFAFVEFEDP 71

Query: 61 E-AVDKVFSTDSHVLEGSRLSIQPS 84
            A D V+  D +  +G RL ++  
Sbjct: 72 RDAEDAVYGRDGYDYDGYRLRVEFP 96

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 75.8 bits (187), Expect = 3e-17
 Identities = 15/54 (27%), Positives = 26/54 (48%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
            +++ NL   V+  +L   F+ + +     + F   TG  +G  F+TF NKE 
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEI 79

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 75.4 bits (185), Expect = 4e-17
 Identities = 16/86 (18%), Positives = 34/86 (39%), Gaps = 2/86 (2%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDK--NTGLSKGFGFVTFQNKEAVDKV 66
           K+FVG LP  +  +E+   F  +G ++       +  +    KG+ F+ FQ + +V  +
Sbjct: 9  RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68

Query: 67 FSTDSHVLEGSRLSIQPSDSHNRMAE 92
                      L +      ++  +
Sbjct: 69 IDACLEEDGKLYLCVSSPTIKDKPVQ 94

>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 = 74.6 bits (184), Expect = 4e-17
 Identities = 12/57 (21%), Positives = 27/57 (47%), Gaps = 5/57 (8%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
            +   NL + ++ +ELK+ F +  +     +      G SKG  ++ F+++   +K
Sbjct: 17 RTLLAKNLSFNITEDELKEVFEDALE-----IRLVSQDGKSKGIAYIEFKSEADAEK 68

>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 = 75.0 bits (185), Expect = 4e-17
 Identities = 20/76 (26%), Positives = 32/76 (42%), Gaps = 3/76 (3%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
           K+FVG L    S  ++ + F  +G I   +V+   + G SKG  FV F +         
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD-GSSKGCAFVKFSSHTEAQAAIH 74

Query: 69 T--DSHVLEGSRLSIQ 82
              S  + G+  S+ 
Sbjct: 75 ALHGSQTMPGASSSLV 90

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 74.3 bits (183), Expect = 5e-17
 Identities = 12/61 (19%), Positives = 25/61 (40%), Gaps = 2/61 (3%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQ--IMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
          + I + N+      + +    S Y    + N  ++ DK T  ++GF FV   +     ++
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 67 F 67
           
Sbjct: 70 L 70

>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 = 75.1 bits (185), Expect = 5e-17
 Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 8/68 (11%)

Query: 6  RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMN--------ASVMFDKNTGLSKGFGFVTF 57
             + I+V  L  +V+ ++L  FF + G +            +  DK TG  KG   V++
Sbjct: 13 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSY 72

Query: 58 QNKEAVDK 65
          ++      
Sbjct: 73 EDPPTAKA 80

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 75.1 bits (185), Expect = 5e-17
 Identities = 16/65 (24%), Positives = 25/65 (38%), Gaps = 8/65 (12%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNAS--------VMFDKNTGLSKGFGFVTFQNK 60
          N IFV  L   V+   +  +F + G I            +  D+ TG  KG   V+F + 
Sbjct: 8  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67

Query: 61 EAVDK 65
           +   
Sbjct: 68 PSAKA 72

>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 = 74.6 bits (184), Expect = 6e-17
 Identities = 18/73 (24%), Positives = 35/73 (47%), Gaps = 2/73 (2%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKN-TGLSKGFGFVTFQNKEAVDKVFS 68
            F+GNLP+ V+   +K+FF     I    +  + +     KGFG+  F++ +++    S
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 69 TDSHVLEGSRLSI 81
           +   L   R+ +
Sbjct: 76 LNEESLGNKRIRV 88

>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 = 74.2 bits (183), Expect = 7e-17
 Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 2/78 (2%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNT-GLSKGFGFVTFQNKEAVDKVFS 68
            F+GNLP+ V+   +K+FF     I    +  + +     KGFG+  F++ +++    S
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79

Query: 69 TDSHVLEGSRLSIQPSDS 86
           +   L   R+ +  +D 
Sbjct: 80 LNEESLGNRRIRVDVADQ 97

>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 = 74.4 bits (183), Expect = 7e-17
 Identities = 16/89 (17%), Positives = 33/89 (37%), Gaps = 1/89 (1%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
               + N+P++++  ++ +F        NA  +   N G   G   V F+N++   K   
Sbjct: 16  VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER 75

Query: 69  TDSHVLEGSRLSIQPSDSHNRMAENMEDR 97
                L G    +    +   M E  ++ 
Sbjct: 76  LHRKKLNGREAFVHVV-TLEDMREIEKNP 103

>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 = 75.6 bits (186), Expect = 9e-17
 Identities = 15/57 (26%), Positives = 30/57 (52%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
             +FV ++      +E+++ F +YG+I N  +  D+ TG SKG+  V ++  +    
Sbjct: 73  WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALA 129

>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 = 73.9 bits (182), Expect = 1e-16
 Identities = 12/57 (21%), Positives = 25/57 (43%), Gaps = 4/57 (7%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
            + + NL ++ +   L++ F +   I     +     G SKG+ F+ F + E   +
Sbjct: 16 KTLVLSNLSYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEFASFEDAKE 68

>3ehr_A Osteoclast-stimulating factor 1; beta barrel, helix-turn-helix, SH3, ankyrin repeat, signaling protein, ANK repeat, cytoplasm, phosphoprotein; 1.95A {Homo sapiens} PDB: 3ehq_A Length = 222

 Score = 76.9 bits (190), Expect = 1e-16
 Identities = 25/102 (24%), Positives = 43/102 (42%), Gaps = 8/102 (7%)

Query: 251 LDDNEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKV 304
               E+           AK G L   +++        +N LD+ G   L+WAC  GH  +
Sbjct: 64  NYVAEQAESIDNPLHEAAKRGNLSW-LRECLD-NRVGVNGLDKAGSTALYWACHGGHKDI 121

Query: 305 VQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           V+ L  +   ++N  +  GD  L  A    + D+++ L+  G
Sbjct: 122 VEMLFTQPNIELNQQNKLGDTALHAAAWKGYADIVQLLLAKG 163

>3ehr_A Osteoclast-stimulating factor 1; beta barrel, helix-turn-helix, SH3, ankyrin repeat, signaling protein, ANK repeat, cytoplasm, phosphoprotein; 1.95A {Homo sapiens} PDB: 3ehq_A Length = 222

 Score = 72.3 bits (178), Expect = 4e-15
 Identities = 21/99 (21%), Positives = 39/99 (39%), Gaps = 8/99 (8%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N  +             G  D+ V+ L    +  +NQ ++ G   LH A  +G+  +VQ 
Sbjct: 100 NGLDKAGSTALYWACHGGHKDI-VEMLFTQPNIELNQQNKLGDTALHAAAWKGYADIVQL 158

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L+ K GA  ++ + +     D A       L++    + 
Sbjct: 159 LLAK-GARTDLRNIEKKLAFDMATNAACASLLKKKQGTD 196

>3ehr_A Osteoclast-stimulating factor 1; beta barrel, helix-turn-helix, SH3, ankyrin repeat, signaling protein, ANK repeat, cytoplasm, phosphoprotein; 1.95A {Homo sapiens} PDB: 3ehq_A Length = 222

 Score = 62.3 bits (152), Expect = 1e-11
 Identities = 20/99 (20%), Positives = 35/99 (35%), Gaps = 14/99 (14%)

Query: 252 DDNEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVV 305
           D                 +G+  ++           + +  E+  N LH A  RG+L  +
Sbjct: 37  DIIYITDMSDTNWWKGTSKGRTGLI-------PSNYVAEQAESIDNPLHEAAKRGNLSWL 89

Query: 306 QHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVN 344
           +  ++     VN  D  G   L +A    H D++E L  
Sbjct: 90  RECLDN-RVGVNGLDKAGSTALYWACHGGHKDIVEMLFT 127

>3ehr_A Osteoclast-stimulating factor 1; beta barrel, helix-turn-helix, SH3, ankyrin repeat, signaling protein, ANK repeat, cytoplasm, phosphoprotein; 1.95A {Homo sapiens} PDB: 3ehq_A Length = 222

 Score = 53.8 bits (130), Expect = 1e-08
 Identities = 10/83 (12%), Positives = 28/83 (33%), Gaps = 9/83 (10%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N++N          A +G  D+ V+ L   K    +  +         A +     +++ 
Sbjct: 134 NQQNKLGDTALHAAAWKGYADI-VQLLLA-KGARTDLRNIEKKLAFDMATNAACASLLKK 191

Query: 308 LIEKCGADVNVTDSDGDYGLDYA 330
                 A   +++++     + +
Sbjct: 192 KQGT-DAVRTLSNAEDYLDDEDS 213

>3ehr_A Osteoclast-stimulating factor 1; beta barrel, helix-turn-helix, SH3, ankyrin repeat, signaling protein, ANK repeat, cytoplasm, phosphoprotein; 1.95A {Homo sapiens} PDB: 3ehq_A Length = 222

 Score = 50.3 bits (121), Expect = 2e-07
 Identities = 8/62 (12%), Positives = 15/62 (24%), Gaps = 1/62 (1%)

Query: 283 NQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYL 342
            +  + G   +  A      +    L  +   D+       D       +   T LI   
Sbjct: 6   PKPVKPGQVKVFRALYTFEPRTPDELYIE-EGDIIYITDMSDTNWWKGTSKGRTGLIPSN 64

Query: 343 VN 344
             
Sbjct: 65  YV 66

>3ehr_A Osteoclast-stimulating factor 1; beta barrel, helix-turn-helix, SH3, ankyrin repeat, signaling protein, ANK repeat, cytoplasm, phosphoprotein; 1.95A {Homo sapiens} PDB: 3ehq_A Length = 222

 Score = 46.9 bits (112), Expect = 3e-06
 Identities = 6/66 (9%), Positives = 17/66 (25%), Gaps = 6/66 (9%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           +I  + +           +G   ++          V       D  L  A    +   + 
Sbjct: 37  DIIYITDMSDTNWWKGTSKGRTGLIP------SNYVAEQAESIDNPLHEAAKRGNLSWLR 90

Query: 341 YLVNSG 346
             +++ 
Sbjct: 91  ECLDNR 96

>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 = 73.4 bits (181), Expect = 1e-16
 Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 3/57 (5%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
            +FV  L    +   LK+ F        A ++ D+ TG SKGFGFV F ++E    
Sbjct: 16 KTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKA 69

>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 = 76.9 bits (190), Expect = 3e-16
 Identities = 12/109 (11%), Positives = 35/109 (32%), Gaps = 5/109 (4%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK-VF 67
             +++ N P + +   ++    +   +  +  +       S+ F ++   +KE     V 
Sbjct: 118 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 177

Query: 68  STDSHVLEGSRLSIQPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSST 116
             +   +EG  L  + S+   +                   ++ L +  
Sbjct: 178 KLNGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIM----IRNLSTEL 222

>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 = 76.9 bits (190), Expect = 3e-16
 Identities = 15/83 (18%), Positives = 32/83 (38%), Gaps = 2/83 (2%)

Query: 6   RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
           R+L  + V NLP + + N++ K+F   G I++  V        +  F  + F   +    
Sbjct: 39  RELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALA 96

Query: 66  VFSTDSHVLEGSRLSIQPSDSHN 88
             +    V+  + + +       
Sbjct: 97  AITKTHKVVGQNEIIVSHLTECT 119

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 75.8 bits (187), Expect = 9e-16
 Identities = 16/82 (19%), Positives = 37/82 (45%), Gaps = 2/82 (2%)

Query: 7   QLNKIFVGNLPWTVSH-NELKKFFSEYGQIMNASVMFD-KNTGLSKGFGFVTFQNKEAVD 64
           +  +I + NL   +   N L++ F  +G I   ++    K    +    F+ F+NK++ +
Sbjct: 209 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 268

Query: 65  KVFSTDSHVLEGSRLSIQPSDS 86
           +    +  +L    +S+  +D 
Sbjct: 269 RALQMNRSLLGNREISVSLADK 290

>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 = 74.1 bits (182), Expect = 3e-16
 Identities = 14/57 (24%), Positives = 28/57 (49%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
            ++VGNL +  +  ++ + FS+ G I    +  DK    + GF FV + ++   + 
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 75.4 bits (186), Expect = 3e-16
 Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 3/93 (3%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
             IF+ NL  ++ +  L   FS +G I++  V+ D     SKG+GFV F+ +EA ++   
Sbjct: 104 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIE 161

Query: 69  T-DSHVLEGSRLSIQPSDSHNRMAENMEDRFNQ 100
             +  +L   ++ +    S       +  R  +
Sbjct: 162 KMNGMLLNDRKVFVGRFKSRKEREAELGARAKE 194

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 70.8 bits (174), Expect = 1e-14
 Identities = 18/59 (30%), Positives = 29/59 (49%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          ++VG+L   V+   L + FS  G I++  V  D  T  S G+ +V FQ     ++   T
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 72.1 bits (177), Expect = 5e-16
 Identities = 19/89 (21%), Positives = 40/89 (44%), Gaps = 3/89 (3%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
            +++   P   + +++K++  + GQ++N  +    +    KG  FV F + E+  K   
Sbjct: 12 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE 70

Query: 69 TDSHVLEGSRLSIQPSDSHNRMAENMEDR 97
          T     + + L I   D  +  A+  E+R
Sbjct: 71 TPGQKYKETDLLILFKD--DYFAKKNEER 97

>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 = 72.6 bits (178), Expect = 5e-16
 Identities = 14/87 (16%), Positives = 34/87 (39%), Gaps = 1/87 (1%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
             +++  LP+   +  +  FF +   + ++  +     G + G GFV F+N+        
Sbjct: 26  FCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC 85

Query: 69  TDSHVLEGSRLSIQPSDSHNRMAENME 95
                +    + + P  +   M E ++
Sbjct: 86  RHKQYMGNRFIQVHPI-TKKGMLEKID 111

>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 = 71.2 bits (175), Expect = 7e-16
 Identities = 17/79 (21%), Positives = 33/79 (41%), Gaps = 1/79 (1%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
            I V N+P+TVS +E+  FF  Y  I  +  +     G+  G   V F++++       
Sbjct: 16 TVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75

Query: 69 T-DSHVLEGSRLSIQPSDS 86
            +   +   ++ +    S
Sbjct: 76 DLNDRPIGSRKVKLSGPSS 94

>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 = 71.1 bits (175), Expect = 8e-16
 Identities = 12/57 (21%), Positives = 27/57 (47%), Gaps = 6/57 (10%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          NK+++GNL   V+ ++L++ F +    +           L  G+ FV + ++    +
Sbjct: 9  NKLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIR 59

>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 = 70.7 bits (174), Expect = 1e-15
 Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 7/72 (9%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK-VF 67
          +++FVGNLP  ++  E++K F +YG+     +  D      KGFGF+  + +   +    
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKV 69

Query: 68 STDSHVLEGSRL 79
            D+  L G +L
Sbjct: 70 ELDNMPLRGKQL 81

>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 = 70.5 bits (173), Expect = 1e-15
 Identities = 18/74 (24%), Positives = 30/74 (40%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          + +  LP+  S  E+ +FFS    + N   +     G S G  FV F ++E  +K     
Sbjct: 18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKH 77

Query: 71 SHVLEGSRLSIQPS 84
             +    + I  S
Sbjct: 78 KERIGHRYIEIFKS 91

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 70.8 bits (174), Expect = 2e-15
 Identities = 17/77 (22%), Positives = 28/77 (36%), Gaps = 9/77 (11%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE-AVDKVF 67
            ++FV   P  V  +EL + F  +G +    ++         GF FV F+  E A   + 
Sbjct: 32  TRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIE 83

Query: 68  STDSHVLEGSRLSIQPS 84
                      L +  S
Sbjct: 84  EVHGKSFANQPLEVVYS 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 = 69.8 bits (171), Expect = 2e-15
 Identities = 14/82 (17%), Positives = 35/82 (42%), Gaps = 5/82 (6%)

Query: 5  IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVM-----FDKNTGLSKGFGFVTFQN 59
          +    +++VGN+P+ ++   +  FF+   ++   +               K F F+ F++
Sbjct: 3  LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRS 62

Query: 60 KEAVDKVFSTDSHVLEGSRLSI 81
           +   +  + D  + +G  L I
Sbjct: 63 VDETTQAMAFDGIIFQGQSLKI 84

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 69.9 bits (172), Expect = 2e-15
 Identities = 27/97 (27%), Positives = 46/97 (47%), Gaps = 10/97 (10%)

Query: 3  NSIRQLNKIFVGNLPW-TVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          ++I   +++F+GNLP   VS  +L + FS YG IM  ++           FGF+ F N +
Sbjct: 5  HNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQ 56

Query: 62 -AVDKVFSTDSHVLEGSRLSIQPSDSHNRMAENMEDR 97
             D +      +  G +L ++ S S+ R   +  D 
Sbjct: 57 SVRDAIECESQEMNFGKKLILEVSSSNARPQFDHGDH 93

>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 = 70.0 bits (172), Expect = 2e-15
 Identities = 15/69 (21%), Positives = 34/69 (49%), Gaps = 1/69 (1%)

Query: 2  SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQ-IMNASVMFDKNTGLSKGFGFVTFQNK 60
          S S      +++G+L   +  N + + F+  G+ +M+  ++ ++ TG+  G+ FV F + 
Sbjct: 3  SGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADL 62

Query: 61 EAVDKVFST 69
             +K    
Sbjct: 63 ATAEKCLHK 71

>3f6q_A Integrin-linked protein kinase; ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK, IPP; 1.60A {Homo sapiens} PDB: 3ixe_A 2kbx_A Length = 179

 Score = 72.1 bits (178), Expect = 2e-15
 Identities = 29/99 (29%), Positives = 47/99 (47%), Gaps = 9/99 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N  N  +       A  G  D+ V++L +    +IN ++E+G   LH+AC  G  +V + 
Sbjct: 66  NVMNRGDDTPLHLAASHGHRDI-VQKLLQ-YKADINAVNEHGNVPLHYACFWGQDQVAED 123

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L+   GA V++ +  G+  +D AKA     L E     G
Sbjct: 124 LVAN-GALVSICNKYGEMPVDKAKAPLRELLRERAEKMG 161

>3f6q_A Integrin-linked protein kinase; ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK, IPP; 1.60A {Homo sapiens} PDB: 3ixe_A 2kbx_A Length = 179

 Score = 69.8 bits (172), Expect = 1e-14
 Identities = 28/89 (31%), Positives = 46/89 (51%), Gaps = 2/89 (2%)

Query: 258 IYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVN 317
           I+   +EG     V+      + ++NQ D++G + LHWAC  G   VV+ LI + GA +N
Sbjct: 9   IFTQCREGNAVA-VRLWLDNTENDLNQGDDHGFSPLHWACREGRSAVVEMLIMR-GARIN 66

Query: 318 VTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           V +   D  L  A +  H D+++ L+   
Sbjct: 67  VMNRGDDTPLHLAASHGHRDIVQKLLQYK 95

>3f6q_A Integrin-linked protein kinase; ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK, IPP; 1.60A {Homo sapiens} PDB: 3ixe_A 2kbx_A Length = 179

 Score = 66.7 bits (164), Expect = 2e-13
 Identities = 26/99 (26%), Positives = 45/99 (45%), Gaps = 9/99 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N+ + + +       +EG+  + V+ L   +   IN ++      LH A   GH  +VQ 
Sbjct: 33  NQGDDHGFSPLHWACREGRSAV-VEMLIM-RGARINVMNRGDDTPLHLAASHGHRDIVQK 90

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L++   AD+N  +  G+  L YA       + E LV +G
Sbjct: 91  LLQY-KADINAVNEHGNVPLHYACFWGQDQVAEDLVANG 128

>3f6q_A Integrin-linked protein kinase; ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK, IPP; 1.60A {Homo sapiens} PDB: 3ixe_A 2kbx_A Length = 179

 Score = 57.1 bits (139), Expect = 5e-10
 Identities = 12/61 (19%), Positives = 25/61 (40%)

Query: 286 DENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNS 345
               ++ +   C  G+   V+  ++    D+N  D  G   L +A     + ++E L+  
Sbjct: 2   SPEFMDDIFTQCREGNAVAVRLWLDNTENDLNQGDDHGFSPLHWACREGRSAVVEMLIMR 61

Query: 346 G 346
           G
Sbjct: 62  G 62

>3f6q_A Integrin-linked protein kinase; ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK, IPP; 1.60A {Homo sapiens} PDB: 3ixe_A 2kbx_A Length = 179

 Score = 50.1 bits (121), Expect = 1e-07
 Identities = 8/73 (10%), Positives = 22/73 (30%), Gaps = 9/73 (12%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N  N +           G+  +  + L       ++  ++ G   +  A       + + 
Sbjct: 99  NAVNEHGNVPLHYACFWGQDQV-AEDLVA-NGALVSICNKYGEMPVDKAKAPLRELLRER 156

Query: 308 LIEKCGADVNVTD 320
             +  G ++N   
Sbjct: 157 AEKM-GQNLNRIP 168

>1n11_A Ankyrin; clathrin, BAND 3, anion exchanger, structural protein; 2.70A {Homo sapiens} SCOP: d.211.1.1 Length = 437

 Score = 75.2 bits (186), Expect = 3e-15
 Identities = 27/99 (27%), Positives = 42/99 (42%), Gaps = 9/99 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N  N          A+EG + +    L K     ++     G   LH A   G++K+V+ 
Sbjct: 272 NLGNKSGLTPLHLVAQEGHVPV-ADVLIK-HGVMVDATTRMGYTPLHVASHYGNIKLVKF 329

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L++   ADVN     G   L  A    HTD++  L+ +G
Sbjct: 330 LLQH-QADVNAKTKLGYSPLHQAAQQGHTDIVTLLLKNG 367

>1n11_A Ankyrin; clathrin, BAND 3, anion exchanger, structural protein; 2.70A {Homo sapiens} SCOP: d.211.1.1 Length = 437

 Score = 71.8 bits (177), Expect = 5e-14
 Identities = 23/100 (23%), Positives = 41/100 (41%), Gaps = 9/100 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           +      +      +  G + + VK L +    ++N   + G + LH A  +GH  +V  
Sbjct: 305 DATTRMGYTPLHVASHYGNIKL-VKFLLQ-HQADVNAKTKLGYSPLHQAAQQGHTDIVTL 362

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
           L++  GA  N   SDG   L  AK + +  + + L     
Sbjct: 363 LLKN-GASPNEVSSDGTTPLAIAKRLGYISVTDVLKVVTD 401

>1n11_A Ankyrin; clathrin, BAND 3, anion exchanger, structural protein; 2.70A {Homo sapiens} SCOP: d.211.1.1 Length = 437

 Score = 70.6 bits (174), Expect = 1e-13
 Identities = 20/99 (20%), Positives = 40/99 (40%), Gaps = 9/99 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           +      +      AK+ ++++  + L +    + N     G+  LH A   GH ++V  
Sbjct: 206 HSPAWNGYTPLHIAAKQNQVEV-ARSLLQ-YGGSANAESVQGVTPLHLAAQEGHAEMVAL 263

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L+ K  A+ N+ +  G   L       H  + + L+  G
Sbjct: 264 LLSK-QANGNLGNKSGLTPLHLVAQEGHVPVADVLIKHG 301

>1n11_A Ankyrin; clathrin, BAND 3, anion exchanger, structural protein; 2.70A {Homo sapiens} SCOP: d.211.1.1 Length = 437

 Score = 70.2 bits (173), Expect = 1e-13
 Identities = 27/99 (27%), Positives = 43/99 (43%), Gaps = 9/99 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N +++         A+EG  +M V  L   K  N N  +++GL  LH     GH+ V   
Sbjct: 239 NAESVQGVTPLHLAAQEGHAEM-VALLLS-KQANGNLGNKSGLTPLHLVAQEGHVPVADV 296

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           LI+  G  V+ T   G   L  A    +  L+++L+   
Sbjct: 297 LIKH-GVMVDATTRMGYTPLHVASHYGNIKLVKFLLQHQ 334

>1n11_A Ankyrin; clathrin, BAND 3, anion exchanger, structural protein; 2.70A {Homo sapiens} SCOP: d.211.1.1 Length = 437

 Score = 70.2 bits (173), Expect = 1e-13
 Identities = 22/99 (22%), Positives = 40/99 (40%), Gaps = 9/99 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
                  +      AK GK+ +  + L + +D + N   +NGL  LH A    +L +V+ 
Sbjct: 140 ACMTKKGFTPLHVAAKYGKVRV-AELLLE-RDAHPNAAGKNGLTPLHVAVHHNNLDIVKL 197

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L+ + G   +    +G   L  A      ++   L+  G
Sbjct: 198 LLPR-GGSPHSPAWNGYTPLHIAAKQNQVEVARSLLQYG 235

>1n11_A Ankyrin; clathrin, BAND 3, anion exchanger, structural protein; 2.70A {Homo sapiens} SCOP: d.211.1.1 Length = 437

 Score = 67.5 bits (166), Expect = 1e-12
 Identities = 22/99 (22%), Positives = 39/99 (39%), Gaps = 9/99 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N  N+         A+ G  ++  K L +     +N   ++    LH A   GH  +V+ 
Sbjct: 41  NVSNVKVETPLHMAARAGHTEV-AKYLLQ-NKAKVNAKAKDDQTPLHCAARIGHTNMVKL 98

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L+E   A+ N+  + G   L  A    H + +  L+   
Sbjct: 99  LLEN-NANPNLATTAGHTPLHIAAREGHVETVLALLEKE 136

>1n11_A Ankyrin; clathrin, BAND 3, anion exchanger, structural protein; 2.70A {Homo sapiens} SCOP: d.211.1.1 Length = 437

 Score = 67.1 bits (165), Expect = 1e-12
 Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 1/66 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           +     E+GL  LH A   GHL +V++L+++ GA  NV++   +  L  A    HT++ +
Sbjct: 6   SGGGGGESGLTPLHVASFMGHLPIVKNLLQR-GASPNVSNVKVETPLHMAARAGHTEVAK 64

Query: 341 YLVNSG 346
           YL+ + 
Sbjct: 65  YLLQNK 70

>1n11_A Ankyrin; clathrin, BAND 3, anion exchanger, structural protein; 2.70A {Homo sapiens} SCOP: d.211.1.1 Length = 437

 Score = 66.4 bits (163), Expect = 3e-12
 Identities = 26/99 (26%), Positives = 36/99 (36%), Gaps = 9/99 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N K   +       A+ G  +M VK L +  + N N     G   LH A   GH++ V  
Sbjct: 74  NAKAKDDQTPLHCAARIGHTNM-VKLLLE-NNANPNLATTAGHTPLHIAAREGHVETVLA 131

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L+EK  A        G   L  A       + E L+   
Sbjct: 132 LLEK-EASQACMTKKGFTPLHVAAKYGKVRVAELLLERD 169

>1n11_A Ankyrin; clathrin, BAND 3, anion exchanger, structural protein; 2.70A {Homo sapiens} SCOP: d.211.1.1 Length = 437

 Score = 52.5 bits (127), Expect = 9e-08
 Identities = 18/86 (20%), Positives = 31/86 (36%), Gaps = 10/86 (11%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N K    +      A++G  D+ V  L K    + N++  +G   L  A   G++ V   
Sbjct: 338 NAKTKLGYSPLHQAAQQGHTDI-VTLLLK-NGASPNEVSSDGTTPLAIAKRLGYISVTDV 395

Query: 308 LIEKC--GADVNVTDSDGDYGLDYAK 331
           L       + V V+D       +   
Sbjct: 396 LKVVTDETSFVLVSDKHRMSFPETVD 421

>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 = 69.6 bits (171), Expect = 3e-15
 Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 1/77 (1%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK-VF 67
            I V N+P+TVS +E+  FF  Y  I  +  +     G+  G   V F++++     V 
Sbjct: 16 TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 75

Query: 68 STDSHVLEGSRLSIQPS 84
            +   +   ++ +   
Sbjct: 76 DLNDRPIGSRKVKLVLG 92

>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 = 70.3 bits (172), Expect = 3e-15
 Identities = 16/84 (19%), Positives = 30/84 (35%)

Query: 1   MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
            S        + +  LP+  +  E+ +FFS    + N   +     G   G  FV F ++
Sbjct: 35  NSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQ 94

Query: 61  EAVDKVFSTDSHVLEGSRLSIQPS 84
           E  +K        +    + +  S
Sbjct: 95  ELAEKALGKHKERIGHRYIEVFKS 118

>3v30_A DNA-binding protein rfxank; structural genomics consortium, SGC, rfxank, ANK repeat, Pro binding; 1.57A {Homo sapiens} PDB: 3uxg_A Length = 172

 Score = 71.7 bits (177), Expect = 4e-15
 Identities = 24/99 (24%), Positives = 42/99 (42%), Gaps = 9/99 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           +             +  G  D+ V  L + +D +IN  D NG   L +A    H+K V+ 
Sbjct: 63  HILAKERESALSLASTGGYTDI-VGLLLE-RDVDINIYDWNGGTPLLYAVRGNHVKCVEA 120

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L+ + GAD+      G   +D A A+ +  + + + N  
Sbjct: 121 LLAR-GADLTTEADSGYTPMDLAVALGYRKVQQVIENHI 158

>3v30_A DNA-binding protein rfxank; structural genomics consortium, SGC, rfxank, ANK repeat, Pro binding; 1.57A {Homo sapiens} PDB: 3uxg_A Length = 172

 Score = 69.0 bits (170), Expect = 3e-14
 Identities = 25/85 (29%), Positives = 44/85 (51%), Gaps = 2/85 (2%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
           A +G+LD  +K+  +  D  +N+ DE G   L WA   G ++ V+ L+E  GAD ++   
Sbjct: 10  AAQGELDQ-LKEHLRKGDNLVNKPDERGFTPLIWASAFGEIETVRFLLEW-GADPHILAK 67

Query: 322 DGDYGLDYAKAIEHTDLIEYLVNSG 346
           + +  L  A    +TD++  L+   
Sbjct: 68  ERESALSLASTGGYTDIVGLLLERD 92

>3v30_A DNA-binding protein rfxank; structural genomics consortium, SGC, rfxank, ANK repeat, Pro binding; 1.57A {Homo sapiens} PDB: 3uxg_A Length = 172

 Score = 61.3 bits (150), Expect = 1e-11
 Identities = 9/76 (11%), Positives = 24/76 (31%), Gaps = 9/76 (11%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N  +           +   +   V+ L   +  ++    ++G   +  A   G+ KV Q 
Sbjct: 96  NIYDWNGGTPLLYAVRGNHVKC-VEALLA-RGADLTTEADSGYTPMDLAVALGYRKVQQV 153

Query: 308 LIEKCGADVNVTDSDG 323
           +       +  ++   
Sbjct: 154 IENH-ILKLFQSNLVP 168

>3v30_A DNA-binding protein rfxank; structural genomics consortium, SGC, rfxank, ANK repeat, Pro binding; 1.57A {Homo sapiens} PDB: 3uxg_A Length = 172

 Score = 50.1 bits (121), Expect = 1e-07
 Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 2/55 (3%)

Query: 293 LHWACDRGHLKVVQHLIEKCGAD-VNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           +H    +G L  ++  + K G + VN  D  G   L +A A    + + +L+  G
Sbjct: 6   IHQLAAQGELDQLKEHLRK-GDNLVNKPDERGFTPLIWASAFGEIETVRFLLEWG 59

>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 = 69.3 bits (170), Expect = 4e-15
 Identities = 25/91 (27%), Positives = 43/91 (47%), Gaps = 10/91 (10%)

Query: 1  MSNSIRQLNKIFVGNLPW-TVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN 59
          +       +++F+GNLP   VS  +L + FS YG IM  ++           FGF+ F N
Sbjct: 15 VPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDN 66

Query: 60 KEAVDK-VFSTDSHVLEGSRLSIQPSDSHNR 89
           ++V   +      +  G +L ++ S S+ R
Sbjct: 67 PQSVRDAIEXESQEMNFGKKLILEVSSSNAR 97

>3v31_A Ankyrin repeat family A protein 2; structural genomics consortium, SGC, ankra2, ANK repeat, Pro binding, HDAC4; 1.57A {Homo sapiens} PDB: 3v2x_A 3v2o_A 3so8_A Length = 167

 Score = 71.3 bits (176), Expect = 4e-15
 Identities = 23/99 (23%), Positives = 40/99 (40%), Gaps = 9/99 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
                           +G  D+ VK L      ++N+ D NG   L +A    H+K V+ 
Sbjct: 63  QLLGKGRESALSLACSKGYTDI-VKMLLD-CGVDVNEYDWNGGTPLLYAVHGNHVKCVKM 120

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L+E  GAD  +    G   +D A A+ +  + + + +  
Sbjct: 121 LLES-GADPTIETDSGYNSMDLAVALGYRSVQQVIESHL 158

>3v31_A Ankyrin repeat family A protein 2; structural genomics consortium, SGC, ankra2, ANK repeat, Pro binding, HDAC4; 1.57A {Homo sapiens} PDB: 3v2x_A 3v2o_A 3so8_A Length = 167

 Score = 69.3 bits (171), Expect = 2e-14
 Identities = 23/85 (27%), Positives = 43/85 (50%), Gaps = 3/85 (3%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
           A +G++   +    + ++  IN  DE G   L WA   G + VV+ L++  GAD  +   
Sbjct: 11  AAQGEMLY-LATRIE-QENVINHTDEEGFTPLMWAAAHGQIAVVEFLLQN-GADPQLLGK 67

Query: 322 DGDYGLDYAKAIEHTDLIEYLVNSG 346
             +  L  A +  +TD+++ L++ G
Sbjct: 68  GRESALSLACSKGYTDIVKMLLDCG 92

>3v31_A Ankyrin repeat family A protein 2; structural genomics consortium, SGC, ankra2, ANK repeat, Pro binding, HDAC4; 1.57A {Homo sapiens} PDB: 3v2x_A 3v2o_A 3so8_A Length = 167

 Score = 55.1 bits (134), Expect = 2e-09
 Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 293 LHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           +H    +G +  +   IE+    +N TD +G   L +A A     ++E+L+ +G
Sbjct: 7   VHQLAAQGEMLYLATRIEQ-ENVINHTDEEGFTPLMWAAAHGQIAVVEFLLQNG 59

>2fo1_E LIN-12 protein; beta-barrel, protein-DNA complex, double helix, ankyrin repeat, gene regulation/signalling protein/DNA complex; 3.12A {Caenorhabditis elegans} SCOP: d.211.1.1 Length = 373

 Score = 74.6 bits (184), Expect = 4e-15
 Identities = 22/108 (20%), Positives = 45/108 (41%), Gaps = 8/108 (7%)

Query: 245 INDESQLDDNEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACD 298
           ++ +     + +           A+   + + VK L   K  N ++ DE+G   +  A  
Sbjct: 264 VDYDGAARKDSEKYKGRTALHYAAQVSNMPI-VKYLVGEKGSNKDKQDEDGKTPIMLAAQ 322

Query: 299 RGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
            G ++VV +LI++ GA V   D+        A+A  H ++++      
Sbjct: 323 EGRIEVVMYLIQQ-GASVEAVDATDHTARQLAQANNHHNIVDIFDRCR 369

>2fo1_E LIN-12 protein; beta-barrel, protein-DNA complex, double helix, ankyrin repeat, gene regulation/signalling protein/DNA complex; 3.12A {Caenorhabditis elegans} SCOP: d.211.1.1 Length = 373

 Score = 60.4 bits (147), Expect = 2e-10
 Identities = 17/104 (16%), Positives = 34/104 (32%), Gaps = 13/104 (12%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N  +  E           +  + V  L K    +    +++  + LH A       ++ +
Sbjct: 160 NAMDCDENTPLMLAVLARRRRL-VAYLMK-AGADPTIYNKSERSALHQAAANRDFGMMVY 217

Query: 308 LIEKC--GADVNVTDSDGDYGLDYAKAIEHTDLI---EYLVNSG 346
           ++       D+   D +G   L      E  D +   + LV  G
Sbjct: 218 MLNSTKLKGDIEELDRNGMTALMIVAHNEGRDQVASAKLLVEKG 261

>2fo1_E LIN-12 protein; beta-barrel, protein-DNA complex, double helix, ankyrin repeat, gene regulation/signalling protein/DNA complex; 3.12A {Caenorhabditis elegans} SCOP: d.211.1.1 Length = 373

 Score = 59.6 bits (145), Expect = 3e-10
 Identities = 23/107 (21%), Positives = 35/107 (32%), Gaps = 15/107 (14%)

Query: 252 DDNEKNIYEW-----AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQ 306
              E              G   +  + +T+ +  NI     +    LHW       +  +
Sbjct: 86  IPTEPEPESPIKLHTEAAGSYAI-TEPITR-ESVNIID-PRHNRTVLHWIASNSSAEKSE 142

Query: 307 HLIEK-------CGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
            LI          GADVN  D D +  L  A       L+ YL+ +G
Sbjct: 143 DLIVHEAKECIAAGADVNAMDCDENTPLMLAVLARRRRLVAYLMKAG 189

>2fo1_E LIN-12 protein; beta-barrel, protein-DNA complex, double helix, ankyrin repeat, gene regulation/signalling protein/DNA complex; 3.12A {Caenorhabditis elegans} SCOP: d.211.1.1 Length = 373

 Score = 59.2 bits (144), Expect = 5e-10
 Identities = 19/108 (17%), Positives = 38/108 (35%), Gaps = 15/108 (13%)

Query: 254 NEKNIYEW------AKEGKLDML--VKQL-------TKLKDFNINQLDENGLNCLHWACD 298
            E +          A     D +   K L               +     G   LH+A  
Sbjct: 229 EELDRNGMTALMIVAHNEGRDQVASAKLLVEKGAKVDYDGAARKDSEKYKGRTALHYAAQ 288

Query: 299 RGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
             ++ +V++L+ + G++ +  D DG   +  A      +++ YL+  G
Sbjct: 289 VSNMPIVKYLVGEKGSNKDKQDEDGKTPIMLAAQEGRIEVVMYLIQQG 336

>2fo1_E LIN-12 protein; beta-barrel, protein-DNA complex, double helix, ankyrin repeat, gene regulation/signalling protein/DNA complex; 3.12A {Caenorhabditis elegans} SCOP: d.211.1.1 Length = 373

 Score = 58.0 bits (141), Expect = 1e-09
 Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 1/64 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           ++N +D +    L  A      ++V +L++  GAD  + +      L  A A     ++ 
Sbjct: 158 DVNAMDCDENTPLMLAVLARRRRLVAYLMKA-GADPTIYNKSERSALHQAAANRDFGMMV 216

Query: 341 YLVN 344
           Y++N
Sbjct: 217 YMLN 220

>2fo1_E LIN-12 protein; beta-barrel, protein-DNA complex, double helix, ankyrin repeat, gene regulation/signalling protein/DNA complex; 3.12A {Caenorhabditis elegans} SCOP: d.211.1.1 Length = 373

 Score = 53.8 bits (130), Expect = 3e-08
 Identities = 7/69 (10%), Positives = 14/69 (20%), Gaps = 2/69 (2%)

Query: 278 KDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTD 337
                N+L    L         G+  +               + +    L    A     
Sbjct: 50  IKRQRNELQHYSLYPNPQGYGNGNDFLGDFNHTN-LQIPTEPEPESPIKLHTE-AAGSYA 107

Query: 338 LIEYLVNSG 346
           + E +    
Sbjct: 108 ITEPITRES 116

>2fo1_E LIN-12 protein; beta-barrel, protein-DNA complex, double helix, ankyrin repeat, gene regulation/signalling protein/DNA complex; 3.12A {Caenorhabditis elegans} SCOP: d.211.1.1 Length = 373

 Score = 45.3 bits (108), Expect = 1e-05
 Identities = 14/113 (12%), Positives = 43/113 (38%), Gaps = 16/113 (14%)

Query: 217 EINWDESQESGSKENEGQT-------KGWVNVSSMINDESQLDDNEKNIYEW------AK 263
           ++++D +    S++ +G+T          + +   +  E   + ++++          A+
Sbjct: 263 KVDYDGAARKDSEKYKGRTALHYAAQVSNMPIVKYLVGEKGSNKDKQDEDGKTPIMLAAQ 322

Query: 264 EGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADV 316
           EG++++ V  L + +  ++  +D         A    H  +V         + 
Sbjct: 323 EGRIEV-VMYLIQ-QGASVEAVDATDHTARQLAQANNHHNIVDIFDRC-RPER 372

>1n0r_A 4ANK, 4 ankyrin repeats; structural protein; 1.50A {} SCOP: k.37.1.1 Length = 126

 Score = 69.7 bits (172), Expect = 6e-15
 Identities = 34/99 (34%), Positives = 52/99 (52%), Gaps = 9/99 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N K+          A+ G L++ VK L +    ++N  D+NG   LH A   GHL+VV+ 
Sbjct: 29  NAKDKNGRTPLHLAARNGHLEV-VKLLLE-AGADVNAKDKNGRTPLHLAARNGHLEVVKL 86

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L+E  GADVN  D +G   L  A    H ++++ L+ +G
Sbjct: 87  LLEA-GADVNAKDKNGRTPLHLAARNGHLEVVKLLLEAG 124

>1n0r_A 4ANK, 4 ankyrin repeats; structural protein; 1.50A {} SCOP: k.37.1.1 Length = 126

 Score = 63.9 bits (157), Expect = 7e-13
 Identities = 26/66 (39%), Positives = 39/66 (59%), Gaps = 1/66 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           ++N  D+NG   LH A   GHL+VV+ L+E  GADVN  D +G   L  A    H ++++
Sbjct: 27  DVNAKDKNGRTPLHLAARNGHLEVVKLLLEA-GADVNAKDKNGRTPLHLAARNGHLEVVK 85

Query: 341 YLVNSG 346
            L+ +G
Sbjct: 86  LLLEAG 91

>1n0r_A 4ANK, 4 ankyrin repeats; structural protein; 1.50A {} SCOP: k.37.1.1 Length = 126

 Score = 56.2 bits (137), Expect = 3e-10
 Identities = 24/59 (40%), Positives = 34/59 (57%), Gaps = 1/59 (1%)

Query: 288 NGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           NG   LH A   GHL+VV+ L+E  GADVN  D +G   L  A    H ++++ L+ +G
Sbjct: 1   NGRTPLHLAARNGHLEVVKLLLEA-GADVNAKDKNGRTPLHLAARNGHLEVVKLLLEAG 58

>1n0r_A 4ANK, 4 ankyrin repeats; structural protein; 1.50A {} SCOP: k.37.1.1 Length = 126

 Score = 47.7 bits (115), Expect = 3e-07
 Identities = 24/67 (35%), Positives = 35/67 (52%), Gaps = 9/67 (13%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N K+          A+ G L++ VK L +    ++N  D+NG   LH A   GHL+VV+ 
Sbjct: 62  NAKDKNGRTPLHLAARNGHLEV-VKLLLE-AGADVNAKDKNGRTPLHLAARNGHLEVVKL 119

Query: 308 LIEKCGA 314
           L+E  GA
Sbjct: 120 LLEA-GA 125

>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 = 70.3 bits (172), Expect = 6e-15
 Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 6/81 (7%)

Query: 10  KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE-AVDKVFS 68
           K++VGNL    +  EL++ F  YG + +  V  +       GF FV F++   A D V  
Sbjct: 75  KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRE 129

Query: 69  TDSHVLEGSRLSIQPSDSHNR 89
            D   L G R+ ++ S+   R
Sbjct: 130 LDGRTLCGCRVRVELSNGEKR 150

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 68.4 bits (167), Expect = 1e-14
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 3/76 (3%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
            + V  LP  V    L  +F    +     V+  +  G     G +TF+     ++V +
Sbjct: 9  VAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG---CGGVLTFREPADAERVLA 65

Query: 69 TDSHVLEGSRLSIQPS 84
             H L G++LS++P+
Sbjct: 66 QADHELHGAQLSLRPA 81

>3aaa_C Myotrophin, protein V-1; actin capping protein, barbed END capping, inhibition, prote binding, actin capping, actin-binding, cytoskeleton, ANK RE; 2.20A {Homo sapiens} PDB: 1myo_A 2kxp_C 2myo_A Length = 123

 Score = 68.6 bits (169), Expect = 1e-14
 Identities = 28/85 (32%), Positives = 42/85 (49%), Gaps = 3/85 (3%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
            K G LD  VK     K  ++N+  E G   LH+A D G L++++ L+ K GAD+N  D 
Sbjct: 15  LKNGDLDE-VKDYVA-KGEDVNRTLEGGRKPLHYAADCGQLEILEFLLLK-GADINAPDK 71

Query: 322 DGDYGLDYAKAIEHTDLIEYLVNSG 346
                L  A    H   ++ L++ G
Sbjct: 72  HHITPLLSAVYEGHVSCVKLLLSKG 96

>3aaa_C Myotrophin, protein V-1; actin capping protein, barbed END capping, inhibition, prote binding, actin capping, actin-binding, cytoskeleton, ANK RE; 2.20A {Homo sapiens} PDB: 1myo_A 2kxp_C 2myo_A Length = 123

 Score = 65.9 bits (162), Expect = 1e-13
 Identities = 23/93 (24%), Positives = 38/93 (40%), Gaps = 9/93 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N             A  G+L++ ++ L   K  +IN  D++ +  L  A   GH+  V+ 
Sbjct: 34  NRTLEGGRKPLHYAADCGQLEI-LEFLLL-KGADINAPDKHHITPLLSAVYEGHVSCVKL 91

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           L+ K GAD  V   DG    +         L++
Sbjct: 92  LLSK-GADKTVKGPDGLTAFEATDNQAIKALLQ 123

>3aaa_C Myotrophin, protein V-1; actin capping protein, barbed END capping, inhibition, prote binding, actin capping, actin-binding, cytoskeleton, ANK RE; 2.20A {Homo sapiens} PDB: 1myo_A 2kxp_C 2myo_A Length = 123

 Score = 57.8 bits (141), Expect = 9e-11
 Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 285 LDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVN 344
           L         WA   G L  V+  + K G DVN T   G   L YA      +++E+L+ 
Sbjct: 3   LGSMCDKEFMWALKNGDLDEVKDYVAK-GEDVNRTLEGGRKPLHYAADCGQLEILEFLLL 61

Query: 345 SG 346
            G
Sbjct: 62  KG 63

>3c5r_A BARD-1, BRCA1-associated ring domain protein 1; ankyrin repeat, helix, extended loop, four repeat, PR ANK repeat, disease mutation, metal-binding; 2.00A {Homo sapiens} SCOP: k.37.1.1 Length = 137

 Score = 68.2 bits (168), Expect = 2e-14
 Identities = 23/100 (23%), Positives = 37/100 (37%), Gaps = 9/100 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N K+   W         G L + V+ L +     +N       + LH A   GH+ +V+ 
Sbjct: 37  NVKDHAGWTPLHEACNHGHLKV-VELLLQ-HKALVNTTGYQNDSPLHDAAKNGHVDIVKL 94

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
           L+   GA  N  +  G   +DY        L+     + S
Sbjct: 95  LLSY-GASRNAVNIFGLRPVDYTDDESMKSLLLLPEKNES 133

>3c5r_A BARD-1, BRCA1-associated ring domain protein 1; ankyrin repeat, helix, extended loop, four repeat, PR ANK repeat, disease mutation, metal-binding; 2.00A {Homo sapiens} SCOP: k.37.1.1 Length = 137

 Score = 65.1 bits (160), Expect = 3e-13
 Identities = 25/66 (37%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           + N  D  G   LH AC+ GHLKVV+ L++   A VN T    D  L  A    H D+++
Sbjct: 35  DPNVKDHAGWTPLHEACNHGHLKVVELLLQH-KALVNTTGYQNDSPLHDAAKNGHVDIVK 93

Query: 341 YLVNSG 346
            L++ G
Sbjct: 94  LLLSYG 99

>3c5r_A BARD-1, BRCA1-associated ring domain protein 1; ankyrin repeat, helix, extended loop, four repeat, PR ANK repeat, disease mutation, metal-binding; 2.00A {Homo sapiens} SCOP: k.37.1.1 Length = 137

 Score = 61.3 bits (150), Expect = 6e-12
 Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 2/66 (3%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           +    +  G   LH A  +G +  V++L++  G+D NV D  G   L  A    H  ++E
Sbjct: 3   DPFT-NHRGETLLHIASIKGDIPSVEYLLQN-GSDPNVKDHAGWTPLHEACNHGHLKVVE 60

Query: 341 YLVNSG 346
            L+   
Sbjct: 61  LLLQHK 66

>1wdy_A 2-5A-dependent ribonuclease; hydrolase, RNA-binding; HET: 25A; 1.80A {Homo sapiens} SCOP: d.211.1.1 Length = 285

 Score = 71.3 bits (176), Expect = 2e-14
 Identities = 26/102 (25%), Positives = 41/102 (40%), Gaps = 10/102 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKL---KDFNINQLDENGLNCLHWACDRGHLKV 304
           N  +                   V+ +T L      ++N   E G   L  A ++ HL +
Sbjct: 176 NACDNMGRNALIHALLSSDDSD-VEAITHLLLDHGADVNVRGERGKTPLILAVEKKHLGL 234

Query: 305 VQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           VQ L+E+   ++N TDSDG   L  A  ++   + E L   G
Sbjct: 235 VQRLLEQEHIEINDTDSDGKTALLLAVELKLKKIAELLCKRG 276

>1wdy_A 2-5A-dependent ribonuclease; hydrolase, RNA-binding; HET: 25A; 1.80A {Homo sapiens} SCOP: d.211.1.1 Length = 285

 Score = 63.3 bits (155), Expect = 1e-11
 Identities = 16/66 (24%), Positives = 26/66 (39%), Gaps = 1/66 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           +     +NG      A   G +K+++  + K GADVN  D  G      A        ++
Sbjct: 64  DPVLRKKNGATPFLLAAIAGSVKLLKLFLSK-GADVNECDFYGFTAFMEAAVYGKVKALK 122

Query: 341 YLVNSG 346
           +L   G
Sbjct: 123 FLYKRG 128

>1wdy_A 2-5A-dependent ribonuclease; hydrolase, RNA-binding; HET: 25A; 1.80A {Homo sapiens} SCOP: d.211.1.1 Length = 285

 Score = 60.9 bits (149), Expect = 8e-11
 Identities = 28/113 (24%), Positives = 50/113 (44%), Gaps = 22/113 (19%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNC----------LHWAC 297
           NE + Y +      A  GK+   +K L K +  N+N   +   +           L  A 
Sbjct: 99  NECDFYGFTAFMEAAVYGKVKA-LKFLYK-RGANVNLRRKTKEDQERLRKGGATALMDAA 156

Query: 298 DRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTD----LIEYLVNSG 346
           ++GH++V++ L+++ GADVN  D+ G   L +A           +   L++ G
Sbjct: 157 EKGHVEVLKILLDEMGADVNACDNMGRNALIHALLSSDDSDVEAITHLLLDHG 209

>1wdy_A 2-5A-dependent ribonuclease; hydrolase, RNA-binding; HET: 25A; 1.80A {Homo sapiens} SCOP: d.211.1.1 Length = 285

 Score = 57.5 bits (140), Expect = 1e-09
 Identities = 20/86 (23%), Positives = 36/86 (41%), Gaps = 4/86 (4%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLD-ENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTD 320
            +   +D+ V+QL +    N+N  + E G   LH A       +V+ L+   GAD  +  
Sbjct: 13  VQNEDVDL-VQQLLE-GGANVNFQEEEGGWTPLHNAVQMSREDIVELLLRH-GADPVLRK 69

Query: 321 SDGDYGLDYAKAIEHTDLIEYLVNSG 346
            +G      A       L++  ++ G
Sbjct: 70  KNGATPFLLAAIAGSVKLLKLFLSKG 95

>1wdy_A 2-5A-dependent ribonuclease; hydrolase, RNA-binding; HET: 25A; 1.80A {Homo sapiens} SCOP: d.211.1.1 Length = 285

 Score = 53.2 bits (129), Expect = 3e-08
 Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 2/62 (3%)

Query: 286 DENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY-GLDYAKAIEHTDLIEYLVN 344
                + L  A     + +VQ L+E  GA+VN  + +G +  L  A  +   D++E L+ 
Sbjct: 2   AVEDNHLLIKAVQNEDVDLVQQLLEG-GANVNFQEEEGGWTPLHNAVQMSREDIVELLLR 60

Query: 345 SG 346
            G
Sbjct: 61  HG 62

>3hra_A Ankyrin repeat family protein; structural protein; 1.69A {Enterococcus faecalis} Length = 201

 Score = 69.8 bits (172), Expect = 2e-14
 Identities = 21/104 (20%), Positives = 47/104 (45%), Gaps = 12/104 (11%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N +N            +G+ ++ +  + K    ++N+ +  G N L  A ++GH+  V+ 
Sbjct: 66  NLQNSISDSPYLYAGAQGRTEI-LAYMLKHATPDLNKHNRYGGNALIPAAEKGHIDNVKL 124

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIE-----HTDLIEYLVNSG 346
           L+E    D++  +  G   L  A  +      + D+++ L+ +G
Sbjct: 125 LLEDGREDIDFQNDFGYTALIEAVGLREGNQLYQDIVKLLMENG 168

>3hra_A Ankyrin repeat family protein; structural protein; 1.69A {Enterococcus faecalis} Length = 201

 Score = 65.2 bits (160), Expect = 1e-12
 Identities = 27/103 (26%), Positives = 50/103 (48%), Gaps = 13/103 (12%)

Query: 252 DDNEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWAC-----DRG 300
           D N+ N Y        A++G +D  VK L +    +I+  ++ G   L  A      ++ 
Sbjct: 98  DLNKHNRYGGNALIPAAEKGHIDN-VKLLLEDGREDIDFQNDFGYTALIEAVGLREGNQL 156

Query: 301 HLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLV 343
           +  +V+ L+E  GAD ++ D+ G   +DYA    +T++ + L 
Sbjct: 157 YQDIVKLLMEN-GADQSIKDNSGRTAMDYANQKGYTEISKILA 198

>3hra_A Ankyrin repeat family protein; structural protein; 1.69A {Enterococcus faecalis} Length = 201

 Score = 64.0 bits (157), Expect = 2e-12
 Identities = 20/95 (21%), Positives = 44/95 (46%), Gaps = 2/95 (2%)

Query: 252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEK 311
                 + E A +     + + L     + ++++D  G   L+ A     +++ + LI++
Sbjct: 3   TYEVGALLEAANQRDTKKVKEILQD-TTYQVDEVDTEGNTPLNIAVHNNDIEIAKALIDR 61

Query: 312 CGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
            GAD+N+ +S  D    YA A   T+++ Y++   
Sbjct: 62  -GADINLQNSISDSPYLYAGAQGRTEILAYMLKHA 95

>3hra_A Ankyrin repeat family protein; structural protein; 1.69A {Enterococcus faecalis} Length = 201

 Score = 62.5 bits (153), Expect = 9e-12
 Identities = 16/100 (16%), Positives = 39/100 (39%), Gaps = 8/100 (8%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           +E +               +++  K L   +  +IN  +    +   +A  +G  +++ +
Sbjct: 33  DEVDTEGNTPLNIAVHNNDIEI-AKALID-RGADINLQNSISDSPYLYAGAQGRTEILAY 90

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
           +++    D+N  +  G   L  A    H D ++ L+  G 
Sbjct: 91  MLKHATPDLNKHNRYGGNALIPAAEKGHIDNVKLLLEDGR 130

>3hra_A Ankyrin repeat family protein; structural protein; 1.69A {Enterococcus faecalis} Length = 201

 Score = 39.7 bits (94), Expect = 5e-04
 Identities = 10/68 (14%), Positives = 29/68 (42%), Gaps = 9/68 (13%)

Query: 252 DDNEKNIYEW------AKEGKLDMLVKQLTKL---KDFNINQLDENGLNCLHWACDRGHL 302
           D + +N + +          + + L + + KL      + +  D +G   + +A  +G+ 
Sbjct: 132 DIDFQNDFGYTALIEAVGLREGNQLYQDIVKLLMENGADQSIKDNSGRTAMDYANQKGYT 191

Query: 303 KVVQHLIE 310
           ++ + L +
Sbjct: 192 EISKILAQ 199

>1d9s_A Cyclin-dependent kinase 4 inhibitor B; helix-turn-helix, ankyrin repeat, signaling protein; NMR {Mus musculus} SCOP: i.11.1.1 Length = 136

 Score = 68.2 bits (168), Expect = 2e-14
 Identities = 23/99 (23%), Positives = 35/99 (35%), Gaps = 9/99 (9%)

Query: 254 NEKNIYEW-----AKEGKLDMLVKQLTKLKDFNINQLDENGLNC-LHWACDRGHLKVVQH 307
           N  N +          G   +  + L        N  D   L   +H A   G L  +  
Sbjct: 39  NALNRFGRRPIQVMMMGSAQV-AELLLL-HGAEPNCADPATLTRPVHDAAREGFLDTLVV 96

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L    GA ++V D+ G   +D A+   H D+  YL  + 
Sbjct: 97  LHRA-GARLDVCDAWGRLPVDLAEEQGHRDIARYLHAAT 134

>1d9s_A Cyclin-dependent kinase 4 inhibitor B; helix-turn-helix, ankyrin repeat, signaling protein; NMR {Mus musculus} SCOP: i.11.1.1 Length = 136

 Score = 64.8 bits (159), Expect = 4e-13
 Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 2/66 (3%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
            I+ L  +    L  A  RG ++ V+ L+E  GAD N  +  G   +     +    + E
Sbjct: 4   GIHMLGGSSDAGLATAAARGQVETVRQLLEA-GADPNALNRFGRRPIQVM-MMGSAQVAE 61

Query: 341 YLVNSG 346
            L+  G
Sbjct: 62  LLLLHG 67

>1d9s_A Cyclin-dependent kinase 4 inhibitor B; helix-turn-helix, ankyrin repeat, signaling protein; NMR {Mus musculus} SCOP: i.11.1.1 Length = 136

 Score = 49.4 bits (119), Expect = 9e-08
 Identities = 14/71 (19%), Positives = 27/71 (38%), Gaps = 10/71 (14%)

Query: 252 DDNEKNIYEW-------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKV 304
           + N  +           A+EG LD  +  L +     ++  D  G   +  A ++GH  +
Sbjct: 69  EPNCADPATLTRPVHDAAREGFLDT-LVVLHR-AGARLDVCDAWGRLPVDLAEEQGHRDI 126

Query: 305 VQHLIEKCGAD 315
            ++L      D
Sbjct: 127 ARYLHAA-TGD 136

>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 = 67.4 bits (165), Expect = 3e-14
 Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 10/83 (12%)

Query: 9   NKIFVGNLPW-TVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK-V 66
           +++F+GNL    V  ++++  FS+YG++   SV         KG+ FV + N+      V
Sbjct: 28  SRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARAAV 79

Query: 67  FSTDSHVLEGSRLSIQPSDSHNR 89
              +  VL G  L I  +     
Sbjct: 80  LGENGRVLAGQTLDINMAGEPKP 102

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 66.9 bits (164), Expect = 3e-14
 Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 11 IFVGNLPWTVSHNELKKFFSE-YGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          +FVG+L   V    L +FF + Y       V+ D+ TG+SKG+GFV F ++    +
Sbjct: 12 LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKR 66

>2vge_A RELA-associated inhibitor; iaspp, nucleus, apoptosis, repressor, cytoplasm, phosphorylation, P53 binding protein, ANK repeat, SH3 domain; 2.10A {Homo sapiens} Length = 229

 Score = 70.0 bits (172), Expect = 3e-14
 Identities = 28/104 (26%), Positives = 43/104 (41%), Gaps = 12/104 (11%)

Query: 252 DDNEKNIYEW---------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHL 302
              +               A  G+L++ V+Q  K +  + +Q +E G+  LH A    + 
Sbjct: 10  SPRKARRARLNPLVLLLDAALTGELEV-VQQAVK-EMNDPSQPNEEGITALHNAICGANY 67

Query: 303 KVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
            +V  LI   GA+VN  DS G   L  A +   T +   LV  G
Sbjct: 68  SIVDFLITA-GANVNSPDSHGWTPLHCAASCNDTVICMALVQHG 110

>2vge_A RELA-associated inhibitor; iaspp, nucleus, apoptosis, repressor, cytoplasm, phosphorylation, P53 binding protein, ANK repeat, SH3 domain; 2.10A {Homo sapiens} Length = 229

 Score = 51.9 bits (125), Expect = 6e-08
 Identities = 13/102 (12%), Positives = 27/102 (26%), Gaps = 13/102 (12%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDEN-GLNCLHWA--CDRGHLKV 304
           N  + + W      A      +    L +     I     + G            G+   
Sbjct: 81  NSPDSHGWTPLHCAASCNDTVI-CMALVQ-HGAAIFATTLSDGATAFEKCDPYREGYADC 138

Query: 305 VQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
             +L +     + + +S   Y L    + E  D + +     
Sbjct: 139 ATYLADV-EQSMGLMNSGAVYALWDY-SAEFGDELSFREGES 178

>3ljn_A Hypothetical protein; ankyrin, structural genomics, PSI, structural genomics of pathogenic protozoa consortium, SGPP, ANK repeat; 2.90A {Leishmania major} Length = 364

 Score = 71.4 bits (176), Expect = 5e-14
 Identities = 16/102 (15%), Positives = 35/102 (34%), Gaps = 10/102 (9%)

Query: 254 NEKNIYEW------AKEGKLDM---LVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKV 304
             K+  +        +    +    ++  +       ++  ++ G + LHWA       V
Sbjct: 167 TAKDKADETPLMRAMEFRNREALDLMMDTVPSKSSLRLDYANKQGNSHLHWAILINWEDV 226

Query: 305 VQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
               +E  G DVN+ D++    L  +       L + L+   
Sbjct: 227 AMRFVEM-GIDVNMEDNEHTVPLYLSVRAAMVLLTKELLQKT 267

>3ljn_A Hypothetical protein; ankyrin, structural genomics, PSI, structural genomics of pathogenic protozoa consortium, SGPP, ANK repeat; 2.90A {Leishmania major} Length = 364

 Score = 69.1 bits (170), Expect = 2e-13
 Identities = 18/74 (24%), Positives = 29/74 (39%), Gaps = 1/74 (1%)

Query: 273 QLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKA 332
            +T     N  + D+  +  +H A  +G    V+ LIE  G    + +  G   L  A  
Sbjct: 4   SMTDFPKLNRIKSDDENMEKIHVAARKGQTDEVRRLIET-GVSPTIQNRFGCTALHLACK 62

Query: 333 IEHTDLIEYLVNSG 346
               D  +YL + G
Sbjct: 63  FGCVDTAKYLASVG 76

>3ljn_A Hypothetical protein; ankyrin, structural genomics, PSI, structural genomics of pathogenic protozoa consortium, SGPP, ANK repeat; 2.90A {Leishmania major} Length = 364

 Score = 66.0 bits (162), Expect = 3e-12
 Identities = 15/111 (13%), Positives = 32/111 (28%), Gaps = 20/111 (18%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQL-----------TKLKD-FNINQLDENGLNCLHW 295
           N ++           +   + +  K+L               +   +       L+ +  
Sbjct: 238 NMEDNEHTVPLYLSVRAAMVLL-TKELLQKTDVFLIQACPYHNGTTVLPDRVVWLDFVPA 296

Query: 296 ACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           A D    +V+Q L EK   +V  + + G  G    K      +    +   
Sbjct: 297 AADPSKQEVLQLLQEK-LDEVVRSLNTGAGGAVKRKKKAAPAVKRMKLAPS 346

>3ljn_A Hypothetical protein; ankyrin, structural genomics, PSI, structural genomics of pathogenic protozoa consortium, SGPP, ANK repeat; 2.90A {Leishmania major} Length = 364

 Score = 58.3 bits (142), Expect = 9e-10
 Identities = 16/109 (14%), Positives = 38/109 (34%), Gaps = 14/109 (12%)

Query: 250 QLDDNEKNIYEW------AKEGK--LDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGH 301
           ++  + K+             G   L+M +K L +    +    D+     L  A +  +
Sbjct: 128 EIGSHVKHCKGQTALHWCVGLGPEYLEM-IKILVQ-LGASPTAKDKADETPLMRAMEFRN 185

Query: 302 LKVVQHLIEKC----GADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
            + +  +++         ++  +  G+  L +A  I   D+    V  G
Sbjct: 186 REALDLMMDTVPSKSSLRLDYANKQGNSHLHWAILINWEDVAMRFVEMG 234

>3ljn_A Hypothetical protein; ankyrin, structural genomics, PSI, structural genomics of pathogenic protozoa consortium, SGPP, ANK repeat; 2.90A {Leishmania major} Length = 364

 Score = 57.2 bits (139), Expect = 2e-09
 Identities = 11/102 (10%), Positives = 25/102 (24%), Gaps = 9/102 (8%)

Query: 236 KGWVNVSSMINDESQLDDNEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENG 289
           K  V +       +        +         A   K ++ ++ L + K   + +    G
Sbjct: 266 KTDVFLIQACPYHNGTTVLPDRVVWLDFVPAAADPSKQEV-LQLLQE-KLDEVVRSLNTG 323

Query: 290 LNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAK 331
                    +    V +  +    A V             +K
Sbjct: 324 AGGAVKRKKKAAPAVKRMKLAP-SAPVRTRSRSRARSSAVSK 364

>3ljn_A Hypothetical protein; ankyrin, structural genomics, PSI, structural genomics of pathogenic protozoa consortium, SGPP, ANK repeat; 2.90A {Leishmania major} Length = 364

 Score = 49.5 bits (119), Expect = 7e-07
 Identities = 13/97 (13%), Positives = 26/97 (26%), Gaps = 17/97 (17%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
             +N +         K G +D   K L        +    +G   +H A       +V  
Sbjct: 47  TIQNRFGCTALHLACKFGCVDT-AKYLAS-VGEVHS--LWHGQKPIHLAVMANKTDLVVA 102

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVN 344
           L+E    +                  +  ++ E   +
Sbjct: 103 LVEG-AKERGQMP------ESLLNECDEREVNEIGSH 132

>2dzn_A Probable 26S proteasome regulatory subunit P28; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} SCOP: d.211.1.1 PDB: 2dzo_A 1ixv_A 1wg0_A Length = 228

 Score = 69.0 bits (170), Expect = 7e-14
 Identities = 23/97 (23%), Positives = 40/97 (41%), Gaps = 10/97 (10%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
             K+ +        A  G L + ++ L  L    +N  D+ G   L  A   GH      
Sbjct: 134 RIKDKFNQIPLHRAASVGSLKL-IELLCGLGKSAVNWQDKQGWTPLFHALAEGHGDAAVL 192

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVN 344
           L+EK GA+ ++ D+ G    D A    +  + ++ +N
Sbjct: 193 LVEKYGAEYDLVDNKGAKAEDVAL---NEQVKKFFLN 226

>2dzn_A Probable 26S proteasome regulatory subunit P28; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} SCOP: d.211.1.1 PDB: 2dzo_A 1ixv_A 1wg0_A Length = 228

 Score = 66.3 bits (163), Expect = 7e-13
 Identities = 27/86 (31%), Positives = 40/86 (46%), Gaps = 3/86 (3%)

Query: 262 AKEGKLDMLVKQL-TKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTD 320
              G L++ VK L  +    ++N++   G+ CLH A  +   +V Q LIE  GA V + D
Sbjct: 80  CSVGNLEV-VKSLYDRPLKPDLNKITNQGVTCLHLAVGKKWFEVSQFLIEN-GASVRIKD 137

Query: 321 SDGDYGLDYAKAIEHTDLIEYLVNSG 346
                 L  A ++    LIE L   G
Sbjct: 138 KFNQIPLHRAASVGSLKLIELLCGLG 163

>2dzn_A Probable 26S proteasome regulatory subunit P28; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} SCOP: d.211.1.1 PDB: 2dzo_A 1ixv_A 1wg0_A Length = 228

 Score = 64.0 bits (157), Expect = 5e-12
 Identities = 22/99 (22%), Positives = 36/99 (36%), Gaps = 8/99 (8%)

Query: 252 DDNEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVV 305
           D N+              +   ++  + L +    ++   D+     LH A   G LK++
Sbjct: 99  DLNKITNQGVTCLHLAVGKKWFEV-SQFLIE-NGASVRIKDKFNQIPLHRAASVGSLKLI 156

Query: 306 QHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVN 344
           + L     + VN  D  G   L +A A  H D    LV 
Sbjct: 157 ELLCGLGKSAVNWQDKQGWTPLFHALAEGHGDAAVLLVE 195

>2dzn_A Probable 26S proteasome regulatory subunit P28; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} SCOP: d.211.1.1 PDB: 2dzo_A 1ixv_A 1wg0_A Length = 228

 Score = 61.3 bits (150), Expect = 3e-11
 Identities = 18/88 (20%), Positives = 38/88 (43%), Gaps = 5/88 (5%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
             E +   + + L   K   + Q D++G   LHW+      ++   L+ K   +VN+ D 
Sbjct: 10  CMENEFFKVQELLHS-KPSLLLQKDQDGRIPLHWSVSFQAHEITSFLLSK-MENVNLDDY 67

Query: 322 DGDYG---LDYAKAIEHTDLIEYLVNSG 346
             D G      A ++ + ++++ L +  
Sbjct: 68  PDDSGWTPFHIACSVGNLEVVKSLYDRP 95

>2dzn_A Probable 26S proteasome regulatory subunit P28; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} SCOP: d.211.1.1 PDB: 2dzo_A 1ixv_A 1wg0_A Length = 228

 Score = 51.7 bits (125), Expect = 6e-08
 Identities = 12/54 (22%), Positives = 24/54 (44%)

Query: 293 LHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           LH AC       VQ L+    + +   D DG   L ++ + +  ++  +L++  
Sbjct: 6   LHQACMENEFFKVQELLHSKPSLLLQKDQDGRIPLHWSVSFQAHEITSFLLSKM 59

>3b7b_A Euchromatic histone-lysine N-methyltransferase 1; ankyrin repeat, alternative splicing, ANK repeat, chromatin regulator, nucleus, phosphorylation; 2.99A {Homo sapiens} SCOP: k.37.1.1 PDB: 3b95_A* Length = 237

 Score = 69.0 bits (170), Expect = 9e-14
 Identities = 24/101 (23%), Positives = 40/101 (39%), Gaps = 9/101 (8%)

Query: 252 DDNEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVV 305
           D N ++   W       +   +D+ VK L   K  +IN  D     CLHWA   G + + 
Sbjct: 103 DVNCQDDGGWTPMIWATEYKHVDL-VKLLLS-KGSDINIRDNEENICLHWAAFSGCVDIA 160

Query: 306 QHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           + L+     D++  +  GD  L  A      D +   ++  
Sbjct: 161 EILLAA-KCDLHAVNIHGDSPLHIAARENRYDCVVLFLSRD 200

>3b7b_A Euchromatic histone-lysine N-methyltransferase 1; ankyrin repeat, alternative splicing, ANK repeat, chromatin regulator, nucleus, phosphorylation; 2.99A {Homo sapiens} SCOP: k.37.1.1 PDB: 3b95_A* Length = 237

 Score = 66.3 bits (163), Expect = 7e-13
 Identities = 16/99 (16%), Positives = 37/99 (37%), Gaps = 9/99 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N ++  E       A  G +D+  + L      +++ ++ +G + LH A        V  
Sbjct: 138 NIRDNEENICLHWAAFSGCVDI-AEILLA-AKCDLHAVNIHGDSPLHIAARENRYDCVVL 195

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
            + +  +DV + + +G+  L  A           +  + 
Sbjct: 196 FLSR-DSDVTLKNKEGETPLQCASLNSQVWSALQMSKAL 233

>3b7b_A Euchromatic histone-lysine N-methyltransferase 1; ankyrin repeat, alternative splicing, ANK repeat, chromatin regulator, nucleus, phosphorylation; 2.99A {Homo sapiens} SCOP: k.37.1.1 PDB: 3b95_A* Length = 237

 Score = 65.1 bits (160), Expect = 2e-12
 Identities = 29/99 (29%), Positives = 47/99 (47%), Gaps = 8/99 (8%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           +  +  +       A+   L+  VK L K     ++  D  G  CLH A  +GH +VVQ+
Sbjct: 38  DTCSEDQRTPLMEAAENNHLEA-VKYLIK-AGALVDPKDAEGSTCLHLAAKKGHYEVVQY 95

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L+     DVN  D  G   + +A   +H DL++ L++ G
Sbjct: 96  LLSNGQMDVNCQDDGGWTPMIWATEYKHVDLVKLLLSKG 134

>3b7b_A Euchromatic histone-lysine N-methyltransferase 1; ankyrin repeat, alternative splicing, ANK repeat, chromatin regulator, nucleus, phosphorylation; 2.99A {Homo sapiens} SCOP: k.37.1.1 PDB: 3b95_A* Length = 237

 Score = 63.2 bits (155), Expect = 1e-11
 Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 1/66 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           N     +N  + LH A + GH+ +   L++  GA+++    D    L  A    H + ++
Sbjct: 3   NFKMEHQNKRSPLHAAAEAGHVDICHMLVQA-GANIDTCSEDQRTPLMEAAENNHLEAVK 61

Query: 341 YLVNSG 346
           YL+ +G
Sbjct: 62  YLIKAG 67

>3b7b_A Euchromatic histone-lysine N-methyltransferase 1; ankyrin repeat, alternative splicing, ANK repeat, chromatin regulator, nucleus, phosphorylation; 2.99A {Homo sapiens} SCOP: k.37.1.1 PDB: 3b95_A* Length = 237

 Score = 47.8 bits (115), Expect = 1e-06
 Identities = 11/68 (16%), Positives = 23/68 (33%), Gaps = 9/68 (13%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           +  NI+        A+E + D  V      +D ++   ++ G   L  A     +     
Sbjct: 171 HAVNIHGDSPLHIAARENRYDC-VVLFLS-RDSDVTLKNKEGETPLQCASLNSQVWSALQ 228

Query: 308 LIEKCGAD 315
           + +    D
Sbjct: 229 MSKA-LQD 235

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 66.1 bits (161), Expect = 1e-13
 Identities = 16/77 (20%), Positives = 29/77 (37%), Gaps = 3/77 (3%)

Query: 11  IFVGNLPWTVSHNELKKFFSEYGQIMNA--SVMFDKN-TGLSKGFGFVTFQNKEAVDKVF 67
           + +  LP+T +  E+  FF ++  I      ++F     G   G  FV F  +E      
Sbjct: 26  VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85

Query: 68  STDSHVLEGSRLSIQPS 84
                +L    + +  S
Sbjct: 86  RKHKDLLGKRYIELFRS 102

>2y1l_E Darpin-8.4; hydrolase-inhibitor complex, DEVD darpin, ankyrin repeat Pro ribosome display, apoptosis; 1.80A {Synthetic source} PDB: 3noc_D* 4dx5_D* 2j8s_D* 4dx6_D* 4dx7_D* 3nog_D* 1mj0_A 1svx_A 2qyj_A 2bkg_A 2p2c_P 2bkk_B* 2v5q_C 2xee_A 2xeh_A 3q9n_C* 3q9u_C* Length = 169

 Score = 67.0 bits (165), Expect = 1e-13
 Identities = 30/96 (31%), Positives = 43/96 (44%), Gaps = 9/96 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N  +          A  G L++ V+ L K    ++N  D  G   LH A   GHL++V+ 
Sbjct: 74  NAVDHAGMTPLRLAALFGHLEI-VEVLLK-NGADVNANDMEGHTPLHLAAMFGHLEIVEV 131

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLV 343
           L++  GADVN  D  G    D +    + DL E L 
Sbjct: 132 LLKN-GADVNAQDKFGKTAFDISIDNGNEDLAEILQ 166

>2y1l_E Darpin-8.4; hydrolase-inhibitor complex, DEVD darpin, ankyrin repeat Pro ribosome display, apoptosis; 1.80A {Synthetic source} PDB: 3noc_D* 4dx5_D* 2j8s_D* 4dx6_D* 4dx7_D* 3nog_D* 1mj0_A 1svx_A 2qyj_A 2bkg_A 2p2c_P 2bkk_B* 2v5q_C 2xee_A 2xeh_A 3q9n_C* 3q9u_C* Length = 169

 Score = 62.8 bits (154), Expect = 5e-12
 Identities = 29/85 (34%), Positives = 45/85 (52%), Gaps = 3/85 (3%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
           A+ G+ D  V+ L      ++N  D +G   LH A   GHL++V+ L++  GADVN  D 
Sbjct: 22  ARAGRDDE-VRILMA-NGADVNAEDASGWTPLHLAAFNGHLEIVEVLLKN-GADVNAVDH 78

Query: 322 DGDYGLDYAKAIEHTDLIEYLVNSG 346
            G   L  A    H +++E L+ +G
Sbjct: 79  AGMTPLRLAALFGHLEIVEVLLKNG 103

>2y1l_E Darpin-8.4; hydrolase-inhibitor complex, DEVD darpin, ankyrin repeat Pro ribosome display, apoptosis; 1.80A {Synthetic source} PDB: 3noc_D* 4dx5_D* 2j8s_D* 4dx6_D* 4dx7_D* 3nog_D* 1mj0_A 1svx_A 2qyj_A 2bkg_A 2p2c_P 2bkk_B* 2v5q_C 2xee_A 2xeh_A 3q9n_C* 3q9u_C* Length = 169

 Score = 54.3 bits (132), Expect = 4e-09
 Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 2/68 (2%)

Query: 279 DFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDL 338
             + +    +    L  A   G    V+ L+   GADVN  D+ G   L  A    H ++
Sbjct: 5   HHHHHH-GSDLGKKLLEAARAGRDDEVRILMAN-GADVNAEDASGWTPLHLAAFNGHLEI 62

Query: 339 IEYLVNSG 346
           +E L+ +G
Sbjct: 63  VEVLLKNG 70

>2y1l_E Darpin-8.4; hydrolase-inhibitor complex, DEVD darpin, ankyrin repeat Pro ribosome display, apoptosis; 1.80A {Synthetic source} PDB: 3noc_D* 4dx5_D* 2j8s_D* 4dx6_D* 4dx7_D* 3nog_D* 1mj0_A 1svx_A 2qyj_A 2bkg_A 2p2c_P 2bkk_B* 2v5q_C 2xee_A 2xeh_A 3q9n_C* 3q9u_C* Length = 169

 Score = 43.1 bits (103), Expect = 3e-05
 Identities = 13/64 (20%), Positives = 26/64 (40%), Gaps = 8/64 (12%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N  ++         A  G L++ V+ L K    ++N  D+ G      + D G+  + + 
Sbjct: 107 NANDMEGHTPLHLAAMFGHLEI-VEVLLK-NGADVNAQDKFGKTAFDISIDNGNEDLAEI 164

Query: 308 LIEK 311
           L + 
Sbjct: 165 LQKL 168

>1ihb_A P18-INK4C(INK6), cyclin-dependent kinase 6 inhibitor; cell cycle inhibitor, ankyrin repeat, CDK 4/6 inhibitor; 1.95A {Homo sapiens} SCOP: d.211.1.1 PDB: 1bu9_A 1g3n_B 1mx4_A 1mx2_A 1mx6_A Length = 162

 Score = 66.6 bits (164), Expect = 2e-13
 Identities = 24/99 (24%), Positives = 46/99 (46%), Gaps = 8/99 (8%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           + K+   +      A+ G LD  ++ L +    ++N  D  G   LH A   GHL+VV+ 
Sbjct: 64  DLKDRTGFAVIHDAARAGFLDT-LQTLLE-FQADVNIEDNEGNLPLHLAAKEGHLRVVEF 121

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L++   ++V   +  GD   D A+     +++  +  +G
Sbjct: 122 LVKHTASNVGHRNHKGDTACDLARLYGRNEVVSLMQANG 160

>1ihb_A P18-INK4C(INK6), cyclin-dependent kinase 6 inhibitor; cell cycle inhibitor, ankyrin repeat, CDK 4/6 inhibitor; 1.95A {Homo sapiens} SCOP: d.211.1.1 PDB: 1bu9_A 1g3n_B 1mx4_A 1mx2_A 1mx6_A Length = 162

 Score = 66.3 bits (163), Expect = 2e-13
 Identities = 27/98 (27%), Positives = 45/98 (45%), Gaps = 8/98 (8%)

Query: 254 NEKNIYEW-----AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHL 308
           N +N +        K G  ++  ++L   +  N +  D  G   +H A   G L  +Q L
Sbjct: 32  NAQNGFGRTALQVMKLGNPEI-ARRLLL-RGANPDLKDRTGFAVIHDAARAGFLDTLQTL 89

Query: 309 IEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           +E   ADVN+ D++G+  L  A    H  ++E+LV   
Sbjct: 90  LEF-QADVNIEDNEGNLPLHLAAKEGHLRVVEFLVKHT 126

>1ihb_A P18-INK4C(INK6), cyclin-dependent kinase 6 inhibitor; cell cycle inhibitor, ankyrin repeat, CDK 4/6 inhibitor; 1.95A {Homo sapiens} SCOP: d.211.1.1 PDB: 1bu9_A 1g3n_B 1mx4_A 1mx2_A 1mx6_A Length = 162

 Score = 56.6 bits (138), Expect = 5e-10
 Identities = 14/62 (22%), Positives = 26/62 (41%), Gaps = 2/62 (3%)

Query: 285 LDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVN 344
           + E   N L  A  RG L+ +  L++    +VN  +  G   L     + + ++   L+ 
Sbjct: 1   MAEPWGNELASAAARGDLEQLTSLLQN-NVNVNAQNGFGRTALQVM-KLGNPEIARRLLL 58

Query: 345 SG 346
            G
Sbjct: 59  RG 60

>1ihb_A P18-INK4C(INK6), cyclin-dependent kinase 6 inhibitor; cell cycle inhibitor, ankyrin repeat, CDK 4/6 inhibitor; 1.95A {Homo sapiens} SCOP: d.211.1.1 PDB: 1bu9_A 1g3n_B 1mx4_A 1mx2_A 1mx6_A Length = 162

 Score = 53.5 bits (130), Expect = 6e-09
 Identities = 13/66 (19%), Positives = 28/66 (42%), Gaps = 2/66 (3%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           N+N  +  G   L      G+ ++ + L+ + GA+ ++ D  G   +  A      D ++
Sbjct: 30  NVNAQNGFGRTALQVMK-LGNPEIARRLLLR-GANPDLKDRTGFAVIHDAARAGFLDTLQ 87

Query: 341 YLVNSG 346
            L+   
Sbjct: 88  TLLEFQ 93

>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 = 65.2 bits (159), Expect = 2e-13
 Identities = 22/66 (33%), Positives = 27/66 (40%), Gaps = 11/66 (16%)

Query: 4  SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE-- 61
          S R  N++ V  LP + S  +LK    E G +  A V          G G V F  KE  
Sbjct: 11 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGVVEFVRKEDM 63

Query: 62 --AVDK 65
            AV K
Sbjct: 64 TYAVRK 69

>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 = 64.8 bits (158), Expect = 2e-13
 Identities = 12/78 (15%), Positives = 34/78 (43%), Gaps = 5/78 (6%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYG-QIMNASVMFD-KNTGLSKGFGFVTFQNKEAVD-- 64
           ++F+G +P      E+ +  ++    +++  V     +   ++GF FV +++  A    
Sbjct: 9  CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68

Query: 65 -KVFSTDSHVLEGSRLSI 81
           +        L G ++++
Sbjct: 69 RRKLMPGRIQLWGHQIAV 86

>1bi7_B P16INK4A, MTS1, multiple tumor suppressor; cyclin dependent kinase, cyclin dependent kinase inhibitory protein, CDK, cell cycle; 3.40A {Homo sapiens} SCOP: d.211.1.1 PDB: 1a5e_A 1dc2_A 2a5e_A Length = 156

 Score = 66.0 bits (162), Expect = 2e-13
 Identities = 24/99 (24%), Positives = 36/99 (36%), Gaps = 9/99 (9%)

Query: 254 NEKNIYEW-----AKEGKLDMLVKQLTKLKDFNINQLDENGLNC-LHWACDRGHLKVVQH 307
           N  N Y          G   +  + L        N  D   L   +H A   G L  +  
Sbjct: 39  NAPNSYGRRPIQVMMMGSARV-AELLLL-HGAEPNCADPATLTRPVHDAAREGFLDTLVV 96

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L    GA ++V D+ G   +D A+ + H D+  YL  + 
Sbjct: 97  LHRA-GARLDVRDAWGRLPVDLAEELGHRDVARYLRAAA 134

>1bi7_B P16INK4A, MTS1, multiple tumor suppressor; cyclin dependent kinase, cyclin dependent kinase inhibitory protein, CDK, cell cycle; 3.40A {Homo sapiens} SCOP: d.211.1.1 PDB: 1a5e_A 1dc2_A 2a5e_A Length = 156

 Score = 61.7 bits (151), Expect = 7e-12
 Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 2/61 (3%)

Query: 286 DENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNS 345
            E   + L  A  RG ++ V+ L+E  GA+ N  +S G   +     +    + E L+  
Sbjct: 9   MEPSADWLATAAARGRVEEVRALLEA-GANPNAPNSYGRRPIQVM-MMGSARVAELLLLH 66

Query: 346 G 346
           G
Sbjct: 67  G 67

>1bi7_B P16INK4A, MTS1, multiple tumor suppressor; cyclin dependent kinase, cyclin dependent kinase inhibitory protein, CDK, cell cycle; 3.40A {Homo sapiens} SCOP: d.211.1.1 PDB: 1a5e_A 1dc2_A 2a5e_A Length = 156

 Score = 61.3 bits (150), Expect = 1e-11
 Identities = 18/86 (20%), Positives = 32/86 (37%), Gaps = 5/86 (5%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
           A  G+++  V+ L +    N N  +  G   +      G  +V + L+   GA+ N  D 
Sbjct: 20  AARGRVEE-VRALLE-AGANPNAPNSYGRRPIQVMM-MGSARVAELLLLH-GAEPNCADP 75

Query: 322 DGDYG-LDYAKAIEHTDLIEYLVNSG 346
                 +  A      D +  L  +G
Sbjct: 76  ATLTRPVHDAAREGFLDTLVVLHRAG 101

>1bi7_B P16INK4A, MTS1, multiple tumor suppressor; cyclin dependent kinase, cyclin dependent kinase inhibitory protein, CDK, cell cycle; 3.40A {Homo sapiens} SCOP: d.211.1.1 PDB: 1a5e_A 1dc2_A 2a5e_A Length = 156

 Score = 54.4 bits (132), Expect = 3e-09
 Identities = 14/77 (18%), Positives = 26/77 (33%), Gaps = 10/77 (12%)

Query: 254 NEKNIYEW-------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQ 306
           N  +           A+EG LD  +  L +     ++  D  G   +  A + GH  V +
Sbjct: 71  NCADPATLTRPVHDAAREGFLDT-LVVLHR-AGARLDVRDAWGRLPVDLAEELGHRDVAR 128

Query: 307 HLIEKCGADVNVTDSDG 323
           +L          ++   
Sbjct: 129 YLRAA-AGGTRGSNHAR 144

>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 = 64.8 bits (158), Expect = 2e-13
 Identities = 19/62 (30%), Positives = 25/62 (40%), Gaps = 7/62 (11%)

Query: 4  SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAV 63
          S R  N++ V  LP + S  +LK    E G +  A V          G G V F  KE +
Sbjct: 12 SRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVY-------RDGTGVVEFVRKEDM 64

Query: 64 DK 65
            
Sbjct: 65 TY 66

>1k1a_A B-cell lymphoma 3-encoded protein; BCL-3, NF-kappab transcription factors, ikappab proteins; 1.86A {Homo sapiens} SCOP: d.211.1.1 PDB: 1k1b_A Length = 241

 Score = 67.9 bits (167), Expect = 2e-13
 Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 1/66 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           N+N    +G + LH A  RG L +V+ L+   GAD ++ +   D  L  A++    D++ 
Sbjct: 175 NVNAQMYSGSSALHSASGRGLLPLVRTLVRS-GADSSLKNCHNDTPLMVARSRRVIDILR 233

Query: 341 YLVNSG 346
                 
Sbjct: 234 GKATRP 239

>1k1a_A B-cell lymphoma 3-encoded protein; BCL-3, NF-kappab transcription factors, ikappab proteins; 1.86A {Homo sapiens} SCOP: d.211.1.1 PDB: 1k1b_A Length = 241

 Score = 63.6 bits (156), Expect = 6e-12
 Identities = 18/102 (17%), Positives = 29/102 (28%), Gaps = 11/102 (10%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDF---NINQLDENGLNCLHWACDRGHLKV 304
              +            +G L   V +L  L       ++  +      LH A       V
Sbjct: 3   TRADEDGDTPLHIAVVQGNLPA-VHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSV 61

Query: 305 VQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           V+ L+   GA     D  G      A        +  L++S 
Sbjct: 62  VRLLVTA-GASPMALDRHGQTAAHLACEHRSPTCLRALLDSA 102

>1k1a_A B-cell lymphoma 3-encoded protein; BCL-3, NF-kappab transcription factors, ikappab proteins; 1.86A {Homo sapiens} SCOP: d.211.1.1 PDB: 1k1b_A Length = 241

 Score = 63.2 bits (155), Expect = 8e-12
 Identities = 19/103 (18%), Positives = 39/103 (37%), Gaps = 12/103 (11%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTK---LKDFNINQLDENGLNCLHWACDRGHLKV 304
              + +         +       ++ L         ++   + +GL  LH A +    + 
Sbjct: 73  MALDRHGQTAAHLACEHRSPTC-LRALLDSAAPGTLDLEARNYDGLTALHVAVNTECQET 131

Query: 305 VQHLIEKCGADVNVTDS-DGDYGLDYAKAIEHTDLIEYLVNSG 346
           VQ L+E+ GAD++  D   G   L +A       +++ L+  G
Sbjct: 132 VQLLLER-GADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQHG 173

>1k1a_A B-cell lymphoma 3-encoded protein; BCL-3, NF-kappab transcription factors, ikappab proteins; 1.86A {Homo sapiens} SCOP: d.211.1.1 PDB: 1k1b_A Length = 241

 Score = 61.7 bits (151), Expect = 3e-11
 Identities = 26/106 (24%), Positives = 43/106 (40%), Gaps = 10/106 (9%)

Query: 248 ESQLDDNEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLD-ENGLNCLHWACDRG 300
              LD   +N                +  V+ L + +  +I+ +D ++G + L  A +  
Sbjct: 104 PGTLDLEARNYDGLTALHVAVNTECQET-VQLLLE-RGADIDAVDIKSGRSPLIHAVENN 161

Query: 301 HLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
            L +VQ L++  GA+VN     G   L  A       L+  LV SG
Sbjct: 162 SLSMVQLLLQH-GANVNAQMYSGSSALHSASGRGLLPLVRTLVRSG 206

>1k1a_A B-cell lymphoma 3-encoded protein; BCL-3, NF-kappab transcription factors, ikappab proteins; 1.86A {Homo sapiens} SCOP: d.211.1.1 PDB: 1k1b_A Length = 241

 Score = 59.0 bits (144), Expect = 2e-10
 Identities = 19/103 (18%), Positives = 35/103 (33%), Gaps = 13/103 (12%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           +  N                 + V+ L      +   LD +G    H AC+      ++ 
Sbjct: 40  DIYNNLRQTPLHLAVITTLPSV-VRLLVT-AGASPMALDRHGQTAAHLACEHRSPTCLRA 97

Query: 308 LIEKCGA----DVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L++   A    D+   + DG   L  A   E  + ++ L+  G
Sbjct: 98  LLDS-AAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERG 139

>1k1a_A B-cell lymphoma 3-encoded protein; BCL-3, NF-kappab transcription factors, ikappab proteins; 1.86A {Homo sapiens} SCOP: d.211.1.1 PDB: 1k1b_A Length = 241

 Score = 56.3 bits (137), Expect = 2e-09
 Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 3/68 (4%)

Query: 282 INQLDENGLNCLHWACDRGHLKVVQHLIE---KCGADVNVTDSDGDYGLDYAKAIEHTDL 338
             + DE+G   LH A  +G+L  V  L+    + G ++++ ++     L  A       +
Sbjct: 2   ATRADEDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSV 61

Query: 339 IEYLVNSG 346
           +  LV +G
Sbjct: 62  VRLLVTAG 69

>1n0q_A 3ANK, 3 ankyrin repeats; structural protein; 1.26A {} SCOP: k.37.1.1 Length = 93

 Score = 63.9 bits (157), Expect = 3e-13
 Identities = 32/85 (37%), Positives = 49/85 (57%), Gaps = 3/85 (3%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
           A+ G L++ VK L +    ++N  D+NG   LH A   GHL+VV+ L+E  GADVN  D 
Sbjct: 10  ARNGHLEV-VKLLLE-AGADVNAKDKNGRTPLHLAARNGHLEVVKLLLEA-GADVNAKDK 66

Query: 322 DGDYGLDYAKAIEHTDLIEYLVNSG 346
           +G   L  A    H ++++ L+ +G
Sbjct: 67  NGRTPLHLAARNGHLEVVKLLLEAG 91

>1n0q_A 3ANK, 3 ankyrin repeats; structural protein; 1.26A {} SCOP: k.37.1.1 Length = 93

 Score = 58.9 bits (144), Expect = 2e-11
 Identities = 24/59 (40%), Positives = 34/59 (57%), Gaps = 1/59 (1%)

Query: 288 NGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           NG   LH A   GHL+VV+ L+E  GADVN  D +G   L  A    H ++++ L+ +G
Sbjct: 1   NGRTPLHLAARNGHLEVVKLLLEA-GADVNAKDKNGRTPLHLAARNGHLEVVKLLLEAG 58

>1n0q_A 3ANK, 3 ankyrin repeats; structural protein; 1.26A {} SCOP: k.37.1.1 Length = 93

 Score = 48.5 bits (117), Expect = 9e-08
 Identities = 24/67 (35%), Positives = 35/67 (52%), Gaps = 9/67 (13%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N K+          A+ G L++ VK L +    ++N  D+NG   LH A   GHL+VV+ 
Sbjct: 29  NAKDKNGRTPLHLAARNGHLEV-VKLLLE-AGADVNAKDKNGRTPLHLAARNGHLEVVKL 86

Query: 308 LIEKCGA 314
           L+E  GA
Sbjct: 87  LLEA-GA 92

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 64.4 bits (157), Expect = 3e-13
 Identities = 12/74 (16%), Positives = 33/74 (44%), Gaps = 2/74 (2%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          + V  +P++   N+++ FF    ++    ++ D   G + G G V F + +   +    +
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEALKRN 76

Query: 71 SHVLEGSRLSIQPS 84
            ++    + + P+
Sbjct: 77 RMLMIQRYVEVSPA 90

>1awc_B Protein (GA binding protein beta 1); complex (transcription regulation/DNA), DNA-binding, nuclear protein, ETS domain, ankyrin repeats; HET: DNA BRU CBR; 2.15A {Mus musculus} SCOP: d.211.1.1 Length = 153

 Score = 65.5 bits (161), Expect = 4e-13
 Identities = 26/95 (27%), Positives = 42/95 (44%), Gaps = 9/95 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           + +   +       A EG  ++ V+ L K    ++N  D   +  LHWA +  H +VV+ 
Sbjct: 61  DARTKVDRTPLHMAASEGHANI-VEVLLK-HGADVNAKDMLKMTALHWATEHNHQEVVEL 118

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYL 342
           LI+  GADV+          D +    + DL E L
Sbjct: 119 LIKY-GADVHTQSKFCKTAFDISIDNGNEDLAEIL 152

>1awc_B Protein (GA binding protein beta 1); complex (transcription regulation/DNA), DNA-binding, nuclear protein, ETS domain, ankyrin repeats; HET: DNA BRU CBR; 2.15A {Mus musculus} SCOP: d.211.1.1 Length = 153

 Score = 58.2 bits (142), Expect = 1e-10
 Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 1/66 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           + +   +     LH A   GH  +V+ L++  GADVN  D      L +A    H +++E
Sbjct: 59  SRDARTKVDRTPLHMAASEGHANIVEVLLKH-GADVNAKDMLKMTALHWATEHNHQEVVE 117

Query: 341 YLVNSG 346
            L+  G
Sbjct: 118 LLIKYG 123

>1awc_B Protein (GA binding protein beta 1); complex (transcription regulation/DNA), DNA-binding, nuclear protein, ETS domain, ankyrin repeats; HET: DNA BRU CBR; 2.15A {Mus musculus} SCOP: d.211.1.1 Length = 153

 Score = 53.5 bits (130), Expect = 4e-09
 Identities = 15/66 (22%), Positives = 24/66 (36%), Gaps = 2/66 (3%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
                D  G + LH A   GH    + L+   G   +         L  A +  H +++E
Sbjct: 27  PFTT-DWLGTSPLHLAAQYGHFSTTEVLLRA-GVSRDARTKVDRTPLHMAASEGHANIVE 84

Query: 341 YLVNSG 346
            L+  G
Sbjct: 85  VLLKHG 90

>1awc_B Protein (GA binding protein beta 1); complex (transcription regulation/DNA), DNA-binding, nuclear protein, ETS domain, ankyrin repeats; HET: DNA BRU CBR; 2.15A {Mus musculus} SCOP: d.211.1.1 Length = 153

 Score = 44.7 bits (107), Expect = 5e-06
 Identities = 16/59 (27%), Positives = 21/59 (35%), Gaps = 2/59 (3%)

Query: 288 NGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           +    L  A   G    V+ L+   GA    TD  G   L  A    H    E L+ +G
Sbjct: 1   DLGKKLLEAARAGQDDEVRILMAN-GAPFT-TDWLGTSPLHLAAQYGHFSTTEVLLRAG 57

>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 = 63.8 bits (156), Expect = 4e-13
 Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 9/81 (11%)

Query: 2  SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          S+ + ++  +FV NL  TV+   L+K FS++G++     +        K + F+ F  ++
Sbjct: 5  SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERD 56

Query: 62 -AVDKVFSTDSHVLEGSRLSI 81
           AV  +   +   LEG  + I
Sbjct: 57 GAVKAMEEMNGKDLEGENIEI 77

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 63.9 bits (156), Expect = 5e-13
 Identities = 19/91 (20%), Positives = 42/91 (46%), Gaps = 5/91 (5%)

Query: 11  IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE-AVDKVFST 69
           +++ NLP+ ++  E+   F +YG I    V    NT  ++G  +V +++   A + V   
Sbjct: 11  LYIRNLPYKITAEEMYDIFGKYGPIRQIRVG---NTPETRGTAYVVYEDIFDAKNAVDHL 67

Query: 70  DSHVLEGSRLSIQPSDSHNRMAENMEDRFNQ 100
               +    L +   ++ NR  + M+ +  +
Sbjct: 68  SGFNVSNRYLVVLYYNA-NRAFQKMDTKKKE 97

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 63.3 bits (154), Expect = 6e-13
 Identities = 16/83 (19%), Positives = 28/83 (33%), Gaps = 6/83 (7%)

Query: 3  NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
                  ++VGNLP     ++LK+   E G     SV         +   F+ + +  A
Sbjct: 14 EGAPLAADVYVGNLPRDARVSDLKRALRELG-----SVPLRLTWQGPRRRAFLHYPDSAA 68

Query: 63 VDKVFST-DSHVLEGSRLSIQPS 84
            +  S      L    L +  +
Sbjct: 69 AQQAVSCLQGLRLGTDTLRVALA 91

>1ycs_B 53BP2, P53BP2; ankyrin repeats, SH3, tumor suppressor, multigene family, nuclear protein, phosphorylation, disease mutation, polymorphism; 2.20A {Homo sapiens} SCOP: b.34.2.1 d.211.1.1 PDB: 4a63_B Length = 239

 Score = 66.5 bits (163), Expect = 6e-13
 Identities = 25/85 (29%), Positives = 48/85 (56%), Gaps = 3/85 (3%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
           + EG+ D+ V+++   +  + +  ++ G+  LH A   GH ++V+ L++  G +VN  DS
Sbjct: 45  SLEGEFDL-VQRIIY-EVDDPSLPNDEGITALHNAVCAGHTEIVKFLVQF-GVNVNAADS 101

Query: 322 DGDYGLDYAKAIEHTDLIEYLVNSG 346
           DG   L  A +  +  + ++LV SG
Sbjct: 102 DGWTPLHCAASCNNVQVCKFLVESG 126

>1ycs_B 53BP2, P53BP2; ankyrin repeats, SH3, tumor suppressor, multigene family, nuclear protein, phosphorylation, disease mutation, polymorphism; 2.20A {Homo sapiens} SCOP: b.34.2.1 d.211.1.1 PDB: 4a63_B Length = 239

 Score = 59.9 bits (146), Expect = 1e-10
 Identities = 15/85 (17%), Positives = 32/85 (37%), Gaps = 4/85 (4%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
            +         +        +   +   L  L  +   G   +VQ +I +   D ++ + 
Sbjct: 13  KRTNLRKT-GSERIA-HGMRVK-FNPLPLALLLDSSLEGEFDLVQRIIYE-VDDPSLPND 68

Query: 322 DGDYGLDYAKAIEHTDLIEYLVNSG 346
           +G   L  A    HT+++++LV  G
Sbjct: 69  EGITALHNAVCAGHTEIVKFLVQFG 93

>1ycs_B 53BP2, P53BP2; ankyrin repeats, SH3, tumor suppressor, multigene family, nuclear protein, phosphorylation, disease mutation, polymorphism; 2.20A {Homo sapiens} SCOP: b.34.2.1 d.211.1.1 PDB: 4a63_B Length = 239

 Score = 57.2 bits (139), Expect = 1e-09
 Identities = 11/94 (11%), Positives = 27/94 (28%), Gaps = 12/94 (12%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNC---LHWACDRGHLKV 304
           N  +   W      A    + +  K L +     +  +  + +          + G+ + 
Sbjct: 97  NAADSDGWTPLHCAASCNNVQV-CKFLVE-SGAAVFAMTYSDMQTAADKCEEMEEGYTQC 154

Query: 305 VQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDL 338
            Q L       + + +    Y L   +     +L
Sbjct: 155 SQFLYGV-QEKMGIMNKGVIYALWDYEPQNDDEL 187

>1ycs_B 53BP2, P53BP2; ankyrin repeats, SH3, tumor suppressor, multigene family, nuclear protein, phosphorylation, disease mutation, polymorphism; 2.20A {Homo sapiens} SCOP: b.34.2.1 d.211.1.1 PDB: 4a63_B Length = 239

 Score = 52.2 bits (126), Expect = 4e-08
 Identities = 9/61 (14%), Positives = 15/61 (24%), Gaps = 2/61 (3%)

Query: 286 DENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNS 345
           +  G   L         K     I   G  V          L  +      DL++ ++  
Sbjct: 2   EITGQVSLPPGKRTNLRKTGSERIAH-GMRVKFNP-LPLALLLDSSLEGEFDLVQRIIYE 59

Query: 346 G 346
            
Sbjct: 60  V 60

>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 = 63.4 bits (155), Expect = 6e-13
 Identities = 12/59 (20%), Positives = 24/59 (40%), Gaps = 2/59 (3%)

Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          Q   ++VGNL   V+   + + FS+ G   +  ++ +  +     + FV F        
Sbjct: 14 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAA 70

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 62.8 bits (153), Expect = 6e-13
 Identities = 16/83 (19%), Positives = 25/83 (30%), Gaps = 8/83 (9%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          + I V NLP   +  E+     +Y                +K   FVT  N E       
Sbjct: 6  SGILVKNLPQDSNCQEVHDLLKDYDLK-------YCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 69 T-DSHVLEGSRLSIQPSDSHNRM 90
              +   G  L +Q   +   +
Sbjct: 59 MFHQYSFRGKDLIVQLQPTDALL 81

>2l6b_A NR1C; ankyrin, consensus, repeat protein, ising model, DE NOV; NMR {Escherichia coli} Length = 115

 Score = 63.2 bits (155), Expect = 8e-13
 Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           ++N   ++G   LH A   GH ++V+ L+ K GADVN    DG+     AK   H ++++
Sbjct: 34  DVNARSKDGNTPLHLAAKNGHAEIVKLLLAK-GADVNARSKDGNTPEHLAKKNGHHEIVK 92

Query: 341 YLVNSG 346
            L   G
Sbjct: 93  LLDAKG 98

>2l6b_A NR1C; ankyrin, consensus, repeat protein, ising model, DE NOV; NMR {Escherichia coli} Length = 115

 Score = 58.5 bits (143), Expect = 4e-11
 Identities = 22/82 (26%), Positives = 35/82 (42%), Gaps = 9/82 (10%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N ++          AK G  ++ VK L   K  ++N   ++G    H A   GH ++V+ 
Sbjct: 36  NARSKDGNTPLHLAAKNGHAEI-VKLLLA-KGADVNARSKDGNTPEHLAKKNGHHEIVKL 93

Query: 308 LIEKCGADVNVTDSDGDYGLDY 329
           L  K GADVN       +   +
Sbjct: 94  LDAK-GADVNARSWGSSHHHHH 114

>2l6b_A NR1C; ankyrin, consensus, repeat protein, ising model, DE NOV; NMR {Escherichia coli} Length = 115

 Score = 57.8 bits (141), Expect = 8e-11
 Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 3/66 (4%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
                 ++G   LH A   GH + V+ L+ K GADVN    DG+  L  A    H ++++
Sbjct: 3   MWG--SKDGNTPLHNAAKNGHAEEVKKLLSK-GADVNARSKDGNTPLHLAAKNGHAEIVK 59

Query: 341 YLVNSG 346
            L+  G
Sbjct: 60  LLLAKG 65

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 62.5 bits (152), Expect = 9e-13
 Identities = 15/81 (18%), Positives = 34/81 (41%), Gaps = 10/81 (12%)

Query: 6  RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE---- 61
          +++ K+ + N+P  +    L     +YG + +   +   +         VT+ +K+    
Sbjct: 13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKDQARQ 69

Query: 62 AVDKVFSTDSHVLEGSRLSIQ 82
          A+DK+   +   LE   L + 
Sbjct: 70 ALDKL---NGFQLENFTLKVA 87

>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 = 62.3 bits (152), Expect = 9e-13
 Identities = 13/78 (16%), Positives = 33/78 (42%), Gaps = 2/78 (2%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          + + +   P+ V+   + +F +     +   ++ + + G   G+ FV F N+E V +   
Sbjct: 11 HTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAH-GNKTGYIFVDFSNEEEVKQALK 68

Query: 69 TDSHVLEGSRLSIQPSDS 86
           +   + G  + +    S
Sbjct: 69 CNREYMGGRYIEVFREKS 86

>3eu9_A Huntingtin-interacting protein 14; epigenetics, ankyrin repeats, methyllyine binding, huntingti interacting protein 14, acyltransferase, ANK repeat; HET: HIS; 1.99A {Homo sapiens} Length = 240

 Score = 65.9 bits (162), Expect = 1e-12
 Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 1/66 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           ++  +D+     +  A   G  +  + L+E  G DV   D +    L +A      DL++
Sbjct: 1   HMTHIDDYSTWDIVKATQYGIYERCRELVEA-GYDVRQPDKENVTLLHWAAINNRIDLVK 59

Query: 341 YLVNSG 346
           Y ++ G
Sbjct: 60  YYISKG 65

>3eu9_A Huntingtin-interacting protein 14; epigenetics, ankyrin repeats, methyllyine binding, huntingti interacting protein 14, acyltransferase, ANK repeat; HET: HIS; 1.99A {Homo sapiens} Length = 240

 Score = 64.4 bits (158), Expect = 4e-12
 Identities = 21/100 (21%), Positives = 41/100 (41%), Gaps = 10/100 (10%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
              + Y         + G  +   ++L +   +++ Q D+  +  LHWA     + +V++
Sbjct: 3   THIDDYSTWDIVKATQYGIYER-CRELVE-AGYDVRQPDKENVTLLHWAAINNRIDLVKY 60

Query: 308 LIEKCGADVNVTDSD-GDYGLDYAKAIEHTDLIEYLVNSG 346
            I K GA V+    D     L +A    H  ++  L+  G
Sbjct: 61  YISK-GAIVDQLGGDLNSTPLHWATRQGHLSMVVQLMKYG 99

>3eu9_A Huntingtin-interacting protein 14; epigenetics, ankyrin repeats, methyllyine binding, huntingti interacting protein 14, acyltransferase, ANK repeat; HET: HIS; 1.99A {Homo sapiens} Length = 240

 Score = 62.5 bits (153), Expect = 1e-11
 Identities = 20/67 (29%), Positives = 36/67 (53%), Gaps = 2/67 (2%)

Query: 281 NINQLDE-NGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLI 339
           ++N  D+ +    LHWA   G+  V+  L+E  GA+V+  +  G+  LD AK  ++  +I
Sbjct: 168 SVNLGDKYHKNTALHWAVLAGNTTVISLLLEA-GANVDAQNIKGESALDLAKQRKNVWMI 226

Query: 340 EYLVNSG 346
            +L  + 
Sbjct: 227 NHLQEAR 233

>3eu9_A Huntingtin-interacting protein 14; epigenetics, ankyrin repeats, methyllyine binding, huntingti interacting protein 14, acyltransferase, ANK repeat; HET: HIS; 1.99A {Homo sapiens} Length = 240

 Score = 61.7 bits (151), Expect = 3e-11
 Identities = 28/86 (32%), Positives = 43/86 (50%), Gaps = 4/86 (4%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
            ++G L M V QL K    + + +D  G +C+H A   GH  +V +LI K G DV++ D 
Sbjct: 84  TRQGHLSM-VVQLMK-YGADPSLIDGEGCSCIHLAAQFGHTSIVAYLIAK-GQDVDMMDQ 140

Query: 322 DGDYGLDYAKAIEHT-DLIEYLVNSG 346
           +G   L +A    H+ D    L+   
Sbjct: 141 NGMTPLMWAAYRTHSVDPTRLLLTFN 166

>3eu9_A Huntingtin-interacting protein 14; epigenetics, ankyrin repeats, methyllyine binding, huntingti interacting protein 14, acyltransferase, ANK repeat; HET: HIS; 1.99A {Homo sapiens} Length = 240

 Score = 57.4 bits (140), Expect = 9e-10
 Identities = 23/101 (22%), Positives = 43/101 (42%), Gaps = 11/101 (10%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGH-LKVVQ 306
           +  +          A+ G   + V  L   K  +++ +D+NG+  L WA  R H +   +
Sbjct: 103 SLIDGEGCSCIHLAAQFGHTSI-VAYLIA-KGQDVDMMDQNGMTPLMWAAYRTHSVDPTR 160

Query: 307 HLIEKCGADVNVTD-SDGDYGLDYAKAIEHTDLIEYLVNSG 346
            L+      VN+ D    +  L +A    +T +I  L+ +G
Sbjct: 161 LLLTF-NVSVNLGDKYHKNTALHWAVLAGNTTVISLLLEAG 200

>3eu9_A Huntingtin-interacting protein 14; epigenetics, ankyrin repeats, methyllyine binding, huntingti interacting protein 14, acyltransferase, ANK repeat; HET: HIS; 1.99A {Homo sapiens} Length = 240

 Score = 42.4 bits (101), Expect = 8e-05
 Identities = 8/40 (20%), Positives = 17/40 (42%), Gaps = 1/40 (2%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTD 320
           N++  +  G + L  A  R ++ ++ HL E         +
Sbjct: 202 NVDAQNIKGESALDLAKQRKNVWMINHLQEA-RQAKGYDN 240

>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 = 62.3 bits (152), Expect = 1e-12
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 7/73 (9%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE-AVDKVFS 68
           ++V NL  + S   ++K F+         V         + + FV F N+E AV+ + +
Sbjct: 17 ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKA 70

Query: 69 TDSHVLEGSRLSI 81
           +  VL+GS + +
Sbjct: 71 LNGKVLDGSPIEV 83

>1bd8_A P19INK4D CDK4/6 inhibitor; tumor suppressor, ankyrin motif; 1.80A {Homo sapiens} SCOP: d.211.1.1 PDB: 1bi8_B 1ap7_A 1blx_B Length = 156

 Score = 64.0 bits (157), Expect = 1e-12
 Identities = 25/97 (25%), Positives = 40/97 (41%), Gaps = 10/97 (10%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N ++          A+ G LD  +K L +    ++N  D  G   +H A   GH  VV  
Sbjct: 62  NVQDTSGTSPVHDAARTGFLDT-LKVLVE-HGADVNVPDGTGALPIHLAVQEGHTAVVSF 119

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVN 344
           L     +D++  D+ G   L+ A      DL++ L  
Sbjct: 120 LAA--ESDLHRRDARGLTPLELALQRGAQDLVDILQG 154

>1bd8_A P19INK4D CDK4/6 inhibitor; tumor suppressor, ankyrin motif; 1.80A {Homo sapiens} SCOP: d.211.1.1 PDB: 1bi8_B 1ap7_A 1blx_B Length = 156

 Score = 63.6 bits (156), Expect = 2e-12
 Identities = 25/96 (26%), Positives = 41/96 (42%), Gaps = 8/96 (8%)

Query: 254 NEKNIYEW-----AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHL 308
           +  N +          G   +   +L K +  + N  D +G + +H A   G L  ++ L
Sbjct: 30  DALNRFGKTALQVMMFGSTAI-ALELLK-QGASPNVQDTSGTSPVHDAARTGFLDTLKVL 87

Query: 309 IEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVN 344
           +E  GADVNV D  G   +  A    HT ++ +L  
Sbjct: 88  VEH-GADVNVPDGTGALPIHLAVQEGHTAVVSFLAA 122

>1bd8_A P19INK4D CDK4/6 inhibitor; tumor suppressor, ankyrin motif; 1.80A {Homo sapiens} SCOP: d.211.1.1 PDB: 1bi8_B 1ap7_A 1blx_B Length = 156

 Score = 61.3 bits (150), Expect = 1e-11
 Identities = 20/85 (23%), Positives = 35/85 (41%), Gaps = 3/85 (3%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
           A  G +   V++L   +  + + L+  G   L      G   +   L+++ GA  NV D+
Sbjct: 10  AARGDVQE-VRRLLHRELVHPDALNRFGKTALQVMM-FGSTAIALELLKQ-GASPNVQDT 66

Query: 322 DGDYGLDYAKAIEHTDLIEYLVNSG 346
            G   +  A      D ++ LV  G
Sbjct: 67  SGTSPVHDAARTGFLDTLKVLVEHG 91

>1bd8_A P19INK4D CDK4/6 inhibitor; tumor suppressor, ankyrin motif; 1.80A {Homo sapiens} SCOP: d.211.1.1 PDB: 1bi8_B 1ap7_A 1blx_B Length = 156

 Score = 58.2 bits (142), Expect = 1e-10
 Identities = 11/54 (20%), Positives = 20/54 (37%), Gaps = 1/54 (1%)

Query: 293 LHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L  A  RG ++ V+ L+ +     +  +  G   L        T +   L+  G
Sbjct: 6   LSGAAARGDVQEVRRLLHRELVHPDALNRFGKTALQVM-MFGSTAIALELLKQG 58

>2rfm_A Putative ankyrin repeat protein TV1425; ANK repeat, protein binding; HET: BU2 GOL; 1.65A {Thermoplasma volcanium} Length = 192

 Score = 64.7 bits (159), Expect = 1e-12
 Identities = 21/96 (21%), Positives = 36/96 (37%), Gaps = 9/96 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N K+             G  +M    L +    N+N  +  G   L  A   G  ++V+ 
Sbjct: 95  NTKDFSGKTPLMWSIIFGYSEM-SYFLLE-HGANVNDRNLEGETPLIVASKYGRSEIVKK 152

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLV 343
           L+E  GAD++  D  G      A+     ++I+   
Sbjct: 153 LLEL-GADISARDLTGLTAEASARIFGRQEVIKIFT 187

>2rfm_A Putative ankyrin repeat protein TV1425; ANK repeat, protein binding; HET: BU2 GOL; 1.65A {Thermoplasma volcanium} Length = 192

 Score = 61.3 bits (150), Expect = 2e-11
 Identities = 24/99 (24%), Positives = 47/99 (47%), Gaps = 9/99 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
            +K+I          K  +L +  ++L   K  N+N  D +G   L W+   G+ ++   
Sbjct: 62  EDKDIEGSTALIWAVKNNRLGI-AEKLLS-KGSNVNTKDFSGKTPLMWSIIFGYSEMSYF 119

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L+E  GA+VN  + +G+  L  A     +++++ L+  G
Sbjct: 120 LLEH-GANVNDRNLEGETPLIVASKYGRSEIVKKLLELG 157

>2rfm_A Putative ankyrin repeat protein TV1425; ANK repeat, protein binding; HET: BU2 GOL; 1.65A {Thermoplasma volcanium} Length = 192

 Score = 60.1 bits (147), Expect = 5e-11
 Identities = 17/68 (25%), Positives = 25/68 (36%), Gaps = 1/68 (1%)

Query: 279 DFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDL 338
           DF  N  D      L  AC  G    +  L+E     +   D +G   L +A       +
Sbjct: 25  DFLRNYRDSYNRTPLMVACMLGMENAIDKLVEN-FDKLEDKDIEGSTALIWAVKNNRLGI 83

Query: 339 IEYLVNSG 346
            E L++ G
Sbjct: 84  AEKLLSKG 91

>2rfm_A Putative ankyrin repeat protein TV1425; ANK repeat, protein binding; HET: BU2 GOL; 1.65A {Thermoplasma volcanium} Length = 192

 Score = 40.8 bits (97), Expect = 2e-04
 Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 8/63 (12%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N++N+         +K G+ ++ VK+L +    +I+  D  GL     A   G  +V++ 
Sbjct: 128 NDRNLEGETPLIVASKYGRSEI-VKKLLE-LGADISARDLTGLTAEASARIFGRQEVIKI 185

Query: 308 LIE 310
             E
Sbjct: 186 FTE 188

>1yyh_A HN1;, notch 1, ankyrin domain; ankyrin repeats, cell cycle,transcription; 1.90A {Homo sapiens} PDB: 2he0_A 2f8x_K 3nbn_B 3v79_K* 1ot8_A Length = 253

 Score = 65.6 bits (161), Expect = 2e-12
 Identities = 18/99 (18%), Positives = 32/99 (32%), Gaps = 9/99 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N  +          A    +D     L K    N +  +      L  A   G  +  + 
Sbjct: 151 NAVDDLGKSALHWAAAVNNVDA-AVVLLK-NGANKDMQNNREETPLFLAAREGSYETAKV 208

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L++   A+ ++TD       D A+   H D++  L    
Sbjct: 209 LLDH-FANRDITDHMDRLPRDIAQERMHHDIVRLLDLEH 246

>1yyh_A HN1;, notch 1, ankyrin domain; ankyrin repeats, cell cycle,transcription; 1.90A {Homo sapiens} PDB: 2he0_A 2f8x_K 3nbn_B 3v79_K* 1ot8_A Length = 253

 Score = 61.7 bits (151), Expect = 3e-11
 Identities = 17/101 (16%), Positives = 41/101 (40%), Gaps = 9/101 (8%)

Query: 252 DDNEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVV 305
           D + +           A+     M ++ L      ++N +D+ G + LHWA    ++   
Sbjct: 116 DLDARMHDGTTPLILAARLAVEGM-LEDLIN-SHADVNAVDDLGKSALHWAAAVNNVDAA 173

Query: 306 QHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
             L++  GA+ ++ ++  +  L  A      +  + L++  
Sbjct: 174 VVLLKN-GANKDMQNNREETPLFLAAREGSYETAKVLLDHF 213

>1yyh_A HN1;, notch 1, ankyrin domain; ankyrin repeats, cell cycle,transcription; 1.90A {Homo sapiens} PDB: 2he0_A 2f8x_K 3nbn_B 3v79_K* 1ot8_A Length = 253

 Score = 60.2 bits (147), Expect = 1e-10
 Identities = 24/100 (24%), Positives = 37/100 (37%), Gaps = 8/100 (8%)

Query: 253 DNEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQ 306
            N+ +          A+  + D   K+L +    + N  D  G   LH A       V Q
Sbjct: 50  HNQTDRTGETALHLAARYSRSDA-AKRLLE-ASADANIQDNMGRTPLHAAVSADAQGVFQ 107

Query: 307 HLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
            LI     D++    DG   L  A  +    ++E L+NS 
Sbjct: 108 ILIRNRATDLDARMHDGTTPLILAARLAVEGMLEDLINSH 147

>1yyh_A HN1;, notch 1, ankyrin domain; ankyrin repeats, cell cycle,transcription; 1.90A {Homo sapiens} PDB: 2he0_A 2f8x_K 3nbn_B 3v79_K* 1ot8_A Length = 253

 Score = 46.7 bits (112), Expect = 3e-06
 Identities = 14/70 (20%), Positives = 24/70 (34%), Gaps = 9/70 (12%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           + +N  E       A+EG  +   K L      N +  D         A +R H  +V+ 
Sbjct: 184 DMQNNREETPLFLAAREGSYET-AKVLLD-HFANRDITDHMDRLPRDIAQERMHHDIVRL 241

Query: 308 LIEKCGADVN 317
           L  +     +
Sbjct: 242 LDLE-HHHHH 250

>1yyh_A HN1;, notch 1, ankyrin domain; ankyrin repeats, cell cycle,transcription; 1.90A {Homo sapiens} PDB: 2he0_A 2f8x_K 3nbn_B 3v79_K* 1ot8_A Length = 253

 Score = 45.5 bits (109), Expect = 9e-06
 Identities = 17/80 (21%), Positives = 28/80 (35%), Gaps = 15/80 (18%)

Query: 281 NINQLDENGLNCLHWACDRG-------------HLKVVQHLIEKCGADV-NVTDSDGDYG 326
           ++N    +G   L  A   G                V+   I + GA + N TD  G+  
Sbjct: 2   DVNVRGPDGFTPLMIASCSGGGLETGNSEEEEDAPAVISDFIYQ-GASLHNQTDRTGETA 60

Query: 327 LDYAKAIEHTDLIEYLVNSG 346
           L  A     +D  + L+ + 
Sbjct: 61  LHLAARYSRSDAAKRLLEAS 80

>3twr_A Tankyrase-2; ankyrin repeat, protein-protein interaction, substrate recru poly(ADP-ribosyl)ation; HET: PE8; 1.55A {Homo sapiens} PDB: 3tws_A* 3twt_A* 3twv_A* 3tww_A 3twx_A 3twq_A 3twu_A 2y0i_S* Length = 165

 Score = 63.6 bits (156), Expect = 2e-12
 Identities = 21/99 (21%), Positives = 37/99 (37%), Gaps = 10/99 (10%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           + K+             G  ++  + L K     +N  D      LH A  +G  ++ + 
Sbjct: 69  HAKDKGGLVPLHNACSYGHYEV-AELLVK-HGAVVNVADLWKFTPLHEAAAKGKYEICKL 126

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L++  GAD    + DG+  LD       TD+ + L    
Sbjct: 127 LLQH-GADPTKKNRDGNTPLDLV-KDGDTDIQDLLRGDA 163

>3twr_A Tankyrase-2; ankyrin repeat, protein-protein interaction, substrate recru poly(ADP-ribosyl)ation; HET: PE8; 1.55A {Homo sapiens} PDB: 3tws_A* 3twt_A* 3twv_A* 3tww_A 3twx_A 3twq_A 3twu_A 2y0i_S* Length = 165

 Score = 62.8 bits (154), Expect = 3e-12
 Identities = 26/85 (30%), Positives = 43/85 (50%), Gaps = 2/85 (2%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
           AK G ++  VK+L  ++  N   ++      LH+A     + VV++L++  GADV+  D 
Sbjct: 16  AKAGDVET-VKKLCTVQSVNCRDIEGRQSTPLHFAAGYNRVSVVEYLLQH-GADVHAKDK 73

Query: 322 DGDYGLDYAKAIEHTDLIEYLVNSG 346
            G   L  A +  H ++ E LV  G
Sbjct: 74  GGLVPLHNACSYGHYEVAELLVKHG 98

>3twr_A Tankyrase-2; ankyrin repeat, protein-protein interaction, substrate recru poly(ADP-ribosyl)ation; HET: PE8; 1.55A {Homo sapiens} PDB: 3tws_A* 3twt_A* 3twv_A* 3tww_A 3twx_A 3twq_A 3twu_A 2y0i_S* Length = 165

 Score = 62.8 bits (154), Expect = 4e-12
 Identities = 25/101 (24%), Positives = 45/101 (44%), Gaps = 9/101 (8%)

Query: 252 DDNEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVV 305
           +  +    +       A   ++ + V+ L +    +++  D+ GL  LH AC  GH +V 
Sbjct: 34  NCRDIEGRQSTPLHFAAGYNRVSV-VEYLLQ-HGADVHAKDKGGLVPLHNACSYGHYEVA 91

Query: 306 QHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           + L++  GA VNV D      L  A A    ++ + L+  G
Sbjct: 92  ELLVKH-GAVVNVADLWKFTPLHEAAAKGKYEICKLLLQHG 131

>3twr_A Tankyrase-2; ankyrin repeat, protein-protein interaction, substrate recru poly(ADP-ribosyl)ation; HET: PE8; 1.55A {Homo sapiens} PDB: 3tws_A* 3twt_A* 3twv_A* 3tww_A 3twx_A 3twq_A 3twu_A 2y0i_S* Length = 165

 Score = 51.6 bits (125), Expect = 3e-08
 Identities = 12/66 (18%), Positives = 21/66 (31%), Gaps = 3/66 (4%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
             N         L  A   G ++ V+ L      +    +      L +A       ++E
Sbjct: 3   MGN---SEADRQLLEAAKAGDVETVKKLCTVQSVNCRDIEGRQSTPLHFAAGYNRVSVVE 59

Query: 341 YLVNSG 346
           YL+  G
Sbjct: 60  YLLQHG 65

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 61.8 bits (150), Expect = 3e-12
 Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 12/81 (14%)

Query: 6  RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMF-DKNTGLSKGFGFVTFQNKE--- 61
           +  +I + NLP   S  +LK    E          F   NT    G G + F ++E   
Sbjct: 26 AKRYRITMKNLPEGCSWQDLKDLARENS----LETTFSSVNTRDFDGTGALEFPSEEILV 81

Query: 62 -AVDKVFSTDSHVLEGSRLSI 81
           A++++   ++    GS +++
Sbjct: 82 EALERL---NNIEFRGSVITV 99

>2f8y_A Notch homolog 1, translocation-associated (drosophila); ankyrin repeats, transcription; 1.55A {Homo sapiens} PDB: 2qc9_A 1ymp_A Length = 223

 Score = 64.0 bits (157), Expect = 3e-12
 Identities = 18/99 (18%), Positives = 32/99 (32%), Gaps = 9/99 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N  +          A    +D     L K    N +  +      L  A   G  +  + 
Sbjct: 119 NAVDDLGKSALHWAAAVNNVDA-AVVLLK-NGANKDMQNNREETPLFLAAREGSYETAKV 176

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L++   A+ ++TD       D A+   H D++  L    
Sbjct: 177 LLDH-FANRDITDHMDRLPRDIAQERMHHDIVRLLDEYN 214

>2f8y_A Notch homolog 1, translocation-associated (drosophila); ankyrin repeats, transcription; 1.55A {Homo sapiens} PDB: 2qc9_A 1ymp_A Length = 223

 Score = 61.3 bits (150), Expect = 3e-11
 Identities = 17/101 (16%), Positives = 41/101 (40%), Gaps = 9/101 (8%)

Query: 252 DDNEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVV 305
           D + +           A+     M ++ L      ++N +D+ G + LHWA    ++   
Sbjct: 84  DLDARMHDGTTPLILAARLAVEGM-LEDLIN-SHADVNAVDDLGKSALHWAAAVNNVDAA 141

Query: 306 QHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
             L++  GA+ ++ ++  +  L  A      +  + L++  
Sbjct: 142 VVLLKN-GANKDMQNNREETPLFLAAREGSYETAKVLLDHF 181

>2f8y_A Notch homolog 1, translocation-associated (drosophila); ankyrin repeats, transcription; 1.55A {Homo sapiens} PDB: 2qc9_A 1ymp_A Length = 223

 Score = 60.5 bits (148), Expect = 6e-11
 Identities = 24/100 (24%), Positives = 37/100 (37%), Gaps = 8/100 (8%)

Query: 253 DNEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQ 306
            N+ +          A+  + D   K+L +    + N  D  G   LH A       V Q
Sbjct: 18  HNQTDRTGETALHLAARYSRSDA-AKRLLE-ASADANIQDNMGRTPLHAAVSADAQGVFQ 75

Query: 307 HLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
            LI     D++    DG   L  A  +    ++E L+NS 
Sbjct: 76  ILIRNRATDLDARMHDGTTPLILAARLAVEGMLEDLINSH 115

>2f8y_A Notch homolog 1, translocation-associated (drosophila); ankyrin repeats, transcription; 1.55A {Homo sapiens} PDB: 2qc9_A 1ymp_A Length = 223

 Score = 45.1 bits (108), Expect = 8e-06
 Identities = 15/70 (21%), Positives = 24/70 (34%), Gaps = 9/70 (12%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           + +N  E       A+EG  +   K L      N +  D         A +R H  +V+ 
Sbjct: 152 DMQNNREETPLFLAAREGSYET-AKVLLD-HFANRDITDHMDRLPRDIAQERMHHDIVRL 209

Query: 308 LIEKCGADVN 317
           L E      +
Sbjct: 210 LDEY-NLVRS 218

>2jab_A H10-2-G3; HER2, darpin, ankyrin repeat protein, membrane protein, human epidermal growth factor receptor 2, de novo protein; 1.70A {} PDB: 3hg0_D 2xzt_G 2xzd_G 2y0b_G 2v4h_C Length = 136

 Score = 62.0 bits (152), Expect = 4e-12
 Identities = 30/95 (31%), Positives = 44/95 (46%), Gaps = 9/95 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N K+ Y           G L++ V+ L K    ++N +D  G   LH A   GHL++ + 
Sbjct: 41  NAKDEYGLTPLYLATAHGHLEI-VEVLLK-NGADVNAVDAIGFTPLHLAAFIGHLEIAEV 98

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYL 342
           L++  GADVN  D  G    D +    + DL E L
Sbjct: 99  LLKH-GADVNAQDKFGKTAFDISIGNGNEDLAEIL 132

>2jab_A H10-2-G3; HER2, darpin, ankyrin repeat protein, membrane protein, human epidermal growth factor receptor 2, de novo protein; 1.70A {} PDB: 3hg0_D 2xzt_G 2xzd_G 2y0b_G 2v4h_C Length = 136

 Score = 58.9 bits (144), Expect = 5e-11
 Identities = 26/66 (39%), Positives = 38/66 (57%), Gaps = 1/66 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           ++N  DE GL  L+ A   GHL++V+ L++  GADVN  D+ G   L  A  I H ++ E
Sbjct: 39  DVNAKDEYGLTPLYLATAHGHLEIVEVLLKN-GADVNAVDAIGFTPLHLAAFIGHLEIAE 97

Query: 341 YLVNSG 346
            L+  G
Sbjct: 98  VLLKHG 103

>2jab_A H10-2-G3; HER2, darpin, ankyrin repeat protein, membrane protein, human epidermal growth factor receptor 2, de novo protein; 1.70A {} PDB: 3hg0_D 2xzt_G 2xzd_G 2y0b_G 2v4h_C Length = 136

 Score = 50.5 bits (122), Expect = 4e-08
 Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 2/68 (2%)

Query: 279 DFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDL 338
             + +    +    L  A   G    V+ L+   GADVN  D  G   L  A A  H ++
Sbjct: 5   HHHHHH-GSDLGKKLLEAARAGQDDEVRILMAN-GADVNAKDEYGLTPLYLATAHGHLEI 62

Query: 339 IEYLVNSG 346
           +E L+ +G
Sbjct: 63  VEVLLKNG 70

>2jab_A H10-2-G3; HER2, darpin, ankyrin repeat protein, membrane protein, human epidermal growth factor receptor 2, de novo protein; 1.70A {} PDB: 3hg0_D 2xzt_G 2xzd_G 2y0b_G 2v4h_C Length = 136

 Score = 39.7 bits (94), Expect = 2e-04
 Identities = 11/63 (17%), Positives = 24/63 (38%), Gaps = 8/63 (12%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N  +   +      A  G L++  + L K    ++N  D+ G      +   G+  + + 
Sbjct: 74  NAVDAIGFTPLHLAAFIGHLEI-AEVLLK-HGADVNAQDKFGKTAFDISIGNGNEDLAEI 131

Query: 308 LIE 310
           L +
Sbjct: 132 LQK 134

>2zgd_A 3 repeat synthetic ankyrin; ankyrin repeat, hydroxylated, de novo protein; 1.90A {Synthetic} PDB: 2zgg_A 2xen_A Length = 110

 Score = 61.1 bits (149), Expect = 5e-12
 Identities = 24/62 (38%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           ++   D+NG   LH A   GHL+VV+ L+E  GADV   D  G    D +    + DL E
Sbjct: 49  DVAAKDKNGSTPLHLAARNGHLEVVKLLLEA-GADVXAQDKFGKTAFDISIDNGNEDLAE 107

Query: 341 YL 342
            L
Sbjct: 108 IL 109

>2zgd_A 3 repeat synthetic ankyrin; ankyrin repeat, hydroxylated, de novo protein; 1.90A {Synthetic} PDB: 2zgg_A 2xen_A Length = 110

 Score = 55.7 bits (135), Expect = 3e-10
 Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 4/66 (6%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           ++     +    L  A   G    V+ L+   GADV   D +G   L  A    H ++++
Sbjct: 19  HMG---SDLGKKLLEAARAGQDDEVRILMAN-GADVAAKDKNGSTPLHLAARNGHLEVVK 74

Query: 341 YLVNSG 346
            L+ +G
Sbjct: 75  LLLEAG 80

>2zgd_A 3 repeat synthetic ankyrin; ankyrin repeat, hydroxylated, de novo protein; 1.90A {Synthetic} PDB: 2zgg_A 2xen_A Length = 110

 Score = 41.4 bits (98), Expect = 4e-05
 Identities = 10/51 (19%), Positives = 17/51 (33%), Gaps = 4/51 (7%)

Query: 296 ACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
                H      L+ + G+ +    SD    L  A      D +  L+ +G
Sbjct: 1   GSSHHHHHHSSGLVPR-GSHMG---SDLGKKLLEAARAGQDDEVRILMANG 47

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 60.4 bits (147), Expect = 5e-12
 Identities = 11/52 (21%), Positives = 22/52 (42%), Gaps = 6/52 (11%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
           ++GN+P   +  +L   F  +G I++     +      KG  F+ +   E 
Sbjct: 30 AYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDTHEQ 75

>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 = 60.8 bits (148), Expect = 6e-12
 Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 6/52 (11%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
          ++ G +   ++   +++ FS +GQIM   V  +      KG+ FV F   E+
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHES 73

>3deo_A Signal recognition particle 43 kDa protein; chloroplast SRP system, signal sequence, ankyrin repeat, chromodomain, type I turn; 1.50A {Arabidopsis thaliana} SCOP: b.34.13.2 k.37.1.1 PDB: 3dep_A 1x32_A Length = 183

 Score = 62.1 bits (152), Expect = 8e-12
 Identities = 26/86 (30%), Positives = 41/86 (47%), Gaps = 5/86 (5%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
           A++      + QL  L+D +++ +DENG   L +    G  K V+ L E  GAD++  D 
Sbjct: 52  ARKADEQA-LSQL--LEDRDVDAVDENGRTALLFVAGLGSDKCVRLLAEA-GADLDHRDM 107

Query: 322 -DGDYGLDYAKAIEHTDLIEYLVNSG 346
             G   L  A      +++E LV  G
Sbjct: 108 RGGLTALHMAAGYVRPEVVEALVELG 133

>3deo_A Signal recognition particle 43 kDa protein; chloroplast SRP system, signal sequence, ankyrin repeat, chromodomain, type I turn; 1.50A {Arabidopsis thaliana} SCOP: b.34.13.2 k.37.1.1 PDB: 3dep_A 1x32_A Length = 183

 Score = 61.4 bits (150), Expect = 2e-11
 Identities = 26/102 (25%), Positives = 40/102 (39%), Gaps = 10/102 (9%)

Query: 252 DDNEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLD-ENGLNCLHWACDRGHLKV 304
           D +  +          A  G     V+ L +    +++  D   GL  LH A      +V
Sbjct: 68  DVDAVDENGRTALLFVAGLGSDKC-VRLLAE-AGADLDHRDMRGGLTALHMAAGYVRPEV 125

Query: 305 VQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           V+ L+E  GAD+ V D  G   L+ A+ I  T      +  G
Sbjct: 126 VEALVEL-GADIEVEDERGLTALELAREILKTTPKGNPMQFG 166

>3deo_A Signal recognition particle 43 kDa protein; chloroplast SRP system, signal sequence, ankyrin repeat, chromodomain, type I turn; 1.50A {Arabidopsis thaliana} SCOP: b.34.13.2 k.37.1.1 PDB: 3dep_A 1x32_A Length = 183

 Score = 51.0 bits (123), Expect = 6e-08
 Identities = 10/61 (16%), Positives = 20/61 (32%), Gaps = 2/61 (3%)

Query: 286 DENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNS 345
                     A  +   + +  L+E    DV+  D +G   L +   +     +  L  +
Sbjct: 41  VSEYETPWWTAARKADEQALSQLLE--DRDVDAVDENGRTALLFVAGLGSDKCVRLLAEA 98

Query: 346 G 346
           G
Sbjct: 99  G 99

>3deo_A Signal recognition particle 43 kDa protein; chloroplast SRP system, signal sequence, ankyrin repeat, chromodomain, type I turn; 1.50A {Arabidopsis thaliana} SCOP: b.34.13.2 k.37.1.1 PDB: 3dep_A 1x32_A Length = 183

 Score = 44.0 bits (105), Expect = 2e-05
 Identities = 8/40 (20%), Positives = 15/40 (37%), Gaps = 1/40 (2%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTD 320
           +I   DE GL  L  A +        + ++  G  + +  
Sbjct: 135 DIEVEDERGLTALELAREILKTTPKGNPMQF-GRRIGLEK 173

>1ikn_D Protein (I-kappa-B-alpha), protein (NF-kappa-B P50D subunit); transcription factor, IKB/NFKB complex; 2.30A {Homo sapiens} SCOP: d.211.1.1 PDB: 1nfi_E Length = 236

 Score = 63.0 bits (154), Expect = 1e-11
 Identities = 27/105 (25%), Positives = 45/105 (42%), Gaps = 14/105 (13%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTK-----LKDFNINQLDENGLNCLHWACDRGHL 302
             ++           ++G L   V  LT+          +   + NG  CLH A   G+L
Sbjct: 72  ELRDFRGNTPLHLACEQGCLAS-VGVLTQSCTTPHLHSILKATNYNGHTCLHLASIHGYL 130

Query: 303 KVVQHLIEKCGADVNVTD-SDGDYGLDYAKAIEHTDLIEYLVNSG 346
            +V+ L+   GADVN  +  +G   L  A  +++ DL+  L+  G
Sbjct: 131 GIVELLVSL-GADVNAQEPCNGRTALHLAVDLQNPDLVSLLLKCG 174

>1ikn_D Protein (I-kappa-B-alpha), protein (NF-kappa-B P50D subunit); transcription factor, IKB/NFKB complex; 2.30A {Homo sapiens} SCOP: d.211.1.1 PDB: 1nfi_E Length = 236

 Score = 60.6 bits (148), Expect = 7e-11
 Identities = 22/108 (20%), Positives = 34/108 (31%), Gaps = 10/108 (9%)

Query: 246 NDESQLDDNEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDE-NGLNCLHWACD 298
                      N          +  G L + V+ L      ++N  +  NG   LH A D
Sbjct: 103 TPHLHSILKATNYNGHTCLHLASIHGYLGI-VELLVS-LGADVNAQEPCNGRTALHLAVD 160

Query: 299 RGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
             +  +V  L++  GADVN     G            T + + L    
Sbjct: 161 LQNPDLVSLLLKC-GADVNRVTYQGYSPYQLTWGRPSTRIQQQLGQLT 207

>1ikn_D Protein (I-kappa-B-alpha), protein (NF-kappa-B P50D subunit); transcription factor, IKB/NFKB complex; 2.30A {Homo sapiens} SCOP: d.211.1.1 PDB: 1nfi_E Length = 236

 Score = 55.2 bits (134), Expect = 4e-09
 Identities = 22/104 (21%), Positives = 40/104 (38%), Gaps = 13/104 (12%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N +N  +           + ++  + L      +    D  G   LH AC++G L  V  
Sbjct: 39  NFQNNLQQTPLHLAVITNQPEI-AEALLG-AGCDPELRDFRGNTPLHLACEQGCLASVGV 96

Query: 308 LIEKC-----GADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L + C      + +  T+ +G   L  A    +  ++E LV+ G
Sbjct: 97  LTQSCTTPHLHSILKATNYNGHTCLHLASIHGYLGIVELLVSLG 140

>1ikn_D Protein (I-kappa-B-alpha), protein (NF-kappa-B P50D subunit); transcription factor, IKB/NFKB complex; 2.30A {Homo sapiens} SCOP: d.211.1.1 PDB: 1nfi_E Length = 236

 Score = 54.9 bits (133), Expect = 5e-09
 Identities = 13/66 (19%), Positives = 22/66 (33%), Gaps = 1/66 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
            +N  +      LH A      ++ + L+   G D  + D  G+  L  A        + 
Sbjct: 37  FLNFQNNLQQTPLHLAVITNQPEIAEALLGA-GCDPELRDFRGNTPLHLACEQGCLASVG 95

Query: 341 YLVNSG 346
            L  S 
Sbjct: 96  VLTQSC 101

>1ikn_D Protein (I-kappa-B-alpha), protein (NF-kappa-B P50D subunit); transcription factor, IKB/NFKB complex; 2.30A {Homo sapiens} SCOP: d.211.1.1 PDB: 1nfi_E Length = 236

 Score = 54.5 bits (132), Expect = 8e-09
 Identities = 9/60 (15%), Positives = 21/60 (35%), Gaps = 1/60 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           ++N++   G +       R   ++ Q L +    +      + +    Y    E T+  E
Sbjct: 176 DVNRVTYQGYSPYQLTWGRPSTRIQQQLGQL-TLENLQMLPESEDEESYDTESEFTEFTE 234

>1ikn_D Protein (I-kappa-B-alpha), protein (NF-kappa-B P50D subunit); transcription factor, IKB/NFKB complex; 2.30A {Homo sapiens} SCOP: d.211.1.1 PDB: 1nfi_E Length = 236

 Score = 45.2 bits (108), Expect = 9e-06
 Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 5/67 (7%)

Query: 284 QLDENGLNCLHWACDRGH----LKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLI 339
           QL E+G + LH A         ++V++ +     A +N  ++     L  A      ++ 
Sbjct: 3   QLTEDGDSFLHLAIIHEEKALTMEVIRQVKGD-LAFLNFQNNLQQTPLHLAVITNQPEIA 61

Query: 340 EYLVNSG 346
           E L+ +G
Sbjct: 62  EALLGAG 68

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 59.7 bits (145), Expect = 1e-11
 Identities = 13/74 (17%), Positives = 27/74 (36%), Gaps = 2/74 (2%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD 70
          + +  LP+  + N++  FFS     M   +    + G   G   V F   E      + D
Sbjct: 18 VHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEADVEFATHEDAVAAMAKD 75

Query: 71 SHVLEGSRLSIQPS 84
             ++   + +  +
Sbjct: 76 KANMQHRYVELFLN 89

>1s70_B 130 kDa myosin-binding subunit of smooth muscle myosin phophatase (M130), serine/threonine protein phosphatase PP1-beta (OR delta) catalytic subunit; myosin phosphatase; HET: PGE; 2.70A {Gallus gallus} SCOP: d.211.1.1 Length = 299

 Score = 63.3 bits (155), Expect = 2e-11
 Identities = 27/98 (27%), Positives = 48/98 (48%), Gaps = 8/98 (8%)

Query: 254 NEKNIYEW-----AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHL 308
             K             G  +  V +L + +  +IN  + +GL  LH AC   ++ +V+ L
Sbjct: 35  KVKFDDGAVFLAACSSGDTEE-VLRLLE-RGADINYANVDGLTALHQACIDDNVDMVKFL 92

Query: 309 IEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           +E  GA++N  D++G   L  A +  + D+ EYL++ G
Sbjct: 93  VEN-GANINQPDNEGWIPLHAAASCGYLDIAEYLISQG 129

>1s70_B 130 kDa myosin-binding subunit of smooth muscle myosin phophatase (M130), serine/threonine protein phosphatase PP1-beta (OR delta) catalytic subunit; myosin phosphatase; HET: PGE; 2.70A {Gallus gallus} SCOP: d.211.1.1 Length = 299

 Score = 61.0 bits (149), Expect = 8e-11
 Identities = 20/101 (19%), Positives = 35/101 (34%), Gaps = 9/101 (8%)

Query: 252 DDNEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVV 305
           +D              A +G  ++ +K L +   +++N  D +G   LH A   G  +  
Sbjct: 191 NDVRHAKSGGTALHVAAAKGYTEV-LKLLIQ-ARYDVNIKDYDGWTPLHAAAHWGKEEAC 248

Query: 306 QHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           + L+E    D+   +  G    D A       L E      
Sbjct: 249 RILVEN-LCDMEAVNKVGQTAFDVADEDILGYLEELQKKQN 288

>1s70_B 130 kDa myosin-binding subunit of smooth muscle myosin phophatase (M130), serine/threonine protein phosphatase PP1-beta (OR delta) catalytic subunit; myosin phosphatase; HET: PGE; 2.70A {Gallus gallus} SCOP: d.211.1.1 Length = 299

 Score = 59.4 bits (145), Expect = 3e-10
 Identities = 23/95 (24%), Positives = 37/95 (38%), Gaps = 4/95 (4%)

Query: 252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEK 311
           D       E  +    D   +Q       N  +  ++G   LH A  +G+ +V++ LI+ 
Sbjct: 165 DIEAARKEEE-RIMLRD--ARQWLNSGHINDVRHAKSGGTALHVAAAKGYTEVLKLLIQA 221

Query: 312 CGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
              DVN+ D DG   L  A      +    LV + 
Sbjct: 222 -RYDVNIKDYDGWTPLHAAAHWGKEEACRILVENL 255

>1s70_B 130 kDa myosin-binding subunit of smooth muscle myosin phophatase (M130), serine/threonine protein phosphatase PP1-beta (OR delta) catalytic subunit; myosin phosphatase; HET: PGE; 2.70A {Gallus gallus} SCOP: d.211.1.1 Length = 299

 Score = 53.7 bits (130), Expect = 2e-08
 Identities = 15/99 (15%), Positives = 38/99 (38%), Gaps = 15/99 (15%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N+ +   W      A  G LD+  + L   +  ++  ++  G   L  A +    +++Q+
Sbjct: 100 NQPDNEGWIPLHAAASCGYLDI-AEYLIS-QGAHVGAVNSEGDTPLDIAEEEAMEELLQN 157

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
            + + G D+     + +  +         D  ++L +  
Sbjct: 158 EVNRQGVDIEAARKEEERIM-------LRDARQWLNSGH 189

>1s70_B 130 kDa myosin-binding subunit of smooth muscle myosin phophatase (M130), serine/threonine protein phosphatase PP1-beta (OR delta) catalytic subunit; myosin phosphatase; HET: PGE; 2.70A {Gallus gallus} SCOP: d.211.1.1 Length = 299

 Score = 46.0 bits (110), Expect = 8e-06
 Identities = 10/65 (15%), Positives = 18/65 (27%), Gaps = 2/65 (3%)

Query: 282 INQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEY 341
           +   D             G    ++  + K      V   DG      A +   T+ +  
Sbjct: 1   MKMADAKQKRNEQLKRWIGSETDLEPPVVK-RKKTKVKFDDG-AVFLAACSSGDTEEVLR 58

Query: 342 LVNSG 346
           L+  G
Sbjct: 59  LLERG 63

>3utm_A Tankyrase-1; tankyrase, TNKS, ankryin repeat clusters, WNT signaling, POL ribosylation, transferase-signaling protein complex; 2.00A {Mus musculus} Length = 351

 Score = 63.7 bits (156), Expect = 2e-11
 Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 1/66 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           N+N+ +++ +  LH A +R H  V++ L +  GA +N  DS G   L  A    H     
Sbjct: 239 NVNEKNKDFMTPLHVAAERAHNDVMEVLHKH-GAKMNALDSLGQTALHRAALAGHLQTCR 297

Query: 341 YLVNSG 346
            L++ G
Sbjct: 298 LLLSYG 303

>3utm_A Tankyrase-1; tankyrase, TNKS, ankryin repeat clusters, WNT signaling, POL ribosylation, transferase-signaling protein complex; 2.00A {Mus musculus} Length = 351

 Score = 61.0 bits (149), Expect = 1e-10
 Identities = 23/99 (23%), Positives = 44/99 (44%), Gaps = 9/99 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           +  +  +       A   ++ + V+ L +    +++  D+ GL  LH AC  GH +V + 
Sbjct: 52  HASDGRKSTPLHLAAGYNRVRI-VQLLLQ-HGADVHAKDKGGLVPLHNACSYGHYEVTEL 109

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L++  GA VN  D      L  A +    ++   L++ G
Sbjct: 110 LLKH-GACVNAMDLWQFTPLHEAASKNRVEVCSLLLSHG 147

>3utm_A Tankyrase-1; tankyrase, TNKS, ankryin repeat clusters, WNT signaling, POL ribosylation, transferase-signaling protein complex; 2.00A {Mus musculus} Length = 351

 Score = 61.0 bits (149), Expect = 1e-10
 Identities = 22/99 (22%), Positives = 39/99 (39%), Gaps = 14/99 (14%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           NEKN          A+    D+ ++ L K     +N LD  G   LH A   GHL+  + 
Sbjct: 241 NEKNKDFMTPLHVAAERAHNDV-MEVLHK-HGAKMNALDSLGQTALHRAALAGHLQTCRL 298

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L+   G+D ++    G             + ++ +++  
Sbjct: 299 LLSY-GSDPSIISLQGFTAAQMG-----NEAVQQILSES 331

>3utm_A Tankyrase-1; tankyrase, TNKS, ankryin repeat clusters, WNT signaling, POL ribosylation, transferase-signaling protein complex; 2.00A {Mus musculus} Length = 351

 Score = 54.0 bits (131), Expect = 2e-08
 Identities = 24/100 (24%), Positives = 41/100 (41%), Gaps = 6/100 (6%)

Query: 250 QLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGH---LKVVQ 306
             +    ++ + A+E  L  + K L    +    +  ++    LH A    H    +V +
Sbjct: 174 TYEFKGHSLLQAAREADLAKVKKTL--ALEIINFKQPQSHETALHCAVASLHPKRKQVAE 231

Query: 307 HLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
            L+ K GA+VN  + D    L  A    H D++E L   G
Sbjct: 232 LLLRK-GANVNEKNKDFMTPLHVAAERAHNDVMEVLHKHG 270

>3utm_A Tankyrase-1; tankyrase, TNKS, ankryin repeat clusters, WNT signaling, POL ribosylation, transferase-signaling protein complex; 2.00A {Mus musculus} Length = 351

 Score = 52.5 bits (127), Expect = 6e-08
 Identities = 10/67 (14%), Positives = 22/67 (32%), Gaps = 2/67 (2%)

Query: 281 NINQLDENGLNCLHWACDRGHLK-VVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLI 339
                 E   + L  A   G+ + ++  L      + + +D      L  A       ++
Sbjct: 16  KAVLTGEYKKDELLEAARSGNEEKLMALLTPL-NVNCHASDGRKSTPLHLAAGYNRVRIV 74

Query: 340 EYLVNSG 346
           + L+  G
Sbjct: 75  QLLLQHG 81

>3utm_A Tankyrase-1; tankyrase, TNKS, ankryin repeat clusters, WNT signaling, POL ribosylation, transferase-signaling protein complex; 2.00A {Mus musculus} Length = 351

 Score = 47.1 bits (113), Expect = 3e-06
 Identities = 12/122 (9%), Positives = 35/122 (28%), Gaps = 31/122 (25%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N  +++++      A + ++++    L      +   ++ +G + +  A      + + +
Sbjct: 118 NAMDLWQFTPLHEAASKNRVEV-CSLLLS-HGADPTLVNCHGKSAVDMAPTPELRERLTY 175

Query: 308 LIEK--------------------CGADVNVTDSDGDYGLDYAKAIEH---TDLIEYLVN 344
             +                                 +  L  A A  H     + E L+ 
Sbjct: 176 EFKGHSLLQAAREADLAKVKKTLALEIINFKQPQSHETALHCAVASLHPKRKQVAELLLR 235

Query: 345 SG 346
            G
Sbjct: 236 KG 237

>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 = 60.2 bits (146), Expect = 2e-11
 Identities = 13/76 (17%), Positives = 28/76 (36%), Gaps = 2/76 (2%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
           + + +  LP+  + N++  FFS     +   +    + G   G   V F   E      S
Sbjct: 47  HCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAMS 104

Query: 69  TDSHVLEGSRLSIQPS 84
            D   ++   + +  +
Sbjct: 105 KDRANMQHRYIELFLN 120

>3t8k_A Uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center F or structural genomics, MCSG; 1.77A {Leptotrichia buccalis} Length = 186

 Score = 61.6 bits (150), Expect = 2e-11
 Identities = 7/72 (9%), Positives = 24/72 (33%), Gaps = 6/72 (8%)

Query: 281 NINQLDENGLNCLHWACDRGHL------KVVQHLIEKCGADVNVTDSDGDYGLDYAKAIE 334
           +I  L +     +        +       + + +  + G  + + D  G   L++ K  +
Sbjct: 106 DITALYKPYKIVVFKNIFNYFVDENEMIPLYKLIFSQSGLQLLIKDKWGLTALEFVKRCQ 165

Query: 335 HTDLIEYLVNSG 346
               ++ + +  
Sbjct: 166 KPIALKMMEDYI 177

>3t8k_A Uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center F or structural genomics, MCSG; 1.77A {Leptotrichia buccalis} Length = 186

 Score = 52.0 bits (125), Expect = 3e-08
 Identities = 13/87 (14%), Positives = 23/87 (26%), Gaps = 9/87 (10%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKV------VQHLIEKCGAD 315
             E +  +    L   K  +I    + G          G   +       +  +EK GAD
Sbjct: 50  NDEARYKI-SMFLIN-KGADIKSRTKEGTTLFFPLFQGGGNDITGTTELCKIFLEK-GAD 106

Query: 316 VNVTDSDGDYGLDYAKAIEHTDLIEYL 342
           +          +         D  E +
Sbjct: 107 ITALYKPYKIVVFKNIFNYFVDENEMI 133

>3t8k_A Uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center F or structural genomics, MCSG; 1.77A {Leptotrichia buccalis} Length = 186

 Score = 52.0 bits (125), Expect = 3e-08
 Identities = 8/80 (10%), Positives = 20/80 (25%), Gaps = 12/80 (15%)

Query: 254 NEKNIYEW------AKEGKLDM-----LVKQLTKLKDFNINQLDENGLNCLHWACDRGHL 302
                              +D      L K +       +   D+ GL  L +       
Sbjct: 108 TALYKPYKIVVFKNIFNYFVDENEMIPLYKLIFSQSGLQLLIKDKWGLTALEFVKRCQKP 167

Query: 303 KVVQHLIEKCGADVNVTDSD 322
             ++ + +      N+ ++ 
Sbjct: 168 IALKMMEDY-IKKYNLKENS 186

>3t8k_A Uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center F or structural genomics, MCSG; 1.77A {Leptotrichia buccalis} Length = 186

 Score = 50.4 bits (121), Expect = 1e-07
 Identities = 16/101 (15%), Positives = 29/101 (28%), Gaps = 8/101 (7%)

Query: 253 DNEKNIYEWAKEGKLDMLVKQLTKLKDFN-INQLDENGLNCLHWACDRGHLKVVQHLIEK 311
              + +   A  G  +  ++   K  +            + L    D    K+   LI K
Sbjct: 5   SEYRTVSAAAMLGTYEDFLELFEKGYEDKESVLKSNILYDVLRNNNDEARYKISMFLINK 64

Query: 312 CGADVNVTDSDGDYGLDYA------KAIEHTDLIEYLVNSG 346
            GAD+     +G                  T+L +  +  G
Sbjct: 65  -GADIKSRTKEGTTLFFPLFQGGGNDITGTTELCKIFLEKG 104

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 59.5 bits (144), Expect = 2e-11
 Identities = 17/82 (20%), Positives = 38/82 (46%), Gaps = 7/82 (8%)

Query: 5  IRQLNKIFVGNLPWTVSHNEL---KKFFSEYGQIMNASVMFDKNTGLSK---GFGFVTFQ 58
          + Q N +FV  L   ++  E+    ++F ++G+I    +    +   S+      +VT+ 
Sbjct: 12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYI 71

Query: 59 NKE-AVDKVFSTDSHVLEGSRL 79
            E A+  +   ++ V++G  L
Sbjct: 72 RSEDALRAIQCVNNVVVDGRTL 93

>2aja_A Ankyrin repeat family protein; NESG, Q5ZSV0, structural genomics, PSI, protein structure initiative; 2.80A {Legionella pneumophila} SCOP: a.118.24.1 Length = 376

 Score = 63.8 bits (155), Expect = 2e-11
 Identities = 16/89 (17%), Positives = 26/89 (29%), Gaps = 5/89 (5%)

Query: 260 EWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVT 319
                  LD L   LT   D  +  +          A + GHL V+  L E       + 
Sbjct: 101 ITGCSSALDTLCLLLTS--DEIVKVIQAENYQAFRLAAENGHLHVLNRLCEL-APTEIMA 157

Query: 320 D--SDGDYGLDYAKAIEHTDLIEYLVNSG 346
              ++  +    A    H  ++  L    
Sbjct: 158 MIQAENYHAFRLAAENGHLHVLNRLCELA 186

>2aja_A Ankyrin repeat family protein; NESG, Q5ZSV0, structural genomics, PSI, protein structure initiative; 2.80A {Legionella pneumophila} SCOP: a.118.24.1 Length = 376

 Score = 59.2 bits (143), Expect = 5e-10
 Identities = 18/107 (16%), Positives = 38/107 (35%), Gaps = 14/107 (13%)

Query: 252 DDNEKNIYEW------AKEGKLDMLVKQLTKLK-DFNINQLDENGLNCLHWACDRGHLKV 304
                    +      A+ G L + + +L +L     +  +     +    A + GHL V
Sbjct: 120 IVKVIQAENYQAFRLAAENGHLHV-LNRLCELAPTEIMAMIQAENYHAFRLAAENGHLHV 178

Query: 305 VQHLIEKCGADVNVTD--SDGDYGLDYAKAIE--HTDLIEYLVNSGS 347
           +  L E            ++  Y   +A A+   H ++I +L++   
Sbjct: 179 LNRLCEL-APTEATAMIQAENYYAFRWA-AVGRGHHNVINFLLDCPV 223

>2aja_A Ankyrin repeat family protein; NESG, Q5ZSV0, structural genomics, PSI, protein structure initiative; 2.80A {Legionella pneumophila} SCOP: a.118.24.1 Length = 376

 Score = 48.0 bits (114), Expect = 2e-06
 Identities = 8/64 (12%), Positives = 19/64 (29%), Gaps = 4/64 (6%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
               +  +    L  A   G+      L+    + + +T ++  Y     +     DL  
Sbjct: 311 PTATIPGDANELLRLALRLGNQGACALLLSI-PSVLALTKANNYY---INETGGRLDLRA 366

Query: 341 YLVN 344
             + 
Sbjct: 367 VALE 370

>2aja_A Ankyrin repeat family protein; NESG, Q5ZSV0, structural genomics, PSI, protein structure initiative; 2.80A {Legionella pneumophila} SCOP: a.118.24.1 Length = 376

 Score = 41.5 bits (97), Expect = 3e-04
 Identities = 12/87 (13%), Positives = 25/87 (28%), Gaps = 11/87 (12%)

Query: 262 AKEGKLDMLVKQL-TKLKDFNINQLDENGLNCLHWAC-DRGHLKVVQHLIEKCGADVNVT 319
           A+ G L + + +L           +         WA   RGH  V+  L++     +   
Sbjct: 171 AENGHLHV-LNRLCELAPTEATAMIQAENYYAFRWAAVGRGHHNVINFLLDC-PVMLA-- 226

Query: 320 DSDGDYGLDYAKAIEHTDLIEYLVNSG 346
                Y   +        +  ++    
Sbjct: 227 -----YAEIHEFEYGEKYVNPFIARHV 248

>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 = 63.7 bits (154), Expect = 2e-11
 Identities = 14/97 (14%), Positives = 38/97 (39%), Gaps = 1/97 (1%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVD-KVF 67
             +FV  + +  + ++L++ F  YG I    +++ K +G  +G+ F+ ++++  +     
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162

Query: 68  STDSHVLEGSRLSIQPSDSHNRMAENMEDRFNQACDY 104
             D   ++G R+ +                       
Sbjct: 163 HADGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGT 199

>3d9h_A CDNA FLJ77766, highly similar to HOMO sapiens ankyrin repeat and SOCS box-containing...; ASB9, ANK repeat, L-shaped, structural protein; 2.20A {Homo sapiens} Length = 285

 Score = 62.9 bits (154), Expect = 2e-11
 Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 3/85 (3%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
           A  G     ++ L   + + +N +  + ++ LH AC  GHL  V+ L++  GA VN   +
Sbjct: 67  AIHGHQLS-LRNLIS-QGWAVNIITADHVSPLHEACLGGHLSCVKILLKH-GAQVNGVTA 123

Query: 322 DGDYGLDYAKAIEHTDLIEYLVNSG 346
           D    L  A      D +  L+  G
Sbjct: 124 DWHTPLFNACVSGSWDCVNLLLQHG 148

>3d9h_A CDNA FLJ77766, highly similar to HOMO sapiens ankyrin repeat and SOCS box-containing...; ASB9, ANK repeat, L-shaped, structural protein; 2.20A {Homo sapiens} Length = 285

 Score = 61.7 bits (151), Expect = 5e-11
 Identities = 23/99 (23%), Positives = 33/99 (33%), Gaps = 10/99 (10%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N                G L   VK L K     +N +  +    L  AC  G    V  
Sbjct: 86  NIITADHVSPLHEACLGGHLSC-VKILLK-HGAQVNGVTADWHTPLFNACVSGSWDCVNL 143

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L++  GA V   +SD    +  A    H + +  L+  G
Sbjct: 144 LLQH-GASVQ-PESDLASPIHEAARRGHVECVNSLIAYG 180

>3d9h_A CDNA FLJ77766, highly similar to HOMO sapiens ankyrin repeat and SOCS box-containing...; ASB9, ANK repeat, L-shaped, structural protein; 2.20A {Homo sapiens} Length = 285

 Score = 59.4 bits (145), Expect = 3e-10
 Identities = 22/85 (25%), Positives = 34/85 (40%), Gaps = 4/85 (4%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
           A+ G ++  V  L      NI+    +    L+ AC+      V+ L+E  GADVN    
Sbjct: 165 ARRGHVEC-VNSLIA-YGGNIDHKISHLGTPLYLACENQQRACVKKLLES-GADVN-QGK 220

Query: 322 DGDYGLDYAKAIEHTDLIEYLVNSG 346
             D  L         +L   L++ G
Sbjct: 221 GQDSPLHAVVRTASEELACLLMDFG 245

>3d9h_A CDNA FLJ77766, highly similar to HOMO sapiens ankyrin repeat and SOCS box-containing...; ASB9, ANK repeat, L-shaped, structural protein; 2.20A {Homo sapiens} Length = 285

 Score = 57.5 bits (140), Expect = 1e-09
 Identities = 15/99 (15%), Positives = 35/99 (35%), Gaps = 11/99 (11%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           + K  +         +  +    VK+L +    ++NQ  +   + LH        ++   
Sbjct: 184 DHKISHLGTPLYLACENQQRAC-VKKLLE-SGADVNQ-GKGQDSPLHAVVRTASEELACL 240

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L++  GAD    +++G   ++            +L   G
Sbjct: 241 LMDF-GADTQAKNAEGKRPVELVPPESPLA-QLFLEREG 277

>3d9h_A CDNA FLJ77766, highly similar to HOMO sapiens ankyrin repeat and SOCS box-containing...; ASB9, ANK repeat, L-shaped, structural protein; 2.20A {Homo sapiens} Length = 285

 Score = 55.6 bits (135), Expect = 5e-09
 Identities = 18/95 (18%), Positives = 33/95 (34%), Gaps = 4/95 (4%)

Query: 252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEK 311
           D  +  +      G  D              +    +  + +H A   GH   +++LI +
Sbjct: 25  DGKQGGMDGSKPAGPRD-FPGIRLLSNPLMGD--AVSDWSPMHEAAIHGHQLSLRNLISQ 81

Query: 312 CGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
            G  VN+  +D    L  A    H   ++ L+  G
Sbjct: 82  -GWAVNIITADHVSPLHEACLGGHLSCVKILLKHG 115

>3d9h_A CDNA FLJ77766, highly similar to HOMO sapiens ankyrin repeat and SOCS box-containing...; ASB9, ANK repeat, L-shaped, structural protein; 2.20A {Homo sapiens} Length = 285

 Score = 41.7 bits (99), Expect = 2e-04
 Identities = 5/39 (12%), Positives = 12/39 (30%), Gaps = 2/39 (5%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVT 319
           +    +  G   +        L  +   +E+ GA +   
Sbjct: 247 DTQAKNAEGKRPVELVPPESPLAQL--FLEREGASLPKP 283

>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 = 59.5 bits (144), Expect = 2e-11
 Identities = 15/77 (19%), Positives = 29/77 (37%), Gaps = 2/77 (2%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNA-SVMFDKN-TGLSKGFGFVTFQNKEAVDKVFS 68
          + +  LPW+ S  +++ F S+         V F     G   G  FV  ++++ V     
Sbjct: 20 VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALK 79

Query: 69 TDSHVLEGSRLSIQPSD 85
           D   +    + +  S 
Sbjct: 80 KDRESMGHRYIEVFKSH 96

>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 = 61.6 bits (149), Expect = 2e-11
 Identities = 11/81 (13%), Positives = 25/81 (30%), Gaps = 1/81 (1%)

Query: 2   SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
           +      N +   N P  V+     +   E G     SV            G + + +K 
Sbjct: 117 NRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKS 176

Query: 62  -AVDKVFSTDSHVLEGSRLSI 81
            A++ +   + + ++      
Sbjct: 177 DALETLGFLNHYQMKNPNGPY 197

>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 = 48.9 bits (116), Expect = 4e-07
 Identities = 17/106 (16%), Positives = 38/106 (35%), Gaps = 7/106 (6%)

Query: 11  IFVGNL-PWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           + V  L    ++ + +   F  YG +     M  K      G   V   +  AVD+  + 
Sbjct: 7   LMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITH 61

Query: 70  -DSHVLEGSRLSIQPSDSHNRMAENMEDRFNQACDYLPSLVKKLDS 114
            +++ + G ++++  S     M        + +C Y      + + 
Sbjct: 62  LNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNR 107

>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 = 58.4 bits (142), Expect = 3e-11
 Identities = 23/91 (25%), Positives = 38/91 (41%), Gaps = 12/91 (13%)

Query: 9  NKIFVGNLPWTVSHNELKK----FFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVD 64
          + I++ NL   +  +ELKK     FS +GQI++  V     +   +G  FV F+   +  
Sbjct: 9  HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS---RSLKMRGQAFVIFKEVSSAT 65

Query: 65 K-VFSTDSHVLEGSRLSIQ----PSDSHNRM 90
            + S          + IQ     SD   +M
Sbjct: 66 NALRSMQGFPFYDKPMRIQYAKTDSDIIAKM 96

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 59.5 bits (144), Expect = 4e-11
 Identities = 23/92 (25%), Positives = 36/92 (39%), Gaps = 10/92 (10%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQI--MNASVMFD---KNTGLSKGFGFVTFQNKEAV 63
            +I+V NL   V   +LK  F  Y         +MFD      G  KG  F+   N++A 
Sbjct: 46  CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105

Query: 64  DK-VFSTDSHVLEGSRLSIQ----PSDSHNRM 90
            K +   + +VL G  + +Q         +  
Sbjct: 106 AKALKEANGYVLFGKPMVVQFARSARPKQDPK 137

>3kea_A K1L; tropism, ANK repeat, viral protein; 2.30A {Vaccinia virus} Length = 285

 Score = 61.8 bits (151), Expect = 4e-11
 Identities = 13/101 (12%), Positives = 30/101 (29%), Gaps = 12/101 (11%)

Query: 254 NEKNIYEW-------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQ 306
                  W            + + V     L +          L+C+H     GH+ ++ 
Sbjct: 122 MFYGKTGWKTSFYHAVMLNDVSI-VSYF--LSEIPSTFDLAILLSCIHITIKNGHVDMMI 178

Query: 307 HLIEKCGADVNVTDSDGD-YGLDYAKAIEHTDLIEYLVNSG 346
            L++      N  +S      +  A   +  ++++ L    
Sbjct: 179 LLLDY-MTSTNTNNSLLFIPDIKLAIDNKDIEMLQALFKYD 218

>3kea_A K1L; tropism, ANK repeat, viral protein; 2.30A {Vaccinia virus} Length = 285

 Score = 61.8 bits (151), Expect = 4e-11
 Identities = 16/86 (18%), Positives = 35/86 (40%), Gaps = 4/86 (4%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
           A      + VK L      + +Q D+ G   L++A D G+++ V+  ++K    +     
Sbjct: 70  ATLEDTKI-VKILLF-SGLDDSQFDDKGNTALYYAVDSGNMQTVKLFVKK-NWRLMFYGK 126

Query: 322 DGDY-GLDYAKAIEHTDLIEYLVNSG 346
            G      +A  +    ++ Y ++  
Sbjct: 127 TGWKTSFYHAVMLNDVSIVSYFLSEI 152

>3kea_A K1L; tropism, ANK repeat, viral protein; 2.30A {Vaccinia virus} Length = 285

 Score = 58.7 bits (143), Expect = 5e-10
 Identities = 17/76 (22%), Positives = 38/76 (50%), Gaps = 5/76 (6%)

Query: 271 VKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA 330
           +K    L   +  + D +G +  ++A    ++++V  L+   GA  N+   + ++ L  A
Sbjct: 15  LKSF--LSSKDTFKADVHGHSASYYAIADNNVRLVCTLLNA-GALKNLL--ENEFPLHQA 69

Query: 331 KAIEHTDLIEYLVNSG 346
             +E T +++ L+ SG
Sbjct: 70  ATLEDTKIVKILLFSG 85

>3kea_A K1L; tropism, ANK repeat, viral protein; 2.30A {Vaccinia virus} Length = 285

 Score = 47.5 bits (114), Expect = 2e-06
 Identities = 13/104 (12%), Positives = 28/104 (26%), Gaps = 21/104 (20%)

Query: 254 NEKNIYEW-------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQ 306
           N  N   +            ++M ++ L K  D NI        +           ++ +
Sbjct: 188 NTNNSLLFIPDIKLAIDNKDIEM-LQALFK-YDINIY-------SANLENVLLDDAEIAK 238

Query: 307 HLIEKCGADVNVTDSDGD----YGLDYAKAIEHTDLIEYLVNSG 346
            +IEK   +        D          + I     +  +  + 
Sbjct: 239 MIIEK-HVEYKSDSYTKDLDIVKNNKLDEIISKNKELRLMYVNC 281

>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 = 61.8 bits (149), Expect = 5e-11
 Identities = 24/107 (22%), Positives = 42/107 (39%), Gaps = 12/107 (11%)

Query: 4   SIRQLNKIFVGNLPWTVSHNELKK----FFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN 59
             R  + I++ NL   +  +ELKK     FS++GQI++  V     +   +G  FV F+ 
Sbjct: 5   ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS---RSLKMRGQAFVIFKE 61

Query: 60  KEAVDKVFST-DSHVLEGSRLSIQ----PSDSHNRMAENMEDRFNQA 101
             +      +          + IQ     SD   +M     +R  + 
Sbjct: 62  VSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKR 108

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 45.6 bits (107), Expect = 9e-06
 Identities = 10/62 (16%), Positives = 22/62 (35%), Gaps = 5/62 (8%)

Query: 1   MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
             +     + +F+ NLP   +   L   F+++       ++  +         FV F N+
Sbjct: 200 PLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNE 254

Query: 61  EA 62
             
Sbjct: 255 VQ 256

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 57.8 bits (140), Expect = 5e-11
 Identities = 18/63 (28%), Positives = 25/63 (39%), Gaps = 6/63 (9%)

Query: 9  NKIFVGNLP------WTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
            I V   P        V    L   FS+ G+++N     D+ TG +KGF FV   +   
Sbjct: 7  QYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMND 66

Query: 63 VDK 65
            K
Sbjct: 67 AKK 69

>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 = 57.6 bits (140), Expect = 6e-11
 Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 7/75 (9%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE-AVDKVF 67
           +++VG L    S   L + F  +G I   ++   K       F ++ +++ + A     
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSI--RTIDHVKG----DSFAYIQYESLDAAQAACA 71

Query: 68 STDSHVLEGSRLSIQ 82
                L G    ++
Sbjct: 72 KMRGFPLGGPDRRLR 86

>3ui2_A Signal recognition particle 43 kDa protein, chlor; ankyrin repeat, chromodomain, aromatic CAGE, signal recognit particle, protein targeting; 3.18A {Arabidopsis thaliana} PDB: 1x3q_A 2hug_A Length = 244

 Score = 60.7 bits (148), Expect = 7e-11
 Identities = 26/102 (25%), Positives = 40/102 (39%), Gaps = 10/102 (9%)

Query: 252 DDNEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLD-ENGLNCLHWACDRGHLKV 304
           D +  +          A  G     V+ L +    +++  D   GL  LH A      +V
Sbjct: 69  DVDAVDENGRTALLFVAGLGSDKC-VRLLAE-AGADLDHRDMRGGLTALHMAAGYVRPEV 126

Query: 305 VQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           V+ L+E  GAD+ V D  G   L+ A+ I  T      +  G
Sbjct: 127 VEALVEL-GADIEVEDERGLTALELAREILKTTPKGNPMQFG 167

>3ui2_A Signal recognition particle 43 kDa protein, chlor; ankyrin repeat, chromodomain, aromatic CAGE, signal recognit particle, protein targeting; 3.18A {Arabidopsis thaliana} PDB: 1x3q_A 2hug_A Length = 244

 Score = 60.3 bits (147), Expect = 8e-11
 Identities = 26/86 (30%), Positives = 41/86 (47%), Gaps = 5/86 (5%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
           A++      + QL  L+D +++ +DENG   L +    G  K V+ L E  GAD++  D 
Sbjct: 53  ARKADEQA-LSQL--LEDRDVDAVDENGRTALLFVAGLGSDKCVRLLAEA-GADLDHRDM 108

Query: 322 -DGDYGLDYAKAIEHTDLIEYLVNSG 346
             G   L  A      +++E LV  G
Sbjct: 109 RGGLTALHMAAGYVRPEVVEALVELG 134

>3ui2_A Signal recognition particle 43 kDa protein, chlor; ankyrin repeat, chromodomain, aromatic CAGE, signal recognit particle, protein targeting; 3.18A {Arabidopsis thaliana} PDB: 1x3q_A 2hug_A Length = 244

 Score = 50.7 bits (122), Expect = 2e-07
 Identities = 10/54 (18%), Positives = 20/54 (37%), Gaps = 2/54 (3%)

Query: 293 LHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
              A  +   + +  L+E    DV+  D +G   L +   +     +  L  +G
Sbjct: 49  WWTAARKADEQALSQLLE--DRDVDAVDENGRTALLFVAGLGSDKCVRLLAEAG 100

>3ui2_A Signal recognition particle 43 kDa protein, chlor; ankyrin repeat, chromodomain, aromatic CAGE, signal recognit particle, protein targeting; 3.18A {Arabidopsis thaliana} PDB: 1x3q_A 2hug_A Length = 244

 Score = 47.6 bits (114), Expect = 1e-06
 Identities = 10/62 (16%), Positives = 23/62 (37%), Gaps = 4/62 (6%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           +I   DE GL  L  A +        + ++  G  + +        +   +  E+ ++ E
Sbjct: 136 DIEVEDERGLTALELAREILKTTPKGNPMQF-GRRIGLEKVI---NVLEGQVFEYAEVDE 191

Query: 341 YL 342
            +
Sbjct: 192 IV 193

>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 = 56.9 bits (138), Expect = 8e-11
 Identities = 16/75 (21%), Positives = 38/75 (50%), Gaps = 8/75 (10%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK--VF 67
           ++VG L  T++  +L+  F ++G+I   +V+        +   F+ F  ++A +     
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEK 67

Query: 68 STDSHVLEGSRLSIQ 82
          S +  ++ G RL+++
Sbjct: 68 SFNKLIVNGRRLNVK 82

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 56.7 bits (137), Expect = 2e-10
 Identities = 17/77 (22%), Positives = 34/77 (44%), Gaps = 9/77 (11%)

Query: 9  NKIFVGNLPWTVS------HNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
          + I V N+P           N + K FS++G+I   +  + +  G +KG+ F+ + +   
Sbjct: 16 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKIT--NDFYPEEDGKTKGYIFLEYASPAH 73

Query: 63 VDK-VFSTDSHVLEGSR 78
              V + D + L+   
Sbjct: 74 AVDAVKNADGYKLDKQH 90

>1oy3_D Transcription factor inhibitor I-kappa-B-beta; protein-protein complex, transcription factors, nuclear localization, DNA binding protein; 2.05A {Mus musculus} SCOP: d.211.1.1 PDB: 1k3z_D Length = 282

 Score = 59.9 bits (146), Expect = 2e-10
 Identities = 20/100 (20%), Positives = 33/100 (33%), Gaps = 10/100 (10%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDEN-GLNCLHWACDRGHLKVVQ 306
             +N                +M V+ L      ++N+ +   G   LH A +     V++
Sbjct: 152 EAENYDGHTPLHVAVIHKDAEM-VRLLRD-AGADLNKPEPTCGRTPLHLAVEAQAASVLE 209

Query: 307 HLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
            L++  GAD       G   L  A    +  L   L   G
Sbjct: 210 LLLKA-GADPTARMYGGRTPLGSALLRPNPILARLLRAHG 248

>1oy3_D Transcription factor inhibitor I-kappa-B-beta; protein-protein complex, transcription factors, nuclear localization, DNA binding protein; 2.05A {Mus musculus} SCOP: d.211.1.1 PDB: 1k3z_D Length = 282

 Score = 59.5 bits (145), Expect = 2e-10
 Identities = 9/62 (14%), Positives = 17/62 (27%), Gaps = 1/62 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           +       G   L  A  R +  + + L    GA       D       + +   +D  +
Sbjct: 217 DPTARMYGGRTPLGSALLRPNPILARLLRAH-GAPEPEDGGDKLSPCSSSGSDSDSDNRD 275

Query: 341 YL 342
             
Sbjct: 276 EG 277

>1oy3_D Transcription factor inhibitor I-kappa-B-beta; protein-protein complex, transcription factors, nuclear localization, DNA binding protein; 2.05A {Mus musculus} SCOP: d.211.1.1 PDB: 1k3z_D Length = 282

 Score = 57.6 bits (140), Expect = 1e-09
 Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 6/69 (8%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG---LDYAKAIEHTD 337
            +   + +G   LH A      ++V+ L +  GAD+N    +   G   L  A   +   
Sbjct: 150 QLEAENYDGHTPLHVAVIHKDAEMVRLLRDA-GADLNKP--EPTCGRTPLHLAVEAQAAS 206

Query: 338 LIEYLVNSG 346
           ++E L+ +G
Sbjct: 207 VLELLLKAG 215

>1oy3_D Transcription factor inhibitor I-kappa-B-beta; protein-protein complex, transcription factors, nuclear localization, DNA binding protein; 2.05A {Mus musculus} SCOP: d.211.1.1 PDB: 1k3z_D Length = 282

 Score = 56.0 bits (136), Expect = 3e-09
 Identities = 15/66 (22%), Positives = 23/66 (34%), Gaps = 1/66 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
            ++  ++ G   LH A   G    V+ L    GA V V +  G   L  A  +       
Sbjct: 37  YLDLQNDLGQTALHLAAILGEASTVEKLYAA-GAGVLVAERGGHTALHLACRVRAHTCAC 95

Query: 341 YLVNSG 346
            L+   
Sbjct: 96  VLLQPR 101

>1oy3_D Transcription factor inhibitor I-kappa-B-beta; protein-protein complex, transcription factors, nuclear localization, DNA binding protein; 2.05A {Mus musculus} SCOP: d.211.1.1 PDB: 1k3z_D Length = 282

 Score = 52.5 bits (127), Expect = 5e-08
 Identities = 14/68 (20%), Positives = 25/68 (36%), Gaps = 4/68 (5%)

Query: 282 INQLDENGLNCLHWACDRGHLKVVQHLIEKCGAD---VNVTDSDGDYGLDYAKAIEHTDL 338
              + E+G   LH A    H   +  L+    A    +++ +  G   L  A  +     
Sbjct: 2   FGYVTEDGDTALHLAVIHQHEPFLDFLLGF-SAGHEYLDLQNDLGQTALHLAAILGEAST 60

Query: 339 IEYLVNSG 346
           +E L  +G
Sbjct: 61  VEKLYAAG 68

>1oy3_D Transcription factor inhibitor I-kappa-B-beta; protein-protein complex, transcription factors, nuclear localization, DNA binding protein; 2.05A {Mus musculus} SCOP: d.211.1.1 PDB: 1k3z_D Length = 282

 Score = 49.9 bits (120), Expect = 4e-07
 Identities = 15/93 (16%), Positives = 24/93 (25%), Gaps = 11/93 (11%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           + +N          A  G+    V++L       +   +  G   LH AC          
Sbjct: 39  DLQNDLGQTALHLAAILGEAST-VEKLYA-AGAGVLVAERGGHTALHLACRVRAHTCACV 96

Query: 308 LIEKCGADVNVTDSDGDY--GLDYAKAIEHTDL 338
           L++          SD       D      H   
Sbjct: 97  LLQP-RPSHPRDASDTYLTQSQDCTPDTSHAPA 128

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 56.9 bits (137), Expect = 2e-10
 Identities = 16/77 (20%), Positives = 29/77 (37%), Gaps = 2/77 (2%)

Query: 10  KIFVGNLPWTVSHNELKKFFSEYGQIMNA-SVMFDKN-TGLSKGFGFVTFQNKEAVDKVF 67
            + +  LPW+ S  +++ F S+      A  V F     G   G  FV   +++ V    
Sbjct: 46  VVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMAL 105

Query: 68  STDSHVLEGSRLSIQPS 84
             D   +    + +  S
Sbjct: 106 KKDRESMGHRYIEVFKS 122

>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 = 56.0 bits (135), Expect = 2e-10
 Identities = 14/102 (13%), Positives = 36/102 (35%), Gaps = 4/102 (3%)

Query: 1   MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASV--MFDKNTGLSKGFGFVTFQ 58
           +   +  +  I    LPW+ +  ++  FFS+       +         G  +G   +  +
Sbjct: 4   LEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEME 63

Query: 59  NKEAVDKVFSTDSHVLEGSRLSIQPSDSHNRMAENMEDRFNQ 100
           +++ V K        + G R  ++  + +N   + +      
Sbjct: 64  SEQDVQKALEKHRMYM-GQRY-VEVYEINNEDVDALMKSLQV 103

>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 = 5e-10
 Identities = 17/80 (21%), Positives = 36/80 (45%), Gaps = 9/80 (11%)

Query: 1  MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
             + R+ N ++V      ++   L+  FS +G I++ S+         +   FVT++  
Sbjct: 8  ERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKM 59

Query: 61 EAVDK-VFSTDSHVLEGSRL 79
          E+ D+ V   +   +E  +L
Sbjct: 60 ESADQAVAELNGTQVESVQL 79

>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 = 57.3 bits (138), Expect = 9e-10
 Identities = 19/80 (23%), Positives = 29/80 (36%), Gaps = 7/80 (8%)

Query: 11  IFVGNL-PWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK-VFS 68
           + V NL P  V+   L   F  YG +    ++F+K     K    V   +       +  
Sbjct: 37  LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSH 91

Query: 69  TDSHVLEGSRLSIQPSDSHN 88
            + H L G  + I  S   N
Sbjct: 92  LNGHKLHGKPIRITLSKHQN 111

>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 = 56.5 bits (136), Expect = 2e-09
 Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 4/54 (7%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
             + + N+P +VS  +LK  FS  G ++     F K+    +    +   + E 
Sbjct: 152 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEE 201

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 54.4 bits (131), Expect = 9e-10
 Identities = 14/79 (17%), Positives = 28/79 (35%), Gaps = 9/79 (11%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV---F 67
          + V  L  +V   +L +   ++G I    +M  K          V F+N ++  +     
Sbjct: 18 VHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR------QALVEFENIDSAKECVTFA 71

Query: 68 STDSHVLEGSRLSIQPSDS 86
          +     + G +     S S
Sbjct: 72 ADVPVYIAGQQAFFNYSTS 90

>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 = 56.8 bits (136), Expect = 9e-10
 Identities = 16/77 (20%), Positives = 34/77 (44%), Gaps = 1/77 (1%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
             +++   P   + +++K++  + GQ++N  +    +    KG  FV F + E+  K   
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE 168

Query: 69  TDSHVLEGSRLSIQPSD 85
           T     + + L I   D
Sbjct: 169 TPGQKYKETDLLILFKD 185

>2etb_A Transient receptor potential cation channel subfamily V member 2; TRPV2, ankyrin repeat domain, transport protein; 1.65A {Rattus norvegicus} PDB: 2eta_A 2etc_A 2f37_A Length = 256

 Score = 57.5 bits (139), Expect = 1e-09
 Identities = 16/87 (18%), Positives = 30/87 (34%), Gaps = 14/87 (16%)

Query: 274 LTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAI 333
              L +         G + LH A ++  L+ V+ L+E  GADV++      +        
Sbjct: 75  PKPLVNAQCTDEFYQGHSALHIAIEKRSLQCVKLLVEN-GADVHLRACGRFFQKHQGTCF 133

Query: 334 E-------------HTDLIEYLVNSGS 347
                           D++ YL+ +  
Sbjct: 134 YFGELPLSLAACTKQWDVVTYLLENPH 160

>2etb_A Transient receptor potential cation channel subfamily V member 2; TRPV2, ankyrin repeat domain, transport protein; 1.65A {Rattus norvegicus} PDB: 2eta_A 2etc_A 2f37_A Length = 256

 Score = 50.6 bits (121), Expect = 2e-07
 Identities = 17/112 (15%), Positives = 29/112 (25%), Gaps = 19/112 (16%)

Query: 254 NEKNIYEWAKEGKLDMLVKQLTKLK------DFNINQLDENGLNCLHWA---CDRGHLKV 304
           +   ++     G  + L   L  L+        +       G  CL  A      G    
Sbjct: 2   DRDRLFSVVSRGVPEELTGLLEYLRWNSKYLTDSAYTEGSTGKTCLMKAVLNLQDGVNAC 61

Query: 305 VQHLIEKC----------GADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           +  L++             A        G   L  A        ++ LV +G
Sbjct: 62  IMPLLQIDKDSGNPKPLVNAQCTDEFYQGHSALHIAIEKRSLQCVKLLVENG 113

>2etb_A Transient receptor potential cation channel subfamily V member 2; TRPV2, ankyrin repeat domain, transport protein; 1.65A {Rattus norvegicus} PDB: 2eta_A 2etc_A 2f37_A Length = 256

 Score = 48.6 bits (116), Expect = 1e-06
 Identities = 10/64 (15%), Positives = 22/64 (34%), Gaps = 3/64 (4%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
             +G L M   +L           +  GL  L  A   G +++ +H++++          
Sbjct: 196 MYDGLLQM-GARLCP-TVQLEEISNHQGLTPLKLAAKEGKIEIFRHILQR-EFSGAAAHH 252

Query: 322 DGDY 325
              +
Sbjct: 253 HHHH 256

>2etb_A Transient receptor potential cation channel subfamily V member 2; TRPV2, ankyrin repeat domain, transport protein; 1.65A {Rattus norvegicus} PDB: 2eta_A 2etc_A 2f37_A Length = 256

 Score = 48.2 bits (115), Expect = 1e-06
 Identities = 7/65 (10%), Positives = 20/65 (30%), Gaps = 1/65 (1%)

Query: 282 INQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEY 341
           +   +    + L      G L++   L         +++  G   L  A      ++  +
Sbjct: 181 MIADNSPENSALVIHMYDGLLQMGARLCPT-VQLEEISNHQGLTPLKLAAKEGKIEIFRH 239

Query: 342 LVNSG 346
           ++   
Sbjct: 240 ILQRE 244

>2etb_A Transient receptor potential cation channel subfamily V member 2; TRPV2, ankyrin repeat domain, transport protein; 1.65A {Rattus norvegicus} PDB: 2eta_A 2etc_A 2f37_A Length = 256

 Score = 44.4 bits (105), Expect = 2e-05
 Identities = 17/107 (15%), Positives = 29/107 (27%), Gaps = 23/107 (21%)

Query: 252 DDNEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNC------------- 292
              ++            ++  L   VK L +    +++                      
Sbjct: 82  QCTDEFYQGHSALHIAIEKRSLQC-VKLLVE-NGADVHLRACGRFFQKHQGTCFYFGELP 139

Query: 293 LHWACDRGHLKVVQHLIEK--CGADVNVTDSDGDYGLDYAKAIEHTD 337
           L  A       VV +L+E     A +  TDS G+  L     I    
Sbjct: 140 LSLAACTKQWDVVTYLLENPHQPASLEATDSLGNTVLHALVMIADNS 186

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 54.0 bits (130), Expect = 1e-09
 Identities = 14/79 (17%), Positives = 25/79 (31%), Gaps = 9/79 (11%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV---F 67
          + +  L   V   +L +   E+G I    VM        K    V F++           
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYA 77

Query: 68 STDSHVLEGSRLSIQPSDS 86
          + +   + G    +  S S
Sbjct: 78 ADNQIYIAGHPAFVNYSTS 96

>1sw6_A Regulatory protein SWI6; transcription regulation, ankyrin repeats, cell-cycle; 2.10A {Saccharomyces cerevisiae} SCOP: d.211.1.1 Length = 327

 Score = 57.7 bits (139), Expect = 1e-09
 Identities = 19/96 (19%), Positives = 39/96 (40%), Gaps = 3/96 (3%)

Query: 241 VSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDF--NINQLDENGLNCLHWACD 298
           V           + +++        + D +++ L         +N  D NG  CL+ A  
Sbjct: 233 VKKQNRPIQSGTNEKESKPNDKNGERKDSILENLDLKWIIANMLNAQDSNGDTCLNIAAR 292

Query: 299 RGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIE 334
            G++ +V  L++  GAD  + +  G   +D+   +E
Sbjct: 293 LGNISIVDALLDY-GADPFIANKSGLRPVDFGAGLE 327

>1sw6_A Regulatory protein SWI6; transcription regulation, ankyrin repeats, cell-cycle; 2.10A {Saccharomyces cerevisiae} SCOP: d.211.1.1 Length = 327

 Score = 56.2 bits (135), Expect = 4e-09
 Identities = 21/85 (24%), Positives = 42/85 (49%), Gaps = 5/85 (5%)

Query: 243 SMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKL---KDFNIN-QLDENGLNCLHWACD 298
           S+ ND S  +    +  +  +    D L++++         N+N  +DE+G   LHW   
Sbjct: 81  SLNNDSSNRNSEGGSSNQQQQHVSFDSLLQEVNDAFPNTQLNLNIPVDEHGNTPLHWLTS 140

Query: 299 RGHLKVVQHLIEKCGADVNVTDSDG 323
             +L++V+HL++  G++    D+ G
Sbjct: 141 IANLELVKHLVKH-GSNRLYGDNMG 164

>1sw6_A Regulatory protein SWI6; transcription regulation, ankyrin repeats, cell-cycle; 2.10A {Saccharomyces cerevisiae} SCOP: d.211.1.1 Length = 327

 Score = 43.5 bits (102), Expect = 6e-05
 Identities = 21/116 (18%), Positives = 44/116 (37%), Gaps = 6/116 (5%)

Query: 212 DKEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWA-KEGKLDML 270
           ++  E  + ++ Q+  S ++  Q       ++ +N    +D++      W      L++ 
Sbjct: 88  NRNSEGGSSNQQQQHVSFDSLLQEVNDAFPNTQLNLNIPVDEHGNTPLHWLTSIANLEL- 146

Query: 271 VKQLTKLKDFNINQLDENGLNCLHWACDRGH---LKVVQHLIEKCGADVNVTDSDG 323
           VK L K    N    D  G +CL  A    +       + L++     + + DS  
Sbjct: 147 VKHLVKHGS-NRLYGDNMGESCLVKAVKSVNNYDSGTFEALLDYLYPCLILEDSMN 201

>3aji_A 26S proteasome non-ATPase regulatory subunit 10; gankyrin, S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dvw_A 2dwz_A* 1tr4_A 1uoh_A 1qym_A Length = 231

 Score = 56.8 bits (137), Expect = 1e-09
 Identities = 26/95 (27%), Positives = 45/95 (47%), Gaps = 2/95 (2%)

Query: 253 DNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKC 312
            +   I   A  GKLD L +++         + D++    LHWAC  GH ++V+ L++  
Sbjct: 5   VSNIMICNLAYSGKLDELKERILA-DKSLATRTDQDSRTALHWACSAGHTEIVEFLLQL- 62

Query: 313 GADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
           G  VN  D  G   L  A +    ++++ L+  G+
Sbjct: 63  GVPVNDKDDAGWSPLHIAASAGXDEIVKALLVKGA 97

>3aji_A 26S proteasome non-ATPase regulatory subunit 10; gankyrin, S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dvw_A 2dwz_A* 1tr4_A 1uoh_A 1qym_A Length = 231

 Score = 52.2 bits (125), Expect = 4e-08
 Identities = 20/100 (20%), Positives = 45/100 (45%), Gaps = 9/100 (9%)

Query: 254 NEKNIYEW------AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQH 307
           N+K+   W      A  G  +++  +   +K  ++N +++NG   LH+A  +   ++   
Sbjct: 67  NDKDDAGWSPLHIAASAGXDEIV--KALLVKGAHVNAVNQNGCTPLHYAASKNRHEIAVM 124

Query: 308 LIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
           L+E  GA+ +  D      +  A A  +  ++  L+   +
Sbjct: 125 LLEG-GANPDAKDHYDATAMHRAAAKGNLKMVHILLFYKA 163

>3aji_A 26S proteasome non-ATPase regulatory subunit 10; gankyrin, S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dvw_A 2dwz_A* 1tr4_A 1uoh_A 1qym_A Length = 231

 Score = 49.9 bits (119), Expect = 3e-07
 Identities = 22/106 (20%), Positives = 43/106 (40%), Gaps = 5/106 (4%)

Query: 241 VSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRG 300
           +    N +++   +   ++  A +G L M+   +      + N  D  G   LH ACD  
Sbjct: 126 LEGGANPDAKDHYDATAMHRAAAKGNLKMV--HILLFYKASTNIQDTEGNTPLHLACDEE 183

Query: 301 HLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
            ++  + L+ + GA + + + +    L  AK      LI   +  G
Sbjct: 184 RVEEAKFLVTQ-GASIYIENKEEKTPLQVAK--GGLGLILKRLAEG 226

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 54.5 bits (131), Expect = 1e-09
 Identities = 13/79 (16%), Positives = 30/79 (37%), Gaps = 8/79 (10%)

Query: 9   NKIFVGNLPWTVSHNELKK----FFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVD 64
             + + N+   V   +L+       S  G I++  V     +  + G  ++ F  +E+  
Sbjct: 30  QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVD---LSDDNSGKAYIVFATQESAQ 86

Query: 65  KVF-STDSHVLEGSRLSIQ 82
               +   +  +G+ L I 
Sbjct: 87  AFVEAFQGYPFQGNPLVIT 105

>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 = 56.1 bits (135), Expect = 2e-09
 Identities = 19/84 (22%), Positives = 29/84 (34%), Gaps = 7/84 (8%)

Query: 11 IFVGNL-PWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK-VFS 68
          + V NL P  V+   L   F  YG +    ++F+K     K    V   +       +  
Sbjct: 6  LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSH 60

Query: 69 TDSHVLEGSRLSIQPSDSHNRMAE 92
           + H L G  + I  S   N    
Sbjct: 61 LNGHKLHGKPIRITLSKHQNVQLP 84

>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 = 54.5 bits (131), Expect = 5e-09
 Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 4/54 (7%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
             + + N+P +VS  +LK  FS  G ++     F K+    +    +   + E 
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMGSVEE 170

>2pnn_A Transient receptor potential cation channel subfa member 1; TRPV1, ankyrin repeat domain, transport protein; HET: ATP; 2.70A {Rattus norvegicus} PDB: 2nyj_A* Length = 273

 Score = 56.3 bits (136), Expect = 2e-09
 Identities = 14/91 (15%), Positives = 31/91 (34%), Gaps = 15/91 (16%)

Query: 271 VKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA 330
              L +  + +       G   LH A +R ++ +V  L+E  GADV    +   +     
Sbjct: 83  TDSLKQFVNASYTDSYYKGQTALHIAIERRNMTLVTLLVEN-GADVQAAANGDFFKKTKG 141

Query: 331 KAIE--------------HTDLIEYLVNSGS 347
           +                    ++++L+ +  
Sbjct: 142 RPGFYFGELPLSLAACTNQLAIVKFLLQNSW 172

>2pnn_A Transient receptor potential cation channel subfa member 1; TRPV1, ankyrin repeat domain, transport protein; HET: ATP; 2.70A {Rattus norvegicus} PDB: 2nyj_A* Length = 273

 Score = 44.0 bits (104), Expect = 3e-05
 Identities = 11/52 (21%), Positives = 20/52 (38%), Gaps = 2/52 (3%)

Query: 293 LHWACDRGHLKVVQHLIEK--CGADVNVTDSDGDYGLDYAKAIEHTDLIEYL 342
           L  A     L +V+ L++     AD++  DS G+  L     +    +    
Sbjct: 152 LSLAACTNQLAIVKFLLQNSWQPADISARDSVGNTVLHALVEVADNTVDNTK 203

>2pnn_A Transient receptor potential cation channel subfa member 1; TRPV1, ankyrin repeat domain, transport protein; HET: ATP; 2.70A {Rattus norvegicus} PDB: 2nyj_A* Length = 273

 Score = 44.0 bits (104), Expect = 3e-05
 Identities = 8/66 (12%), Positives = 24/66 (36%), Gaps = 2/66 (3%)

Query: 252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEK 311
           +  +   +  +   ++ +L  +L           +  GL  L  A   G + V+ +++++
Sbjct: 197 NTVDNTKFVTSMYNEILILGAKLHP-TLKLEEITNRKGLTPLALAASSGKIGVLAYILQR 255

Query: 312 CGADVN 317
                 
Sbjct: 256 -EIHEP 260

>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 = 53.0 bits (127), Expect = 4e-09
 Identities = 18/79 (22%), Positives = 36/79 (45%), Gaps = 9/79 (11%)

Query: 11  IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV---F 67
           I +  LP  V+  E+      +G++ N  ++  KN        F+    +EA + +   +
Sbjct: 34  IHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKN------QAFIEMNTEEAANTMVNYY 87

Query: 68  STDSHVLEGSRLSIQPSDS 86
           ++ + VL G  + IQ S+ 
Sbjct: 88  TSVTPVLRGQPIYIQFSNH 106

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 52.2 bits (125), Expect = 6e-09
 Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 9/79 (11%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV---F 67
          I +  LP  V+  E+      +G++ N  ++        K   F+    +EA + +   +
Sbjct: 19 IHIRKLPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVNYY 72

Query: 68 STDSHVLEGSRLSIQPSDS 86
          ++ + VL G  + IQ S+ 
Sbjct: 73 TSVTPVLRGQPIYIQFSNH 91

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 52.1 bits (125), Expect = 7e-09
 Identities = 18/82 (21%), Positives = 27/82 (32%), Gaps = 10/82 (12%)

Query: 2  SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
           +S R    I   NLP      E+++ FS +G +    V+  +          V F    
Sbjct: 4  GSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSL--GRVLLPE----GGITAIVEFLEPL 57

Query: 62 AVDKVFSTDSHVLEGSRLSIQP 83
             K F      L  S+    P
Sbjct: 58 EARKAFRH----LAYSKFHHVP 75

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 50.5 bits (121), Expect = 1e-08
 Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 9/77 (11%)

Query: 9  NKIFVGNLPWTVS------HNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE- 61
          + I V N+P           N + K FS++G+I   +  + +  G +KG+ F+ + +   
Sbjct: 2  SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKIT--NDFYPEEDGKTKGYIFLEYASPAH 59

Query: 62 AVDKVFSTDSHVLEGSR 78
          AVD V + D + L+   
Sbjct: 60 AVDAVKNADGYKLDKQH 76

>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 = 51.0 bits (122), Expect = 2e-08
 Identities = 15/77 (19%), Positives = 30/77 (38%), Gaps = 9/77 (11%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV---F 67
          + +  LP  V+  E+      +G++ N  ++        K   F+    +EA   +   +
Sbjct: 18 LHIRKLPGEVTETEVIALGLPFGKVTNILML------KGKNQAFLELATEEAAITMVNYY 71

Query: 68 STDSHVLEGSRLSIQPS 84
          S  +  L    + IQ S
Sbjct: 72 SAVTPHLRNQPIYIQYS 88

>2rfa_A Transient receptor potential cation channel subfa member 6; TRPV6, ankyrin reapeat, ANK RE calcium channel, calcium transport, calmodulin-binding; 1.70A {Mus musculus} Length = 232

 Score = 52.6 bits (127), Expect = 3e-08
 Identities = 21/90 (23%), Positives = 36/90 (40%), Gaps = 7/90 (7%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADV----- 316
           AKE  +  L K L K +   ++Q    G   LH A    +L+    L+E    ++     
Sbjct: 11  AKENDVQALSKLL-KFEGCEVHQRGAMGETALHIAALYDNLEAAMVLMEA-APELVFEPM 68

Query: 317 NVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
                +G   L  A   ++ +L+  L+  G
Sbjct: 69  TSELYEGQTALHIAVINQNVNLVRALLARG 98

>2rfa_A Transient receptor potential cation channel subfa member 6; TRPV6, ankyrin reapeat, ANK RE calcium channel, calcium transport, calmodulin-binding; 1.70A {Mus musculus} Length = 232

 Score = 45.3 bits (108), Expect = 1e-05
 Identities = 9/75 (12%), Positives = 21/75 (28%), Gaps = 9/75 (12%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIE---KCGADVN------VTDSDGDYGLDYAK 331
           +I   D  G   LH    + +      +           +      V ++ G      A 
Sbjct: 146 DIRAQDSLGNTVLHILILQPNKTFACQMYNLLLSYDGGDHLKSLELVPNNQGLTPFKLAG 205

Query: 332 AIEHTDLIEYLVNSG 346
              +  + ++L+   
Sbjct: 206 VEGNIVMFQHLMQKR 220

>2rfa_A Transient receptor potential cation channel subfa member 6; TRPV6, ankyrin reapeat, ANK RE calcium channel, calcium transport, calmodulin-binding; 1.70A {Mus musculus} Length = 232

 Score = 44.9 bits (107), Expect = 1e-05
 Identities = 19/122 (15%), Positives = 39/122 (31%), Gaps = 24/122 (19%)

Query: 247 DESQLDDNEKNIYEW------AKEGKLDMLVKQL------------TKLKDFNINQLDEN 288
           +        +                +++ V+ L              +  +  + L   
Sbjct: 62  ELVFEPMTSELYEGQTALHIAVINQNVNL-VRALLARGASVSARATGSVFHYRPHNLIYY 120

Query: 289 GLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTD----LIEYLVN 344
           G + L +A   G  ++V+ LIE  GAD+   DS G+  L       +      +   L++
Sbjct: 121 GEHPLSFAACVGSEEIVRLLIEH-GADIRAQDSLGNTVLHILILQPNKTFACQMYNLLLS 179

Query: 345 SG 346
             
Sbjct: 180 YD 181

>2rfa_A Transient receptor potential cation channel subfa member 6; TRPV6, ankyrin reapeat, ANK RE calcium channel, calcium transport, calmodulin-binding; 1.70A {Mus musculus} Length = 232

 Score = 44.1 bits (105), Expect = 2e-05
 Identities = 9/54 (16%), Positives = 23/54 (42%)

Query: 293 LHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           L  A     ++ +  L++  G +V+   + G+  L  A   ++ +    L+ + 
Sbjct: 7   LLLAAKENDVQALSKLLKFEGCEVHQRGAMGETALHIAALYDNLEAAMVLMEAA 60

>2b0o_E UPLC1; arfgap, structural genomics, structural genomics consortium, SGC, metal binding protein; 2.06A {Homo sapiens} Length = 301

 Score = 52.7 bits (126), Expect = 5e-08
 Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 1/65 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           +++    +G   LH+A        ++ L+ K  A V   +  G+  LD A+   H +  E
Sbjct: 218 HLDAKAADGNTALHYAALYNQPDCLKLLL-KGRALVGTVNEAGETALDIARKKHHKECEE 276

Query: 341 YLVNS 345
            L  +
Sbjct: 277 LLEQA 281

>1dcq_A PYK2-associated protein beta; zinc-binding module, ankyrin repeats, metal binding protein; 2.10A {Mus musculus} SCOP: d.211.1.1 g.45.1.1 Length = 278

 Score = 51.5 bits (123), Expect = 1e-07
 Identities = 15/65 (23%), Positives = 32/65 (49%), Gaps = 1/65 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           N+++    G   LH+ C   + + ++ L+ +  A + + +  G+  LD AK ++H    E
Sbjct: 197 NLDKQTGKGSTALHYCCLTDNAECLKLLL-RGKASIEIANESGETPLDIAKRLKHEHCEE 255

Query: 341 YLVNS 345
            L  +
Sbjct: 256 LLTQA 260

>1dcq_A PYK2-associated protein beta; zinc-binding module, ankyrin repeats, metal binding protein; 2.10A {Mus musculus} SCOP: d.211.1.1 g.45.1.1 Length = 278

 Score = 42.3 bits (99), Expect = 1e-04
 Identities = 24/171 (14%), Positives = 54/171 (31%), Gaps = 16/171 (9%)

Query: 188 DWKPNQKAMSKYI--ALLNEVDASWEDKEQEEINWDESQESGSKENEG------QTKGWV 239
               ++  ++K I  A  NE+    E     E     +  S     +         + + 
Sbjct: 64  VLGTSELLLAKNIGNAGFNEI---MECCLPSEDPVKPNPGSDMIARKDYITAKYMERRYA 120

Query: 240 NVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWAC-- 297
                 +  ++L    + +      G L      +   +   +    E     LH A   
Sbjct: 121 R-KKHADTAAKLHSLCEAVKTRDIFGLLQAYADGVDLTEKIPLANGHEPDETALHLAVRS 179

Query: 298 -DRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
            DR  L +V  L++    +++     G   L Y    ++ + ++ L+   +
Sbjct: 180 VDRTSLHIVDFLVQN-SGNLDKQTGKGSTALHYCCLTDNAECLKLLLRGKA 229

>3jxi_A Vanilloid receptor-related osmotically activated protein; ankyrin repeats, ANK repeat, ION transport, ionic channel, R transmembrane, transport; 2.30A {Gallus gallus} PDB: 3jxj_A Length = 260

 Score = 50.2 bits (120), Expect = 2e-07
 Identities = 19/90 (21%), Positives = 31/90 (34%), Gaps = 15/90 (16%)

Query: 272 KQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS---------- 321
             + +  +     +   G   LH A +R     V+ L+EK GADV+              
Sbjct: 76  GNMREFINSPFRDVYYRGQTALHIAIERRCKHYVELLVEK-GADVHAQARGRFFQPKDEG 134

Query: 322 ----DGDYGLDYAKAIEHTDLIEYLVNSGS 347
                G+  L  A       ++ YL  +G 
Sbjct: 135 GYFYFGELPLSLAACTNQPHIVHYLTENGH 164

>3jxi_A Vanilloid receptor-related osmotically activated protein; ankyrin repeats, ANK repeat, ION transport, ionic channel, R transmembrane, transport; 2.30A {Gallus gallus} PDB: 3jxj_A Length = 260

 Score = 42.8 bits (101), Expect = 6e-05
 Identities = 9/48 (18%), Positives = 17/48 (35%), Gaps = 1/48 (2%)

Query: 278 KDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY 325
                  L+ +GL+ L  A   G + + QH+I +             +
Sbjct: 214 DTNLEALLNNDGLSPLMMAAKTGKIGIFQHIIRR-EIADAAAHHHHHH 260

>3jxi_A Vanilloid receptor-related osmotically activated protein; ankyrin repeats, ANK repeat, ION transport, ionic channel, R transmembrane, transport; 2.30A {Gallus gallus} PDB: 3jxj_A Length = 260

 Score = 42.5 bits (100), Expect = 9e-05
 Identities = 14/57 (24%), Positives = 19/57 (33%), Gaps = 2/57 (3%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEK--CGADVNVTDSDGDYGLDYAKAIEH 335
           +       G   L  A       +V +L E     AD+   DS G+  L    AI  
Sbjct: 132 DEGGYFYFGELPLSLAACTNQPHIVHYLTENGHKQADLRRQDSRGNTVLHALVAIAD 188

>3jue_A Arfgap with coiled-coil, ANK repeat and PH domain containing protein 1; arfgap domain, zinc-binding module, GTPase activ metal-binding, nitration; 2.30A {Homo sapiens} Length = 368

 Score = 50.9 bits (121), Expect = 2e-07
 Identities = 21/63 (33%), Positives = 29/63 (46%), Gaps = 1/63 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           N+NQ D  G   LH A   GH  +    + K GAD+   DS+G   L  A    + D++ 
Sbjct: 260 NVNQADSAGRGPLHHATILGHTGLACLFL-KRGADLGARDSEGRDPLTIAMETANADIVT 318

Query: 341 YLV 343
            L 
Sbjct: 319 LLR 321

>3jue_A Arfgap with coiled-coil, ANK repeat and PH domain containing protein 1; arfgap domain, zinc-binding module, GTPase activ metal-binding, nitration; 2.30A {Homo sapiens} Length = 368

 Score = 45.2 bits (106), Expect = 2e-05
 Identities = 19/68 (27%), Positives = 28/68 (41%), Gaps = 1/68 (1%)

Query: 279 DFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDL 338
           D N     ++    L  A     L   + L++  GA+VN  DS G   L +A  + HT L
Sbjct: 225 DVNWVNGGQDNATPLIQATAANSLLACEFLLQN-GANVNQADSAGRGPLHHATILGHTGL 283

Query: 339 IEYLVNSG 346
               +  G
Sbjct: 284 ACLFLKRG 291

>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 = 47.2 bits (112), Expect = 3e-07
 Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 10/81 (12%)

Query: 11  IFVGNLPW-TVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV--- 66
           I + NLP    S + + K    YG+I N  +M  K+        F+  + +E    +   
Sbjct: 28  IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKS------QAFIEMETREDAMAMVDH 81

Query: 67  FSTDSHVLEGSRLSIQPSDSH 87
               +   +G  + +  S+ +
Sbjct: 82  CLKKALWFQGRCVKVDLSEKY 102

>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 = 46.8 bits (111), Expect = 5e-07
 Identities = 11/52 (21%), Positives = 21/52 (40%), Gaps = 6/52 (11%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
          +  G L   VS N+L     + G +   +++   N    K + F  ++  E 
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVD--ALLMPPN----KPYSFARYRTTEE 75

>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154

 Score = 42.2 bits (98), Expect = 5e-05
 Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 8/27 (29%)

Query: 109 VKKLDSSTLLKFY------ALYKQATV 129
           +KKL +S  LK Y      AL  +AT+
Sbjct: 22  LKKLQAS--LKLYADDSAPALAIKATM 46

>3lvq_E ARF-GAP with SH3 domain, ANK repeat and PH domain containing protein 3, ADP-ribosylation...; GDP, ASAP3, UPLC1, linkers, alternat splicing; HET: GDP; 3.38A {Homo sapiens} PDB: 3lvr_E* Length = 497

 Score = 41.8 bits (98), Expect = 2e-04
 Identities = 14/69 (20%), Positives = 26/69 (37%), Gaps = 4/69 (5%)

Query: 281 NINQLDENGLNCLHWAC---DRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTD 337
                       LH A    ++  L +V  +I+  G  ++   +DG+  L YA      D
Sbjct: 163 PGPDAQAPEELVLHLAVKVANQASLPLVDFIIQN-GGHLDAKAADGNTALHYAALYNQPD 221

Query: 338 LIEYLVNSG 346
            ++ L+   
Sbjct: 222 CLKLLLKGR 230

>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 = 40.1 bits (93), Expect = 3e-04
 Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 4/55 (7%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          I V NL + V+ + L + FS++G ++   + F KN         + + +  +   
Sbjct: 49 IIVENLFYPVTLDVLHQIFSKFGTVLK-IITFTKNNQFQ---ALLQYADPVSAQH 99

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 38.9 bits (90), Expect = 5e-04
 Identities = 12/52 (23%), Positives = 25/52 (48%), Gaps = 4/52 (7%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEA 62
          I V NL + V+ + L + FS++G ++   + F KN         + + +  +
Sbjct: 31 IIVENLFYPVTLDVLHQIFSKFGTVLK-IITFTKNNQFQ---ALLQYADPVS 78

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	347
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.9
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.9
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.89
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.88
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.88
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.87
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.87
4gpm_A	169	Engineered protein OR264; de novo protein, structu	99.87
1n0q_A	93	3ANK, 3 ankyrin repeats; structural protein; 1.26A	99.86
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.86
1hbk_A	89	ACBP, acyl-COA binding protein; fatty acid metabol	99.86
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.86
1st7_A	86	ACBP, acyl-COA-binding protein; four helix bundle,	99.86
2lbb_A	96	Acyl COA binding protein; protein binding, structu	99.85
2cop_A	109	Acyl-coenzyme A binding domain containing 6; acyl	99.85
3epy_A	89	Acyl-COA-binding domain-containing protein 7; acyl	99.85
2cb8_A	87	Acyl-COA-binding protein; acyl-coenzyme A binding	99.84
4gpm_A	169	Engineered protein OR264; de novo protein, structu	99.84
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.84
2cqu_A	116	Peroxisomal D3,D2-enoyl-COA isomerase; acyl-COA bi	99.84
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.83
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.82
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.82
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.82
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.82
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.81
2wh5_A	106	Acyl-COA-binding domain-containing protein 4; alte	99.8
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.8
3fp5_A	106	Acyl-COA binding protein; ACBP, cacao disease, fat	99.8
3flv_A	119	Acyl-COA-binding domain-containing protein 5; lipi	99.8
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.8
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.8
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.8
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.79
2jab_A	136	H10-2-G3; HER2, darpin, ankyrin repeat protein, me	99.79
1d9s_A	136	Cyclin-dependent kinase 4 inhibitor B; helix-turn-	99.79
3aaa_C	123	Myotrophin, protein V-1; actin capping protein, ba	99.79
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.79
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.79
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.79
3c5r_A	137	BARD-1, BRCA1-associated ring domain protein 1; an	99.79
2l6b_A	115	NR1C; ankyrin, consensus, repeat protein, ising mo	99.79
1d9s_A	136	Cyclin-dependent kinase 4 inhibitor B; helix-turn-	99.78
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.78
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.78
3f6q_A	179	Integrin-linked protein kinase; ILK, integrin-link	99.78
3twr_A	165	Tankyrase-2; ankyrin repeat, protein-protein inter	99.77
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.77
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.77
1n0r_A	126	4ANK, 4 ankyrin repeats; structural protein; 1.50A	99.77
1ihb_A	162	P18-INK4C(INK6), cyclin-dependent kinase 6 inhibit	99.77
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.77
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.77
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.77
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.77
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.77
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.77
1bi7_B	156	P16INK4A, MTS1, multiple tumor suppressor; cyclin	99.77
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.77
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.77
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.76
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.76
1dcq_A	278	PYK2-associated protein beta; zinc-binding module,	99.76
2y1l_E	169	Darpin-8.4; hydrolase-inhibitor complex, DEVD darp	99.76
2div_A	99	TRNA selenocysteine associated protein; structural	99.76
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.76
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.76
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.76
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.76
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.76
1awc_B	153	Protein (GA binding protein beta 1); complex (tran	99.76
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.76
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.76
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.76
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.76
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.76
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.76
3v30_A	172	DNA-binding protein rfxank; structural genomics co	99.76
2jab_A	136	H10-2-G3; HER2, darpin, ankyrin repeat protein, me	99.75
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.75
3v31_A	167	Ankyrin repeat family A protein 2; structural geno	99.75
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.75
4b93_B	269	Ankyrin repeat domain-containing protein 27; endoc	99.75
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.75
1ihb_A	162	P18-INK4C(INK6), cyclin-dependent kinase 6 inhibit	99.75
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.75
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.75
2zgd_A	110	3 repeat synthetic ankyrin; ankyrin repeat, hydrox	99.75
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.75
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.75
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.75
2rfm_A	192	Putative ankyrin repeat protein TV1425; ANK repeat	99.75
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.75
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.75
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.75
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.74
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.74
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.74
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.74
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.74
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.74
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.74
2y1l_E	169	Darpin-8.4; hydrolase-inhibitor complex, DEVD darp	99.74
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.74
3v30_A	172	DNA-binding protein rfxank; structural genomics co	99.74
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.74
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.74
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.74
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.74
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.74
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.74
3twr_A	165	Tankyrase-2; ankyrin repeat, protein-protein inter	99.73
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.73
1bd8_A	156	P19INK4D CDK4/6 inhibitor; tumor suppressor, ankyr	99.73
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.73
1oy3_D	282	Transcription factor inhibitor I-kappa-B-beta; pro	99.73
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.73
1ycs_B	239	53BP2, P53BP2; ankyrin repeats, SH3, tumor suppres	99.73
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.73
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.73
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.73
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.73
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.73
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.73
1bd8_A	156	P19INK4D CDK4/6 inhibitor; tumor suppressor, ankyr	99.73
2vge_A	229	RELA-associated inhibitor; iaspp, nucleus, apoptos	99.73
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.73
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.73
3lvq_E	497	ARF-GAP with SH3 domain, ANK repeat and PH domain	99.73
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.73
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.73
3deo_A	183	Signal recognition particle 43 kDa protein; chloro	99.72
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.72
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.72
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.72
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.72
3ehr_A	222	Osteoclast-stimulating factor 1; beta barrel, heli	99.72
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.72
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.72
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.72
1awc_B	153	Protein (GA binding protein beta 1); complex (tran	99.72
2rfm_A	192	Putative ankyrin repeat protein TV1425; ANK repeat	99.72
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.72
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.72
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.72
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.72
1n0r_A	126	4ANK, 4 ankyrin repeats; structural protein; 1.50A	99.72
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.72
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.72
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.72
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.71
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.71
3ui2_A	244	Signal recognition particle 43 kDa protein, chlor;	99.71
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.71
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.71
1bi7_B	156	P16INK4A, MTS1, multiple tumor suppressor; cyclin	99.71
4b93_B	269	Ankyrin repeat domain-containing protein 27; endoc	99.71
4hbd_A	276	KN motif and ankyrin repeat domain-containing Pro;	99.71
3v31_A	167	Ankyrin repeat family A protein 2; structural geno	99.71
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.71
2f8y_A	223	Notch homolog 1, translocation-associated (drosoph	99.7
2b0o_E	301	UPLC1; arfgap, structural genomics, structural gen	99.7
1yyh_A	253	HN1;, notch 1, ankyrin domain; ankyrin repeats, ce	99.7
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.7
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.7
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.7
2dzn_A	228	Probable 26S proteasome regulatory subunit P28; an	99.7
2vge_A	229	RELA-associated inhibitor; iaspp, nucleus, apoptos	99.7
3f6q_A	179	Integrin-linked protein kinase; ILK, integrin-link	99.7
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.7
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.69
1ikn_D	236	Protein (I-kappa-B-alpha), protein (NF-kappa-B P50	99.69
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.69
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.69
3aji_A	231	26S proteasome non-ATPase regulatory subunit 10; g	99.69
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.69
3hra_A	201	Ankyrin repeat family protein; structural protein;	99.69
2f8y_A	223	Notch homolog 1, translocation-associated (drosoph	99.69
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.69
3utm_A	351	Tankyrase-1; tankyrase, TNKS, ankryin repeat clust	99.69
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.69
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.69
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.69
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.69
1oy3_D	282	Transcription factor inhibitor I-kappa-B-beta; pro	99.69
3ehr_A	222	Osteoclast-stimulating factor 1; beta barrel, heli	99.69
2rfa_A	232	Transient receptor potential cation channel subfa	99.69
1ikn_D	236	Protein (I-kappa-B-alpha), protein (NF-kappa-B P50	99.69
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.69
3ljn_A	364	Hypothetical protein; ankyrin, structural genomics	99.69
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.68
1ycs_B	239	53BP2, P53BP2; ankyrin repeats, SH3, tumor suppres	99.68
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.68
3t8k_A	186	Uncharacterized protein; structural genomics, PSI-	99.68
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.68
1k1a_A	241	B-cell lymphoma 3-encoded protein; BCL-3, NF-kappa	99.68
4g8k_A	337	2-5A-dependent ribonuclease; ankyrin-repeat domain	99.68
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.68
3kea_A	285	K1L; tropism, ANK repeat, viral protein; 2.30A {Va	99.68
3jxi_A	260	Vanilloid receptor-related osmotically activated p	99.68
2etb_A	256	Transient receptor potential cation channel subfam	99.68
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.68
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.68
2etb_A	256	Transient receptor potential cation channel subfam	99.68
2xai_A	261	ASB-9, ankyrin repeat and SOCS box protein 9; tran	99.68
3jue_A	368	Arfgap with coiled-coil, ANK repeat and PH domain	99.68
2rfa_A	232	Transient receptor potential cation channel subfa	99.68
3d9h_A	285	CDNA FLJ77766, highly similar to HOMO sapiens anky	99.68
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.68
3b7b_A	237	Euchromatic histone-lysine N-methyltransferase 1;	99.67
2pnn_A	273	Transient receptor potential cation channel subfa	99.67
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.67
1wdy_A	285	2-5A-dependent ribonuclease; hydrolase, RNA-bindin	99.67
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.67
3jxi_A	260	Vanilloid receptor-related osmotically activated p	99.67
3c5r_A	137	BARD-1, BRCA1-associated ring domain protein 1; an	99.67
3hra_A	201	Ankyrin repeat family protein; structural protein;	99.67
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.67
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.67
2fo1_E	373	LIN-12 protein; beta-barrel, protein-DNA complex,	99.67
3aaa_C	123	Myotrophin, protein V-1; actin capping protein, ba	99.67
2pnn_A	273	Transient receptor potential cation channel subfa	99.66
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.66
3deo_A	183	Signal recognition particle 43 kDa protein; chloro	99.66
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.66
3ui2_A	244	Signal recognition particle 43 kDa protein, chlor;	99.66
1s70_B	299	130 kDa myosin-binding subunit of smooth muscle my	99.66
4g8k_A	337	2-5A-dependent ribonuclease; ankyrin-repeat domain	99.66
1yyh_A	253	HN1;, notch 1, ankyrin domain; ankyrin repeats, ce	99.66
3aji_A	231	26S proteasome non-ATPase regulatory subunit 10; g	99.65
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.65
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.65
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.65
1n11_A	437	Ankyrin; clathrin, BAND 3, anion exchanger, struct	99.65
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.46
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.65
3utm_A	351	Tankyrase-1; tankyrase, TNKS, ankryin repeat clust	99.65
1s70_B	299	130 kDa myosin-binding subunit of smooth muscle my	99.65
3ljn_A	364	Hypothetical protein; ankyrin, structural genomics	99.65
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.65
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.65
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.64
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.64
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.64
4hbd_A	276	KN motif and ankyrin repeat domain-containing Pro;	99.64
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.64
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.64
2dzn_A	228	Probable 26S proteasome regulatory subunit P28; an	99.64
3t8k_A	186	Uncharacterized protein; structural genomics, PSI-	99.64
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.64
3kea_A	285	K1L; tropism, ANK repeat, viral protein; 2.30A {Va	99.64
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.63
1n11_A	437	Ankyrin; clathrin, BAND 3, anion exchanger, struct	99.63
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.63
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.63
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.63
2xai_A	261	ASB-9, ankyrin repeat and SOCS box protein 9; tran	99.63
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.63
1wdy_A	285	2-5A-dependent ribonuclease; hydrolase, RNA-bindin	99.63
3b7b_A	237	Euchromatic histone-lysine N-methyltransferase 1;	99.63
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.62
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.62
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.62
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.62
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.62
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.62
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.62
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.62
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.61
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.61
1k1a_A	241	B-cell lymphoma 3-encoded protein; BCL-3, NF-kappa	99.61
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.61
3d9h_A	285	CDNA FLJ77766, highly similar to HOMO sapiens anky	99.61
2fo1_E	373	LIN-12 protein; beta-barrel, protein-DNA complex,	99.61
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.6
3jue_A	368	Arfgap with coiled-coil, ANK repeat and PH domain	99.6
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.6
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.6
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.6
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.6
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.59
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.59
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.59
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.59
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.59
3eu9_A	240	Huntingtin-interacting protein 14; epigenetics, an	99.59
1sw6_A	327	Regulatory protein SWI6; transcription regulation,	99.59
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.58
1sw6_A	327	Regulatory protein SWI6; transcription regulation,	99.58
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.58
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.58
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.58
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.57
1dcq_A	278	PYK2-associated protein beta; zinc-binding module,	99.56
3eu9_A	240	Huntingtin-interacting protein 14; epigenetics, an	99.56
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.56
3lvq_E	497	ARF-GAP with SH3 domain, ANK repeat and PH domain	99.56
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.56
2b0o_E	301	UPLC1; arfgap, structural genomics, structural gen	99.55
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.55
1x5p_A	97	Negative elongation factor E; structure genomics,	99.55
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.55
1n0q_A	93	3ANK, 3 ankyrin repeats; structural protein; 1.26A	99.54
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.54
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.54
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.53
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.53
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.51
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.51
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.51
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.49
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.45
2aja_A	376	Ankyrin repeat family protein; NESG, Q5ZSV0, struc	99.45
2zgd_A	110	3 repeat synthetic ankyrin; ankyrin repeat, hydrox	99.45
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.44
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.37
2aja_A	376	Ankyrin repeat family protein; NESG, Q5ZSV0, struc	99.36
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.35
2l6b_A	115	NR1C; ankyrin, consensus, repeat protein, ising mo	99.35
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.34
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.33
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.3
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.3
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.29
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.29
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.27
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.17
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.97
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.97
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	98.92
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.88
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.8
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	98.59
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.58
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.3
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	98.08
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.91
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	97.86
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	97.86
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	97.68
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	97.55
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	97.41
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	97.41
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.37
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	97.37
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	97.3
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	97.29
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.28
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	97.28
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	97.28
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	97.24
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	97.24
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	97.21
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	97.2
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	97.2
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	97.19
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	97.19
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	97.18
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	97.17
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	97.16
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	97.16
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	97.14
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	97.12
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	97.11
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	97.11
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	97.09
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	97.09
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	97.08
1x4e_A	85	RNA binding motif, single-stranded interacting pro	97.07
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	97.07
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.07
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	97.06
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	97.05
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	97.04
2div_A	99	TRNA selenocysteine associated protein; structural	97.03
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	96.09
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	97.01
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	97.01
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	97.01
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	97.0
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	97.0
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	96.98
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	96.97
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	96.97
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	96.96
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	96.95
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	96.95
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	96.95
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	96.94
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	96.94
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	96.93
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	96.93
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	96.92
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	96.92
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	96.92
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	96.92
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	96.9
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	96.89
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	96.88
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	96.88
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	96.87
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	96.86
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	96.86
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	96.85
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	96.84
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	96.81
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	96.81
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	96.81
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	96.81
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	96.8
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	96.8
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	96.79
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	96.79
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	96.79
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	96.78
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	96.78
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	96.77
2dis_A	109	Unnamed protein product; structural genomics, RRM	96.76
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.75
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	96.75
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	96.75
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	96.74
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	96.72
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	96.72
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	96.72
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	96.71
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	96.71
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	96.7
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	96.7
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	96.7
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	96.69
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	96.68
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	96.67
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	96.67
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	96.66
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	96.65
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	96.65
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	96.64
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	96.63
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	96.63
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	96.62
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	96.61
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	96.6
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	96.59
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	96.58
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	96.57
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	96.56
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	96.55
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	96.54
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	96.53
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	96.51
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	96.51
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	96.5
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	96.5
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	96.48
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	96.47
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	96.47
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.46
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	96.44
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	96.35
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	96.35
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	96.32
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	96.3
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	96.29
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	96.29
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	96.29
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	96.27
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	96.26
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	96.26
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.25
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.16
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	96.16
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	96.14
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	96.14
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	96.13
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	96.12
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	96.09
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	96.07
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	96.07
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	96.06
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	96.05
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	96.05
1x5o_A	114	RNA binding motif, single-stranded interacting pro	96.05
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.02
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	96.02
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	95.99
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	95.97
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	95.95
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	95.95
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	95.81
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	95.79
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	95.74
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	95.63
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	95.51
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	95.34
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	94.89
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	94.87
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	94.42
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	93.72
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	93.18

>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=2.2e-24  Score=181.52  Aligned_cols=155  Identities=21%  Similarity=0.359  Sum_probs=122.9

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccC
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP   83 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~   83 (347)
                      ++.+.++|||+|||+++|+++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|.+|+..++..+.|+.|.|.+
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~   88 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKR   88 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeec
Confidence            45677899999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCcccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHH
Q psy630           84 SDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAM  163 (347)
Q Consensus        84 ~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~  163 (347)
                      +.+...... ........++||+|||..+++++|+++|+.||.|....+..++.     .|+.|+.|+..  ..+.++|.
T Consensus        89 ~~~~~~~~~-~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~g~~~g~afV~--F~~~~~A~  160 (196)
T 1l3k_A           89 AVSREDSQR-PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRG-----SGKKRGFAFVT--FDDHDSVD  160 (196)
T ss_dssp             CCC------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTT-----TCCEEEEEEEE--ESSHHHHH
T ss_pred             ccCcccccc-cccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCC-----CCCccceEEEE--ECCHHHHH
Confidence            876543221 12223457899999999999999999999999998777765532     22333334443  34577777


Q ss_pred             HHH
Q psy630          164 SKY  166 (347)
Q Consensus       164 ~~y  166 (347)
                      ++.
T Consensus       161 ~A~  163 (196)
T 1l3k_A          161 KIV  163 (196)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            664

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.90  E-value=2.7e-24  Score=183.54  Aligned_cols=146  Identities=21%  Similarity=0.281  Sum_probs=120.1

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ...++|||+|||+++|+++|+++|++||.|.+|+|++++.+++++|||||+|.+.++|.+|+.. ++..+.|+.+++.++
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~   92 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWS   92 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCcccccccc
Confidence            4568999999999999999999999999999999999999999999999999999999999986 999999999999887


Q ss_pred             CcccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHH
Q psy630           85 DSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMS  164 (347)
Q Consensus        85 ~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~  164 (347)
                      ......     ..-...++||+|||..+++++|+++|+.||.|....+..++.       ..|+.|+..  ..+.++|.+
T Consensus        93 ~~~~~~-----~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~-------~~~g~~fV~--f~~~~~a~~  158 (213)
T 4f02_A           93 QRDPSL-----RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-------GSKGYGFVH--FETQEAAER  158 (213)
T ss_dssp             CCCTHH-----HHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT-------EEEEEEEEE--ESSHHHHHH
T ss_pred             cccccc-----cccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCC-------CCceEEEEE--eCCHHHHHH
Confidence            654432     122346799999999999999999999999998777655432       123333333  446777776


Q ss_pred             H
Q psy630          165 K  165 (347)
Q Consensus       165 ~  165 (347)
                      +
T Consensus       159 A  159 (213)
T 4f02_A          159 A  159 (213)
T ss_dssp             H
T ss_pred             H
Confidence            6

>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=99.89  E-value=1.5e-23  Score=171.56  Aligned_cols=144  Identities=20%  Similarity=0.348  Sum_probs=119.8

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCc
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~   86 (347)
                      .++|||+|||+++++++|+++|++||.|..+++++++.+|.++|||||+|.+.++|.+|+.. ++..+.|++|.|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            57999999999999999999999999999999999998999999999999999999999984 99999999999998876


Q ss_pred             ccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           87 HNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        87 ~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ....       ....++||+|||..+++++|+++|+.||.+....+..++.     .|+.++.|+..  ..+.++|.++
T Consensus        82 ~~~~-------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~-----~g~~~g~afV~--f~~~~~A~~A  146 (167)
T 1fxl_A           82 SSAS-------IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQV-----TGVSRGVGFIR--FDKRIEAEEA  146 (167)
T ss_dssp             CCGG-------GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----TCCEEEEEEEE--ESSHHHHHHH
T ss_pred             Cccc-------CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCC-----CCCccceEEEE--eCCHHHHHHH
Confidence            5431       2456799999999999999999999999998777655432     12223333333  3456666666

>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=99.88  E-value=2.1e-23  Score=171.03  Aligned_cols=145  Identities=19%  Similarity=0.304  Sum_probs=120.4

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~~~   85 (347)
                      ..++|||+|||+++++++|+++|++||.|..+++++++.+|.++|||||+|.+.++|.+|+. +++..+.|++|.|.++.
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            45899999999999999999999999999999999999899999999999999999999998 59999999999999887


Q ss_pred             cccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           86 SHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        86 ~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      +....       ....++||+|||..+++++|+++|+.||.+....+..++.     .|+.++.|+..  ..+.++|.++
T Consensus        82 ~~~~~-------~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~-----~~~~~g~afV~--f~~~~~A~~A  147 (168)
T 1b7f_A           82 PGGES-------IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKL-----TGRPRGVAFVR--YNKREEAQEA  147 (168)
T ss_dssp             CCSST-------TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTT-----TCCEEEEEEEE--ESSHHHHHHH
T ss_pred             CCccc-------CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCC-----CCCcceEEEEE--ECCHHHHHHH
Confidence            65432       2446899999999999999999999999998776655442     12222333333  3456676666

>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=99.88  E-value=1.1e-23  Score=172.52  Aligned_cols=144  Identities=22%  Similarity=0.452  Sum_probs=119.7

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCCc
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~~   86 (347)
                      +.++|||+|||+++|+++|+++|++||.|.++++++++.+|.++|||||+|.+.++|.+|+.. +..+.|+.+.|.++.+
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~g~~i~v~~~~~   80 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT-QHILDGKVIDPKRAIP   80 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS-CCEETTEECCCEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc-ccccCCeEcccccccc
Confidence            568999999999999999999999999999999999999999999999999999999999985 6789999999988766


Q ss_pred             ccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           87 HNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        87 ~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...       .-...++||+|||..+++++|+++|+.||.+....+..++.     .|+.|+.|+..  ..+.++|.++
T Consensus        81 ~~~-------~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~-----~g~~~g~afV~--f~~~~~a~~A  145 (167)
T 2cjk_A           81 RDE-------QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKD-----TGQSRGFGFVT--YDSADAVDRV  145 (167)
T ss_dssp             HHH-------HHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSS-----SSTTSEEEEEE--ESSHHHHHHH
T ss_pred             hhh-------ccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCC-----CCccceEEEEE--ECCHHHHHHH
Confidence            432       12346899999999999999999999999998777765532     23344445444  3456666665

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.87  E-value=5.7e-23  Score=167.98  Aligned_cols=144  Identities=19%  Similarity=0.290  Sum_probs=117.2

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccCCCcc
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQPSDSH   87 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~~~~~   87 (347)
                      |+|||+|||+++|+++|+++|++||.|.++++++++. ++++|||||+|.+.++|.+|+. +++..+.|+.+.|.++.+.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKN-NKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC--CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCC-CCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            6899999999999999999999999999999999974 8899999999999999999996 5999999999999988665


Q ss_pred             cccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           88 NRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        88 ~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...     ..-...++||+|||..+++++|+++|+.||.+....+..++.     .|+.|+.||..  ..+.++|..+
T Consensus        80 ~~~-----~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~-----~~~~~g~afV~--f~~~~~A~~A  145 (166)
T 3md3_A           80 QQS-----SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQ-----TGSSRGYGFVS--FTSQDDAQNA  145 (166)
T ss_dssp             CCC-----CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTT-----TCCEEEEEEEE--ESCHHHHHHH
T ss_pred             CCC-----CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCC-----CCCcceEEEEE--eCCHHHHHHH
Confidence            432     122456899999999999999999999999998777765432     12223334433  3456777666

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.87  E-value=1.7e-22  Score=172.62  Aligned_cols=153  Identities=16%  Similarity=0.295  Sum_probs=120.6

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~~   84 (347)
                      ...++|||+|||+++|+++|+++|++||.|..|++++++.+|.++|||||+|.+.++|.+|+. +++..+.|+.|.|.++
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            456899999999999999999999999999999999999899999999999999999999999 5999999999999887


Q ss_pred             Ccccccchh----hhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHH
Q psy630           85 DSHNRMAEN----MEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKS  160 (347)
Q Consensus        85 ~~~~~~~~~----~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~  160 (347)
                      .........    ....-...++||+|||..+++++|+++|+.||.|....+..++.     .|+.|+.||..  ..+.+
T Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~-----~g~~~g~afV~--F~~~~  178 (216)
T 2qfj_A          106 SNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPT-----TGKHKGYGFIE--YEKAQ  178 (216)
T ss_dssp             SCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTT-----TCCEEEEEEEE--ESSHH
T ss_pred             CCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCC-----CCCcCceEEEE--ecCHH
Confidence            765432211    11223447899999999999999999999999998777765532     22333334443  34577


Q ss_pred             HHHHH
Q psy630          161 EAMSK  165 (347)
Q Consensus       161 eA~~~  165 (347)
                      +|.++
T Consensus       179 ~A~~A  183 (216)
T 2qfj_A          179 SSQDA  183 (216)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            77666

>4gpm_A Engineered protein OR264; de novo protein, structural genomics, PSI-biology, northeast structural genomics consortium, NESG; 2.00A {Synthetic construct} PDB: 4gmr_A

Probab=99.87  E-value=1.1e-21  Score=161.22  Aligned_cols=100  Identities=34%  Similarity=0.476  Sum_probs=93.8

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      .+++..+..|.||||+|+..+..+++++|++ .|+++|.+|..|+||||+||..|+.+++++|++ .|++++.+|..|+|
T Consensus        61 ad~~~~d~~g~TpLh~A~~~g~~~~v~~Ll~-~gadvn~~d~~G~TpLh~A~~~g~~~~v~~Ll~-~gad~~~~d~~G~T  138 (169)
T 4gpm_A           61 ADVNAKDSDGRTPLHHAAENGHKEVVKLLIS-KGADVNAKDSDGRTPLHHAAENGHKEVVKLLIS-KGADVNTSDSDGRT  138 (169)
T ss_dssp             CCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCC
T ss_pred             cchhhhccCCCCHHHHHHHcCCHHHHHHHHH-CcCCCCCCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCccccCCCCCC
Confidence            4567788899999999999999999999999 899999999999999999999999999999999 79999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|+..|+.+++++|+++||
T Consensus       139 pL~~A~~~g~~~iv~~Ll~~GA  160 (169)
T 4gpm_A          139 PLDLAREHGNEEVVKLLEKQGG  160 (169)
T ss_dssp             HHHHHHHTTCHHHHHHHHTC--
T ss_pred             HHHHHHHcCCHHHHHHHHHCCC
Confidence            9999999999999999999997

>1n0q_A 3ANK, 3 ankyrin repeats; structural protein; 1.26A {} SCOP: k.37.1.1

Probab=99.86  E-value=1.2e-21  Score=144.20  Aligned_cols=92  Identities=34%  Similarity=0.482  Sum_probs=86.5

Q ss_pred             CCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHc
Q psy630          254 NEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAI  333 (347)
Q Consensus       254 ~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~  333 (347)
                      .|.|+||+|+..+..+++++|++ .+++++.+|..|+||||+|+..|+.+++++|++ .|++++.+|..|+||||+|+..
T Consensus         1 ~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~n~~d~~g~t~L~~A~~~~~~~~v~~Ll~-~ga~~~~~d~~g~t~l~~A~~~   78 (93)
T 1n0q_A            1 NGRTPLHLAARNGHLEVVKLLLE-AGADVNAKDKNGRTPLHLAARNGHLEVVKLLLE-AGADVNAKDKNGRTPLHLAARN   78 (93)
T ss_dssp             --CCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHT
T ss_pred             CCCcHHHHHHHcCCHHHHHHHHH-cCCCCcccCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCccCCCCCCHHHHHHHc
Confidence            36899999998888889999988 799999999999999999999999999999999 7999999999999999999999


Q ss_pred             CCHHHHHHHHhCCC
Q psy630          334 EHTDLIEYLVNSGS  347 (347)
Q Consensus       334 ~~~~~v~~Ll~~GA  347 (347)
                      |+.+++++|+++||
T Consensus        79 ~~~~~~~~Ll~~ga   92 (93)
T 1n0q_A           79 GHLEVVKLLLEAGA   92 (93)
T ss_dssp             TCHHHHHHHHHTTC
T ss_pred             CCHHHHHHHHHcCC
Confidence            99999999999997

>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=99.86  E-value=7.9e-22  Score=151.27  Aligned_cols=109  Identities=21%  Similarity=0.381  Sum_probs=74.3

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ...++|||+|||+++++++|+++|++||.|.+|+|++++  +.++|||||+|.+.++|++|+.. ++..+.|+.|.|.++
T Consensus         3 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a   80 (115)
T 4f25_A            3 LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRF   80 (115)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            456789999999999999999999999999999999986  55899999999999999999975 999999999999988


Q ss_pred             Ccccccchhhh-hhcccccccccCCcccccchh
Q psy630           85 DSHNRMAENME-DRFNQACDYLPSLVKKLDSST  116 (347)
Q Consensus        85 ~~~~~~~~~~~-~~f~~~~~~v~~l~~~~~~e~  116 (347)
                      .++..+..... ..-...++||+|||+.+|++.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           81 KSRKEREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             SCCCC----------------------------
T ss_pred             CCccccccccccccCCCCceEeCCCCCCccccc
Confidence            77654333222 122335789999999988763

>1hbk_A ACBP, acyl-COA binding protein; fatty acid metabolism; HET: COA MYR; 2.0A {Plasmodium falciparum} SCOP: a.11.1.1

Probab=99.86  E-value=1.4e-22  Score=145.42  Aligned_cols=85  Identities=29%  Similarity=0.650  Sum_probs=81.1

Q ss_pred             hhhcccccccccCCc--ccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHH
Q psy630           95 EDRFNQACDYLPSLV--KKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKE  172 (347)
Q Consensus        95 ~~~f~~~~~~v~~l~--~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~  172 (347)
                      +..|..+..+|++++  ..++.+++++||++|+|+++|+|+.++||+++++|++||+||+++++||++|||++||+++++
T Consensus         3 ~~~F~~A~~~v~~l~~~~~~~~~~~L~LYalyKQAt~Gd~~~~~Pg~~d~~~~aKw~AW~~l~gms~eeA~~~YI~~v~~   82 (89)
T 1hbk_A            3 AQVFEECVSFINGLPRTINLPNELKLDLYKYYKQSTIGNCNIKEPSAHKYIDRKKYEAWKSVENLNREDAQKRYVDIVSE   82 (89)
T ss_dssp             HHHHHHHHHHHHHSCTTCCCCHHHHHHHHHHHHHHHTCSCCSCCCCTTSHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCcCCCCHHHHHHHHHHHHHhhcCCCCCCCCCccCHHhHHHHHHHHHhcCCCHHHHHHHHHHHHHH
Confidence            457888999999999  889999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccCCh
Q psy630          173 VDAGWED  179 (347)
Q Consensus       173 l~~~~~~  179 (347)
                      +.+.|.+
T Consensus        83 l~~~~~~   89 (89)
T 1hbk_A           83 IFPYWQD   89 (89)
T ss_dssp             HCTTTTC
T ss_pred             HcccccC
Confidence            9999963

>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=99.86  E-value=1.6e-21  Score=160.80  Aligned_cols=145  Identities=21%  Similarity=0.322  Sum_probs=115.6

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCC--CceeEEEEEEcCHHHHHHHHhc-CCCccC---Ccccc
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTG--LSKGFGFVTFQNKEAVDKVFST-DSHVLE---GSRLS   80 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~--~~~g~afV~f~~~~~a~~a~~~-~~~~~~---g~~l~   80 (347)
                      +.++|||+|||+++|+++|+++|++||.|.++++++++.++  +++|||||+|.+.++|.+|+.. ++..+.   ++.+.
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            56799999999999999999999999999999999999877  8999999999999999999985 777665   46666


Q ss_pred             ccCCCcccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHH
Q psy630           81 IQPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKS  160 (347)
Q Consensus        81 v~~~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~  160 (347)
                      +.++.+....      .....++||+|||..+++++|+++|+.||.|....+..++.|      +.|+.|+..  ..+.+
T Consensus        82 ~~~~~~~~~~------~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g------~~~g~afV~--f~~~~  147 (175)
T 3nmr_A           82 MKPADSEKNN------AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDG------LSRGCAFVT--FTTRA  147 (175)
T ss_dssp             EEECGGGCCS------CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTS------CEEEEEEEE--ESSHH
T ss_pred             Eccccccccc------cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCC------CEEEEEEEE--ECCHH
Confidence            6665543321      234578999999999999999999999999987776655432      233334433  44567


Q ss_pred             HHHHH
Q psy630          161 EAMSK  165 (347)
Q Consensus       161 eA~~~  165 (347)
                      +|.++
T Consensus       148 ~A~~A  152 (175)
T 3nmr_A          148 MAQTA  152 (175)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            77766

>1st7_A ACBP, acyl-COA-binding protein; four helix bundle, transport protein; NMR {Saccharomyces cerevisiae}

Probab=99.86  E-value=1.2e-22  Score=144.91  Aligned_cols=84  Identities=35%  Similarity=0.611  Sum_probs=80.5

Q ss_pred             hhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhh
Q psy630           95 EDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVD  174 (347)
Q Consensus        95 ~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~l~  174 (347)
                      ...|..+..+|++++..++.+++++||++|+|+++|+|+.++||+++++|++||+||+++++||++|||++||++++++.
T Consensus         2 ~~~F~~A~~~v~~l~~~~~~~~~L~lYalyKQAt~Gd~~~~~Pg~~d~~~raKw~AW~~l~gms~eeA~~~YI~~v~~l~   81 (86)
T 1st7_A            2 SQLFEEKAKAVNELPTKPSTDELLELYALYKQATVGDNDKEKPGIFNMKDRYKWEAWENLKGKSQEDAEKEYIALVDQLI   81 (86)
T ss_dssp             HHHHHHHHHHHTSCSSCCCHHHHHHHHHHHHHHHHCSCCCCCCCSSCHHHHHHHHHHHTTTTTHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCCcCHHHHHHHHHHHHHHhhCCCCCCCCCccCHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Confidence            35688899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q psy630          175 AGWE  178 (347)
Q Consensus       175 ~~~~  178 (347)
                      +.|.
T Consensus        82 ~~~~   85 (86)
T 1st7_A           82 AKYS   85 (86)
T ss_dssp             HHHC
T ss_pred             hhhc
Confidence            9885

>2lbb_A Acyl COA binding protein; protein binding, structural genomi seattle structural genomics center for infectious disease,; NMR {Babesia bovis}

Probab=99.85  E-value=2.6e-22  Score=144.50  Aligned_cols=84  Identities=36%  Similarity=0.684  Sum_probs=80.6

Q ss_pred             hhcccccccccCCc-ccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhh
Q psy630           96 DRFNQACDYLPSLV-KKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVD  174 (347)
Q Consensus        96 ~~f~~~~~~v~~l~-~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~l~  174 (347)
                      ..|..+..+|++++ ..++.+++++||++|+|+++|+|+.++||+++++|++||+||+++++||++|||++||++++++.
T Consensus        12 ~~F~~A~~~vk~l~~~~ps~~~~L~LYaLyKQAt~Gd~~~~~Pg~~d~~graKw~AW~~l~gmS~eeAm~~YI~lv~~l~   91 (96)
T 2lbb_A           12 DDFDAAVKYVSNTTTMMASNDDKLCFYKYYKQATVGDCNKPKPGMLQLQEKYKWEAWNALRGMSTESAKEAYVKLLDTLA   91 (96)
T ss_dssp             STHHHHHHHHHHCCCSCCCTTTTTHHHHHHHHTTTSSCCCCCCCSSCSHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCcccHHhHHHHHHHHHhcCCCHHHHHHHHHHHHHHHh
Confidence            46888999999999 99999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCh
Q psy630          175 AGWED  179 (347)
Q Consensus       175 ~~~~~  179 (347)
                      +.|.+
T Consensus        92 ~~~~~   96 (96)
T 2lbb_A           92 PSWRN   96 (96)
T ss_dssp             GGGTC
T ss_pred             chhcC
Confidence            99963

>2cop_A Acyl-coenzyme A binding domain containing 6; acyl COA binding protein, COA binding protein, lipid binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.85  E-value=4.7e-22  Score=147.46  Aligned_cols=88  Identities=40%  Similarity=0.804  Sum_probs=84.7

Q ss_pred             hhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHH
Q psy630           93 NMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKE  172 (347)
Q Consensus        93 ~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~  172 (347)
                      .+...|..|..+|++++..++.+++++||++|+|+++|+|+.++||+++++|++||+||+++++|+++|||++||++|++
T Consensus         7 ~l~~~F~~A~~~vk~l~~~p~~~~~L~LYaLyKQAt~Gd~~~~~Pg~~d~~~raKw~AW~~l~gms~eeAm~~YI~lv~~   86 (109)
T 2cop_A            7 GLAELFEKAAAHLQGLIQVASREQLLYLYARYKQVKVGNCNTPKPSFFDFEGKQKWEAWKALGDSSPSQAMQEYIAVVKK   86 (109)
T ss_dssp             CSHHHHHHHHHHHTTSTTTSCHHHHHHHHHHHHHHHTCSCCSCCCCSSCHHHHHHHHHHHSCTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcccCCCHHHHHHHHHHHHHhhcCCCCCCCCCccCHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHH
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccCChh
Q psy630          173 VDAGWEDK  180 (347)
Q Consensus       173 l~~~~~~~  180 (347)
                      |.+.|...
T Consensus        87 l~~~~~~~   94 (109)
T 2cop_A           87 LDPGWNPQ   94 (109)
T ss_dssp             HCTTCCCC
T ss_pred             Hhhhhccc
Confidence            99999987

>3epy_A Acyl-COA-binding domain-containing protein 7; acyl-COA binding protein, fatty acid, lipid metabolism, structural genomics; HET: COA PLM; 2.00A {Homo sapiens} SCOP: a.11.1.1

Probab=99.85  E-value=4.1e-22  Score=142.35  Aligned_cols=84  Identities=32%  Similarity=0.563  Sum_probs=80.7

Q ss_pred             hhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHh
Q psy630           94 MEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEV  173 (347)
Q Consensus        94 ~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~l  173 (347)
                      ++..|..+..+|++++..++.+++++||++|+|+++|+|+.++||+++++|++||+||+++++||++|||++||+++++|
T Consensus         4 L~~~F~~A~~~vk~l~~~p~~~~~L~lYalyKQAt~Gd~~~~~Pg~~d~~~~aKw~AW~~l~g~s~eeA~~~Yi~~v~~l   83 (89)
T 3epy_A            4 LQADFDRAAEDVRKLKARPDDGELKELYGLYKQAIVGDINIACPGMLDLKGKAKWEAWNLKKGLSTEDATSAYISKAKEL   83 (89)
T ss_dssp             HHHHHHHHHHHGGGCSSCCCHHHHHHHHHHHHHHHTCSCCSCCTTTTCHHHHHHHHHHHTTTTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHHHHhhCCCCCCCCcccchHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHH
Confidence            56779999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccC
Q psy630          174 DAGW  177 (347)
Q Consensus       174 ~~~~  177 (347)
                      .+.|
T Consensus        84 ~~ky   87 (89)
T 3epy_A           84 IEKY   87 (89)
T ss_dssp             HHHH
T ss_pred             hhhh
Confidence            8875

>2cb8_A Acyl-COA-binding protein; acyl-coenzyme A binding protein, fatty acid, acetylation, alternative splicing, lipid-binding, transport; HET: MYA; 1.4A {Homo sapiens} PDB: 2fj9_A 1aca_A* 1hb6_A 1hb8_A 1nti_A 1nvl_A* 2abd_A 2fdq_A

Probab=99.84  E-value=7.5e-22  Score=140.72  Aligned_cols=84  Identities=32%  Similarity=0.587  Sum_probs=79.9

Q ss_pred             hhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhh
Q psy630           95 EDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVD  174 (347)
Q Consensus        95 ~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~l~  174 (347)
                      ...|..+..+|++++..++.+++++||++|+|+++|+|+.++||+++++|++||+||+++++||++|||++||++++++.
T Consensus         3 ~~~F~~A~~~vk~l~~~~~~~~~L~lYalyKQAt~Gd~~~~~Pg~~d~~~~aKw~AW~~l~gms~eeA~~~Yi~~v~~l~   82 (87)
T 2cb8_A            3 QAEFEKAAEEVRHLKTKPSDEEMLFIYGHYKQATVGDINTERPGMLDFTGKAKWDAWNELKGTSKEDAMKAYINKVEELK   82 (87)
T ss_dssp             HHHHHHHHHHGGGCSSCCCHHHHHHHHHHHHHHHTCSCCSCCCCTTCHHHHHHHHHHHTTTTCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHccCCcCHHHHHHHHHHHHhhhhCCCCCCCCCcccHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHH
Confidence            35688899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCC
Q psy630          175 AGWE  178 (347)
Q Consensus       175 ~~~~  178 (347)
                      +.|.
T Consensus        83 ~~~~   86 (87)
T 2cb8_A           83 KKYG   86 (87)
T ss_dssp             HHHC
T ss_pred             HHhC
Confidence            8763

>4gpm_A Engineered protein OR264; de novo protein, structural genomics, PSI-biology, northeast structural genomics consortium, NESG; 2.00A {Synthetic construct} PDB: 4gmr_A

Probab=99.84  E-value=1.2e-20  Score=154.83  Aligned_cols=100  Identities=34%  Similarity=0.474  Sum_probs=95.5

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      .+++..+..|.|++|+|+..+...++++|+. .+++++.+|..|+||||+||..|+.+++++||+ .|+++|.+|..|+|
T Consensus        28 advn~~d~~g~t~l~~a~~~~~~~~~~~ll~-~gad~~~~d~~g~TpLh~A~~~g~~~~v~~Ll~-~gadvn~~d~~G~T  105 (169)
T 4gpm_A           28 ADVNASDSDGRTPLHHAAENGHKEVVKLLIS-KGADVNAKDSDGRTPLHHAAENGHKEVVKLLIS-KGADVNAKDSDGRT  105 (169)
T ss_dssp             CCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCC
T ss_pred             CCCCCcCCCCCCHHHHHHHcCCHHHHHHHHh-cccchhhhccCCCCHHHHHHHcCCHHHHHHHHH-CcCCCCCCCCCCCC
Confidence            4677888999999999999999999999998 899999999999999999999999999999999 79999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|+..|+.++|++|+++||
T Consensus       106 pLh~A~~~g~~~~v~~Ll~~ga  127 (169)
T 4gpm_A          106 PLHHAAENGHKEVVKLLISKGA  127 (169)
T ss_dssp             HHHHHHHTTCHHHHHHHHHTTC
T ss_pred             HHHHHHHcCCHHHHHHHHHcCC
Confidence            9999999999999999999986

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}

Probab=99.84  E-value=7.8e-21  Score=141.44  Aligned_cols=80  Identities=25%  Similarity=0.503  Sum_probs=76.3

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      +.++|||+|||+++|+++|+++|++||.|.++++++++.+|.++|||||+|.+.++|.+|++. |+..+.|++|+|.++.
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            467999999999999999999999999999999999999999999999999999999999985 9999999999999886


Q ss_pred             c
Q psy630           86 S   86 (347)
Q Consensus        86 ~   86 (347)
                      |
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            5

>2cqu_A Peroxisomal D3,D2-enoyl-COA isomerase; acyl-COA binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=1.8e-21  Score=145.23  Aligned_cols=88  Identities=34%  Similarity=0.639  Sum_probs=84.3

Q ss_pred             hhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHh
Q psy630           94 MEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEV  173 (347)
Q Consensus        94 ~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~l  173 (347)
                      +...|..+..+|++++..++.+++++||++|+|+++|+|+.++||++++++++||+||+++++|+++|||++||++|++|
T Consensus        16 ~~~~F~~A~~~vk~l~~~p~~~~~L~LYaLyKQAt~Gd~~~~~Pg~~d~~graKw~AW~~l~gms~eeAm~~YI~lv~~l   95 (116)
T 2cqu_A           16 SQKDFENSMNQVKLLKKDPGNEVKLKLYALYKQATEGPCNMPKPGVFDLINKAKWDAWNALGSLPKEAARQNYVDLVSSL   95 (116)
T ss_dssp             CHHHHHHHHHHHHHCCSCCCHHHHHHHHHHHTTTTTCSCCSCCCCTTCHHHHHHHHHHHHHCSCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHhcCCCCCCCCCcccHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHH
Confidence            35779999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccCChhh
Q psy630          174 DAGWEDKE  181 (347)
Q Consensus       174 ~~~~~~~~  181 (347)
                      .+.|....
T Consensus        96 ~~~~~~~~  103 (116)
T 2cqu_A           96 SPSLESSS  103 (116)
T ss_dssp             CSCCCCCC
T ss_pred             cccccccc
Confidence            99999873

>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=3.6e-21  Score=158.90  Aligned_cols=121  Identities=18%  Similarity=0.220  Sum_probs=104.8

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccC
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP   83 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~   83 (347)
                      ++...++|||+|||+++++++|+++|++||.+.. .++++..+|.++|||||+|.+.++|.+|+++++..+.|++|.|.+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~   87 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEK   87 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEec
Confidence            5677899999999999999999999999998766 344555678999999999999999999998899999999999999


Q ss_pred             CCcccccchhhhhhcccccccccCCcccccchhhHHHHhhcccccee
Q psy630           84 SDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVG  130 (347)
Q Consensus        84 ~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g  130 (347)
                      +.++....     .-...++||+|||..+++++|+++|+.||.|...
T Consensus        88 ~~~~~~~~-----~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~  129 (175)
T 1fje_B           88 PKGRDSKK-----VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV  129 (175)
T ss_dssp             CCCSSCST-----TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE
T ss_pred             CCCccccc-----cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe
Confidence            87754421     2245789999999999999999999999998754

>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=99.82  E-value=5.8e-21  Score=161.51  Aligned_cols=146  Identities=14%  Similarity=0.179  Sum_probs=109.8

Q ss_pred             CCCeEEEeCCC-CCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            7 QLNKIFVGNLP-WTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         7 ~~~~l~V~nLp-~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      +.++|||+||| +.+++++|+++|++||.|.+|+++++     ++|||||+|.+.++|++|++. |+..+.|++|.|.++
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            46799999999 79999999999999999999999865     369999999999999999984 999999999999977


Q ss_pred             Ccccccch-----------------hhhhhc-------------ccccccccCCcccccchhhHHHHhhcccc--ceecc
Q psy630           85 DSHNRMAE-----------------NMEDRF-------------NQACDYLPSLVKKLDSSTLLKFYALYKQA--TVGQC  132 (347)
Q Consensus        85 ~~~~~~~~-----------------~~~~~f-------------~~~~~~v~~l~~~~~~e~l~~~f~~fg~v--~~g~~  132 (347)
                      ........                 .....|             ...++||+|||..+++++|+++|+.||.+  ....+
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            53221000                 000001             13469999999999999999999999998  55554


Q ss_pred             cCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          133 NIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       133 ~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ..++.       +.++.|+.  ...+.++|.++.
T Consensus       158 ~~~~~-------~~~g~gfV--~f~~~~~A~~Ai  182 (205)
T 3tyt_A          158 FSGKS-------ERSSSGLL--EWDSKSDALETL  182 (205)
T ss_dssp             CSCCS-------SSSEEEEE--ECSSHHHHHHHH
T ss_pred             EcCCC-------CCceEEEE--EeCCHHHHHHHH
Confidence            44321       11222333  344677777763

>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=3.3e-20  Score=165.03  Aligned_cols=83  Identities=23%  Similarity=0.390  Sum_probs=74.6

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHH----HHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELK----KFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGS   77 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~----~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~   77 (347)
                      ++.+..++|||+|||+++++++|+    ++|++||.|..|++++   +|+++|||||+|.+.++|.+|+.. ++..+.|+
T Consensus         4 ~~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   80 (282)
T 3pgw_A            4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK   80 (282)
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCc
Confidence            456778999999999999999976    8999999999999875   688999999999999999999964 99999999


Q ss_pred             cccccCCCccc
Q psy630           78 RLSIQPSDSHN   88 (347)
Q Consensus        78 ~l~v~~~~~~~   88 (347)
                      .|.|.++....
T Consensus        81 ~l~v~~a~~~~   91 (282)
T 3pgw_A           81 PMRIQYAKTDS   91 (282)
T ss_pred             EEEEEEeccCc
Confidence            99998875543

>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=99.82  E-value=8.7e-20  Score=162.48  Aligned_cols=147  Identities=18%  Similarity=0.237  Sum_probs=122.6

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~~~   85 (347)
                      ..++|||+|||+++++++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|.+|+. +++..+.|+.|.|.++.
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~  173 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD  173 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            45789999999999999999999999999999999999999999999999999999999996 59999999999999987


Q ss_pred             cccccchhhhhhcccccccccCCcccc-cchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHH
Q psy630           86 SHNRMAENMEDRFNQACDYLPSLVKKL-DSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMS  164 (347)
Q Consensus        86 ~~~~~~~~~~~~f~~~~~~v~~l~~~~-~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~  164 (347)
                      +.....    ......++||+|||..+ ++++|+++|+.||.|....+..+..|      +.|+.||.  ...+.++|.+
T Consensus       174 ~~~~~~----~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g------~~~g~afV--~f~~~~~A~~  241 (284)
T 3smz_A          174 AGQLTP----ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDG------QLKGFAVL--EYETAEMAEE  241 (284)
T ss_dssp             GGGCCT----TTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSC------CEEEEEEE--ECSSHHHHHH
T ss_pred             CCCCCc----ccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCC------CcccEEEE--EeCCHHHHHH
Confidence            755422    22455789999999995 89999999999999987776665432      23333333  3556777777


Q ss_pred             H
Q psy630          165 K  165 (347)
Q Consensus       165 ~  165 (347)
                      +
T Consensus       242 A  242 (284)
T 3smz_A          242 A  242 (284)
T ss_dssp             H
T ss_pred             H
Confidence            6

>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=99.82  E-value=1e-20  Score=155.57  Aligned_cols=117  Identities=15%  Similarity=0.379  Sum_probs=100.9

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhcc----C-------CeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCcc
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEY----G-------QIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVL   74 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~----G-------~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~   74 (347)
                      ++.++|||+|||+++|+++|+++|++|    |       .|..+.+      +.++|||||+|.+.++|.+|+.+++..+
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~------~~~~g~afV~f~~~~~A~~A~~~~~~~~   75 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAMAFDGIIF   75 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEE------ETTTTEEEEEESSHHHHHHHGGGTTCEE
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEe------cCCCCEEEEEeCCHHHHHHHHHhCCcEe
Confidence            467899999999999999999999999    6       6666666      3457999999999999999996699999


Q ss_pred             CCccccccCCCcccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCC
Q psy630           75 EGSRLSIQPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus        75 ~g~~l~v~~~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                      .|++|.|.++.+....       -...++||+|||..+++++|+++|+.||.+....+..+
T Consensus        76 ~g~~i~v~~~~~~~~~-------~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~  129 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQPL-------PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKD  129 (172)
T ss_dssp             TTEECEEECCSSCCCC-------TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEEC
T ss_pred             cCceeeecCCcccCCC-------CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEec
Confidence            9999999987664432       12578999999999999999999999999987776554

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.81  E-value=1.3e-20  Score=138.15  Aligned_cols=82  Identities=23%  Similarity=0.434  Sum_probs=76.3

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccC-CeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc--CCCccCCccccccCC
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYG-QIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST--DSHVLEGSRLSIQPS   84 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G-~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~--~~~~~~g~~l~v~~~   84 (347)
                      +++|||+|||+++|+++|+++|++|| .|.+|+|++++.||.++|||||+|.+.++|.+|++.  ++..+.|++|.|.++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            36899999999999999999999999 899999999999999999999999999999999974  677899999999999


Q ss_pred             Ccccc
Q psy630           85 DSHNR   89 (347)
Q Consensus        85 ~~~~~   89 (347)
                      .++..
T Consensus        81 ~~~~~   85 (91)
T 2lxi_A           81 DPKPK   85 (91)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            88655

>2wh5_A Acyl-COA-binding domain-containing protein 4; alternative splicing, fatty acid metabolism, lipid transport, lipid binding protein; HET: STE ST9 COA; 2.60A {Homo sapiens}

Probab=99.80  E-value=9.3e-21  Score=139.41  Aligned_cols=87  Identities=37%  Similarity=0.684  Sum_probs=80.9

Q ss_pred             hhhhcccccccccCCcc----cccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHH
Q psy630           94 MEDRFNQACDYLPSLVK----KLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIAL  169 (347)
Q Consensus        94 ~~~~f~~~~~~v~~l~~----~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~  169 (347)
                      +...|..+..+|++++.    .++.+++++||++|+|+++|+|+.++||+++++|++||+||+++++|+++|||++||++
T Consensus         8 l~~~F~~A~~~vk~l~~~g~~~ps~e~~L~LYaLyKQAt~Gd~~~~~Pg~~d~~~~aKw~AW~~l~gms~eeA~~~YI~~   87 (106)
T 2wh5_A            8 CQKQFQAAVSVIQNLPKNGSYRPSYEEMLRFYSYYKQATMGPCLVPRPGFWDPIGRYKWDAWNSLGKMSREEAMSAYITE   87 (106)
T ss_dssp             -CHHHHHHHHHHHHSCSSCSCCCCHHHHHHHHHHHHHHHHCSCCSCCCCTTCHHHHHHHHHHHTTTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccccCCCCCCHHHHHHHHHHHhhhccCCCCCCCCCcccHHHHHHHHHHHHhcCCCHHHHHHHHHHH
Confidence            45679999999999987    68999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhccCChh
Q psy630          170 LKEVDAGWEDK  180 (347)
Q Consensus       170 ~~~l~~~~~~~  180 (347)
                      +++|.+.+.+.
T Consensus        88 v~~l~~k~~~t   98 (106)
T 2wh5_A           88 MKLVAQKVIDT   98 (106)
T ss_dssp             HHHHHHHHHTC
T ss_pred             HHHHHHHhhcc
Confidence            99998877654

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.80  E-value=1.4e-19  Score=137.15  Aligned_cols=85  Identities=15%  Similarity=0.221  Sum_probs=79.1

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      +...++|||+|||+++++++|+++|++||.|.+|+|++++.||+++|||||+|.+.++|++|++. |+..+.|+.|.|.+
T Consensus         3 ~~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~   82 (110)
T 3s8s_A            3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQL   82 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34678999999999999999999999999999999999999999999999999999999999985 99999999999998


Q ss_pred             CCcccc
Q psy630           84 SDSHNR   89 (347)
Q Consensus        84 ~~~~~~   89 (347)
                      +.....
T Consensus        83 a~~~~~   88 (110)
T 3s8s_A           83 DIKGQQ   88 (110)
T ss_dssp             CSTTHH
T ss_pred             CCCCcH
Confidence            866543

>3fp5_A Acyl-COA binding protein; ACBP, cacao disease, fatty acid metabolism, lipid binding protein; HET: MES; 1.61A {Moniliophthora perniciosa} SCOP: a.11.1.0

Probab=99.80  E-value=1.6e-20  Score=138.02  Aligned_cols=82  Identities=35%  Similarity=0.594  Sum_probs=78.4

Q ss_pred             hhhcccccccccCCcc----cccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHH
Q psy630           95 EDRFNQACDYLPSLVK----KLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALL  170 (347)
Q Consensus        95 ~~~f~~~~~~v~~l~~----~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~  170 (347)
                      +..|..+..+|++++.    .++.++++.||++|+|+++|+|+.++||+++++|++||+||+++++||++|||++||+++
T Consensus         5 ~~~F~~A~~~vk~l~~~g~~~ps~~~~L~LYalyKQAt~Gd~~~~~Pg~~d~~~raKw~AW~~l~gmS~eeA~~~YI~~v   84 (106)
T 3fp5_A            5 KAKFDKAVEIVQSLPKDGPIKPTQDEQLYFYKYFKQATVGDVNISRPGLMDFTGKAKWDAWKSVEGTSKEVAYQKYVEKL   84 (106)
T ss_dssp             HHHHHHHHHHHHHCCSSSSSCCCHHHHHHHHHHHHHHHTCSCCSCCCCTTCHHHHHHHHHHHTTTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcccccCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCccchHHHHHHHHHHHccCCCHHHHHHHHHHHH
Confidence            5679999999999985    689999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhcc
Q psy630          171 KEVDAG  176 (347)
Q Consensus       171 ~~l~~~  176 (347)
                      +++.+.
T Consensus        85 ~~l~~~   90 (106)
T 3fp5_A           85 LEILKK   90 (106)
T ss_dssp             HHHHHH
T ss_pred             HHHhcc
Confidence            999998

>3flv_A Acyl-COA-binding domain-containing protein 5; lipid binding, structural genomics, struct genomics consortium, SGC, lipid-binding, membrane; HET: STE COA; 1.70A {Homo sapiens}

Probab=99.80  E-value=1.4e-20  Score=140.23  Aligned_cols=90  Identities=36%  Similarity=0.644  Sum_probs=82.5

Q ss_pred             chhhhhhcccccccccCCcc----cccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630           91 AENMEDRFNQACDYLPSLVK----KLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus        91 ~~~~~~~f~~~~~~v~~l~~----~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ...+...|..|..+|+++|.    .++.++++.||++|+|+++|+|+.++||+++++|++||+||+++++||+++||++|
T Consensus        21 ~~dLe~~F~~A~~~Vk~l~~~g~~~ps~d~~L~LYaLyKQAT~Gd~~~~~Pg~~d~~graKw~AW~~l~gmS~eeAm~~Y  100 (119)
T 3flv_A           21 QSMHETRFEAAVKVIQSLPKNGSFQPTNEMMLKFYSFYKQATEGPCKLSRPGFWDPIGRYKWDAWSSLGDMTKEEAMIAY  100 (119)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHSSCCCCHHHHHHHHHHHHHHHTCSCCSCCCCTTCHHHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHHHhCcccCCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCccCHHHHHHHHHHHHccCCCHHHHHHHH
Confidence            34567889999999999986    58999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhccCChh
Q psy630          167 IALLKEVDAGWEDK  180 (347)
Q Consensus       167 i~~~~~l~~~~~~~  180 (347)
                      |+++++|.+++...
T Consensus       101 I~~v~~l~~~~~~~  114 (119)
T 3flv_A          101 VEEMKKIIETMPMT  114 (119)
T ss_dssp             HHHHHHHHHHSCC-
T ss_pred             HHHHHHHHhhCCCC
Confidence            99999998887654

>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=99.80  E-value=7.6e-20  Score=163.52  Aligned_cols=138  Identities=14%  Similarity=0.178  Sum_probs=110.0

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      .+..++|||+|||+++|+++|+++|++||.|..|++++++. + ++|||||+|.+.++|.+|+.+++..+.|+.|.|.++
T Consensus        38 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-~-~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~~  115 (292)
T 2ghp_A           38 NRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK-K-NFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL  115 (292)
T ss_dssp             ----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT-S-SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC-C-CcEEEEEEECCHHHHHHHHHhCCcEeCCcEEEEEEC
Confidence            45678999999999999999999999999999999999874 3 589999999999999999988999999999999876


Q ss_pred             CcccccchhhhhhcccccccccCCcccccchhhHHHHhhcc-ccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHH
Q psy630           85 DSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYK-QATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAM  163 (347)
Q Consensus        85 ~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg-~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~  163 (347)
                      .              ..++||+|||..+++++|.++|+.|| .+....+..++.      |+.++.||..  ..+.++|.
T Consensus       116 ~--------------~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~------~~~~g~afV~--f~~~~~a~  173 (292)
T 2ghp_A          116 T--------------ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF------NTSRRFAYID--VTSKEDAR  173 (292)
T ss_dssp             C--------------SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------------CCEEEEE--CSSHHHHH
T ss_pred             C--------------CCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC------CCcceEEEEE--ECCHHHHH
Confidence            3              45789999999999999999999999 988766654432      3334444443  44566776


Q ss_pred             HHH
Q psy630          164 SKY  166 (347)
Q Consensus       164 ~~y  166 (347)
                      .+.
T Consensus       174 ~A~  176 (292)
T 2ghp_A          174 YCV  176 (292)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            663

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.80  E-value=3.9e-20  Score=136.16  Aligned_cols=83  Identities=18%  Similarity=0.357  Sum_probs=75.4

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCC--eeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCC----ccCC
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQ--IMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSH----VLEG   76 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~--i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~----~~~g   76 (347)
                      ....+.+|||+|||+++|+++|+++|++||.  +.+|++++|+.||+++|||||+|.+.++|.+|++. |+.    .++|
T Consensus         5 ~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~G   84 (95)
T 2lkz_A            5 HHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDG   84 (95)
T ss_dssp             SSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETT
T ss_pred             cCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECC
Confidence            4567899999999999999999999999995  67999999999999999999999999999999985 654    5899


Q ss_pred             ccccccCCCc
Q psy630           77 SRLSIQPSDS   86 (347)
Q Consensus        77 ~~l~v~~~~~   86 (347)
                      |+|.|.+|.+
T Consensus        85 r~i~V~~Aks   94 (95)
T 2lkz_A           85 KTIGVDFAKS   94 (95)
T ss_dssp             EEEEEEECCC
T ss_pred             EEEEEEEccC
Confidence            9999998864

>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=99.80  E-value=2.6e-19  Score=130.09  Aligned_cols=82  Identities=33%  Similarity=0.770  Sum_probs=76.5

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCcccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ   82 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~   82 (347)
                      +...+.++|||+|||+++++++|+++|++||.|..+++++++.+|+++|||||+|.+.++|.+|++.++..+.|+.|.|.
T Consensus         6 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v~   85 (87)
T 3s7r_A            6 KNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPK   85 (87)
T ss_dssp             -CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEEE
Confidence            45677889999999999999999999999999999999999999999999999999999999999888889999999987


Q ss_pred             CC
Q psy630           83 PS   84 (347)
Q Consensus        83 ~~   84 (347)
                      +|
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            64

>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=99.79  E-value=2.3e-20  Score=164.11  Aligned_cols=135  Identities=19%  Similarity=0.347  Sum_probs=112.1

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~   83 (347)
                      ..+.++|||+|||+++|+++|+++|++||.|..|.+.+      ++|||||+|.+.++|.+|+. .++..+.|+.|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~   92 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR------DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRF   92 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeee
Confidence            34557999999999999999999999999999999854      36899999999999999998 599999999999998


Q ss_pred             CCcccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHH
Q psy630           84 SDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAM  163 (347)
Q Consensus        84 ~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~  163 (347)
                      +.+             ..++||+|||..+++++|+++|+.||.|....+..+..      |+.++.||..  ..+.++|.
T Consensus        93 a~~-------------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~------g~~~g~afV~--f~~~~~A~  151 (261)
T 3sde_A           93 ATH-------------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDR------GRATGKGFVE--FAAKPPAR  151 (261)
T ss_dssp             CCC-------------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT------SCEEEEEEEE--ESSHHHHH
T ss_pred             ccc-------------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCC------CCcCcEEEEE--eCCHHHHH
Confidence            864             34799999999999999999999999998777766532      3333344444  44567776


Q ss_pred             HHH
Q psy630          164 SKY  166 (347)
Q Consensus       164 ~~y  166 (347)
                      .+.
T Consensus       152 ~A~  154 (261)
T 3sde_A          152 KAL  154 (261)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            664

>2jab_A H10-2-G3; HER2, darpin, ankyrin repeat protein, membrane protein, human epidermal growth factor receptor 2, de novo protein; 1.70A {} PDB: 3hg0_D 2xzt_G 2xzd_G 2y0b_G 2v4h_C

Probab=99.79  E-value=3.1e-19  Score=140.85  Aligned_cols=98  Identities=29%  Similarity=0.325  Sum_probs=91.6

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..|.|+||+|+..+..+++++|++ .+++++.+|..|.||||+|+..|+.+++++|++ +|++++.+|..|+||
T Consensus        39 ~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~d~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~tp  116 (136)
T 2jab_A           39 DVNAKDEYGLTPLYLATAHGHLEIVEVLLK-NGADVNAVDAIGFTPLHLAAFIGHLEIAEVLLK-HGADVNAQDKFGKTA  116 (136)
T ss_dssp             CTTCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTCCCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTSCCH
T ss_pred             CCCCcCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCcCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCcCcCCCCCCH
Confidence            456677889999999999888899999998 799999999999999999999999999999999 799999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSG  346 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~G  346 (347)
                      ||+|+..|+.+++++|+++|
T Consensus       117 l~~A~~~~~~~~~~~Ll~~G  136 (136)
T 2jab_A          117 FDISIGNGNEDLAEILQKLN  136 (136)
T ss_dssp             HHHHHHTTCHHHHHHHHHC-
T ss_pred             HHHHHHCCCHHHHHHHHHcC
Confidence            99999999999999999987

>1d9s_A Cyclin-dependent kinase 4 inhibitor B; helix-turn-helix, ankyrin repeat, signaling protein; NMR {Mus musculus} SCOP: i.11.1.1

Probab=99.79  E-value=6e-20  Score=144.98  Aligned_cols=99  Identities=21%  Similarity=0.204  Sum_probs=92.6

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCC-CchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCC
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDEN-GLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGD  324 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~-g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~  324 (347)
                      .+.+..+..+.|+||+|+. +...++++|++ .+++++.+|.. |+||||+|+..|+.+++++|++ .|++++.+|..|.
T Consensus        36 ~~~~~~~~~g~t~L~~A~~-~~~~~v~~Ll~-~g~~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~ga~~~~~d~~g~  112 (136)
T 1d9s_A           36 ADPNALNRFGRRPIQVMMM-GSAQVAELLLL-HGAEPNCADPATLTRPVHDAAREGFLDTLVVLHR-AGARLDVCDAWGR  112 (136)
T ss_dssp             CCTTCCCTTCCTTTTTSTT-SCHHHHHHHHH-HTCCSSCCBTTTTBCHHHHHHHHTCHHHHHHHHH-TCCCCCCCSSSSS
T ss_pred             CCcCCcCCCCCCHHHHHHc-CCHHHHHHHHH-CCCCCCCcCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCccCCCCC
Confidence            3566778889999999999 88889999988 79999999999 9999999999999999999999 7999999999999


Q ss_pred             cHHHHHHHcCCHHHHHHHHhCCC
Q psy630          325 YGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       325 TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||||+|+..++.+++++|+++||
T Consensus       113 tpl~~A~~~~~~~~~~~Ll~~Ga  135 (136)
T 1d9s_A          113 LPVDLAEEQGHRDIARYLHAATG  135 (136)
T ss_dssp             CHHHHHHHHTCHHHHHHHHHHHC
T ss_pred             CHHHHHHHcCCHHHHHHHHHcCC
Confidence            99999999999999999999987

>3aaa_C Myotrophin, protein V-1; actin capping protein, barbed END capping, inhibition, prote binding, actin capping, actin-binding, cytoskeleton, ANK RE; 2.20A {Homo sapiens} PDB: 1myo_A 2kxp_C 2myo_A

Probab=99.79  E-value=3.3e-19  Score=138.16  Aligned_cols=94  Identities=27%  Similarity=0.323  Sum_probs=84.2

Q ss_pred             CCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHH
Q psy630          252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAK  331 (347)
Q Consensus       252 ~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~  331 (347)
                      +..+.++||+|+..+...++++|++ .+.+++.+|..|+||||+||..|+.+++++|++ .|++++.+|..|+||||+|+
T Consensus         4 ~~~~~~~l~~A~~~~~~~~v~~ll~-~~~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~d~~g~tpL~~A~   81 (123)
T 3aaa_C            4 GSMCDKEFMWALKNGDLDEVKDYVA-KGEDVNRTLEGGRKPLHYAADCGQLEILEFLLL-KGADINAPDKHHITPLLSAV   81 (123)
T ss_dssp             ---CHHHHHHHHHTTCHHHHHHHHH-TTCCTTSCCTTSSCHHHHHHHTTCHHHHHHHHT-TTCCTTCCCTTSCCHHHHHH
T ss_pred             ccccchHHHHHHHcCCHHHHHHHHH-cCCCcCccCCCCCcHHHHHHHcCCHHHHHHHHH-cCCCCCcCCCCCCCHHHHHH
Confidence            4567789999888888888888888 789999999999999999999999999999998 79999999999999999999


Q ss_pred             HcCCHHHHHHHHhCCC
Q psy630          332 AIEHTDLIEYLVNSGS  347 (347)
Q Consensus       332 ~~~~~~~v~~Ll~~GA  347 (347)
                      ..|+.+++++|+++||
T Consensus        82 ~~~~~~~v~~Ll~~ga   97 (123)
T 3aaa_C           82 YEGHVSCVKLLLSKGA   97 (123)
T ss_dssp             HHTCHHHHHHHHHTTC
T ss_pred             HcCCHHHHHHHHHcCC
Confidence            9999999999999986

>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=99.79  E-value=2.1e-19  Score=154.86  Aligned_cols=124  Identities=18%  Similarity=0.175  Sum_probs=102.4

Q ss_pred             ccCCCeEEEeCCCC-CCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCcccccc
Q psy630            5 IRQLNKIFVGNLPW-TVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQ   82 (347)
Q Consensus         5 ~~~~~~l~V~nLp~-~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~   82 (347)
                      ....++|||+|||+ ++++++|+++|++||.|..|++++++     +|||||+|.+.++|.+|+. +++..+.|+.|.|.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~  105 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRIT  105 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            45678999999999 99999999999999999999998765     7899999999999999998 59999999999998


Q ss_pred             CCCcccccc----h-------------------hh-----hhhcccccccccCCcccccchhhHHHHhhcc-ccceeccc
Q psy630           83 PSDSHNRMA----E-------------------NM-----EDRFNQACDYLPSLVKKLDSSTLLKFYALYK-QATVGQCN  133 (347)
Q Consensus        83 ~~~~~~~~~----~-------------------~~-----~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg-~v~~g~~~  133 (347)
                      ++.+.....    .                   ..     ...-...++||+|||..+++++|+++|+.|| .+....+.
T Consensus       106 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~  185 (229)
T 2adc_A          106 LSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF  185 (229)
T ss_dssp             CCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC
T ss_pred             EecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEE
Confidence            876541100    0                   00     0011246799999999999999999999999 88766653

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.79  E-value=5.5e-20  Score=154.77  Aligned_cols=125  Identities=14%  Similarity=0.337  Sum_probs=100.0

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhcc----C-------CeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCcc
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEY----G-------QIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVL   74 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~----G-------~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~   74 (347)
                      ...++|||+|||+++++++|+++|++|    |       .|..+.+      +.++|||||+|.+.++|.+|+.+++..+
T Consensus         2 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al~l~g~~~   75 (198)
T 2yh0_A            2 AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAMAFDGIIF   75 (198)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHGGGTTEEE
T ss_pred             CceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHHHhcCCEE
Confidence            356899999999999999999999999    4       5555554      5668999999999999999997799999


Q ss_pred             CCccccccCCCcccccch-------------hhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCC
Q psy630           75 EGSRLSIQPSDSHNRMAE-------------NMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDK  136 (347)
Q Consensus        75 ~g~~l~v~~~~~~~~~~~-------------~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~  136 (347)
                      .|+.|.|.++.+......             .....-...++||+|||..+++++|+++|+.||.+....+..++
T Consensus        76 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~  150 (198)
T 2yh0_A           76 QGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDS  150 (198)
T ss_dssp             TTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECT
T ss_pred             cCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecC
Confidence            999999998766422110             00011244789999999999999999999999999876665543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=5.1e-19  Score=131.82  Aligned_cols=87  Identities=26%  Similarity=0.655  Sum_probs=81.5

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCcccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ   82 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~   82 (347)
                      .+....++|||+|||+++++++|+++|++||.|..|.+++++.++.++|||||+|.+.++|.+|+.+++..+.|+.|.|.
T Consensus         5 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~   84 (99)
T 2dgs_A            5 SSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVK   84 (99)
T ss_dssp             CCCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEE
Confidence            45567789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcccc
Q psy630           83 PSDSHNR   89 (347)
Q Consensus        83 ~~~~~~~   89 (347)
                      ++.++..
T Consensus        85 ~a~~~~~   91 (99)
T 2dgs_A           85 RAEPRDS   91 (99)
T ss_dssp             ECCCCCC
T ss_pred             ECCCCcc
Confidence            9887654

>3c5r_A BARD-1, BRCA1-associated ring domain protein 1; ankyrin repeat, helix, extended loop, four repeat, PR ANK repeat, disease mutation, metal-binding; 2.00A {Homo sapiens} SCOP: k.37.1.1

Probab=99.79  E-value=4.9e-19  Score=139.80  Aligned_cols=96  Identities=29%  Similarity=0.325  Sum_probs=89.4

Q ss_pred             ccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHH
Q psy630          250 QLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDY  329 (347)
Q Consensus       250 ~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~  329 (347)
                      ..+..|.|+||+|+..+...++++|++ .+++++.+|..|+||||+|+..|+.+++++|++ +|++++.+|..|.||||+
T Consensus         5 ~~~~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~~~~g~t~L~~   82 (137)
T 3c5r_A            5 FTNHRGETLLHIASIKGDIPSVEYLLQ-NGSDPNVKDHAGWTPLHEACNHGHLKVVELLLQ-HKALVNTTGYQNDSPLHD   82 (137)
T ss_dssp             CCCTTCCCHHHHHHHHTCHHHHHHHHH-TTCCSCCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCGGGCCHHHH
T ss_pred             CcCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCcCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCcccCcCCCCCCHHHH
Confidence            456789999999988888888888888 799999999999999999999999999999999 799999999999999999


Q ss_pred             HHHcCCHHHHHHHHhCCC
Q psy630          330 AKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       330 A~~~~~~~~v~~Ll~~GA  347 (347)
                      |+..|+.+++++|+++||
T Consensus        83 A~~~~~~~~v~~Ll~~ga  100 (137)
T 3c5r_A           83 AAKNGHVDIVKLLLSYGA  100 (137)
T ss_dssp             HHHTTCHHHHHHHHHTTC
T ss_pred             HHHcCCHHHHHHHHHcCC
Confidence            999999999999999986

>2l6b_A NR1C; ankyrin, consensus, repeat protein, ising model, DE NOV; NMR {Escherichia coli}

Probab=99.79  E-value=2.2e-19  Score=137.41  Aligned_cols=95  Identities=27%  Similarity=0.362  Sum_probs=90.1

Q ss_pred             cCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHH
Q psy630          251 LDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA  330 (347)
Q Consensus       251 ~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A  330 (347)
                      .|..|.++||+|+..+...++++|+. .+++++.+|..|.||||+|+..++.+++++|++ .|++++.+|..|+||||+|
T Consensus         5 ~d~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~d~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~d~~g~tpl~~A   82 (115)
T 2l6b_A            5 GSKDGNTPLHNAAKNGHAEEVKKLLS-KGADVNARSKDGNTPLHLAAKNGHAEIVKLLLA-KGADVNARSKDGNTPEHLA   82 (115)
T ss_dssp             CSCSSCCHHHHHHHHTCHHHHHHHTT-TTCCSSCCCSSSCCTTHHHHTTTCHHHHHHHTT-TTCCTTCCCTTCCCTTHHH
T ss_pred             cCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCCcCCCCCCHHHHHHHcCcHHHHHHHHH-cCCCCcccCCCCCCHHHHH
Confidence            46789999999998888889999998 799999999999999999999999999999999 7999999999999999999


Q ss_pred             HHcCCHHHHHHHHhCCC
Q psy630          331 KAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       331 ~~~~~~~~v~~Ll~~GA  347 (347)
                      +..++.+++++|+++||
T Consensus        83 ~~~~~~~~~~~Ll~~ga   99 (115)
T 2l6b_A           83 KKNGHHEIVKLLDAKGA   99 (115)
T ss_dssp             HTTTCHHHHHHHHTTSS
T ss_pred             HHCCCHHHHHHHHHcCC
Confidence            99999999999999997

>1d9s_A Cyclin-dependent kinase 4 inhibitor B; helix-turn-helix, ankyrin repeat, signaling protein; NMR {Mus musculus} SCOP: i.11.1.1

Probab=99.78  E-value=3.5e-19  Score=140.59  Aligned_cols=98  Identities=19%  Similarity=0.122  Sum_probs=92.3

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCC-CCc
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSD-GDY  325 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~-g~T  325 (347)
                      +.+..+..+.++||+|+..+..+++++|++ .+++++.+|..|+||||+|+. |+.+++++|++ +|++++.+|.. |+|
T Consensus         4 ~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~-~~~~~v~~Ll~-~g~~~~~~~~~~g~t   80 (136)
T 1d9s_A            4 GIHMLGGSSDAGLATAAARGQVETVRQLLE-AGADPNALNRFGRRPIQVMMM-GSAQVAELLLL-HGAEPNCADPATLTR   80 (136)
T ss_dssp             CCSCCCCCCSCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTCCTTTTTSTT-SCHHHHHHHHH-HTCCSSCCBTTTTBC
T ss_pred             CccCCCCCCccHHHHHHHcCCHHHHHHHHH-cCCCcCCcCCCCCCHHHHHHc-CCHHHHHHHHH-CCCCCCCcCCCCCCC
Confidence            456678899999999999999999999998 799999999999999999999 99999999999 79999999999 999


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|+..|+.+++++|+++||
T Consensus        81 ~L~~A~~~~~~~~v~~Ll~~ga  102 (136)
T 1d9s_A           81 PVHDAAREGFLDTLVVLHRAGA  102 (136)
T ss_dssp             HHHHHHHHTCHHHHHHHHHTCC
T ss_pred             HHHHHHHcCCHHHHHHHHHcCC
Confidence            9999999999999999999986

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens}

Probab=99.78  E-value=1.3e-18  Score=131.60  Aligned_cols=86  Identities=26%  Similarity=0.568  Sum_probs=79.9

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI   81 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v   81 (347)
                      +.....++|||+|||+++++++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|.+|+.. ++..+.|+.|.|
T Consensus        21 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  100 (108)
T 2jrs_A           21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV  100 (108)
T ss_dssp             CSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            4456778999999999999999999999999999999999999999999999999999999999984 999999999999


Q ss_pred             cCCCccc
Q psy630           82 QPSDSHN   88 (347)
Q Consensus        82 ~~~~~~~   88 (347)
                      .++.++.
T Consensus       101 ~~a~~k~  107 (108)
T 2jrs_A          101 GHVTERT  107 (108)
T ss_dssp             ECSCSSC
T ss_pred             EEcccCC
Confidence            9987653

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=5.7e-19  Score=132.12  Aligned_cols=81  Identities=20%  Similarity=0.309  Sum_probs=75.9

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      ....++|||+|||+++|+++|+++|++||.|.+|+|++++. |.++|||||+|.+.++|.+|+..++..+.|+.|.|.++
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFK   86 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEEH
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            44568999999999999999999999999999999999987 99999999999999999999999999999999999876


Q ss_pred             Cc
Q psy630           85 DS   86 (347)
Q Consensus        85 ~~   86 (347)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            55

>3f6q_A Integrin-linked protein kinase; ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK, IPP; 1.60A {Homo sapiens} PDB: 3ixe_A 2kbx_A

Probab=99.78  E-value=1.8e-18  Score=143.01  Aligned_cols=99  Identities=29%  Similarity=0.407  Sum_probs=80.2

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..|.|+||+|+..+...++++|++ .+++++.+|..|.||||+|+..|+.+++++|++ +|++++.+|..|.||
T Consensus        31 ~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~d~~g~t~  108 (179)
T 3f6q_A           31 DLNQGDDHGFSPLHWACREGRSAVVEMLIM-RGARINVMNRGDDTPLHLAASHGHRDIVQKLLQ-YKADINAVNEHGNVP  108 (179)
T ss_dssp             CTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCH
T ss_pred             cccccCCCCCCHHHHHHHcCcHHHHHHHHH-cCCCCCCcCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCccCCCCCCH
Confidence            345566777888888888777778888877 688888888888888888888888888888887 688888888888888


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+..|+.+++++|+++||
T Consensus       109 L~~A~~~~~~~~v~~Ll~~ga  129 (179)
T 3f6q_A          109 LHYACFWGQDQVAEDLVANGA  129 (179)
T ss_dssp             HHHHHHTTCHHHHHHHHHTTC
T ss_pred             HHHHHHcCCHHHHHHHHHCCC
Confidence            888888888888888888875

>3twr_A Tankyrase-2; ankyrin repeat, protein-protein interaction, substrate recru poly(ADP-ribosyl)ation; HET: PE8; 1.55A {Homo sapiens} SCOP: d.211.1.0 PDB: 3tws_A* 3twt_A* 3twv_A* 3tww_A 3twx_A 3twq_A 3twu_A 2y0i_S*

Probab=99.77  E-value=2e-18  Score=140.56  Aligned_cols=92  Identities=27%  Similarity=0.320  Sum_probs=45.0

Q ss_pred             CCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHH
Q psy630          253 DNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKA  332 (347)
Q Consensus       253 ~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~  332 (347)
                      ..+.|+||+|+..+..+++++|++ .+++++.+|..|+||||+|+..|+.+++++|++ +|++++.+|..|+||||+|+.
T Consensus        40 ~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~  117 (165)
T 3twr_A           40 GRQSTPLHFAAGYNRVSVVEYLLQ-HGADVHAKDKGGLVPLHNACSYGHYEVAELLVK-HGAVVNVADLWKFTPLHEAAA  117 (165)
T ss_dssp             TTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTCCCHHHHHHH
T ss_pred             cCCCCHHHHHHHcChHHHHHHHHh-cCCCCCccCCCCCCHHHHHHHcCcHHHHHHHHh-CCCCCCCcCCCCCCHHHHHHH
Confidence            334444444444444444444444 444444444445555555555555555555554 355555444445555555555


Q ss_pred             cCCHHHHHHHHhCC
Q psy630          333 IEHTDLIEYLVNSG  346 (347)
Q Consensus       333 ~~~~~~v~~Ll~~G  346 (347)
                      .|+.+++++|+++|
T Consensus       118 ~~~~~~v~~Ll~~g  131 (165)
T 3twr_A          118 KGKYEICKLLLQHG  131 (165)
T ss_dssp             TTCHHHHHHHHHTT
T ss_pred             cCCHHHHHHHHHcC
Confidence            55555555554444

>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=99.77  E-value=1.2e-18  Score=125.28  Aligned_cols=79  Identities=28%  Similarity=0.570  Sum_probs=75.5

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCcc
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDSH   87 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~~   87 (347)
                      .+|||+|||+++++++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|.+|+.. ++..+.|+.|.|.++.++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            5899999999999999999999999999999999999999999999999999999999985 999999999999998765

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.77  E-value=3.8e-19  Score=130.03  Aligned_cols=81  Identities=22%  Similarity=0.480  Sum_probs=71.1

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccC--CeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccCCC
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYG--QIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQPSD   85 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G--~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~~~   85 (347)
                      .+|||+|||+++++++|+++|++||  .|.++++++++.+|+++|||||+|.+.++|++|++ +|+..+.|+.|.|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4799999999999999999999999  99999999999999999999999999999999997 59999999999999987


Q ss_pred             cccc
Q psy630           86 SHNR   89 (347)
Q Consensus        86 ~~~~   89 (347)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            7543

>1n0r_A 4ANK, 4 ankyrin repeats; structural protein; 1.50A {} SCOP: k.37.1.1

Probab=99.77  E-value=1.8e-18  Score=133.92  Aligned_cols=99  Identities=33%  Similarity=0.471  Sum_probs=92.7

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..+.+++|+|+..+..+++++|.+ .+++++.+|..|.||||+|+..++.+++++|++ .|++++.+|..|.||
T Consensus        27 ~~~~~~~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~~~~g~t~l~~A~~~~~~~~~~~Ll~-~g~~~~~~~~~g~t~  104 (126)
T 1n0r_A           27 DVNAKDKNGRTPLHLAARNGHLEVVKLLLE-AGADVNAKDKNGRTPLHLAARNGHLEVVKLLLE-AGADVNAKDKNGRTP  104 (126)
T ss_dssp             CTTCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCH
T ss_pred             CCCCcCCCCCcHHHHHHHcCcHHHHHHHHH-cCCCCcccCCCCCcHHHHHHHcChHHHHHHHHH-cCCCCcccCCCCCCH
Confidence            345566788999999999888899999998 799999999999999999999999999999999 799999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+..|+.+++++|+++||
T Consensus       105 l~~A~~~~~~~~~~~Ll~~Ga  125 (126)
T 1n0r_A          105 LHLAARNGHLEVVKLLLEAGA  125 (126)
T ss_dssp             HHHHHHTTCHHHHHHHHHHTC
T ss_pred             HHHHHHcCcHHHHHHHHHcCC
Confidence            999999999999999999997

>1ihb_A P18-INK4C(INK6), cyclin-dependent kinase 6 inhibitor; cell cycle inhibitor, ankyrin repeat, CDK 4/6 inhibitor; 1.95A {Homo sapiens} SCOP: d.211.1.1 PDB: 1bu9_A 1g3n_B 1mx4_A 1mx2_A 1mx6_A

Probab=99.77  E-value=1.3e-18  Score=141.12  Aligned_cols=100  Identities=22%  Similarity=0.303  Sum_probs=93.0

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCC-ccccCCCCC
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGAD-VNVTDSDGD  324 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~-i~~~d~~g~  324 (347)
                      .+.+..+..|.|+||+|+..+...++++|++ .+++++.+|..|.||||+|+..|+.+++++|++ .|++ ++.+|..|.
T Consensus        61 ~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~~g~  138 (162)
T 1ihb_A           61 ANPDLKDRTGFAVIHDAARAGFLDTLQTLLE-FQADVNIEDNEGNLPLHLAAKEGHLRVVEFLVK-HTASNVGHRNHKGD  138 (162)
T ss_dssp             CCTTCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-HSCCCTTCCCTTSC
T ss_pred             CCCCCCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCCcCCCCCCHHHHHHHcCCHHHHHHHHH-ccCCCCCCcCCCCC
Confidence            3567778899999999999998999999998 799999999999999999999999999999999 6998 699999999


Q ss_pred             cHHHHHHHcCCHHHHHHHHhCCC
Q psy630          325 YGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       325 TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||||+|+..|+.+++++|+++||
T Consensus       139 t~l~~A~~~~~~~~~~~Ll~~GA  161 (162)
T 1ihb_A          139 TACDLARLYGRNEVVSLMQANGA  161 (162)
T ss_dssp             CHHHHHHHTTCHHHHHHHHHTC-
T ss_pred             cHHHHHHHcCCHHHHHHHHHhCC
Confidence            99999999999999999999997

>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=99.77  E-value=6.2e-19  Score=157.60  Aligned_cols=154  Identities=11%  Similarity=0.130  Sum_probs=114.5

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccC-CeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYG-QIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQP   83 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G-~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~   83 (347)
                      ...++|||+|||+++++++|+++|++|| .|..+.+++++. |.++|||||+|.+.++|.+|+. +++..+.|+.|.|.+
T Consensus       115 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  193 (292)
T 2ghp_A          115 LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKV  193 (292)
T ss_dssp             CCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3568999999999999999999999999 999999999875 8899999999999999999999 599999999999999


Q ss_pred             CCcccccchhhhhhcccccccccCCccc-ccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHH
Q psy630           84 SDSHNRMAENMEDRFNQACDYLPSLVKK-LDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEA  162 (347)
Q Consensus        84 ~~~~~~~~~~~~~~f~~~~~~v~~l~~~-~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA  162 (347)
                      +.+...............++||+|||.. +++++|+++|+.||.|....+..+..    ..|+.|+.|+..  ..+.++|
T Consensus       194 a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~----~tg~~~g~afV~--F~~~~~A  267 (292)
T 2ghp_A          194 SNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQK----EHSFNNCCAFMV--FENKDSA  267 (292)
T ss_dssp             CCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC-------CCCEEEEEE--ESSHHHH
T ss_pred             CCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCC----cCCCCceEEEEE--eCCHHHH
Confidence            8775543222123345578999999999 99999999999999998776655432    013333334433  4457777


Q ss_pred             HHHH
Q psy630          163 MSKY  166 (347)
Q Consensus       163 ~~~y  166 (347)
                      .++.
T Consensus       268 ~~A~  271 (292)
T 2ghp_A          268 ERAL  271 (292)
T ss_dssp             HHHG
T ss_pred             HHHH
Confidence            7663

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.77  E-value=5.9e-19  Score=124.40  Aligned_cols=75  Identities=35%  Similarity=0.690  Sum_probs=72.1

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630           10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus        10 ~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      +|||+|||+++++++|+++|++||.|..+.+++++.+|+++|||||+|.+.++|++|+++++..+.|++|.|.++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEeC
Confidence            599999999999999999999999999999999998999999999999999999999999999999999999865

>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=99.77  E-value=1.1e-18  Score=126.20  Aligned_cols=81  Identities=22%  Similarity=0.389  Sum_probs=76.4

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      ...+.++|||+|||+++++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|.+|+.. ++..+.|+.|+|.
T Consensus         3 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   82 (85)
T 3mdf_A            3 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   82 (85)
T ss_dssp             CCCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            456788999999999999999999999999999999999998999999999999999999999975 9999999999998


Q ss_pred             CC
Q psy630           83 PS   84 (347)
Q Consensus        83 ~~   84 (347)
                      ++
T Consensus        83 ~a   84 (85)
T 3mdf_A           83 LA   84 (85)
T ss_dssp             EC
T ss_pred             Ec
Confidence            76

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.77  E-value=6.9e-19  Score=133.41  Aligned_cols=87  Identities=30%  Similarity=0.574  Sum_probs=76.9

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCcccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ   82 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~   82 (347)
                      +...+.++|||+|||+++++++|+++|++||.|..|++++++.+|.++|||||+|.+.++|.+|+...+..+.|+.|.|.
T Consensus        20 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~   99 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPK   99 (109)
T ss_dssp             ------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEE
Confidence            45667889999999999999999999999999999999999999999999999999999999999986799999999999


Q ss_pred             CCCcccc
Q psy630           83 PSDSHNR   89 (347)
Q Consensus        83 ~~~~~~~   89 (347)
                      ++.++..
T Consensus       100 ~a~~~~~  106 (109)
T 2rs2_A          100 VAFPRRA  106 (109)
T ss_dssp             ECCCCCC
T ss_pred             EccCCCC
Confidence            9877654

>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=99.77  E-value=1.2e-18  Score=126.59  Aligned_cols=82  Identities=28%  Similarity=0.474  Sum_probs=75.0

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      .+.++|||+|||+++++++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|.+|+.. ++..+.|+.|.|.++
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   83 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   83 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEec
Confidence            4567999999999999999999999999999999999998999999999999999999999985 999999999999988


Q ss_pred             Ccc
Q psy630           85 DSH   87 (347)
Q Consensus        85 ~~~   87 (347)
                      .++
T Consensus        84 ~~k   86 (87)
T 3bs9_A           84 TRK   86 (87)
T ss_dssp             C--
T ss_pred             CCC
Confidence            654

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.2e-18  Score=131.22  Aligned_cols=86  Identities=33%  Similarity=0.764  Sum_probs=80.8

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccC
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP   83 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~   83 (347)
                      .....++|||+|||+++++++|+++|++||.|..|.|++++.++.++|||||+|.+.++|.+|+..++..+.|+.|.|.+
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKP   91 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEEE
Confidence            45677899999999999999999999999999999999999999999999999999999999998899999999999999


Q ss_pred             CCcccc
Q psy630           84 SDSHNR   89 (347)
Q Consensus        84 ~~~~~~   89 (347)
                      +.++..
T Consensus        92 a~~~~~   97 (105)
T 2dh8_A           92 CTPRGM   97 (105)
T ss_dssp             SCCSSC
T ss_pred             ccCCCC
Confidence            987654

>1bi7_B P16INK4A, MTS1, multiple tumor suppressor; cyclin dependent kinase, cyclin dependent kinase inhibitory protein, CDK, cell cycle; 3.40A {Homo sapiens} SCOP: d.211.1.1 PDB: 1a5e_A 1dc2_A 2a5e_A

Probab=99.77  E-value=4.5e-19  Score=143.36  Aligned_cols=98  Identities=20%  Similarity=0.227  Sum_probs=89.8

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCch-HHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLN-CLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~t-pLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      +.+..+..|.|+||+|+ .+...++++|++ .+++++.+|..|+| |||+|+..|+.+++++|++ +|++++.+|..|+|
T Consensus        37 ~~~~~~~~g~t~L~~A~-~~~~~~v~~Ll~-~g~~~~~~d~~g~ttpL~~A~~~~~~~~v~~Ll~-~ga~~~~~d~~g~t  113 (156)
T 1bi7_B           37 NPNAPNSYGRRPIQVMM-MGSARVAELLLL-HGAEPNCADPATLTRPVHDAAREGFLDTLVVLHR-AGARLDVRDAWGRL  113 (156)
T ss_dssp             CTTCCCSSSCCTTTSSC-TTCHHHHHHHHT-TTCCCCCCCTTTCCCHHHHHHHHTCHHHHHHHHH-HTCCSSCCCTTCCC
T ss_pred             CCCCCCCCCCCHHHHHH-cCCHHHHHHHHH-cCCCCCCcCCCCCcHHHHHHHHCCCHHHHHHHHH-cCCCCcccCCCCCC
Confidence            56677889999999996 566678888888 79999999999999 9999999999999999999 69999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|+..|+.+++++|+++||
T Consensus       114 pl~~A~~~~~~~~v~~Ll~~ga  135 (156)
T 1bi7_B          114 PVDLAEELGHRDVARYLRAAAG  135 (156)
T ss_dssp             HHHHHHHHTCHHHHHHHSSCC-
T ss_pred             HHHHHHHhCHHHHHHHHHHcCC
Confidence            9999999999999999999996

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.77  E-value=3.6e-19  Score=149.89  Aligned_cols=122  Identities=18%  Similarity=0.187  Sum_probs=100.6

Q ss_pred             CCeEEEeCCCC-CCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccCCC
Q psy630            8 LNKIFVGNLPW-TVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQPSD   85 (347)
Q Consensus         8 ~~~l~V~nLp~-~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~~~   85 (347)
                      .++|||+|||+ ++++++|+++|++||.|..|++++++     +|||||+|.+.++|.+|+. +++..+.|+.|.|.++.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            57999999999 99999999999999999999998764     6899999999999999998 59999999999998776


Q ss_pred             cccccchh-----------------------h-----hhhcccccccccCCcccccchhhHHHHhhcc-ccceecccC
Q psy630           86 SHNRMAEN-----------------------M-----EDRFNQACDYLPSLVKKLDSSTLLKFYALYK-QATVGQCNI  134 (347)
Q Consensus        86 ~~~~~~~~-----------------------~-----~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg-~v~~g~~~~  134 (347)
                      +.......                       .     ...-...++||+|||..+++++|+++|+.|| .+....+..
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~  155 (198)
T 1qm9_A           78 HQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ  155 (198)
T ss_dssp             CCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESS
T ss_pred             CCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEe
Confidence            43210000                       0     0001246799999999999999999999999 888666643

>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=99.77  E-value=1.1e-18  Score=130.04  Aligned_cols=87  Identities=33%  Similarity=0.539  Sum_probs=80.9

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSI   81 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v   81 (347)
                      ....+.++|||+|||+++++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|.+|+. +++..+.|+.|.|
T Consensus         3 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (99)
T 1whw_A            3 SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHV   82 (99)
T ss_dssp             CCCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            456778899999999999999999999999999999999999899999999999999999999996 5999999999999


Q ss_pred             cCCCcccc
Q psy630           82 QPSDSHNR   89 (347)
Q Consensus        82 ~~~~~~~~   89 (347)
                      .++.++..
T Consensus        83 ~~a~~~~~   90 (99)
T 1whw_A           83 LPSTIKKE   90 (99)
T ss_dssp             EECCCCST
T ss_pred             EEcCCCcc
Confidence            99887654

>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=99.76  E-value=2.6e-19  Score=159.41  Aligned_cols=134  Identities=22%  Similarity=0.266  Sum_probs=109.0

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      ....++|||+|||+++|+++|+++|++|| |..+.+      ++++|||||+|.+.++|.+|+.. ++..+.|+.|.|.+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~------~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~   91 (284)
T 3smz_A           19 FRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQL   91 (284)
T ss_dssp             HHCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE------ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEe
Confidence            34678999999999999999999999999 999887      56689999999999999999975 99999999999987


Q ss_pred             CCcccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHH
Q psy630           84 SDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAM  163 (347)
Q Consensus        84 ~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~  163 (347)
                      +.+             ..++||+|||..+++++|.++|+.||.+....+..++.     .|+.|+.||..  ..+.++|.
T Consensus        92 ~~~-------------~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~-----~g~~~g~afV~--f~~~~~a~  151 (284)
T 3smz_A           92 QPT-------------DALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER-----TGQSKGYGFAE--YMKKDSAA  151 (284)
T ss_dssp             CCC-------------SCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----TCCEEEEEEEE--ESSHHHHH
T ss_pred             cCC-------------CCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCC-----CCccceEEEEE--ECCHHHHH
Confidence            542             25799999999999999999999999998776655432     12233334433  34566666


Q ss_pred             HH
Q psy630          164 SK  165 (347)
Q Consensus       164 ~~  165 (347)
                      .+
T Consensus       152 ~A  153 (284)
T 3smz_A          152 RA  153 (284)
T ss_dssp             HH
T ss_pred             HH
Confidence            65

>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=99.76  E-value=1.1e-18  Score=133.74  Aligned_cols=106  Identities=14%  Similarity=0.249  Sum_probs=93.8

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~   82 (347)
                      ++...++|||+|||+++++++|+++|++||.|..+.++++   +.++|||||+|.+.++|.+|+. +++..+.|+.|.|.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   80 (115)
T 3lqv_A            4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVL   80 (115)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            4567789999999999999999999999999999999865   5569999999999999999998 59999999999999


Q ss_pred             CCCcccccchhhhhhcccccccccCCcccccchhhHHHHhhcccc
Q psy630           83 PSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQA  127 (347)
Q Consensus        83 ~~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v  127 (347)
                      ++.+....               ++++....++++.++|+.||.-
T Consensus        81 ~a~~~~~~---------------~~~~~~~~~~~l~~~~~~~g~~  110 (115)
T 3lqv_A           81 YYNANRAF---------------QKMDTKKKEEQLKLLKEKYGIN  110 (115)
T ss_dssp             ECCHHHHT---------------TTSCHHHHHHHHHHHHHHHCCC
T ss_pred             EecCChhh---------------hhhhHhHhHHHHHHHHHHhCCC
Confidence            98765431               5677788899999999999953

>1dcq_A PYK2-associated protein beta; zinc-binding module, ankyrin repeats, metal binding protein; 2.10A {Mus musculus} SCOP: d.211.1.1 g.45.1.1

Probab=99.76  E-value=1.2e-18  Score=154.57  Aligned_cols=96  Identities=20%  Similarity=0.315  Sum_probs=89.8

Q ss_pred             ccCCCCCcHHHHHHcC---ChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          250 QLDDNEKNIYEWAKEG---KLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       250 ~~~~~~~~~l~~a~~~---~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      ..+..|.|+||+|+..   +...++++|++ .|+++|.+|..|+||||+|+..|+.+++++||+ +|++++.+|..|.||
T Consensus       164 ~~~~~g~t~Lh~A~~~~~~~~~~~v~~Ll~-~ga~in~~d~~g~TpLh~A~~~g~~~~v~~Ll~-~gad~~~~d~~g~tp  241 (278)
T 1dcq_A          164 NGHEPDETALHLAVRSVDRTSLHIVDFLVQ-NSGNLDKQTGKGSTALHYCCLTDNAECLKLLLR-GKASIEIANESGETP  241 (278)
T ss_dssp             SCSSTTCBHHHHHHHHCCTTTHHHHHHHHH-HCSCTTCCCTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCH
T ss_pred             ccccCCCCcchHHHHhcccchHHHHHHHHH-CCCCccccCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCCccCCCCCH
Confidence            3467799999999887   77889999988 799999999999999999999999999999999 799999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+..|+.+++++|+++||
T Consensus       242 L~~A~~~~~~~~v~~Ll~~ga  262 (278)
T 1dcq_A          242 LDIAKRLKHEHCEELLTQALS  262 (278)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHHHcCCHHHHHHHHHcCC
Confidence            999999999999999999886

>2y1l_E Darpin-8.4; hydrolase-inhibitor complex, DEVD darpin, ankyrin repeat Pro ribosome display, apoptosis; 1.80A {Synthetic source} PDB: 3noc_D* 4dx5_D* 2j8s_D* 4dx6_D* 4dx7_D* 3nog_D* 1mj0_A 1svx_A 2qyj_A 2bkg_A 2p2c_P 2bkk_B* 2v5q_C 2xee_A 2xeh_A 3q9n_C* 3q9u_C*

Probab=99.76  E-value=3.4e-18  Score=139.99  Aligned_cols=98  Identities=30%  Similarity=0.309  Sum_probs=84.5

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..+.++||+|+..+...++++|++ .+++++.+|..|.||||+|+..|+.+++++|++ .|++++.+|..|.||
T Consensus        72 ~~~~~~~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~  149 (169)
T 2y1l_E           72 DVNAVDHAGMTPLRLAALFGHLEIVEVLLK-NGADVNANDMEGHTPLHLAAMFGHLEIVEVLLK-NGADVNAQDKFGKTA  149 (169)
T ss_dssp             CTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCH
T ss_pred             CCCccCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCCCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCCcCCCCCCH
Confidence            466777888888988888888888888888 788888888889999999999999999999988 699998888889999


Q ss_pred             HHHHHHcCCHHHHHHHHhCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSG  346 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~G  346 (347)
                      ||+|+..|+.+++++|++.|
T Consensus       150 l~~A~~~~~~~~~~~L~~~G  169 (169)
T 2y1l_E          150 FDISIDNGNEDLAEILQKLN  169 (169)
T ss_dssp             HHHHHHTTCHHHHHHHHTC-
T ss_pred             HHHHHHhCCHHHHHHHHHcC
Confidence            99999999999999988876

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=2.6e-18  Score=127.90  Aligned_cols=86  Identities=17%  Similarity=0.391  Sum_probs=79.8

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCee-EEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcc--
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIM-NASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSR--   78 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~-~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~--   78 (347)
                      ......++|||+|||+++++++|+++|++||.|. .+++++++.++.++|||||+|.+.++|++|+.. ++..+.|+.  
T Consensus         4 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~   83 (99)
T 2div_A            4 GSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPA   83 (99)
T ss_dssp             CCCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSC
T ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcc
Confidence            4566789999999999999999999999999999 999999999999999999999999999999985 999999999  


Q ss_pred             --ccccCCCccc
Q psy630           79 --LSIQPSDSHN   88 (347)
Q Consensus        79 --l~v~~~~~~~   88 (347)
                        |+|.++.+..
T Consensus        84 ~~l~v~~a~~~~   95 (99)
T 2div_A           84 KRFKLNYATYSG   95 (99)
T ss_dssp             EECCEEETTCCS
T ss_pred             eeEEEeecCCCC
Confidence              9999887643

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.76  E-value=2.6e-18  Score=125.28  Aligned_cols=81  Identities=26%  Similarity=0.603  Sum_probs=76.4

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCCc
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~~   86 (347)
                      +.++|||+|||+++++++|+++|++||.|..+++++++.+++++|||||+|.+.++|.+|+.+++..+.|+.|.|.++.+
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEETTT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEEccC
Confidence            45799999999999999999999999999999999999899999999999999999999996699999999999998865


Q ss_pred             c
Q psy630           87 H   87 (347)
Q Consensus        87 ~   87 (347)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.76  E-value=2.7e-18  Score=127.84  Aligned_cols=82  Identities=23%  Similarity=0.360  Sum_probs=77.2

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeE--------EEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMN--------ASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHV   73 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~--------~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~   73 (347)
                      ..+...++|||+|||+++++++|+++|++||.|..        +++++++.+|+++|||||+|.+.++|++|++. ++..
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            45677889999999999999999999999999999        99999999999999999999999999999984 9999


Q ss_pred             cCCccccccCC
Q psy630           74 LEGSRLSIQPS   84 (347)
Q Consensus        74 ~~g~~l~v~~~   84 (347)
                      +.|+.|+|.++
T Consensus        88 ~~g~~l~V~~A   98 (99)
T 2la6_A           88 FSGNPIKVSFA   98 (99)
T ss_dssp             SSSSBCEEEEC
T ss_pred             eCCcEEEEEec
Confidence            99999999876

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=2.8e-18  Score=126.73  Aligned_cols=85  Identities=26%  Similarity=0.532  Sum_probs=79.5

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~   83 (347)
                      +...++|||+|||+++++++|+++|++||.|..+.+++++.+++++|||||+|.+.++|.+|+. +++..+.|+.|.|.+
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   81 (95)
T 2dnz_A            2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGH   81 (95)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            3567899999999999999999999999999999999999999999999999999999999998 499999999999999


Q ss_pred             CCcccc
Q psy630           84 SDSHNR   89 (347)
Q Consensus        84 ~~~~~~   89 (347)
                      +.++..
T Consensus        82 a~~~~~   87 (95)
T 2dnz_A           82 VTERLD   87 (95)
T ss_dssp             SSCCCC
T ss_pred             cccccC
Confidence            877654

>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=99.76  E-value=1.9e-18  Score=131.52  Aligned_cols=87  Identities=21%  Similarity=0.452  Sum_probs=81.0

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-C------CCccC
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-D------SHVLE   75 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~------~~~~~   75 (347)
                      +.+...++|||+|||+++++++|+++|++||.|..|+|++++.++.++|||||+|.+.++|.+|+.. +      +..+.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~   89 (111)
T 1x4h_A           10 SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLD   89 (111)
T ss_dssp             CCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESS
T ss_pred             CcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEc
Confidence            4456788999999999999999999999999999999999999999999999999999999999985 8      99999


Q ss_pred             CccccccCCCcccc
Q psy630           76 GSRLSIQPSDSHNR   89 (347)
Q Consensus        76 g~~l~v~~~~~~~~   89 (347)
                      |+.|.|.++.++..
T Consensus        90 g~~l~v~~a~~~~~  103 (111)
T 1x4h_A           90 GRQLKVDLAVTRDE  103 (111)
T ss_dssp             SCEEEEECCCCCCC
T ss_pred             CEEEEEEECCCCcc
Confidence            99999999987654

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=2.5e-18  Score=127.03  Aligned_cols=84  Identities=25%  Similarity=0.446  Sum_probs=78.5

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI   81 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v   81 (347)
                      .++...++|||+|||+++++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|.+|+.. ++..+.|+.|.|
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   89 (95)
T 2cqc_A           10 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   89 (95)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            3456678999999999999999999999999999999999999999999999999999999999985 999999999999


Q ss_pred             cCCCc
Q psy630           82 QPSDS   86 (347)
Q Consensus        82 ~~~~~   86 (347)
                      .++.+
T Consensus        90 ~~a~~   94 (95)
T 2cqc_A           90 SGPSS   94 (95)
T ss_dssp             ECCSC
T ss_pred             EecCC
Confidence            98864

>1awc_B Protein (GA binding protein beta 1); complex (transcription regulation/DNA), DNA-binding, nuclear protein, ETS domain, ankyrin repeats; HET: DNA BRU CBR; 2.15A {Mus musculus} SCOP: d.211.1.1

Probab=99.76  E-value=3e-18  Score=137.85  Aligned_cols=94  Identities=26%  Similarity=0.337  Sum_probs=62.3

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..|.|+||+|+..+...++++|++ .+++++.+|..|.||||+|+..|+.+++++|++ +|++++.+|..|.||
T Consensus        59 ~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~ga~~~~~~~~g~t~  136 (153)
T 1awc_B           59 SRDARTKVDRTPLHMAASEGHANIVEVLLK-HGADVNAKDMLKMTALHWATEHNHQEVVELLIK-YGADVHTQSKFCKTA  136 (153)
T ss_dssp             CTTCCCTTCCCHHHHHHHHTCHHHHHHHHT-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCH
T ss_pred             CCCCCCCCCCCHHHHHHHcChHHHHHHHHH-cCCCCCCCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCccccCCCCCCH
Confidence            345556666666666666666666666666 566666666666666666666666666666666 466666666666666


Q ss_pred             HHHHHHcCCHHHHHHH
Q psy630          327 LDYAKAIEHTDLIEYL  342 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~L  342 (347)
                      ||+|+..|+.+++++|
T Consensus       137 l~~A~~~~~~~i~~~L  152 (153)
T 1awc_B          137 FDISIDNGNEDLAEIL  152 (153)
T ss_dssp             HHHHHHTTCHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHh
Confidence            6666666666666665

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=3.1e-18  Score=129.24  Aligned_cols=83  Identities=20%  Similarity=0.360  Sum_probs=77.5

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ...++|||+|||+++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|++|+.. ++..+.|+.|.|.++
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            4457899999999999999999999999999999999999999999999999999999999985 999999999999988


Q ss_pred             Cccc
Q psy630           85 DSHN   88 (347)
Q Consensus        85 ~~~~   88 (347)
                      .++.
T Consensus       101 ~~~~  104 (106)
T 1p27_B          101 FVRG  104 (106)
T ss_dssp             EESS
T ss_pred             cCCC
Confidence            7643

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.76  E-value=4.1e-19  Score=132.49  Aligned_cols=84  Identities=26%  Similarity=0.375  Sum_probs=77.9

Q ss_pred             cCCCeEEEeCCCC------CCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCC-c
Q psy630            6 RQLNKIFVGNLPW------TVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEG-S   77 (347)
Q Consensus         6 ~~~~~l~V~nLp~------~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g-~   77 (347)
                      ...++|||+|||+      ++++++|+++|++||.|.+|+|++++.||+++|||||+|.+.++|.+|+.. |+..+.| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            3457899999999      999999999999999999999999999999999999999999999999974 9999999 9


Q ss_pred             cccccCCCcccc
Q psy630           78 RLSIQPSDSHNR   89 (347)
Q Consensus        78 ~l~v~~~~~~~~   89 (347)
                      .|.|.++.++.+
T Consensus        84 ~l~V~~a~~~~~   95 (100)
T 3ns6_A           84 RLFLYTMKDVER   95 (100)
T ss_dssp             BCEEEESHHHHH
T ss_pred             EEEEEECchhhh
Confidence            999999876543

>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=99.76  E-value=2.6e-18  Score=129.44  Aligned_cols=86  Identities=29%  Similarity=0.467  Sum_probs=80.2

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      .....++|||+|||+++++++|+++|++||.|..|.+++++.++.++|||||+|.+.++|.+|+.. ++..+.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   90 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   90 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            456678999999999999999999999999999999999998999999999999999999999984 9999999999999


Q ss_pred             CCCcccc
Q psy630           83 PSDSHNR   89 (347)
Q Consensus        83 ~~~~~~~   89 (347)
                      ++.++..
T Consensus        91 ~a~~~~~   97 (105)
T 1x5u_A           91 KASAHNK   97 (105)
T ss_dssp             ETTTTSC
T ss_pred             ECCCCCc
Confidence            9877654

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=1.7e-18  Score=129.93  Aligned_cols=87  Identities=23%  Similarity=0.459  Sum_probs=80.5

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSI   81 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v   81 (347)
                      +...+.++|||+|||+++++++|+++|++||.|..+.|++++.++.++|||||+|.+.++|++|+. +++..+.|+.|.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2dnm_A            8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRV   87 (103)
T ss_dssp             SCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            345667899999999999999999999999999999999999999999999999999999999999 4999999999999


Q ss_pred             cCCCcccc
Q psy630           82 QPSDSHNR   89 (347)
Q Consensus        82 ~~~~~~~~   89 (347)
                      .++.+...
T Consensus        88 ~~a~~~~~   95 (103)
T 2dnm_A           88 QVARYGRR   95 (103)
T ss_dssp             EECSSCCS
T ss_pred             EECCcCCC
Confidence            99877543

>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=99.76  E-value=2.8e-18  Score=127.00  Aligned_cols=82  Identities=23%  Similarity=0.475  Sum_probs=77.8

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCc
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~   86 (347)
                      .++|||+|||+++++++|+++|++||.|..+++++++.+|.++|||||+|.+.++|.+|+.. ++..+.|+.|.|.++.+
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            57999999999999999999999999999999999999999999999999999999999975 99999999999999987


Q ss_pred             ccc
Q psy630           87 HNR   89 (347)
Q Consensus        87 ~~~   89 (347)
                      +..
T Consensus        82 ~~~   84 (96)
T 2x1f_A           82 SDI   84 (96)
T ss_dssp             SSG
T ss_pred             CCC
Confidence            654

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=6e-18  Score=127.14  Aligned_cols=86  Identities=27%  Similarity=0.463  Sum_probs=79.4

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhc-cCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCc-cCCccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSE-YGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHV-LEGSRL   79 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~-~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~-~~g~~l   79 (347)
                      +++...++|||+|||+++++++|+++|++ ||.|..|+|++++ +|.++|||||+|.+.++|.+|+. +++.. +.|+.|
T Consensus         4 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l   82 (104)
T 2dhg_A            4 GSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPV   82 (104)
T ss_dssp             CCSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeE
Confidence            34567789999999999999999999999 9999999999998 89999999999999999999998 49999 999999


Q ss_pred             cccCCCcccc
Q psy630           80 SIQPSDSHNR   89 (347)
Q Consensus        80 ~v~~~~~~~~   89 (347)
                      .|.++.++..
T Consensus        83 ~v~~a~~~~~   92 (104)
T 2dhg_A           83 RLSVAIPKAS   92 (104)
T ss_dssp             CCCBCCCCCS
T ss_pred             EEEEccCCCc
Confidence            9999877654

>3v30_A DNA-binding protein rfxank; structural genomics consortium, SGC, rfxank, ANK repeat, Pro binding; 1.57A {Homo sapiens} PDB: 3uxg_A

Probab=99.76  E-value=4.4e-18  Score=139.56  Aligned_cols=100  Identities=26%  Similarity=0.313  Sum_probs=86.9

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      .+.+..+..+.++||+|+..+...++++|++ .+++++.+|..|.||||+|+..|+.+++++|++ .|++++.+|..|.|
T Consensus        60 ~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~ga~~~~~~~~g~t  137 (172)
T 3v30_A           60 ADPHILAKERESALSLASTGGYTDIVGLLLE-RDVDINIYDWNGGTPLLYAVRGNHVKCVEALLA-RGADLTTEADSGYT  137 (172)
T ss_dssp             CCTTCCCTTCCCHHHHHHHTTCHHHHHHHHT-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCC
T ss_pred             CCchhhcccCCCHHHHHHHCCCHHHHHHHHH-cCCCCCCCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCccccCCCCCC
Confidence            3567778888899999888888888888888 788889888899999999999999999999998 69999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|+..|+.+++++|+++|+
T Consensus       138 ~l~~A~~~~~~~~~~~L~~~~~  159 (172)
T 3v30_A          138 PMDLAVALGYRKVQQVIENHIL  159 (172)
T ss_dssp             HHHHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHHHhCcHHHHHHHHHHHH
Confidence            9999999999999999888763

>2jab_A H10-2-G3; HER2, darpin, ankyrin repeat protein, membrane protein, human epidermal growth factor receptor 2, de novo protein; 1.70A {} PDB: 3hg0_D 2xzt_G 2xzd_G 2y0b_G 2v4h_C

Probab=99.75  E-value=1.8e-18  Score=136.50  Aligned_cols=94  Identities=32%  Similarity=0.375  Sum_probs=87.5

Q ss_pred             CCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHH
Q psy630          252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAK  331 (347)
Q Consensus       252 ~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~  331 (347)
                      ...+.+++|+|+..+..+++++|++ .+++++.+|..|+||||+||..|+.+++++|++ .|++++.+|..|.||||+|+
T Consensus        11 ~~~~~t~l~~A~~~g~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~d~~g~t~L~~A~   88 (136)
T 2jab_A           11 GSDLGKKLLEAARAGQDDEVRILMA-NGADVNAKDEYGLTPLYLATAHGHLEIVEVLLK-NGADVNAVDAIGFTPLHLAA   88 (136)
T ss_dssp             -CHHHHHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTCCCHHHHHH
T ss_pred             cccccHHHHHHHHhCCHHHHHHHHH-cCCCCCCcCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCcCCCCCCCHHHHHH
Confidence            3567799999988888888898888 799999999999999999999999999999999 79999999999999999999


Q ss_pred             HcCCHHHHHHHHhCCC
Q psy630          332 AIEHTDLIEYLVNSGS  347 (347)
Q Consensus       332 ~~~~~~~v~~Ll~~GA  347 (347)
                      ..|+.+++++|+++||
T Consensus        89 ~~~~~~~v~~Ll~~g~  104 (136)
T 2jab_A           89 FIGHLEIAEVLLKHGA  104 (136)
T ss_dssp             HHTCHHHHHHHHHTTC
T ss_pred             HcCCHHHHHHHHHcCC
Confidence            9999999999999986

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.75  E-value=4.2e-18  Score=127.79  Aligned_cols=84  Identities=21%  Similarity=0.473  Sum_probs=78.2

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      ....++|||+|||+++++++|+++|++|| |..|+|++++.+++++|||||+|.+.++|.+|+.+++..+.|+.|.|.++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a   90 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIA   90 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEEEEe
Confidence            45668999999999999999999999997 99999999999999999999999999999999966999999999999998


Q ss_pred             Ccccc
Q psy630           85 DSHNR   89 (347)
Q Consensus        85 ~~~~~   89 (347)
                      .++..
T Consensus        91 ~~~~~   95 (103)
T 2dng_A           91 EGRKQ   95 (103)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            77654

>3v31_A Ankyrin repeat family A protein 2; structural genomics consortium, SGC, ankra2, ANK repeat, Pro binding, HDAC4; 1.57A {Homo sapiens} PDB: 3v2x_A 3v2o_A 3so8_A

Probab=99.75  E-value=5.9e-18  Score=138.08  Aligned_cols=98  Identities=24%  Similarity=0.302  Sum_probs=66.2

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..+.+++|+|+..+...++++|++ .+++++.+|..|.||||+|+..|+.+++++|++ +|++++.+|..|.||
T Consensus        61 ~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~  138 (167)
T 3v31_A           61 DPQLLGKGRESALSLACSKGYTDIVKMLLD-CGVDVNEYDWNGGTPLLYAVHGNHVKCVKMLLE-SGADPTIETDSGYNS  138 (167)
T ss_dssp             CTTCCCTTCCCHHHHHHHHTCHHHHHHHHH-HTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCH
T ss_pred             CCCCcCCCCCcHHHHHHHcCCHHHHHHHHH-CCCCCCcCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCCcCCCCCCH
Confidence            445556666677776666666666666666 566666666677777777777777777777776 577777777777777


Q ss_pred             HHHHHHcCCHHHHHHHHhCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSG  346 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~G  346 (347)
                      ||+|+..|+.+++++|++++
T Consensus       139 l~~A~~~~~~~~~~~L~~~~  158 (167)
T 3v31_A          139 MDLAVALGYRSVQQVIESHL  158 (167)
T ss_dssp             HHHHHHHTCHHHHHHHHHHH
T ss_pred             HHHHHHcCcHHHHHHHHHHH
Confidence            77777777777777766654

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=4.1e-18  Score=127.14  Aligned_cols=84  Identities=18%  Similarity=0.432  Sum_probs=78.1

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      ..+.++|||+|||+++++++|+++|++||.|..++++.++ +|+++|||||+|.+.++|.+|+.. ++..+.|+.|.|.+
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   92 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4557899999999999999999999999999999999998 899999999999999999999975 99999999999999


Q ss_pred             CCcccc
Q psy630           84 SDSHNR   89 (347)
Q Consensus        84 ~~~~~~   89 (347)
                      +.++..
T Consensus        93 a~~~~~   98 (100)
T 2do4_A           93 SNSGPS   98 (100)
T ss_dssp             CCCCSC
T ss_pred             CCCCCC
Confidence            887653

>4b93_B Ankyrin repeat domain-containing protein 27; endocytosis, exocytosis, snare; 2.00A {Homo sapiens}

Probab=99.75  E-value=2.1e-18  Score=152.25  Aligned_cols=99  Identities=24%  Similarity=0.330  Sum_probs=83.1

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..|.++++.|+..+...++++|++ .++++|.+|..|+||||+||..|+.+++++||+ .|+++|.+|..|+||
T Consensus       111 ~~~~~~~~g~t~l~~a~~~~~~~~~~~Ll~-~g~~~n~~d~~g~TpL~~A~~~g~~~~v~~Ll~-~gadvn~~~~~g~t~  188 (269)
T 4b93_B          111 NAGARNADQAVPLHLACQQGHFQVVKCLLD-SNAKPNKKDLSGNTPLIYACSGGHHELVALLLQ-HGASINASNNKGNTA  188 (269)
T ss_dssp             CTTCCCTTCCCHHHHHHHHTCHHHHHHHHH-TTCCSCCCCTTCCCHHHHHHHTTCGGGHHHHHH-TTCCTTCBCTTSCBH
T ss_pred             CcCccCCCCCCccccccccChHHHHHHHHH-CCCCCCCCCCCCCCHHHHHHHCCCHHHHHHHHH-CCCCCCccccCCCcH
Confidence            456667778888888888888888888887 788888888888888888888888888888888 688888888888888


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+..|+.++|++||++||
T Consensus       189 Lh~A~~~g~~~~v~~Ll~~Ga  209 (269)
T 4b93_B          189 LHEAVIEKHVFVVELLLLHGA  209 (269)
T ss_dssp             HHHHHHTTCHHHHHHHHHTTC
T ss_pred             HHHHHHcCCHHHHHHHHHCCC
Confidence            888888888888888888886

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=2.4e-18  Score=129.08  Aligned_cols=85  Identities=24%  Similarity=0.392  Sum_probs=79.6

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~   83 (347)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|++++.++.++|||||+|.+.++|.+|+. +++..+.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   91 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            4567899999999999999999999999999999999999899999999999999999999998 599999999999999


Q ss_pred             CCcccc
Q psy630           84 SDSHNR   89 (347)
Q Consensus        84 ~~~~~~   89 (347)
                      +.++..
T Consensus        92 a~~~~~   97 (103)
T 2cq0_A           92 AKPSTN   97 (103)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            887654

>1ihb_A P18-INK4C(INK6), cyclin-dependent kinase 6 inhibitor; cell cycle inhibitor, ankyrin repeat, CDK 4/6 inhibitor; 1.95A {Homo sapiens} SCOP: d.211.1.1 PDB: 1bu9_A 1g3n_B 1mx4_A 1mx2_A 1mx6_A

Probab=99.75  E-value=2.6e-18  Score=139.38  Aligned_cols=98  Identities=24%  Similarity=0.358  Sum_probs=91.0

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..+.|+||+|+. +..+++++|++ .+++++.+|..|.||||+|+..|+.+++++|++ .|++++.+|..|+||
T Consensus        30 ~~~~~~~~g~t~L~~A~~-~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~  106 (162)
T 1ihb_A           30 NVNAQNGFGRTALQVMKL-GNPEIARRLLL-RGANPDLKDRTGFAVIHDAARAGFLDTLQTLLE-FQADVNIEDNEGNLP  106 (162)
T ss_dssp             CTTCCCTTSCCHHHHCCS-SCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTSCCH
T ss_pred             CccccCccCccHHHHHHc-CcHHHHHHHHH-cCCCCCCCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCCcCCCCCCH
Confidence            456667889999999999 77778888888 799999999999999999999999999999999 799999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+..|+.+++++|+++|+
T Consensus       107 L~~A~~~~~~~~v~~Ll~~g~  127 (162)
T 1ihb_A          107 LHLAAKEGHLRVVEFLVKHTA  127 (162)
T ss_dssp             HHHHHHTTCHHHHHHHHHHSC
T ss_pred             HHHHHHcCCHHHHHHHHHccC
Confidence            999999999999999999885

>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=99.75  E-value=4e-18  Score=130.55  Aligned_cols=84  Identities=29%  Similarity=0.520  Sum_probs=78.8

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ...++|||+|||+++++++|+++|++||.|..|+|++++.+++++|||||+|.+.++|++|+.. ++..+.|+.|.|.++
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  102 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK  102 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            4568999999999999999999999999999999999998999999999999999999999975 999999999999998


Q ss_pred             Ccccc
Q psy630           85 DSHNR   89 (347)
Q Consensus        85 ~~~~~   89 (347)
                      .++..
T Consensus       103 ~~~~~  107 (115)
T 2cpz_A          103 RSKND  107 (115)
T ss_dssp             CCSCC
T ss_pred             CCCCc
Confidence            87654

>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=99.75  E-value=5.7e-18  Score=127.03  Aligned_cols=85  Identities=33%  Similarity=0.645  Sum_probs=78.6

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccC
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP   83 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~   83 (347)
                      .....++|||+|||+++++++|+++|++||.|..|.|++++.+|.++|||||+|.+.++|.+|+. +++.+.|+.|.|.+
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEEEC
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH-cCCeeCCeEEEEEe
Confidence            34567899999999999999999999999999999999999999999999999999999999998 47899999999999


Q ss_pred             CCcccc
Q psy630           84 SDSHNR   89 (347)
Q Consensus        84 ~~~~~~   89 (347)
                      +.++..
T Consensus        90 a~~~~~   95 (103)
T 2cqg_A           90 PNSKQS   95 (103)
T ss_dssp             CCTTCC
T ss_pred             cCCCCc
Confidence            987654

>2zgd_A 3 repeat synthetic ankyrin; ankyrin repeat, hydroxylated, de novo protein; 1.90A {Synthetic} PDB: 2zgg_A 2xen_A

Probab=99.75  E-value=2.7e-18  Score=130.42  Aligned_cols=94  Identities=31%  Similarity=0.363  Sum_probs=83.6

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      .....+..+.++||+|+..+...++++|+. .+++++.+|..|.||||+||..|+.+++++|++ +|++++.+|..|+||
T Consensus        16 ~~~~~~~~g~t~L~~A~~~g~~~~v~~Ll~-~g~~i~~~d~~g~tpLh~A~~~~~~~~v~~Ll~-~ga~~~~~d~~g~tp   93 (110)
T 2zgd_A           16 RGSHMGSDLGKKLLEAARAGQDDEVRILMA-NGADVAAKDKNGSTPLHLAARNGHLEVVKLLLE-AGADVXAQDKFGKTA   93 (110)
T ss_dssp             ------CCHHHHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCH
T ss_pred             cccccCCccchHHHHHHHcCCHHHHHHHHH-cCCCCCccCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCccccccCCCcH
Confidence            355677889999999988888888898888 799999999999999999999999999999999 799999999999999


Q ss_pred             HHHHHHcCCHHHHHHH
Q psy630          327 LDYAKAIEHTDLIEYL  342 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~L  342 (347)
                      ||+|+..|+.+++++|
T Consensus        94 l~~A~~~~~~~~~~~L  109 (110)
T 2zgd_A           94 FDISIDNGNEDLAEIL  109 (110)
T ss_dssp             HHHHHHHTCHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHh
Confidence            9999999999999987

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.75  E-value=4.8e-18  Score=130.13  Aligned_cols=86  Identities=28%  Similarity=0.476  Sum_probs=80.0

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~   82 (347)
                      +..+.++|||+|||+++++++|+++|++||.|..|+|++++.++.++|||||+|.+.++|++|+. +++..+.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           11 DTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             CSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            44567899999999999999999999999999999999998899999999999999999999998 49999999999999


Q ss_pred             CCCcccc
Q psy630           83 PSDSHNR   89 (347)
Q Consensus        83 ~~~~~~~   89 (347)
                      ++.++..
T Consensus        91 ~a~~~~~   97 (115)
T 2dgo_A           91 WATRKPP   97 (115)
T ss_dssp             ESSCCCC
T ss_pred             EccCCCC
Confidence            9887654

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=2.2e-18  Score=129.11  Aligned_cols=87  Identities=29%  Similarity=0.582  Sum_probs=79.9

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI   81 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v   81 (347)
                      ....+.++|||+|||+++++++|+++|++||.|..+++++++.++.++|||||+|.+.++|.+|+.. ++..+.|+.|.|
T Consensus         7 ~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   86 (102)
T 1x5s_A            7 GMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRV   86 (102)
T ss_dssp             CCCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            3456778999999999999999999999999999999999998999999999999999999999975 999999999999


Q ss_pred             cCCCcccc
Q psy630           82 QPSDSHNR   89 (347)
Q Consensus        82 ~~~~~~~~   89 (347)
                      .++.++..
T Consensus        87 ~~a~~~~~   94 (102)
T 1x5s_A           87 DQAGKSSD   94 (102)
T ss_dssp             EEEECCCC
T ss_pred             EECCCCCC
Confidence            98876543

>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=99.75  E-value=4.4e-18  Score=132.86  Aligned_cols=85  Identities=25%  Similarity=0.427  Sum_probs=79.6

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      ++...++|||+|||+++++++|+++|++||.|..|++++++.+|+++|||||+|.+.++|++|+.. ++..+.|+.|.|.
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~  121 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD  121 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEES
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            456678999999999999999999999999999999999999999999999999999999999985 9999999999999


Q ss_pred             CCCccc
Q psy630           83 PSDSHN   88 (347)
Q Consensus        83 ~~~~~~   88 (347)
                      ++.++.
T Consensus       122 ~a~~~~  127 (129)
T 2kxn_B          122 FSITKR  127 (129)
T ss_dssp             CCSSSS
T ss_pred             EecCCC
Confidence            987754

>2rfm_A Putative ankyrin repeat protein TV1425; ANK repeat, protein binding; HET: BU2 GOL; 1.65A {Thermoplasma volcanium}

Probab=99.75  E-value=5.9e-18  Score=141.44  Aligned_cols=98  Identities=20%  Similarity=0.230  Sum_probs=78.2

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..|.|+||+|+..+...++++|++ .+++++.+|..|.||||+|+..|+.+++++|++ +|++++.+|..|.||
T Consensus        93 ~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~ga~~~~~~~~g~t~  170 (192)
T 2rfm_A           93 NVNTKDFSGKTPLMWSIIFGYSEMSYFLLE-HGANVNDRNLEGETPLIVASKYGRSEIVKKLLE-LGADISARDLTGLTA  170 (192)
T ss_dssp             CTTCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCSSCCCTTCCCHHHHHHHHTCHHHHHHHHH-TTCCTTCBCTTSCBH
T ss_pred             CCCCCCCCCCcHHHHHHHcCCHHHHHHHHH-CCCCCCCCCCCCCCHHHHHHHcCCHHHHHHHHH-CCCCCCCcCCCCCCH
Confidence            466677778888888877777777777777 678888888888888888888888888888887 688888888888888


Q ss_pred             HHHHHHcCCHHHHHHHHhCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSG  346 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~G  346 (347)
                      ||+|+..|+.+++++|+++|
T Consensus       171 l~~A~~~~~~~~v~~Ll~~~  190 (192)
T 2rfm_A          171 EASARIFGRQEVIKIFTEVR  190 (192)
T ss_dssp             HHHHHHTTCHHHHHHHHHHH
T ss_pred             HHHHHHhCcHHHHHHHHhcc
Confidence            88888888888888887764

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=2.3e-18  Score=127.46  Aligned_cols=84  Identities=26%  Similarity=0.454  Sum_probs=78.8

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEE-EEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNA-SVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQP   83 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~-~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~   83 (347)
                      ...++|||+|||+++++++|+++|++||.|..+ +|++++.++.++|||||+|.+.++|++|+. +++..+.|+.|.|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            467899999999999999999999999999999 999998899999999999999999999999 599999999999999


Q ss_pred             CCcccc
Q psy630           84 SDSHNR   89 (347)
Q Consensus        84 ~~~~~~   89 (347)
                      +.++..
T Consensus        83 a~~~~~   88 (96)
T 1x5t_A           83 AFKKDS   88 (96)
T ss_dssp             SCCCCC
T ss_pred             ecccCC
Confidence            877654

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=4.8e-18  Score=126.23  Aligned_cols=84  Identities=29%  Similarity=0.548  Sum_probs=77.8

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCC---CCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccc
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKN---TGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI   81 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~---t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v   81 (347)
                      .+.++|||+|||+++++++|+++|++||.|..|.+++++.   |+.++|||||+|.+.++|.+|+.. ++..+.|+.|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            5678999999999999999999999999999999999876   679999999999999999999995 999999999999


Q ss_pred             cCCCcccc
Q psy630           82 QPSDSHNR   89 (347)
Q Consensus        82 ~~~~~~~~   89 (347)
                      .++.++..
T Consensus        83 ~~a~~~~~   90 (98)
T 2cpf_A           83 RISERATK   90 (98)
T ss_dssp             ECSSCSSC
T ss_pred             EEccCCCC
Confidence            99877554

>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=99.75  E-value=1.2e-18  Score=122.82  Aligned_cols=75  Identities=28%  Similarity=0.573  Sum_probs=71.7

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630           10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus        10 ~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      +|||+|||+++++++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|.+|+..++..+.|+.|.|.++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEC
Confidence            599999999999999999999999999999999999999999999999999999999999999999999998754

>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=99.74  E-value=2.9e-18  Score=128.23  Aligned_cols=83  Identities=16%  Similarity=0.255  Sum_probs=75.6

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccC
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP   83 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~   83 (347)
                      .+...++|||+|||+++|+++|+++|++|| +..|+|++++ +|+++|||||+|.+.++|++|+..++..+.||.|.|.+
T Consensus        11 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G-~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~   88 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFL   88 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcC-ceEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEE
Confidence            456678999999999999999999999999 4599999998 89999999999999999999998899999999999987


Q ss_pred             CCccc
Q psy630           84 SDSHN   88 (347)
Q Consensus        84 ~~~~~   88 (347)
                      +.+..
T Consensus        89 ~~~~~   93 (102)
T 1wez_A           89 NSTAG   93 (102)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            76543

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=2.3e-18  Score=124.42  Aligned_cols=82  Identities=22%  Similarity=0.408  Sum_probs=76.4

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      +...++|||+|||+++++++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|.+|+.. |+..+.|+.+++.+
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~   81 (85)
T 1x4e_A            2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSG   81 (85)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecC
Confidence            35678999999999999999999999999999999999999999999999999999999999985 99999999999987


Q ss_pred             CCc
Q psy630           84 SDS   86 (347)
Q Consensus        84 ~~~   86 (347)
                      +.+
T Consensus        82 ~~s   84 (85)
T 1x4e_A           82 PSS   84 (85)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.74  E-value=4.6e-18  Score=137.03  Aligned_cols=82  Identities=21%  Similarity=0.512  Sum_probs=76.7

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccC--CeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYG--QIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G--~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      ..++|||+|||+++++++|+++|++||  .|..|+|++|+.+|+++|||||+|.+.++|.+|+.. ++..+.|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            457999999999999999999999999  999999999999999999999999999999999986 99999999999999


Q ss_pred             CCccc
Q psy630           84 SDSHN   88 (347)
Q Consensus        84 ~~~~~   88 (347)
                      +.++.
T Consensus       134 a~~~~  138 (156)
T 3n9u_C          134 ATRQN  138 (156)
T ss_dssp             CCHHH
T ss_pred             cCCCc
Confidence            87643

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=3.7e-18  Score=125.81  Aligned_cols=81  Identities=27%  Similarity=0.551  Sum_probs=76.0

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~   82 (347)
                      .+...++|||+|||+++++++|+++|++||.|..+.+++++.++.++|||||+|.+.++|.+|++ +++..+.|+.|.|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   91 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS   91 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999997 59999999999998


Q ss_pred             CC
Q psy630           83 PS   84 (347)
Q Consensus        83 ~~   84 (347)
                      ++
T Consensus        92 ~a   93 (94)
T 2e5h_A           92 IA   93 (94)
T ss_dssp             EC
T ss_pred             ec
Confidence            76

>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=99.74  E-value=4.8e-18  Score=127.63  Aligned_cols=84  Identities=23%  Similarity=0.319  Sum_probs=76.4

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeE-EEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMN-ASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSI   81 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~-~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v   81 (347)
                      ++....++|||+|||+++++++|+++|++||.|.. |+|+.+ .+|+++|||||+|.+.++|++|+..++..+.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v   88 (104)
T 1wg5_A           10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEI   88 (104)
T ss_dssp             SSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEE
Confidence            34456789999999999999999999999999987 888888 6899999999999999999999999999999999999


Q ss_pred             cCCCcc
Q psy630           82 QPSDSH   87 (347)
Q Consensus        82 ~~~~~~   87 (347)
                      .++.+.
T Consensus        89 ~~~~~~   94 (104)
T 1wg5_A           89 FKSSRA   94 (104)
T ss_dssp             EEECTT
T ss_pred             EECCHH
Confidence            877553

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=2.8e-18  Score=131.63  Aligned_cols=84  Identities=26%  Similarity=0.610  Sum_probs=79.1

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSD   85 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~   85 (347)
                      ...++|||+|||+++++++|+++|++||.|..|.|++++.++.++|||||+|.+.++|.+|+..++..+.|+.|.|.++.
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEECC
Confidence            34589999999999999999999999999999999999999999999999999999999999989999999999999998


Q ss_pred             cccc
Q psy630           86 SHNR   89 (347)
Q Consensus        86 ~~~~   89 (347)
                      ++..
T Consensus       105 ~~~~  108 (116)
T 1x4b_A          105 AREE  108 (116)
T ss_dssp             SCCC
T ss_pred             CCcc
Confidence            7654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=9e-18  Score=125.95  Aligned_cols=84  Identities=30%  Similarity=0.520  Sum_probs=78.0

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      ...+.++|||+|||+++++++|+++|++||.|..|.++++  ++.++|||||+|.+.++|.+|+.. ++..+.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVA   88 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            3457789999999999999999999999999999999998  799999999999999999999985 9999999999999


Q ss_pred             CCCcccc
Q psy630           83 PSDSHNR   89 (347)
Q Consensus        83 ~~~~~~~   89 (347)
                      ++.++..
T Consensus        89 ~a~~~~~   95 (103)
T 2d9p_A           89 LAQRKEE   95 (103)
T ss_dssp             ECSSCCC
T ss_pred             Eeccccc
Confidence            9887654

>2y1l_E Darpin-8.4; hydrolase-inhibitor complex, DEVD darpin, ankyrin repeat Pro ribosome display, apoptosis; 1.80A {Synthetic source} PDB: 3noc_D* 4dx5_D* 2j8s_D* 4dx6_D* 4dx7_D* 3nog_D* 1mj0_A 1svx_A 2qyj_A 2bkg_A 2p2c_P 2bkk_B* 2v5q_C 2xee_A 2xeh_A 3q9n_C* 3q9u_C*

Probab=99.74  E-value=1.2e-17  Score=136.78  Aligned_cols=99  Identities=29%  Similarity=0.403  Sum_probs=92.8

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..|.++||+|+..+..+++++|++ .+++++..|..|.||||+|+..|+.+++++|++ +|++++.+|..|.||
T Consensus        39 ~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~~~~g~t~  116 (169)
T 2y1l_E           39 DVNAEDASGWTPLHLAAFNGHLEIVEVLLK-NGADVNAVDHAGMTPLRLAALFGHLEIVEVLLK-NGADVNANDMEGHTP  116 (169)
T ss_dssp             CTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCH
T ss_pred             CCCCCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCccCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCCCCCCCCCH
Confidence            345566788999999999999999999998 799999999999999999999999999999999 799999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+..|+.+++++|+++||
T Consensus       117 L~~A~~~~~~~~v~~Ll~~g~  137 (169)
T 2y1l_E          117 LHLAAMFGHLEIVEVLLKNGA  137 (169)
T ss_dssp             HHHHHHTTCHHHHHHHHHTTC
T ss_pred             HHHHHHcCCHHHHHHHHHcCC
Confidence            999999999999999999986

>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=99.74  E-value=2.4e-18  Score=128.35  Aligned_cols=82  Identities=24%  Similarity=0.473  Sum_probs=74.2

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeC-CCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDK-NTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~-~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~   83 (347)
                      ....++|||+|||+++++++|+++|++|| |..|+|++++ .+|+++|||||+|.+.++|.+|+.+++..+.|+.|.|.+
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~l~V~~   94 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDV   94 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBCCCCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeEEEEEe
Confidence            45678999999999999999999999999 9999999998 689999999999999999999996699999999999998


Q ss_pred             CCcc
Q psy630           84 SDSH   87 (347)
Q Consensus        84 ~~~~   87 (347)
                      +.++
T Consensus        95 a~~~   98 (100)
T 2j76_E           95 ADQA   98 (100)
T ss_dssp             CCCS
T ss_pred             ccCC
Confidence            8764

>3v30_A DNA-binding protein rfxank; structural genomics consortium, SGC, rfxank, ANK repeat, Pro binding; 1.57A {Homo sapiens} PDB: 3uxg_A

Probab=99.74  E-value=6.5e-18  Score=138.54  Aligned_cols=98  Identities=23%  Similarity=0.233  Sum_probs=92.3

Q ss_pred             CcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHH
Q psy630          248 ESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGL  327 (347)
Q Consensus       248 ~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpL  327 (347)
                      .+..+..|.|+||+|+..+..+++++|++ .+++++.+|..|.||||+|+..|+.+++++|++ .|++++.+|..|+|||
T Consensus        29 ~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L  106 (172)
T 3v30_A           29 VNKPDERGFTPLIWASAFGEIETVRFLLE-WGADPHILAKERESALSLASTGGYTDIVGLLLE-RDVDINIYDWNGGTPL  106 (172)
T ss_dssp             GGCCCTTSCCHHHHHHHTTCHHHHHHHHH-HTCCTTCCCTTCCCHHHHHHHTTCHHHHHHHHT-TTCCTTCCCTTSCCHH
T ss_pred             ccCCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCchhhcccCCCHHHHHHHCCCHHHHHHHHH-cCCCCCCCCCCCCCHH
Confidence            45567789999999999999999999998 799999999999999999999999999999999 7999999999999999


Q ss_pred             HHHHHcCCHHHHHHHHhCCC
Q psy630          328 DYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       328 h~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |+|+..|+.+++++|+++||
T Consensus       107 ~~A~~~~~~~~v~~Ll~~ga  126 (172)
T 3v30_A          107 LYAVRGNHVKCVEALLARGA  126 (172)
T ss_dssp             HHHHHTTCHHHHHHHHHTTC
T ss_pred             HHHHHcCCHHHHHHHHHcCC
Confidence            99999999999999999986

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=2.2e-18  Score=129.07  Aligned_cols=86  Identities=21%  Similarity=0.357  Sum_probs=79.8

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      .....++|||+|||+++++++|+++|++||.|..|.|++++.++.++|||||+|.+.++|.+|+.. ++..+.|+.|.|.
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            345678999999999999999999999999999999999999999999999999999999999975 9999999999999


Q ss_pred             CCCcccc
Q psy630           83 PSDSHNR   89 (347)
Q Consensus        83 ~~~~~~~   89 (347)
                      ++.++..
T Consensus        88 ~a~~~~~   94 (102)
T 2cqb_A           88 LAKPMRI   94 (102)
T ss_dssp             ECCCCCC
T ss_pred             eCCCCCC
Confidence            9877654

>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=99.74  E-value=4.5e-18  Score=128.32  Aligned_cols=86  Identities=29%  Similarity=0.566  Sum_probs=79.0

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCcc---CCccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVL---EGSRL   79 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~---~g~~l   79 (347)
                      .....++|||+|||+++++++|+++|++||.|..|++++++.+++++|||||+|.+.++|.+|+.. ++..+   .|+.|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            345678999999999999999999999999999999999999999999999999999999999984 88887   88999


Q ss_pred             cccCCCcccc
Q psy630           80 SIQPSDSHNR   89 (347)
Q Consensus        80 ~v~~~~~~~~   89 (347)
                      .|.++.++..
T Consensus        89 ~v~~a~~~~~   98 (106)
T 2dgp_A           89 QVKPADSESR   98 (106)
T ss_dssp             EEEECCCCSC
T ss_pred             EEEECCcccc
Confidence            9999877654

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=99.74  E-value=9.4e-18  Score=123.88  Aligned_cols=82  Identities=27%  Similarity=0.446  Sum_probs=75.9

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~   82 (347)
                      .....++|||+|||+++++++|+++|++||.|..|++++++. ++++|||||+|.+.++|.+|+. +++..+.|+.|.|.
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVS   90 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEE
Confidence            345668999999999999999999999999999999999985 9999999999999999999998 49999999999999


Q ss_pred             CCCc
Q psy630           83 PSDS   86 (347)
Q Consensus        83 ~~~~   86 (347)
                      ++..
T Consensus        91 ~a~~   94 (95)
T 2ywk_A           91 GPSS   94 (95)
T ss_dssp             CCCC
T ss_pred             EcCC
Confidence            8754

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=4.1e-18  Score=128.03  Aligned_cols=85  Identities=29%  Similarity=0.642  Sum_probs=79.2

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~   83 (347)
                      ....++|||+|||+++++++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|.+|+. +++..+.|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   84 (104)
T 1p1t_A            5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN   84 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEE
T ss_pred             CCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Confidence            3456899999999999999999999999999999999999899999999999999999999997 599999999999999


Q ss_pred             CCcccc
Q psy630           84 SDSHNR   89 (347)
Q Consensus        84 ~~~~~~   89 (347)
                      +.++..
T Consensus        85 a~~~~~   90 (104)
T 1p1t_A           85 AASEKN   90 (104)
T ss_dssp             TTCTTH
T ss_pred             CCCccc
Confidence            887654

>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=99.74  E-value=1.3e-17  Score=125.51  Aligned_cols=83  Identities=24%  Similarity=0.386  Sum_probs=77.1

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCC---ccccc
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEG---SRLSI   81 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g---~~l~v   81 (347)
                      ...++|||+|||+++++++|+++|++||.|..|+|++++ +|.++|||||+|.+.++|.+|+.. ++..+.|   +.|.|
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            457899999999999999999999999999999999998 799999999999999999999985 9999988   99999


Q ss_pred             cCCCcccc
Q psy630           82 QPSDSHNR   89 (347)
Q Consensus        82 ~~~~~~~~   89 (347)
                      .++.++..
T Consensus        92 ~~a~~~~~   99 (105)
T 2dnh_A           92 KFADTDKE   99 (105)
T ss_dssp             EESCSSCC
T ss_pred             EECccCcc
Confidence            99887654

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=7e-18  Score=125.42  Aligned_cols=80  Identities=23%  Similarity=0.315  Sum_probs=72.1

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-C--CCccCCcccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-D--SHVLEGSRLS   80 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~--~~~~~g~~l~   80 (347)
                      ++...++|||+|||+++|+++|+++|++||.|.+|+|+++      +|||||+|.+.++|..|++. +  +..+.|++|.
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~   85 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY   85 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            5677899999999999999999999999999999999864      68999999999999999983 3  5789999999


Q ss_pred             ccCCCcccc
Q psy630           81 IQPSDSHNR   89 (347)
Q Consensus        81 v~~~~~~~~   89 (347)
                      |.++.++..
T Consensus        86 V~~A~~~~~   94 (105)
T 1sjq_A           86 IQFSNHKEL   94 (105)
T ss_dssp             BCCCSSSSC
T ss_pred             EEEcCCCCC
Confidence            999977543

>3twr_A Tankyrase-2; ankyrin repeat, protein-protein interaction, substrate recru poly(ADP-ribosyl)ation; HET: PE8; 1.55A {Homo sapiens} SCOP: d.211.1.0 PDB: 3tws_A* 3twt_A* 3twv_A* 3tww_A 3twx_A 3twq_A 3twu_A 2y0i_S*

Probab=99.73  E-value=3.6e-18  Score=139.09  Aligned_cols=99  Identities=23%  Similarity=0.228  Sum_probs=91.5

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      .+.+..+..|.|+||+|+..+..+++++|++ .+++++.+|..|+||||+|+..|+.+++++|++ +|++++.+|..|.|
T Consensus        66 ~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~ga~~~~~~~~g~t  143 (165)
T 3twr_A           66 ADVHAKDKGGLVPLHNACSYGHYEVAELLVK-HGAVVNVADLWKFTPLHEAAAKGKYEICKLLLQ-HGADPTKKNRDGNT  143 (165)
T ss_dssp             CCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCC
T ss_pred             CCCCccCCCCCCHHHHHHHcCcHHHHHHHHh-CCCCCCCcCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCcccCCCCCC
Confidence            3567778899999999999999999999999 899999999999999999999999999999999 79999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|+. ++.+++++|+++||
T Consensus       144 ~l~~a~~-~~~~i~~~L~~~gA  164 (165)
T 3twr_A          144 PLDLVKD-GDTDIQDLLRGDAA  164 (165)
T ss_dssp             TGGGSCT-TCHHHHHHHHTC--
T ss_pred             hhHhHhc-CChHHHHHHhhccc
Confidence            9999877 99999999999997

>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=99.73  E-value=5.7e-18  Score=128.64  Aligned_cols=84  Identities=19%  Similarity=0.349  Sum_probs=78.0

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~~   84 (347)
                      .+.++|||+|||+++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|.+|+. +++..+.|+.|.|.++
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  103 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  103 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEc
Confidence            455789999999999999999999999999999999999999999999999999999999998 4999999999999998


Q ss_pred             Ccccc
Q psy630           85 DSHNR   89 (347)
Q Consensus        85 ~~~~~   89 (347)
                      .++..
T Consensus       104 ~~~~~  108 (110)
T 1oo0_B          104 FVKGP  108 (110)
T ss_dssp             EESSC
T ss_pred             ccCCC
Confidence            76543

>1bd8_A P19INK4D CDK4/6 inhibitor; tumor suppressor, ankyrin motif; 1.80A {Homo sapiens} SCOP: d.211.1.1 PDB: 1bi8_B 1ap7_A 1blx_B

Probab=99.73  E-value=1.4e-17  Score=134.28  Aligned_cols=97  Identities=23%  Similarity=0.226  Sum_probs=90.7

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      .+.+..+..|.|+||+|+..+...++++|++ .|++++.+|..|.||||+|+..|+.+++++|++ . ++++.+|..|.|
T Consensus        59 ~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~-~~~~~~~~~g~t  135 (156)
T 1bd8_A           59 ASPNVQDTSGTSPVHDAARTGFLDTLKVLVE-HGADVNVPDGTGALPIHLAVQEGHTAVVSFLAA-E-SDLHRRDARGLT  135 (156)
T ss_dssp             CCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCSCCCCTTSCCHHHHHHHHTCHHHHHHHHT-T-SCTTCCCTTSCC
T ss_pred             CCCCCcCCCCCCHHHHHHHcCcHHHHHHHHH-cCCCCCCcCCCCCcHHHHHHHhChHHHHHHHHh-c-cCCCCcCCCCCC
Confidence            4567778899999999999999999999998 899999999999999999999999999999998 6 999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHHhC
Q psy630          326 GLDYAKAIEHTDLIEYLVNS  345 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~  345 (347)
                      |||+|+..|+.+++++|+++
T Consensus       136 ~l~~A~~~~~~~~v~~Ll~~  155 (156)
T 1bd8_A          136 PLELALQRGAQDLVDILQGH  155 (156)
T ss_dssp             HHHHHHHSCCHHHHHHHHTT
T ss_pred             HHHHHHHcCcHHHHHHHHhh
Confidence            99999999999999999975

>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=99.73  E-value=8.8e-18  Score=128.73  Aligned_cols=84  Identities=24%  Similarity=0.452  Sum_probs=78.2

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~   83 (347)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+.++ +|.++|||||+|.+.++|++|+. +++..+.|+.|.|.+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4677899999999999999999999999999999999998 89999999999999999999998 499999999999998


Q ss_pred             CCcccc
Q psy630           84 SDSHNR   89 (347)
Q Consensus        84 ~~~~~~   89 (347)
                      +.+...
T Consensus        83 a~~~~~   88 (116)
T 2fy1_A           83 AKKPSF   88 (116)
T ss_dssp             CCCSSC
T ss_pred             CCCCCC
Confidence            876543

>1oy3_D Transcription factor inhibitor I-kappa-B-beta; protein-protein complex, transcription factors, nuclear localization, DNA binding protein; 2.05A {Mus musculus} SCOP: d.211.1.1 PDB: 1k3z_D

Probab=99.73  E-value=1.2e-17  Score=147.59  Aligned_cols=100  Identities=20%  Similarity=0.154  Sum_probs=93.5

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCC-CCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCC
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDE-NGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGD  324 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~-~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~  324 (347)
                      .+.+..+..|.|+||+|+..+...++++|++ .|++++.++. .|+||||+|+..|+.+++++||+ +|++++.+|..|+
T Consensus       149 ~~~~~~~~~g~t~L~~A~~~g~~~~v~~Ll~-~g~~~~~~~~~~g~tpL~~A~~~~~~~~v~~Ll~-~gad~~~~d~~g~  226 (282)
T 1oy3_D          149 LQLEAENYDGHTPLHVAVIHKDAEMVRLLRD-AGADLNKPEPTCGRTPLHLAVEAQAASVLELLLK-AGADPTARMYGGR  226 (282)
T ss_dssp             GGTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-HTCCTTCCCTTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSC
T ss_pred             hcCCCcCCCCcCHHHHHHHcCCHHHHHHHHH-cCCCCCCCCCCCCcCHHHHHHHcCCHHHHHHHHH-cCCCCcccccCCC
Confidence            3467778899999999999999999999998 7999999986 49999999999999999999999 7999999999999


Q ss_pred             cHHHHHHHcCCHHHHHHHHhCCC
Q psy630          325 YGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       325 TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||||+|+..|+.+++++|+++||
T Consensus       227 tpL~~A~~~~~~~~v~~Ll~~ga  249 (282)
T 1oy3_D          227 TPLGSALLRPNPILARLLRAHGA  249 (282)
T ss_dssp             CHHHHHHTSSCHHHHHHHHHTTC
T ss_pred             CHHHHHHHcCCcHHHHHHHHcCC
Confidence            99999999999999999999997

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1e-17  Score=128.45  Aligned_cols=84  Identities=30%  Similarity=0.648  Sum_probs=77.7

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      .....++|||+|||+++++++|+++|++||.|..|+|++++.+++++|||||+|.+.++|++|+.. ++ .+.|+.|.|.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~   91 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   91 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEE
Confidence            445678999999999999999999999999999999999999999999999999999999999997 76 8999999999


Q ss_pred             CCCccc
Q psy630           83 PSDSHN   88 (347)
Q Consensus        83 ~~~~~~   88 (347)
                      ++.+..
T Consensus        92 ~a~~~~   97 (116)
T 2cqd_A           92 LAYLGA   97 (116)
T ss_dssp             ESTTTC
T ss_pred             EcccCC
Confidence            986643

>1ycs_B 53BP2, P53BP2; ankyrin repeats, SH3, tumor suppressor, multigene family, nuclear protein, phosphorylation, disease mutation, polymorphism; 2.20A {Homo sapiens} SCOP: b.34.2.1 d.211.1.1 PDB: 4a63_B

Probab=99.73  E-value=6.6e-18  Score=146.37  Aligned_cols=93  Identities=25%  Similarity=0.307  Sum_probs=66.8

Q ss_pred             CCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHH
Q psy630          253 DNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKA  332 (347)
Q Consensus       253 ~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~  332 (347)
                      ..+.++||.|+..+...++++|++ .++++|.+|..|+||||+||..|+.+++++|++ +|+++|.+|..|+||||+|+.
T Consensus        35 ~~~~t~L~~A~~~g~~~~v~~Ll~-~g~~~~~~d~~g~t~L~~A~~~g~~~~v~~Ll~-~ga~~~~~d~~g~tpL~~A~~  112 (239)
T 1ycs_B           35 PLPLALLLDSSLEGEFDLVQRIIY-EVDDPSLPNDEGITALHNAVCAGHTEIVKFLVQ-FGVNVNAADSDGWTPLHCAAS  112 (239)
T ss_dssp             --CHHHHHHHHHHTCHHHHHHHTS-TTSSCCCCCTTSCCHHHHHHHHTCHHHHHHHHH-HTCCTTCCCTTCCCHHHHHHH
T ss_pred             chhhHHHHHHHHcCCHHHHHHHHH-cCCCCCCcCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCccCCCCCCHHHHHHH
Confidence            455677777766666666666666 566777777777777777777777777777777 577777777777777777777


Q ss_pred             cCCHHHHHHHHhCCC
Q psy630          333 IEHTDLIEYLVNSGS  347 (347)
Q Consensus       333 ~~~~~~v~~Ll~~GA  347 (347)
                      .|+.+++++|+++||
T Consensus       113 ~~~~~~v~~Ll~~ga  127 (239)
T 1ycs_B          113 CNNVQVCKFLVESGA  127 (239)
T ss_dssp             TTCHHHHHHHHHTTC
T ss_pred             cCCHHHHHHHHHcCC
Confidence            777777777777765

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=1.1e-17  Score=126.44  Aligned_cols=86  Identities=31%  Similarity=0.573  Sum_probs=79.4

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeee-CCCCCceeEEEEEEcCHHHHHHHHh-c-CCCccCCcccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFD-KNTGLSKGFGFVTFQNKEAVDKVFS-T-DSHVLEGSRLS   80 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~-~~t~~~~g~afV~f~~~~~a~~a~~-~-~~~~~~g~~l~   80 (347)
                      .....++|||+|||+++++++|+++|++||.|..|+|+++ +.++.++|||||+|.+.++|.+|+. + ++..+.|+.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            3456789999999999999999999999999999999999 7889999999999999999999997 5 89999999999


Q ss_pred             ccCCCcccc
Q psy630           81 IQPSDSHNR   89 (347)
Q Consensus        81 v~~~~~~~~   89 (347)
                      |.++.++..
T Consensus        91 v~~a~~~~~   99 (107)
T 2cph_A           91 LEWADSEVT   99 (107)
T ss_dssp             EEECCCCCC
T ss_pred             EEeCCCCCC
Confidence            999887654

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.73  E-value=2.3e-17  Score=121.00  Aligned_cols=85  Identities=26%  Similarity=0.490  Sum_probs=77.4

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI   81 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v   81 (347)
                      ......++|||+|||+++++++|+++|++||.|..+.++++  ++.++|||||+|.+.++|.+|+.. ++..+.|+.|.|
T Consensus         3 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v   80 (92)
T 2dgv_A            3 SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDV   80 (92)
T ss_dssp             CSSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            34567789999999999999999999999999999999984  799999999999999999999985 999999999999


Q ss_pred             cCCCcccc
Q psy630           82 QPSDSHNR   89 (347)
Q Consensus        82 ~~~~~~~~   89 (347)
                      .++.+...
T Consensus        81 ~~a~~~~~   88 (92)
T 2dgv_A           81 RIDRNASG   88 (92)
T ss_dssp             EECSCCSS
T ss_pred             EEcCCCCC
Confidence            99877543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.73  E-value=9.8e-18  Score=132.90  Aligned_cols=87  Identities=25%  Similarity=0.497  Sum_probs=80.8

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSI   81 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v   81 (347)
                      ++....++|||+|||+++++++|+++|++||.|..|.|++++.+|+++|||||+|.+.++|.+|+. +++..+.|+.|+|
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  116 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV  116 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            345667899999999999999999999999999999999999999999999999999999999998 4999999999999


Q ss_pred             cCCCcccc
Q psy630           82 QPSDSHNR   89 (347)
Q Consensus        82 ~~~~~~~~   89 (347)
                      .++.++..
T Consensus       117 ~~a~~~~~  124 (139)
T 1u6f_A          117 ALAASGHQ  124 (139)
T ss_dssp             EESSCCCC
T ss_pred             EECCCCCC
Confidence            99877654

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.73  E-value=2.7e-18  Score=121.60  Aligned_cols=75  Identities=35%  Similarity=0.720  Sum_probs=71.4

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ++|||+|||+++++++|+++|++||.|..+.+++++.+|+++|||||+|.+.++|.+|+.. + ..+.|++|.|.++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            5799999999999999999999999999999999998999999999999999999999997 6 9999999999765

>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=99.73  E-value=6.6e-18  Score=126.93  Aligned_cols=83  Identities=23%  Similarity=0.469  Sum_probs=77.2

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCC-CCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNT-GLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t-~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      ...++|||+|||+++++++|+++|++|| |..|.|++++.+ |+++|||||+|.+.++|++|+.+++..+.|+.|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a   91 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEEEEEc
Confidence            4567999999999999999999999999 999999999988 99999999999999999999966999999999999998


Q ss_pred             Ccccc
Q psy630           85 DSHNR   89 (347)
Q Consensus        85 ~~~~~   89 (347)
                      .++..
T Consensus        92 ~~~~~   96 (104)
T 1wi8_A           92 DQAQD   96 (104)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            87654

>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=99.73  E-value=5.5e-18  Score=123.24  Aligned_cols=82  Identities=22%  Similarity=0.460  Sum_probs=75.8

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCC-ceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGL-SKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~-~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ..++|||+|||+++++++|+++|++||.|..+.++.++.++. ++|||||+|.+.++|.+|+.. ++..+.|+.|.|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            467999999999999999999999999999999999987766 899999999999999999995 999999999999987


Q ss_pred             Cccc
Q psy630           85 DSHN   88 (347)
Q Consensus        85 ~~~~   88 (347)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6643

>1bd8_A P19INK4D CDK4/6 inhibitor; tumor suppressor, ankyrin motif; 1.80A {Homo sapiens} SCOP: d.211.1.1 PDB: 1bi8_B 1ap7_A 1blx_B

Probab=99.73  E-value=1.7e-17  Score=133.76  Aligned_cols=96  Identities=26%  Similarity=0.316  Sum_probs=88.1

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..|.|+||+ +..+..+++++|++ .|++++.+|..|.||||+|+..|+.+++++|++ .|++++.+|..|+||
T Consensus        28 ~~~~~~~~g~t~L~~-~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~  104 (156)
T 1bd8_A           28 HPDALNRFGKTALQV-MMFGSTAIALELLK-QGASPNVQDTSGTSPVHDAARTGFLDTLKVLVE-HGADVNVPDGTGALP  104 (156)
T ss_dssp             CTTCCCTTSCCHHHH-SCTTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCSCCCCTTSCCH
T ss_pred             CccccCCCCCcHHHH-HHcCCHHHHHHHHH-CCCCCCCcCCCCCCHHHHHHHcCcHHHHHHHHH-cCCCCCCcCCCCCcH
Confidence            455667889999999 76677778888888 799999999999999999999999999999999 799999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhC
Q psy630          327 LDYAKAIEHTDLIEYLVNS  345 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~  345 (347)
                      ||+|+..|+.+++++|+++
T Consensus       105 L~~A~~~~~~~~v~~Ll~~  123 (156)
T 1bd8_A          105 IHLAVQEGHTAVVSFLAAE  123 (156)
T ss_dssp             HHHHHHHTCHHHHHHHHTT
T ss_pred             HHHHHHhChHHHHHHHHhc
Confidence            9999999999999999975

>2vge_A RELA-associated inhibitor; iaspp, nucleus, apoptosis, repressor, cytoplasm, phosphorylation, P53 binding protein, ANK repeat, SH3 domain; 2.10A {Homo sapiens}

Probab=99.73  E-value=9.2e-18  Score=144.61  Aligned_cols=99  Identities=24%  Similarity=0.256  Sum_probs=65.8

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccC-CCCCc
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTD-SDGDY  325 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d-~~g~T  325 (347)
                      +++..+..|.|+||+|+..+..+++++|++ .|+++|.+|..|+||||+||..|+.+++++|++ .|++++.++ ..|+|
T Consensus        46 ~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~-~ga~~n~~d~~g~tpLh~A~~~g~~~~v~~Ll~-~ga~~~~~~~~~g~t  123 (229)
T 2vge_A           46 DPSQPNEEGITALHNAICGANYSIVDFLIT-AGANVNSPDSHGWTPLHCAASCNDTVICMALVQ-HGAAIFATTLSDGAT  123 (229)
T ss_dssp             CTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTCCCHHHHHHHTTCHHHHHHHHT-TTCCTTCCCSSTTCC
T ss_pred             CCCCCCCCCCCHHHHHHHcCCHHHHHHHHH-CCCCCCCCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCcccccCCCCCC
Confidence            455566666666666666666666666666 566666666666667777666666666666666 566666665 46666


Q ss_pred             HHHHH--HHcCCHHHHHHHHhCCC
Q psy630          326 GLDYA--KAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A--~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|  +..|+.+++++|+++||
T Consensus       124 pL~~A~a~~~~~~~~v~~Ll~~ga  147 (229)
T 2vge_A          124 AFEKCDPYREGYADCATYLADVEQ  147 (229)
T ss_dssp             TGGGCCTTSTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcChHHHHHHHHHcCC
Confidence            77666  66666666666666553

>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=99.73  E-value=4e-18  Score=133.72  Aligned_cols=84  Identities=15%  Similarity=0.315  Sum_probs=78.0

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCC---eeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQ---IMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRL   79 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~---i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l   79 (347)
                      +...+.++|||+|||+++|+++|+++|++||.   |..|+|++++. |+++|||||+|.+.++|++|+.+++..+.||.|
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 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALKKDRESMGHRYI  117 (136)
T ss_dssp             SSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHTTTEEESSSSEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCEECCEEE
Confidence            45567789999999999999999999999999   88999999987 999999999999999999999999999999999


Q ss_pred             cccCCCcc
Q psy630           80 SIQPSDSH   87 (347)
Q Consensus        80 ~v~~~~~~   87 (347)
                      .|.++.++
T Consensus       118 ~V~~a~~~  125 (136)
T 2hgl_A          118 EVFKSHRT  125 (136)
T ss_dssp             EEEECCHH
T ss_pred             EEEECChH
Confidence            99888653

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.73  E-value=2.6e-18  Score=125.62  Aligned_cols=81  Identities=27%  Similarity=0.673  Sum_probs=72.8

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCc
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~   86 (347)
                      .++|||+|||+++++++|+++|++||.|..+.+++++.+|.++|||||+|.+.+ |.+|+.. ++..+.|+.|.|.++.+
T Consensus         1 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~   79 (90)
T 2ki2_A            1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANP   79 (90)
T ss_dssp             CEEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC--
T ss_pred             CcEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCC
Confidence            368999999999999999999999999999999999999999999999999999 9999985 99999999999999877


Q ss_pred             ccc
Q psy630           87 HNR   89 (347)
Q Consensus        87 ~~~   89 (347)
                      ...
T Consensus        80 ~~~   82 (90)
T 2ki2_A           80 KKS   82 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            543

>3lvq_E ARF-GAP with SH3 domain, ANK repeat and PH domain containing protein 3, ADP-ribosylation...; GDP, ASAP3, UPLC1, linkers, alternat splicing; HET: GDP; 3.38A {Homo sapiens} PDB: 3lvr_E*

Probab=99.73  E-value=9.8e-18  Score=160.86  Aligned_cols=94  Identities=19%  Similarity=0.229  Sum_probs=89.3

Q ss_pred             CCCCCcHHHHHHc---CChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHH
Q psy630          252 DDNEKNIYEWAKE---GKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLD  328 (347)
Q Consensus       252 ~~~~~~~l~~a~~---~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh  328 (347)
                      +..|.|+||+|+.   .+...++++|++ .|+++|.+|..|+||||+||..|+.+++++||+ +||+++.+|..|+||||
T Consensus       168 ~~~g~t~Lh~A~~~a~~g~~~~v~~Ll~-~ga~vn~~d~~g~TpLh~A~~~g~~~~v~~Ll~-~ga~~~~~d~~g~tpl~  245 (497)
T 3lvq_E          168 QAPEELVLHLAVKVANQASLPLVDFIIQ-NGGHLDAKAADGNTALHYAALYNQPDCLKLLLK-GRALVGTVNEAGETALD  245 (497)
T ss_dssp             CCSCBCHHHHHHHTCCTTTHHHHHHHHH-HSCCTTCCCSSSCCHHHHHTTTTCHHHHHHHHH-TCCCCSCCCTTCCCHHH
T ss_pred             ccccchHHHHHHHhcccccHHHHHHHHH-cCCCCCccCCCCCcHHHHHHHcCCHHHHHHHHH-cCCCCCCcCCCCCCHHH
Confidence            6789999999965   788889999998 799999999999999999999999999999999 79999999999999999


Q ss_pred             HHHHcCCHHHHHHHHhCCC
Q psy630          329 YAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       329 ~A~~~~~~~~v~~Ll~~GA  347 (347)
                      +|+..|+.+++++|+++||
T Consensus       246 ~A~~~~~~~~~~~Ll~~ga  264 (497)
T 3lvq_E          246 IARKKHHKECEELLEQAQA  264 (497)
T ss_dssp             HHHHTTCHHHHHHHHHTCC
T ss_pred             HHHHcCCHHHHHHHHHhCC
Confidence            9999999999999999997

>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=99.73  E-value=2.8e-18  Score=131.15  Aligned_cols=84  Identities=15%  Similarity=0.244  Sum_probs=78.2

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCe-eEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQI-MNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i-~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~   82 (347)
                      .+.+.++|||+|||+++|+++|+++|++||.| ..|+|++++ +|+++|||||+|.+.++|++|+..++..+.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~v~   89 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVH   89 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEE
T ss_pred             CCCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEEE
Confidence            35667899999999999999999999999999 889999998 8999999999999999999999999999999999999


Q ss_pred             CCCccc
Q psy630           83 PSDSHN   88 (347)
Q Consensus        83 ~~~~~~   88 (347)
                      ++.++.
T Consensus        90 ~a~~~~   95 (114)
T 2cpy_A           90 VVTLED   95 (114)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            887654

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1e-17  Score=127.93  Aligned_cols=86  Identities=22%  Similarity=0.369  Sum_probs=79.6

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCee--------EEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCcc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIM--------NASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVL   74 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~--------~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~   74 (347)
                      +..+.++|||+|||+++++++|+++|++||.|.        .|+|+.++.+++++|||||+|.+.++|.+|+.. ++..+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            345678999999999999999999999999999        699999988999999999999999999999985 99999


Q ss_pred             CCccccccCCCcccc
Q psy630           75 EGSRLSIQPSDSHNR   89 (347)
Q Consensus        75 ~g~~l~v~~~~~~~~   89 (347)
                      .|+.|.|.++.++..
T Consensus        91 ~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           91 QGSKLKVSLARKKPP  105 (113)
T ss_dssp             TTEECEEECSSCCCC
T ss_pred             CCCEEEEEECCCCCC
Confidence            999999999887654

>3deo_A Signal recognition particle 43 kDa protein; chloroplast SRP system, signal sequence, ankyrin repeat, chromodomain, type I turn; 1.50A {Arabidopsis thaliana} SCOP: b.34.13.2 k.37.1.1 PDB: 3dep_A 1x32_A

Probab=99.72  E-value=6.7e-18  Score=140.19  Aligned_cols=95  Identities=26%  Similarity=0.342  Sum_probs=86.0

Q ss_pred             ccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccC-CCCCcHHH
Q psy630          250 QLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTD-SDGDYGLD  328 (347)
Q Consensus       250 ~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d-~~g~TpLh  328 (347)
                      ..+..|.|+||+|+..+...++++|+.  +.+++.+|..|+||||+||..|+.+++++|++ +|+++|.+| ..|+||||
T Consensus        39 ~~~~~g~t~L~~A~~~g~~~~v~~Ll~--~~~~~~~d~~g~t~L~~A~~~~~~~~v~~Ll~-~ga~~~~~~~~~g~tpL~  115 (183)
T 3deo_A           39 DVVSEYETPWWTAARKADEQALSQLLE--DRDVDAVDENGRTALLFVAGLGSDKCVRLLAE-AGADLDHRDMRGGLTALH  115 (183)
T ss_dssp             HHHHHHHHHHHHHHHTTCHHHHHHHTT--TSCTTCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCSSSSCCHHH
T ss_pred             cCCCCCCCHHHHHHHcCCHHHHHHHHh--cCCCCCcCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCcCCCCCCCCHHH
Confidence            345678899999998888888888888  88999999999999999999999999999998 799999998 88999999


Q ss_pred             HHHHcCCHHHHHHHHhCCC
Q psy630          329 YAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       329 ~A~~~~~~~~v~~Ll~~GA  347 (347)
                      +|+..|+.+++++|+++||
T Consensus       116 ~A~~~~~~~~v~~Ll~~ga  134 (183)
T 3deo_A          116 MAAGYVRPEVVEALVELGA  134 (183)
T ss_dssp             HHHHTTCHHHHHHHHHHTC
T ss_pred             HHHhcCcHHHHHHHHHcCC
Confidence            9999999999999999886

>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=99.72  E-value=5.8e-18  Score=125.03  Aligned_cols=82  Identities=21%  Similarity=0.359  Sum_probs=74.4

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      ....++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|+.. ++..+.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            34457999999999999999999999999999999999999999999999999999999999985 99999999999988


Q ss_pred             CCc
Q psy630           84 SDS   86 (347)
Q Consensus        84 ~~~   86 (347)
                      +.+
T Consensus        92 a~s   94 (95)
T 2ek1_A           92 PSS   94 (95)
T ss_dssp             CC-
T ss_pred             ccC
Confidence            754

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=1.4e-17  Score=121.85  Aligned_cols=84  Identities=17%  Similarity=0.341  Sum_probs=77.6

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCcccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ   82 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~   82 (347)
                      +.....++|||+|||+++++++|+++|++| .|..++++++ .+|+++|||||+|.+.++|.+|+.+++..+.|+.|.|.
T Consensus         5 ~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~   82 (91)
T 2dgw_A            5 SSGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVF   82 (91)
T ss_dssp             CCCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEE
T ss_pred             CCCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEE
Confidence            345667899999999999999999999999 8999999999 68999999999999999999999999999999999999


Q ss_pred             CCCccc
Q psy630           83 PSDSHN   88 (347)
Q Consensus        83 ~~~~~~   88 (347)
                      ++.++.
T Consensus        83 ~a~~~~   88 (91)
T 2dgw_A           83 REKSGP   88 (91)
T ss_dssp             EESSCC
T ss_pred             ECCcCC
Confidence            887653

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.72  E-value=9.2e-18  Score=129.16  Aligned_cols=80  Identities=29%  Similarity=0.505  Sum_probs=75.3

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~   83 (347)
                      ..+.++|||+|||+++++++|+++|++||.|..+++++++.+|+++|||||+|.+.++|++|+. +++..+.|+.|+|.+
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            4556899999999999999999999999999999999999899999999999999999999998 499999999999987


Q ss_pred             C
Q psy630           84 S   84 (347)
Q Consensus        84 ~   84 (347)
                      +
T Consensus       117 a  117 (118)
T 2khc_A          117 K  117 (118)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.72  E-value=1.7e-18  Score=132.39  Aligned_cols=83  Identities=24%  Similarity=0.439  Sum_probs=77.1

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSD   85 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~   85 (347)
                      ...++|||+|||+++++++|+++|++||.|..|.|++++.+|.++|||||+|.+.++|++|+.+++..+.|+.|.|.++.
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~  102 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQ  102 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeEEEEEecC
Confidence            44579999999999999999999999999999999999999999999999999999999999659999999999999876


Q ss_pred             ccc
Q psy630           86 SHN   88 (347)
Q Consensus        86 ~~~   88 (347)
                      ++.
T Consensus       103 ~~~  105 (114)
T 2cq4_A          103 AEK  105 (114)
T ss_dssp             HHH
T ss_pred             CCc
Confidence            644

>3ehr_A Osteoclast-stimulating factor 1; beta barrel, helix-turn-helix, SH3, ankyrin repeat, signaling protein, ANK repeat, cytoplasm, phosphoprotein; 1.95A {Homo sapiens} PDB: 3ehq_A

Probab=99.72  E-value=8.4e-18  Score=143.86  Aligned_cols=95  Identities=23%  Similarity=0.355  Sum_probs=67.1

Q ss_pred             cCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhc-CCCccccCCCCCcHHHH
Q psy630          251 LDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKC-GADVNVTDSDGDYGLDY  329 (347)
Q Consensus       251 ~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~-ga~i~~~d~~g~TpLh~  329 (347)
                      .+..+.|+||+|+..+...++++|++ .+++++.+|..|+||||+||..|+.+++++||+ . |++++.+|..|+||||+
T Consensus        69 ~~~~g~t~L~~A~~~g~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~~g~~~~~~d~~g~tpL~~  146 (222)
T 3ehr_A           69 QAESIDNPLHEAAKRGNLSWLRECLD-NRVGVNGLDKAGSTALYWACHGGHKDIVEMLFT-QPNIELNQQNKLGDTALHA  146 (222)
T ss_dssp             HEEEESCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHTT-STTCCCCCCCTTSCCHHHH
T ss_pred             cccccccccccccccCcHHHHHHHHh-CCCCccccCCCCCCHHHHHHHcCCHHHHHHHHc-CCCCCccccCCCCCCHHHH
Confidence            34556677777666666666666666 567777777777777777777777777777776 4 77777777777777777


Q ss_pred             HHHcCCHHHHHHHHhCCC
Q psy630          330 AKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       330 A~~~~~~~~v~~Ll~~GA  347 (347)
                      |+..|+.+++++|+++||
T Consensus       147 A~~~~~~~~v~~Ll~~ga  164 (222)
T 3ehr_A          147 AAWKGYADIVQLLLAKGA  164 (222)
T ss_dssp             HHHHTCHHHHHHHHHHTC
T ss_pred             HHHcCCHHHHHHHHHcCC
Confidence            777777777777777665

>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=99.72  E-value=1.7e-17  Score=125.30  Aligned_cols=81  Identities=28%  Similarity=0.501  Sum_probs=75.6

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      .....++|||+|||+.+++++|+++|++||.|..+.+++++ +|+++|||||+|.+.++|.+|+.. ++..+.|+.|.|.
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  103 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34567899999999999999999999999999999999998 899999999999999999999995 9999999999998


Q ss_pred             CCC
Q psy630           83 PSD   85 (347)
Q Consensus        83 ~~~   85 (347)
                      ++.
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            764

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.72  E-value=4e-18  Score=133.69  Aligned_cols=83  Identities=17%  Similarity=0.368  Sum_probs=76.8

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeE--EEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCC----ccCCcc
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMN--ASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSH----VLEGSR   78 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~--~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~----~~~g~~   78 (347)
                      ...++|||+|||+++|+++|+++|++||.|..  |+|++++.+|+++|||||+|.+. +|.+|+.. ++.    .+.|+.
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~   99 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKT   99 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEE
Confidence            45679999999999999999999999999977  99999999999999999999999 99999985 998    999999


Q ss_pred             ccccCCCcccc
Q psy630           79 LSIQPSDSHNR   89 (347)
Q Consensus        79 l~v~~~~~~~~   89 (347)
                      |.|.++.++..
T Consensus       100 l~V~~a~~~~~  110 (131)
T 2m2b_A          100 INVEFAKGSKR  110 (131)
T ss_dssp             CCCEECCCSCC
T ss_pred             EEEEECCCCCC
Confidence            99999877543

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.72  E-value=1.8e-17  Score=128.67  Aligned_cols=82  Identities=24%  Similarity=0.575  Sum_probs=76.9

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCCc
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~~   86 (347)
                      +.++|||+|||+++++++|+++|++||.|..|.+++++.+|.++|||||+|.+.++|.+|+.+++..+.|+.|.|.++.+
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETTEECEEEESSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCC
Confidence            45899999999999999999999999999999999999899999999999999999999996699999999999998866


Q ss_pred             cc
Q psy630           87 HN   88 (347)
Q Consensus        87 ~~   88 (347)
                      ..
T Consensus       115 ~~  116 (124)
T 2jwn_A          115 NM  116 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>1awc_B Protein (GA binding protein beta 1); complex (transcription regulation/DNA), DNA-binding, nuclear protein, ETS domain, ankyrin repeats; HET: DNA BRU CBR; 2.15A {Mus musculus} SCOP: d.211.1.1

Probab=99.72  E-value=2.7e-17  Score=132.28  Aligned_cols=94  Identities=23%  Similarity=0.265  Sum_probs=89.3

Q ss_pred             CCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHH
Q psy630          252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAK  331 (347)
Q Consensus       252 ~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~  331 (347)
                      +..|.|+||+|+..+..+++++|++ .+++++.+|..|+||||+|+..|+.+++++|++ +|++++.+|..|.||||+|+
T Consensus        31 ~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~  108 (153)
T 1awc_B           31 DWLGTSPLHLAAQYGHFSTTEVLLR-AGVSRDARTKVDRTPLHMAASEGHANIVEVLLK-HGADVNAKDMLKMTALHWAT  108 (153)
T ss_dssp             CTTCCCHHHHHHHHTCHHHHHHHHT-TTCCTTCCCTTCCCHHHHHHHHTCHHHHHHHHT-TTCCTTCCCTTSCCHHHHHH
T ss_pred             CCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCCCCCCCCCHHHHHHHcChHHHHHHHHH-cCCCCCCCCCCCCCHHHHHH
Confidence            5678899999998888889999998 899999999999999999999999999999999 79999999999999999999


Q ss_pred             HcCCHHHHHHHHhCCC
Q psy630          332 AIEHTDLIEYLVNSGS  347 (347)
Q Consensus       332 ~~~~~~~v~~Ll~~GA  347 (347)
                      ..|+.+++++|+++||
T Consensus       109 ~~~~~~~v~~Ll~~ga  124 (153)
T 1awc_B          109 EHNHQEVVELLIKYGA  124 (153)
T ss_dssp             HTTCHHHHHHHHHTTC
T ss_pred             HcCCHHHHHHHHHcCC
Confidence            9999999999999986

>2rfm_A Putative ankyrin repeat protein TV1425; ANK repeat, protein binding; HET: BU2 GOL; 1.65A {Thermoplasma volcanium}

Probab=99.72  E-value=1.9e-17  Score=138.27  Aligned_cols=99  Identities=23%  Similarity=0.306  Sum_probs=93.6

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..|.|+||+|+..+...++++|++ .+++++.+|..|.||||+|+..|+.+++++|++ +|++++.+|..|.||
T Consensus        60 ~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~  137 (192)
T 2rfm_A           60 KLEDKDIEGSTALIWAVKNNRLGIAEKLLS-KGSNVNTKDFSGKTPLMWSIIFGYSEMSYFLLE-HGANVNDRNLEGETP  137 (192)
T ss_dssp             CTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-HTCCTTCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCSSCCCTTCCCH
T ss_pred             ccccccccCccHHHHHHHcCCHHHHHHHHH-CCCCCCCCCCCCCcHHHHHHHcCCHHHHHHHHH-CCCCCCCCCCCCCCH
Confidence            566677889999999999999999999998 799999999999999999999999999999999 799999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+..|+.+++++|+++||
T Consensus       138 L~~A~~~~~~~~v~~Ll~~ga  158 (192)
T 2rfm_A          138 LIVASKYGRSEIVKKLLELGA  158 (192)
T ss_dssp             HHHHHHHTCHHHHHHHHHTTC
T ss_pred             HHHHHHcCCHHHHHHHHHCCC
Confidence            999999999999999999986

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.72  E-value=7.8e-18  Score=125.81  Aligned_cols=96  Identities=26%  Similarity=0.384  Sum_probs=80.4

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCcc
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDSH   87 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~~   87 (347)
                      ++|||+|||+++++++|+++|++||.|..+.++++     ++|||||+|.+.++|.+|+.. ++..+.|+.|.|.++.++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            58999999999999999999999999999999876     689999999999999999985 999999999999988775


Q ss_pred             cccchh---hhhhcccccccccCCc
Q psy630           88 NRMAEN---MEDRFNQACDYLPSLV  109 (347)
Q Consensus        88 ~~~~~~---~~~~f~~~~~~v~~l~  109 (347)
                      ......   ....-...++||++|+
T Consensus        76 ~~~~~~~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           76 PRRSRFDRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             CCSSCCCSCCCSCCCCSCCCSCCCC
T ss_pred             CCcccCCCCCccccCCCceecCCCC
Confidence            532211   1111224678999986

>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=99.72  E-value=5.8e-18  Score=127.88  Aligned_cols=85  Identities=13%  Similarity=0.347  Sum_probs=78.6

Q ss_pred             CccccCCCeEEEeCCCCCCCHHHHHHHHhccCC---eeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCcc
Q psy630            2 SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQ---IMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSR   78 (347)
Q Consensus         2 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~---i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~   78 (347)
                      +++....++|||+|||+++|+++|+++|+.||.   |..|+|++++. |+++|||||+|.+.++|++|+.+++..+.|+.
T Consensus         5 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~   83 (107)
T 2lmi_A            5 EEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALEKHRMYMGQRY   83 (107)
T ss_dssp             CCCCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHTTTTCCSSSSC
T ss_pred             cCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHHhCcceeCCeE
Confidence            345677889999999999999999999999988   89999999987 99999999999999999999999999999999


Q ss_pred             ccccCCCcc
Q psy630           79 LSIQPSDSH   87 (347)
Q Consensus        79 l~v~~~~~~   87 (347)
                      |.|.++.++
T Consensus        84 i~V~~a~~~   92 (107)
T 2lmi_A           84 VEVYEINNE   92 (107)
T ss_dssp             CCCEECCHH
T ss_pred             EEEEECCHH
Confidence            999988664

>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=99.72  E-value=1.1e-17  Score=123.67  Aligned_cols=84  Identities=12%  Similarity=0.178  Sum_probs=76.1

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHH----HHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELK----KFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGS   77 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~----~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~   77 (347)
                      .+..+.++|||+|||+++++++|+    ++|++||.|..|+|++++.+   +|||||+|.+.++|++|+.. |+..+.|+
T Consensus         4 ~~~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr   80 (96)
T 2dgx_A            4 GSSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSK   80 (96)
T ss_dssp             CCCSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCe
Confidence            445667899999999999999999    99999999999999998765   88999999999999999984 99999999


Q ss_pred             cccccCCCcccc
Q psy630           78 RLSIQPSDSHNR   89 (347)
Q Consensus        78 ~l~v~~~~~~~~   89 (347)
                      .|+|.++.+...
T Consensus        81 ~l~V~~a~~~~~   92 (96)
T 2dgx_A           81 KILVSLATGASG   92 (96)
T ss_dssp             EEEEEECCCSSC
T ss_pred             EEEEEEcCCCCC
Confidence            999999876543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.72  E-value=8.3e-18  Score=129.29  Aligned_cols=83  Identities=16%  Similarity=0.352  Sum_probs=76.9

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCC---eeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCcccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQ---IMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLS   80 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~---i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~   80 (347)
                      ...+.++|||+|||+++|+++|+++|+.||.   |..|+|++++. |+++|||||+|.+.++|++|+.+++..+.|+.|.
T Consensus        13 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~   91 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALKKDRESMGHRYIE   91 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEE
Confidence            4566789999999999999999999999999   89999999987 9999999999999999999999999999999999


Q ss_pred             ccCCCcc
Q psy630           81 IQPSDSH   87 (347)
Q Consensus        81 v~~~~~~   87 (347)
                      |.++..+
T Consensus        92 V~~a~~~   98 (118)
T 2db1_A           92 VFKSHRT   98 (118)
T ss_dssp             EEEECHH
T ss_pred             EEECCHH
Confidence            9887543

>1n0r_A 4ANK, 4 ankyrin repeats; structural protein; 1.50A {} SCOP: k.37.1.1

Probab=99.72  E-value=2.8e-17  Score=127.04  Aligned_cols=92  Identities=34%  Similarity=0.482  Sum_probs=86.2

Q ss_pred             CCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHc
Q psy630          254 NEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAI  333 (347)
Q Consensus       254 ~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~  333 (347)
                      .|.|+||.|+..+...++++|++ .+.+++..|..|.||||+|+..++.+++++|++ .|++++.+|..|.||||+|+..
T Consensus         1 ~g~t~L~~A~~~~~~~~v~~Ll~-~~~~~~~~~~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~~~~g~t~l~~A~~~   78 (126)
T 1n0r_A            1 NGRTPLHLAARNGHLEVVKLLLE-AGADVNAKDKNGRTPLHLAARNGHLEVVKLLLE-AGADVNAKDKNGRTPLHLAARN   78 (126)
T ss_dssp             CCCCHHHHHHHHTCHHHHHHHHH-HTCCTTCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHT
T ss_pred             CCccHHHHHHHcCcHHHHHHHHH-cCCCCCCcCCCCCcHHHHHHHcCcHHHHHHHHH-cCCCCcccCCCCCcHHHHHHHc
Confidence            47899999988888888888888 689999999999999999999999999999999 7999999999999999999999


Q ss_pred             CCHHHHHHHHhCCC
Q psy630          334 EHTDLIEYLVNSGS  347 (347)
Q Consensus       334 ~~~~~v~~Ll~~GA  347 (347)
                      |+.+++++|+++|+
T Consensus        79 ~~~~~~~~Ll~~g~   92 (126)
T 1n0r_A           79 GHLEVVKLLLEAGA   92 (126)
T ss_dssp             TCHHHHHHHHHTTC
T ss_pred             ChHHHHHHHHHcCC
Confidence            99999999999985

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.72  E-value=6.3e-18  Score=126.59  Aligned_cols=85  Identities=29%  Similarity=0.621  Sum_probs=77.5

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCcccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ   82 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~   82 (347)
                      +.....++|||+|||+++++++|+++|++||.|..+++++++ +|.++|||||+|.+.++|++|+. ++..++|+.|.|.
T Consensus         4 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~-~~~~~~g~~l~v~   81 (102)
T 2xs2_A            4 EGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKLKLG   81 (102)
T ss_dssp             CCEEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT-CCCEETTEECEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh-CCCeECCEEEEEE
Confidence            445566899999999999999999999999999999999998 89999999999999999999999 9999999999998


Q ss_pred             CCCcccc
Q psy630           83 PSDSHNR   89 (347)
Q Consensus        83 ~~~~~~~   89 (347)
                      ++.++..
T Consensus        82 ~a~~~~~   88 (102)
T 2xs2_A           82 PAIRKQN   88 (102)
T ss_dssp             EEEECC-
T ss_pred             ECCcCcc
Confidence            8766543

>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=99.72  E-value=1.1e-17  Score=129.25  Aligned_cols=82  Identities=20%  Similarity=0.344  Sum_probs=74.7

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCee--EEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCcccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIM--NASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLS   80 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~--~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~   80 (347)
                      ..+.+.++|||+|||+++|+++|+++|++| .|.  .|+|++++. |+++|||||+|.+.++|++|+..++..+.||.|.
T Consensus        37 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~  114 (126)
T 2hgm_A           37 ADSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGKHKERIGHRYIE  114 (126)
T ss_dssp             TCSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHCCCEECCEEEE
Confidence            345667899999999999999999999999 577  899999987 9999999999999999999999888999999999


Q ss_pred             ccCCCc
Q psy630           81 IQPSDS   86 (347)
Q Consensus        81 v~~~~~   86 (347)
                      |.++.+
T Consensus       115 V~~a~~  120 (126)
T 2hgm_A          115 VFKSSQ  120 (126)
T ss_dssp             CEEECH
T ss_pred             EEECCH
Confidence            987754

>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=99.72  E-value=3.4e-17  Score=122.79  Aligned_cols=85  Identities=27%  Similarity=0.629  Sum_probs=77.2

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI   81 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v   81 (347)
                      +.....++|||+|||+++++++|+++|++||.|..|+|++++.  .++|||||+|.+.++|.+|+.. ++..+.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   87 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            3456778999999999999999999999999999999998864  3899999999999999999985 999999999999


Q ss_pred             cCCCcccc
Q psy630           82 QPSDSHNR   89 (347)
Q Consensus        82 ~~~~~~~~   89 (347)
                      .++.++..
T Consensus        88 ~~a~~~~~   95 (103)
T 2cq3_A           88 NNATARVM   95 (103)
T ss_dssp             EECCSSCC
T ss_pred             EEcccCCC
Confidence            99887654

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.9e-17  Score=125.45  Aligned_cols=85  Identities=14%  Similarity=0.267  Sum_probs=77.7

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCC-eeEEEEe-eeCCCCCceeEEEEEEcCHHHHHHHHhc-C--CCccCCccc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQ-IMNASVM-FDKNTGLSKGFGFVTFQNKEAVDKVFST-D--SHVLEGSRL   79 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~-i~~~~i~-~~~~t~~~~g~afV~f~~~~~a~~a~~~-~--~~~~~g~~l   79 (347)
                      ..+.++|||+|||+++++++|+++|++||. |..+.++ .++.+|.++|||||+|.+.++|.+|+.. +  +..+.|+.|
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l   84 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeE
Confidence            456789999999999999999999999998 9999998 8888899999999999999999999985 5  589999999


Q ss_pred             cccCCCcccc
Q psy630           80 SIQPSDSHNR   89 (347)
Q Consensus        80 ~v~~~~~~~~   89 (347)
                      .|.++.++..
T Consensus        85 ~V~~a~~~~~   94 (109)
T 2dis_A           85 AVDWAEPEID   94 (109)
T ss_dssp             EEEESCSSCS
T ss_pred             EEEEcCCCCC
Confidence            9999987654

>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=99.71  E-value=9.6e-18  Score=124.59  Aligned_cols=83  Identities=19%  Similarity=0.327  Sum_probs=76.3

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~   83 (347)
                      ....++|||+|||+++++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|+. +++..+.|+.|+|.+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            3455789999999999999999999999999999999999999999999999999999999996 599999999999998


Q ss_pred             CCcc
Q psy630           84 SDSH   87 (347)
Q Consensus        84 ~~~~   87 (347)
                      +...
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            7653

>3ui2_A Signal recognition particle 43 kDa protein, chlor; ankyrin repeat, chromodomain, aromatic CAGE, signal recognit particle, protein targeting; 3.18A {Arabidopsis thaliana} PDB: 1x3q_A 2hug_A

Probab=99.71  E-value=1.1e-17  Score=145.57  Aligned_cols=96  Identities=26%  Similarity=0.342  Sum_probs=88.7

Q ss_pred             cccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccC-CCCCcHH
Q psy630          249 SQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTD-SDGDYGL  327 (347)
Q Consensus       249 ~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d-~~g~TpL  327 (347)
                      ...+..|.|+||+|+..+...++++|+.  ++++|.+|..|+||||+||..|+.+++++|++ +|+++|.++ ..|+|||
T Consensus        39 ~~~~~~g~t~L~~A~~~g~~~~v~~Ll~--~~~~~~~d~~g~t~L~~A~~~g~~~~v~~Ll~-~ga~~~~~~~~~g~t~L  115 (244)
T 3ui2_A           39 ADVVSEYETPWWTAARKADEQALSQLLE--DRDVDAVDENGRTALLFVAGLGSDKCVRLLAE-AGADLDHRDMRGGLTAL  115 (244)
T ss_dssp             HHHHHHHHHHHHHHHTTTCHHHHHHTTT--TCCTTCBCTTSCBHHHHHHHHTCHHHHHHHHH-TTCCTTCCCSSSCCCHH
T ss_pred             cccccCCCCHHHHHHHcCCHHHHHHHHc--CCCCCCcCCCCCCHHHHHHHCCCHHHHHHHHH-cCCCCCcCCCCCCCCHH
Confidence            3344678899999999999999999988  88999999999999999999999999999999 799999998 7899999


Q ss_pred             HHHHHcCCHHHHHHHHhCCC
Q psy630          328 DYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       328 h~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |+|+..|+.+++++|+++||
T Consensus       116 ~~A~~~g~~~~v~~Ll~~ga  135 (244)
T 3ui2_A          116 HMAAGYVRPEVVEALVELGA  135 (244)
T ss_dssp             HHHHHTTCHHHHHHHHHTTC
T ss_pred             HHHHHcCCHHHHHHHHHCCC
Confidence            99999999999999999986

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=2.6e-17  Score=123.42  Aligned_cols=84  Identities=15%  Similarity=0.312  Sum_probs=76.3

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~   82 (347)
                      .....++|||+|||+++++++|+++|++||.|..|+|++++.  .++|||||+|.+.++|.+|+. +++..+.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   88 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEE
Confidence            456678999999999999999999999999999999999864  378999999999999999998 59999999999999


Q ss_pred             CCCcccc
Q psy630           83 PSDSHNR   89 (347)
Q Consensus        83 ~~~~~~~   89 (347)
                      ++.++..
T Consensus        89 ~a~~~~~   95 (103)
T 2cqi_A           89 WATTPSS   95 (103)
T ss_dssp             ECCCTTC
T ss_pred             ECCCCcc
Confidence            9887554

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.71  E-value=2.6e-17  Score=117.74  Aligned_cols=72  Identities=24%  Similarity=0.412  Sum_probs=66.7

Q ss_pred             CeEEEeCCCCCC------CHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCc-ccc
Q psy630            9 NKIFVGNLPWTV------SHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGS-RLS   80 (347)
Q Consensus         9 ~~l~V~nLp~~~------t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~-~l~   80 (347)
                      ++|||+|||+.+      ++++|+++|++||.|..+.++  +.+|+++|||||+|.+.++|.+|+.. |+..+.|+ +|+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            689999999999      779999999999999999987  45799999999999999999999985 99999999 888


Q ss_pred             cc
Q psy630           81 IQ   82 (347)
Q Consensus        81 v~   82 (347)
                      |.
T Consensus        80 V~   81 (81)
T 2krb_A           80 VN   81 (81)
T ss_dssp             CC
T ss_pred             eC
Confidence            73

>1bi7_B P16INK4A, MTS1, multiple tumor suppressor; cyclin dependent kinase, cyclin dependent kinase inhibitory protein, CDK, cell cycle; 3.40A {Homo sapiens} SCOP: d.211.1.1 PDB: 1a5e_A 1dc2_A 2a5e_A

Probab=99.71  E-value=7.4e-18  Score=136.14  Aligned_cols=95  Identities=18%  Similarity=0.103  Sum_probs=86.5

Q ss_pred             ccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc-HHH
Q psy630          250 QLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY-GLD  328 (347)
Q Consensus       250 ~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T-pLh  328 (347)
                      ..+..+.++||+|+..+...++++|++ .+++++.+|..|+||||+|+ .|+.+++++|++ .|++++.+|..|+| |||
T Consensus         7 ~~~~~~~t~L~~A~~~g~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~-~~~~~~v~~Ll~-~g~~~~~~d~~g~ttpL~   83 (156)
T 1bi7_B            7 SSMEPSADWLATAAARGRVEEVRALLE-AGANPNAPNSYGRRPIQVMM-MGSARVAELLLL-HGAEPNCADPATLTRPVH   83 (156)
T ss_dssp             ---CCSTTHHHHHHHHTCHHHHHHHHT-TTCCTTCCCSSSCCTTTSSC-TTCHHHHHHHHT-TTCCCCCCCTTTCCCHHH
T ss_pred             CCCccchHHHHHHHHcCCHHHHHHHHH-cCCCCCCCCCCCCCHHHHHH-cCCHHHHHHHHH-cCCCCCCcCCCCCcHHHH
Confidence            345678899999998888889999888 79999999999999999996 999999999999 79999999999999 999


Q ss_pred             HHHHcCCHHHHHHHHhCCC
Q psy630          329 YAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       329 ~A~~~~~~~~v~~Ll~~GA  347 (347)
                      +|+..|+.+++++|+++||
T Consensus        84 ~A~~~~~~~~v~~Ll~~ga  102 (156)
T 1bi7_B           84 DAAREGFLDTLVVLHRAGA  102 (156)
T ss_dssp             HHHHHTCHHHHHHHHHHTC
T ss_pred             HHHHCCCHHHHHHHHHcCC
Confidence            9999999999999999886

>4b93_B Ankyrin repeat domain-containing protein 27; endocytosis, exocytosis, snare; 2.00A {Homo sapiens}

Probab=99.71  E-value=3.2e-17  Score=144.70  Aligned_cols=102  Identities=25%  Similarity=0.289  Sum_probs=96.2

Q ss_pred             cccCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCC
Q psy630          244 MINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDG  323 (347)
Q Consensus       244 ~~~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g  323 (347)
                      ...+++..+..|.||||+|+..+..+++++|+. .+++++.++..|.||||+|+..++.+++++|++ .|+++|.+|..|
T Consensus        75 ~Gadvn~~d~~G~TpLh~A~~~g~~~~v~~Ll~-~~a~~~~~~~~g~t~l~~a~~~~~~~~~~~Ll~-~g~~~n~~d~~g  152 (269)
T 4b93_B           75 SGLGVNVTSQDGSSPLHVAALHGRADLIPLLLK-HGANAGARNADQAVPLHLACQQGHFQVVKCLLD-SNAKPNKKDLSG  152 (269)
T ss_dssp             CCCCTTCCCTTSCCHHHHHHHTTCTTHHHHHHH-TTCCTTCCCTTCCCHHHHHHHHTCHHHHHHHHH-TTCCSCCCCTTC
T ss_pred             CCCCCCCcCCCCCCHHHHHHHcCcHHHHHHHHh-cCCCcCccCCCCCCccccccccChHHHHHHHHH-CCCCCCCCCCCC
Confidence            334678889999999999999999999999998 899999999999999999999999999999999 799999999999


Q ss_pred             CcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          324 DYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       324 ~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      +||||+|+..|+.++|++||++||
T Consensus       153 ~TpL~~A~~~g~~~~v~~Ll~~ga  176 (269)
T 4b93_B          153 NTPLIYACSGGHHELVALLLQHGA  176 (269)
T ss_dssp             CCHHHHHHHTTCGGGHHHHHHTTC
T ss_pred             CCHHHHHHHCCCHHHHHHHHHCCC
Confidence            999999999999999999999986

>4hbd_A KN motif and ankyrin repeat domain-containing Pro; structural genomics consortium, SGC, protein binding; 1.72A {Homo sapiens}

Probab=99.71  E-value=3.9e-17  Score=144.67  Aligned_cols=99  Identities=21%  Similarity=0.285  Sum_probs=92.4

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      ..+..+..|.|+||+|+..+..+++++|++ .|+++|.+|..|+||||+||..|+.+++++||+..|++++.+|..|+||
T Consensus       175 ~~~~~~~~g~tpLh~A~~~g~~~~v~~Ll~-~gad~n~~d~~G~TpLh~A~~~g~~~iv~~Ll~~~gad~~~~d~~g~Tp  253 (276)
T 4hbd_A          175 INAKASQAGQTALMLAVSHGRVDVVKALLA-CEADVNVQDDDGSTALMCACEHGHKEIAGLLLAVPSCDISLTDRDGSTA  253 (276)
T ss_dssp             TTCCCTTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHHTCHHHHHHHHTSTTCCTTCCCTTSCCH
T ss_pred             CccccCCCCCCHHHHHHHcCCHHHHHHHHh-CCCCCCCCCCCCCCHHHHHHHCCCHHHHHHHHhcCCCCCcCcCCCCCCH
Confidence            455667789999999999999999999999 8999999999999999999999999999999984599999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSG  346 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~G  346 (347)
                      ||+|+..|+.+++++|++++
T Consensus       254 L~~A~~~g~~~iv~~Ll~~~  273 (276)
T 4hbd_A          254 LMVALDAGQSEIASMLYSRM  273 (276)
T ss_dssp             HHHHHHHTCHHHHHHHHHHC
T ss_pred             HHHHHHcCCHHHHHHHHhcc
Confidence            99999999999999999875

>3v31_A Ankyrin repeat family A protein 2; structural genomics consortium, SGC, ankra2, ANK repeat, Pro binding, HDAC4; 1.57A {Homo sapiens} PDB: 3v2x_A 3v2o_A 3so8_A

Probab=99.71  E-value=1.8e-17  Score=135.18  Aligned_cols=99  Identities=26%  Similarity=0.386  Sum_probs=93.3

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..|.|+||+|+..+..+++++|++ .+++++..|..|.||||+|+..|+.+++++|++ +|++++.+|..|.||
T Consensus        28 ~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~  105 (167)
T 3v31_A           28 VINHTDEEGFTPLMWAAAHGQIAVVEFLLQ-NGADPQLLGKGRESALSLACSKGYTDIVKMLLD-CGVDVNEYDWNGGTP  105 (167)
T ss_dssp             CTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTCCCHHHHHHHHTCHHHHHHHHH-HTCCTTCCCTTSCCH
T ss_pred             CcCCCCCCCCCHHHHHHHCCCHHHHHHHHH-cCCCCCCcCCCCCcHHHHHHHcCCHHHHHHHHH-CCCCCCcCCCCCCCH
Confidence            356667889999999999999999999999 799999999999999999999999999999999 799999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+..|+.+++++|+++||
T Consensus       106 L~~A~~~~~~~~v~~Ll~~g~  126 (167)
T 3v31_A          106 LLYAVHGNHVKCVKMLLESGA  126 (167)
T ss_dssp             HHHHHHTTCHHHHHHHHHTTC
T ss_pred             HHHHHHcCCHHHHHHHHHcCC
Confidence            999999999999999999986

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.71  E-value=1.4e-17  Score=131.03  Aligned_cols=86  Identities=27%  Similarity=0.522  Sum_probs=79.6

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      +..+.++|||+|||+++++++|+++|++||.|..|.|++++.+++++|||||+|.+.++|++|+.. ++..+.|+.|.|.
T Consensus        43 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  122 (135)
T 2lea_A           43 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQ  122 (135)
T ss_dssp             SGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            455678999999999999999999999999999999999998999999999999999999999985 9999999999999


Q ss_pred             CCCcccc
Q psy630           83 PSDSHNR   89 (347)
Q Consensus        83 ~~~~~~~   89 (347)
                      ++.+...
T Consensus       123 ~a~~~~~  129 (135)
T 2lea_A          123 MARYGRP  129 (135)
T ss_dssp             ECCCCCC
T ss_pred             ECCCCCC
Confidence            9877543

>2f8y_A Notch homolog 1, translocation-associated (drosophila); ankyrin repeats, transcription; 1.55A {Homo sapiens} PDB: 2qc9_A 1ymp_A

Probab=99.70  E-value=6.1e-17  Score=138.24  Aligned_cols=100  Identities=21%  Similarity=0.204  Sum_probs=94.1

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      .+.+..+..+.|+||+|+..+...++++|++ .+++++.+|..|.||||+|+..|+.+++++|++ +|++++.+|..|.|
T Consensus       116 ~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~ga~~~~~~~~g~t  193 (223)
T 2f8y_A          116 ADVNAVDDLGKSALHWAAAVNNVDAAVVLLK-NGANKDMQNNREETPLFLAAREGSYETAKVLLD-HFANRDITDHMDRL  193 (223)
T ss_dssp             CCTTCBCTTSCBHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTCCCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTCCC
T ss_pred             CCCcCcCCCCCcHHHHHHHcCCHHHHHHHHH-cCCCCCCcCCCCcCHHHHHHHcCCHHHHHHHHH-cCCCCccccccCCC
Confidence            3566777889999999999999999999999 799999999999999999999999999999999 79999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|+..++.+++++|+++||
T Consensus       194 ~l~~A~~~~~~~i~~~L~~~g~  215 (223)
T 2f8y_A          194 PRDIAQERMHHDIVRLLDEYNL  215 (223)
T ss_dssp             HHHHHHHTTCHHHHHHHHHTTC
T ss_pred             HHHHHHHhcchHHHHHHHHcCC
Confidence            9999999999999999999986

>2b0o_E UPLC1; arfgap, structural genomics, structural genomics consortium, SGC, metal binding protein; 2.06A {Homo sapiens}

Probab=99.70  E-value=2e-17  Score=148.40  Aligned_cols=95  Identities=19%  Similarity=0.215  Sum_probs=88.4

Q ss_pred             cCCCCCcHHHHHHcC---ChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHH
Q psy630          251 LDDNEKNIYEWAKEG---KLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGL  327 (347)
Q Consensus       251 ~~~~~~~~l~~a~~~---~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpL  327 (347)
                      .+..|.|+||+|+..   +...++++|++ .|+++|.+|..|+||||+|+..|+.+++++||+ +|++++.+|..|.|||
T Consensus       186 ~~~~g~t~Lh~A~~~~~~~~~~iv~~Ll~-~gadvn~~d~~G~TpLh~A~~~g~~~~v~~Ll~-~gad~~~~d~~G~TpL  263 (301)
T 2b0o_E          186 AQAPEELVLHLAVKVANQASLPLVDFIIQ-NGGHLDAKAADGNTALHYAALYNQPDCLKLLLK-GRALVGTVNEAGETAL  263 (301)
T ss_dssp             SCSCEECHHHHHHHTCCTTTHHHHHHHHH-HSSCTTCCCTTCCCHHHHHHHTTCHHHHHHHHH-TTCCCSCCCTTSCCHH
T ss_pred             cCCCCccHHHHHHHhcccCcHHHHHHHHh-cCCCCCCCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCCcCCCCCCHH
Confidence            467889999999975   67788898888 699999999999999999999999999999999 7999999999999999


Q ss_pred             HHHHHcCCHHHHHHHHhCCC
Q psy630          328 DYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       328 h~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |+|+..|+.+++++|+++||
T Consensus       264 ~~A~~~~~~~iv~~Ll~~ga  283 (301)
T 2b0o_E          264 DIARKKHHKECEELLEQAQA  283 (301)
T ss_dssp             HHHHHHTCHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHhcC
Confidence            99999999999999998874

>1yyh_A HN1;, notch 1, ankyrin domain; ankyrin repeats, cell cycle,transcription; 1.90A {Homo sapiens} PDB: 2he0_A 2f8x_K 3nbn_B 3v79_K* 1ot8_A

Probab=99.70  E-value=3.4e-17  Score=143.02  Aligned_cols=98  Identities=21%  Similarity=0.208  Sum_probs=83.7

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      .+.+..+..|.|+||+|+..+...++++|++ .|++++.+|..|.||||+|+..|+.+++++|++ +|++++.+|..|.|
T Consensus       148 ~~~~~~d~~g~t~L~~A~~~~~~~~v~~Ll~-~ga~~~~~~~~g~tpL~~A~~~~~~~~v~~Ll~-~ga~~~~~d~~g~t  225 (253)
T 1yyh_A          148 ADVNAVDDLGKSALHWAAAVNNVDAAVVLLK-NGANKDMQNNREETPLFLAAREGSYETAKVLLD-HFANRDITDHMDRL  225 (253)
T ss_dssp             CCTTCBCTTSCBHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTCCC
T ss_pred             CCCCCcCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCCcCCCCCCHHHHHHHCCCHHHHHHHHH-cCCCccccccCCCC
Confidence            4567778888899988888888888888888 788888888889999999999999999999998 69999988889999


Q ss_pred             HHHHHHHcCCHHHHHHHHhC
Q psy630          326 GLDYAKAIEHTDLIEYLVNS  345 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~  345 (347)
                      |||+|+..|+.+++++|...
T Consensus       226 pl~~A~~~g~~~i~~~l~~~  245 (253)
T 1yyh_A          226 PRDIAQERMHHDIVRLLDLE  245 (253)
T ss_dssp             HHHHHHHTTCHHHHHHHHC-
T ss_pred             HHHHHHHcCCHHHHHHHHHH
Confidence            99999999999999888753

>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=99.70  E-value=2.6e-17  Score=128.12  Aligned_cols=85  Identities=20%  Similarity=0.341  Sum_probs=78.2

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~   83 (347)
                      ..+.++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+|+. +++..+.|+.|.|.+
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   98 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   98 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            3456799999999999999999999999999999999999899999999999999999999997 499999999999998


Q ss_pred             CCcccc
Q psy630           84 SDSHNR   89 (347)
Q Consensus        84 ~~~~~~   89 (347)
                      +.++..
T Consensus        99 a~~~~~  104 (126)
T 3ex7_B           99 CFVRGP  104 (126)
T ss_dssp             SEESSS
T ss_pred             ecCCCC
Confidence            876543

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=9.7e-18  Score=130.19  Aligned_cols=84  Identities=14%  Similarity=0.316  Sum_probs=76.8

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      ....++|||+|||+++|+++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|.+|+.+++..+.|+.|.|.++
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEEC
Confidence            34568999999999999999999999999999877777778999999999999999999999999999999999999988


Q ss_pred             Cccc
Q psy630           85 DSHN   88 (347)
Q Consensus        85 ~~~~   88 (347)
                      .++.
T Consensus       102 ~~~~  105 (124)
T 1wel_A          102 TKKG  105 (124)
T ss_dssp             CHHH
T ss_pred             CHHH
Confidence            6643

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=7.1e-17  Score=123.37  Aligned_cols=83  Identities=28%  Similarity=0.444  Sum_probs=76.4

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      .....++|||+|||+++++++|+++|++||.|..|.|++++ +++++|||||+|.+.++|++|+.. ++..+.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   89 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVK   89 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEE
Confidence            34567899999999999999999999999999999999998 599999999999999999999984 9999999999999


Q ss_pred             CCCcc
Q psy630           83 PSDSH   87 (347)
Q Consensus        83 ~~~~~   87 (347)
                      ++...
T Consensus        90 ~a~~~   94 (114)
T 2do0_A           90 MDERA   94 (114)
T ss_dssp             ECSCC
T ss_pred             EcccC
Confidence            87653

>2dzn_A Probable 26S proteasome regulatory subunit P28; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} SCOP: d.211.1.1 PDB: 2dzo_A 1ixv_A 1wg0_A

Probab=99.70  E-value=7.9e-17  Score=137.93  Aligned_cols=99  Identities=25%  Similarity=0.207  Sum_probs=92.2

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcC-CCccccCCCCCc
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCG-ADVNVTDSDGDY  325 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~g-a~i~~~d~~g~T  325 (347)
                      +.+..+..|.++||+|+..+...++++|++ .|++++.+|..|.||||+|+..|+.+++++|++ .| ++++.+|..|+|
T Consensus        99 ~~~~~~~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~d~~g~t  176 (228)
T 2dzn_A           99 DLNKITNQGVTCLHLAVGKKWFEVSQFLIE-NGASVRIKDKFNQIPLHRAASVGSLKLIELLCG-LGKSAVNWQDKQGWT  176 (228)
T ss_dssp             CTTCCCTTCCCHHHHHHHTTCHHHHHHHHH-TTCCSCCCCTTSCCHHHHHHHTTCHHHHHHHHT-TTCCCSCCCCTTSCC
T ss_pred             ccccCCcCCCCHHHHHHHcCCHhHHHHHHH-cCCCccccCCCCCCHHHHHHHcCCHHHHHHHHh-cCcccccCcCCCCCC
Confidence            456667889999999999999999999998 799999999999999999999999999999999 68 999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHH-hCCC
Q psy630          326 GLDYAKAIEHTDLIEYLV-NSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll-~~GA  347 (347)
                      |||+|+..|+.+++++|+ ++||
T Consensus       177 ~L~~A~~~~~~~~v~~Ll~~~ga  199 (228)
T 2dzn_A          177 PLFHALAEGHGDAAVLLVEKYGA  199 (228)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHCC
T ss_pred             HHHHHHHcCCHHHHHHHHHhcCC
Confidence            999999999999999999 7776

>2vge_A RELA-associated inhibitor; iaspp, nucleus, apoptosis, repressor, cytoplasm, phosphorylation, P53 binding protein, ANK repeat, SH3 domain; 2.10A {Homo sapiens}

Probab=99.70  E-value=9.6e-18  Score=144.50  Aligned_cols=96  Identities=28%  Similarity=0.231  Sum_probs=88.4

Q ss_pred             ccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHH
Q psy630          250 QLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDY  329 (347)
Q Consensus       250 ~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~  329 (347)
                      ..+..+.++||+|+..+..+++++|++ .+++++.+|..|+||||+||..|+.+++++|++ .|+++|.+|..|+||||+
T Consensus        16 ~~~~~~~t~L~~A~~~g~~~~v~~Ll~-~g~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~-~ga~~n~~d~~g~tpLh~   93 (229)
T 2vge_A           16 RARLNPLVLLLDAALTGELEVVQQAVK-EMNDPSQPNEEGITALHNAICGANYSIVDFLIT-AGANVNSPDSHGWTPLHC   93 (229)
T ss_dssp             CTTSCHHHHHHHHHHHTCHHHHHHHHH-HSSCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTCCCHHHH
T ss_pred             ccccchhHHHHHHHHcCCHHHHHHHHh-cCCCCCCCCCCCCCHHHHHHHcCCHHHHHHHHH-CCCCCCCCCCCCCCHHHH
Confidence            345667788999888888888888887 799999999999999999999999999999999 799999999999999999


Q ss_pred             HHHcCCHHHHHHHHhCCC
Q psy630          330 AKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       330 A~~~~~~~~v~~Ll~~GA  347 (347)
                      |+..|+.+++++|+++||
T Consensus        94 A~~~g~~~~v~~Ll~~ga  111 (229)
T 2vge_A           94 AASCNDTVICMALVQHGA  111 (229)
T ss_dssp             HHHTTCHHHHHHHHTTTC
T ss_pred             HHHcCCHHHHHHHHHcCC
Confidence            999999999999999986

>3f6q_A Integrin-linked protein kinase; ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK, IPP; 1.60A {Homo sapiens} PDB: 3ixe_A 2kbx_A

Probab=99.70  E-value=1.6e-17  Score=137.22  Aligned_cols=100  Identities=25%  Similarity=0.301  Sum_probs=94.7

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      .+.+..+..|.|+||+|+..+...++++|++ .+++++.+|..|.||||+|+..|+.+++++|++ +|++++.+|..|.|
T Consensus        63 ~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~d~~g~t~L~~A~~~~~~~~v~~Ll~-~ga~~~~~~~~g~t  140 (179)
T 3f6q_A           63 ARINVMNRGDDTPLHLAASHGHRDIVQKLLQ-YKADINAVNEHGNVPLHYACFWGQDQVAEDLVA-NGALVSICNKYGEM  140 (179)
T ss_dssp             CCTTCCCTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCSSBCCTTSCC
T ss_pred             CCCCCcCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCccCCCCCCHHHHHHHcCCHHHHHHHHH-CCCCcchhccCCCC
Confidence            3567778889999999999999999999999 799999999999999999999999999999999 79999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|+..++.+++++|+++||
T Consensus       141 pl~~A~~~~~~~~~~~L~~~g~  162 (179)
T 3f6q_A          141 PVDKAKAPLRELLRERAEKMGQ  162 (179)
T ss_dssp             GGGGSCHHHHHHHHHHHHHTTC
T ss_pred             cHHHHHHHHHHHHHHHHHHhhc
Confidence            9999999999999999999986

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=3e-17  Score=124.32  Aligned_cols=82  Identities=28%  Similarity=0.664  Sum_probs=75.2

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      .....++|||+|||+++++++|+++|++||.|..+++++++  +.++|||||+|.+.++|++|+.. ++..+.|+.|.|.
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  102 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN  102 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45567899999999999999999999999999999999886  45899999999999999999985 9999999999999


Q ss_pred             CCCcc
Q psy630           83 PSDSH   87 (347)
Q Consensus        83 ~~~~~   87 (347)
                      ++.++
T Consensus       103 ~a~~~  107 (109)
T 2err_A          103 NATAR  107 (109)
T ss_dssp             ECCCS
T ss_pred             ECCCC
Confidence            88764

>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=99.69  E-value=7.4e-17  Score=130.41  Aligned_cols=85  Identities=18%  Similarity=0.370  Sum_probs=79.1

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      ....++|||+|||+++|+++|+++|++||.|..|.|++++.++.++|||||+|.+.++|++|+.. ++..|.|+.|.|.+
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  115 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW  115 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34678999999999999999999999999999999999999999999999999999999999984 99999999999999


Q ss_pred             CCcccc
Q psy630           84 SDSHNR   89 (347)
Q Consensus        84 ~~~~~~   89 (347)
                      +.+...
T Consensus       116 a~~~~~  121 (156)
T 1h2v_Z          116 DAGFKE  121 (156)
T ss_dssp             ESCCCT
T ss_pred             CCCCCC
Confidence            876443

>1ikn_D Protein (I-kappa-B-alpha), protein (NF-kappa-B P50D subunit); transcription factor, IKB/NFKB complex; 2.30A {Homo sapiens} SCOP: d.211.1.1 PDB: 1nfi_E

Probab=99.69  E-value=2.6e-17  Score=142.05  Aligned_cols=97  Identities=23%  Similarity=0.219  Sum_probs=91.3

Q ss_pred             cccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCC-CCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHH
Q psy630          249 SQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDE-NGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGL  327 (347)
Q Consensus       249 ~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~-~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpL  327 (347)
                      +..+..|.++||+|+..+...++++|++ .|++++.++. .|.||||+|+..|+.+++++|++ +|++++.+|..|.|||
T Consensus       111 ~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~~g~tpL~~A~~~~~~~~v~~Ll~-~ga~~~~~~~~g~tpl  188 (236)
T 1ikn_D          111 KATNYNGHTCLHLASIHGYLGIVELLVS-LGADVNAQEPCNGRTALHLAVDLQNPDLVSLLLK-CGADVNRVTYQGYSPY  188 (236)
T ss_dssp             GCCCTTCCCHHHHHHHTTCHHHHHHHHH-HTCCTTCCCTTTCCCHHHHHHHTTCHHHHHHHHT-TTCCSCCCCTTCCCGG
T ss_pred             hccCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCCCCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCcccCCCCCHH
Confidence            4456788999999999999999999998 7999999998 99999999999999999999999 7999999999999999


Q ss_pred             HHHHHcCCHHHHHHHHhCCC
Q psy630          328 DYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       328 h~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |+|+..|+.+++++|+++||
T Consensus       189 ~~A~~~~~~~~~~~Ll~~ga  208 (236)
T 1ikn_D          189 QLTWGRPSTRIQQQLGQLTL  208 (236)
T ss_dssp             GGCTTSSCHHHHHHHHTTSC
T ss_pred             HHHHccCchHHHHHHHHcch
Confidence            99999999999999999997

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.69  E-value=4.1e-18  Score=127.37  Aligned_cols=84  Identities=24%  Similarity=0.353  Sum_probs=76.7

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      ....++|||+|||+++++++|+++|++||.|.. .++.++.+|.++|||||+|.+.++|.+|+++++..+.|+.|.|.++
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEEEc
Confidence            346789999999999999999999999999988 6777777899999999999999999999999999999999999999


Q ss_pred             Ccccc
Q psy630           85 DSHNR   89 (347)
Q Consensus        85 ~~~~~   89 (347)
                      .++..
T Consensus        93 ~~~~~   97 (101)
T 1fj7_A           93 KGRDG   97 (101)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87654

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.69  E-value=3.9e-17  Score=129.54  Aligned_cols=81  Identities=23%  Similarity=0.400  Sum_probs=75.3

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~   82 (347)
                      .....++|||+|||+++++++|+++|++||.|..+++++++.+|+++|||||+|.+.++|.+|++ +++..+.|+.|+|.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999997 59999999999997


Q ss_pred             CC
Q psy630           83 PS   84 (347)
Q Consensus        83 ~~   84 (347)
                      +|
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            64

>3aji_A 26S proteasome non-ATPase regulatory subunit 10; gankyrin, S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dvw_A 2dwz_A* 1tr4_A 1uoh_A 1qym_A

Probab=99.69  E-value=9.8e-17  Score=137.69  Aligned_cols=98  Identities=22%  Similarity=0.318  Sum_probs=69.0

Q ss_pred             CcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHH
Q psy630          248 ESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGL  327 (347)
Q Consensus       248 ~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpL  327 (347)
                      .+..+..|.++||+|+..+..+++++|++ .+++++.+|..|.||||+|+..|+.+++++|++ +|++++.+|..|.|||
T Consensus        99 ~~~~~~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L  176 (231)
T 3aji_A           99 VNAVNQNGCTPLHYAASKNRHEIAVMLLE-GGANPDAKDHYDATAMHRAAAKGNLKMVHILLF-YKASTNIQDTEGNTPL  176 (231)
T ss_dssp             TTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCSCCCCTTSCCHH
T ss_pred             CCCCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCCcCCCCCcHHHHHHHcCCHHHHHHHHh-cCCCccccCCCCCCHH
Confidence            44455666777777776666667776666 567777777777777777777777777777776 5777777777777777


Q ss_pred             HHHHHcCCHHHHHHHHhCCC
Q psy630          328 DYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       328 h~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |+|+..|+.+++++|+++||
T Consensus       177 ~~A~~~~~~~~v~~Ll~~ga  196 (231)
T 3aji_A          177 HLACDEERVEEAKFLVTQGA  196 (231)
T ss_dssp             HHHHHTTCHHHHHHHHHTTC
T ss_pred             HHHHHCCCHHHHHHHHHCCC
Confidence            77777777777777777665

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.3e-17  Score=125.83  Aligned_cols=77  Identities=16%  Similarity=0.346  Sum_probs=72.2

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCCc
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~~   86 (347)
                      .++|||+|||+++|+++|+++|++| .|..|+|++++. |+++|||||+|.+.++|++|+.+++..+.||.|.|..+.+
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCc
Confidence            4689999999999999999999999 899999999986 9999999999999999999998899999999999987754

>3hra_A Ankyrin repeat family protein; structural protein; 1.69A {Enterococcus faecalis}

Probab=99.69  E-value=1.1e-16  Score=134.45  Aligned_cols=99  Identities=24%  Similarity=0.211  Sum_probs=91.6

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCC-----HHHHHHHHhhcCCCccccCC
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGH-----LKVVQHLIEKCGADVNVTDS  321 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~-----~~~v~~Ll~~~ga~i~~~d~  321 (347)
                      +.+..+..+.+++|+|+..+...++++|++..+.+++.+|..|+||||+|+..+.     .+++++|++ .|++++.+|.
T Consensus        98 ~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~~g~~~~~~~~~~g~t~L~~A~~~~~~~~~~~~~v~~Ll~-~ga~~~~~~~  176 (201)
T 3hra_A           98 DLNKHNRYGGNALIPAAEKGHIDNVKLLLEDGREDIDFQNDFGYTALIEAVGLREGNQLYQDIVKLLME-NGADQSIKDN  176 (201)
T ss_dssp             CTTCCCTTSCCSHHHHHHTTCHHHHHHHHHHCCCCTTCCCTTSCCHHHHHHHSSCCSHHHHHHHHHHHH-TTCCTTCCCT
T ss_pred             ccccccCCCCcHHHHHHHcCCHHHHHHHHHcCCCCcCCCCCCCCCHHHHHHHhccchhhHHHHHHHHHH-CCCCCCccCC
Confidence            4566778899999999999999999999984449999999999999999999998     999999999 7999999999


Q ss_pred             CCCcHHHHHHHcCCHHHHHHHHhCC
Q psy630          322 DGDYGLDYAKAIEHTDLIEYLVNSG  346 (347)
Q Consensus       322 ~g~TpLh~A~~~~~~~~v~~Ll~~G  346 (347)
                      .|.||||+|+..|+.+++++|+++|
T Consensus       177 ~g~t~l~~A~~~~~~~~~~~Ll~~G  201 (201)
T 3hra_A          177 SGRTAMDYANQKGYTEISKILAQYN  201 (201)
T ss_dssp             TSCCHHHHHHHHTCHHHHHHHHTCC
T ss_pred             CCCCHHHHHHHcCCHhHHHHHHhcC
Confidence            9999999999999999999999987

>2f8y_A Notch homolog 1, translocation-associated (drosophila); ankyrin repeats, transcription; 1.55A {Homo sapiens} PDB: 2qc9_A 1ymp_A

Probab=99.69  E-value=1.1e-16  Score=136.74  Aligned_cols=99  Identities=16%  Similarity=0.230  Sum_probs=92.5

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..+.+++|+|+..+...++++|++ .+++++..|..|.||||+|+..|+.+++++|++ .|++++.+|..|.||
T Consensus        84 ~~~~~~~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~  161 (223)
T 2f8y_A           84 DLDARMHDGTTPLILAARLAVEGMLEDLIN-SHADVNAVDDLGKSALHWAAAVNNVDAAVVLLK-NGANKDMQNNREETP  161 (223)
T ss_dssp             CTTCCCTTCCCHHHHHHHHTCHHHHHHHHH-TTCCTTCBCTTSCBHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTCCCH
T ss_pred             CcccCCCCCCcHHHHHHHhCcHHHHHHHHH-cCCCCcCcCCCCCcHHHHHHHcCCHHHHHHHHH-cCCCCCCcCCCCcCH
Confidence            345566788999999999888889999998 899999999999999999999999999999999 699999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+..|+.+++++|+++||
T Consensus       162 L~~A~~~~~~~~v~~Ll~~ga  182 (223)
T 2f8y_A          162 LFLAAREGSYETAKVLLDHFA  182 (223)
T ss_dssp             HHHHHHHTCHHHHHHHHHTTC
T ss_pred             HHHHHHcCCHHHHHHHHHcCC
Confidence            999999999999999999986

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.69  E-value=4.1e-17  Score=126.68  Aligned_cols=84  Identities=27%  Similarity=0.457  Sum_probs=77.8

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~   82 (347)
                      .....++|||+|||+++++++|+++|++||.|..|+|++++ +|+++|||||+|.+.++|.+|+. +++..+.|+.|.|.
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            44566899999999999999999999999999999999998 89999999999999999999998 59999999999999


Q ss_pred             CCCccc
Q psy630           83 PSDSHN   88 (347)
Q Consensus        83 ~~~~~~   88 (347)
                      ++.+..
T Consensus       110 ~a~~~~  115 (124)
T 2kt5_A          110 LVASQI  115 (124)
T ss_dssp             EECCTT
T ss_pred             EeCCCC
Confidence            887644

>3utm_A Tankyrase-1; tankyrase, TNKS, ankryin repeat clusters, WNT signaling, POL ribosylation, transferase-signaling protein complex; 2.00A {Mus musculus}

Probab=99.69  E-value=1.3e-16  Score=145.31  Aligned_cols=99  Identities=24%  Similarity=0.278  Sum_probs=93.8

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..|.|+||+|+..+...++++|++ .|++++.+|..|+||||+|+..|+.+++++|++ +|++++..|..|.||
T Consensus        50 ~~~~~d~~g~t~L~~A~~~g~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~g~~~iv~~Ll~-~g~~~~~~~~~g~t~  127 (351)
T 3utm_A           50 NCHASDGRKSTPLHLAAGYNRVRIVQLLLQ-HGADVHAKDKGGLVPLHNACSYGHYEVTELLLK-HGACVNAMDLWQFTP  127 (351)
T ss_dssp             TCCCSSTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTCCCH
T ss_pred             CcccCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCccCCCCCcHHHHHHHCCCHHHHHHHHH-CCCCCCCCCCCCCCH
Confidence            456677889999999999999999999999 799999999999999999999999999999999 799999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+..|+.+++++|+++||
T Consensus       128 L~~A~~~~~~~~v~~Ll~~g~  148 (351)
T 3utm_A          128 LHEAASKNRVEVCSLLLSHGA  148 (351)
T ss_dssp             HHHHHHTTCHHHHHHHHHTTC
T ss_pred             HHHHHHcCCHHHHHHHHHcCC
Confidence            999999999999999999986

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.69  E-value=4.1e-17  Score=122.72  Aligned_cols=80  Identities=21%  Similarity=0.336  Sum_probs=73.0

Q ss_pred             CCCeEEEeCCCCCC------CHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCc-c
Q psy630            7 QLNKIFVGNLPWTV------SHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGS-R   78 (347)
Q Consensus         7 ~~~~l~V~nLp~~~------t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~-~   78 (347)
                      ..++|||+|||+.+      ++++|+++|++||.|..|.|+  +.+|+++|||||+|.+.++|.+|+.. |+..+.|+ +
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~   91 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT   91 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCE
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCce
Confidence            35799999999999      789999999999999999998  45799999999999999999999985 99999998 9


Q ss_pred             ccccCCCccc
Q psy630           79 LSIQPSDSHN   88 (347)
Q Consensus        79 l~v~~~~~~~   88 (347)
                      |.|.++....
T Consensus        92 l~V~~a~~~~  101 (105)
T 2nlw_A           92 FRVNLFTDFD  101 (105)
T ss_dssp             EEEECSCCCC
T ss_pred             EEEEEcchHh
Confidence            9999987643

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=2.5e-17  Score=126.90  Aligned_cols=80  Identities=19%  Similarity=0.262  Sum_probs=73.5

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCe----eEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccc
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQI----MNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSI   81 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i----~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v   81 (347)
                      .+.++|||+|||+++|+++|+++|++||.|    ..|+|++++ +|+++|||||+|.+.++|++|+..++..+.||.|.|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~V   99 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIEL   99 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEE
Confidence            456899999999999999999999999975    689999985 899999999999999999999999999999999999


Q ss_pred             cCCCc
Q psy630           82 QPSDS   86 (347)
Q Consensus        82 ~~~~~   86 (347)
                      ..+.+
T Consensus       100 ~~a~~  104 (123)
T 2dha_A          100 FRSTA  104 (123)
T ss_dssp             EEECH
T ss_pred             EECCH
Confidence            87754

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.69  E-value=3.9e-17  Score=115.80  Aligned_cols=73  Identities=12%  Similarity=0.277  Sum_probs=68.1

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      ....|||+||++.+|+++|+++|.+||+|.++++..      ++|||||+|.+.++|.+|++. |+..+.|++|+|..|.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            467899999999999999999999999999999864      689999999999999999986 9999999999999883

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=1e-16  Score=122.45  Aligned_cols=81  Identities=21%  Similarity=0.511  Sum_probs=72.1

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccC--------
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLE--------   75 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~--------   75 (347)
                      ..+.++|||+|||+++++++|+++|++||.|..++|++++ ++.++|||||+|.+.++|.+|+.. |+..+.        
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            3466899999999999999999999999999999999998 899999999999999999999984 999984        


Q ss_pred             CccccccCCCc
Q psy630           76 GSRLSIQPSDS   86 (347)
Q Consensus        76 g~~l~v~~~~~   86 (347)
                      +++|.|.++.+
T Consensus       101 ~~~l~v~~a~p  111 (114)
T 1x5o_A          101 TEPLLCKFSGP  111 (114)
T ss_dssp             SSCBEEEECCC
T ss_pred             CCceeEEccCC
Confidence            55566666654

>1oy3_D Transcription factor inhibitor I-kappa-B-beta; protein-protein complex, transcription factors, nuclear localization, DNA binding protein; 2.05A {Mus musculus} SCOP: d.211.1.1 PDB: 1k3z_D

Probab=99.69  E-value=5e-17  Score=143.61  Aligned_cols=97  Identities=18%  Similarity=0.202  Sum_probs=90.0

Q ss_pred             cccCCCCCcHHHHHHcCChHHHHHHHhhcCCCC---ccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          249 SQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFN---INQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       249 ~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~---~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      +..+..|.|+||+|+..+...++++|+. .+.+   ++.+|..|+||||+||..|+.+++++|++ +|++++.+|..|+|
T Consensus         3 ~~~d~~g~t~L~~A~~~g~~~~v~~Ll~-~g~~~~~~~~~~~~g~t~L~~A~~~g~~~~v~~Ll~-~ga~~~~~~~~g~t   80 (282)
T 1oy3_D            3 GYVTEDGDTALHLAVIHQHEPFLDFLLG-FSAGHEYLDLQNDLGQTALHLAAILGEASTVEKLYA-AGAGVLVAERGGHT   80 (282)
T ss_dssp             CCCCTTCCCHHHHHHHTTCHHHHHHHHH-HHTTSGGGGCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCSSCCCTTSCC
T ss_pred             CccCCCCCcHHHHHHHcCCHHHHHHHHh-cCCCcccccccCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCCCCCCCCC
Confidence            4567899999999999999999999987 5666   88999999999999999999999999999 79999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|+..|+.+++++|+++|+
T Consensus        81 pL~~A~~~~~~~~v~~Ll~~~~  102 (282)
T 1oy3_D           81 ALHLACRVRAHTCACVLLQPRP  102 (282)
T ss_dssp             HHHHHTTTTCHHHHHHHSSSCC
T ss_pred             HHHHHHHcCCcchhHhhhccCC
Confidence            9999999999999999999875

>3ehr_A Osteoclast-stimulating factor 1; beta barrel, helix-turn-helix, SH3, ankyrin repeat, signaling protein, ANK repeat, cytoplasm, phosphoprotein; 1.95A {Homo sapiens} PDB: 3ehq_A

Probab=99.69  E-value=1.7e-17  Score=141.98  Aligned_cols=100  Identities=22%  Similarity=0.305  Sum_probs=87.8

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..|.|+||+|+..+...++++|+...+++++.+|..|+||||+|+..|+.+++++||+ .|++++.+|..|.||
T Consensus        98 ~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~~~g~~~~~~d~~g~tpL~~A~~~~~~~~v~~Ll~-~ga~~~~~~~~g~t~  176 (222)
T 3ehr_A           98 GVNGLDKAGSTALYWACHGGHKDIVEMLFTQPNIELNQQNKLGDTALHAAAWKGYADIVQLLLA-KGARTDLRNIEKKLA  176 (222)
T ss_dssp             CTTCCCTTSCCHHHHHHHTTCHHHHHHHTTSTTCCCCCCCTTSCCHHHHHHHHTCHHHHHHHHH-HTCCSCCCCTTSCCH
T ss_pred             CccccCCCCCCHHHHHHHcCCHHHHHHHHcCCCCCccccCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCccccCCCCCH
Confidence            4566778899999999999999999999994499999999999999999999999999999999 699999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+..++.++++.|+..||
T Consensus       177 l~~A~~~~~~~~l~~l~~~~~  197 (222)
T 3ehr_A          177 FDMATNAACASLLKKKQGTDA  197 (222)
T ss_dssp             HHHCCSHHHHHHHC-------
T ss_pred             HHHhcchhHHHHHHHHhccch
Confidence            999999999999999998875

>2rfa_A Transient receptor potential cation channel subfa member 6; TRPV6, ankyrin reapeat, ANK RE calcium channel, calcium transport, calmodulin-binding; 1.70A {Mus musculus}

Probab=99.69  E-value=1.5e-16  Score=136.69  Aligned_cols=97  Identities=21%  Similarity=0.190  Sum_probs=89.5

Q ss_pred             cccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCC-------------CCchHHHHHHHcCCHHHHHHHHhhcCCC
Q psy630          249 SQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDE-------------NGLNCLHWACDRGHLKVVQHLIEKCGAD  315 (347)
Q Consensus       249 ~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~-------------~g~tpLh~A~~~g~~~~v~~Ll~~~ga~  315 (347)
                      +..+..|.|+||+|+..+..+++++|++ .+++++..+.             .|.||||+|+..|+.+++++|++ .|++
T Consensus        69 ~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~~~~~~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~ga~  146 (232)
T 2rfa_A           69 TSELYEGQTALHIAVINQNVNLVRALLA-RGASVSARATGSVFHYRPHNLIYYGEHPLSFAACVGSEEIVRLLIE-HGAD  146 (232)
T ss_dssp             CSTTTTTCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCCSGGGSCCTTCSCCCCSSHHHHHHHHTCHHHHHHHHH-TTCC
T ss_pred             cccCCCCcCHHHHHHHcCCHHHHHHHHh-CCCCCCcccCCcceeecccccccCCCCHHHHHHHcCCHHHHHHHHH-CCCC
Confidence            4456789999999999999999999999 7999988765             79999999999999999999999 7999


Q ss_pred             ccccCCCCCcHHHHHHHcCCHHHH----HHHHhCCC
Q psy630          316 VNVTDSDGDYGLDYAKAIEHTDLI----EYLVNSGS  347 (347)
Q Consensus       316 i~~~d~~g~TpLh~A~~~~~~~~v----~~Ll~~GA  347 (347)
                      ++.+|..|+||||+|+..|+.+++    ++|+++||
T Consensus       147 ~~~~d~~g~t~L~~A~~~~~~~~~~~i~~~Ll~~g~  182 (232)
T 2rfa_A          147 IRAQDSLGNTVLHILILQPNKTFACQMYNLLLSYDG  182 (232)
T ss_dssp             TTCCCTTSCCHHHHHHTCSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCCCHHHHHHHcCChHHHHHHHHHHHhcCC
Confidence            999999999999999999999988    99999986

>1ikn_D Protein (I-kappa-B-alpha), protein (NF-kappa-B P50D subunit); transcription factor, IKB/NFKB complex; 2.30A {Homo sapiens} SCOP: d.211.1.1 PDB: 1nfi_E

Probab=99.69  E-value=1.5e-16  Score=137.26  Aligned_cols=100  Identities=29%  Similarity=0.375  Sum_probs=90.7

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCC------ccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCcccc
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFN------INQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVT  319 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~------~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~  319 (347)
                      .+++..+..|.++||+|+..+...++++|+. .+.+      ++..+..|.||||+|+..|+.+++++|++ .|++++.+
T Consensus        69 ~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~~~~~~~~~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~  146 (236)
T 1ikn_D           69 CDPELRDFRGNTPLHLACEQGCLASVGVLTQ-SCTTPHLHSILKATNYNGHTCLHLASIHGYLGIVELLVS-LGADVNAQ  146 (236)
T ss_dssp             CCSCCCCTTCCCHHHHHHHHTCHHHHHHHHH-STTTTSSSCGGGCCCTTCCCHHHHHHHTTCHHHHHHHHH-HTCCTTCC
T ss_pred             CCCCCcCCCCCCHHHHHHHcCCHHHHHHHHh-cccchhHHHHhhccCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCCC
Confidence            3567778899999999999888889999988 5543      57788899999999999999999999999 79999999


Q ss_pred             CC-CCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          320 DS-DGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       320 d~-~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      +. .|.||||+|+..|+.+++++|+++||
T Consensus       147 ~~~~g~tpL~~A~~~~~~~~v~~Ll~~ga  175 (236)
T 1ikn_D          147 EPCNGRTALHLAVDLQNPDLVSLLLKCGA  175 (236)
T ss_dssp             CTTTCCCHHHHHHHTTCHHHHHHHHTTTC
T ss_pred             CCCCCCCHHHHHHHcCCHHHHHHHHHcCC
Confidence            98 99999999999999999999999986

>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=99.69  E-value=3e-17  Score=124.80  Aligned_cols=83  Identities=18%  Similarity=0.307  Sum_probs=75.8

Q ss_pred             cCCCeEEEeCCCCCCCHHHHH---HHHhccCCeeEEEEeeeCCCC---CceeEEEEEEcCHHHHHHHHhc-CCCccCCcc
Q psy630            6 RQLNKIFVGNLPWTVSHNELK---KFFSEYGQIMNASVMFDKNTG---LSKGFGFVTFQNKEAVDKVFST-DSHVLEGSR   78 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~---~~f~~~G~i~~~~i~~~~~t~---~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~   78 (347)
                      .+.++|||+|||+++++++|+   ++|++||.|..|.|++++.++   .++|||||+|.+.++|++|+.. |+..+.|+.
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~   92 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   92 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEE
Confidence            456799999999999999999   999999999999999988754   5669999999999999999996 999999999


Q ss_pred             ccccCCCccc
Q psy630           79 LSIQPSDSHN   88 (347)
Q Consensus        79 l~v~~~~~~~   88 (347)
                      |.|.++.++.
T Consensus        93 l~V~~a~~k~  102 (111)
T 2cpi_A           93 LKASLGTTKY  102 (111)
T ss_dssp             EEEESCCCCS
T ss_pred             EEEEeccccc
Confidence            9999998765

>3ljn_A Hypothetical protein; ankyrin, structural genomics, PSI, structural genomics of pathogenic protozoa consortium, SGPP, ANK repeat; 2.90A {Leishmania major}

Probab=99.69  E-value=6.2e-17  Score=148.84  Aligned_cols=100  Identities=18%  Similarity=0.193  Sum_probs=93.1

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCC-----ccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccC
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFN-----INQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTD  320 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~-----~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d  320 (347)
                      .+++..+..|.|+||+|+..+..+++++|++ .+++     ++..|..|+||||+||..|+.+++++||+ +|++++.+|
T Consensus       164 a~~~~~d~~g~t~L~~A~~~g~~~~v~~Ll~-~g~~~~~~~~~~~~~~g~t~L~~A~~~g~~~~v~~Ll~-~gad~~~~d  241 (364)
T 3ljn_A          164 ASPTAKDKADETPLMRAMEFRNREALDLMMD-TVPSKSSLRLDYANKQGNSHLHWAILINWEDVAMRFVE-MGIDVNMED  241 (364)
T ss_dssp             CCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-HCSCSSSCCTTCCCTTCCCTTHHHHTTTCHHHHHHHHT-TTCCTTCCC
T ss_pred             CCCcccCCCCCCHHHHHHHcCCHHHHHHHHh-cccccccccccccCCCCCcHHHHHHHcCCHHHHHHHHH-cCCCCCCCC
Confidence            4677888899999999999999999999998 6777     99999999999999999999999999999 799999999


Q ss_pred             CCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          321 SDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       321 ~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ..|.||||+|+..|+.+++++|+++||
T Consensus       242 ~~g~tpL~~A~~~g~~~~v~~Ll~~~~  268 (364)
T 3ljn_A          242 NEHTVPLYLSVRAAMVLLTKELLQKTD  268 (364)
T ss_dssp             TTSCCHHHHHHHTCCHHHHHHHHHHSC
T ss_pred             CCCCCHHHHHHHhChHHHHHHHHHcCC
Confidence            999999999999999999999999875

>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=99.68  E-value=4.3e-17  Score=132.14  Aligned_cols=84  Identities=27%  Similarity=0.516  Sum_probs=78.3

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~~   84 (347)
                      ...++|||+|||+++++++|+++|++||.|..|++++++.+|.++|||||+|.+.++|.+|+. +++..+.|++|.|.++
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  147 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  147 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            446899999999999999999999999999999999999899999999999999999999998 4999999999999998


Q ss_pred             Ccccc
Q psy630           85 DSHNR   89 (347)
Q Consensus        85 ~~~~~   89 (347)
                      .++..
T Consensus       148 ~~~~~  152 (158)
T 2kn4_A          148 RYGRP  152 (158)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            77543

>1ycs_B 53BP2, P53BP2; ankyrin repeats, SH3, tumor suppressor, multigene family, nuclear protein, phosphorylation, disease mutation, polymorphism; 2.20A {Homo sapiens} SCOP: b.34.2.1 d.211.1.1 PDB: 4a63_B

Probab=99.68  E-value=1.7e-17  Score=143.84  Aligned_cols=99  Identities=23%  Similarity=0.213  Sum_probs=92.1

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCC-c
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGD-Y  325 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~-T  325 (347)
                      +.+..+..|.|+||+|+..++..++++|+. .++++|.+|..|+||||+||..|+.+++++|++ +|++++.++..|. |
T Consensus        62 ~~~~~d~~g~t~L~~A~~~g~~~~v~~Ll~-~ga~~~~~d~~g~tpL~~A~~~~~~~~v~~Ll~-~ga~~~~~~~~~~~t  139 (239)
T 1ycs_B           62 DPSLPNDEGITALHNAVCAGHTEIVKFLVQ-FGVNVNAADSDGWTPLHCAASCNNVQVCKFLVE-SGAAVFAMTYSDMQT  139 (239)
T ss_dssp             SCCCCCTTSCCHHHHHHHHTCHHHHHHHHH-HTCCTTCCCTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCSSSCCC
T ss_pred             CCCCcCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCccCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCcceecCCCCcc
Confidence            567778899999999999999999999998 799999999999999999999999999999999 7999999998877 9


Q ss_pred             HHHHH--HHcCCHHHHHHHHhCCC
Q psy630          326 GLDYA--KAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A--~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|  +..|+.+++++|+++||
T Consensus       140 ~l~~a~~~~~g~~~~~~~Ll~~~a  163 (239)
T 1ycs_B          140 AADKCEEMEEGYTQCSQFLYGVQE  163 (239)
T ss_dssp             HHHHCCSSSTTCCCHHHHHHHHHH
T ss_pred             hHHHHHHhhhccHHHHHHHHHhhh
Confidence            99999  78899999999998764

>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=99.68  E-value=2.1e-17  Score=130.00  Aligned_cols=82  Identities=16%  Similarity=0.267  Sum_probs=74.3

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      +...++|||+|||+++|+++|+++|++|| |..|+|++++. |+++|||||+|.+.++|++|+.+++..+.|+.|.|..+
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLN  120 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEEC
Confidence            45667999999999999999999999999 77999999986 99999999999999999999977999999999999887


Q ss_pred             Cccc
Q psy630           85 DSHN   88 (347)
Q Consensus        85 ~~~~   88 (347)
                      .+..
T Consensus       121 ~~~~  124 (139)
T 2hgn_A          121 STTG  124 (139)
T ss_dssp             CCSC
T ss_pred             CCCC
Confidence            7644

>3t8k_A Uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center F or structural genomics, MCSG; 1.77A {Leptotrichia buccalis}

Probab=99.68  E-value=8.6e-18  Score=140.01  Aligned_cols=101  Identities=12%  Similarity=0.077  Sum_probs=84.7

Q ss_pred             cccCCcccCCCCCcHHHHHHcCCh------HHHHHHHhhcCCCCccccCCCCc-hHHHHHHHcC-----CHHHHHHHHhh
Q psy630          244 MINDESQLDDNEKNIYEWAKEGKL------DMLVKQLTKLKDFNINQLDENGL-NCLHWACDRG-----HLKVVQHLIEK  311 (347)
Q Consensus       244 ~~~~~~~~~~~~~~~l~~a~~~~~------~~~~~lL~~~~~~~~~~~d~~g~-tpLh~A~~~g-----~~~~v~~Ll~~  311 (347)
                      ...+++..+..|.||||+|+..+.      .+++++|+. .|+++|.+|..|+ ||||+|+..+     +.+++++||++
T Consensus        64 ~Gadvn~~d~~g~TpLh~a~~~~~~~~~~~~~iv~~Ll~-~Gadin~~d~~g~ttpLh~A~~~~~~~~~~~~iv~~Ll~~  142 (186)
T 3t8k_A           64 KGADIKSRTKEGTTLFFPLFQGGGNDITGTTELCKIFLE-KGADITALYKPYKIVVFKNIFNYFVDENEMIPLYKLIFSQ  142 (186)
T ss_dssp             TTCCSSCCCTTCCCTHHHHHHHCTTCHHHHHHHHHHHHH-TTCCSSSCBGGGTBCTTGGGGGCCSCHHHHHHHHHHHHTS
T ss_pred             CCCCCCCCCCCCCcHHHHHHHcCCcchhhHHHHHHHHHH-CCCCCCccCCCcCchHHHHHHHcCCChhhHHHHHHHHHHh
Confidence            345788888999999998876554      467888888 7999999999999 9999999854     35688999973


Q ss_pred             cCCCccccCCCCCcHHHHHHHcCCHHHHHHHHhC
Q psy630          312 CGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNS  345 (347)
Q Consensus       312 ~ga~i~~~d~~g~TpLh~A~~~~~~~~v~~Ll~~  345 (347)
                      +|++++.+|..|.||||+|+..|+.++|++|++.
T Consensus       143 ~gad~~~~d~~G~TpL~~A~~~~~~~~v~~L~~~  176 (186)
T 3t8k_A          143 SGLQLLIKDKWGLTALEFVKRCQKPIALKMMEDY  176 (186)
T ss_dssp             TTCCTTCCCTTSCCHHHHHHTTTCHHHHHHHHHH
T ss_pred             cCCCCcccCCCCCCHHHHHHHcCCHHHHHHHHHH
Confidence            4999999999999999999999999999998764

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.68  E-value=8.1e-17  Score=124.83  Aligned_cols=82  Identities=17%  Similarity=0.309  Sum_probs=72.9

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHH----HHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELK----KFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRL   79 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~----~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l   79 (347)
                      ....++|||+|||+.+++++|+    ++|++||.|..|.+.+   +++++|||||+|.+.++|..|+.. |+..+.|++|
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l  102 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPL  102 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEE
Confidence            3456899999999999999876    6999999999988753   688999999999999999999975 9999999999


Q ss_pred             cccCCCcccc
Q psy630           80 SIQPSDSHNR   89 (347)
Q Consensus        80 ~v~~~~~~~~   89 (347)
                      .|.++.++..
T Consensus       103 ~V~~a~~~~~  112 (127)
T 2a3j_A          103 VITFSETPQS  112 (127)
T ss_dssp             EEEECCCCCH
T ss_pred             EEEEccCcch
Confidence            9999987654

>1k1a_A B-cell lymphoma 3-encoded protein; BCL-3, NF-kappab transcription factors, ikappab proteins; 1.86A {Homo sapiens} SCOP: d.211.1.1 PDB: 1k1b_A

Probab=99.68  E-value=1.6e-16  Score=137.13  Aligned_cols=99  Identities=25%  Similarity=0.289  Sum_probs=79.3

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccC-CCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLD-ENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d-~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      +.+..+..+.+++|+|+..+..+++++|++ .+++++..+ ..|.||||+|+..|+.+++++|++ +|++++.+|..|+|
T Consensus       108 ~~~~~~~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t  185 (241)
T 1k1a_A          108 DLEARNYDGLTALHVAVNTECQETVQLLLE-RGADIDAVDIKSGRSPLIHAVENNSLSMVQLLLQ-HGANVNAQMYSGSS  185 (241)
T ss_dssp             CTTCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCBCTTSCB
T ss_pred             cccccCcCCCcHHHHHHHcCCHHHHHHHHH-cCCCcccccccCCCcHHHHHHHcCCHHHHHHHHH-cCCCCCCcCCCCCC
Confidence            344556677888888887777778888777 678888877 678888888888888888888887 68888888888888


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|+..|+.+++++|+++||
T Consensus       186 ~L~~A~~~~~~~~v~~Ll~~ga  207 (241)
T 1k1a_A          186 ALHSASGRGLLPLVRTLVRSGA  207 (241)
T ss_dssp             HHHHHHHHTCHHHHHHHHHTTC
T ss_pred             HHHHHHHcCCHHHHHHHHhcCC
Confidence            8888888888888888888875

>4g8k_A 2-5A-dependent ribonuclease; ankyrin-repeat domain, single-stranded RNA, hydrolase; 2.40A {Homo sapiens} PDB: 4g8l_A*

Probab=99.68  E-value=1.1e-16  Score=145.67  Aligned_cols=96  Identities=23%  Similarity=0.215  Sum_probs=88.0

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      .+++..+..|.|+||+|+..+...++++|+...++++|.+|..|+||||+||..|+.++|++||+ +||++|.+     |
T Consensus       230 ad~n~~d~~g~t~L~~a~~~~~~~~v~~Ll~~~~~~vn~~d~~G~TpL~~A~~~g~~~iv~~Ll~-~GAd~n~~-----~  303 (337)
T 4g8k_A          230 ADVNVRGERGKTPLILAVEKKHLGLVQRLLEQEHIEINDTDSDGKTALLLAVELKLKKIAELLCK-RGASTDCG-----D  303 (337)
T ss_dssp             CCTTCCCGGGCCHHHHHHHTTCHHHHHHHHTSTTCCTTCBCTTSCBHHHHHHHTTCHHHHHHHHT-TSCSSTTC-----C
T ss_pred             CCCCCcCCCCCCHHHHHHHhhhhHHHHHHHHhcCCcccCcCCCCCCHHHHHHHcCCHHHHHHHHH-CCCCCCCC-----C
Confidence            46777888999999999998888888888876789999999999999999999999999999999 79999865     5


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|+..|+.++|++||++||
T Consensus       304 ~L~~A~~~~~~~iv~~Ll~~GA  325 (337)
T 4g8k_A          304 LVMTARRNYDHSLVKVLLSHGA  325 (337)
T ss_dssp             HHHHHHHTTCHHHHHHHHHTTC
T ss_pred             HHHHHHHcCCHHHHHHHHHCcC
Confidence            9999999999999999999998

>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=99.68  E-value=1.8e-16  Score=120.06  Aligned_cols=83  Identities=23%  Similarity=0.386  Sum_probs=74.4

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~   82 (347)
                      .....++|||+|||+++++++|+++|++||.|..|.|+.+   +.++|||||+|.+.++|++|++ +++..+.|+.|.|.
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   94 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   94 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            3456789999999999999999999999999999999653   5689999999999999999996 49999999999999


Q ss_pred             CCCcccc
Q psy630           83 PSDSHNR   89 (347)
Q Consensus        83 ~~~~~~~   89 (347)
                      ++.++..
T Consensus        95 ~a~~~~~  101 (109)
T 1x4a_A           95 FPRSGRG  101 (109)
T ss_dssp             CCCCCCC
T ss_pred             EcccCCC
Confidence            9877654

>3kea_A K1L; tropism, ANK repeat, viral protein; 2.30A {Vaccinia virus}

Probab=99.68  E-value=7.3e-17  Score=143.59  Aligned_cols=92  Identities=16%  Similarity=0.226  Sum_probs=85.5

Q ss_pred             CCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCC-CcHHHHHHH
Q psy630          254 NEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDG-DYGLDYAKA  332 (347)
Q Consensus       254 ~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g-~TpLh~A~~  332 (347)
                      .|.|+||+|+..+..+++++|++ .|++++.+|..|+||||+|+..|+.+++++|++ +|++++.+|..| .||||+|+.
T Consensus        61 ~g~t~L~~A~~~g~~~~v~~Ll~-~ga~~~~~d~~g~t~L~~A~~~g~~~~v~~Ll~-~ga~~~~~~~~g~~t~L~~A~~  138 (285)
T 3kea_A           61 ENEFPLHQAATLEDTKIVKILLF-SGLDDSQFDDKGNTALYYAVDSGNMQTVKLFVK-KNWRLMFYGKTGWKTSFYHAVM  138 (285)
T ss_dssp             TTCCHHHHHTTSSSCHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-HCGGGGGCSSSGGGSHHHHHHH
T ss_pred             CCCCHHHHHHHcCCHHHHHHHHH-CCCCCCCcCCCCCcHHHHHHHcCCHHHHHHHHh-cCCCCCccCCCCCCCHHHHHHH
Confidence            48999999999888889999998 799999999999999999999999999999999 699999999999 799999999


Q ss_pred             cCCHHHHHHHHhCCC
Q psy630          333 IEHTDLIEYLVNSGS  347 (347)
Q Consensus       333 ~~~~~~v~~Ll~~GA  347 (347)
                      .|+.+++++|+++|+
T Consensus       139 ~~~~~~v~~Ll~~g~  153 (285)
T 3kea_A          139 LNDVSIVSYFLSEIP  153 (285)
T ss_dssp             TTCHHHHHHHHTTSC
T ss_pred             cCCHHHHHHHHhCCC
Confidence            999999999999885

>3jxi_A Vanilloid receptor-related osmotically activated protein; ankyrin repeats, ANK repeat, ION transport, ionic channel, R transmembrane, transport; 2.30A {Gallus gallus} PDB: 3jxj_A 4dx1_A 4dx2_A*

Probab=99.68  E-value=7.6e-17  Score=141.11  Aligned_cols=97  Identities=22%  Similarity=0.176  Sum_probs=88.6

Q ss_pred             ccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccC--------------CCCchHHHHHHHcCCHHHHHHHHhh--cC
Q psy630          250 QLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLD--------------ENGLNCLHWACDRGHLKVVQHLIEK--CG  313 (347)
Q Consensus       250 ~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d--------------~~g~tpLh~A~~~g~~~~v~~Ll~~--~g  313 (347)
                      ..+..|.|+||+|+..+..+++++|++ .|++++..+              ..|+||||+|+..|+.+++++|++.  .|
T Consensus        88 ~~d~~g~t~L~~A~~~g~~~~v~~Ll~-~ga~~~~~~~~~~~~~~~~~~~~~~g~tpL~~A~~~g~~~~v~~Ll~~~~~g  166 (260)
T 3jxi_A           88 DVYYRGQTALHIAIERRCKHYVELLVE-KGADVHAQARGRFFQPKDEGGYFYFGELPLSLAACTNQPHIVHYLTENGHKQ  166 (260)
T ss_dssp             CSSEESBCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCEECCCSSSCCCCSCCSCSSHHHHHHHTTCHHHHHHHHHCSSCC
T ss_pred             ccccCCCCHHHHHHHcCCHHHHHHHHh-CCCCcCccccccccCcccccccccCCCCHHHHHHHcCCHHHHHHHHhccccC
Confidence            345588999999999999999999999 899999998              6899999999999999999999982  49


Q ss_pred             CCccccCCCCCcHHHHHHHcCC---------HHHHHHHHhCCC
Q psy630          314 ADVNVTDSDGDYGLDYAKAIEH---------TDLIEYLVNSGS  347 (347)
Q Consensus       314 a~i~~~d~~g~TpLh~A~~~~~---------~~~v~~Ll~~GA  347 (347)
                      ++++.+|..|+||||+|+..++         .+++++|+++||
T Consensus       167 a~~~~~d~~g~TpLh~A~~~~~~~~~~~~~~~~~v~~Ll~~ga  209 (260)
T 3jxi_A          167 ADLRRQDSRGNTVLHALVAIADNTRENTKFVTKMYDLLLIKCA  209 (260)
T ss_dssp             CCTTCCCTTSCCHHHHHHHHCCSSHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCcccCCCCCcHHHHHHHhccCchhHHHHHHHHHHHHHHhCc
Confidence            9999999999999999999887         799999999875

>2etb_A Transient receptor potential cation channel subfamily V member 2; TRPV2, ankyrin repeat domain, transport protein; 1.65A {Rattus norvegicus} PDB: 2eta_A 2etc_A 2f37_A

Probab=99.68  E-value=4e-17  Score=142.61  Aligned_cols=94  Identities=15%  Similarity=0.099  Sum_probs=87.6

Q ss_pred             CCCCcHHHHHHcCChHHHHHHHhhc--CCCCccccCCCCchHHHHHHH--cCCHH-------HHHHHHhhcCCCc-----
Q psy630          253 DNEKNIYEWAKEGKLDMLVKQLTKL--KDFNINQLDENGLNCLHWACD--RGHLK-------VVQHLIEKCGADV-----  316 (347)
Q Consensus       253 ~~~~~~l~~a~~~~~~~~~~lL~~~--~~~~~~~~d~~g~tpLh~A~~--~g~~~-------~v~~Ll~~~ga~i-----  316 (347)
                      ..|.|+||+|+..+..+++++|++.  .|+++|.+|..|+||||+|+.  .++.+       ++++|++ +|+++     
T Consensus       134 ~~g~tpL~~A~~~~~~~~v~~Ll~~~~~ga~~n~~d~~g~TpLh~A~~~~~~~~~~~~~~~~iv~~Ll~-~ga~~~~~~~  212 (256)
T 2etb_A          134 YFGELPLSLAACTKQWDVVTYLLENPHQPASLEATDSLGNTVLHALVMIADNSPENSALVIHMYDGLLQ-MGARLCPTVQ  212 (256)
T ss_dssp             CSCSSHHHHHHHTTCHHHHHHHHHCSSCCCCTTCCCTTSCCHHHHHHHHCCSCHHHHHHHHHHHHHHHH-HHHHHSTTCC
T ss_pred             cCCCCHHHHHHHcCCHHHHHHHHhccccCCCcCccCCCCCCHHHHHHHcccCCchhhHHHHHHHHHHHH-cCCCcccccc
Confidence            3499999999999999999999985  689999999999999999999  88888       9999999 79999     


Q ss_pred             --cccCCCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          317 --NVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       317 --~~~d~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                        +.+|..|+||||+|+..|+.+++++||++|+
T Consensus       213 ~~~~~d~~g~tpL~~A~~~g~~~~v~~Ll~~g~  245 (256)
T 2etb_A          213 LEEISNHQGLTPLKLAAKEGKIEIFRHILQREF  245 (256)
T ss_dssp             GGGCCCTTSCCHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cccccCCCCCCHHHHHHHhCCHHHHHHHHhCCC
Confidence              9999999999999999999999999999874

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C

Probab=99.68  E-value=8.8e-17  Score=137.95  Aligned_cols=82  Identities=21%  Similarity=0.453  Sum_probs=76.1

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccC--CeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYG--QIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQP   83 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G--~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~   83 (347)
                      ..++|||+|||+++|+++|+++|++||  .|..|+|++++.+|+++|||||+|.+.++|++|+. +|+..|.|+.|.|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            567899999999999999999999999  99999999999999999999999999999999998 499999999999999


Q ss_pred             CCccc
Q psy630           84 SDSHN   88 (347)
Q Consensus        84 ~~~~~   88 (347)
                      +.+..
T Consensus       147 a~~~~  151 (229)
T 3q2s_C          147 VNKQF  151 (229)
T ss_dssp             CCHHH
T ss_pred             CCCCc
Confidence            87643

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=1.7e-16  Score=115.84  Aligned_cols=80  Identities=25%  Similarity=0.639  Sum_probs=72.9

Q ss_pred             CccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccc
Q psy630            2 SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLS   80 (347)
Q Consensus         2 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~   80 (347)
                      ++.....++|||+|||+++++++|+++|++||.|..+.++        +|||||+|.+.++|++|+.. ++..+.|+.|.
T Consensus         2 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   73 (90)
T 2dnq_A            2 SSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNIN   73 (90)
T ss_dssp             CSCSSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCE
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEE
Confidence            3456778999999999999999999999999999999987        57999999999999999975 99999999999


Q ss_pred             ccCCCcccc
Q psy630           81 IQPSDSHNR   89 (347)
Q Consensus        81 v~~~~~~~~   89 (347)
                      |.++.++..
T Consensus        74 v~~a~~~~~   82 (90)
T 2dnq_A           74 VEASKNKSK   82 (90)
T ss_dssp             EECSSCCCC
T ss_pred             EEECCCCCC
Confidence            999887654

>2etb_A Transient receptor potential cation channel subfamily V member 2; TRPV2, ankyrin repeat domain, transport protein; 1.65A {Rattus norvegicus} PDB: 2eta_A 2etc_A 2f37_A

Probab=99.68  E-value=1.1e-16  Score=139.84  Aligned_cols=96  Identities=21%  Similarity=0.117  Sum_probs=88.4

Q ss_pred             cCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCC-------------CchHHHHHHHcCCHHHHHHHHhh--cCCC
Q psy630          251 LDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDEN-------------GLNCLHWACDRGHLKVVQHLIEK--CGAD  315 (347)
Q Consensus       251 ~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~-------------g~tpLh~A~~~g~~~~v~~Ll~~--~ga~  315 (347)
                      .+..|.|+||+|+..+..+++++|++ .|++++.+|..             |.||||+|+..|+.+++++|+++  .|++
T Consensus        86 ~d~~g~t~L~~A~~~g~~~~v~~Ll~-~ga~~~~~~~~~~~~~~~~~~~~~g~tpL~~A~~~~~~~~v~~Ll~~~~~ga~  164 (256)
T 2etb_A           86 EFYQGHSALHIAIEKRSLQCVKLLVE-NGADVHLRACGRFFQKHQGTCFYFGELPLSLAACTKQWDVVTYLLENPHQPAS  164 (256)
T ss_dssp             TTTTTCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCCSGGGSCCSSSCCCSCSSHHHHHHHTTCHHHHHHHHHCSSCCCC
T ss_pred             ccccCCCHHHHHHHcCCHHHHHHHHH-cCCCCCcccccccccccccccccCCCCHHHHHHHcCCHHHHHHHHhccccCCC
Confidence            34679999999999999999999999 79999999886             99999999999999999999983  4999


Q ss_pred             ccccCCCCCcHHHHHHH--cCCHH-------HHHHHHhCCC
Q psy630          316 VNVTDSDGDYGLDYAKA--IEHTD-------LIEYLVNSGS  347 (347)
Q Consensus       316 i~~~d~~g~TpLh~A~~--~~~~~-------~v~~Ll~~GA  347 (347)
                      +|.+|..|+||||+|+.  .++.+       ++++|+++||
T Consensus       165 ~n~~d~~g~TpLh~A~~~~~~~~~~~~~~~~iv~~Ll~~ga  205 (256)
T 2etb_A          165 LEATDSLGNTVLHALVMIADNSPENSALVIHMYDGLLQMGA  205 (256)
T ss_dssp             TTCCCTTSCCHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCccCCCCCCHHHHHHHcccCCchhhHHHHHHHHHHHHcCC
Confidence            99999999999999999  88888       9999999875

>3jue_A Arfgap with coiled-coil, ANK repeat and PH domain containing protein 1; arfgap domain, zinc-binding module, GTPase activ metal-binding, nitration; 2.30A {Homo sapiens} PDB: 3t9k_A 4f1p_A

Probab=99.68  E-value=1.1e-16  Score=147.17  Aligned_cols=99  Identities=23%  Similarity=0.268  Sum_probs=92.5

Q ss_pred             cCCcccC--CCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCC
Q psy630          246 NDESQLD--DNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDG  323 (347)
Q Consensus       246 ~~~~~~~--~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g  323 (347)
                      .+++..+  ..+.|+||+|+..+...++++|++ .|+++|.+|..|+||||+|+..|+.+++++||+ +|++++.+|..|
T Consensus       224 advn~~~~~~~g~TpLh~Aa~~g~~~iv~~LL~-~Gadvn~~d~~G~TpLh~A~~~g~~~~v~~LL~-~Gad~~~~d~~G  301 (368)
T 3jue_A          224 ADVNWVNGGQDNATPLIQATAANSLLACEFLLQ-NGANVNQADSAGRGPLHHATILGHTGLACLFLK-RGADLGARDSEG  301 (368)
T ss_dssp             CCTTCCCTTTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTS
T ss_pred             CCCCccccccCCCCHHHHHHHCCCHHHHHHHHH-cCCCCCCCCCCCCCHHHHHHHcCcHHHHHHHHH-CcCCCCCcCCCC
Confidence            4566666  789999999999999999999999 799999999999999999999999999999999 799999999999


Q ss_pred             CcHHHHHHHcCCHHHHHHHHhCC
Q psy630          324 DYGLDYAKAIEHTDLIEYLVNSG  346 (347)
Q Consensus       324 ~TpLh~A~~~~~~~~v~~Ll~~G  346 (347)
                      .||||+|+..++.+++++|+.+|
T Consensus       302 ~TpL~~A~~~g~~~iv~lLl~~~  324 (368)
T 3jue_A          302 RDPLTIAMETANADIVTLLRLAK  324 (368)
T ss_dssp             CCHHHHHHHTTCHHHHHHHHHHH
T ss_pred             CCHHHHHHHCCCHHHHHHHHHcC
Confidence            99999999999999999999765

>2rfa_A Transient receptor potential cation channel subfa member 6; TRPV6, ankyrin reapeat, ANK RE calcium channel, calcium transport, calmodulin-binding; 1.70A {Mus musculus}

Probab=99.68  E-value=1.8e-16  Score=136.14  Aligned_cols=99  Identities=17%  Similarity=0.199  Sum_probs=89.9

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCc-----cccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCC
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNI-----NQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS  321 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~-----~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~  321 (347)
                      +.+..+..|.|+||+|+..+..+++++|++ .++++     +..|..|.||||+|+..|+.+++++|++ .|++++..+.
T Consensus        29 ~~~~~~~~g~t~L~~A~~~g~~~~v~~Ll~-~~~~~~~~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~  106 (232)
T 2rfa_A           29 EVHQRGAMGETALHIAALYDNLEAAMVLME-AAPELVFEPMTSELYEGQTALHIAVINQNVNLVRALLA-RGASVSARAT  106 (232)
T ss_dssp             CTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-HCGGGGGCCCCSTTTTTCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCC
T ss_pred             CcccCCCCCCCHHHHHHHcCCHHHHHHHHH-cCchhccccccccCCCCcCHHHHHHHcCCHHHHHHHHh-CCCCCCcccC
Confidence            456678899999999999999999999988 67766     6678899999999999999999999999 7999999876


Q ss_pred             -------------CCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          322 -------------DGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       322 -------------~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                                   .|.||||+|+..|+.+++++|+++||
T Consensus       107 ~~~~~~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~~ga  145 (232)
T 2rfa_A          107 GSVFHYRPHNLIYYGEHPLSFAACVGSEEIVRLLIEHGA  145 (232)
T ss_dssp             SGGGSCCTTCSCCCCSSHHHHHHHHTCHHHHHHHHHTTC
T ss_pred             CcceeecccccccCCCCHHHHHHHcCCHHHHHHHHHCCC
Confidence                         79999999999999999999999986

>3d9h_A CDNA FLJ77766, highly similar to HOMO sapiens ankyrin repeat and SOCS box-containing...; ASB9, ANK repeat, L-shaped, structural protein; 2.20A {Homo sapiens}

Probab=99.68  E-value=2.1e-16  Score=140.63  Aligned_cols=97  Identities=23%  Similarity=0.239  Sum_probs=62.6

Q ss_pred             cccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHH
Q psy630          249 SQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLD  328 (347)
Q Consensus       249 ~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh  328 (347)
                      +..+..|.|+||+|+..+...++++|+. .+++++.+|..|+||||+||..|+.+++++|++ .|++++.+|..|.||||
T Consensus        53 ~~~~~~g~t~L~~Aa~~g~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~g~~~~v~~Ll~-~ga~~~~~~~~g~t~L~  130 (285)
T 3d9h_A           53 MGDAVSDWSPMHEAAIHGHQLSLRNLIS-QGWAVNIITADHVSPLHEACLGGHLSCVKILLK-HGAQVNGVTADWHTPLF  130 (285)
T ss_dssp             CSSSCCSCCHHHHHHHTTCHHHHHHHHH-TTCCSCEECTTCCCHHHHHHHTTCHHHHHHHHH-TTCCSSCCCTTCCCHHH
T ss_pred             cCCCccCCCHHHHHHHcCCHHHHHHHHH-CCCCCCCcCCCCCCHHHHHHHCCcHHHHHHHHH-CCCCCCCCCCCCCCHHH
Confidence            3445566666666666666666666665 566666666666666666666666666666666 46666666666666666


Q ss_pred             HHHHcCCHHHHHHHHhCCC
Q psy630          329 YAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       329 ~A~~~~~~~~v~~Ll~~GA  347 (347)
                      +|+..|+.+++++|+++|+
T Consensus       131 ~A~~~~~~~~v~~Ll~~g~  149 (285)
T 3d9h_A          131 NACVSGSWDCVNLLLQHGA  149 (285)
T ss_dssp             HHHHHTCHHHHHHHHHTTC
T ss_pred             HHHHcCHHHHHHHHHHCCC
Confidence            6666666666666666654

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=3.3e-16  Score=115.26  Aligned_cols=81  Identities=27%  Similarity=0.592  Sum_probs=72.4

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCcccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ   82 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~   82 (347)
                      ......++|||+|||+++++++|+++|++||.|..|  +.++.+|+   ||||+|.+.++|.+|+.+++..+.|+.|.|.
T Consensus         3 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~l~g~~~~g~~l~V~   77 (94)
T 2e5g_A            3 SGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLSQSQHSLGGHRLRVR   77 (94)
T ss_dssp             SCCTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHTCSCCEETTEECCCB
T ss_pred             CccCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHhcCCeEECCEEEEEE
Confidence            445677899999999999999999999999999987  66666665   9999999999999999999999999999999


Q ss_pred             CCCccc
Q psy630           83 PSDSHN   88 (347)
Q Consensus        83 ~~~~~~   88 (347)
                      ++.++.
T Consensus        78 ~a~~~~   83 (94)
T 2e5g_A           78 PREQKE   83 (94)
T ss_dssp             CSCCSC
T ss_pred             ECCcCC
Confidence            887654

>3b7b_A Euchromatic histone-lysine N-methyltransferase 1; ankyrin repeat, alternative splicing, ANK repeat, chromatin regulator, nucleus, phosphorylation; 2.99A {Homo sapiens} SCOP: k.37.1.1 PDB: 3b95_A*

Probab=99.67  E-value=2.7e-16  Score=135.45  Aligned_cols=99  Identities=29%  Similarity=0.373  Sum_probs=87.5

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..|.+++|+|+..+...++++|++ .+++++.+|..|.||||+|+..|+.+++++|++ .|++++.+|..|.||
T Consensus       103 ~~~~~~~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~~~~g~t~  180 (237)
T 3b7b_A          103 DVNCQDDGGWTPMIWATEYKHVDLVKLLLS-KGSDINIRDNEENICLHWAAFSGCVDIAEILLA-AKCDLHAVNIHGDSP  180 (237)
T ss_dssp             CTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHHCCHHHHHHHHT-TTCCTTCCCTTCCCH
T ss_pred             CcccCCCCCCCHHHHHHHcCCHHHHHHHHH-CCCCCCccCCCCCCHHHHHHHCCCHHHHHHHHH-cCCCCCCcCCCCCCH
Confidence            345566778899999988888888888888 788999999999999999999999999999998 699999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+..|+.+++++|+++||
T Consensus       181 L~~A~~~~~~~~v~~Ll~~ga  201 (237)
T 3b7b_A          181 LHIAARENRYDCVVLFLSRDS  201 (237)
T ss_dssp             HHHHHHTTCHHHHHHHHTTTC
T ss_pred             HHHHHHhCCHhHHHHHHHcCC
Confidence            999999999999999999886

>2pnn_A Transient receptor potential cation channel subfa member 1; TRPV1, ankyrin repeat domain, transport protein; HET: ATP; 2.70A {Rattus norvegicus} PDB: 2nyj_A*

Probab=99.67  E-value=5.1e-17  Score=143.37  Aligned_cols=96  Identities=17%  Similarity=0.132  Sum_probs=88.6

Q ss_pred             cCCCCCcHHHHHHcCChHHHHHHHhhc--CCCCccccCCCCchHHHHHHHcCC---------HHHHHHHHhhcCCCcc--
Q psy630          251 LDDNEKNIYEWAKEGKLDMLVKQLTKL--KDFNINQLDENGLNCLHWACDRGH---------LKVVQHLIEKCGADVN--  317 (347)
Q Consensus       251 ~~~~~~~~l~~a~~~~~~~~~~lL~~~--~~~~~~~~d~~g~tpLh~A~~~g~---------~~~v~~Ll~~~ga~i~--  317 (347)
                      .+..|.|+||+|+..+..+++++|++.  .|++++.+|..|+||||+|+..|+         .+++++|++ .|+++|  
T Consensus       144 ~~~~g~tpL~~A~~~g~~~~v~~Ll~~~~~gad~~~~d~~g~tpLh~A~~~~~~~~~~~~~~~~~v~~Ll~-~ga~~n~~  222 (273)
T 2pnn_A          144 GFYFGELPLSLAACTNQLAIVKFLLQNSWQPADISARDSVGNTVLHALVEVADNTVDNTKFVTSMYNEILI-LGAKLHPT  222 (273)
T ss_dssp             CCCSCBSHHHHHHHTTCHHHHHHHHHCSSCCCCTTCCCTTSCCHHHHHHHHCCSCHHHHHHHHHHHHHHHH-HHHHHCTT
T ss_pred             cccCCCCHHHHHHHcCCHHHHHHHHhcccCCCCceeeCCCCCcHHHHHHHccCcchhHHHHHHHHHHHHHH-hhhhcccc
Confidence            345799999999999999999999885  689999999999999999999998         899999999 799997  


Q ss_pred             -----ccCCCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          318 -----VTDSDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       318 -----~~d~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                           .+|..|+||||+|+..|+.+++++||++||
T Consensus       223 ~~~~~~~d~~g~TpL~~A~~~g~~~iv~~Ll~~ga  257 (273)
T 2pnn_A          223 LKLEEITNRKGLTPLALAASSGKIGVLAYILQREI  257 (273)
T ss_dssp             CCGGGCCCTTSCCHHHHHHHTTCHHHHHHHHHHHT
T ss_pred             cccccccCCCCCCHHHHHHHhChHHHHHHHHHCCC
Confidence                 489999999999999999999999999987

>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=99.67  E-value=1.3e-16  Score=130.07  Aligned_cols=83  Identities=19%  Similarity=0.368  Sum_probs=76.5

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      ..++|||+|||+.+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|+.. ++..|.|+.|.|.++.
T Consensus        71 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  150 (165)
T 1rk8_A           71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF  150 (165)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            346799999999999999999999999999999999999999999999999999999999985 9999999999999987


Q ss_pred             cccc
Q psy630           86 SHNR   89 (347)
Q Consensus        86 ~~~~   89 (347)
                      ++..
T Consensus       151 ~~~~  154 (165)
T 1rk8_A          151 VKGP  154 (165)
T ss_dssp             ECC-
T ss_pred             CCCC
Confidence            6543

>1wdy_A 2-5A-dependent ribonuclease; hydrolase, RNA-binding; HET: 25A; 1.80A {Homo sapiens} SCOP: d.211.1.1

Probab=99.67  E-value=2.3e-16  Score=139.15  Aligned_cols=101  Identities=27%  Similarity=0.326  Sum_probs=93.8

Q ss_pred             cCCcccCCCCCcHHHHHHcCCh----HHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCC
Q psy630          246 NDESQLDDNEKNIYEWAKEGKL----DMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS  321 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~----~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~  321 (347)
                      .+.+..+..|.+++|+|+..+.    ..++++|.+ .|++++.+|..|.||||+|+..|+.+++++|+++.|++++.+|.
T Consensus       173 ~~~~~~~~~g~t~l~~a~~~~~~~~~~~i~~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~~~g~~~~~~~~  251 (285)
T 1wdy_A          173 ADVNACDNMGRNALIHALLSSDDSDVEAITHLLLD-HGADVNVRGERGKTPLILAVEKKHLGLVQRLLEQEHIEINDTDS  251 (285)
T ss_dssp             CCTTCCCTTSCCHHHHHHHCSCTTTHHHHHHHHHH-TTCCSSCCCTTSCCHHHHHHHTTCHHHHHHHHHSSSCCTTCCCT
T ss_pred             CCCCccCCCCCCHHHHHHHccccchHHHHHHHHHH-cCCCCCCcCCCCCcHHHHHHHcCCHHHHHHHHhccCCCccccCC
Confidence            3567778889999999988777    889999998 89999999999999999999999999999999856999999999


Q ss_pred             CCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          322 DGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       322 ~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      .|.||||+|+..|+.+++++|+++||
T Consensus       252 ~g~t~l~~A~~~~~~~i~~~Ll~~Ga  277 (285)
T 1wdy_A          252 DGKTALLLAVELKLKKIAELLCKRGA  277 (285)
T ss_dssp             TSCCHHHHHHHTTCHHHHHHHHHHSS
T ss_pred             CCCcHHHHHHHcCcHHHHHHHHHcCC
Confidence            99999999999999999999999997

>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=99.67  E-value=1e-16  Score=122.17  Aligned_cols=79  Identities=22%  Similarity=0.310  Sum_probs=70.6

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-C--CCccCCccccc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-D--SHVLEGSRLSI   81 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~--~~~~~g~~l~v   81 (347)
                      ....++|||+|||+++++++|+++|++||.|..|.|+++      +|||||+|.+.++|.+|+.. +  +..+.|++|.|
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            455689999999999999999999999999999999865      68999999999999999984 4  57899999999


Q ss_pred             cCCCcccc
Q psy630           82 QPSDSHNR   89 (347)
Q Consensus        82 ~~~~~~~~   89 (347)
                      .++.++..
T Consensus       102 ~~a~~k~~  109 (119)
T 2ad9_A          102 QFSNHKEL  109 (119)
T ss_dssp             EECSSSSC
T ss_pred             EEccCCCC
Confidence            99877543

>3jxi_A Vanilloid receptor-related osmotically activated protein; ankyrin repeats, ANK repeat, ION transport, ionic channel, R transmembrane, transport; 2.30A {Gallus gallus} PDB: 3jxj_A 4dx1_A 4dx2_A*

Probab=99.67  E-value=4.8e-17  Score=142.36  Aligned_cols=95  Identities=17%  Similarity=0.103  Sum_probs=87.7

Q ss_pred             CCCCCcHHHHHHcCChHHHHHHHhhc--CCCCccccCCCCchHHHHHHHcCC---------HHHHHHHHhhcCCCc----
Q psy630          252 DDNEKNIYEWAKEGKLDMLVKQLTKL--KDFNINQLDENGLNCLHWACDRGH---------LKVVQHLIEKCGADV----  316 (347)
Q Consensus       252 ~~~~~~~l~~a~~~~~~~~~~lL~~~--~~~~~~~~d~~g~tpLh~A~~~g~---------~~~v~~Ll~~~ga~i----  316 (347)
                      +..|.|+||+|+..+..+++++|++.  .|++++.+|..|+||||+||..++         .+++++|++ .|+++    
T Consensus       137 ~~~g~tpL~~A~~~g~~~~v~~Ll~~~~~ga~~~~~d~~g~TpLh~A~~~~~~~~~~~~~~~~~v~~Ll~-~ga~~~~~~  215 (260)
T 3jxi_A          137 FYFGELPLSLAACTNQPHIVHYLTENGHKQADLRRQDSRGNTVLHALVAIADNTRENTKFVTKMYDLLLI-KCAKLFPDT  215 (260)
T ss_dssp             CCSCSSHHHHHHHTTCHHHHHHHHHCSSCCCCTTCCCTTSCCHHHHHHHHCCSSHHHHHHHHHHHHHHHH-HHHHHCTTC
T ss_pred             ccCCCCHHHHHHHcCCHHHHHHHHhccccCCCCcccCCCCCcHHHHHHHhccCchhHHHHHHHHHHHHHH-hCccccccc
Confidence            36799999999999999999999885  689999999999999999999888         799999999 79999    


Q ss_pred             ---cccCCCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          317 ---NVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       317 ---~~~d~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                         +.+|..|+||||+|+..|+.+++++||++|+
T Consensus       216 ~~~~~~d~~g~tpL~~A~~~g~~~~v~~Ll~~g~  249 (260)
T 3jxi_A          216 NLEALLNNDGLSPLMMAAKTGKIGIFQHIIRREI  249 (260)
T ss_dssp             CGGGCCCTTSCCHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             chhhcccCCCCCHHHHHHHcCCHHHHHHHHHhCC
Confidence               7799999999999999999999999999874

>3c5r_A BARD-1, BRCA1-associated ring domain protein 1; ankyrin repeat, helix, extended loop, four repeat, PR ANK repeat, disease mutation, metal-binding; 2.00A {Homo sapiens} SCOP: k.37.1.1

Probab=99.67  E-value=1.2e-17  Score=131.76  Aligned_cols=98  Identities=20%  Similarity=0.153  Sum_probs=88.4

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..|.|+||+|+..+...++++|++ .+++++.+|..|.||||+|+..|+.+++++|++ +|++++.+|..|.||
T Consensus        35 ~~~~~~~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~ga~~~~~~~~g~tp  112 (137)
T 3c5r_A           35 DPNVKDHAGWTPLHEACNHGHLKVVELLLQ-HKALVNTTGYQNDSPLHDAAKNGHVDIVKLLLS-YGASRNAVNIFGLRP  112 (137)
T ss_dssp             CSCCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCGGGCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCG
T ss_pred             CCCcCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCcccCcCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCCCCCCCCCH
Confidence            556677889999999999999999999998 899999999999999999999999999999999 799999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSG  346 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~G  346 (347)
                      ||+|+..++.+++.+|.+.+
T Consensus       113 l~~A~~~~~~~~l~~l~~~~  132 (137)
T 3c5r_A          113 VDYTDDESMKSLLLLPEKNE  132 (137)
T ss_dssp             GGGCCCHHHHHHHSCC----
T ss_pred             HHHHhhccHHHHHhhccccc
Confidence            99999999999988877654

>3hra_A Ankyrin repeat family protein; structural protein; 1.69A {Enterococcus faecalis}

Probab=99.67  E-value=2.5e-16  Score=132.12  Aligned_cols=101  Identities=22%  Similarity=0.315  Sum_probs=92.3

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcC-CCccccCCCCC
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCG-ADVNVTDSDGD  324 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~g-a~i~~~d~~g~  324 (347)
                      .+++..+..+.+++|+|+..+..+++++|+...+.+++..|..|.||||+|+..|+.+++++|++ .| ++++.+|..|+
T Consensus        63 ~~~~~~~~~g~t~l~~A~~~~~~~~~~~Ll~~~~~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~~g~  141 (201)
T 3hra_A           63 ADINLQNSISDSPYLYAGAQGRTEILAYMLKHATPDLNKHNRYGGNALIPAAEKGHIDNVKLLLE-DGREDIDFQNDFGY  141 (201)
T ss_dssp             CCTTCCCTTSCCHHHHHHHTTCHHHHHHHHHHSCCCTTCCCTTSCCSHHHHHHTTCHHHHHHHHH-HCCCCTTCCCTTSC
T ss_pred             CCCCCCCCCCCCHHHHHHHcCCHHHHHHHHhccCcccccccCCCCcHHHHHHHcCCHHHHHHHHH-cCCCCcCCCCCCCC
Confidence            35677788899999999999999999998855888999999999999999999999999999999 58 99999999999


Q ss_pred             cHHHHHHHcCC-----HHHHHHHHhCCC
Q psy630          325 YGLDYAKAIEH-----TDLIEYLVNSGS  347 (347)
Q Consensus       325 TpLh~A~~~~~-----~~~v~~Ll~~GA  347 (347)
                      ||||+|+..++     .+++++|+++||
T Consensus       142 t~L~~A~~~~~~~~~~~~~v~~Ll~~ga  169 (201)
T 3hra_A          142 TALIEAVGLREGNQLYQDIVKLLMENGA  169 (201)
T ss_dssp             CHHHHHHHSSCCSHHHHHHHHHHHHTTC
T ss_pred             CHHHHHHHhccchhhHHHHHHHHHHCCC
Confidence            99999999998     999999999986

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.67  E-value=1.2e-16  Score=117.57  Aligned_cols=77  Identities=18%  Similarity=0.185  Sum_probs=68.2

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCC--ccCCccccc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSH--VLEGSRLSI   81 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~--~~~g~~l~v   81 (347)
                      ..+.++|||+|||+++|+++|+++|++||.|.++.+++      ++|||||+|.+.++|.+|+.. ++.  .+.|++|.|
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V   91 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEE
Confidence            34678999999999999999999999999999999974      368999999999999999985 555  488999999


Q ss_pred             cCCCcc
Q psy630           82 QPSDSH   87 (347)
Q Consensus        82 ~~~~~~   87 (347)
                      .++.++
T Consensus        92 ~~S~~k   97 (100)
T 3r27_A           92 NYSTSQ   97 (100)
T ss_dssp             EECSCS
T ss_pred             Eecccc
Confidence            998764

>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=99.67  E-value=1.4e-16  Score=118.40  Aligned_cols=79  Identities=18%  Similarity=0.210  Sum_probs=70.3

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc---CCCccCCccccc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST---DSHVLEGSRLSI   81 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~---~~~~~~g~~l~v   81 (347)
                      ....++|||+|||+++++++|+++|++||.|..|.++++      +|||||+|.+.++|.+|+..   ++..+.|++|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   85 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   85 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEE
Confidence            345689999999999999999999999999999998754      68999999999999999983   678899999999


Q ss_pred             cCCCcccc
Q psy630           82 QPSDSHNR   89 (347)
Q Consensus        82 ~~~~~~~~   89 (347)
                      .++.++..
T Consensus        86 ~~a~~~~~   93 (101)
T 2cq1_A           86 QYSNHKEL   93 (101)
T ss_dssp             EECSCSSC
T ss_pred             EEcCcccC
Confidence            99876543

>2fo1_E LIN-12 protein; beta-barrel, protein-DNA complex, double helix, ankyrin repeat, gene regulation/signalling protein/DNA complex; 3.12A {Caenorhabditis elegans} SCOP: d.211.1.1

Probab=99.67  E-value=2.5e-16  Score=145.53  Aligned_cols=96  Identities=23%  Similarity=0.287  Sum_probs=90.3

Q ss_pred             cCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHH
Q psy630          251 LDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA  330 (347)
Q Consensus       251 ~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A  330 (347)
                      .+..|.|+||+|+..+..+++++|+...+++++.+|..|.||||+|+..|+.+++++|++ +|++++.+|..|.||||+|
T Consensus       275 ~d~~g~t~Lh~A~~~g~~~~v~~Ll~~~~~~~n~~d~~g~TpL~~A~~~g~~~iv~~Ll~-~gad~~~~d~~g~t~l~~A  353 (373)
T 2fo1_E          275 EKYKGRTALHYAAQVSNMPIVKYLVGEKGSNKDKQDEDGKTPIMLAAQEGRIEVVMYLIQ-QGASVEAVDATDHTARQLA  353 (373)
T ss_dssp             SSCCCCCTHHHHHSSCCHHHHHHHHHHSCCCTTCCCTTCCCHHHHHHHHTCHHHHHHHHH-TTCCSSCCCSSSCCHHHHH
T ss_pred             ccccCCCHHHHHHHhCCHHHHHHHHHhcCCCccCcCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCccCCCCCCCCHHHHH
Confidence            566899999999999999999999975669999999999999999999999999999999 7999999999999999999


Q ss_pred             HHcCCHHHHHHHHhCCC
Q psy630          331 KAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       331 ~~~~~~~~v~~Ll~~GA  347 (347)
                      +..|+.+++++|+++||
T Consensus       354 ~~~g~~~iv~~Ll~~~a  370 (373)
T 2fo1_E          354 QANNHHNIVDIFDRCRP  370 (373)
T ss_dssp             HHTTCHHHHHHHHTTC-
T ss_pred             HHcCCHHHHHHHHhcCc
Confidence            99999999999999986

>3aaa_C Myotrophin, protein V-1; actin capping protein, barbed END capping, inhibition, prote binding, actin capping, actin-binding, cytoskeleton, ANK RE; 2.20A {Homo sapiens} PDB: 1myo_A 2kxp_C 2myo_A

Probab=99.67  E-value=2.7e-16  Score=121.56  Aligned_cols=85  Identities=22%  Similarity=0.253  Sum_probs=78.8

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..|.|+||+|+..+...++++|++ .+++++.+|..|+||||+|+..|+.+++++|++ +|++++.+|..|.||
T Consensus        32 ~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~d~~g~tpL~~A~~~~~~~~v~~Ll~-~ga~~~~~~~~g~t~  109 (123)
T 3aaa_C           32 DVNRTLEGGRKPLHYAADCGQLEILEFLLL-KGADINAPDKHHITPLLSAVYEGHVSCVKLLLS-KGADKTVKGPDGLTA  109 (123)
T ss_dssp             CTTSCCTTSSCHHHHHHHTTCHHHHHHHHT-TTCCTTCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTSCCH
T ss_pred             CcCccCCCCCcHHHHHHHcCCHHHHHHHHH-cCCCCCcCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCCcCCCCCCH
Confidence            456677889999999999999999999998 899999999999999999999999999999999 799999999999999


Q ss_pred             HHHHHHc
Q psy630          327 LDYAKAI  333 (347)
Q Consensus       327 Lh~A~~~  333 (347)
                      ||+|+..
T Consensus       110 l~~A~~~  116 (123)
T 3aaa_C          110 FEATDNQ  116 (123)
T ss_dssp             HHHCCCH
T ss_pred             HHHhCCH
Confidence            9999443

>2pnn_A Transient receptor potential cation channel subfa member 1; TRPV1, ankyrin repeat domain, transport protein; HET: ATP; 2.70A {Rattus norvegicus} PDB: 2nyj_A*

Probab=99.66  E-value=1.8e-16  Score=139.80  Aligned_cols=96  Identities=20%  Similarity=0.188  Sum_probs=88.6

Q ss_pred             cCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCC--------------CCchHHHHHHHcCCHHHHHHHHhh--cCC
Q psy630          251 LDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDE--------------NGLNCLHWACDRGHLKVVQHLIEK--CGA  314 (347)
Q Consensus       251 ~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~--------------~g~tpLh~A~~~g~~~~v~~Ll~~--~ga  314 (347)
                      .+..|.|+||+|+..+..+++++|++ .|++++.++.              .|.||||+|+..|+.+++++||++  .|+
T Consensus        97 ~d~~g~tpL~~A~~~g~~~~v~~Ll~-~ga~~~~~~~~~~~~~~~~~~~~~~g~tpL~~A~~~g~~~~v~~Ll~~~~~ga  175 (273)
T 2pnn_A           97 SYYKGQTALHIAIERRNMTLVTLLVE-NGADVQAAANGDFFKKTKGRPGFYFGELPLSLAACTNQLAIVKFLLQNSWQPA  175 (273)
T ss_dssp             TTTTTCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCBCSGGGSSCSSSCCCCSCBSHHHHHHHTTCHHHHHHHHHCSSCCC
T ss_pred             ccCCCCCHHHHHHHcCCHHHHHHHHH-CCCCcCccccccccccccccccccCCCCHHHHHHHcCCHHHHHHHHhcccCCC
Confidence            45689999999999999999999999 7999999987              799999999999999999999983  499


Q ss_pred             CccccCCCCCcHHHHHHHcCC---------HHHHHHHHhCCC
Q psy630          315 DVNVTDSDGDYGLDYAKAIEH---------TDLIEYLVNSGS  347 (347)
Q Consensus       315 ~i~~~d~~g~TpLh~A~~~~~---------~~~v~~Ll~~GA  347 (347)
                      +++.+|..|+||||+|+..|+         .+++++|+++||
T Consensus       176 d~~~~d~~g~tpLh~A~~~~~~~~~~~~~~~~~v~~Ll~~ga  217 (273)
T 2pnn_A          176 DISARDSVGNTVLHALVEVADNTVDNTKFVTSMYNEILILGA  217 (273)
T ss_dssp             CTTCCCTTSCCHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CceeeCCCCCcHHHHHHHccCcchhHHHHHHHHHHHHHHhhh
Confidence            999999999999999999998         899999998874

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.66  E-value=2.2e-16  Score=117.91  Aligned_cols=77  Identities=17%  Similarity=0.382  Sum_probs=70.4

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      .+...++|||+|||+++++++|+++|++||.|..++++      +++|||||+|.+.++|.+|+.. ++..+.|+.|+|.
T Consensus        23 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   96 (101)
T 2la4_A           23 APPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTG   96 (101)
T ss_dssp             SCSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCC
T ss_pred             CCCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            44567899999999999999999999999999999987      3579999999999999999975 9999999999999


Q ss_pred             CCCc
Q psy630           83 PSDS   86 (347)
Q Consensus        83 ~~~~   86 (347)
                      ++.+
T Consensus        97 ~a~~  100 (101)
T 2la4_A           97 WGKE  100 (101)
T ss_dssp             BCCC
T ss_pred             eccC
Confidence            8865

>3deo_A Signal recognition particle 43 kDa protein; chloroplast SRP system, signal sequence, ankyrin repeat, chromodomain, type I turn; 1.50A {Arabidopsis thaliana} SCOP: b.34.13.2 k.37.1.1 PDB: 3dep_A 1x32_A

Probab=99.66  E-value=2.2e-16  Score=130.96  Aligned_cols=97  Identities=28%  Similarity=0.395  Sum_probs=86.6

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccC-CCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLD-ENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d-~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      +.+..+..|.|+||+|+..+...++++|++ .+++++.+| ..|+||||+|+..|+.+++++|++ +|++++.+|..|+|
T Consensus        68 ~~~~~d~~g~t~L~~A~~~~~~~~v~~Ll~-~ga~~~~~~~~~g~tpL~~A~~~~~~~~v~~Ll~-~ga~~~~~d~~g~t  145 (183)
T 3deo_A           68 DVDAVDENGRTALLFVAGLGSDKCVRLLAE-AGADLDHRDMRGGLTALHMAAGYVRPEVVEALVE-LGADIEVEDERGLT  145 (183)
T ss_dssp             CTTCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCSSSSCCHHHHHHHTTCHHHHHHHHH-HTCCTTCCCTTSCC
T ss_pred             CCCCcCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCcCCCCCCCCHHHHHHhcCcHHHHHHHHH-cCCCCcCCCCCCCC
Confidence            456677889999999999999999999999 899999998 899999999999999999999999 69999999999999


Q ss_pred             HHHHHHHc----------------CCHHHHHHHHhC
Q psy630          326 GLDYAKAI----------------EHTDLIEYLVNS  345 (347)
Q Consensus       326 pLh~A~~~----------------~~~~~v~~Ll~~  345 (347)
                      |||+|+..                |+.+++++|.++
T Consensus       146 pl~~A~~~~~~~~~~~~l~~a~~~~~~~i~~~L~~~  181 (183)
T 3deo_A          146 ALELAREILKTTPKGNPMQFGRRIGLEKVINVLEGQ  181 (183)
T ss_dssp             HHHHHHHHHHTCCCCSHHHHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHhccCcccccHHHHHHHcCHHHHHHHHHHh
Confidence            99998875                566777777654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.66  E-value=6.5e-17  Score=122.20  Aligned_cols=82  Identities=22%  Similarity=0.255  Sum_probs=70.9

Q ss_pred             CccccCCCeEEEeCCCCCCCHHHHHHHHhccC-CeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccc
Q psy630            2 SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYG-QIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRL   79 (347)
Q Consensus         2 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G-~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l   79 (347)
                      +..+...++|||+|||+++++++|+++|++|| .|..+.++.    +.++|||||+|.+.++|++|++ +|+..+.|+.|
T Consensus        22 ~~~p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i   97 (111)
T 2jvr_A           22 SKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVI   97 (111)
T ss_dssp             ---CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            34566778999999999999999999999999 899998853    3578999999999999999997 59999999999


Q ss_pred             cccCCCcc
Q psy630           80 SIQPSDSH   87 (347)
Q Consensus        80 ~v~~~~~~   87 (347)
                      .|.++...
T Consensus        98 ~V~~a~~~  105 (111)
T 2jvr_A           98 TVERDDNP  105 (111)
T ss_dssp             EEEESCC-
T ss_pred             EEEECCCC
Confidence            99887653

>3ui2_A Signal recognition particle 43 kDa protein, chlor; ankyrin repeat, chromodomain, aromatic CAGE, signal recognit particle, protein targeting; 3.18A {Arabidopsis thaliana} PDB: 1x3q_A 2hug_A

Probab=99.66  E-value=1.4e-16  Score=138.48  Aligned_cols=97  Identities=28%  Similarity=0.393  Sum_probs=89.1

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccC-CCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLD-ENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d-~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      +++..+..|.|+||+|+..++..++++|+. .|+++|.+| ..|+||||+||..|+.+++++|++ +|++++.+|..|+|
T Consensus        69 ~~~~~d~~g~t~L~~A~~~g~~~~v~~Ll~-~ga~~~~~~~~~g~t~L~~A~~~g~~~~v~~Ll~-~ga~~~~~d~~g~t  146 (244)
T 3ui2_A           69 DVDAVDENGRTALLFVAGLGSDKCVRLLAE-AGADLDHRDMRGGLTALHMAAGYVRPEVVEALVE-LGADIEVEDERGLT  146 (244)
T ss_dssp             CTTCBCTTSCBHHHHHHHHTCHHHHHHHHH-TTCCTTCCCSSSCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTCCC
T ss_pred             CCCCcCCCCCCHHHHHHHCCCHHHHHHHHH-cCCCCCcCCCCCCCCHHHHHHHcCCHHHHHHHHH-CCCCCCCCCCCCCc
Confidence            556778889999999999999999999999 899999998 789999999999999999999999 79999999999999


Q ss_pred             HHHHHH----------------HcCCHHHHHHHHhC
Q psy630          326 GLDYAK----------------AIEHTDLIEYLVNS  345 (347)
Q Consensus       326 pLh~A~----------------~~~~~~~v~~Ll~~  345 (347)
                      |||+|+                ..|+.+++++|+++
T Consensus       147 ~l~~A~~~~~~~~~~~~l~~a~~~g~~~iv~~L~~~  182 (244)
T 3ui2_A          147 ALELAREILKTTPKGNPMQFGRRIGLEKVINVLEGQ  182 (244)
T ss_dssp             HHHHHHHHHTTCCCSSHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccCCCCHHHHHHHcChHHHHHHHHHh
Confidence            999988                66889999999874

>1s70_B 130 kDa myosin-binding subunit of smooth muscle myosin phophatase (M130), serine/threonine protein phosphatase PP1-beta (OR delta) catalytic subunit; myosin phosphatase; HET: PGE; 2.70A {Gallus gallus} SCOP: d.211.1.1

Probab=99.66  E-value=1.7e-16  Score=141.68  Aligned_cols=94  Identities=28%  Similarity=0.405  Sum_probs=73.2

Q ss_pred             CCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHH
Q psy630          252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAK  331 (347)
Q Consensus       252 ~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~  331 (347)
                      +..+.++|++|+..+...++++|+. .|+++|..|..|.||||+||..|+.+++++|++ +|++++.+|..|.||||+|+
T Consensus        37 ~~~~~t~l~~A~~~g~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~g~~~~v~~Ll~-~ga~~~~~~~~g~tpL~~A~  114 (299)
T 1s70_B           37 KFDDGAVFLAACSSGDTEEVLRLLE-RGADINYANVDGLTALHQACIDDNVDMVKFLVE-NGANINQPDNEGWIPLHAAA  114 (299)
T ss_dssp             EECHHHHHHHHHHHTCHHHHHHHHH-HCCCTTCBCTTCCBHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHH
T ss_pred             ccCCccHHHHHHHcCCHHHHHHHHH-cCCCCcccCCCCCCHHHHHHHcCCHHHHHHHHH-CCCCCCCCCCCCCcHHHHHH
Confidence            3455677777766666666666666 578888888888888888888888888888887 68888888888888888888


Q ss_pred             HcCCHHHHHHHHhCCC
Q psy630          332 AIEHTDLIEYLVNSGS  347 (347)
Q Consensus       332 ~~~~~~~v~~Ll~~GA  347 (347)
                      ..|+.+++++|+++||
T Consensus       115 ~~g~~~~v~~Ll~~g~  130 (299)
T 1s70_B          115 SCGYLDIAEYLISQGA  130 (299)
T ss_dssp             HHTCHHHHHHHHHTTC
T ss_pred             HcCCHHHHHHHHhCCC
Confidence            8888888888888775

>4g8k_A 2-5A-dependent ribonuclease; ankyrin-repeat domain, single-stranded RNA, hydrolase; 2.40A {Homo sapiens} PDB: 4g8l_A*

Probab=99.66  E-value=4.3e-16  Score=141.69  Aligned_cols=101  Identities=27%  Similarity=0.364  Sum_probs=90.2

Q ss_pred             cCCcccCCCCCcHHHHHH----cCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCC
Q psy630          246 NDESQLDDNEKNIYEWAK----EGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS  321 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~----~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~  321 (347)
                      .+++..+..|.++++.++    .++...++++|++ .|+++|.+|..|+||||+|+..|+.+++++|+...|+++|.+|.
T Consensus       193 ad~n~~d~~g~t~l~~~~~~~~~~~~~~i~~lLl~-~gad~n~~d~~g~t~L~~a~~~~~~~~v~~Ll~~~~~~vn~~d~  271 (337)
T 4g8k_A          193 ADVNACDNMGRNALIHALLSSDDSDVEAITHLLLD-HGADVNVRGERGKTPLILAVEKKHLGLVQRLLEQEHIEINDTDS  271 (337)
T ss_dssp             CCTTCCCTTSCCHHHHHHHHSCTTTHHHHHHHHHH-TTCCTTCCCGGGCCHHHHHHHTTCHHHHHHHHTSTTCCTTCBCT
T ss_pred             CCcCccCCCCCcHHHHHHHHcCcccHHHHHHHHHH-CCCCCCCcCCCCCCHHHHHHHhhhhHHHHHHHHhcCCcccCcCC
Confidence            356778888888887654    3445678888888 89999999999999999999999999999999855899999999


Q ss_pred             CCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          322 DGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       322 ~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      .|+||||+|+..|+.++|++||++||
T Consensus       272 ~G~TpL~~A~~~g~~~iv~~Ll~~GA  297 (337)
T 4g8k_A          272 DGKTALLLAVELKLKKIAELLCKRGA  297 (337)
T ss_dssp             TSCBHHHHHHHTTCHHHHHHHHTTSC
T ss_pred             CCCCHHHHHHHcCCHHHHHHHHHCCC
Confidence            99999999999999999999999997

>1yyh_A HN1;, notch 1, ankyrin domain; ankyrin repeats, cell cycle,transcription; 1.90A {Homo sapiens} PDB: 2he0_A 2f8x_K 3nbn_B 3v79_K* 1ot8_A

Probab=99.66  E-value=3.3e-16  Score=136.68  Aligned_cols=99  Identities=16%  Similarity=0.230  Sum_probs=92.5

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..|.++||+|+..+...++++|+. .+++++.+|..|+||||+|+..|+.+++++|++ .|++++.+|..|.||
T Consensus       116 ~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~d~~g~t~L~~A~~~~~~~~v~~Ll~-~ga~~~~~~~~g~tp  193 (253)
T 1yyh_A          116 DLDARMHDGTTPLILAARLAVEGMLEDLIN-SHADVNAVDDLGKSALHWAAAVNNVDAAVVLLK-NGANKDMQNNREETP  193 (253)
T ss_dssp             CTTCCCTTCCCHHHHHHHHTCSSHHHHHHH-TTCCTTCBCTTSCBHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTSCCH
T ss_pred             CccccCCCCCcHHHHHHHcChHHHHHHHHH-cCCCCCCcCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCCcCCCCCCH
Confidence            345567789999999998888889999998 799999999999999999999999999999999 799999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+..|+.+++++|+++||
T Consensus       194 L~~A~~~~~~~~v~~Ll~~ga  214 (253)
T 1yyh_A          194 LFLAAREGSYETAKVLLDHFA  214 (253)
T ss_dssp             HHHHHHHTCHHHHHHHHHTTC
T ss_pred             HHHHHHCCCHHHHHHHHHcCC
Confidence            999999999999999999986

>3aji_A 26S proteasome non-ATPase regulatory subunit 10; gankyrin, S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dvw_A 2dwz_A* 1tr4_A 1uoh_A 1qym_A

Probab=99.65  E-value=5.2e-16  Score=133.13  Aligned_cols=99  Identities=22%  Similarity=0.287  Sum_probs=92.4

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..|.|+||+|+..+..+++++|++ .+++++.+|..|.||||+|+..++.+++++|++ .|++++.+|..|.||
T Consensus        65 ~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~~~~g~t~  142 (231)
T 3aji_A           65 PVNDKDDAGWSPLHIAASAGXDEIVKALLV-KGAHVNAVNQNGCTPLHYAASKNRHEIAVMLLE-GGANPDAKDHYDATA  142 (231)
T ss_dssp             CSCCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCH
T ss_pred             CCCCcCCCCCCHHHHHHHcCHHHHHHHHHH-cCCCCCCCCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCCcCCCCCcH
Confidence            456677889999999999889999999998 799999999999999999999999999999999 799999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+..|+.+++++|+++|+
T Consensus       143 L~~A~~~~~~~~v~~Ll~~g~  163 (231)
T 3aji_A          143 MHRAAAKGNLKMVHILLFYKA  163 (231)
T ss_dssp             HHHHHHHTCHHHHHHHHHTTC
T ss_pred             HHHHHHcCCHHHHHHHHhcCC
Confidence            999999999999999999885

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=3e-16  Score=117.37  Aligned_cols=83  Identities=24%  Similarity=0.438  Sum_probs=75.1

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      .....++|||+|||+++++++|+++|+.|+   .+.++.++.++.++|||||+|.+.++|++|+.. ++..+.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLD   87 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            356678999999999999999999999774   788888988999999999999999999999984 9999999999999


Q ss_pred             CCCcccc
Q psy630           83 PSDSHNR   89 (347)
Q Consensus        83 ~~~~~~~   89 (347)
                      ++.++..
T Consensus        88 ~a~~~~~   94 (102)
T 2fc8_A           88 WAKPKGE   94 (102)
T ss_dssp             ECCCCCS
T ss_pred             EecCCCC
Confidence            9987654

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.65  E-value=1.5e-16  Score=118.83  Aligned_cols=82  Identities=18%  Similarity=0.387  Sum_probs=73.2

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~   82 (347)
                      .....++|||+|||+++++++|+++|++||.|   +++.+ .+++++|||||+|.+.++|++|+. +++..+.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            34567899999999999999999999999977   56666 579999999999999999999998 59999999999999


Q ss_pred             CCCcccc
Q psy630           83 PSDSHNR   89 (347)
Q Consensus        83 ~~~~~~~   89 (347)
                      ++.++..
T Consensus        87 ~a~~~~~   93 (101)
T 2fc9_A           87 LQGPRGS   93 (101)
T ss_dssp             ECSSCCC
T ss_pred             EcCCCCC
Confidence            9877643

>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=99.65  E-value=7.1e-17  Score=119.89  Aligned_cols=79  Identities=11%  Similarity=0.207  Sum_probs=69.6

Q ss_pred             ccCCCeEEEeCCCC-CCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-C--CCccCCcccc
Q psy630            5 IRQLNKIFVGNLPW-TVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-D--SHVLEGSRLS   80 (347)
Q Consensus         5 ~~~~~~l~V~nLp~-~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~--~~~~~g~~l~   80 (347)
                      ....++|||+|||+ ++|+++|+++|++||.|.+|.|+++      +|||||+|.+.++|..|+.. +  +..+.|++|.
T Consensus        12 ~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~   85 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   85 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEE
Confidence            45678999999999 9999999999999999999999865      47999999999999999984 4  5569999999


Q ss_pred             ccCCCcccc
Q psy630           81 IQPSDSHNR   89 (347)
Q Consensus        81 v~~~~~~~~   89 (347)
                      |.++..+..
T Consensus        86 V~~a~~~~~   94 (102)
T 1x4d_A           86 VHLSQKYKR   94 (102)
T ss_dssp             EEEECCCTT
T ss_pred             EEECCCCCC
Confidence            999876543

>1n11_A Ankyrin; clathrin, BAND 3, anion exchanger, structural protein; 2.70A {Homo sapiens} SCOP: d.211.1.1

Probab=99.65  E-value=2.7e-16  Score=148.12  Aligned_cols=99  Identities=22%  Similarity=0.274  Sum_probs=83.3

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..|.|+||+|+..+...++++|.+ .+++++.+|..|+||||+|+..|+.+++++|++ +|+++|.+|..|+||
T Consensus       270 ~~~~~~~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~~~~g~t~L~~A~~~g~~~~v~~Ll~-~gad~n~~~~~g~t~  347 (437)
T 1n11_A          270 NGNLGNKSGLTPLHLVAQEGHVPVADVLIK-HGVMVDATTRMGYTPLHVASHYGNIKLVKFLLQ-HQADVNAKTKLGYSP  347 (437)
T ss_dssp             CTTCCCTTCCCHHHHHHHHTCHHHHHHHHH-HTCCTTCCCSSCCCHHHHHHHSSCSHHHHHHHH-TTCCTTCCCTTSCCH
T ss_pred             CCCCCCCCCCCHHHHHHHcCCHHHHHHHHh-CCccCCCCCCCCCCHHHHHHHcCcHHHHHHHHh-cCCCCCCCCCCCCCH
Confidence            456667778888888888777778888887 688888888888888888888888888888888 688888888888888


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+..|+.++|++|+++||
T Consensus       348 L~~A~~~g~~~iv~~Ll~~ga  368 (437)
T 1n11_A          348 LHQAAQQGHTDIVTLLLKNGA  368 (437)
T ss_dssp             HHHHHHTTCHHHHHHHHHTTC
T ss_pred             HHHHHHCChHHHHHHHHHCcC
Confidence            888888888888888888886

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.46  E-value=9.3e-18  Score=128.72  Aligned_cols=86  Identities=21%  Similarity=0.329  Sum_probs=79.5

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeE--------EEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCcc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMN--------ASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVL   74 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~--------~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~   74 (347)
                      +..+.++|||+|||+++++++|+++|++||.|..        |++++++.++.++|||||+|.+.++|.+|+.. ++..+
T Consensus         3 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   82 (116)
T 2lcw_A            3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   82 (116)
Confidence            3456789999999999999999999999999998        99999988999999999999999999999984 99999


Q ss_pred             CCccccccCCCcccc
Q psy630           75 EGSRLSIQPSDSHNR   89 (347)
Q Consensus        75 ~g~~l~v~~~~~~~~   89 (347)
                      .|+.|.|.++.++..
T Consensus        83 ~g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           83 SGNPIKVSFATRRAD   97 (116)
Confidence            999999999887654

>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=99.65  E-value=4.6e-16  Score=116.31  Aligned_cols=78  Identities=18%  Similarity=0.200  Sum_probs=69.0

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc---CCCccCCccccc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST---DSHVLEGSRLSI   81 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~---~~~~~~g~~l~v   81 (347)
                      ....++|||+|||+++++++|+++|++||.|..|.++++      +|||||+|.+.++|.+|+..   ++..+.|++|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V   85 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            345689999999999999999999999999999998753      68999999999999999984   456699999999


Q ss_pred             cCCCccc
Q psy630           82 QPSDSHN   88 (347)
Q Consensus        82 ~~~~~~~   88 (347)
                      .++..+.
T Consensus        86 ~~a~~~~   92 (104)
T 1wex_A           86 NYSTSKR   92 (104)
T ss_dssp             EECSSSS
T ss_pred             EEccCcc
Confidence            9987654

>3utm_A Tankyrase-1; tankyrase, TNKS, ankryin repeat clusters, WNT signaling, POL ribosylation, transferase-signaling protein complex; 2.00A {Mus musculus}

Probab=99.65  E-value=6e-16  Score=140.81  Aligned_cols=95  Identities=26%  Similarity=0.319  Sum_probs=87.6

Q ss_pred             cCCCCCcHHHHHHcC---ChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHH
Q psy630          251 LDDNEKNIYEWAKEG---KLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGL  327 (347)
Q Consensus       251 ~~~~~~~~l~~a~~~---~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpL  327 (347)
                      .+..+.+++|+|+..   +...++++|.. .+++++.+|..|+||||+|+..|+.+++++|++ +|+++|.+|..|+|||
T Consensus       207 ~~~~~~t~L~~A~~~~~~~~~~~~~~Ll~-~g~~~~~~~~~g~t~L~~A~~~g~~~~v~~Ll~-~ga~~n~~d~~g~t~L  284 (351)
T 3utm_A          207 QPQSHETALHCAVASLHPKRKQVAELLLR-KGANVNEKNKDFMTPLHVAAERAHNDVMEVLHK-HGAKMNALDSLGQTAL  284 (351)
T ss_dssp             CTTTCCCHHHHHHHCCSTTHHHHHHHHHH-TTCCTTCCCTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCHH
T ss_pred             CCCCCCCHHHHHHHHhCccHHHHHHHHHH-cCCCcCCcCCCCCCHHHHHHHcCCHHHHHHHHH-CCCCCCCcCCCCCCHH
Confidence            456788999999887   66788899988 899999999999999999999999999999999 7999999999999999


Q ss_pred             HHHHHcCCHHHHHHHHhCCC
Q psy630          328 DYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       328 h~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |+|+..|+.+++++|+++||
T Consensus       285 ~~A~~~~~~~~v~~Ll~~ga  304 (351)
T 3utm_A          285 HRAALAGHLQTCRLLLSYGS  304 (351)
T ss_dssp             HHHHHHTCHHHHHHHHHTTC
T ss_pred             HHHHHcCcHHHHHHHHHcCC
Confidence            99999999999999999986

>1s70_B 130 kDa myosin-binding subunit of smooth muscle myosin phophatase (M130), serine/threonine protein phosphatase PP1-beta (OR delta) catalytic subunit; myosin phosphatase; HET: PGE; 2.70A {Gallus gallus} SCOP: d.211.1.1

Probab=99.65  E-value=4.7e-16  Score=138.73  Aligned_cols=99  Identities=22%  Similarity=0.212  Sum_probs=81.9

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccC----------------------------------------
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLD----------------------------------------  286 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d----------------------------------------  286 (347)
                      +.+..+..|.|+||+|+..+..+++++|+. .+++++..|                                        
T Consensus        98 ~~~~~~~~g~tpL~~A~~~g~~~~v~~Ll~-~g~~~~~~~~~g~t~l~~A~~~~~~~~~~~ll~~~~~~~~~~~~~~~~~  176 (299)
T 1s70_B           98 NINQPDNEGWIPLHAAASCGYLDIAEYLIS-QGAHVGAVNSEGDTPLDIAEEEAMEELLQNEVNRQGVDIEAARKEEERI  176 (299)
T ss_dssp             CTTCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCCCCCCCCcHHHHHHHcCCHHHHHHHHh-CCCCCCCcCCCCCCHHHHHHhcchHHHHHHHHhhcCCCchhhhhhhhhH
Confidence            445556667777777777666667777766 566655443                                        


Q ss_pred             --------------------CCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCCHHHHHHHHhCC
Q psy630          287 --------------------ENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG  346 (347)
Q Consensus       287 --------------------~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~~~v~~Ll~~G  346 (347)
                                          ..|.||||+||..|+.+++++|++ +|+++|.+|..|.||||+|+..|+.+++++|+++|
T Consensus       177 ~~~~~~~~l~~~~~~~~~~~~~g~t~L~~A~~~g~~~~v~~Ll~-~g~d~~~~d~~g~tpL~~A~~~~~~~~v~~Ll~~g  255 (299)
T 1s70_B          177 MLRDARQWLNSGHINDVRHAKSGGTALHVAAAKGYTEVLKLLIQ-ARYDVNIKDYDGWTPLHAAAHWGKEEACRILVENL  255 (299)
T ss_dssp             HHHHHHHHHHHTCCCCCCCTTTCCCHHHHHHHHTCHHHHHHHHT-TTCCTTCCCTTCCCHHHHHHHTTCHHHHHHHHHTT
T ss_pred             HHHHHHHHHhccCcchhhhcCCCCCHHHHHHHCCcHHHHHHHHH-cCCCCCCcCCCCCcHHHHHHhcCCHHHHHHHHHcC
Confidence                                457789999999999999999999 79999999999999999999999999999999998


Q ss_pred             C
Q psy630          347 S  347 (347)
Q Consensus       347 A  347 (347)
                      |
T Consensus       256 a  256 (299)
T 1s70_B          256 C  256 (299)
T ss_dssp             C
T ss_pred             C
Confidence            6

>3ljn_A Hypothetical protein; ankyrin, structural genomics, PSI, structural genomics of pathogenic protozoa consortium, SGPP, ANK repeat; 2.90A {Leishmania major}

Probab=99.65  E-value=2.5e-16  Score=144.78  Aligned_cols=98  Identities=13%  Similarity=0.151  Sum_probs=92.2

Q ss_pred             CcccCCCCCcHHHHHHcCC--hHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCC-----ccccC
Q psy630          248 ESQLDDNEKNIYEWAKEGK--LDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGAD-----VNVTD  320 (347)
Q Consensus       248 ~~~~~~~~~~~l~~a~~~~--~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~-----i~~~d  320 (347)
                      .+..+..+.|+||+|+..+  ..+++++|++ .|++++.+|..|+||||+||..|+.+++++|++ +|++     +|.+|
T Consensus       131 ~~~~~~~g~t~L~~A~~~g~~~~~~v~~Ll~-~ga~~~~~d~~g~t~L~~A~~~g~~~~v~~Ll~-~g~~~~~~~~~~~~  208 (364)
T 3ljn_A          131 SHVKHCKGQTALHWCVGLGPEYLEMIKILVQ-LGASPTAKDKADETPLMRAMEFRNREALDLMMD-TVPSKSSLRLDYAN  208 (364)
T ss_dssp             TEEEEESCCCHHHHHHHSCGGGHHHHHHHHH-HTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-HCSCSSSCCTTCCC
T ss_pred             cccCCCCCCCHHHHHHHcCCchHHHHHHHHH-cCCCCcccCCCCCCHHHHHHHcCCHHHHHHHHh-cccccccccccccC
Confidence            4456778999999999999  8899999999 699999999999999999999999999999999 6999     99999


Q ss_pred             CCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          321 SDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       321 ~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ..|+||||+|+..|+.++|++||++||
T Consensus       209 ~~g~t~L~~A~~~g~~~~v~~Ll~~ga  235 (364)
T 3ljn_A          209 KQGNSHLHWAILINWEDVAMRFVEMGI  235 (364)
T ss_dssp             TTCCCTTHHHHTTTCHHHHHHHHTTTC
T ss_pred             CCCCcHHHHHHHcCCHHHHHHHHHcCC
Confidence            999999999999999999999999986

>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=99.65  E-value=1.1e-16  Score=118.50  Aligned_cols=83  Identities=23%  Similarity=0.388  Sum_probs=74.4

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHH----HHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELK----KFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSR   78 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~----~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~   78 (347)
                      +....++|||+|||+++++++|+    ++|++||.|..+.+++   +|.++|||||+|.+.++|.+|+.. ++..+.|+.
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   80 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcE
Confidence            45677899999999999999999    9999999999999873   578899999999999999999985 999999999


Q ss_pred             ccccCCCcccc
Q psy630           79 LSIQPSDSHNR   89 (347)
Q Consensus        79 l~v~~~~~~~~   89 (347)
                      |.|.++.++..
T Consensus        81 l~v~~a~~~~~   91 (97)
T 1nu4_A           81 MRIQYAKTDSD   91 (97)
T ss_dssp             CEEEECSSCCT
T ss_pred             EEEEEccCCCc
Confidence            99999887654

>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=99.65  E-value=4.5e-16  Score=115.27  Aligned_cols=79  Identities=18%  Similarity=0.325  Sum_probs=71.3

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccC--Cccccc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLE--GSRLSI   81 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~--g~~l~v   81 (347)
                      +...++|||+|||+++++++|+++|++||.|..+.++++      +|||||+|.+.++|++|+.. ++..+.  |+.|.|
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V   87 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRV   87 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEE
Confidence            455689999999999999999999999999999998753      68999999999999999985 999999  999999


Q ss_pred             cCCCcccc
Q psy630           82 QPSDSHNR   89 (347)
Q Consensus        82 ~~~~~~~~   89 (347)
                      .++.++..
T Consensus        88 ~~a~~~~~   95 (97)
T 1why_A           88 DFAKSGPS   95 (97)
T ss_dssp             EECCCCCC
T ss_pred             EECCCCCC
Confidence            99887643

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=4e-16  Score=115.51  Aligned_cols=79  Identities=18%  Similarity=0.323  Sum_probs=70.4

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      ....++|||+|||+++++++|+++|++||.|. +.++.    +.++|||||+|.+.++|++|+.. ++..+.|+.|.|.+
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   90 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVAL   90 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            44578999999999999999999999999997 66665    46789999999999999999975 99999999999999


Q ss_pred             CCccc
Q psy630           84 SDSHN   88 (347)
Q Consensus        84 ~~~~~   88 (347)
                      +.++.
T Consensus        91 a~~~~   95 (97)
T 2e5j_A           91 ARQQR   95 (97)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            87654

>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=99.64  E-value=6.2e-16  Score=111.51  Aligned_cols=76  Identities=20%  Similarity=0.481  Sum_probs=69.2

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-c-CCCccCCcccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-T-DSHVLEGSRLS   80 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~-~~~~~~g~~l~   80 (347)
                      +.....++|||+|||+++++++|+++|++||.|..++++++      +|||||+|.+.++|.+|+. + ++..+.|++|.
T Consensus         7 ~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~   80 (85)
T 2ytc_A            7 GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLN   80 (85)
T ss_dssp             CSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECC
T ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEE
Confidence            34566789999999999999999999999999999999863      6899999999999999998 5 99999999999


Q ss_pred             ccCC
Q psy630           81 IQPS   84 (347)
Q Consensus        81 v~~~   84 (347)
                      |.++
T Consensus        81 v~~a   84 (85)
T 2ytc_A           81 VKWG   84 (85)
T ss_dssp             EEEC
T ss_pred             EEec
Confidence            9876

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.64  E-value=1.9e-16  Score=119.81  Aligned_cols=78  Identities=15%  Similarity=0.264  Sum_probs=69.7

Q ss_pred             CeEEEeCC----CCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcC----H-HH---HHHHHh--c-CCCc
Q psy630            9 NKIFVGNL----PWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN----K-EA---VDKVFS--T-DSHV   73 (347)
Q Consensus         9 ~~l~V~nL----p~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~----~-~~---a~~a~~--~-~~~~   73 (347)
                      ++|||+||    |+.+++.+|+++|++||+|.++.++.|+.||.|+|||||+|.+    . ++   |.+|+.  . ++..
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            57999999    9999999999999999999999999999999999999999995    2 22   788877  4 9999


Q ss_pred             cCCccccccCCCc
Q psy630           74 LEGSRLSIQPSDS   86 (347)
Q Consensus        74 ~~g~~l~v~~~~~   86 (347)
                      |.|+.|+|.....
T Consensus        83 I~Gr~irV~ln~~   95 (136)
T 2j8a_A           83 IMGFKFEVILNKH   95 (136)
T ss_dssp             ETTEEEEEEECCT
T ss_pred             ecCcEEEEEECcc
Confidence            9999999986654

>4hbd_A KN motif and ankyrin repeat domain-containing Pro; structural genomics consortium, SGC, protein binding; 1.72A {Homo sapiens}

Probab=99.64  E-value=3.6e-16  Score=138.45  Aligned_cols=99  Identities=23%  Similarity=0.250  Sum_probs=88.7

Q ss_pred             CCcccCCCCCcHHHHHH-----cCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCC
Q psy630          247 DESQLDDNEKNIYEWAK-----EGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS  321 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~-----~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~  321 (347)
                      +.+..+..|.|++|+|+     ..+...++++|.. .+..++..|..|+||||+||..|+.+++++||+ +|+++|.+|.
T Consensus       137 ~~~~~~~~g~tpL~~a~~~~~~~~~~~~~v~~Ll~-~g~~~~~~~~~g~tpLh~A~~~g~~~~v~~Ll~-~gad~n~~d~  214 (276)
T 4hbd_A          137 KVDKQNRAGYSPIMLTALATLKTQDDIETVLQLFR-LGNINAKASQAGQTALMLAVSHGRVDVVKALLA-CEADVNVQDD  214 (276)
T ss_dssp             CTTCCCTTSCCHHHHGGGCCCCSHHHHHHHHHHHH-HSCTTCCCTTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCT
T ss_pred             cCCCCCCCCCCHHHHHHHHHhhhhhhHHHHHHHHH-cCCCccccCCCCCCHHHHHHHcCCHHHHHHHHh-CCCCCCCCCC
Confidence            56677888999999988     4566677777777 678888889999999999999999999999999 7999999999


Q ss_pred             CCCcHHHHHHHcCCHHHHHHHHh-CCC
Q psy630          322 DGDYGLDYAKAIEHTDLIEYLVN-SGS  347 (347)
Q Consensus       322 ~g~TpLh~A~~~~~~~~v~~Ll~-~GA  347 (347)
                      .|+||||+|+..|+.+++++|++ .||
T Consensus       215 ~G~TpLh~A~~~g~~~iv~~Ll~~~ga  241 (276)
T 4hbd_A          215 DGSTALMCACEHGHKEIAGLLLAVPSC  241 (276)
T ss_dssp             TSCCHHHHHHHHTCHHHHHHHHTSTTC
T ss_pred             CCCCHHHHHHHCCCHHHHHHHHhcCCC
Confidence            99999999999999999999999 775

>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=99.64  E-value=8.1e-17  Score=123.25  Aligned_cols=84  Identities=23%  Similarity=0.360  Sum_probs=72.0

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ...++|||+|||+++++++|+++|++||.|..+.+..+..+++++|||||+|.+.++|.+|+.. ++..+.|+.|.|.++
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            4568999999999999999999999999985433332223789999999999999999999984 999999999999998


Q ss_pred             Ccccc
Q psy630           85 DSHNR   89 (347)
Q Consensus        85 ~~~~~   89 (347)
                      .++..
T Consensus       103 ~~~~~  107 (115)
T 2cpx_A          103 KNKKQ  107 (115)
T ss_dssp             CCCSC
T ss_pred             cCCCC
Confidence            87654

>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=99.64  E-value=2.1e-16  Score=119.04  Aligned_cols=80  Identities=20%  Similarity=0.304  Sum_probs=70.4

Q ss_pred             cccCCCeEEEeCCCCC-CCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc---CCCccCCccc
Q psy630            4 SIRQLNKIFVGNLPWT-VSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST---DSHVLEGSRL   79 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~-~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~---~~~~~~g~~l   79 (347)
                      +....++|||+|||++ +++++|+++|++||.|..|.|++      ++|||||+|.+.++|..|+..   ++..+.|++|
T Consensus        21 ~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l   94 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCV   94 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCC
T ss_pred             cCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            3556789999999998 99999999999999999999964      468999999999999999984   5677999999


Q ss_pred             cccCCCcccc
Q psy630           80 SIQPSDSHNR   89 (347)
Q Consensus        80 ~v~~~~~~~~   89 (347)
                      .|.++..+..
T Consensus        95 ~V~~a~~~~~  104 (112)
T 1x4f_A           95 KVDLSEKYKK  104 (112)
T ss_dssp             EEEEECSCSS
T ss_pred             EEEECccccc
Confidence            9999876543

>2dzn_A Probable 26S proteasome regulatory subunit P28; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} SCOP: d.211.1.1 PDB: 2dzo_A 1ixv_A 1wg0_A

Probab=99.64  E-value=9e-16  Score=131.30  Aligned_cols=94  Identities=30%  Similarity=0.391  Sum_probs=88.5

Q ss_pred             cCCCCCcHHHHHHcCChHHHHHHHhhcCC--CCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHH
Q psy630          251 LDDNEKNIYEWAKEGKLDMLVKQLTKLKD--FNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLD  328 (347)
Q Consensus       251 ~~~~~~~~l~~a~~~~~~~~~~lL~~~~~--~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh  328 (347)
                      .+..|.|+||+|+..+..+++++|++ .+  .+++..|..|.||||+|+..|+.+++++|++ .|++++.+|..|.||||
T Consensus        68 ~~~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~~~~~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~~~~g~t~L~  145 (228)
T 2dzn_A           68 PDDSGWTPFHIACSVGNLEVVKSLYD-RPLKPDLNKITNQGVTCLHLAVGKKWFEVSQFLIE-NGASVRIKDKFNQIPLH  145 (228)
T ss_dssp             CCTTSCCHHHHHHHHCCHHHHHHHHS-SSSCCCTTCCCTTCCCHHHHHHHTTCHHHHHHHHH-TTCCSCCCCTTSCCHHH
T ss_pred             CCCCCCCHHHHHHHcCCHHHHHHHHh-CCCCcccccCCcCCCCHHHHHHHcCCHhHHHHHHH-cCCCccccCCCCCCHHH
Confidence            56788999999998888889999888 56  8899999999999999999999999999999 79999999999999999


Q ss_pred             HHHHcCCHHHHHHHHhCC
Q psy630          329 YAKAIEHTDLIEYLVNSG  346 (347)
Q Consensus       329 ~A~~~~~~~~v~~Ll~~G  346 (347)
                      +|+..|+.+++++|+++|
T Consensus       146 ~A~~~~~~~~v~~Ll~~g  163 (228)
T 2dzn_A          146 RAASVGSLKLIELLCGLG  163 (228)
T ss_dssp             HHHHTTCHHHHHHHHTTT
T ss_pred             HHHHcCCHHHHHHHHhcC
Confidence            999999999999999998

>3t8k_A Uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center F or structural genomics, MCSG; 1.77A {Leptotrichia buccalis}

Probab=99.64  E-value=9.5e-17  Score=133.67  Aligned_cols=93  Identities=15%  Similarity=0.070  Sum_probs=83.3

Q ss_pred             CCCCcHHHHHHcCC----hHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCC------HHHHHHHHhhcCCCccccCCC
Q psy630          253 DNEKNIYEWAKEGK----LDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGH------LKVVQHLIEKCGADVNVTDSD  322 (347)
Q Consensus       253 ~~~~~~l~~a~~~~----~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~------~~~v~~Ll~~~ga~i~~~d~~  322 (347)
                      ..|.||||+|+..+    ...++++|++ .|+++|.+|..|+||||+|+..++      .+++++||+ +|+++|.+|..
T Consensus        36 ~~g~T~Lh~A~~~~~~~~~~~iv~~Ll~-~Gadvn~~d~~g~TpLh~a~~~~~~~~~~~~~iv~~Ll~-~Gadin~~d~~  113 (186)
T 3t8k_A           36 VLKSNILYDVLRNNNDEARYKISMFLIN-KGADIKSRTKEGTTLFFPLFQGGGNDITGTTELCKIFLE-KGADITALYKP  113 (186)
T ss_dssp             HHTTTHHHHHTTCSCHHHHHHHHHHHHH-TTCCSSCCCTTCCCTHHHHHHHCTTCHHHHHHHHHHHHH-TTCCSSSCBGG
T ss_pred             cCCCCHHHHHHHcCCcchHHHHHHHHHH-CCCCCCCCCCCCCcHHHHHHHcCCcchhhHHHHHHHHHH-CCCCCCccCCC
Confidence            56889999998876    3778899888 899999999999999999999987      688999999 79999999999


Q ss_pred             CC-cHHHHHHHcC-----CHHHHHHHHh-CCC
Q psy630          323 GD-YGLDYAKAIE-----HTDLIEYLVN-SGS  347 (347)
Q Consensus       323 g~-TpLh~A~~~~-----~~~~v~~Ll~-~GA  347 (347)
                      |+ ||||+|+..+     +.+++++|++ +||
T Consensus       114 g~ttpLh~A~~~~~~~~~~~~iv~~Ll~~~ga  145 (186)
T 3t8k_A          114 YKIVVFKNIFNYFVDENEMIPLYKLIFSQSGL  145 (186)
T ss_dssp             GTBCTTGGGGGCCSCHHHHHHHHHHHHTSTTC
T ss_pred             cCchHHHHHHHcCCChhhHHHHHHHHHHhcCC
Confidence            99 9999999954     4569999999 886

>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=99.64  E-value=7.3e-16  Score=114.05  Aligned_cols=76  Identities=32%  Similarity=0.615  Sum_probs=69.1

Q ss_pred             cccCCCeEEEeCCCC-CCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccc
Q psy630            4 SIRQLNKIFVGNLPW-TVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI   81 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~-~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v   81 (347)
                      .....++|||+|||+ ++++++|+++|++||.|..+++.        +|||||+|.+.++|.+|+.. ++..+.|+.|.|
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V   89 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLIL   89 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            356678999999998 99999999999999999999983        68999999999999999985 999999999999


Q ss_pred             cCCCcc
Q psy630           82 QPSDSH   87 (347)
Q Consensus        82 ~~~~~~   87 (347)
                      .++.++
T Consensus        90 ~~a~~~   95 (97)
T 2xnq_A           90 EVSSSN   95 (97)
T ss_dssp             EECCCC
T ss_pred             EecCCC
Confidence            988664

>3kea_A K1L; tropism, ANK repeat, viral protein; 2.30A {Vaccinia virus}

Probab=99.64  E-value=4.1e-16  Score=138.73  Aligned_cols=99  Identities=16%  Similarity=0.121  Sum_probs=88.7

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCC-chHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCC
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENG-LNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGD  324 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g-~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~  324 (347)
                      .+++..+..|.|+||+|+..+..+++++|++ .|++++.+|..| .||||+|+..|+.+++++|++ .|+++... ..|.
T Consensus        86 a~~~~~d~~g~t~L~~A~~~g~~~~v~~Ll~-~ga~~~~~~~~g~~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~-~~g~  162 (285)
T 3kea_A           86 LDDSQFDDKGNTALYYAVDSGNMQTVKLFVK-KNWRLMFYGKTGWKTSFYHAVMLNDVSIVSYFLS-EIPSTFDL-AILL  162 (285)
T ss_dssp             CCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-HCGGGGGCSSSGGGSHHHHHHHTTCHHHHHHHHT-TSCTTCCC-STHH
T ss_pred             CCCCCcCCCCCcHHHHHHHcCCHHHHHHHHh-cCCCCCccCCCCCCCHHHHHHHcCCHHHHHHHHh-CCCccccc-cCCc
Confidence            3577788899999999999999999999998 699999999999 799999999999999999999 69887332 2899


Q ss_pred             cHHHHHHHcCCHHHHHHHHhCCC
Q psy630          325 YGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       325 TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||||+|+..|+.+++++|+++||
T Consensus       163 t~L~~A~~~g~~~~v~~Ll~~ga  185 (285)
T 3kea_A          163 SCIHITIKNGHVDMMILLLDYMT  185 (285)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHH
T ss_pred             cHHHHHHHcChHHHHHHHHHcCC
Confidence            99999999999999999998874

>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=99.63  E-value=2.9e-16  Score=114.17  Aligned_cols=80  Identities=21%  Similarity=0.499  Sum_probs=62.9

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCcccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ   82 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~   82 (347)
                      ..+....+|||+|||+++|+++|+++|++||.|.+|+|+++     ++|||||+|.+.++|+++.. ....+.|+.|.|.
T Consensus         6 ~~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~~~~-~~~~~~g~~v~v~   79 (89)
T 3d2w_A            6 HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCG-EDLIIKGISVHIS   79 (89)
T ss_dssp             -----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHHHTT-CEEEETTEEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHHHcC-CCcccCCEEEEEE
Confidence            34567789999999999999999999999999999999864     78999999999999885432 2444569999999


Q ss_pred             CCCccc
Q psy630           83 PSDSHN   88 (347)
Q Consensus        83 ~~~~~~   88 (347)
                      ++.++.
T Consensus        80 ~a~~k~   85 (89)
T 3d2w_A           80 NAEPKH   85 (89)
T ss_dssp             ECC---
T ss_pred             EcCCCC
Confidence            887754

>1n11_A Ankyrin; clathrin, BAND 3, anion exchanger, structural protein; 2.70A {Homo sapiens} SCOP: d.211.1.1

Probab=99.63  E-value=4.4e-16  Score=146.68  Aligned_cols=99  Identities=19%  Similarity=0.223  Sum_probs=76.8

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +++..+..+.|+||+|+..++.+++++|++ .+++++.+|..|+||||+||..|+.+++++|++ +|++++..+..|.||
T Consensus        39 ~~~~~~~~~~t~L~~A~~~g~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~g~~~~v~~Ll~-~ga~~~~~~~~g~t~  116 (437)
T 1n11_A           39 SPNVSNVKVETPLHMAARAGHTEVAKYLLQ-NKAKVNAKAKDDQTPLHCAARIGHTNMVKLLLE-NNANPNLATTAGHTP  116 (437)
T ss_dssp             CSCCSSSCCCCHHHHHHHHTCHHHHHHHHH-HTCCSSCCCTTSCCHHHHHHHHTCHHHHHHHHH-HTCCTTCCCTTCCCH
T ss_pred             CCCCCCCCCCCHHHHHHHcCCHHHHHHHHh-CCCCCCCCCCCCCCHHHHHHHCCCHHHHHHHHh-CCCCCCCCCCCCCcH
Confidence            456666777788887777777777777777 677778778888888888888888888888887 588888888888888


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+..|+.+++++|+++|+
T Consensus       117 L~~A~~~g~~~~v~~Ll~~~~  137 (437)
T 1n11_A          117 LHIAAREGHVETVLALLEKEA  137 (437)
T ss_dssp             HHHHHHHTCHHHHHHHHHTTC
T ss_pred             HHHHHHcCCHHHHHHHHhCCC
Confidence            888888888888888877764

>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=99.63  E-value=6.4e-16  Score=117.02  Aligned_cols=80  Identities=21%  Similarity=0.414  Sum_probs=72.7

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      .....++|||+|||+++++++|+++|++||.|..|+++++      +|||||+|.+.++|.+|+.. ++..+.|+.|.|.
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   94 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY   94 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            3456789999999999999999999999999999999865      68999999999999999975 9999999999999


Q ss_pred             CCCcccc
Q psy630           83 PSDSHNR   89 (347)
Q Consensus        83 ~~~~~~~   89 (347)
                      ++.++..
T Consensus        95 ~a~~~~~  101 (109)
T 1x4g_A           95 WGKESPD  101 (109)
T ss_dssp             CCCCCCS
T ss_pred             ecCCCCC
Confidence            9887654

>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=99.63  E-value=4.7e-16  Score=115.62  Aligned_cols=79  Identities=28%  Similarity=0.544  Sum_probs=71.4

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      ..+.++|||+|||+++++++|+++|++||.|..++++++      +|||||+|.+.++|.+|+.. ++..+.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   85 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEE
Confidence            456689999999999999999999999999999999753      68999999999999999975 99999999999999


Q ss_pred             CCcccc
Q psy630           84 SDSHNR   89 (347)
Q Consensus        84 ~~~~~~   89 (347)
                      +.++..
T Consensus        86 a~~~~~   91 (99)
T 2cpj_A           86 ACHSAS   91 (99)
T ss_dssp             SSCCSC
T ss_pred             cCCCCC
Confidence            877543

>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=99.63  E-value=5.5e-16  Score=117.14  Aligned_cols=78  Identities=26%  Similarity=0.373  Sum_probs=71.1

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCC-----cc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEG-----SR   78 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g-----~~   78 (347)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+       |||||+|.+.++|++|++ +|+..+.|     +.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~   84 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   84 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceE
Confidence            456789999999999999999999999999999999865       899999999999999998 59999999     99


Q ss_pred             ccccCCCcccc
Q psy630           79 LSIQPSDSHNR   89 (347)
Q Consensus        79 l~v~~~~~~~~   89 (347)
                      |.|.++.++..
T Consensus        85 i~V~~a~~~~~   95 (108)
T 1x4c_A           85 IRVKVDGPRSP   95 (108)
T ss_dssp             EEEEESSCCSC
T ss_pred             EEEEeCCCCCC
Confidence            99998877543

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.63  E-value=6.5e-16  Score=116.65  Aligned_cols=78  Identities=22%  Similarity=0.463  Sum_probs=70.6

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      .....++|||+|||+++++++|+++|++||.|..+.++        +|||||+|.+.++|.+|+.. ++..+.|+.|.|.
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   98 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            44567899999999999999999999999999999987        68999999999999999985 9999999999999


Q ss_pred             CCCcccc
Q psy630           83 PSDSHNR   89 (347)
Q Consensus        83 ~~~~~~~   89 (347)
                      ++.++..
T Consensus        99 ~a~~~~~  105 (108)
T 2jvo_A           99 YSKLPAK  105 (108)
T ss_dssp             SCSCCC-
T ss_pred             EecCCCC
Confidence            9877554

>1wdy_A 2-5A-dependent ribonuclease; hydrolase, RNA-binding; HET: 25A; 1.80A {Homo sapiens} SCOP: d.211.1.1

Probab=99.63  E-value=1.8e-15  Score=133.42  Aligned_cols=94  Identities=19%  Similarity=0.194  Sum_probs=89.7

Q ss_pred             CCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHH
Q psy630          252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAK  331 (347)
Q Consensus       252 ~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~  331 (347)
                      +..|.++||+|+..+..+++++|++ .+++++.+|..|.||||+|+..|+.+++++|++ .|++++..|..|.||||+|+
T Consensus        36 ~~~g~t~L~~A~~~g~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~  113 (285)
T 1wdy_A           36 EEGGWTPLHNAVQMSREDIVELLLR-HGADPVLRKKNGATPFLLAAIAGSVKLLKLFLS-KGADVNECDFYGFTAFMEAA  113 (285)
T ss_dssp             TTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTCCCHHHHHHHHTCHHHHHHHHH-TTCCTTCBCTTCCBHHHHHH
T ss_pred             CCCCCcHHHHHHHcCCHHHHHHHHH-cCCCCcccCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCCCccCcccCCHHHHHH
Confidence            5678899999999999999999999 799999999999999999999999999999999 79999999999999999999


Q ss_pred             HcCCHHHHHHHHhCCC
Q psy630          332 AIEHTDLIEYLVNSGS  347 (347)
Q Consensus       332 ~~~~~~~v~~Ll~~GA  347 (347)
                      ..|+.+++++|+++|+
T Consensus       114 ~~~~~~~~~~Ll~~g~  129 (285)
T 1wdy_A          114 VYGKVKALKFLYKRGA  129 (285)
T ss_dssp             HTTCHHHHHHHHHTTC
T ss_pred             HhCCHHHHHHHHHhCC
Confidence            9999999999999985

>3b7b_A Euchromatic histone-lysine N-methyltransferase 1; ankyrin repeat, alternative splicing, ANK repeat, chromatin regulator, nucleus, phosphorylation; 2.99A {Homo sapiens} SCOP: k.37.1.1 PDB: 3b95_A*

Probab=99.63  E-value=1.5e-15  Score=130.70  Aligned_cols=99  Identities=31%  Similarity=0.446  Sum_probs=85.2

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcC-CCccccCCCCCc
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCG-ADVNVTDSDGDY  325 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~g-a~i~~~d~~g~T  325 (347)
                      +.+..+..|.++||+|+..+..+++++|++ .+++++.++..|.||||+|+..|+.+++++|++ .| ++++..+..|.|
T Consensus        36 ~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~L~~A~~~~~~~~~~~Ll~-~~~~~~~~~~~~g~t  113 (237)
T 3b7b_A           36 NIDTCSEDQRTPLMEAAENNHLEAVKYLIK-AGALVDPKDAEGSTCLHLAAKKGHYEVVQYLLS-NGQMDVNCQDDGGWT  113 (237)
T ss_dssp             CTTCCCTTCCCHHHHHHHTTCHHHHHHHHT-TTCCCCCCCTTSCCHHHHHHHTTCHHHHHHHHT-TTCCCTTCCCTTSCC
T ss_pred             CcCccCCCCCCHHHHHHHhCCHHHHHHHHh-CCCCCCCCCCCCCcHHHHHHHcCCHHHHHHHHh-CCCCCcccCCCCCCC
Confidence            566777888888888888888888888888 788888888889999999999999999999988 56 888888888999


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|+..++.+++++|+++|+
T Consensus       114 ~L~~A~~~~~~~~~~~Ll~~g~  135 (237)
T 3b7b_A          114 PMIWATEYKHVDLVKLLLSKGS  135 (237)
T ss_dssp             HHHHHHHTTCHHHHHHHHHTTC
T ss_pred             HHHHHHHcCCHHHHHHHHHCCC
Confidence            9999999999999999988875

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.62  E-value=4e-16  Score=119.14  Aligned_cols=82  Identities=21%  Similarity=0.368  Sum_probs=70.2

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCC---CCceeEEEEEEcCHHHHHHHHhcCCCccCCccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNT---GLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRL   79 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t---~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l   79 (347)
                      +.....++|||+|||+++++++|+++|++||.|. +.++.++.+   |+++|||||+|.+.++|++|+..- ..++|+.+
T Consensus         3 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~-~~~~G~~~   80 (114)
T 2dnl_A            3 SGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDAC-LEEDGKLY   80 (114)
T ss_dssp             CSSSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHS-EEETTEEE
T ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhh-hhcCCcEE
Confidence            4556789999999999999999999999999999 888888777   799999999999999999999752 23778877


Q ss_pred             cccCCCc
Q psy630           80 SIQPSDS   86 (347)
Q Consensus        80 ~v~~~~~   86 (347)
                      .+..+.+
T Consensus        81 ~~~~~~~   87 (114)
T 2dnl_A           81 LCVSSPT   87 (114)
T ss_dssp             EEECCSS
T ss_pred             EeccCCC
Confidence            7765543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=9.4e-16  Score=111.84  Aligned_cols=79  Identities=22%  Similarity=0.464  Sum_probs=71.4

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI   81 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v   81 (347)
                      ..+...++|||+|||+++++++|+++|++||.|..+.+++        +||||+|.+.++|++|+.. ++..+.|+.|.|
T Consensus         4 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   75 (90)
T 2dnp_A            4 GSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINV   75 (90)
T ss_dssp             CSSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            3456778999999999999999999999999999999973        4999999999999999985 999999999999


Q ss_pred             cCCCcccc
Q psy630           82 QPSDSHNR   89 (347)
Q Consensus        82 ~~~~~~~~   89 (347)
                      .++.+...
T Consensus        76 ~~a~~~~~   83 (90)
T 2dnp_A           76 ELSTKGQK   83 (90)
T ss_dssp             EESCCCCC
T ss_pred             EECCCCCC
Confidence            99877544

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.62  E-value=6.6e-16  Score=127.12  Aligned_cols=83  Identities=28%  Similarity=0.461  Sum_probs=76.9

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~   83 (347)
                      +...++|||+|||+++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|.+|+. +++..+.|+.|.|.+
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~  163 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4456799999999999999999999999999999999998 89999999999999999999998 599999999999998


Q ss_pred             CCccc
Q psy630           84 SDSHN   88 (347)
Q Consensus        84 ~~~~~   88 (347)
                      +....
T Consensus       164 a~~~~  168 (177)
T 2f3j_A          164 VASQI  168 (177)
T ss_dssp             ESSGG
T ss_pred             ecCCC
Confidence            86643

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.62  E-value=2.3e-16  Score=116.61  Aligned_cols=80  Identities=20%  Similarity=0.434  Sum_probs=71.2

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~   83 (347)
                      ....++|||+|||+++++++|+++|++||.|..+     ..++.++|||||+|.+.++|.+|+. +++..+.|+.|.|.+
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   87 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY   87 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            4456899999999999999999999999988766     2468999999999999999999999 599999999999999


Q ss_pred             CCcccc
Q psy630           84 SDSHNR   89 (347)
Q Consensus        84 ~~~~~~   89 (347)
                      +.++..
T Consensus        88 a~~~~~   93 (96)
T 1fjc_A           88 TGEKGG   93 (96)
T ss_dssp             CSSSCC
T ss_pred             cCCCCC
Confidence            877553

>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=99.62  E-value=7.7e-16  Score=123.56  Aligned_cols=79  Identities=27%  Similarity=0.441  Sum_probs=72.2

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~   83 (347)
                      ....++|||+|||+++++++|+++|++||.|..|+++++     ++|||||+|.+.++|.+|+. +++..+.|++|.|.+
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  144 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVEL  144 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            345689999999999999999999999999999999875     57999999999999999998 499999999999999


Q ss_pred             CCccc
Q psy630           84 SDSHN   88 (347)
Q Consensus        84 ~~~~~   88 (347)
                      +.++.
T Consensus       145 a~~~~  149 (150)
T 2i2y_A          145 SNGEK  149 (150)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            87653

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=99.62  E-value=1.3e-15  Score=127.53  Aligned_cols=84  Identities=31%  Similarity=0.642  Sum_probs=76.0

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCCc
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~~   86 (347)
                      ..++|||+|||+++++++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|.+|+..++..++|+.|.|.++.+
T Consensus       103 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~~~~~~~G~~i~v~~a~~  182 (196)
T 1l3k_A          103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALS  182 (196)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEECC-
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHhCCcEECCEEEEEEecCC
Confidence            45799999999999999999999999999999999999899999999999999999999998899999999999999988


Q ss_pred             cccc
Q psy630           87 HNRM   90 (347)
Q Consensus        87 ~~~~   90 (347)
                      +...
T Consensus       183 k~~~  186 (196)
T 1l3k_A          183 KQEM  186 (196)
T ss_dssp             ----
T ss_pred             hhHh
Confidence            6653

>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=99.62  E-value=4e-16  Score=114.55  Aligned_cols=81  Identities=21%  Similarity=0.430  Sum_probs=70.6

Q ss_pred             CccccCCCeEEEeCCCCCCCHHHHHHHHhccCC-eeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CC-CccCCcc
Q psy630            2 SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQ-IMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DS-HVLEGSR   78 (347)
Q Consensus         2 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~-i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~-~~~~g~~   78 (347)
                      +..+...++|||+|||+++++++|+++|++||. |..+.+.       ++|||||+|.+.++|.+|+.. ++ ..+.|+.
T Consensus         2 s~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~   74 (93)
T 2cqh_A            2 SSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKI   74 (93)
T ss_dssp             CCCCCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEE
Confidence            345677889999999999999999999999999 5555552       468999999999999999985 99 9999999


Q ss_pred             ccccCCCcccc
Q psy630           79 LSIQPSDSHNR   89 (347)
Q Consensus        79 l~v~~~~~~~~   89 (347)
                      |.|.++.++..
T Consensus        75 l~v~~a~~~~~   85 (93)
T 2cqh_A           75 MEVDYSVSKKL   85 (93)
T ss_dssp             CEEEECCCCCC
T ss_pred             EEEEEccCccc
Confidence            99999887654

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.62  E-value=9.6e-16  Score=112.29  Aligned_cols=79  Identities=28%  Similarity=0.489  Sum_probs=71.4

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI   81 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v   81 (347)
                      +.....++|||+|||+++++++|+++|++||.|..+.+++        +||||+|.+.++|.+|+.. ++..+.|+.|.|
T Consensus         5 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   76 (92)
T 2dgt_A            5 SSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHV   76 (92)
T ss_dssp             CCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEE
Confidence            3456778999999999999999999999999999999873        4999999999999999975 999999999999


Q ss_pred             cCCCcccc
Q psy630           82 QPSDSHNR   89 (347)
Q Consensus        82 ~~~~~~~~   89 (347)
                      .++.++..
T Consensus        77 ~~a~~~~~   84 (92)
T 2dgt_A           77 QLSTSRLR   84 (92)
T ss_dssp             EESSCCCS
T ss_pred             EEccCCCC
Confidence            99877654

>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=99.61  E-value=9.8e-16  Score=114.74  Aligned_cols=78  Identities=24%  Similarity=0.500  Sum_probs=70.7

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      .....++|||+|||+++++++|+++|++||.|..|.++        ++||||+|.+.++|.+|+.. ++..+.|+.|.|.
T Consensus         7 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   78 (103)
T 2dgu_A            7 GMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIV   78 (103)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEE
Confidence            44567899999999999999999999999999999986        45999999999999999985 9999999999999


Q ss_pred             CCCcccc
Q psy630           83 PSDSHNR   89 (347)
Q Consensus        83 ~~~~~~~   89 (347)
                      ++.++..
T Consensus        79 ~a~~~~~   85 (103)
T 2dgu_A           79 FAKPPDQ   85 (103)
T ss_dssp             ECCCCCC
T ss_pred             EcCCCcc
Confidence            9877654

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.61  E-value=8.7e-16  Score=113.46  Aligned_cols=78  Identities=33%  Similarity=0.655  Sum_probs=68.9

Q ss_pred             cccCCCeEEEeCCCC-CCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccc
Q psy630            4 SIRQLNKIFVGNLPW-TVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI   81 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~-~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v   81 (347)
                      +..+.++|||+|||+ ++++++|+++|++||.|..+.+.        +|||||+|.+.++|..|+.. ++..+.|+.|.|
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   77 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLIL   77 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCE
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            356778999999998 99999999999999999999984        68999999999999999985 999999999999


Q ss_pred             cCCCcccc
Q psy630           82 QPSDSHNR   89 (347)
Q Consensus        82 ~~~~~~~~   89 (347)
                      .++.++..
T Consensus        78 ~~a~~~~~   85 (96)
T 2kvi_A           78 EVSSSNAR   85 (96)
T ss_dssp             EEEECCCC
T ss_pred             EEcCcCCC
Confidence            98866543

>1k1a_A B-cell lymphoma 3-encoded protein; BCL-3, NF-kappab transcription factors, ikappab proteins; 1.86A {Homo sapiens} SCOP: d.211.1.1 PDB: 1k1b_A

Probab=99.61  E-value=3.2e-15  Score=128.87  Aligned_cols=100  Identities=23%  Similarity=0.313  Sum_probs=88.0

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCC----CccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccC-
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDF----NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTD-  320 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~----~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d-  320 (347)
                      .+.+..+..+.+++|+|+..+...++++|+. .+.    +++..|..|.||||+|+..|+.+++++|++ .|++++..+ 
T Consensus        70 ~~~~~~~~~g~t~l~~A~~~~~~~~~~~Ll~-~~~~~~~~~~~~~~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~~~  147 (241)
T 1k1a_A           70 ASPMALDRHGQTAAHLACEHRSPTCLRALLD-SAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLE-RGADIDAVDI  147 (241)
T ss_dssp             CCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-HSCTTSCCTTCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCT
T ss_pred             CCccccCCCCCCHHHHHHHcCCHHHHHHHHH-cCCCccccccccCcCCCcHHHHHHHcCCHHHHHHHHH-cCCCcccccc
Confidence            3567778889999999998888888888887 444    788889999999999999999999999998 699999998 


Q ss_pred             CCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          321 SDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       321 ~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ..|.||||+|+..|+.+++++|+++||
T Consensus       148 ~~g~t~L~~A~~~~~~~~v~~Ll~~g~  174 (241)
T 1k1a_A          148 KSGRSPLIHAVENNSLSMVQLLLQHGA  174 (241)
T ss_dssp             TTCCCHHHHHHHTTCHHHHHHHHHTTC
T ss_pred             cCCCcHHHHHHHcCCHHHHHHHHHcCC
Confidence            789999999999999999999999886

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.61  E-value=4.9e-16  Score=126.79  Aligned_cols=81  Identities=37%  Similarity=0.710  Sum_probs=76.9

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCCc
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~~   86 (347)
                      ..++|||+|||+++++++|+++|++||.|..+++++++.+|.++|||||+|.+.++|.+|+..++..+.|++|.|.++.+
T Consensus        86 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~V~~a~p  165 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEP  165 (167)
T ss_dssp             HCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHHCSEECSSSSCEEEEECCC
T ss_pred             CCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHhCCCEEeCCeEEEEeecCC
Confidence            35689999999999999999999999999999999998899999999999999999999999999999999999999877


Q ss_pred             c
Q psy630           87 H   87 (347)
Q Consensus        87 ~   87 (347)
                      +
T Consensus       166 k  166 (167)
T 2cjk_A          166 R  166 (167)
T ss_dssp             C
T ss_pred             C
Confidence            5

>3d9h_A CDNA FLJ77766, highly similar to HOMO sapiens ankyrin repeat and SOCS box-containing...; ASB9, ANK repeat, L-shaped, structural protein; 2.20A {Homo sapiens}

Probab=99.61  E-value=2.2e-15  Score=133.93  Aligned_cols=98  Identities=18%  Similarity=0.125  Sum_probs=73.8

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..|.|+||+|+..+..+++++|++ .+++++.. ..|.||||+|+..|+.+++++|++ .|++++.+|..|.||
T Consensus       117 ~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~-~~g~t~L~~A~~~g~~~~v~~Ll~-~g~~~~~~d~~g~t~  193 (285)
T 3d9h_A          117 QVNGVTADWHTPLFNACVSGSWDCVNLLLQ-HGASVQPE-SDLASPIHEAARRGHVECVNSLIA-YGGNIDHKISHLGTP  193 (285)
T ss_dssp             CSSCCCTTCCCHHHHHHHHTCHHHHHHHHH-TTCCSSCS-CTTSCHHHHHHHHTCHHHHHHHHH-TTCCTTCCBTTTBCH
T ss_pred             CCCCCCCCCCCHHHHHHHcCHHHHHHHHHH-CCCCCCCC-CCCCCHHHHHHHcCCHHHHHHHHH-CCCCCCCcCCCCCCH
Confidence            456666777777777777777777777777 66666653 347777888887788888888887 688888888888888


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+..|+.+++++|+++||
T Consensus       194 L~~A~~~~~~~~v~~Ll~~ga  214 (285)
T 3d9h_A          194 LYLACENQQRACVKKLLESGA  214 (285)
T ss_dssp             HHHHHHTTCHHHHHHHHHTTC
T ss_pred             HHHHHHcCcHHHHHHHHHCCC
Confidence            888888888888888887775

>2fo1_E LIN-12 protein; beta-barrel, protein-DNA complex, double helix, ankyrin repeat, gene regulation/signalling protein/DNA complex; 3.12A {Caenorhabditis elegans} SCOP: d.211.1.1

Probab=99.61  E-value=2.3e-15  Score=139.05  Aligned_cols=100  Identities=21%  Similarity=0.325  Sum_probs=90.2

Q ss_pred             CCcccCCCCCcHHHHHHcCC---hHHHHHHHhhcCCCCccc--------cCCCCchHHHHHHHcCCHHHHHHHHhhcCCC
Q psy630          247 DESQLDDNEKNIYEWAKEGK---LDMLVKQLTKLKDFNINQ--------LDENGLNCLHWACDRGHLKVVQHLIEKCGAD  315 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~---~~~~~~lL~~~~~~~~~~--------~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~  315 (347)
                      +.+..+..|.|+||+|+..+   ...++++|++ .+++++.        .|..|.||||+||..|+.+++++|+++.|++
T Consensus       227 ~~~~~d~~g~t~L~~A~~~~~~~~~~~v~~Ll~-~g~~~~~~~~~~~~~~d~~g~t~Lh~A~~~g~~~~v~~Ll~~~~~~  305 (373)
T 2fo1_E          227 DIEELDRNGMTALMIVAHNEGRDQVASAKLLVE-KGAKVDYDGAARKDSEKYKGRTALHYAAQVSNMPIVKYLVGEKGSN  305 (373)
T ss_dssp             TTSCCCTTSCCHHHHHHHSCSTTHHHHHHHHHH-HTCCSSCCSGGGTSSSSCCCCCTHHHHHSSCCHHHHHHHHHHSCCC
T ss_pred             ChhhcCCCCCCHHHHHHHhCCcchHHHHHHHHH-CCCCcccccccccCcccccCCCHHHHHHHhCCHHHHHHHHHhcCCC
Confidence            56677889999999998776   8889999888 6888876        6779999999999999999999999843599


Q ss_pred             ccccCCCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          316 VNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       316 i~~~d~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ++.+|..|+||||+|+..|+.++|++|+++||
T Consensus       306 ~n~~d~~g~TpL~~A~~~g~~~iv~~Ll~~ga  337 (373)
T 2fo1_E          306 KDKQDEDGKTPIMLAAQEGRIEVVMYLIQQGA  337 (373)
T ss_dssp             TTCCCTTCCCHHHHHHHHTCHHHHHHHHHTTC
T ss_pred             ccCcCCCCCCHHHHHHHcCCHHHHHHHHHcCC
Confidence            99999999999999999999999999999986

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.60  E-value=2.8e-15  Score=121.96  Aligned_cols=81  Identities=27%  Similarity=0.553  Sum_probs=76.2

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      ....++|||+|||+++++++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|.+|+.. ++..+.|++|.|.+
T Consensus        84 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  163 (166)
T 3md3_A           84 SDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW  163 (166)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Confidence            44567899999999999999999999999999999999999999999999999999999999984 99999999999988


Q ss_pred             CC
Q psy630           84 SD   85 (347)
Q Consensus        84 ~~   85 (347)
                      +.
T Consensus       164 a~  165 (166)
T 3md3_A          164 AA  165 (166)
T ss_dssp             SC
T ss_pred             cC
Confidence            75

>3jue_A Arfgap with coiled-coil, ANK repeat and PH domain containing protein 1; arfgap domain, zinc-binding module, GTPase activ metal-binding, nitration; 2.30A {Homo sapiens} PDB: 3t9k_A 4f1p_A

Probab=99.60  E-value=2.4e-15  Score=138.20  Aligned_cols=92  Identities=21%  Similarity=0.209  Sum_probs=84.4

Q ss_pred             CCCcHHHHHHcC-ChHHHHHHHhhcCCCCccccC--CCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHH
Q psy630          254 NEKNIYEWAKEG-KLDMLVKQLTKLKDFNINQLD--ENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA  330 (347)
Q Consensus       254 ~~~~~l~~a~~~-~~~~~~~lL~~~~~~~~~~~d--~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A  330 (347)
                      .+.++||+|+.. +...++++|+. .|+++|..+  ..|.||||+||..|+.+++++||+ +|+++|.+|..|+||||+|
T Consensus       198 ~~~t~L~~Aa~~~g~~~~v~~LL~-~Gadvn~~~~~~~g~TpLh~Aa~~g~~~iv~~LL~-~Gadvn~~d~~G~TpLh~A  275 (368)
T 3jue_A          198 HPGALLFRASGHPPSLPTMADALA-HGADVNWVNGGQDNATPLIQATAANSLLACEFLLQ-NGANVNQADSAGRGPLHHA  275 (368)
T ss_dssp             CHHHHHHHHTSSSCCHHHHHHHHH-TTCCTTCCCTTTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHH
T ss_pred             CCCcHHHHHHHccCCHHHHHHHHH-cCCCCCccccccCCCCHHHHHHHCCCHHHHHHHHH-cCCCCCCCCCCCCCHHHHH
Confidence            456789988877 77777777777 799999998  899999999999999999999999 7999999999999999999


Q ss_pred             HHcCCHHHHHHHHhCCC
Q psy630          331 KAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       331 ~~~~~~~~v~~Ll~~GA  347 (347)
                      +..|+.+++++||++||
T Consensus       276 ~~~g~~~~v~~LL~~Ga  292 (368)
T 3jue_A          276 TILGHTGLACLFLKRGA  292 (368)
T ss_dssp             HHHTCHHHHHHHHHTTC
T ss_pred             HHcCcHHHHHHHHHCcC
Confidence            99999999999999987

>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=99.60  E-value=2.9e-16  Score=125.02  Aligned_cols=85  Identities=25%  Similarity=0.339  Sum_probs=72.0

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEE--E---eeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNAS--V---MFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSR   78 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~--i---~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~   78 (347)
                      ....++|||+|||+++|+++|+++|++||.|..+.  +   ++...+|.++|||||+|.+.++|.+|+.. |+..+.|+.
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~  121 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKP  121 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            35668999999999999999999999999987641  1   11123689999999999999999999995 999999999


Q ss_pred             ccccCCCcccc
Q psy630           79 LSIQPSDSHNR   89 (347)
Q Consensus        79 l~v~~~~~~~~   89 (347)
                      |.|.++.+...
T Consensus       122 l~V~~a~~~~~  132 (143)
T 3egn_A          122 MVVQFARSARP  132 (143)
T ss_dssp             CEEEECCCSCC
T ss_pred             EEEEECCCCCC
Confidence            99999876543

>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=99.60  E-value=2e-15  Score=109.30  Aligned_cols=73  Identities=22%  Similarity=0.603  Sum_probs=66.5

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhcc----C-------CeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEY----G-------QIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHV   73 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~----G-------~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~   73 (347)
                      .+..++|||+|||+++++++|+++|++|    |       .|.++++.++      +|||||+|.+.++|.+|+.+++..
T Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~~l~g~~   76 (87)
T 2hzc_A            3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAMAFDGII   76 (87)
T ss_dssp             SGGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHGGGTTCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHHhcCCCE
Confidence            4567899999999999999999999999    8       8999988644      699999999999999999669999


Q ss_pred             cCCccccccC
Q psy630           74 LEGSRLSIQP   83 (347)
Q Consensus        74 ~~g~~l~v~~   83 (347)
                      +.|+.|+|++
T Consensus        77 ~~g~~l~V~r   86 (87)
T 2hzc_A           77 FQGQSLKIRR   86 (87)
T ss_dssp             ETTEECEEEC
T ss_pred             ECCeEEEEeC
Confidence            9999999875

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.60  E-value=1.5e-15  Score=112.19  Aligned_cols=79  Identities=19%  Similarity=0.311  Sum_probs=70.6

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEE-EEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCcccccc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNA-SVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQ   82 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~-~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~   82 (347)
                      ....++|||+|||+++++++|+++|++||.|..+ .++.++.++    .|||+|.+.++|.+|+. +++..+.|++|.|.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   87 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLKVA   87 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            3456899999999999999999999999999999 488776543    39999999999999998 59999999999999


Q ss_pred             CCCcc
Q psy630           83 PSDSH   87 (347)
Q Consensus        83 ~~~~~   87 (347)
                      ++.++
T Consensus        88 ~a~~~   92 (96)
T 2e44_A           88 YIPDE   92 (96)
T ss_dssp             ECCCC
T ss_pred             EcCcc
Confidence            98775

>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=99.60  E-value=7.6e-16  Score=116.90  Aligned_cols=75  Identities=19%  Similarity=0.183  Sum_probs=68.1

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      +..++|||+|||+++++++|+++|++||.|..|.++.      ++|||||+|.+.++|++|+.. |+..+.|+.|.|.++
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   81 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            3457999999999999999999999999999998863      568999999999999999985 999999999999887


Q ss_pred             Cc
Q psy630           85 DS   86 (347)
Q Consensus        85 ~~   86 (347)
                      ..
T Consensus        82 ~~   83 (111)
T 1whx_A           82 PI   83 (111)
T ss_dssp             ET
T ss_pred             CC
Confidence            54

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=3.9e-15  Score=110.57  Aligned_cols=77  Identities=21%  Similarity=0.458  Sum_probs=69.5

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhcc--CCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEY--GQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSI   81 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~--G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v   81 (347)
                      ....++|||+|||+++++++|+++|++|  |.|..+.++        +|||||+|.+.++|.+|+. +++..+.|+.|.|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEV   83 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEE
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            4556899999999999999999999999  899988764        5799999999999999998 5999999999999


Q ss_pred             cCCCcccc
Q psy630           82 QPSDSHNR   89 (347)
Q Consensus        82 ~~~~~~~~   89 (347)
                      .++.++..
T Consensus        84 ~~a~~~~~   91 (99)
T 2cpd_A           84 TLAKPVDK   91 (99)
T ss_dssp             ECCCCCCC
T ss_pred             EECCCCCC
Confidence            99887554

>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=99.59  E-value=3.8e-15  Score=124.39  Aligned_cols=80  Identities=20%  Similarity=0.302  Sum_probs=73.2

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCCcc
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDSH   87 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~~~   87 (347)
                      .++|||+|||+++++++|+++|++||.|..|+++++. +|.++|||||+|.+.++|.+|+...+..+.|+.|.|.++...
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDY  187 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTTC
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHHH
Confidence            4899999999999999999999999999999999987 499999999999999999999998667999999999887654


Q ss_pred             c
Q psy630           88 N   88 (347)
Q Consensus        88 ~   88 (347)
                      .
T Consensus       188 ~  188 (193)
T 2voo_A          188 F  188 (193)
T ss_dssp             -
T ss_pred             H
Confidence            3

>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=99.59  E-value=3.3e-15  Score=122.43  Aligned_cols=80  Identities=24%  Similarity=0.525  Sum_probs=75.2

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ...++|||+|||+++++++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|.+|+.. ++..+.|+.|.|.+|
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            3468999999999999999999999999999999999988999999999999999999999985 999999999999876


Q ss_pred             C
Q psy630           85 D   85 (347)
Q Consensus        85 ~   85 (347)
                      .
T Consensus       172 s  172 (172)
T 2g4b_A          172 S  172 (172)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=4.1e-15  Score=106.39  Aligned_cols=76  Identities=16%  Similarity=0.343  Sum_probs=65.9

Q ss_pred             cccCCCe-EEEeCCCCCCCHHH----HHHHHhcc-CCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCC
Q psy630            4 SIRQLNK-IFVGNLPWTVSHNE----LKKFFSEY-GQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEG   76 (347)
Q Consensus         4 ~~~~~~~-l~V~nLp~~~t~~~----l~~~f~~~-G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g   76 (347)
                      ...+..+ |||+|||+++++++    |+++|++| |+|..|       |+   |+|||+|.+.++|.+|++. ++..+.|
T Consensus         4 ~~~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~g   73 (96)
T 2diu_A            4 GSSGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFG   73 (96)
T ss_dssp             SCCCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSS
T ss_pred             CCCCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCC
Confidence            3444555 99999999999988    55899999 599888       34   9999999999999999985 9999999


Q ss_pred             ccccccCCCcccc
Q psy630           77 SRLSIQPSDSHNR   89 (347)
Q Consensus        77 ~~l~v~~~~~~~~   89 (347)
                      |+|+|.++..++.
T Consensus        74 r~i~v~~A~~~sd   86 (96)
T 2diu_A           74 NRIIVSFTPKNRE   86 (96)
T ss_dssp             SCCEEESSCCSCC
T ss_pred             ceEEEEecCCCcc
Confidence            9999999987654

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=7.7e-16  Score=111.83  Aligned_cols=79  Identities=23%  Similarity=0.502  Sum_probs=68.0

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      ....++|||+|||+++++++|+++|++||.|..++++++     ++|||||+|.+.++|+++... ...+.|+.|.|.++
T Consensus         2 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~-~~~~~g~~l~v~~a   75 (88)
T 1wf0_A            2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE-DLIIKGISVHISNA   75 (88)
T ss_dssp             CSCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC-EEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC-CceeCCEEEEEEec
Confidence            346789999999999999999999999999999999754     689999999999999876443 45668999999998


Q ss_pred             Ccccc
Q psy630           85 DSHNR   89 (347)
Q Consensus        85 ~~~~~   89 (347)
                      .++..
T Consensus        76 ~~~~~   80 (88)
T 1wf0_A           76 EPKHN   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            77654

>3eu9_A Huntingtin-interacting protein 14; epigenetics, ankyrin repeats, methyllyine binding, huntingti interacting protein 14, acyltransferase, ANK repeat; HET: HIS; 1.99A {Homo sapiens}

Probab=99.59  E-value=3.2e-15  Score=128.48  Aligned_cols=99  Identities=26%  Similarity=0.374  Sum_probs=90.1

Q ss_pred             CCcccCCCCCcHHHHHH-cCChHHHHHHHhhcCCCCccccCC-CCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCC
Q psy630          247 DESQLDDNEKNIYEWAK-EGKLDMLVKQLTKLKDFNINQLDE-NGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGD  324 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~-~~~~~~~~~lL~~~~~~~~~~~d~-~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~  324 (347)
                      +.+..+..+.+++|.|+ .++...++++|.. .+++++..+. .|.||||+|+..|+.+++++|++ .|++++.+|..|.
T Consensus       134 ~~~~~~~~g~t~l~~a~~~~~~~~~~~~L~~-~~~~~~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~  211 (240)
T 3eu9_A          134 DVDMMDQNGMTPLMWAAYRTHSVDPTRLLLT-FNVSVNLGDKYHKNTALHWAVLAGNTTVISLLLE-AGANVDAQNIKGE  211 (240)
T ss_dssp             CTTCCCTTSCCHHHHHHHHCCSSTTHHHHHH-TTCCTTCCCTTTCCCHHHHHHHHTCHHHHHHHHH-HTCCTTCBCTTSC
T ss_pred             CccccCCCCCcHHHHHHHhCChHHHHHHHHh-cCCCcchhhccCCCcHHHHHHHcCCHHHHHHHHH-cCCCCCCcCCCCC
Confidence            46667788999999988 6666788888888 8999999987 89999999999999999999999 6999999999999


Q ss_pred             cHHHHHHHcCCHHHHHHHHhCCC
Q psy630          325 YGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       325 TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||||+|+..|+.+++++|+++|+
T Consensus       212 t~l~~A~~~~~~~~v~~L~~~~~  234 (240)
T 3eu9_A          212 SALDLAKQRKNVWMINHLQEARQ  234 (240)
T ss_dssp             BHHHHHHHTTCHHHHHHHHHHC-
T ss_pred             CHHHHHHHcCcHHHHHHHHHhhh
Confidence            99999999999999999999875

>1sw6_A Regulatory protein SWI6; transcription regulation, ankyrin repeats, cell-cycle; 2.10A {Saccharomyces cerevisiae} SCOP: d.211.1.1

Probab=99.59  E-value=1.1e-15  Score=138.71  Aligned_cols=101  Identities=16%  Similarity=0.108  Sum_probs=81.5

Q ss_pred             cCCcccCCCCCcHHHHHHcCCh---HHHHHHHhhcCCCCccccCCCCchHHHHHHH----cCCHHHHHHHHhhcCC----
Q psy630          246 NDESQLDDNEKNIYEWAKEGKL---DMLVKQLTKLKDFNINQLDENGLNCLHWACD----RGHLKVVQHLIEKCGA----  314 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~---~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~----~g~~~~v~~Ll~~~ga----  314 (347)
                      .+++..+..|.||||+|+..++   ..++..|++....+++.+|..|+||||+|+.    .|+.+++++|++ .++    
T Consensus       155 ad~n~~d~~g~TpLh~A~~~g~~~~~~~~~~ll~~~~~~~~~~d~~g~tpLh~A~~~~~~~g~~~~v~~Ll~-~~~~~~~  233 (327)
T 1sw6_A          155 SNRLYGDNMGESCLVKAVKSVNNYDSGTFEALLDYLYPCLILEDSMNRTILHHIIITSGMTGCSAAAKYYLD-ILMGWIV  233 (327)
T ss_dssp             CCTTBCCTTCCCHHHHHHHSSHHHHTTCHHHHHHHHGGGGGEECTTCCCHHHHHHHHHTSTTCHHHHHHHHH-HHHHHHH
T ss_pred             CCCCCcCCCCCCHHHHHHHhcccccHHHHHHHHHhhhccccCCCCCCCCHHHHHHHHccccccHHHHHHHHH-HHHHHHh
Confidence            4567778888999999888776   3344444442346788889999999999998    889999999987 443    


Q ss_pred             -----------------------------------------CccccCCCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          315 -----------------------------------------DVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       315 -----------------------------------------~i~~~d~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                                                               ++|.+|..|+||||+|+..|+.++|++||++||
T Consensus       234 ~~~~~~i~~~~~~~g~~~~~~~~~g~t~L~~a~~~~~Ll~~~~n~~d~~G~TpLh~A~~~g~~~~v~~Ll~~Ga  307 (327)
T 1sw6_A          234 KKQNRPIQSGTNEKESKPNDKNGERKDSILENLDLKWIIANMLNAQDSNGDTCLNIAARLGNISIVDALLDYGA  307 (327)
T ss_dssp             HGGGCCEEEC----------------CHHHHHCSHHHHHHHTTTCCCTTSCCHHHHHHHHCCHHHHHHHHHTTC
T ss_pred             cccchHHHhhhhcccCCcccccccCCChhHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHcCCHHHHHHHHHcCC
Confidence                                                     588889999999999999999999999999987

>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=99.58  E-value=3.2e-15  Score=113.34  Aligned_cols=74  Identities=28%  Similarity=0.570  Sum_probs=67.6

Q ss_pred             CCCeEEEeCCCCC-CCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            7 QLNKIFVGNLPWT-VSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         7 ~~~~l~V~nLp~~-~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ..++|||+|||++ +++++|+++|++||.|..|.+        ++|||||+|.+.++|++|+.. ++..+.|+.|.|.++
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   97 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA   97 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEES
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            3479999999999 999999999999999999998        478999999999999999965 999999999999998


Q ss_pred             Cccc
Q psy630           85 DSHN   88 (347)
Q Consensus        85 ~~~~   88 (347)
                      .+..
T Consensus        98 ~~~~  101 (110)
T 1wf1_A           98 GEPK  101 (110)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7533

>1sw6_A Regulatory protein SWI6; transcription regulation, ankyrin repeats, cell-cycle; 2.10A {Saccharomyces cerevisiae} SCOP: d.211.1.1

Probab=99.58  E-value=1.4e-15  Score=138.02  Aligned_cols=100  Identities=18%  Similarity=0.097  Sum_probs=90.5

Q ss_pred             cCCcc-cCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCC---HHHHHHHHhhcCCCccccCC
Q psy630          246 NDESQ-LDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGH---LKVVQHLIEKCGADVNVTDS  321 (347)
Q Consensus       246 ~~~~~-~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~---~~~v~~Ll~~~ga~i~~~d~  321 (347)
                      .+++. .+..|.||||+|+..+..+++++|++ .|++++.+|..|+||||+|+..|+   .+++..|++..+++++.+|.
T Consensus       121 ~dvn~~~d~~g~TpLh~Aa~~g~~~~v~~Ll~-~Gad~n~~d~~g~TpLh~A~~~g~~~~~~~~~~ll~~~~~~~~~~d~  199 (327)
T 1sw6_A          121 LNLNIPVDEHGNTPLHWLTSIANLELVKHLVK-HGSNRLYGDNMGESCLVKAVKSVNNYDSGTFEALLDYLYPCLILEDS  199 (327)
T ss_dssp             CCSCSCCSTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTBCCTTCCCHHHHHHHSSHHHHTTCHHHHHHHHGGGGGEECT
T ss_pred             CCcccccCCCCCcHHHHHHHcCCHHHHHHHHH-cCCCCCCcCCCCCCHHHHHHHhcccccHHHHHHHHHhhhccccCCCC
Confidence            35666 78899999999999999999999999 899999999999999999999998   78888888843388999999


Q ss_pred             CCCcHHHHHHH----cCCHHHHHHHHhCC
Q psy630          322 DGDYGLDYAKA----IEHTDLIEYLVNSG  346 (347)
Q Consensus       322 ~g~TpLh~A~~----~~~~~~v~~Ll~~G  346 (347)
                      .|+||||+|+.    .|+.+++++|++.|
T Consensus       200 ~g~tpLh~A~~~~~~~g~~~~v~~Ll~~~  228 (327)
T 1sw6_A          200 MNRTILHHIIITSGMTGCSAAAKYYLDIL  228 (327)
T ss_dssp             TCCCHHHHHHHHHTSTTCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHccccccHHHHHHHHHHH
Confidence            99999999999    99999999999763

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.58  E-value=5.4e-15  Score=124.00  Aligned_cols=84  Identities=23%  Similarity=0.508  Sum_probs=78.8

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ...++|||+|||+++++++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|.+|+.. ++..+.|+.|.|.++
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4568999999999999999999999999999999999988999999999999999999999985 999999999999998


Q ss_pred             Ccccc
Q psy630           85 DSHNR   89 (347)
Q Consensus        85 ~~~~~   89 (347)
                      .++..
T Consensus       192 ~~~~~  196 (198)
T 2yh0_A          192 SVGAK  196 (198)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            77653

>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=99.58  E-value=1.9e-15  Score=109.72  Aligned_cols=75  Identities=23%  Similarity=0.322  Sum_probs=68.7

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      +..++|||+|||+++++++|+++|++| .|..+++.      +++|||||+|.+.++|++|+.. ++..+.|++|+|.++
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   75 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEc
Confidence            467899999999999999999999999 99999884      5789999999999999999985 999999999999988


Q ss_pred             Ccc
Q psy630           85 DSH   87 (347)
Q Consensus        85 ~~~   87 (347)
                      ...
T Consensus        76 ~~~   78 (88)
T 1wg1_A           76 PTD   78 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.58  E-value=8.1e-15  Score=124.68  Aligned_cols=83  Identities=25%  Similarity=0.529  Sum_probs=78.1

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ...++|||+|||+++++++|+++|++||.|..+++++++.+|+++|||||+|.+.++|.+|+.. ++..+.|+.|.|.++
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            4568999999999999999999999999999999999998999999999999999999999995 999999999999998


Q ss_pred             Cccc
Q psy630           85 DSHN   88 (347)
Q Consensus        85 ~~~~   88 (347)
                      .++.
T Consensus       203 ~~~~  206 (216)
T 2qfj_A          203 VTPP  206 (216)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            7754

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.57  E-value=5.5e-15  Score=125.71  Aligned_cols=81  Identities=27%  Similarity=0.543  Sum_probs=74.7

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      ..++|||+|||+++++++|+++|++||.|..++|++++  +.++|||||+|.+.++|.+|++. |+..+.|++|.|.++.
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~  179 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK  179 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45789999999999999999999999999999999986  55899999999999999999985 9999999999999998


Q ss_pred             cccc
Q psy630           86 SHNR   89 (347)
Q Consensus        86 ~~~~   89 (347)
                      ++..
T Consensus       180 ~~~~  183 (213)
T 4f02_A          180 SRKE  183 (213)
T ss_dssp             CHHH
T ss_pred             CCcc
Confidence            7654

>1dcq_A PYK2-associated protein beta; zinc-binding module, ankyrin repeats, metal binding protein; 2.10A {Mus musculus} SCOP: d.211.1.1 g.45.1.1

Probab=99.56  E-value=1.2e-14  Score=128.82  Aligned_cols=88  Identities=16%  Similarity=0.292  Sum_probs=74.6

Q ss_pred             cHHHHHHcCChHHHHHHHhhcCCCC------ccccCCCCchHHHHHHHc---CCHHHHHHHHhhcCCCccccCCCCCcHH
Q psy630          257 NIYEWAKEGKLDMLVKQLTKLKDFN------INQLDENGLNCLHWACDR---GHLKVVQHLIEKCGADVNVTDSDGDYGL  327 (347)
Q Consensus       257 ~~l~~a~~~~~~~~~~lL~~~~~~~------~~~~d~~g~tpLh~A~~~---g~~~~v~~Ll~~~ga~i~~~d~~g~TpL  327 (347)
                      .++.++..++...+..++..  +.+      ++..|..|+||||+||..   |+.+++++|++ +|+++|.+|..|+|||
T Consensus       133 ~l~~a~~~~d~~~~~~ll~~--g~~~~~~~~l~~~~~~g~t~Lh~A~~~~~~~~~~~v~~Ll~-~ga~in~~d~~g~TpL  209 (278)
T 1dcq_A          133 SLCEAVKTRDIFGLLQAYAD--GVDLTEKIPLANGHEPDETALHLAVRSVDRTSLHIVDFLVQ-NSGNLDKQTGKGSTAL  209 (278)
T ss_dssp             HHHHHHHTTCHHHHHHHHHT--TCCTTSBCCCSSCSSTTCBHHHHHHHHCCTTTHHHHHHHHH-HCSCTTCCCTTCCCHH
T ss_pred             hhhhHhhhcccHHHHHHHHh--hcchhhhccccccccCCCCcchHHHHhcccchHHHHHHHHH-CCCCccccCCCCCCHH
Confidence            34445566666665555544  666      455588999999999999   89999999999 7999999999999999


Q ss_pred             HHHHHcCCHHHHHHHHhCCC
Q psy630          328 DYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       328 h~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |+|+..|+.++|++||++||
T Consensus       210 h~A~~~g~~~~v~~Ll~~ga  229 (278)
T 1dcq_A          210 HYCCLTDNAECLKLLLRGKA  229 (278)
T ss_dssp             HHHHHTTCHHHHHHHHHTTC
T ss_pred             HHHHHcCCHHHHHHHHHcCC
Confidence            99999999999999999997

>3eu9_A Huntingtin-interacting protein 14; epigenetics, ankyrin repeats, methyllyine binding, huntingti interacting protein 14, acyltransferase, ANK repeat; HET: HIS; 1.99A {Homo sapiens}

Probab=99.56  E-value=1.6e-14  Score=124.09  Aligned_cols=98  Identities=31%  Similarity=0.497  Sum_probs=58.4

Q ss_pred             CcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccC-CCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          248 ESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLD-ENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       248 ~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d-~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      .+..+..|.++||+|+..+...++++|++ .+.+++..+ ..|.||||+|+..|+.+++++|++ .|++++.++..|.||
T Consensus        35 ~~~~~~~g~t~L~~A~~~~~~~~v~~Ll~-~~~~~~~~~~~~~~t~L~~A~~~~~~~~v~~Ll~-~g~~~~~~~~~g~t~  112 (240)
T 3eu9_A           35 VRQPDKENVTLLHWAAINNRIDLVKYYIS-KGAIVDQLGGDLNSTPLHWATRQGHLSMVVQLMK-YGADPSLIDGEGCSC  112 (240)
T ss_dssp             TTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCBTTTTBCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTSCCH
T ss_pred             cCCCCCCCCCHHHHHHHhCCHHHHHHHHH-cCCcchhhcCCcCCChhHHHHHcCCHHHHHHHHH-cCCCCcccCCCCCCH
Confidence            34444556666666666666666666665 455554333 336666666666666666666665 466666666666666


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+..|+.+++++|+++|+
T Consensus       113 l~~A~~~~~~~~~~~Ll~~~~  133 (240)
T 3eu9_A          113 IHLAAQFGHTSIVAYLIAKGQ  133 (240)
T ss_dssp             HHHHHHTTCHHHHHHHHHTTC
T ss_pred             HHHHHHcCHHHHHHHHHhcCC
Confidence            666666666666666666553

>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=99.56  E-value=7.5e-15  Score=117.50  Aligned_cols=81  Identities=16%  Similarity=0.256  Sum_probs=71.0

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCC--cccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEG--SRLS   80 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g--~~l~   80 (347)
                      .+....+|||+|||+.+|+++|+++|++||.|.+|.|...    .++|||||+|.+.++|+.|++. +|..|.|  +.|+
T Consensus        42 ~ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~  117 (164)
T 1sjr_A           42 GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLR  117 (164)
T ss_dssp             CCCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEE
T ss_pred             CCCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEE
Confidence            3455668999999999999999999999999999998643    3579999999999999999985 9999965  9999


Q ss_pred             ccCCCccc
Q psy630           81 IQPSDSHN   88 (347)
Q Consensus        81 v~~~~~~~   88 (347)
                      |.++.++.
T Consensus       118 V~~Ak~~~  125 (164)
T 1sjr_A          118 IDFSKLTS  125 (164)
T ss_dssp             EEECSSSS
T ss_pred             EEEecCCc
Confidence            99987753

>3lvq_E ARF-GAP with SH3 domain, ANK repeat and PH domain containing protein 3, ADP-ribosylation...; GDP, ASAP3, UPLC1, linkers, alternat splicing; HET: GDP; 3.38A {Homo sapiens} PDB: 3lvr_E*

Probab=99.56  E-value=6.6e-15  Score=141.16  Aligned_cols=88  Identities=18%  Similarity=0.301  Sum_probs=75.6

Q ss_pred             cHHHHHHcCChHHHHHHHhhcCCCCcccc------CCCCchHHHHHHH---cCCHHHHHHHHhhcCCCccccCCCCCcHH
Q psy630          257 NIYEWAKEGKLDMLVKQLTKLKDFNINQL------DENGLNCLHWACD---RGHLKVVQHLIEKCGADVNVTDSDGDYGL  327 (347)
Q Consensus       257 ~~l~~a~~~~~~~~~~lL~~~~~~~~~~~------d~~g~tpLh~A~~---~g~~~~v~~Ll~~~ga~i~~~d~~g~TpL  327 (347)
                      .++.++..|+...+.. |+. .|+++|.+      |..|+||||+||.   .|+.+++++||+ +|+++|.+|..|+|||
T Consensus       135 ~L~~A~~~g~~~~v~~-ll~-~g~~~n~~~~~~~~~~~g~t~Lh~A~~~a~~g~~~~v~~Ll~-~ga~vn~~d~~g~TpL  211 (497)
T 3lvq_E          135 RLWTAICNRDLLSVLE-AFA-NGQDFGQPLPGPDAQAPEELVLHLAVKVANQASLPLVDFIIQ-NGGHLDAKAADGNTAL  211 (497)
T ss_dssp             HHHHHHHHTCHHHHHH-HHH-TTCCSSSCBCCSSSCCSCBCHHHHHHHTCCTTTHHHHHHHHH-HSCCTTCCCSSSCCHH
T ss_pred             HHHHHHhccCHHHHHH-HHh-hcccccCCCCCcccccccchHHHHHHHhcccccHHHHHHHHH-cCCCCCccCCCCCcHH
Confidence            3445555666655544 445 48999887      8899999999966   999999999999 7999999999999999


Q ss_pred             HHHHHcCCHHHHHHHHhCCC
Q psy630          328 DYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       328 h~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |+|+..|+.++|++||++||
T Consensus       212 h~A~~~g~~~~v~~Ll~~ga  231 (497)
T 3lvq_E          212 HYAALYNQPDCLKLLLKGRA  231 (497)
T ss_dssp             HHHTTTTCHHHHHHHHHTCC
T ss_pred             HHHHHcCCHHHHHHHHHcCC
Confidence            99999999999999999997

>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=99.56  E-value=5.9e-15  Score=138.25  Aligned_cols=82  Identities=17%  Similarity=0.556  Sum_probs=76.8

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      ..++|||+|||+.+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++|.+|+.. |+..|.|+.|.|.++.
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~  180 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  180 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            457999999999999999999999999999999999999999999999999999999999975 9999999999999887


Q ss_pred             ccc
Q psy630           86 SHN   88 (347)
Q Consensus        86 ~~~   88 (347)
                      +..
T Consensus       181 ~~~  183 (437)
T 3pgw_S          181 GRT  183 (437)
T ss_pred             CCC
Confidence            643

>2b0o_E UPLC1; arfgap, structural genomics, structural genomics consortium, SGC, metal binding protein; 2.06A {Homo sapiens}

Probab=99.55  E-value=1.4e-14  Score=129.84  Aligned_cols=88  Identities=18%  Similarity=0.312  Sum_probs=76.2

Q ss_pred             cHHHHHHcCChHHHHHHHhhcCCCCccc------cCCCCchHHHHHHHc---CCHHHHHHHHhhcCCCccccCCCCCcHH
Q psy630          257 NIYEWAKEGKLDMLVKQLTKLKDFNINQ------LDENGLNCLHWACDR---GHLKVVQHLIEKCGADVNVTDSDGDYGL  327 (347)
Q Consensus       257 ~~l~~a~~~~~~~~~~lL~~~~~~~~~~------~d~~g~tpLh~A~~~---g~~~~v~~Ll~~~ga~i~~~d~~g~TpL  327 (347)
                      .++.++..++...+..+| . .+.+++.      .+..|+||||+||..   ++.+++++||+ +|+++|.+|..|+|||
T Consensus       154 ~L~~A~~~g~~~~v~~ll-~-~g~d~~~~~~~~~~~~~g~t~Lh~A~~~~~~~~~~iv~~Ll~-~gadvn~~d~~G~TpL  230 (301)
T 2b0o_E          154 RLWTAICNRDLLSVLEAF-A-NGQDFGQPLPGPDAQAPEELVLHLAVKVANQASLPLVDFIIQ-NGGHLDAKAADGNTAL  230 (301)
T ss_dssp             HHHHHHHTTCHHHHHHHH-H-TTCCTTSCEECSSSCSCEECHHHHHHHTCCTTTHHHHHHHHH-HSSCTTCCCTTCCCHH
T ss_pred             HHhhhhhccCHHHHHHHH-h-cCCcccccCCCcccCCCCccHHHHHHHhcccCcHHHHHHHHh-cCCCCCCCCCCCCCHH
Confidence            345555566666555555 4 5889988      689999999999997   89999999999 7999999999999999


Q ss_pred             HHHHHcCCHHHHHHHHhCCC
Q psy630          328 DYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       328 h~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |+|+..|+.+++++||++||
T Consensus       231 h~A~~~g~~~~v~~Ll~~ga  250 (301)
T 2b0o_E          231 HYAALYNQPDCLKLLLKGRA  250 (301)
T ss_dssp             HHHHHTTCHHHHHHHHHTTC
T ss_pred             HHHHHcCCHHHHHHHHHcCC
Confidence            99999999999999999997

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.55  E-value=1.1e-14  Score=112.25  Aligned_cols=80  Identities=18%  Similarity=0.326  Sum_probs=70.1

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeE-EEEEEcCHHHHHHHHhc-CCCccCC--ccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGF-GFVTFQNKEAVDKVFST-DSHVLEG--SRL   79 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~-afV~f~~~~~a~~a~~~-~~~~~~g--~~l   79 (347)
                      .+...-+|||+|||+.+|+++|+++|++||.|.+|+++...     +|| |||+|.+.++|..|+.. ||..+.|  +.|
T Consensus        24 ~ps~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~L   98 (130)
T 3zzy_A           24 GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTL   98 (130)
T ss_dssp             -CCSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEE
T ss_pred             CCCceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEE
Confidence            34566689999999999999999999999999999987642     577 99999999999999986 9999988  889


Q ss_pred             cccCCCccc
Q psy630           80 SIQPSDSHN   88 (347)
Q Consensus        80 ~v~~~~~~~   88 (347)
                      +|.++.+..
T Consensus        99 rI~~ak~~~  107 (130)
T 3zzy_A           99 RIDFSKLTS  107 (130)
T ss_dssp             EEEECSCSS
T ss_pred             EEEecCCCc
Confidence            999987643

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.55  E-value=1.3e-14  Score=107.30  Aligned_cols=78  Identities=21%  Similarity=0.367  Sum_probs=69.5

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      .+...++|||+||  ++++++|+++|++||.|..|.+.      .++|||||+|.+.++|.+|+.. ++..+.|+.|.|.
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~   82 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVN   82 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            3456789999996  89999999999999999999984      5679999999999999999975 9999999999999


Q ss_pred             CCCcccc
Q psy630           83 PSDSHNR   89 (347)
Q Consensus        83 ~~~~~~~   89 (347)
                      ++.++..
T Consensus        83 ~a~~~~~   89 (97)
T 1x5p_A           83 IARKQPM   89 (97)
T ss_dssp             CCSSCCC
T ss_pred             ECCCCCC
Confidence            9977654

>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=99.55  E-value=2.4e-14  Score=116.74  Aligned_cols=79  Identities=29%  Similarity=0.601  Sum_probs=73.5

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCC--cccccc
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEG--SRLSIQ   82 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g--~~l~v~   82 (347)
                      ...++|||+|||+++++++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|.+|+.. ++..+.|  ++|.|.
T Consensus        87 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~  166 (168)
T 1b7f_A           87 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR  166 (168)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEE
Confidence            4567999999999999999999999999999999999998899999999999999999999985 9999988  888887


Q ss_pred             CC
Q psy630           83 PS   84 (347)
Q Consensus        83 ~~   84 (347)
                      +|
T Consensus       167 ~A  168 (168)
T 1b7f_A          167 LA  168 (168)
T ss_dssp             EC
T ss_pred             eC
Confidence            64

>1n0q_A 3ANK, 3 ankyrin repeats; structural protein; 1.26A {} SCOP: k.37.1.1

Probab=99.54  E-value=9.8e-15  Score=106.89  Aligned_cols=59  Identities=41%  Similarity=0.650  Sum_probs=55.7

Q ss_pred             CCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          288 NGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       288 ~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      +|+||||+||..|+.+++++|++ .|+++|.+|..|+||||+|+..|+.+++++|+++||
T Consensus         1 ~g~t~L~~A~~~~~~~~v~~Ll~-~g~~~n~~d~~g~t~L~~A~~~~~~~~v~~Ll~~ga   59 (93)
T 1n0q_A            1 NGRTPLHLAARNGHLEVVKLLLE-AGADVNAKDKNGRTPLHLAARNGHLEVVKLLLEAGA   59 (93)
T ss_dssp             --CCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHHTTC
T ss_pred             CCCcHHHHHHHcCCHHHHHHHHH-cCCCCcccCCCCCCHHHHHHHcCCHHHHHHHHHcCC
Confidence            48999999999999999999999 799999999999999999999999999999999986

>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=99.54  E-value=4.3e-15  Score=111.94  Aligned_cols=77  Identities=17%  Similarity=0.255  Sum_probs=66.4

Q ss_pred             cccCCCeEEE--eCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCcc-----C
Q psy630            4 SIRQLNKIFV--GNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVL-----E   75 (347)
Q Consensus         4 ~~~~~~~l~V--~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~-----~   75 (347)
                      .....++|||  ||||+++++++|+++|++||.|..|.++.      .+|||||+|.+.++|++|+.. ||..+     .
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~   94 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQ   94 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSC
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCC
Confidence            3456789999  77999999999999999999999998753      368999999999999999985 99887     6


Q ss_pred             CccccccCCCc
Q psy630           76 GSRLSIQPSDS   86 (347)
Q Consensus        76 g~~l~v~~~~~   86 (347)
                      |++|.|.++..
T Consensus        95 g~~l~v~~a~~  105 (114)
T 2cq2_A           95 KITLYLNFVEK  105 (114)
T ss_dssp             EEECEEEEESC
T ss_pred             CcEEEEEeccc
Confidence            78888877654

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=99.54  E-value=7.5e-15  Score=112.15  Aligned_cols=70  Identities=29%  Similarity=0.375  Sum_probs=61.9

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCcccccc
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQ   82 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~   82 (347)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.+       |||||+|.+.++|++|+. +|+..+.|+.+.|.
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~   84 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETA   84 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeE
Confidence            45689999999999999999999999999999999765       899999999999999998 49999999994443

>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=99.53  E-value=3.5e-14  Score=115.49  Aligned_cols=79  Identities=25%  Similarity=0.604  Sum_probs=72.0

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcc--ccc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSR--LSI   81 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~--l~v   81 (347)
                      ....++|||+|||+++++++|+++|++||.|..+++++++.+|.++|||||+|.+.++|.+|+.. ++..+.|+.  |.|
T Consensus        85 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v  164 (167)
T 1fxl_A           85 SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV  164 (167)
T ss_dssp             GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEE
Confidence            34567899999999999999999999999999999999998999999999999999999999985 999999976  555


Q ss_pred             cC
Q psy630           82 QP   83 (347)
Q Consensus        82 ~~   83 (347)
                      .+
T Consensus       165 ~~  166 (167)
T 1fxl_A          165 KF  166 (167)
T ss_dssp             EE
T ss_pred             Ee
Confidence            54

>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=99.53  E-value=2.9e-14  Score=125.05  Aligned_cols=134  Identities=23%  Similarity=0.354  Sum_probs=95.5

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc--CCCccC---Cccccc
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST--DSHVLE---GSRLSI   81 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~--~~~~~~---g~~l~v   81 (347)
                      ..++|||+|||+.+|+++|+++|++||.|..|.+++++ +|.++|||||+|.+.++|.+|+..  ++..+.   |++|.|
T Consensus        95 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v  173 (261)
T 3sde_A           95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIV  173 (261)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEE
T ss_pred             cCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCC-CCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEE
Confidence            45789999999999999999999999999999999994 899999999999999999999985  555555   899999


Q ss_pred             cCCCcccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHH
Q psy630           82 QPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSE  161 (347)
Q Consensus        82 ~~~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~e  161 (347)
                      .++.+......               ++....... ..+....    ........||.+.+....+|.++.++.....+.
T Consensus       174 ~~~~~~~~~~~---------------~~~~~~~~~-~~~~~~r----~~~p~~~~pgs~~~~~~~~~~~~~~~~~~~~~~  233 (261)
T 3sde_A          174 EPMEQFDDEDG---------------LPEKLMQKT-QQYHKER----EQPPRFAQPGTFEFEYASRWKALDEMEKQQREQ  233 (261)
T ss_dssp             EECCCEESSSC---------------CCGGGSCCC-HHHHHHH----TSCSEECCTTSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             eeccccCccCC---------------Ccchhhhcc-hhhhhhc----cCCCCCCCCCcccccccchHHHHHHHHHHHHHH
Confidence            98876543111               111000000 1111111    112344567888887788888887754433333

>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=99.51  E-value=5.3e-14  Score=115.41  Aligned_cols=79  Identities=24%  Similarity=0.471  Sum_probs=71.2

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccC---Cccccc
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLE---GSRLSI   81 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~---g~~l~v   81 (347)
                      ...++|||+|||+++|+++|+++|++||.|..+++++++ +|.++|||||+|.+.++|.+|+.. ++..+.   |++|.|
T Consensus        93 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V  171 (175)
T 3nmr_A           93 VEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVV  171 (175)
T ss_dssp             GGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEE
T ss_pred             CCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEE
Confidence            356799999999999999999999999999999999996 599999999999999999999975 887665   489999


Q ss_pred             cCCC
Q psy630           82 QPSD   85 (347)
Q Consensus        82 ~~~~   85 (347)
                      .++.
T Consensus       172 ~~ad  175 (175)
T 3nmr_A          172 KFAD  175 (175)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            8763

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.51  E-value=5.3e-14  Score=107.99  Aligned_cols=77  Identities=12%  Similarity=0.217  Sum_probs=66.9

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeE-EEEEEcCHHHHHHHHhc-CCCccCC--ccccc
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGF-GFVTFQNKEAVDKVFST-DSHVLEG--SRLSI   81 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~-afV~f~~~~~a~~a~~~-~~~~~~g--~~l~v   81 (347)
                      .....|||+|||+.+++++|+++|++||.|..|+|.. +     .|| |||+|.+.++|..|+.. ||..|.|  +.|+|
T Consensus        23 s~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V   96 (124)
T 2e5i_A           23 NKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKI   96 (124)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEE
T ss_pred             CcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEE
Confidence            3444678999999999999999999999999999865 2     276 99999999999999985 9999988  58999


Q ss_pred             cCCCccc
Q psy630           82 QPSDSHN   88 (347)
Q Consensus        82 ~~~~~~~   88 (347)
                      .++.++.
T Consensus        97 ~~Ak~~~  103 (124)
T 2e5i_A           97 EYARPTR  103 (124)
T ss_dssp             ECCSCSC
T ss_pred             EEecCCc
Confidence            9987654

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.51  E-value=5.7e-14  Score=105.04  Aligned_cols=82  Identities=12%  Similarity=0.062  Sum_probs=72.3

Q ss_pred             ccCCCeEEEeCCCC-----CCCHHHHHHHHhccCCeeEEEEeeeCCC-CCceeEEEEEEcCHHHHHHHHhc-CCCccCCc
Q psy630            5 IRQLNKIFVGNLPW-----TVSHNELKKFFSEYGQIMNASVMFDKNT-GLSKGFGFVTFQNKEAVDKVFST-DSHVLEGS   77 (347)
Q Consensus         5 ~~~~~~l~V~nLp~-----~~t~~~l~~~f~~~G~i~~~~i~~~~~t-~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~   77 (347)
                      +...+.|+|+||..     +-++++|++.|++||.|.+|.|++++.+ +.++|||||+|.+.++|.+|+.. ||..+.||
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            46678999999963     2378999999999999999999998754 68999999999999999999985 99999999


Q ss_pred             cccccCCCc
Q psy630           78 RLSIQPSDS   86 (347)
Q Consensus        78 ~l~v~~~~~   86 (347)
                      .|.|.++..
T Consensus        85 ~i~v~~a~~   93 (105)
T 2pe8_A           85 VVKACFYNL   93 (105)
T ss_dssp             ECEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999998865

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.45  E-value=7.2e-14  Score=114.80  Aligned_cols=77  Identities=21%  Similarity=0.440  Sum_probs=69.9

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ...++|||+|||+++++++|+++|++||.|..+     ..++.++|||||+|.+.++|.+|+.. ++..+.|+.|.|.++
T Consensus        97 ~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  171 (175)
T 1fje_B           97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT  171 (175)
T ss_dssp             GGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEEC
T ss_pred             ccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEec
Confidence            356799999999999999999999999987665     45799999999999999999999995 999999999999998


Q ss_pred             Ccc
Q psy630           85 DSH   87 (347)
Q Consensus        85 ~~~   87 (347)
                      .++
T Consensus       172 ~~k  174 (175)
T 1fje_B          172 GEK  174 (175)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            765

>2aja_A Ankyrin repeat family protein; NESG, Q5ZSV0, structural genomics, PSI, protein structure initiative; 2.80A {Legionella pneumophila} SCOP: a.118.24.1

Probab=99.45  E-value=5.9e-15  Score=136.04  Aligned_cols=93  Identities=18%  Similarity=0.300  Sum_probs=80.2

Q ss_pred             CCCCCcHHHHHHcCChHHHHHHHhhcCCCCc---cccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccc--cCCCCCcH
Q psy630          252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNI---NQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNV--TDSDGDYG  326 (347)
Q Consensus       252 ~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~---~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~--~d~~g~Tp  326 (347)
                      +..+.++||+|+..++.+++++|++ .|+++   +..+.+ .||||+||.+||.+++++|++ +|++++.  +|..|.||
T Consensus       125 ~~~~~tpL~~Aa~~G~~eiv~~Ll~-~gad~~~~~i~~~~-~TpLh~Aa~~G~~eiv~~Ll~-~ga~~~~~~~d~~g~Tp  201 (376)
T 2aja_A          125 QAENYQAFRLAAENGHLHVLNRLCE-LAPTEIMAMIQAEN-YHAFRLAAENGHLHVLNRLCE-LAPTEATAMIQAENYYA  201 (376)
T ss_dssp             CHHHHHHHHHHHHTTCHHHHHHHHH-SCTTTHHHHHSHHH-HHHHHHHHHTTCHHHHHHHHH-SCGGGHHHHHHHHHHHH
T ss_pred             ccCCCCHHHHHHHcCCHHHHHHHHh-CCCCccccccCCCC-CCHHHHHHHCCCHHHHHHHHH-cCCccchhccCCCCCCH
Confidence            3456789999999999999999998 67642   222223 999999999999999999999 7999988  88999999


Q ss_pred             HHHHH-HcCCHHHHHHHHhCCC
Q psy630          327 LDYAK-AIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~-~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+ ..|+.++|++|+++|+
T Consensus       202 L~~Aa~~~G~~eiv~~Ll~~ga  223 (376)
T 2aja_A          202 FRWAAVGRGHHNVINFLLDCPV  223 (376)
T ss_dssp             HHHHHSTTCCHHHHHHHTTSHH
T ss_pred             HHHHHHHCCCHHHHHHHHhCCC
Confidence            99999 9999999999998763

>2zgd_A 3 repeat synthetic ankyrin; ankyrin repeat, hydroxylated, de novo protein; 1.90A {Synthetic} PDB: 2zgg_A 2xen_A

Probab=99.45  E-value=1.4e-13  Score=104.03  Aligned_cols=67  Identities=24%  Similarity=0.285  Sum_probs=58.5

Q ss_pred             CCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          280 FNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       280 ~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ..+...|.+|.||||+||..|+.+++++|++ .|++++.+|..|+||||+|+..|+.+++++|+++||
T Consensus        15 ~~~~~~~~~g~t~L~~A~~~g~~~~v~~Ll~-~g~~i~~~d~~g~tpLh~A~~~~~~~~v~~Ll~~ga   81 (110)
T 2zgd_A           15 PRGSHMGSDLGKKLLEAARAGQDDEVRILMA-NGADVAAKDKNGSTPLHLAARNGHLEVVKLLLEAGA   81 (110)
T ss_dssp             -------CCHHHHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTCCCHHHHHHHTTCHHHHHHHHHTTC
T ss_pred             CcccccCCccchHHHHHHHcCCHHHHHHHHH-cCCCCCccCCCCCCHHHHHHHcCCHHHHHHHHHcCC
Confidence            3456678899999999999999999999999 799999999999999999999999999999999986

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.44  E-value=1.2e-13  Score=117.93  Aligned_cols=79  Identities=20%  Similarity=0.354  Sum_probs=68.7

Q ss_pred             ccCCCeEEEeCCCCCC---------CHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCcc
Q psy630            5 IRQLNKIFVGNLPWTV---------SHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVL   74 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~---------t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~   74 (347)
                      ....++|||+|||+.+         ++++|+++|++||.|.+|+|+.      ++|||||+|.+.++|+.|++. ++..+
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            4567899999999998         7999999999999999999985      479999999999999999985 88888


Q ss_pred             ------------CCccccccCCCcccc
Q psy630           75 ------------EGSRLSIQPSDSHNR   89 (347)
Q Consensus        75 ------------~g~~l~v~~~~~~~~   89 (347)
                                  .|+.|.|.++.....
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             eccccccccccCCCCEEEEEEccCCCC
Confidence                        899999999976543

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.37  E-value=1.5e-12  Score=98.81  Aligned_cols=83  Identities=22%  Similarity=0.397  Sum_probs=69.9

Q ss_pred             ccccCCCeEEEeCCCCCCC-----------HHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cC
Q psy630            3 NSIRQLNKIFVGNLPWTVS-----------HNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TD   70 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t-----------~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~   70 (347)
                      ..+...++|+|+||.....           +++|+++|++||.|..|.| .++   .++|||||+|.+.++|.+|+. +|
T Consensus        10 ~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~ln   85 (112)
T 2dit_A           10 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLD   85 (112)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHST
T ss_pred             CCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcC
Confidence            4567789999999944332           5799999999999999966 443   379999999999999999997 49


Q ss_pred             CCccCCccccccCCCcccc
Q psy630           71 SHVLEGSRLSIQPSDSHNR   89 (347)
Q Consensus        71 ~~~~~g~~l~v~~~~~~~~   89 (347)
                      +..+.|++|.|.++.++..
T Consensus        86 g~~~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           86 GRWFGGRQITAQAWDGTTD  104 (112)
T ss_dssp             TCEETTEECEEEECCSCCC
T ss_pred             CCEECCcEEEEEEeCCCCC
Confidence            9999999999999877543

>2aja_A Ankyrin repeat family protein; NESG, Q5ZSV0, structural genomics, PSI, protein structure initiative; 2.80A {Legionella pneumophila} SCOP: a.118.24.1

Probab=99.36  E-value=2e-13  Score=125.78  Aligned_cols=91  Identities=14%  Similarity=0.163  Sum_probs=72.7

Q ss_pred             CCCcHHHHHHcCChHHHHHHHhhcCCCC---ccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCC---ccccCCCCCcHH
Q psy630          254 NEKNIYEWAKEGKLDMLVKQLTKLKDFN---INQLDENGLNCLHWACDRGHLKVVQHLIEKCGAD---VNVTDSDGDYGL  327 (347)
Q Consensus       254 ~~~~~l~~a~~~~~~~~~~lL~~~~~~~---~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~---i~~~d~~g~TpL  327 (347)
                      .+.|+||+|+..+..+++++|+. .+..   .+..+..|.||||+||.+||.+++++|++ +|++   ++..+.+ .|||
T Consensus        91 ~~~T~Lh~Aa~~G~~e~v~~Ll~-~ga~~~~~~~~~~~~~tpL~~Aa~~G~~eiv~~Ll~-~gad~~~~~i~~~~-~TpL  167 (376)
T 2aja_A           91 KSEVICFVAAITGCSSALDTLCL-LLTSDEIVKVIQAENYQAFRLAAENGHLHVLNRLCE-LAPTEIMAMIQAEN-YHAF  167 (376)
T ss_dssp             CHHHHHHHHHHHCCHHHHHHHTT-C--CCSSCC--CHHHHHHHHHHHHTTCHHHHHHHHH-SCTTTHHHHHSHHH-HHHH
T ss_pred             CcCCHHHHHHHcCCHHHHHHHHH-cCCcHHHHHHhccCCCCHHHHHHHcCCHHHHHHHHh-CCCCccccccCCCC-CCHH
Confidence            34599999998888889999988 5552   22345578999999999999999999999 7976   2333333 9999


Q ss_pred             HHHHHcCCHHHHHHHHhCCC
Q psy630          328 DYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       328 h~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |+|+..|+.++|++|+++||
T Consensus       168 h~Aa~~G~~eiv~~Ll~~ga  187 (376)
T 2aja_A          168 RLAAENGHLHVLNRLCELAP  187 (376)
T ss_dssp             HHHHHTTCHHHHHHHHHSCG
T ss_pred             HHHHHCCCHHHHHHHHHcCC
Confidence            99999999999999999986

>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=99.35  E-value=2.5e-13  Score=101.40  Aligned_cols=71  Identities=20%  Similarity=0.336  Sum_probs=62.4

Q ss_pred             EeCCCCCCCHHHHHHHH------------hccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccc
Q psy630           13 VGNLPWTVSHNELKKFF------------SEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRL   79 (347)
Q Consensus        13 V~nLp~~~t~~~l~~~f------------~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l   79 (347)
                      +.|||+.+++++|++.|            ++||.|.+|.|++++. ++++|||||+|.+.++|.+|+.. ||..+.||+|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56777778888777666            9999999999998874 89999999999999999999985 9999999999


Q ss_pred             cccCC
Q psy630           80 SIQPS   84 (347)
Q Consensus        80 ~v~~~   84 (347)
                      .|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99765

>2l6b_A NR1C; ankyrin, consensus, repeat protein, ising model, DE NOV; NMR {Escherichia coli}

Probab=99.35  E-value=8.1e-13  Score=100.44  Aligned_cols=79  Identities=24%  Similarity=0.233  Sum_probs=71.6

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..|.|+||+|+..+...++++|++ .+++++.+|..|+||||+|+..++.+++++|++ +|+++|.++..|.||
T Consensus        34 ~~~~~d~~g~t~L~~A~~~~~~~~~~~Ll~-~g~~~~~~d~~g~tpl~~A~~~~~~~~~~~Ll~-~ga~~n~~~~~~~~~  111 (115)
T 2l6b_A           34 DVNARSKDGNTPLHLAAKNGHAEIVKLLLA-KGADVNARSKDGNTPEHLAKKNGHHEIVKLLDA-KGADVNARSWGSSHH  111 (115)
T ss_dssp             CSSCCCSSSCCTTHHHHTTTCHHHHHHHTT-TTCCTTCCCTTCCCTTHHHHTTTCHHHHHHHHT-TSSSHHHHSCCCC--
T ss_pred             CCCCcCCCCCCHHHHHHHcCcHHHHHHHHH-cCCCCcccCCCCCCHHHHHHHCCCHHHHHHHHH-cCCCCCcCCcccccc
Confidence            456677889999999999999999999999 799999999999999999999999999999999 799999999999998


Q ss_pred             H
Q psy630          327 L  327 (347)
Q Consensus       327 L  327 (347)
                      -
T Consensus       112 ~  112 (115)
T 2l6b_A          112 H  112 (115)
T ss_dssp             -
T ss_pred             c
Confidence            4

>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=99.34  E-value=9e-13  Score=111.09  Aligned_cols=69  Identities=14%  Similarity=0.205  Sum_probs=62.5

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCe--eEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcc
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQI--MNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSR   78 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i--~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~   78 (347)
                      .++|||+|||+++|+++|+++|++||.|  .+++++.++  +.++|||||+|.+.++|.+|+.. |+..+.|+.
T Consensus       123 ~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~  194 (205)
T 3tyt_A          123 SNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPN  194 (205)
T ss_dssp             CSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSS
T ss_pred             cceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCC
Confidence            4689999999999999999999999999  899998775  56679999999999999999985 999998873

>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=99.33  E-value=2.6e-12  Score=113.86  Aligned_cols=75  Identities=15%  Similarity=0.274  Sum_probs=68.5

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccC-CccccccC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLE-GSRLSIQP   83 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~-g~~l~v~~   83 (347)
                      ...++|||+|||+++++++|+++|++||.|..++++.++     +|||||+|.+.++|.+|+.. ++..+. |+.|+|.+
T Consensus       205 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~  279 (282)
T 3pgw_A          205 PPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISF  279 (282)
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEE
Confidence            356789999999999999999999999999999998654     58999999999999999985 999999 99999988


Q ss_pred             CC
Q psy630           84 SD   85 (347)
Q Consensus        84 ~~   85 (347)
                      +.
T Consensus       280 ak  281 (282)
T 3pgw_A          280 AK  281 (282)
T ss_pred             ec
Confidence            74

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.30  E-value=2e-11  Score=90.03  Aligned_cols=76  Identities=17%  Similarity=0.192  Sum_probs=63.7

Q ss_pred             CCeEEEeCCC-------CCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCcccc
Q psy630            8 LNKIFVGNLP-------WTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLS   80 (347)
Q Consensus         8 ~~~l~V~nLp-------~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~   80 (347)
                      .++|-|.-.+       .++++++|+++|++||.|..|.|+     ++++|||||+|.+.++|..|+.. ...+.|++|.
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~-~~~~~g~~l~   83 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQN-EVGLVDNPLK   83 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHT-CCBCSSSBCE
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHh-cCCCCCCeEE
Confidence            4567666554       468999999999999999999997     46789999999999999999987 4446899999


Q ss_pred             ccCCCcccc
Q psy630           81 IQPSDSHNR   89 (347)
Q Consensus        81 v~~~~~~~~   89 (347)
                      |.++.++..
T Consensus        84 V~~a~~~~~   92 (100)
T 2d9o_A           84 ISWLEGQPQ   92 (100)
T ss_dssp             EECSSCCCC
T ss_pred             EEEccCCCC
Confidence            999877543

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.30  E-value=3.2e-12  Score=107.07  Aligned_cols=75  Identities=20%  Similarity=0.317  Sum_probs=68.3

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccC-CeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccC-CccccccC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYG-QIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLE-GSRLSIQP   83 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G-~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~-g~~l~v~~   83 (347)
                      ..++|||+|||+.+++++|+++|++|| .|..++++.+     ++|||||+|.+.++|.+|+.. ++..+. |++|.|.+
T Consensus       119 ~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~  193 (198)
T 1qm9_A          119 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF  193 (198)
T ss_dssp             CCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEe
Confidence            468899999999999999999999999 9999999653     268999999999999999985 999999 99999998


Q ss_pred             CCc
Q psy630           84 SDS   86 (347)
Q Consensus        84 ~~~   86 (347)
                      +.+
T Consensus       194 a~~  196 (198)
T 1qm9_A          194 SKS  196 (198)
T ss_dssp             ECC
T ss_pred             ecc
Confidence            765

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=99.29  E-value=2.9e-12  Score=95.77  Aligned_cols=80  Identities=14%  Similarity=0.148  Sum_probs=68.9

Q ss_pred             CCCeEEEeCC--CCCCC--------HHHHHHHHhccCCeeEEEEeeeCCC--CCceeEEEEEEcCHHHHHHHHhc-CCCc
Q psy630            7 QLNKIFVGNL--PWTVS--------HNELKKFFSEYGQIMNASVMFDKNT--GLSKGFGFVTFQNKEAVDKVFST-DSHV   73 (347)
Q Consensus         7 ~~~~l~V~nL--p~~~t--------~~~l~~~f~~~G~i~~~~i~~~~~t--~~~~g~afV~f~~~~~a~~a~~~-~~~~   73 (347)
                      .++.|.+.|+  |.+..        +++|++.|++||.|.+|.|++++.+  +.++|+|||+|.+.++|.+|+.. ||..
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            5678899998  44443        3689999999999999999988764  36899999999999999999985 9999


Q ss_pred             cCCccccccCCCc
Q psy630           74 LEGSRLSIQPSDS   86 (347)
Q Consensus        74 ~~g~~l~v~~~~~   86 (347)
                      +.||.|.|.++..
T Consensus        84 f~GR~i~v~~~~~   96 (105)
T 3v4m_A           84 FANRVVVTKYCDP   96 (105)
T ss_dssp             ETTEECEEEEECH
T ss_pred             eCCCEEEEEEeCH
Confidence            9999999987654

>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=99.29  E-value=6.6e-12  Score=107.80  Aligned_cols=75  Identities=20%  Similarity=0.317  Sum_probs=68.2

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccC-CeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccC-CccccccC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYG-QIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLE-GSRLSIQP   83 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G-~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~-g~~l~v~~   83 (347)
                      ..++|||+|||+++++++|+++|++|| .|..++++.+     ++|||||+|.+.++|.+|+.. ++..+. |+.|.|.+
T Consensus       150 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~  224 (229)
T 2adc_A          150 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF  224 (229)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEE
Confidence            358899999999999999999999999 9999999643     368999999999999999984 999999 99999998


Q ss_pred             CCc
Q psy630           84 SDS   86 (347)
Q Consensus        84 ~~~   86 (347)
                      +.+
T Consensus       225 a~~  227 (229)
T 2adc_A          225 SKS  227 (229)
T ss_dssp             CSS
T ss_pred             ecC
Confidence            865

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=99.27  E-value=8.9e-12  Score=94.92  Aligned_cols=81  Identities=12%  Similarity=0.188  Sum_probs=69.6

Q ss_pred             cCCCeEEEeCCC--CCC---CHHHHHHHHhccCCeeEEEEeeeCC----CCCceeEEEEEEcCHHHHHHHHhc-CCCccC
Q psy630            6 RQLNKIFVGNLP--WTV---SHNELKKFFSEYGQIMNASVMFDKN----TGLSKGFGFVTFQNKEAVDKVFST-DSHVLE   75 (347)
Q Consensus         6 ~~~~~l~V~nLp--~~~---t~~~l~~~f~~~G~i~~~~i~~~~~----t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~   75 (347)
                      ...+.|+++|+-  .++   -+++|++.|++||.|.+|.|++++.    ++.++|++||+|.+.++|.+|+.. ||..+.
T Consensus        18 ~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~   97 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA   97 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            357899999993  222   3689999999999999999999865    467889999999999999999985 999999


Q ss_pred             CccccccCCCc
Q psy630           76 GSRLSIQPSDS   86 (347)
Q Consensus        76 g~~l~v~~~~~   86 (347)
                      ||.|.|.++..
T Consensus        98 GR~i~v~~~~~  108 (118)
T 3ue2_A           98 GRKVVAEVYDQ  108 (118)
T ss_dssp             TEECEEEEECH
T ss_pred             CcEEEEEEcCh
Confidence            99999987654

>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=99.17  E-value=3.6e-11  Score=108.16  Aligned_cols=76  Identities=18%  Similarity=0.273  Sum_probs=63.8

Q ss_pred             cccCCCeEEEeC--CCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccC---Cc
Q psy630            4 SIRQLNKIFVGN--LPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLE---GS   77 (347)
Q Consensus         4 ~~~~~~~l~V~n--Lp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~---g~   77 (347)
                      ....+++|||+|  |++.+|+++|+++|++||.|.+|.+..      +||||||+|.+.++|++|++. ||..+.   |+
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~   87 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQ   87 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSC
T ss_pred             cCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCC
Confidence            456778999999  589999999999999999999987743      479999999999999999985 998873   44


Q ss_pred             --cccccCCC
Q psy630           78 --RLSIQPSD   85 (347)
Q Consensus        78 --~l~v~~~~   85 (347)
                        .+.|.+..
T Consensus        88 ~~~ly~~~~~   97 (345)
T 3tht_A           88 KITLYLNFVE   97 (345)
T ss_dssp             EEECEEEECS
T ss_pred             ceEEEEEEee
Confidence              46666654

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.97  E-value=1.1e-09  Score=77.62  Aligned_cols=72  Identities=19%  Similarity=0.260  Sum_probs=61.7

Q ss_pred             CCCeEEEeCCC----CCCCH----HHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCcc
Q psy630            7 QLNKIFVGNLP----WTVSH----NELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSR   78 (347)
Q Consensus         7 ~~~~l~V~nLp----~~~t~----~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~   78 (347)
                      ...||+|.-.|    .....    .+|.+.|.+||.|..++++.++        +||+|.+.++|.+|+.++|..+.||.
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~mnG~~v~Gr~   77 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLSLNGKELLNRT   77 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGGGTTCEETTEE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHhcCCeEeCCeE
Confidence            45678888877    23434    5789999999999999998764        89999999999999999999999999


Q ss_pred             ccccCCCc
Q psy630           79 LSIQPSDS   86 (347)
Q Consensus        79 l~v~~~~~   86 (347)
                      |+|+.+.+
T Consensus        78 LkV~lkt~   85 (91)
T 2dnr_A           78 ITIALKSP   85 (91)
T ss_dssp             EEEEECCC
T ss_pred             EEEEeCCC
Confidence            99998865

>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=98.97  E-value=9e-10  Score=83.17  Aligned_cols=78  Identities=9%  Similarity=0.046  Sum_probs=63.9

Q ss_pred             ccCCCeEEEeCCCCCC----------CHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCc
Q psy630            5 IRQLNKIFVGNLPWTV----------SHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHV   73 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~----------t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~   73 (347)
                      +..++.|.+.|+=..-          -+++|++.|++||.|.+|.|.++.    ++|++||+|.+.++|.+|+.. ||..
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~   79 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRW   79 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCE
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            4567788888882221          124789999999999999997653    589999999999999999985 9999


Q ss_pred             cCCccccccCCCc
Q psy630           74 LEGSRLSIQPSDS   86 (347)
Q Consensus        74 ~~g~~l~v~~~~~   86 (347)
                      +.||.|.|.++..
T Consensus        80 f~GR~i~v~~~~~   92 (114)
T 3s6e_A           80 FAGKMITAAYVPL   92 (114)
T ss_dssp             ETTEECEEEEECH
T ss_pred             ECCEEEEEEEEcH
Confidence            9999999988753

>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=98.92  E-value=1.9e-10  Score=92.65  Aligned_cols=119  Identities=13%  Similarity=0.102  Sum_probs=75.2

Q ss_pred             EEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CC-CccCCccccccCCCccc------ccchhhhhhcccccccccCC
Q psy630           37 NASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DS-HVLEGSRLSIQPSDSHN------RMAENMEDRFNQACDYLPSL  108 (347)
Q Consensus        37 ~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~-~~~~g~~l~v~~~~~~~------~~~~~~~~~f~~~~~~v~~l  108 (347)
                      .+.|+.+.  .+++|||||+|.+.++|++|+.. ++ ..+.|.. .+.......      .............++||+||
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl   78 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYANDNGVDGEW-TYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNL   78 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEE-EEETTTTEEEEECCCCCSSCCCCCCBCCEEEEESC
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhcccCCCCCcc-cccCccccccccccccccccccCCCCCCEEEEeCC
Confidence            46677775  46899999999999999999964 32 2222221 111111100      00001111234578999999


Q ss_pred             cccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          109 VKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       109 ~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      |..+++++|+++|+.||.|....+..++.     .|+.|+.||..  ..+.++|.++
T Consensus        79 ~~~~~~~~l~~~F~~~G~v~~~~i~~~~~-----~g~~~g~afV~--f~~~~~a~~A  128 (158)
T 2kn4_A           79 TYRTSPDTLRRVFEKYGRVGDVYIPRDRY-----TKESRGFAFVR--FHDKRDAEDA  128 (158)
T ss_dssp             CTTCCHHHHHHHHHHHSCEEEEECCCCSS-----CTTSCCEEEEE--ESBHHHHHHH
T ss_pred             CCCCCHHHHHHHHHhcCCeEEEEEeecCC-----CCccceEEEEE--ECCHHHHHHH
Confidence            99999999999999999998777765532     23344445444  3456677666

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.88  E-value=3.4e-09  Score=80.14  Aligned_cols=74  Identities=11%  Similarity=0.074  Sum_probs=62.6

Q ss_pred             cCCCeEEEeCCCCC-CCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcC-HHHHHHHHhc---CCCccCCcccc
Q psy630            6 RQLNKIFVGNLPWT-VSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQN-KEAVDKVFST---DSHVLEGSRLS   80 (347)
Q Consensus         6 ~~~~~l~V~nLp~~-~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~-~~~a~~a~~~---~~~~~~g~~l~   80 (347)
                      ....-|||+|||++ ++.++|+++|++||.|..|.++++..      .|||.|.+ .++|..|+..   ++..|.|..+.
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~   89 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   89 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEE
Confidence            45678999999999 99999999999999999999987764      59999999 7888888863   67888887777


Q ss_pred             ccCCC
Q psy630           81 IQPSD   85 (347)
Q Consensus        81 v~~~~   85 (347)
                      +....
T Consensus        90 ~evL~   94 (121)
T 1owx_A           90 WEVLE   94 (121)
T ss_dssp             EEECC
T ss_pred             EEECC
Confidence            65443

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.80  E-value=5.1e-09  Score=74.54  Aligned_cols=72  Identities=21%  Similarity=0.232  Sum_probs=61.5

Q ss_pred             CCCeEEEeCCCCC-----CCH----HHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCc
Q psy630            7 QLNKIFVGNLPWT-----VSH----NELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGS   77 (347)
Q Consensus         7 ~~~~l~V~nLp~~-----~t~----~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~   77 (347)
                      ...||+|.-+++.     +..    .+|.+.|.+||.|..++++.++        +||+|.+.++|.+|+.+++..+.||
T Consensus        14 pD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~ldG~~v~Gr   85 (95)
T 1ufw_A           14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLDVDGMKVKGR   85 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHHGGGSEETTE
T ss_pred             CCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHhcCCeeeCCe
Confidence            4568999988753     222    4688999999999999998774        9999999999999999999999999


Q ss_pred             cccccCCCc
Q psy630           78 RLSIQPSDS   86 (347)
Q Consensus        78 ~l~v~~~~~   86 (347)
                      .|+|+...+
T Consensus        86 ~L~V~~k~~   94 (95)
T 1ufw_A           86 AVKISGPSS   94 (95)
T ss_dssp             EEEEECCCC
T ss_pred             EEEEeccCC
Confidence            999987654

>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=98.59  E-value=8.4e-09  Score=82.19  Aligned_cols=88  Identities=11%  Similarity=0.101  Sum_probs=69.6

Q ss_pred             CCceeEEEEEEcCHHHHHHHHh-c-CCCccCCccccccCCCcccccc---------hhhhhhcccccccccCCcccccch
Q psy630           47 GLSKGFGFVTFQNKEAVDKVFS-T-DSHVLEGSRLSIQPSDSHNRMA---------ENMEDRFNQACDYLPSLVKKLDSS  115 (347)
Q Consensus        47 ~~~~g~afV~f~~~~~a~~a~~-~-~~~~~~g~~l~v~~~~~~~~~~---------~~~~~~f~~~~~~v~~l~~~~~~e  115 (347)
                      ..-+|+++|+|.+.++|++|+. + |+..+.| .+.+.++.......         ..........++||+|||..++++
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~   88 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKT   88 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCH
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCCCCCCHH
Confidence            4568999999999999999996 5 8999999 89998876532211         111222345789999999999999


Q ss_pred             hhHHHHhhccccceecccCC
Q psy630          116 TLLKFYALYKQATVGQCNID  135 (347)
Q Consensus       116 ~l~~~f~~fg~v~~g~~~~~  135 (347)
                      +|+++|+.||.|....+..+
T Consensus        89 ~l~~~F~~~G~i~~v~i~~~  108 (150)
T 2i2y_A           89 ELERAFGYYGPLRSVWVARN  108 (150)
T ss_dssp             HHHHHHHHHSCEEEEEECSS
T ss_pred             HHHHHHHhhCCEEEEEEeeC
Confidence            99999999999987766554

>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=98.58  E-value=9.7e-08  Score=81.19  Aligned_cols=67  Identities=13%  Similarity=0.174  Sum_probs=59.1

Q ss_pred             CCHHHHHHHHhccCCeeEEEEeeeCC----CCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCc
Q psy630           20 VSHNELKKFFSEYGQIMNASVMFDKN----TGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDS   86 (347)
Q Consensus        20 ~t~~~l~~~f~~~G~i~~~~i~~~~~----t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~   86 (347)
                      -.+++|++.|++||.|.++.|+++..    ++.++|++||+|.+.++|.+|+.. +|..+.||.|.+.+...
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            45678999999999999999986654    458999999999999999999985 99999999999988753

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.30  E-value=1.1e-05  Score=58.07  Aligned_cols=91  Identities=22%  Similarity=0.294  Sum_probs=73.6

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhc-----cCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSE-----YGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRL   79 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~-----~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l   79 (347)
                      ..-.++|.|.|||+.+.++.|.-+|+.     -|+|..++...        +-|+|+|.+...|++.++...+.++|..|
T Consensus         5 ~~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~~H~L~~~~L   76 (104)
T 2dhx_A            5 SSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQADHELHGAQL   76 (104)
T ss_dssp             CCCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCSCCBSSSSBC
T ss_pred             ccCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCCcceecCeEE
Confidence            445679999999999999999999976     25677776532        46899999999999999988899999999


Q ss_pred             cccCCCcccccchhhhhhcccccccccCCcccccc
Q psy630           80 SIQPSDSHNRMAENMEDRFNQACDYLPSLVKKLDS  114 (347)
Q Consensus        80 ~v~~~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~  114 (347)
                      .|.+..+..           ..++++.+|++.++.
T Consensus        77 sV~P~~~~~-----------~~r~ll~gl~~~t~~  100 (104)
T 2dhx_A           77 SLRPAPPRA-----------PARLLLQGLPPGTSG  100 (104)
T ss_dssp             EEEECCCCC-----------CCCCCCCSCCCCCCC
T ss_pred             EEEcCCCCC-----------cceEeeecCCCCCCC
Confidence            998765533           356789999877654

>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=98.08  E-value=2.1e-07  Score=86.99  Aligned_cols=59  Identities=12%  Similarity=0.057  Sum_probs=44.3

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..+|||+|||..+++++|..+|+.||.|....+..++.     .++.|+.||+.  +.+.++|..+
T Consensus       102 ~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~-----tg~~kG~aFV~--F~~~e~A~~A  160 (437)
T 3pgw_S          102 FKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKR-----SGKPRGYAFIE--YEHERDMHSA  160 (437)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCC-----CCCccceEEEe--eccHHHHHHH
Confidence            36899999999999999999999999998777655432     34556666665  3445666555

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.91  E-value=2.8e-05  Score=56.44  Aligned_cols=71  Identities=15%  Similarity=0.143  Sum_probs=62.1

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhcc-----CCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHH-hcCCCccCCcccc
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEY-----GQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF-STDSHVLEGSRLS   80 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~-----G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~-~~~~~~~~g~~l~   80 (347)
                      ..++|-+=|||..+++..++.+.+++     |.+..+.+..|-      +-|+|+|.+...|-+|. ..+|..|.||+|+
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            46888899999999999999999999     999999987764      46999999988777666 5699999999998


Q ss_pred             ccC
Q psy630           81 IQP   83 (347)
Q Consensus        81 v~~   83 (347)
                      +..
T Consensus        94 ~gT   96 (117)
T 2l9w_A           94 SGT   96 (117)
T ss_dssp             EEC
T ss_pred             ecC
Confidence            864

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=97.86  E-value=2.3e-06  Score=66.59  Aligned_cols=100  Identities=12%  Similarity=0.008  Sum_probs=46.1

Q ss_pred             eEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCcccccchhhhhhcccccccccCCcccccchhhHHHHhhccccce
Q psy630           51 GFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATV  129 (347)
Q Consensus        51 g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~  129 (347)
                      -++|.+|.+...+..|+.. ++....|+. .+....+..       ..-...++||+|||..+++++|+++|+.||.|..
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~-~~~~~~~~~-------~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~   76 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRG-SMSYGRPPP-------DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGD   76 (135)
T ss_dssp             -------------------------------CCSCCSCS-------SGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSE
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCC-CCCcCCCCC-------CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEE
Confidence            3677788888888888875 655555543 222222211       1224578999999999999999999999999987


Q ss_pred             ecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          130 GQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       130 g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..+..++.     .++.|+.||..  ..+.++|.++
T Consensus        77 v~i~~~~~-----~g~~~G~afV~--F~~~~~A~~A  105 (135)
T 2lea_A           77 VYIPRDRY-----TKESRGFAFVR--FHDKRDAEDA  105 (135)
T ss_dssp             EECCCCSS-----SSSCCSCCEEE--CSCHHHHHHH
T ss_pred             EEEEecCC-----CCccceEEEEE--ECCHHHHHHH
Confidence            77765432     12333344443  4456677665

>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=97.86  E-value=8.5e-07  Score=65.09  Aligned_cols=62  Identities=11%  Similarity=0.086  Sum_probs=46.0

Q ss_pred             hcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           97 RFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        97 ~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      .+...++||+|||..+++++|+++|+.||+|....+..++.     .|+.|+.||..  ..+.++|.++
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~-----tg~~kG~afV~--f~~~~~A~~A   77 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKV-----AGHSLGYGFVN--YVTAKDAERA   77 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSS-----SCCEEEEEEEE--ESSHHHHHHH
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCC-----CCcccccEEEE--ECCHHHHHHH
Confidence            35667899999999999999999999999998877765543     23334444443  4467777776

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=97.68  E-value=3.2e-06  Score=60.88  Aligned_cols=58  Identities=14%  Similarity=-0.053  Sum_probs=42.4

Q ss_pred             ccccccCCcccccchhhHHHHhhcc-ccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYK-QATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg-~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      .++||+|||..+++++|+++|+.|| .+....+..++.     .|+.|+.|+..  ..+.++|.++
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~-----t~~~rg~aFV~--F~~~~~A~~A   60 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKS-----SGQSRGFAFVE--FSHLQDATRW   60 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSS-----SCCCSSEEEEE--CSSHHHHHHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCC-----CCCcCceEEEE--ecCHHHHHHH
Confidence            4789999999999999999999999 787666655432     23334444443  4567777776

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=97.55  E-value=4.3e-06  Score=60.70  Aligned_cols=61  Identities=10%  Similarity=0.065  Sum_probs=42.1

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      -.++||+|||+.+++++|+++|+.||.+....|...+.   ...|+.|+.||..  ..+.++|.++
T Consensus         9 m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d---~~tg~srG~aFV~--f~~~~~A~~A   69 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKD---KQTQQNRGFAFVQ--LSSAMDASQL   69 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCC---SSSSSCSSEEEEE--CSSSHHHHHH
T ss_pred             cCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEec---CCCCCCceEeEEE--ECCHHHHHHH
Confidence            36899999999999999999999999765555554321   0134455555554  4456666655

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=97.41  E-value=9.4e-06  Score=60.66  Aligned_cols=59  Identities=10%  Similarity=-0.067  Sum_probs=44.1

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+||+..+++++|+++|+.||.|....+..++.     .++.|+.||..  ..+.++|.++
T Consensus         6 ~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~-----tg~~rG~aFV~--f~~~~~A~~A   64 (110)
T 3s8s_A            6 LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPR-----TRKHLGLARVL--FTSTRGAKET   64 (110)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTT-----TCCEEEEEEEE--ESSHHHHHHH
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCC-----CCceeeEEEEE--ECCHHHHHHH
Confidence            46799999999999999999999999999877765542     23444445544  4457777666

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.41  E-value=2.1e-05  Score=58.00  Aligned_cols=54  Identities=9%  Similarity=-0.023  Sum_probs=40.5

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|+...+..+           |+.||.+  ..+.++|..+
T Consensus        15 ~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~-----------kGfaFVe--F~~~~~A~~A   68 (105)
T 1sjq_A           15 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----------KNQAFIE--MNTEEAANTM   68 (105)
T ss_dssp             CCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT-----------TTEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-----------CCEEEEE--ECCHHHHHHH
Confidence            3468999999999999999999999999987666543           2334443  3346666666

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.37  E-value=0.00078  Score=47.84  Aligned_cols=69  Identities=14%  Similarity=0.219  Sum_probs=54.0

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCC--ceeEEEEEEcCHHHHHHHHhc-CCCccCCc
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGL--SKGFGFVTFQNKEAVDKVFST-DSHVLEGS   77 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~--~~g~afV~f~~~~~a~~a~~~-~~~~~~g~   77 (347)
                      ++|.|++||+.+|++++.+.+..+..+........+.+.+  ..+-|||.|.+.+++..-... +|+.|.+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~   73 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDN   73 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECT
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcC
Confidence            5799999999999999999999888776666665544333  235699999999888877765 88877543

>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=97.37  E-value=1.4e-05  Score=62.35  Aligned_cols=102  Identities=14%  Similarity=0.110  Sum_probs=42.2

Q ss_pred             eEEEEEEcCHHHHHHHHhcCCCccCCccccccCCCcccccchhhhhhcccccccccCCcccccchhhHHHHhhcccccee
Q psy630           51 GFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVG  130 (347)
Q Consensus        51 g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g  130 (347)
                      |+||..|.....+..+.........|....-.....     ......-...++||+|||..+++++|+++|+.|| +...
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~gg~~~g~~~g~~-----~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v   75 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSGDS-----EFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRV   75 (139)
T ss_dssp             ------------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEE
T ss_pred             CcccccccCccccchhcccchhccCCCCCCCCCCCc-----ccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEE
Confidence            577888877776666554322223332221111000     1111223456899999999999999999999999 5555


Q ss_pred             cccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          131 QCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       131 ~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      .+..++.      ++.|..||..  ..+.++|.++.
T Consensus        76 ~i~~d~~------g~srGfaFV~--F~~~e~A~~Al  103 (139)
T 2hgn_A           76 HIEIGPD------GRVTGEADVE--FATHEEAVAAM  103 (139)
T ss_dssp             ECCCSSS------SCSSCCCEEE--CSHHHHHHHHT
T ss_pred             EEEECCC------CCCceEEEEE--eCCHHHHHHHH
Confidence            5544432      4555555554  34566776663

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=97.30  E-value=2.6e-05  Score=53.59  Aligned_cols=57  Identities=5%  Similarity=0.053  Sum_probs=40.7

Q ss_pred             cccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          102 CDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       102 ~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ++||+|||..+++++|+++|+.||.+....+..++.     .++.|+.||..  ..+.++|..+
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~~~~~g~afV~--f~~~~~a~~a   57 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKT-----TNRHRGFGFVT--FESEDIVEKV   57 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSS-----STTSCBEEEEE--CSCHHHHHHH
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCC-----CCCcCcEEEEE--ECCHHHHHHH
Confidence            479999999999999999999999998777665542     23334444444  3345666544

>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=97.29  E-value=2e-05  Score=54.24  Aligned_cols=57  Identities=5%  Similarity=0.061  Sum_probs=39.9

Q ss_pred             cccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          102 CDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       102 ~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ++||+|||..+++++|+++|+.||.+....+..++.     .++.|+.||..  ..+.++|.++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~~~~~g~afV~--f~~~~~a~~A   57 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNK-----TNKRRGFCFIT--FKEEEPVKKI   57 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCC-----CSSSCCCEEEE--CSSSHHHHHH
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC-----CCCcCCEEEEE--ECCHHHHHHH
Confidence            479999999999999999999999998766655432     12333344444  3345555555

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.28  E-value=0.00089  Score=49.79  Aligned_cols=74  Identities=16%  Similarity=0.246  Sum_probs=59.4

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCC-ccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEG-SRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g-~~l~v~~   83 (347)
                      ....+.|-|-+.|+.. ...+..+|++||.|.+....      ....+-+|.|.++.+|++|+..||..+.| -.|-|.+
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~------~~~NWihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV~p   93 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKP   93 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEE
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC------CCCCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEEEE
Confidence            3456788899999996 55678899999999988762      12468999999999999999999999985 5566666


Q ss_pred             CC
Q psy630           84 SD   85 (347)
Q Consensus        84 ~~   85 (347)
                      ..
T Consensus        94 ~~   95 (119)
T 1wwh_A           94 CI   95 (119)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=97.28  E-value=1.7e-05  Score=56.81  Aligned_cols=58  Identities=10%  Similarity=-0.064  Sum_probs=39.5

Q ss_pred             ccccccCCcccccchhhHHHHhhcc--ccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYK--QATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg--~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      .++||+|||..+++++|+++|+.||  .+....+..++.     .|+.|+.|+..  ..+.++|.++
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~-----~g~~kG~afV~--f~~~~~a~~A   61 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRA-----NGQSKGFALVG--VGSEASSKKL   61 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTT-----TCCEEEEEEEC--C-CHHHHHHH
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCC-----CCccCcEEEEE--ECCHHHHHHH
Confidence            4789999999999999999999999  777666655432     23334444443  4456666655

>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=97.28  E-value=1.7e-05  Score=63.84  Aligned_cols=60  Identities=13%  Similarity=0.116  Sum_probs=42.9

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...+|||+|||..+++++|..+|+.||.|....+..++.     .|+.|+.||..  ..+.++|..+
T Consensus        71 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~-----~g~~~g~afV~--f~~~~~A~~A  130 (165)
T 1rk8_A           71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR-----TGFSKGYALVE--YETHKQALAA  130 (165)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----TSSEEEEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCC-----CCcEeeEEEEE--ECCHHHHHHH
Confidence            346799999999999999999999999998777765532     22333334443  3456666665

>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=97.24  E-value=2.4e-05  Score=55.18  Aligned_cols=60  Identities=17%  Similarity=0.153  Sum_probs=42.5

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.+....+..++.     .++.|..||..  ..+.++|..+
T Consensus         6 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~-----~~~~~g~afV~--f~~~~~a~~A   65 (85)
T 3mdf_A            6 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-----TEKHRGFAFVE--FELAEDAAAA   65 (85)
T ss_dssp             CSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETT-----TTEECSEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCC-----CCccccEEEEE--ECCHHHHHHH
Confidence            346899999999999999999999999998766654422     22333334443  3456666665

>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=97.24  E-value=5.2e-05  Score=57.24  Aligned_cols=54  Identities=9%  Similarity=-0.023  Sum_probs=40.2

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..+           |..||.+  ..+.++|..+
T Consensus        30 ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~-----------kG~AFVe--F~~~e~A~~A   83 (119)
T 2ad9_A           30 PSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG-----------KNQAFIE--MNTEEAANTM   83 (119)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG-----------GTEEEEE--CSCHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC-----------CCEEEEE--ECCHHHHHHH
Confidence            3468999999999999999999999999987665432           3334443  3456666655

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=97.21  E-value=1.9e-05  Score=57.89  Aligned_cols=59  Identities=10%  Similarity=0.000  Sum_probs=44.1

Q ss_pred             cccccccCCcc------cccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVK------KLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~------~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||.      .+++++|+++|+.||.|....+..++.     .|+.|+.|+..  ..+.++|.++
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~-----tg~~kG~afV~--f~~~~~A~~A   70 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEA-----TGKTKGFLFVE--CGSMNDAKKI   70 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETT-----TTEECSEEEEE--ESSHHHHHHH
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCC-----CCccceEEEEE--ECCHHHHHHH
Confidence            35799999999      999999999999999999777665543     24455545544  4457777766

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.20  E-value=3.5e-05  Score=53.20  Aligned_cols=57  Identities=9%  Similarity=0.098  Sum_probs=40.0

Q ss_pred             cccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          102 CDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       102 ~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ++||+|||..+++++|+++|+.||.+....+..++.     .|+.|+.||..+  .+.++|.++
T Consensus         2 ~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~-----~~~~~g~afV~f--~~~~~a~~a   58 (77)
T 1uaw_A            2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL-----TKRSRGFGFVTF--MDQAGVDKV   58 (77)
T ss_dssp             CEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCC-----SSSCSSEEEECC--CCTTHHHHH
T ss_pred             EEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCC-----CCCcCceEEEEE--cCHHHHHHH
Confidence            689999999999999999999999998766655432     123344444443  345555544

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.20  E-value=4.5e-05  Score=55.88  Aligned_cols=60  Identities=17%  Similarity=0.148  Sum_probs=43.2

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|..||.  ...+.++|..+
T Consensus        11 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~-----~~~~~g~afV--~f~~~~~A~~A   70 (102)
T 2cqb_A           11 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-----TEKHRGFAFV--EFELAEDAAAA   70 (102)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSS-----SCCCSSEEEE--CCSSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCC-----CCCcceEEEE--EECCHHHHHHH
Confidence            457899999999999999999999999998776655432     1223333443  34567777666

>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=97.19  E-value=3.4e-05  Score=57.33  Aligned_cols=60  Identities=15%  Similarity=0.085  Sum_probs=43.4

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .|+.|+.||..  ..+.++|.++
T Consensus        25 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-----~g~~~g~afV~--F~~~~~A~~A   84 (108)
T 2jrs_A           25 GPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSE-----TGRSKGYGFIT--FSDSECAKKA   84 (108)
T ss_dssp             SCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETT-----TTEEEEEEEEE--ESCHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCC-----CCccceEEEEE--ECCHHHHHHH
Confidence            446899999999999999999999999998766655432     23334444444  3456777665

>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=97.19  E-value=3.3e-05  Score=57.04  Aligned_cols=60  Identities=12%  Similarity=0.119  Sum_probs=43.5

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|..||..  ..+.++|..+
T Consensus        12 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~g~~~g~afV~--f~~~~~A~~A   71 (106)
T 2dgp_A           12 DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRF-----TGMHKGCAFLT--YCERESALKA   71 (106)
T ss_dssp             TCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSS-----SCSCCSEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCC-----CCCcceEEEEE--ECCHHHHHHH
Confidence            456899999999999999999999999998777765432     22333344443  3456677665

>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=97.18  E-value=2.1e-05  Score=59.20  Aligned_cols=57  Identities=14%  Similarity=0.148  Sum_probs=42.2

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.|....+..++.       +.|+.||..  ..+.++|.++
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~-------~~kg~afV~--f~~~~~A~~A   61 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN-------GSKGYGFVH--FETQEAAERA   61 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT-------EEEEEEEEE--ESCHHHHHHH
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCC-------CCCceEEEE--ECCHHHHHHH
Confidence            35799999999999999999999999998777655432       123334443  4567777766

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=97.17  E-value=0.00027  Score=51.44  Aligned_cols=35  Identities=6%  Similarity=0.023  Sum_probs=30.8

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceeccc
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCN  133 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~  133 (347)
                      ...++||+|||..+++++|+++|+.||+|+...+.
T Consensus        20 ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~   54 (100)
T 3r27_A           20 ASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVM   54 (100)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEE
Confidence            34689999999999999999999999999876554

>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=97.16  E-value=4.2e-05  Score=55.43  Aligned_cols=58  Identities=16%  Similarity=0.061  Sum_probs=42.3

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      .++||+|||..+++++|+++|+.||.|....+..++.     .|+.|+.||..  ..+.++|.++
T Consensus         3 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~g~~~g~afV~--f~~~~~A~~A   60 (96)
T 2x1f_A            3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQ-----TGRSKGYAFIE--FRDLESSASA   60 (96)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTT-----TCCBCSEEEEE--ESSHHHHHHH
T ss_pred             cEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCC-----CCccceEEEEE--ECCHHHHHHH
Confidence            5789999999999999999999999998777665532     22334444443  3456677665

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.16  E-value=4.5e-05  Score=55.86  Aligned_cols=60  Identities=12%  Similarity=0.114  Sum_probs=43.0

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|..||..  ..+.++|..+
T Consensus        11 ~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~-----~~~~~g~afV~--f~~~~~A~~A   70 (102)
T 1x5s_A           11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRE-----TQRSRGFGFVT--FENIDDAKDA   70 (102)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSS-----SCSCCSEEEEE--CSSHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCC-----CCCcccEEEEE--ECCHHHHHHH
Confidence            346899999999999999999999999998777765432     12223334433  4456777666

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=97.14  E-value=5.3e-05  Score=58.38  Aligned_cols=60  Identities=18%  Similarity=0.047  Sum_probs=41.7

Q ss_pred             cccccccccCCcccccchhhHHHHhhccccce--ecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           98 FNQACDYLPSLVKKLDSSTLLKFYALYKQATV--GQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        98 f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~--g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ....++||+|||..+++++|+++|+.||.|..  ..+..++.     .|+.|+.||..+  .+. +|.++
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~-----tg~~rG~aFV~f--~~~-~a~~A   82 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQ-----TQLNRGFAFIQL--STI-EAAQL   82 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSS-----SSSBCSCEEEEC--CHH-HHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCC-----CCCcceEEEEEE--CCH-HHHHH
Confidence            34578999999999999999999999999976  44544431     234444455443  334 55554

>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=97.12  E-value=3.1e-05  Score=54.88  Aligned_cols=59  Identities=15%  Similarity=0.164  Sum_probs=42.4

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.+....+..++.     .++.|+.||..  ..+.++|..+
T Consensus         6 ~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~~~~~g~afV~--f~~~~~A~~A   64 (87)
T 3bs9_A            6 HFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMA-----TGKSKGYGFVS--FFNKWDAENA   64 (87)
T ss_dssp             CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----TCCEEEEEEEE--ESSHHHHHHH
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCC-----CCccceEEEEE--ECCHHHHHHH
Confidence            46899999999999999999999999998776655432     22333334444  3456666665

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=97.11  E-value=4.6e-05  Score=56.70  Aligned_cols=60  Identities=8%  Similarity=0.095  Sum_probs=43.4

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .|+.|+.||..+  .+.++|.++
T Consensus        24 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~-----tg~~kg~afV~f--~~~~~A~~A   83 (109)
T 2rs2_A           24 SGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL-----TKRSRGFGFVTF--MDQAGVDKV   83 (109)
T ss_dssp             --CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTT-----TCCCTTCEEEEE--SSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCC-----CCCcCcEEEEEE--CCHHHHHHH
Confidence            457899999999999999999999999998777665432     234444555543  356666665

>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=97.11  E-value=3.9e-05  Score=55.88  Aligned_cols=60  Identities=18%  Similarity=0.154  Sum_probs=42.9

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|..||..  ..+.++|..+
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~~~~~g~afV~--f~~~~~a~~A   66 (99)
T 1whw_A            7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSL-----TKKPKGFAFVT--FMFPEHAVKA   66 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTT-----TCCCCSEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCC-----CCCcCeEEEEE--ECCHHHHHHH
Confidence            346899999999999999999999999998777765542     12233334443  3456666665

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.09  E-value=4.4e-05  Score=55.22  Aligned_cols=59  Identities=12%  Similarity=0.083  Sum_probs=41.8

Q ss_pred             cccccccCCcccccchhhHHHHhhcccccee-cccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVG-QCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g-~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.|... .+..++.     .++.|..||..  ..+.++|.++
T Consensus         5 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~-----~g~~~g~afV~--f~~~~~A~~A   64 (96)
T 1x5t_A            5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPD-----TGNSKGYAFIN--FASFDASDAA   64 (96)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTT-----TCSCCSEEEEE--BSSHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCC-----CCCcCeEEEEE--ECCHHHHHHH
Confidence            4689999999999999999999999999866 5554422     22333334443  3456677666

>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=97.09  E-value=5.2e-05  Score=56.44  Aligned_cols=60  Identities=12%  Similarity=0.081  Sum_probs=42.8

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|..||..  ..+.++|..+
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~g~~~g~afV~--f~~~~~A~~A   73 (111)
T 1x4h_A           14 EGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPD-----TEHSKGCAFAQ--FMTQEAAQKC   73 (111)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSS-----SCCBCSEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCC-----CCCCccEEEEE--ECCHHHHHHH
Confidence            346899999999999999999999999998777765532     12233334433  3456666665

>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=97.08  E-value=2.2e-05  Score=55.79  Aligned_cols=60  Identities=7%  Similarity=0.071  Sum_probs=42.6

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.+....+..++.     .|+.|+.||..  ..+.++|.++
T Consensus        10 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~g~~~g~afV~--f~~~~~a~~A   69 (87)
T 3s7r_A           10 DAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPN-----TGRSRGFGFIL--FKDAASVEKV   69 (87)
T ss_dssp             CTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTT-----TCCEEEEEEEE--ESSTHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCC-----CCccccEEEEE--ECCHHHHHHH
Confidence            456899999999999999999999999998777665432     22333344444  3345566554

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.07  E-value=2.9e-05  Score=54.80  Aligned_cols=60  Identities=18%  Similarity=0.164  Sum_probs=42.5

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ..++||+|||..+++++|+++|+.||.|....+..++.     .++.|..||..  ..+.++|..+.
T Consensus         5 ~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~-----~~~~~g~afV~--f~~~~~a~~A~   64 (85)
T 1x4e_A            5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKT-----TNKCKGYGFVD--FDSPSAAQKAV   64 (85)
T ss_dssp             CCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSS-----SCSCCSEEEEE--ESCHHHHHHHH
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC-----CCCcCcEEEEE--ECCHHHHHHHH
Confidence            46899999999999999999999999998777665532     12233334433  34566666653

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.07  E-value=5.8e-05  Score=55.78  Aligned_cols=61  Identities=3%  Similarity=0.028  Sum_probs=43.0

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..+.+    ..++.|+.||..  ..+.++|..+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~----~~~~~~g~afV~--f~~~~~a~~A   74 (107)
T 2cph_A           14 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMT----GTGAHRGFGFVD--FITKQDAKKA   74 (107)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCS----SSCSSCSEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCC----CCCCcCceEEEE--ECCHHHHHHH
Confidence            457899999999999999999999999998777655520    022233334433  4456677665

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.07  E-value=0.0016  Score=46.25  Aligned_cols=52  Identities=23%  Similarity=0.390  Sum_probs=43.5

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc
Q psy630           10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST   69 (347)
Q Consensus        10 ~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~   69 (347)
                      .||+=++|+.+...+|.++|+.||. ..|+++-|.       -|||.|.+++.|..|+..
T Consensus        17 HVf~l~FP~ewKt~DI~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~~   68 (100)
T 1whv_A           17 HVLHVTFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNT   68 (100)
T ss_dssp             SEEEEECCTTCCHHHHHHHHTTTCS-CCCEEEETT-------EEEEECSCHHHHHHHHHH
T ss_pred             eEEEEeCChhhhhHHHHHHhhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHHh
Confidence            4444499999999999999999994 477777663       699999999999988863

>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=97.06  E-value=3.3e-05  Score=54.17  Aligned_cols=58  Identities=16%  Similarity=0.146  Sum_probs=41.1

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      .++||+|||..+++++|+++|+.||.+....+..++.     .++.++.||..  ..+.++|..+
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~-----~~~~~g~afV~--f~~~~~a~~a   59 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQ-----TGSSRGYGFVS--FTSQDDAQNA   59 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTT-----TCCEEEEEEEE--ESCHHHHHHH
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCC-----CCCccceEEEE--ECCHHHHHHH
Confidence            3689999999999999999999999998776655432     12233334433  3456666665

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.05  E-value=5.1e-05  Score=54.66  Aligned_cols=60  Identities=22%  Similarity=0.217  Sum_probs=42.8

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|..||..  ..+.++|.++
T Consensus        15 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~-----~~~~~g~afV~--f~~~~~A~~A   74 (94)
T 2e5h_A           15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKD-----TRKSKGVAFIL--FLDKDSAQNC   74 (94)
T ss_dssp             CTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSS-----SCCCTTCEEEE--ESCHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCC-----CCCcccEEEEE--ECCHHHHHHH
Confidence            346899999999999999999999999998777765533     12233334443  3456666665

>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=97.04  E-value=5.8e-05  Score=56.65  Aligned_cols=60  Identities=18%  Similarity=0.199  Sum_probs=43.3

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|..||..  ..+.++|.++
T Consensus        24 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~g~~~g~afV~--f~~~~~a~~A   83 (115)
T 2cpz_A           24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQ-----TNLSKCFGFVS--YDNPVSAQAA   83 (115)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSS-----SCSEEEEEEEE--CSSHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC-----CCCcCccEEEE--ECCHHHHHHH
Confidence            347899999999999999999999999998777765542     12233334433  4456677665

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.03  E-value=4.6e-05  Score=55.48  Aligned_cols=60  Identities=8%  Similarity=-0.011  Sum_probs=42.8

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccc-eecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQAT-VGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~-~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.+. ...+..++.     .++.|..||..  ..+.++|..+
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~-----~g~~~g~afV~--f~~~~~a~~A   68 (99)
T 2div_A            8 MAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRL-----TGIPAGYCFVE--FADLATAEKC   68 (99)
T ss_dssp             SSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSS-----SCCEEEEEEEE--CSCHHHHHHH
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCC-----CCCcCCEEEEE--eCCHHHHHHH
Confidence            357899999999999999999999999988 776665542     12223333333  4467777666

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=96.09  E-value=9.8e-05  Score=55.51  Aligned_cols=60  Identities=12%  Similarity=0.102  Sum_probs=43.5

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccce--------ecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATV--------GQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~--------g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.+..        ..+..++     ..++.|..||..+..  .++|..+
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~-----~~g~~~g~afV~f~~--~~~A~~A   73 (116)
T 2lcw_A            6 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDR-----ETGKLKGEATVSFDD--PPSAKAA   73 (116)
Confidence            3468999999999999999999999999875        3333322     246677788877543  4455444

>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=97.01  E-value=7.3e-05  Score=55.59  Aligned_cols=60  Identities=13%  Similarity=0.116  Sum_probs=43.3

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .|+.|+.||..  ..+.++|..+
T Consensus        25 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~~~~~g~afV~--f~~~~~A~~A   84 (110)
T 1oo0_B           25 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR-----TGFSKGYALVE--YETHKQALAA   84 (110)
T ss_dssp             TBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTT-----TSSBCSEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC-----CCCcceEEEEE--ECCHHHHHHH
Confidence            457899999999999999999999999998777655432     22333344444  3456666665

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.01  E-value=5.6e-05  Score=54.53  Aligned_cols=59  Identities=14%  Similarity=0.037  Sum_probs=42.3

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.|....+..++.     .++.|..||..  ..+.++|.++
T Consensus         5 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~-----~~~~~g~afV~--f~~~~~a~~A   63 (95)
T 2dnz_A            5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSD-----TGRSKGYGFIT--FSDSECARRA   63 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSS-----SCCCCSEEEEE--ESCHHHHHHH
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCC-----CCceeeEEEEE--ECCHHHHHHH
Confidence            46899999999999999999999999998777665432     12233334444  3456666665

>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=97.01  E-value=5.2e-05  Score=55.88  Aligned_cols=60  Identities=12%  Similarity=0.133  Sum_probs=43.1

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|+.||..  ..+.++|.++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~~~~~g~afV~--f~~~~~a~~A   73 (105)
T 1x5u_A           14 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRV-----TGQHQGYGFVE--FLSEEDADYA   73 (105)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSS-----SCSBCSCEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC-----CCcCCcEEEEE--ECCHHHHHHH
Confidence            447899999999999999999999999998777765542     12233334443  3456666665

>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=97.00  E-value=7.9e-05  Score=54.60  Aligned_cols=35  Identities=6%  Similarity=-0.047  Sum_probs=30.6

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceeccc
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCN  133 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~  133 (347)
                      ...++||+|||..+++++|+++|+.||.|....+.
T Consensus        14 p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~   48 (101)
T 2cq1_A           14 PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML   48 (101)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE
Confidence            34689999999999999999999999999865554

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=97.00  E-value=5.4e-05  Score=55.18  Aligned_cols=60  Identities=12%  Similarity=0.061  Sum_probs=42.1

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccce--------ecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATV--------GQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~--------g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.+..        ..+..++.     .|+.|+.||..  ..+.++|.++
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~-----~g~~~G~afV~--f~~~~~a~~A   79 (99)
T 2la6_A           12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRE-----TGKLKGEATVS--FDDPPSAKAA   79 (99)
T ss_dssp             CCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTT-----TCSEEEEEEEE--BSSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCC-----CCCeeeEEEEE--ECCHHHHHHH
Confidence            3468999999999999999999999999987        44544432     23334444444  3456666655

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=96.98  E-value=5.5e-05  Score=55.85  Aligned_cols=60  Identities=12%  Similarity=0.053  Sum_probs=43.1

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .|+.|+.||..  ..+.++|..+
T Consensus        22 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~-----~~~~~g~afV~--f~~~~~a~~A   81 (106)
T 1p27_B           22 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR-----TGYLKGYTLVE--YETYKEAQAA   81 (106)
T ss_dssp             TBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----TSSEEEEEEEE--ESCHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCC-----CCceeeEEEEE--ECCHHHHHHH
Confidence            456899999999999999999999999998777655443     12333334443  3456666665

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=96.97  E-value=5.2e-05  Score=54.67  Aligned_cols=60  Identities=13%  Similarity=0.050  Sum_probs=42.2

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|..||..  ..+.++|.++
T Consensus        14 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~-----~~~~~g~afV~--f~~~~~A~~A   73 (95)
T 2cqc_A           14 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQ-----SRRSRGFAFVY--FENVDDAKEA   73 (95)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSS-----SSSEEEEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCC-----CCCcccEEEEE--ECCHHHHHHH
Confidence            346899999999999999999999999998776655432     12223334433  3456666665

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.97  E-value=5.6e-05  Score=55.06  Aligned_cols=61  Identities=5%  Similarity=0.035  Sum_probs=43.3

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|..||..  ..+.++|..+.
T Consensus         9 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~~~~~g~afV~--f~~~~~a~~A~   69 (99)
T 2dgs_A            9 KSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAE-----KQRPRGFGFIT--FEDEQSVDQAV   69 (99)
T ss_dssp             SCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTT-----TCSCCSEEEEE--ESSHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCC-----CCCCCceEEEE--ECCHHHHHHHH
Confidence            446899999999999999999999999998777655432     12333334444  34566666663

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=96.96  E-value=8.8e-05  Score=55.42  Aligned_cols=60  Identities=18%  Similarity=0.176  Sum_probs=42.3

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccc--------eecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQAT--------VGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~--------~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|.        ...+..++.     .++.|..||..  ..+.++|..+
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~-----~g~~~g~afV~--f~~~~~A~~A   81 (113)
T 2cpe_A           14 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE-----TGKPKGDATVS--YEDPPTAKAA   81 (113)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTT-----TCSBCSEEEEE--BSSHHHHHHH
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCC-----CCCeeeEEEEE--ECCHHHHHHH
Confidence            457899999999999999999999999997        344444422     23334445544  4456666665

>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=96.95  E-value=7.9e-05  Score=56.10  Aligned_cols=58  Identities=12%  Similarity=0.058  Sum_probs=43.3

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|.++|+.||.|....+..++.      |+.|+.||..  ..+.++|..+
T Consensus         7 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~------g~~~g~afV~--F~~~~~A~~A   64 (116)
T 2fy1_A            7 PGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRT------SKSRGFAFIT--FENPADAKNA   64 (116)
T ss_dssp             CCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTT------TTCCCEEEEE--CSSHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCC------CCcccEEEEE--ECCHHHHHHH
Confidence            46899999999999999999999999998777665542      3334444444  4457777666

>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=96.95  E-value=0.00013  Score=52.85  Aligned_cols=57  Identities=12%  Similarity=0.031  Sum_probs=42.3

Q ss_pred             ccccccccCCcccccchhhH----HHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLL----KFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~----~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+    ++|+.||.|....+..++.+        |..||..  ..+.++|.++
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~--------rg~afV~--f~~~~~A~~A   68 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY--------QLKAVVQ--MENLQDAIGA   68 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST--------TCCEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC--------CeEEEEE--ECCHHHHHHH
Confidence            34689999999999999999    99999999998777665432        2223333  4456777666

>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=96.95  E-value=7.4e-05  Score=57.42  Aligned_cols=60  Identities=13%  Similarity=0.050  Sum_probs=42.9

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|+.||..  ..+.++|.++
T Consensus        45 ~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~-----tg~~~G~afV~--F~~~~~A~~A  104 (129)
T 2kxn_B           45 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQ-----SRRSRGFAFVY--FENVDDAKEA  104 (129)
T ss_dssp             CSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSS-----SSCCCCEEEEE--ESCHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC-----CCccceEEEEE--ECCHHHHHHH
Confidence            346899999999999999999999999998777765432     12233334443  3456677665

>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=96.94  E-value=4.7e-05  Score=55.90  Aligned_cols=61  Identities=11%  Similarity=0.055  Sum_probs=43.4

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|+.||..  ..+.++|..+.
T Consensus        14 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~g~~~g~afV~--f~~~~~a~~A~   74 (103)
T 2cqg_A           14 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLK-----TGHSKGFGFVR--FTEYETQVKVM   74 (103)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSS-----SCSEEEEEEEE--ESSHHHHHHHH
T ss_pred             CCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCC-----CCCccceEEEE--ECCHHHHHHHH
Confidence            346899999999999999999999999998777765532     12333334444  33566666653

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=96.94  E-value=9.2e-05  Score=55.64  Aligned_cols=60  Identities=12%  Similarity=0.080  Sum_probs=43.0

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|..||..  ..+.++|..+
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-----~g~~~g~afV~--f~~~~~a~~A   85 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPA-----SKRSRGFGFVT--FSSMAEVDAA   85 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTT-----TSSCCSEEEEE--CSSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-----CCCcCceEEEE--eCCHHHHHHH
Confidence            347899999999999999999999999998777765532     12233334443  3456666665

>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=96.93  E-value=9.6e-05  Score=56.41  Aligned_cols=60  Identities=12%  Similarity=0.053  Sum_probs=42.8

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|.++|+.||.|....+..++.     .++.|+.||..  ..+.++|..+
T Consensus        21 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~~~~~g~afV~--f~~~~~a~~A   80 (126)
T 3ex7_B           21 EGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR-----TGYLKGYTLVE--YETYKEAQAA   80 (126)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTT-----TSSBCSCEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC-----CCccceEEEEE--ECCHHHHHHH
Confidence            356899999999999999999999999998777765532     22233334433  3456666665

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.93  E-value=6.5e-05  Score=54.80  Aligned_cols=59  Identities=12%  Similarity=0.009  Sum_probs=43.0

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.      |+.|..||..  ..+.++|..+
T Consensus        16 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~------g~~~g~afV~--f~~~~~a~~A   74 (100)
T 2do4_A           16 EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRA------GKPKGLAYVE--YENESQASQA   74 (100)
T ss_dssp             CCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTT------SCEEEEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCC------CCEEeEEEEE--ECCHHHHHHH
Confidence            457899999999999999999999999998777665543      2233334443  3456666665

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.92  E-value=9.9e-05  Score=55.33  Aligned_cols=61  Identities=10%  Similarity=-0.001  Sum_probs=41.9

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.|. ..+..++..  ...|+.|+.||..  ..+.++|.++
T Consensus         8 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~--~~~g~~~G~aFV~--f~~~~~a~~A   68 (114)
T 2dnl_A            8 SRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAES--KSYFPPKGYAFLL--FQEESSVQAL   68 (114)
T ss_dssp             CCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSS--CCCSCTTSEEEEC--CSSHHHHHHH
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCC--CCCCCcccEEEEE--ECCHHHHHHH
Confidence            46899999999999999999999999998 334333210  0114455555544  4557777666

>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=96.92  E-value=7.1e-05  Score=56.08  Aligned_cols=61  Identities=11%  Similarity=0.094  Sum_probs=43.2

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|+.||..+  .+.++|.++.
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~g~~~g~afV~f--~~~~~a~~A~   84 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRN-----SRRSKGIAYVEF--CEIQSVPLAI   84 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCC-----SSSCCCCEEEEE--SCGGGHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCC-----CCccCcEEEEEe--CcHHHHHHHH
Confidence            457899999999999999999999999998777765543     122333344443  3455666554

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=96.92  E-value=6.7e-05  Score=56.40  Aligned_cols=60  Identities=12%  Similarity=0.135  Sum_probs=43.2

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|..||..  ..+.++|.++
T Consensus        16 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~~~~~g~afV~--f~~~~~a~~A   75 (116)
T 2cqd_A           16 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQ-----TGKSRGYGFVT--MADRAAAERA   75 (116)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSS-----SCCCCSEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCC-----CCccceEEEEE--ECCHHHHHHH
Confidence            457899999999999999999999999998776665432     12333344444  3456666665

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=96.92  E-value=0.00057  Score=50.85  Aligned_cols=55  Identities=7%  Similarity=-0.110  Sum_probs=39.7

Q ss_pred             cccccccCCcccccchhhHHHHhhcc-ccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYK-QATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg-~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.|| .|....+...++         |+.||..  ..+.++|.++
T Consensus        28 ~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~---------rGfaFV~--F~~~e~A~~A   83 (111)
T 2jvr_A           28 RYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDF---------DGTGALE--FPSEEILVEA   83 (111)
T ss_dssp             CEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSS---------SCCEEEE--ESSHHHHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCC---------CCEEEEE--ECCHHHHHHH
Confidence            36899999999999999999999999 888766643322         2223333  3456677666

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=96.90  E-value=0.00036  Score=51.19  Aligned_cols=59  Identities=8%  Similarity=-0.063  Sum_probs=44.1

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.      |+.|+.||..+  .+.++|..+
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~------g~~rG~aFV~F--~~~e~a~~A   68 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH------KAFKGSIFVVF--DSIESAKKF   68 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT------TSCCCEEEEEE--SSHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC------CCCccEEEEEE--CCHHHHHHH
Confidence            346899999999999999999999999998777766542      34444455443  356666665

>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=96.89  E-value=6.7e-05  Score=55.10  Aligned_cols=59  Identities=10%  Similarity=0.074  Sum_probs=43.2

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.+....+..++.     .|+.|+.||..  ..+.++|.++
T Consensus         8 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~-----~g~~~g~afV~--f~~~~~a~~A   66 (104)
T 1p1t_A            8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRE-----TGKPKGYGFCE--YQDQETALSA   66 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETT-----TTEEEEEEEEE--CSCHHHHHHH
T ss_pred             ccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCC-----CCccceEEEEE--ECCHHHHHHH
Confidence            46899999999999999999999999998776665432     23333344443  4567777766

>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=96.88  E-value=5.9e-05  Score=55.55  Aligned_cols=59  Identities=14%  Similarity=0.097  Sum_probs=43.6

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.      ++.|..||..  ..+.++|..+
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~------g~~~g~afV~--f~~~~~A~~A   72 (105)
T 2dnh_A           14 RDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPD------GSSKGCAFVK--FSSHTEAQAA   72 (105)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSS------SCEEEEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC------CCcCcEEEEE--eCCHHHHHHH
Confidence            357899999999999999999999999998777765543      2333344444  3456677665

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=96.88  E-value=0.00012  Score=54.39  Aligned_cols=59  Identities=7%  Similarity=0.007  Sum_probs=43.0

Q ss_pred             cccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           98 FNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        98 f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      -...++||+|||..+++++|+++|+.||.|....+..++.       +.|+.||..  ..+.++|.++
T Consensus        27 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~-------~~kg~afV~--f~~~~~A~~A   85 (109)
T 2err_A           27 SQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER-------GSKGFGFVT--FENSADADRA   85 (109)
T ss_dssp             TCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT-------BCTTEEEEE--CCCSHHHHHH
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC-------CCceEEEEE--ECCHHHHHHH
Confidence            3557899999999999999999999999998766655431       234444444  4456666655

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=96.87  E-value=5.5e-05  Score=60.24  Aligned_cols=59  Identities=12%  Similarity=0.012  Sum_probs=42.7

Q ss_pred             cccccccCCcccccchhhHHHHhhcc--ccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYK--QATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg--~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||  .|....+..++.     .|+.|+.||..  ..+.++|..+
T Consensus        55 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~-----tg~skGfaFV~--f~~~~~A~~A  115 (156)
T 3n9u_C           55 RAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRA-----NGQSKGYAEVV--VASENSVHKL  115 (156)
T ss_dssp             -CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTT-----TCCEEEEEEEE--ESCHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCC-----CCccceEEEEE--ECCHHHHHHH
Confidence            46899999999999999999999999  777666655532     33444445544  3456777666

>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=96.86  E-value=4.5e-05  Score=54.26  Aligned_cols=60  Identities=12%  Similarity=0.010  Sum_probs=42.4

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.+....+..++.     .++.|+.||..+  .+.++|.++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~~~~~g~afV~f--~~~~~a~~a   64 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKF-----SGHPKGFAYIEF--SDKESVRTS   64 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCS-----SSSCCEEEEEEE--SSTHHHHHH
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCC-----CCCcceEEEEEE--CCHHHHHHH
Confidence            346899999999999999999999999998777665432     122333344443  345666655

>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=96.86  E-value=0.00052  Score=48.85  Aligned_cols=37  Identities=8%  Similarity=0.135  Sum_probs=31.8

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCC
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..+
T Consensus        10 ~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~   46 (89)
T 3d2w_A           10 HGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP   46 (89)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC
Confidence            3468999999999999999999999999987666553

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=96.85  E-value=0.0002  Score=53.05  Aligned_cols=37  Identities=5%  Similarity=0.095  Sum_probs=32.1

Q ss_pred             hcccccccccCCcccccchhhHHHHhhccccceeccc
Q psy630           97 RFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCN  133 (347)
Q Consensus        97 ~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~  133 (347)
                      .....++||+|||..+++++|+++|+.||.|....+.
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~   64 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL   64 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE
Confidence            3456799999999999999999999999999866554

>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=96.84  E-value=4.9e-05  Score=54.85  Aligned_cols=59  Identities=12%  Similarity=0.109  Sum_probs=40.8

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.+....+..++.     .++.|..||..  ..+.++|.++
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~-----~g~~~g~afV~--f~~~~~a~~A   73 (95)
T 2ek1_A           15 PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE-----KGMPTGEAMVA--FESRDEATAA   73 (95)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECT-----TSCEEEEEEEE--ESSHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCC-----CCCEeeEEEEE--ECCHHHHHHH
Confidence            46899999999999999999999999987544444322     22333334443  3456666665

>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=96.81  E-value=0.0001  Score=55.25  Aligned_cols=59  Identities=10%  Similarity=0.121  Sum_probs=43.1

Q ss_pred             ccccccccCCcccccchhhHHHHhhcccc-ceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQA-TVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v-~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.+ ....+..++.      |+.|+.||..  ..+.++|.++
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~------g~~~G~afV~--F~~~~~a~~A   73 (114)
T 2cpy_A           14 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNN------GQGLGQALVQ--FKNEDDARKS   73 (114)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTT------SSCSSCEEEE--CSSHHHHHHH
T ss_pred             CccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCC------CCcceEEEEE--ECCHHHHHHH
Confidence            44689999999999999999999999998 6555554432      3444445544  4457777776

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=96.81  E-value=7e-05  Score=56.17  Aligned_cols=60  Identities=17%  Similarity=0.169  Sum_probs=43.0

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|+.||..  ..+.++|..+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~~~~~g~afV~--f~~~~~a~~A   73 (115)
T 2dgo_A           14 NHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMA-----TGKSKGYGFVS--FFNKWDAENA   73 (115)
T ss_dssp             TCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----TCCEEEEEEEE--ESSHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCC-----CCCcceEEEEE--ECCHHHHHHH
Confidence            457899999999999999999999999998777765432     22233334443  3456666665

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.81  E-value=0.00011  Score=53.78  Aligned_cols=60  Identities=8%  Similarity=0.055  Sum_probs=42.5

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|..||..+.  +.++|..+
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~-----~~~~~g~afV~f~--~~~~A~~A   71 (103)
T 2dnm_A           12 GMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPH-----TKAPRGFAFVRFH--DRRDAQDA   71 (103)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSS-----SCSBCSCEEEEES--SSSHHHHH
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCC-----CCCCCeEEEEEEC--CHHHHHHH
Confidence            347899999999999999999999999998777665432     1333444555543  34455544

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.81  E-value=8.8e-05  Score=54.62  Aligned_cols=60  Identities=12%  Similarity=0.060  Sum_probs=42.7

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|..||..+..  .++|..+
T Consensus        15 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~-----~g~~~g~afV~f~~--~~~a~~a   74 (105)
T 2dh8_A           15 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKT-----TNQSRGFGFVKFKD--PNCVGTV   74 (105)
T ss_dssp             SSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSS-----SCCEEEEEEEEESS--TTHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCC-----CCCcceEEEEEECC--HHHHHHH
Confidence            447899999999999999999999999998777665532     22334445555443  4455554

>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=96.80  E-value=0.00037  Score=51.01  Aligned_cols=37  Identities=8%  Similarity=-0.050  Sum_probs=32.4

Q ss_pred             ccccccccCCcc-cccchhhHHHHhhccccceecccCC
Q psy630           99 NQACDYLPSLVK-KLDSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus        99 ~~~~~~v~~l~~-~~~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                      ...++||+|||. .+++++|+++|+.||.|+...+..+
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~   51 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK   51 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC
Confidence            356899999999 9999999999999999997776544

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=96.80  E-value=0.00011  Score=57.06  Aligned_cols=60  Identities=17%  Similarity=0.153  Sum_probs=43.7

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|+.||..  ..+.++|.++
T Consensus        62 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~-----~~~~~g~afV~--f~~~~~a~~A  121 (140)
T 2ku7_A           62 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-----TEKHRGFAFVE--FELAEDAAAA  121 (140)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTT-----TCCCCSEEEEE--ESCHHHHHHH
T ss_pred             CCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCC-----CCCcCcEEEEE--ECCHHHHHHH
Confidence            457899999999999999999999999998777655432     22334444444  3456666665

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=96.79  E-value=9.9e-05  Score=55.91  Aligned_cols=50  Identities=6%  Similarity=-0.029  Sum_probs=40.2

Q ss_pred             ccccccCC----cccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcC
Q psy630          101 ACDYLPSL----VKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLG  155 (347)
Q Consensus       101 ~~~~v~~l----~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~  155 (347)
                      ..|||+||    |..+++.+|+.+|+.||+|.+..+..++-     .|++|+.+|..+.
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~-----Tg~slGfgfVef~   56 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPN-----SALPLHVYLIKYA   56 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTT-----TCCEEEEEEEECC
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC-----CCceeeEEEEEEC
Confidence            46899999    99999999999999999999888877653     4455555555554

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=96.79  E-value=0.00035  Score=49.28  Aligned_cols=52  Identities=15%  Similarity=0.043  Sum_probs=39.7

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      .-+||+||++.+++++|+++|..||+|....+..+           |+.|+.  +..+.+||.++
T Consensus         8 ~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~~-----------kGfaFV--ey~~~~eA~~A   59 (89)
T 2wbr_A            8 SWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLN-----------QGIALC--KYTTREEANKA   59 (89)
T ss_dssp             CEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEETT-----------TTEEEE--EESSHHHHHHH
T ss_pred             ceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcCC-----------CcEEEE--EECCHHHHHHH
Confidence            46899999999999999999999999987555432           333333  35567788777

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.79  E-value=9.7e-05  Score=56.21  Aligned_cols=60  Identities=12%  Similarity=0.005  Sum_probs=42.6

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccc----eecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQAT----VGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~----~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ...++||+|||..+++++|+++|+.||.|.    ...+..++      .|+.|+.||..  ..+.++|.++.
T Consensus        22 ~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~------~gr~~G~aFV~--F~~~~~A~~Al   85 (123)
T 2dha_A           22 NQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP------DGRPTGDAFVL--FACEEYAQNAL   85 (123)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT------TSCEEEEEEEC--CSSHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC------CCCEeeEEEEE--ECCHHHHHHHH
Confidence            346899999999999999999999999863    33333332      34555555554  45677777764

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=96.78  E-value=9.6e-05  Score=56.22  Aligned_cols=62  Identities=10%  Similarity=0.009  Sum_probs=43.9

Q ss_pred             cccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630           98 FNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus        98 f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      -...++||+|||..+++++|+++|+.||.|....+..++.     .|+.|+.||..  ..+.++|..+.
T Consensus        34 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~~~~~g~afV~--f~~~~~a~~A~   95 (124)
T 2jwn_A           34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKF-----SGHPKGYAYIE--FAERNSVDAAV   95 (124)
T ss_dssp             HHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECT-----TSSCEEEEEEE--ESSHHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCC-----CCCcccEEEEE--ECCHHHHHHHH
Confidence            3457899999999999999999999999998766655431     22333334443  34566776664

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=96.78  E-value=8.9e-05  Score=51.79  Aligned_cols=56  Identities=9%  Similarity=0.087  Sum_probs=38.5

Q ss_pred             ccccccCCcccc------cchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKL------DSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~------~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      .++||+|||..+      ++++|+++|+.||.+....+. ..      .|+.|+.||..  ..+.++|..+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~-~~------~g~~~g~afV~--f~~~~~A~~A   63 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EE------DGKTKGYIFLE--YASPAHAVDA   63 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC-CB------TTBCCCEEEEE--ESSHHHHHHH
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec-CC------CCcEeEEEEEE--ECCHHHHHHH
Confidence            478999999998      679999999999999876654 21      23334344443  3346666555

>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=96.77  E-value=8.4e-05  Score=54.73  Aligned_cols=60  Identities=13%  Similarity=0.091  Sum_probs=42.4

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccce-ecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATV-GQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~-g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ...++||+|||..+++++|+++|+.||.+.. ..+..+.      .|+.|+.|+..  ..+.++|..+.
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~------~g~~~G~afV~--F~~~~~a~~A~   74 (104)
T 1wg5_A           14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDF------QGRSTGEAFVQ--FASQEIAEKAL   74 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCS------SSCBCSEEEEE--ESSHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECC------CCCcceEEEEE--ECCHHHHHHHH
Confidence            3468999999999999999999999999875 4444432      23444445544  34567776663

>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=96.76  E-value=0.00013  Score=54.02  Aligned_cols=60  Identities=10%  Similarity=-0.022  Sum_probs=42.5

Q ss_pred             ccccccccCCcccccchhhHHHHhhccc-cceeccc-CCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQ-ATVGQCN-IDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~-v~~g~~~-~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||. +....+. .++.     .|+.|+.||..  ..+.++|..+
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~-----~g~~~g~afV~--f~~~~~A~~A   68 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAAD-----KMKNRGFAFVE--YESHRAAAMA   68 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCT-----TTTTCCEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCC-----CCCcCcEEEEE--ecCHHHHHHH
Confidence            3468999999999999999999999998 8766655 2221     23444445544  3456777665

>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=96.75  E-value=0.0037  Score=45.17  Aligned_cols=73  Identities=10%  Similarity=0.055  Sum_probs=59.1

Q ss_pred             CCeEEEeCCCCCC-CH----HHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccc
Q psy630            8 LNKIFVGNLPWTV-SH----NELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI   81 (347)
Q Consensus         8 ~~~l~V~nLp~~~-t~----~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v   81 (347)
                      .++|+|.||+.++ ..    +.++++|.+|+++......+.-      .=.-|.|.+.++|.+|... ++..+.|+.++|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            4689999999876 32    4678999999998887776432      2357999999999998875 999999999999


Q ss_pred             cCCCc
Q psy630           82 QPSDS   86 (347)
Q Consensus        82 ~~~~~   86 (347)
                      -.+++
T Consensus        79 YFgq~   83 (104)
T 1wey_A           79 YFAQT   83 (104)
T ss_dssp             ECCCC
T ss_pred             EecCC
Confidence            88874

>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=96.75  E-value=0.00075  Score=47.71  Aligned_cols=36  Identities=8%  Similarity=0.103  Sum_probs=31.6

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCC
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                      ..++||+|||..+++++|+++|+.||.|....+..+
T Consensus         5 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~   40 (88)
T 1wf0_A            5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP   40 (88)
T ss_dssp             CCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC
Confidence            468999999999999999999999999987666543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=96.75  E-value=4.6e-05  Score=55.96  Aligned_cols=60  Identities=17%  Similarity=0.131  Sum_probs=42.7

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|..||..  ..+.++|..+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~-----~~~~~g~afV~--f~~~~~A~~A   73 (103)
T 2cq0_A           14 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKT-----TGQSKGFAFIS--FHRREDAARA   73 (103)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSS-----SCSEEEEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCC-----CCceeeEEEEE--ECCHHHHHHH
Confidence            457899999999999999999999999998777665432     12223334433  3456666665

>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=96.74  E-value=9.4e-05  Score=54.01  Aligned_cols=61  Identities=8%  Similarity=0.061  Sum_probs=42.3

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ...++||+|||..+++++|+++|+.|| +....+..++.    ..|+.|+.||..  ..+.++|.++.
T Consensus        18 ~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~----~~g~~~g~afV~--f~~~~~a~~Ai   78 (100)
T 2j76_E           18 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPS----NPERLKGFGYAE--FEDLDSLLSAL   78 (100)
T ss_dssp             --CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTT----TTCCCCSCEEEE--ECCHHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCC----cCCccCeEEEEE--ECCHHHHHHHH
Confidence            457899999999999999999999999 88766655431    123334444444  34577777664

>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=96.72  E-value=0.00094  Score=49.63  Aligned_cols=35  Identities=3%  Similarity=-0.068  Sum_probs=30.5

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceeccc
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCN  133 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~  133 (347)
                      ...++||+|||..+++++|+++|+.||.|....+.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~   43 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP   43 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEe
Confidence            34689999999999999999999999999865544

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.72  E-value=0.00011  Score=55.04  Aligned_cols=59  Identities=15%  Similarity=0.054  Sum_probs=42.7

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.      ++.|..||..  ..+.++|..+
T Consensus        14 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~------g~~~g~afV~--f~~~~~a~~A   72 (114)
T 2do0_A           14 LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD------GKSRGIGTVT--FEQSIEAVQA   72 (114)
T ss_dssp             CCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTT------CSEEEEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC------CCeeeEEEEE--ECCHHHHHHH
Confidence            346899999999999999999999999998766665543      2333334443  3456666665

>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=96.72  E-value=0.00042  Score=51.96  Aligned_cols=36  Identities=8%  Similarity=-0.093  Sum_probs=31.1

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCC
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                      ..++||+|||..+++++|+++|+.||.|....+..+
T Consensus        16 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~   51 (115)
T 3beg_B           16 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD   51 (115)
T ss_dssp             -CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC
Confidence            468999999999999999999999999987666544

>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=96.71  E-value=0.0013  Score=48.75  Aligned_cols=55  Identities=15%  Similarity=0.211  Sum_probs=41.0

Q ss_pred             cCCccccccCCCcccccchhhhhhcccccccccCCccc-ccchhhHHHHhhccccceecc
Q psy630           74 LEGSRLSIQPSDSHNRMAENMEDRFNQACDYLPSLVKK-LDSSTLLKFYALYKQATVGQC  132 (347)
Q Consensus        74 ~~g~~l~v~~~~~~~~~~~~~~~~f~~~~~~v~~l~~~-~~~e~l~~~f~~fg~v~~g~~  132 (347)
                      ..|.++.+..+.......    ..-...++||+|||.. +++++|+++|+.||.|....+
T Consensus         5 ~~g~~~~~~~s~~~~~~~----~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i   60 (110)
T 1wf1_A            5 SSGMSLKLQASNVTNKND----PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV   60 (110)
T ss_dssp             CCSCCCCCCCCCSCCSCC----CTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE
T ss_pred             CCCcccccccCCCCCCCC----CCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE
Confidence            456778777665533221    1223468999999999 999999999999999987655

>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=96.71  E-value=5.2e-05  Score=55.07  Aligned_cols=59  Identities=12%  Similarity=0.103  Sum_probs=40.5

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.+....+..++.     .|+.|..||..  ..+.++|.++
T Consensus        15 ~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~-----~g~~~g~afV~--f~~~~~a~~A   73 (98)
T 2cqp_A           15 PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE-----KGMPTGEAMVA--FESRDEATAA   73 (98)
T ss_dssp             SEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECS-----SSCEEEEEEEE--ESCHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECC-----CCCeeeEEEEE--ECCHHHHHHH
Confidence            46899999999999999999999999987544433322     22333334444  3456666665

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.70  E-value=7.8e-05  Score=54.70  Aligned_cols=59  Identities=17%  Similarity=0.211  Sum_probs=42.5

Q ss_pred             cccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           98 FNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        98 f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ....++||+|||..+++++|+++|+.||.|....+..+ .      ++.|..||..  ..+.++|..+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~-~------g~~~g~afV~--f~~~~~A~~A   71 (103)
T 2d9p_A           13 YQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME-G------GRSKGFGFVC--FSSPEEATKA   71 (103)
T ss_dssp             SSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC-S------SSEEEEEEEE--ESSHHHHHHH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC-C------CCcCEEEEEE--ECCHHHHHHH
Confidence            35678999999999999999999999999987666544 2      2233334443  3456666655

>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=96.70  E-value=0.00016  Score=53.52  Aligned_cols=59  Identities=8%  Similarity=0.047  Sum_probs=42.5

Q ss_pred             ccccccccCCcccccchhhHHHHhhccc---cceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQ---ATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~---v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.   +....+..++.      |+.|+.|+..+  .+.++|..+
T Consensus        10 ~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~------g~~~G~afV~F--~~~~~a~~A   71 (107)
T 2lmi_A           10 DVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD------GKRRGDALIEM--ESEQDVQKA   71 (107)
T ss_dssp             SCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT------STTCSEEEEEB--SSHHHHHHH
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC------CCEeeEEEEEE--CCHHHHHHH
Confidence            3468999999999999999999999998   66555554432      44555555553  456666665

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=96.70  E-value=0.00015  Score=55.17  Aligned_cols=59  Identities=12%  Similarity=0.112  Sum_probs=43.1

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.      |+.|+.||..  ..+.++|..+
T Consensus        34 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~------g~~~g~afV~--f~~~~~A~~A   92 (124)
T 2kt5_A           34 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS------GRSLGTADVH--FERRADALKA   92 (124)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSS------SSCCSEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCC------CCEeeEEEEE--ECCHHHHHHH
Confidence            457899999999999999999999999998777765542      2233334433  3456666665

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=96.69  E-value=0.00011  Score=52.63  Aligned_cols=58  Identities=10%  Similarity=-0.021  Sum_probs=41.2

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.+....+..+ .      ++.|..||..  ..+.++|..+
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~-~------g~~~g~afV~--f~~~~~a~~a   64 (92)
T 2dgv_A            7 GACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME-N------GKSKGCGVVK--FESPEVAERA   64 (92)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES-S------SCEEEEEEEE--ESSHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc-C------CCcceEEEEE--ECCHHHHHHH
Confidence            3468999999999999999999999999987666542 1      2233334443  3456666665

>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=96.68  E-value=0.0026  Score=45.73  Aligned_cols=36  Identities=6%  Similarity=-0.024  Sum_probs=31.4

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCC
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                      ..++||+|||..+++++|+++|+.||.|....+...
T Consensus        17 ~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~   52 (97)
T 1why_A           17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG   52 (97)
T ss_dssp             CSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC
Confidence            468999999999999999999999999987666543

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.67  E-value=0.00014  Score=54.00  Aligned_cols=58  Identities=5%  Similarity=0.012  Sum_probs=43.3

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ..++||+|||..+++++|+++|+.| .|....+..++      .|+.|+.||..  ..+.++|.++.
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~------~g~~~G~afV~--F~~~~~a~~Al   73 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH------VGRNNGNGLVK--FLSPQDTFEAL   73 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT------TCCCCSEEEEE--CSSHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC------CCCCCeEEEEE--ECCHHHHHHHH
Confidence            3689999999999999999999999 67766665543      24555556655  44577777774

>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=96.67  E-value=0.0011  Score=49.28  Aligned_cols=35  Identities=17%  Similarity=0.037  Sum_probs=31.0

Q ss_pred             ccccccccCCccc-ccchhhHHHHhhccccceeccc
Q psy630           99 NQACDYLPSLVKK-LDSSTLLKFYALYKQATVGQCN  133 (347)
Q Consensus        99 ~~~~~~v~~l~~~-~~~e~l~~~f~~fg~v~~g~~~  133 (347)
                      ...++||+|||.. +++++|+++|+.||.|....+.
T Consensus        24 p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~   59 (112)
T 1x4f_A           24 LGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILM   59 (112)
T ss_dssp             CCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEE
T ss_pred             CCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEe
Confidence            3568999999998 9999999999999999876664

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.66  E-value=0.0007  Score=48.35  Aligned_cols=35  Identities=6%  Similarity=-0.059  Sum_probs=30.9

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceeccc
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCN  133 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~  133 (347)
                      ...++||+|||..+++++|+++|+.||.|....+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~   43 (92)
T 2dgt_A            9 ASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV   43 (92)
T ss_dssp             SSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEE
Confidence            45789999999999999999999999999866554

>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=96.65  E-value=0.00011  Score=54.00  Aligned_cols=61  Identities=8%  Similarity=0.078  Sum_probs=42.5

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ...++||+|||..+++++|+++|+.|| |....+..++..    .++.|..||..  ..+.++|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~----~g~~~g~afV~--f~~~~~a~~A~   74 (104)
T 1wi8_A           14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSN----PERLKGFGYAE--FEDLDSLLSAL   74 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSC----TTSBCSCEEEE--ESSHHHHHHHH
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCC----CCCcCeEEEEE--ECCHHHHHHHH
Confidence            346899999999999999999999999 876666554320    03334444444  34567776663

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=96.65  E-value=0.00031  Score=51.18  Aligned_cols=34  Identities=6%  Similarity=0.068  Sum_probs=30.4

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceeccc
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCN  133 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~  133 (347)
                      ..++||+|||..+++++|+++|+.||.|....+.
T Consensus        27 ~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~   60 (101)
T 2la4_A           27 VTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY   60 (101)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE
T ss_pred             CCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe
Confidence            4689999999999999999999999999866554

>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=96.64  E-value=5e-05  Score=54.22  Aligned_cols=36  Identities=14%  Similarity=0.174  Sum_probs=31.4

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCC
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDK  136 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~  136 (347)
                      .++||+|||..+++++|+++|+.||.+....+..++
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~   37 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDR   37 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCS
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcC
Confidence            468999999999999999999999999877666543

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=96.63  E-value=6.5e-05  Score=56.65  Aligned_cols=38  Identities=13%  Similarity=0.216  Sum_probs=33.0

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCC
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDK  136 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~  136 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++
T Consensus        39 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~   76 (118)
T 2khc_A           39 EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDK   76 (118)
T ss_dssp             CSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCC
Confidence            45789999999999999999999999999877766543

>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=96.63  E-value=0.00047  Score=49.75  Aligned_cols=57  Identities=16%  Similarity=0.106  Sum_probs=42.3

Q ss_pred             ccccccccCCcccccchhhH----HHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLL----KFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~----~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+    ++|+.||.+....+.        ..|+.|+.||..  ..+.++|..+
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~--------~~~~~~g~afV~--f~~~~~A~~A   67 (97)
T 1nu4_A            7 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS--------RSLKMRGQAFVI--FKEVSSATNA   67 (97)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECC--------HHHHHTTCEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEE--------cCCCcCcEEEEE--eCCHHHHHHH
Confidence            34689999999999999999    999999998865443        145556555554  3456777666

>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=96.62  E-value=0.00046  Score=51.04  Aligned_cols=37  Identities=8%  Similarity=-0.083  Sum_probs=32.0

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCC
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..+
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~   50 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD   50 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC
Confidence            3468999999999999999999999999987666544

>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=96.61  E-value=0.00011  Score=56.90  Aligned_cols=58  Identities=9%  Similarity=-0.042  Sum_probs=42.5

Q ss_pred             cccccccCCcccccchhhHHHHhhccc---cceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQ---ATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~---v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.   +....+..++.      |+.|+.||..  ..+.++|.++
T Consensus        44 ~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~------g~srG~aFV~--F~~~e~a~~A  104 (136)
T 2hgl_A           44 GFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE------GRQSGEAFVE--LGSEDDVKMA  104 (136)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS------SCEEEEEEEE--CSSHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC------CCCCeEEEEE--ECCHHHHHHH
Confidence            468999999999999999999999999   66555544432      4455555555  3457777766

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.60  E-value=0.00079  Score=47.83  Aligned_cols=35  Identities=9%  Similarity=0.005  Sum_probs=30.9

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceeccc
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCN  133 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~  133 (347)
                      ...++||+|||..+++++|+++|+.||.|....+.
T Consensus         8 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~   42 (90)
T 2dnp_A            8 NTWKIFVGNVSAACTSQELRSLFERRGRVIECDVV   42 (90)
T ss_dssp             CSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEE
Confidence            45689999999999999999999999999866654

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.59  E-value=0.00029  Score=50.19  Aligned_cols=34  Identities=6%  Similarity=0.110  Sum_probs=30.2

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceeccc
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCN  133 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~  133 (347)
                      ..++||+|||..+++++|+++|+.||.|....+.
T Consensus         8 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~   41 (90)
T 2dnq_A            8 MVKLFIGNLPREATEQEIRSLFEQYGKVLECDII   41 (90)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE
T ss_pred             CeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE
Confidence            4689999999999999999999999999865554

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=96.58  E-value=0.0018  Score=47.05  Aligned_cols=35  Identities=11%  Similarity=0.067  Sum_probs=30.6

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCC
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                      +++||+|||..+++++|+++|+.||.|....+..+
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~   35 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN   35 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC
Confidence            36899999999999999999999999987666554

>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=96.57  E-value=8.4e-05  Score=56.63  Aligned_cols=60  Identities=12%  Similarity=0.196  Sum_probs=41.1

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..+++     .|+.|+.||..+.  +.++|..+
T Consensus        24 ~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~-----~g~~~G~afV~F~--~~~~a~~A   83 (124)
T 1wel_A           24 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGP-----NGKATGEGFVEFR--NEADYKAA   83 (124)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECT-----TSSEEEEEEEEBS--SSHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECC-----CCCCCeEEEEEEC--CHHHHHHH
Confidence            447899999999999999999999999987533322221     3344445555543  45566555

>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=96.56  E-value=0.00032  Score=51.99  Aligned_cols=37  Identities=8%  Similarity=0.094  Sum_probs=32.2

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCC
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..+
T Consensus        24 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~   60 (109)
T 1x4g_A           24 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE   60 (109)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC
Confidence            4578999999999999999999999999987666544

>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=96.55  E-value=0.001  Score=48.94  Aligned_cols=59  Identities=12%  Similarity=0.098  Sum_probs=43.1

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|.++|+.||.|....+..++.+      +.|+.||..  ..+.++|..+
T Consensus        28 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g------~~~g~afV~--f~~~~~a~~A   86 (107)
T 3ulh_A           28 TGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSG------RSLGTADVH--FERKADALKA   86 (107)
T ss_dssp             CSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTS------CEEEEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC------CcceEEEEE--ECCHHHHHHH
Confidence            3468999999999999999999999999987777655432      233334443  3456666665

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=96.54  E-value=0.00012  Score=56.90  Aligned_cols=60  Identities=12%  Similarity=0.065  Sum_probs=43.6

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.     .++.|..||..  ..+.++|..+
T Consensus        41 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-----~~~~~g~afV~--f~~~~~a~~A  100 (139)
T 1u6f_A           41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRE-----TRQSRGYGFVK--FQSGSSAQQA  100 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETT-----TTEEEEEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCC-----CCCcceEEEEE--ECCHHHHHHH
Confidence            447899999999999999999999999998777655432     23334445544  3456666665

>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=96.53  E-value=0.00099  Score=48.91  Aligned_cols=54  Identities=9%  Similarity=-0.092  Sum_probs=39.5

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ..++||+|||..+++++|+++|+.||.|....+...           |..||.+  ..+.++|..+.
T Consensus        15 ~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~-----------kg~aFVe--f~~~~~A~~Ai   68 (104)
T 1wex_A           15 SPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----------KRQALVE--FENIDSAKECV   68 (104)
T ss_dssp             CSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----------TTEEEEE--ESSHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC-----------CCEEEEE--ECCHHHHHHHH
Confidence            468999999999999999999999999987555332           2334444  33466666664

>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=96.51  E-value=0.00098  Score=53.01  Aligned_cols=54  Identities=7%  Similarity=-0.039  Sum_probs=39.8

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..+||+||+..+++++|+++|+.||.|....+...+++.+         ||.+  ..+.++|..+
T Consensus        47 l~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgf---------AFVe--F~d~~~A~~A  100 (164)
T 1sjr_A           47 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQ---------ALLQ--YADPVSAQHA  100 (164)
T ss_dssp             EEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEE---------EEEE--ESCHHHHHHH
T ss_pred             EEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCE---------EEEE--ECCHHHHHHH
Confidence            4689999999999999999999999998777644433222         3333  3456777766

>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=96.51  E-value=0.0005  Score=51.39  Aligned_cols=56  Identities=11%  Similarity=0.106  Sum_probs=40.5

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.+....+..+..        .++.||..  ..+.++|..+
T Consensus         8 ~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~--------~~g~afV~--f~~~~~A~~A   63 (115)
T 3lqv_A            8 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE--------TRGTAYVV--YEDIFDAKNA   63 (115)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTT--------TTTCEEEE--ESSHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCC--------CCcEEEEE--ECCHHHHHHH
Confidence            35899999999999999999999999998766654321        13334433  4456677665

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=96.50  E-value=0.00012  Score=55.19  Aligned_cols=59  Identities=8%  Similarity=-0.017  Sum_probs=42.5

Q ss_pred             ccccccccCCcccccchhhHHHHhhccc---cceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQ---ATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~---v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.   |....+..++.      |+.|+.|+..+  .+.++|.++
T Consensus        16 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~------g~~~G~afV~F--~~~~~a~~A   77 (118)
T 2db1_A           16 EGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE------GRQSGEAFVEL--ESEDDVKLA   77 (118)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS------SCEEEEEEEEB--SSHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC------CCCCeEEEEEE--CCHHHHHHH
Confidence            3468999999999999999999999999   66555554432      34454555553  356666666

>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=96.50  E-value=8e-05  Score=54.67  Aligned_cols=59  Identities=10%  Similarity=0.130  Sum_probs=42.0

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ...++||+|||..+++++|+++|+.||.+ ...+..++.      ++.|..||..  ..+.++|.++.
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~------g~~~G~afV~--F~~~~~a~~Al   72 (102)
T 1wez_A           14 TGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPD------GRVTGEADVE--FATHEDAVAAM   72 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSS------SCEEEEEEEE--CSSSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCC------CCEeeEEEEE--ECCHHHHHHHH
Confidence            44689999999999999999999999954 445544432      4445555555  44566777664

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=96.48  E-value=0.0011  Score=50.66  Aligned_cols=54  Identities=7%  Similarity=-0.025  Sum_probs=39.0

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..+||+||+..+++++|.++|+.||.|....+.....|+         .||.+  ..+.++|..+
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gf---------qAFVe--f~~~~~A~~A   82 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQF---------QALLQ--YADPVSAQHA   82 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEE---------EEEEE--ESCHHHHHHH
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCc---------EEEEE--ECCHHHHHHH
Confidence            467899999999999999999999999876554322221         13333  3457777776

>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=96.47  E-value=0.0019  Score=53.14  Aligned_cols=100  Identities=9%  Similarity=0.026  Sum_probs=61.7

Q ss_pred             CHHHHHHHHhc---CCCccCCccccccCCCccc--ccchhhhhhcccccccccCCcccccchhhHHHHhhccccceeccc
Q psy630           59 NKEAVDKVFST---DSHVLEGSRLSIQPSDSHN--RMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCN  133 (347)
Q Consensus        59 ~~~~a~~a~~~---~~~~~~g~~l~v~~~~~~~--~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~  133 (347)
                      +.+.+..|+..   ....+.+....|.+.....  .............++||+|||..+++++|.++|+.||.|....+.
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~~p~p~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~  142 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMR  142 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTTSCCCCCCHHHHHHHHHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEE
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEecccCCCcccchhhhhccccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEE
Confidence            45666777764   2344555555554442211  111111123455789999999999999999999999999877666


Q ss_pred             CCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          134 IDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       134 ~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      .+..      ++.|+.|+..  ..+.++|..+.
T Consensus       143 ~~~~------~~~kG~aFVe--F~~~e~A~~A~  167 (193)
T 2voo_A          143 RTLH------KAFKGSIFVV--FDSIESAKKFV  167 (193)
T ss_dssp             ECTT------CCEEEEEEEE--ESSHHHHHHHH
T ss_pred             ECCC------CCcccEEEEE--ECCHHHHHHHH
Confidence            5432      3344445544  34577777663

>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=96.47  E-value=0.00018  Score=57.07  Aligned_cols=60  Identities=8%  Similarity=0.060  Sum_probs=43.1

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...+|||+|||..+++++|.++|+.||.|....+..++.     .++.|..||..  ..+.++|..+
T Consensus        38 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~-----~~~~~g~afV~--f~~~~~A~~A   97 (156)
T 1h2v_Z           38 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-----KKTACGFCFVE--YYSRADAENA   97 (156)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----TCCEEEEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC-----CCccceEEEEE--ECCHHHHHHH
Confidence            447899999999999999999999999998777655432     12233334443  3456677665

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.46  E-value=0.0015  Score=49.26  Aligned_cols=78  Identities=19%  Similarity=0.362  Sum_probs=56.0

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEE-EEeee--------CCCC-----CceeEEEEEEcCHHHHHHHHhcCCCc
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNA-SVMFD--------KNTG-----LSKGFGFVTFQNKEAVDKVFSTDSHV   73 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~-~i~~~--------~~t~-----~~~g~afV~f~~~~~a~~a~~~~~~~   73 (347)
                      ...|.|=+.|+..+.. +-++|++||.|.+- ...+.        +.+.     .......|+|.+..+|.+|+..||.+
T Consensus         7 e~~VtVFGFp~~~~~~-VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~i   85 (132)
T 3p3d_A            7 ELAILVFGYPETMANQ-VIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGAV   85 (132)
T ss_dssp             -CEEEEECCCGGGHHH-HHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTCE
T ss_pred             ceEEEEEecCHHHHHH-HHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCeE
Confidence            3457777898877554 67789999998762 11110        0001     12467799999999999999999999


Q ss_pred             cCCccccccCCCc
Q psy630           74 LEGSRLSIQPSDS   86 (347)
Q Consensus        74 ~~g~~l~v~~~~~   86 (347)
                      |.|..|-|.+..+
T Consensus        86 i~G~mIGV~Py~~   98 (132)
T 3p3d_A           86 FNGVLLGVIPYTK   98 (132)
T ss_dssp             ETTEECEEEECCH
T ss_pred             eCcEEEEEEECCH
Confidence            9999888887754

>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=96.44  E-value=0.0011  Score=48.44  Aligned_cols=34  Identities=9%  Similarity=0.090  Sum_probs=30.1

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceeccc
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCN  133 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~  133 (347)
                      ..++||+|||..+++++|+++|+.||.|....+.
T Consensus        11 ~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~   44 (103)
T 2dgu_A           11 VKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL   44 (103)
T ss_dssp             CCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE
Confidence            4689999999999999999999999999865543

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=96.35  E-value=0.00032  Score=56.98  Aligned_cols=58  Identities=12%  Similarity=0.111  Sum_probs=42.9

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.|....+..++.      ++.|..||..  ..+.++|..+
T Consensus        88 ~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~------g~~kG~afV~--F~~~~~A~~A  145 (177)
T 2f3j_A           88 GAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRS------GRSLGTADVH--FERRADALKA  145 (177)
T ss_dssp             CEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTT------SSCSCCEEEE--ESCHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC------CCEeeEEEEE--eCCHHHHHHH
Confidence            47899999999999999999999999998777765542      2333344444  3456677665

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.35  E-value=0.0022  Score=46.18  Aligned_cols=54  Identities=13%  Similarity=0.032  Sum_probs=38.2

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.|. ..+...         +.|..||..  ..+.++|..+
T Consensus        19 ~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~---------~~~g~afV~--f~~~~~a~~A   72 (97)
T 2e5j_A           19 AADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ---------GPRRRAFLH--YPDSAAAQQA   72 (97)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE---------TTTTEEEEE--CSSHHHHHHH
T ss_pred             CCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC---------CCCcEEEEE--ECCHHHHHHH
Confidence            46899999999999999999999999985 233222         233334433  4456677665

>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=96.32  E-value=0.0025  Score=47.46  Aligned_cols=54  Identities=11%  Similarity=0.022  Sum_probs=38.9

Q ss_pred             cccccc--cCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          100 QACDYL--PSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       100 ~~~~~v--~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ..++||  +||+..+++++|+++|+.||.|....+...+           ..||.  ...+.++|..++
T Consensus        25 t~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~r-----------gfaFV--~f~~~~~A~~Ai   80 (114)
T 2cq2_A           25 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK-----------PYSFA--RYRTTEESKRAY   80 (114)
T ss_dssp             CSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTC-----------SCEEE--EESSHHHHHHHH
T ss_pred             CCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCC-----------CEEEE--EECCHHHHHHHH
Confidence            457999  7799999999999999999999865554321           12332  244677777773

>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=96.30  E-value=0.0015  Score=45.96  Aligned_cols=37  Identities=5%  Similarity=0.254  Sum_probs=32.1

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCC
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDK  136 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~  136 (347)
                      ..++||+|||..+++++|+++|+.||.+....+..++
T Consensus         4 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~   40 (88)
T 4a8x_A            4 PTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVER   40 (88)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEET
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCC
Confidence            4689999999999999999999999999876665543

>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=96.29  E-value=0.00055  Score=49.00  Aligned_cols=29  Identities=14%  Similarity=0.155  Sum_probs=26.6

Q ss_pred             cccccccCCcccccchhhHHHHhhccc-cc
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQ-AT  128 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~-v~  128 (347)
                      ..++||+|||..+++++|+++|+.||. +.
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~   37 (93)
T 2cqh_A            8 MNKLYIGNLSPAVTADDLRQLFGDRKLPLA   37 (93)
T ss_dssp             CCCEEEECCCTTCCHHHHHHHHHHTTCCCS
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHHcCCceE
Confidence            468999999999999999999999998 54

>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=96.29  E-value=0.00011  Score=55.00  Aligned_cols=60  Identities=13%  Similarity=0.165  Sum_probs=39.4

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.+....+.....     .++.|+.||..  ..+.++|..+
T Consensus        24 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~-----~g~~~g~afV~--f~~~~~a~~A   83 (115)
T 2cpx_A           24 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM-----TGRMRGQAFIT--FPNKEIAWQA   83 (115)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE-----CSSSCSEEEEE--CSSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC-----CCccceEEEEE--ECCHHHHHHH
Confidence            347899999999999999999999999985322222110     22333334443  4456666665

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=96.29  E-value=0.00012  Score=53.41  Aligned_cols=58  Identities=5%  Similarity=-0.072  Sum_probs=41.1

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.+.. .+..++     ..++.|..||..  ..+.++|.++
T Consensus        17 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~-----~~g~~~g~afV~--f~~~~~a~~A   74 (101)
T 1fj7_A           17 PFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDV-----RTGTNRKFGYVD--FESAEDLEKA   74 (101)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEE-----EEETTTTEEEEE--ESSHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecC-----CCCCcCcEEEEE--ECCHHHHHHH
Confidence            468999999999999999999999999875 232221     134455555554  3456666666

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=96.27  E-value=0.002  Score=48.89  Aligned_cols=33  Identities=3%  Similarity=-0.176  Sum_probs=29.3

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceeccc
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCN  133 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~  133 (347)
                      ..+||+||+..+++++|.++|+.||.|....+.
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~   58 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIF   58 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEE
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEE
Confidence            357899999999999999999999999876664

>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=96.26  E-value=0.002  Score=46.14  Aligned_cols=59  Identities=10%  Similarity=0.076  Sum_probs=42.2

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.      ++.|..||..+  .+.++|.++
T Consensus        15 ~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~------g~~~g~afV~f--~~~~~a~~A   73 (95)
T 2ywk_A           15 ADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE------GKPKSFGFVCF--KHPESVSYA   73 (95)
T ss_dssp             GGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT------SCEEEEEEEEE--SSTHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC------CCCceEEEEEE--CCHHHHHHH
Confidence            346899999999999999999999999998766665542      23333444443  345566555

>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=96.26  E-value=0.00028  Score=59.87  Aligned_cols=60  Identities=12%  Similarity=0.025  Sum_probs=42.6

Q ss_pred             ccccccccCCcccccchhhHHHHhhcc--ccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYK--QATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg--~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...+|||+||+..+++++|+++|+.||  .|....+..++.     .++.|..||..+.  +.++|.++
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~-----tg~skGfaFV~f~--~~~~a~~A  128 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRA-----NGQSKGFALVGVG--SEASSKKL  128 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTT-----TCCEEEEEEEEES--CTTHHHHH
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCC-----CCccceEEEEEEC--CHHHHHHH
Confidence            346899999999999999999999999  888777766542     3445555555544  34455444

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.25  E-value=0.0076  Score=42.94  Aligned_cols=52  Identities=23%  Similarity=0.365  Sum_probs=44.0

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc
Q psy630           10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST   69 (347)
Q Consensus        10 ~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~   69 (347)
                      .||+-++|+.+...+|.++|+.|| -..|+++-|.       -|||.|.+++.|..|+..
T Consensus         7 HV~~l~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~   58 (101)
T 3ctr_A            7 HVLHVTFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNT   58 (101)
T ss_dssp             EEEEEECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHH
T ss_pred             eEEEEeCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHh
Confidence            455559999999999999999999 5577777663       699999999999988873

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.16  E-value=0.0035  Score=58.25  Aligned_cols=57  Identities=21%  Similarity=0.341  Sum_probs=43.6

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcC
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTD   70 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~   70 (347)
                      .|+|||. .|..+++.+|.++|++||.|.++.+..++     .-||.|+|.+.+++..++...
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~~~  109 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQNGT  109 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHSSC
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHhcc
Confidence            4799997 79999999999999999999999887544     279999999999988887653

>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=96.16  E-value=0.00038  Score=53.09  Aligned_cols=59  Identities=15%  Similarity=0.124  Sum_probs=41.1

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccc--eecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQAT--VGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~--~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ...++||+|||..+++++|+++|+.| .+.  ...+..++      .|+.|+.||..+.  +.++|.++.
T Consensus        41 ~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~------~GrsrGfaFV~F~--~~e~A~~Al  101 (126)
T 2hgm_A           41 NDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDP------EGKITGEAFVQFA--SQELAEKAL  101 (126)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCS------SSSSCSEEEEEES--STTHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECC------CCCCceEEEEEEC--CHHHHHHHH
Confidence            34679999999999999999999999 455  44444433      2455666666644  455665553

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.14  E-value=0.0022  Score=46.06  Aligned_cols=36  Identities=14%  Similarity=0.067  Sum_probs=31.1

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceec-ccCC
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQ-CNID  135 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~-~~~~  135 (347)
                      ..++||+|||..+++++|+++|+.||.|...+ +..+
T Consensus        15 ~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~   51 (96)
T 2e44_A           15 IRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTD   51 (96)
T ss_dssp             CCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCS
T ss_pred             CCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecC
Confidence            46899999999999999999999999998763 4444

>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=96.14  E-value=0.0024  Score=46.49  Aligned_cols=58  Identities=9%  Similarity=0.147  Sum_probs=42.3

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++..       .|..||..  ..+.++|..+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~-------~~g~afV~--f~~~~~a~~A   71 (103)
T 2cqi_A           14 QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS-------NDPYCFVE--FYEHRDAAAA   71 (103)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS-------SCCEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC-------CCCEEEEE--ECCHHHHHHH
Confidence            4578999999999999999999999999987776665322       12233333  3456777666

>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=96.13  E-value=0.0009  Score=47.35  Aligned_cols=52  Identities=10%  Similarity=0.110  Sum_probs=38.0

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.| .+....+.           +.|+.||.  ...+.++|.++
T Consensus         5 ~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~-----------~~~g~afV--~f~~~~~a~~A   56 (88)
T 1wg1_A            5 SSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD-----------RNKRTAFV--TLLNGEQAQNA   56 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE-----------GGGTEEEE--CCSCHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe-----------CCCcEEEE--EECCHHHHHHH
Confidence            4689999999999999999999999 77755442           23333443  34567777766

>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=96.12  E-value=0.00017  Score=56.31  Aligned_cols=62  Identities=16%  Similarity=0.142  Sum_probs=40.1

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecc--cCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQC--NIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~--~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+.+|+.||.|....+  ..+  -.....|+.|+.||..  ..+.++|..+
T Consensus        45 ~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~d--i~~~~~g~~~g~afV~--f~~~~~A~~A  108 (143)
T 3egn_A           45 NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFD--IRLMKEGRMKGQAFIG--LPNEKAAAKA  108 (143)
T ss_dssp             CSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCE--EEEEEETTTEEEEEEE--CSSHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceee--EEeccCCCcccEEEEE--eCCHHHHHHH
Confidence            468999999999999999999999999875311  111  0000123444444444  4466777666

>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=96.09  E-value=0.0026  Score=46.34  Aligned_cols=58  Identities=7%  Similarity=0.031  Sum_probs=42.3

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.+       .|..||..  ..+.++|..+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~-------~~g~afV~--f~~~~~a~~A   71 (103)
T 2cq3_A           14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-------SKGFGFVT--FENSADADRA   71 (103)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-------TCCEEEEE--ESCHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC-------CcEEEEEE--ECCHHHHHHH
Confidence            4578999999999999999999999999987776654321       23334433  3456777666

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=96.07  E-value=0.00041  Score=49.43  Aligned_cols=58  Identities=7%  Similarity=-0.023  Sum_probs=41.2

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.| .+....+..+..      |+.|+.||..  ..+.++|.++
T Consensus         9 ~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~------g~~~g~afV~--f~~~~~a~~A   66 (91)
T 2dgw_A            9 TCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAH------GNKTGYIFVD--FSNEEEVKQA   66 (91)
T ss_dssp             CCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTT------SCEEEEEEEE--CSSHHHHHHH
T ss_pred             CccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCC------CCCceEEEEE--ECCHHHHHHH
Confidence            44689999999999999999999999 787666655432      2333344443  4456666665

>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=96.07  E-value=0.003  Score=46.57  Aligned_cols=57  Identities=11%  Similarity=0.044  Sum_probs=40.7

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.        .|..||..  ..+.++|.++
T Consensus        21 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~--------~~g~afV~--f~~~~~A~~A   77 (109)
T 1x4a_A           21 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG--------GPPFAFVE--FEDPRDAEDA   77 (109)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSS--------SSCCEEEE--ESCHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCC--------CCcEEEEE--ECCHHHHHHH
Confidence            446899999999999999999999999998766644321        22233333  3456666665

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=96.06  E-value=0.00052  Score=50.46  Aligned_cols=57  Identities=9%  Similarity=0.107  Sum_probs=40.1

Q ss_pred             cccccccCCcccc------cchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKL------DSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~------~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+      ++++|+++|+.||.|....+. ..      .|+.|+.||..+.  +.++|..+
T Consensus        15 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~-~~------~g~~~G~afV~f~--~~~~A~~A   77 (105)
T 2nlw_A           15 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP-EE------DGKTKGYIFLEYA--SPAHAVDA   77 (105)
T ss_dssp             CSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC-CB------TTBSCCEEEEEEC--SSSHHHHH
T ss_pred             CCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee-CC------CCCeeeEEEEEEC--CHHHHHHH
Confidence            4689999999988      679999999999999876554 11      3444555655544  34455544

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=96.05  E-value=0.00026  Score=51.86  Aligned_cols=60  Identities=10%  Similarity=-0.066  Sum_probs=41.6

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ...++||+|||..+++++|+++|+.|| |....+..++.     .++.|..||..  ..+.++|..+.
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~-----~g~~~g~afV~--f~~~~~a~~A~   73 (103)
T 2dng_A           14 PPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKD-----TDKFKGFCYVE--FDEVDSLKEAL   73 (103)
T ss_dssp             SCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSS-----SCSEEEEEEEE--ESSHHHHHHHG
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCC-----CCccceEEEEE--ECCHHHHHHHH
Confidence            346899999999999999999999997 77666655432     12333334444  34567776664

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=96.05  E-value=0.0018  Score=46.74  Aligned_cols=60  Identities=10%  Similarity=-0.036  Sum_probs=42.2

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCC--CccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKP--SWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p--~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.|....+..++.  |    .++.|..||..  ..+.++|..+
T Consensus         5 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~g----t~~~~g~afV~--f~~~~~a~~A   66 (98)
T 2cpf_A            5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAG----VLLSMGFGFVE--YKKPEQAQKA   66 (98)
T ss_dssp             CCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTC----CEEEEEEEEEE--ESSHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCC----CcCcccEEEEE--ECCHHHHHHH
Confidence            46899999999999999999999999998766654322  1    11333334444  3456666665

>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=96.05  E-value=0.0021  Score=47.74  Aligned_cols=59  Identities=12%  Similarity=0.128  Sum_probs=42.8

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.+      +.|+.||..  ..+.++|.++
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g------~~~g~afV~--f~~~~~a~~A   82 (114)
T 1x5o_A           24 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSG------TSRGVGFAR--MESTEKCEAV   82 (114)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSS------CEEEEEEEE--ESCHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCC------CcceEEEEE--ECCHHHHHHH
Confidence            4478999999999999999999999999987776655422      233334443  3456666665

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.02  E-value=0.0052  Score=43.87  Aligned_cols=70  Identities=10%  Similarity=0.105  Sum_probs=46.0

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCC--ceeEEEEEEcCHHHHHHHHhc-CCCccCCc
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGL--SKGFGFVTFQNKEAVDKVFST-DSHVLEGS   77 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~--~~g~afV~f~~~~~a~~a~~~-~~~~~~g~   77 (347)
                      .-+|.|+.|||.+|++++.+.+..+=.+........+.+.+  .-.-|||.|.+.++...-... +|..+-+.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~   81 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDS   81 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECT
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeC
Confidence            34799999999999998877776543332222222222211  125589999999988877765 87777543

>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=96.02  E-value=0.0024  Score=44.65  Aligned_cols=36  Identities=8%  Similarity=0.084  Sum_probs=31.2

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccC
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNI  134 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~  134 (347)
                      ...++||+|||..+++++|+++|+.||.+....+..
T Consensus        11 ~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~   46 (85)
T 2ytc_A           11 TITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQ   46 (85)
T ss_dssp             SCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEG
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEEC
Confidence            346899999999999999999999999988665543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=95.99  E-value=0.0035  Score=45.40  Aligned_cols=56  Identities=18%  Similarity=0.091  Sum_probs=38.6

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.|..   ..+.      .++.|..||..  ..+.++|.++
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~---~~~~------~g~~~g~afV~--f~~~~~A~~A   69 (101)
T 2fc9_A           14 ESKTLVLSNLSYSATEETLQEVFEKATFIKV---PQNQ------NGKSKGYAFIE--FASFEDAKEA   69 (101)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHCSSCSEEEC---CBCS------SSCBCSEEEEE--CSSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCEEEE---EECC------CCCEeeEEEEE--ECCHHHHHHH
Confidence            4578999999999999999999999998842   2221      12233334443  4457777666

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=95.97  E-value=0.003  Score=45.91  Aligned_cols=52  Identities=15%  Similarity=0.198  Sum_probs=39.1

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCC
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQ  156 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~  156 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.      |+.|+.||..+..
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~------g~~~g~afV~f~~   59 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT------GVSKGYGFVSFYN   59 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT------SCEEEEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCC------CCccceEEEEECC
Confidence            446899999999999999999999999998766665542      3334445555443

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=95.95  E-value=0.0032  Score=45.89  Aligned_cols=59  Identities=17%  Similarity=0.248  Sum_probs=42.8

Q ss_pred             ccccccccCCcccccchhhHHHHhh-ccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYAL-YKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~-fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+. ||.|....+..++.+      +.|..||..  ..+.++|..+
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g------~~~g~afV~--f~~~~~a~~A   67 (104)
T 2dhg_A            8 PEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTG------VSKGYGFVK--FTDELEQKRA   67 (104)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTC------CEEEEEEEE--ESCHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCC------CccceEEEE--ECCHHHHHHH
Confidence            3468999999999999999999999 999987777655432      233334433  3456666665

>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=95.95  E-value=0.0029  Score=45.73  Aligned_cols=35  Identities=11%  Similarity=0.184  Sum_probs=30.7

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceeccc
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCN  133 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~  133 (347)
                      ...++||+|||..+++++|+++|+.||.|....+.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~   48 (99)
T 2cpj_A           14 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH   48 (99)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEe
Confidence            34689999999999999999999999999865554

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=95.81  E-value=0.00059  Score=52.14  Aligned_cols=56  Identities=7%  Similarity=-0.035  Sum_probs=38.7

Q ss_pred             cccccccCCcccccchhhH----HHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLL----KFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~----~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+    ++|+.||.|....+  .+.      ++.|+.||..  ..+.++|..+
T Consensus        29 ~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i--~~~------~~~rG~aFV~--F~~~~~A~~A   88 (127)
T 2a3j_A           29 SQVVLITNINPEVPKEKLQALLYALASSQGDILDIVV--DLS------DDNSGKAYIV--FATQESAQAF   88 (127)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEE--CCC------CSSCCCEEEE--ESSHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEe--ccC------CCcCCEEEEE--ECCHHHHHHH
Confidence            4689999999999998865    69999999975444  221      2334445544  3456777766

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=95.79  E-value=0.0037  Score=44.86  Aligned_cols=34  Identities=9%  Similarity=0.197  Sum_probs=30.3

Q ss_pred             ccccccccCCcc-cccchhhHHHHhhccccceecc
Q psy630           99 NQACDYLPSLVK-KLDSSTLLKFYALYKQATVGQC  132 (347)
Q Consensus        99 ~~~~~~v~~l~~-~~~~e~l~~~f~~fg~v~~g~~  132 (347)
                      ...++||+|||. .+++++|+++|+.||.|....+
T Consensus         9 ~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i   43 (96)
T 2kvi_A            9 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI   43 (96)
T ss_dssp             CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEE
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE
Confidence            456899999998 9999999999999999986555

>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=95.74  E-value=0.0026  Score=47.17  Aligned_cols=64  Identities=9%  Similarity=0.185  Sum_probs=43.3

Q ss_pred             cccccccccCCcccccchhhH---HHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           98 FNQACDYLPSLVKKLDSSTLL---KFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        98 f~~~~~~v~~l~~~~~~e~l~---~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ....++||+|||..+++++|+   ++|+.||.|....+..++..  ...++.|+.||..  ..+.++|.++
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~--~~~~~~~G~afV~--f~~~~~A~~A   79 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSY--AGSQGPSASAYVT--YIRSEDALRA   79 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSC--CSSSCCCEEEEEE--ESSHHHHHHH
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCc--CccCCCCeEEEEE--ECcHHHHHHH
Confidence            345789999999999999999   99999999987777554321  0011122334433  3456677666

>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=95.63  E-value=0.0049  Score=44.39  Aligned_cols=34  Identities=9%  Similarity=0.184  Sum_probs=30.3

Q ss_pred             ccccccccCCcc-cccchhhHHHHhhccccceecc
Q psy630           99 NQACDYLPSLVK-KLDSSTLLKFYALYKQATVGQC  132 (347)
Q Consensus        99 ~~~~~~v~~l~~-~~~~e~l~~~f~~fg~v~~g~~  132 (347)
                      ...++||+|||. .+++++|+++|+.||.|....+
T Consensus        21 ~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i   55 (97)
T 2xnq_A           21 MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI   55 (97)
T ss_dssp             TTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEE
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEE
Confidence            457899999998 9999999999999999986655

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=95.51  E-value=0.0065  Score=43.35  Aligned_cols=31  Identities=10%  Similarity=0.275  Sum_probs=28.3

Q ss_pred             cccccccCCcccccchhhHHHHhhcccccee
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVG  130 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g  130 (347)
                      ..++||+|||..+++++|+++|+.||.|...
T Consensus         8 ~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v   38 (94)
T 2e5g_A            8 LRSVFVSGFPRGVDSAQLSEYFLAFGPVASV   38 (94)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHGGGTSCEEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCeEEE
Confidence            3589999999999999999999999999864

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=95.34  E-value=0.0067  Score=51.47  Aligned_cols=85  Identities=9%  Similarity=-0.049  Sum_probs=50.5

Q ss_pred             HHHhcCCCccCCccccccCCCcccccchhhhhhcccccccccCCcccc---------cchhhHHHHhhccccceecccCC
Q psy630           65 KVFSTDSHVLEGSRLSIQPSDSHNRMAENMEDRFNQACDYLPSLVKKL---------DSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus        65 ~a~~~~~~~~~g~~l~v~~~~~~~~~~~~~~~~f~~~~~~v~~l~~~~---------~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                      .++..+.....|+.....+........   ...-...++||+||+..+         ++++|+.+|+.||.|....+...
T Consensus       102 ~~~~~~~~D~fGr~k~~~~~d~~~g~g---s~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~  178 (240)
T 3u1l_A          102 LALRTEVLDCFGREKFADYREDMGGIG---SFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES  178 (240)
T ss_dssp             HHHHCSSBCTTSSBCGGGTC------------CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG
T ss_pred             hcccccCcccccchhcccchhcccCcC---ccccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC
Confidence            333334455557655444443322211   112245789999999988         79999999999999987665432


Q ss_pred             CCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          136 KPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       136 ~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                                 |+.||..  ..+.++|..+
T Consensus       179 -----------kG~AFV~--F~~~~~Ae~A  195 (240)
T 3u1l_A          179 -----------KNCGFVK--FKYQANAEFA  195 (240)
T ss_dssp             -----------GTEEEEE--ESSHHHHHHH
T ss_pred             -----------CCEEEEE--eCCHHHHHHH
Confidence                       3334443  4457777766

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=94.89  E-value=0.011  Score=42.47  Aligned_cols=32  Identities=9%  Similarity=0.002  Sum_probs=27.7

Q ss_pred             ccccccccCCcccccchhhHHHHhhc--ccccee
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALY--KQATVG  130 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~f--g~v~~g  130 (347)
                      ...++||+|||..+++++|+++|+.|  |.|...
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~   47 (99)
T 2cpd_A           14 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV   47 (99)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEE
T ss_pred             CcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEE
Confidence            34689999999999999999999999  766643

>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=94.87  E-value=0.013  Score=40.89  Aligned_cols=25  Identities=8%  Similarity=0.232  Sum_probs=23.6

Q ss_pred             cccccccCCcccccchhhHHHHhhc
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALY  124 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~f  124 (347)
                      ..++||+|||..+++++|+++|+.|
T Consensus         6 ~~~l~V~nLp~~~t~~~l~~~F~~~   30 (87)
T 2hzc_A            6 ARRLYVGNIPFGITEEAMMDFFNAQ   30 (87)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHH
Confidence            4689999999999999999999999

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=94.42  E-value=0.012  Score=42.07  Aligned_cols=32  Identities=6%  Similarity=-0.033  Sum_probs=28.4

Q ss_pred             ccccccccCCcccccchhhHHHHhhcccccee
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVG  130 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g  130 (347)
                      ...++||+|||..+++++|+++|+.||.|...
T Consensus        15 ~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~   46 (96)
T 1fjc_A           15 AARTLLAKNLSFNITEDELKEVFEDALEIRLV   46 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSEEEECCE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe
Confidence            44689999999999999999999999988643

>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=93.18  E-value=0.048  Score=48.82  Aligned_cols=54  Identities=11%  Similarity=0.041  Sum_probs=38.3

Q ss_pred             cccccccC--CcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          100 QACDYLPS--LVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       100 ~~~~~v~~--l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ..++||+|  |+..+++++|+++|+.||+|....+...           |..||..  .-+.++|+.++
T Consensus        18 s~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~~-----------kgfaFV~--f~~~~~A~~Ai   73 (345)
T 3tht_A           18 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN-----------KPYSFAR--YRTTEESKRAY   73 (345)
T ss_dssp             CSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCTT-----------CSEEEEE--ESSHHHHHHHH
T ss_pred             CCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC-----------CCEEEEE--ECCHHHHHHHH
Confidence            35789999  5789999999999999999986544321           2223333  34577777774

---

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	347
d1hbka_	89	a.11.1.1 (A:) Acyl-CoA binding protein {Plasmodium	5e-28
d1hb6a_	86	a.11.1.1 (A:) Acyl-CoA binding protein {Cow (Bos t	2e-24
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-17
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-17
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	8e-17
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-16
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-16
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	6e-16
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-15
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-15
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-14
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	5e-14
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-13
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	4e-13
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	5e-13
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	6e-13
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-12
d1wdya_	285	d.211.1.1 (A:) RNase L, 2-5a-dependent ribonucleas	2e-12
d1wdya_	285	d.211.1.1 (A:) RNase L, 2-5a-dependent ribonucleas	2e-08
d1wdya_	285	d.211.1.1 (A:) RNase L, 2-5a-dependent ribonucleas	9e-07
d1wdya_	285	d.211.1.1 (A:) RNase L, 2-5a-dependent ribonucleas	3e-05
d1wdya_	285	d.211.1.1 (A:) RNase L, 2-5a-dependent ribonucleas	4e-05
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	2e-12
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	3e-12
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	6e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	7e-12
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	7e-12
d2fo1e1	277	d.211.1.1 (E:1021-1297) Lin-12 {Caenorhabditis ele	1e-11
d2fo1e1	277	d.211.1.1 (E:1021-1297) Lin-12 {Caenorhabditis ele	1e-04
d2fo1e1	277	d.211.1.1 (E:1021-1297) Lin-12 {Caenorhabditis ele	2e-04
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-11
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-11
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-11
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-11
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-11
d1n11a_	408	d.211.1.1 (A:) Ankyrin-R {Human (Homo sapiens) [Ta	4e-11
d1n11a_	408	d.211.1.1 (A:) Ankyrin-R {Human (Homo sapiens) [Ta	2e-10
d1n11a_	408	d.211.1.1 (A:) Ankyrin-R {Human (Homo sapiens) [Ta	6e-09
d1n11a_	408	d.211.1.1 (A:) Ankyrin-R {Human (Homo sapiens) [Ta	6e-08
d1n11a_	408	d.211.1.1 (A:) Ankyrin-R {Human (Homo sapiens) [Ta	1e-06
d1n11a_	408	d.211.1.1 (A:) Ankyrin-R {Human (Homo sapiens) [Ta	4e-04
d1n11a_	408	d.211.1.1 (A:) Ankyrin-R {Human (Homo sapiens) [Ta	7e-04
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	4e-11
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-11
d1sw6a_	301	d.211.1.1 (A:) Swi6 ankyrin-repeat fragment {Baker	2e-10
d1sw6a_	301	d.211.1.1 (A:) Swi6 ankyrin-repeat fragment {Baker	9e-09
d1sw6a_	301	d.211.1.1 (A:) Swi6 ankyrin-repeat fragment {Baker	1e-05
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-10
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-10
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	4e-10
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	4e-10
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-10
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	8e-10
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-09
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-09
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	1e-09
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-09
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-09
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-09
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-09
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	4e-09
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	4e-09
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	6e-09
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	6e-09
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	9e-09
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-08
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	3e-08
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	4e-08
d2ajaa1	346	a.118.24.1 (A:3-348) Hypothetical protein LPG2416	4e-08
d2ajaa1	346	a.118.24.1 (A:3-348) Hypothetical protein LPG2416	7e-06
d2ajaa1	346	a.118.24.1 (A:3-348) Hypothetical protein LPG2416	4e-04
d1k1aa_	228	d.211.1.1 (A:) bcl-3 {Human (Homo sapiens) [TaxId:	5e-08
d1k1aa_	228	d.211.1.1 (A:) bcl-3 {Human (Homo sapiens) [TaxId:	2e-06
d1k1aa_	228	d.211.1.1 (A:) bcl-3 {Human (Homo sapiens) [TaxId:	0.003
d1s70b_	291	d.211.1.1 (B:) Myosin phosphatase targeting subuni	7e-08
d1s70b_	291	d.211.1.1 (B:) Myosin phosphatase targeting subuni	2e-06
d1s70b_	291	d.211.1.1 (B:) Myosin phosphatase targeting subuni	6e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	8e-08
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	9e-08
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-07
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	1e-07
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-07
d1ixva_	229	d.211.1.1 (A:) 26S proteasome non-ATPase regulator	2e-07
d1ixva_	229	d.211.1.1 (A:) 26S proteasome non-ATPase regulator	1e-06
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-07
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	3e-07
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	3e-07
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	3e-07
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	3e-07
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	3e-07
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-07
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	3e-07
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	4e-07
d1uoha_	223	d.211.1.1 (A:) 26S proteasome non-ATPase regulator	6e-07
d1uoha_	223	d.211.1.1 (A:) 26S proteasome non-ATPase regulator	2e-05
d1uoha_	223	d.211.1.1 (A:) 26S proteasome non-ATPase regulator	2e-04
d1uoha_	223	d.211.1.1 (A:) 26S proteasome non-ATPase regulator	0.002
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-06
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-06
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-06
d1oy3d_	255	d.211.1.1 (D:) Transcription factor inhibitor I-ka	2e-06
d1oy3d_	255	d.211.1.1 (D:) Transcription factor inhibitor I-ka	2e-06
d1oy3d_	255	d.211.1.1 (D:) Transcription factor inhibitor I-ka	1e-04
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-05
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	1e-05
d1ot8a_	209	d.211.1.1 (A:) Neurogenic locus notch receptor dom	1e-05
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-05
d1ihba_	156	d.211.1.1 (A:) p18ink4C(ink6) {Human (Homo sapiens	4e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	5e-05
d1bd8a_	156	d.211.1.1 (A:) Cell cycle inhibitor p19ink4D {Huma	7e-05
d1bd8a_	156	d.211.1.1 (A:) Cell cycle inhibitor p19ink4D {Huma	0.002
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 7e-05
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	2e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	2e-04
d1iknd_	221	d.211.1.1 (D:) I-kappa-B-alpha {Human (Homo sapien	3e-04
d1iknd_	221	d.211.1.1 (D:) I-kappa-B-alpha {Human (Homo sapien	3e-04
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	3e-04
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	5e-04
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	0.001
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	0.001
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	0.001
d1awcb_	153	d.211.1.1 (B:) GA bindinig protein (GABP) beta 1 {	0.002
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	0.002
d1ycsb1	130	d.211.1.1 (B:327-456) 53BP2 {Human (Homo sapiens)	0.003

>d1hbka_ a.11.1.1 (A:) Acyl-CoA binding protein {Plasmodium falciparum [TaxId: 5833]} Length = 89

class: All alpha proteins
fold: Acyl-CoA binding protein-like
superfamily: Acyl-CoA binding protein
family: Acyl-CoA binding protein
domain: Acyl-CoA binding protein
species: Plasmodium falciparum [TaxId: 5833]

 Score =  102 bits (256), Expect = 5e-28
 Identities = 26/89 (29%), Positives = 47/89 (52%), Gaps = 2/89 (2%)

Query: 93  NMEDRFNQACDYLPSLVK--KLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNA 150
           +M   F +   ++  L +   L +   L  Y  YKQ+T+G CNI +PS +    + KY A
Sbjct: 1   HMAQVFEECVSFINGLPRTINLPNELKLDLYKYYKQSTIGNCNIKEPSAHKYIDRKKYEA 60

Query: 151 WNSLGQMAKSEAMSKYIALLKEVDAGWED 179
           W S+  + + +A  +Y+ ++ E+   W+D
Sbjct: 61  WKSVENLNREDAQKRYVDIVSEIFPYWQD 89

>d1hb6a_ a.11.1.1 (A:) Acyl-CoA binding protein {Cow (Bos taurus) [TaxId: 9913]} Length = 86

class: All alpha proteins
fold: Acyl-CoA binding protein-like
superfamily: Acyl-CoA binding protein
family: Acyl-CoA binding protein
domain: Acyl-CoA binding protein
species: Cow (Bos taurus) [TaxId: 9913]

 Score = 93.0 bits (231), Expect = 2e-24
 Identities = 27/83 (32%), Positives = 47/83 (56%)

Query: 95  EDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSL 154
           +  F++A + +  L  K     +L  Y+ YKQATVG  N ++P   + + K+K++AWN L
Sbjct: 2   QAEFDKAAEEVKHLKTKPADEEMLFIYSHYKQATVGDINTERPGMLDFKGKAKWDAWNEL 61

Query: 155 GQMAKSEAMSKYIALLKEVDAGW 177
              +K +AM  YI  ++E+   +
Sbjct: 62  KGTSKEDAMKAYIDKVEELKKKY 84

>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 = 73.1 bits (179), Expect = 3e-17
 Identities = 26/73 (35%), Positives = 43/73 (58%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+F+G L W  +   L+++F ++G++    VM D  T  S+GFGFVTF ++  VDKV + 
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 70 DSHVLEGSRLSIQ 82
            H L+   +  +
Sbjct: 62 SRHELDSKTIDPK 74

>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 = 72.7 bits (178), Expect = 5e-17
 Identities = 21/73 (28%), Positives = 39/73 (53%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          KIFVG L       +++++F  +G++ +  +  D  T   +GF F+TF+ +E V K+   
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 70 DSHVLEGSRLSIQ 82
            H +  S+  I+
Sbjct: 61 KYHNVGLSKCEIK 73

>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 = 73.1 bits (179), Expect = 8e-17
 Identities = 23/91 (25%), Positives = 42/91 (46%), Gaps = 1/91 (1%)

Query: 1   MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
           +S   R    +F   L   +   +L+ FFS  G++ +  ++ D+N+  SKG  +V F   
Sbjct: 11  LSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEI 70

Query: 61  EAVDKVFSTDSHVLEGSRLSIQPSDSH-NRM 90
           ++V          L G  + +Q S +  NR+
Sbjct: 71  QSVPLAIGLTGQRLLGVPIIVQASQAEKNRL 101

>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 = 71.6 bits (175), Expect = 1e-16
 Identities = 27/80 (33%), Positives = 44/80 (55%)

Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
          QL K+F+G L +  +   L+  F ++G + +  VM D NT  S+GFGFVT+   E VD  
Sbjct: 5  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64

Query: 67 FSTDSHVLEGSRLSIQPSDS 86
           +   H ++G  +  + + S
Sbjct: 65 MNARPHKVDGRVVEPKRAVS 84

>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 = 71.5 bits (175), Expect = 2e-16
 Identities = 27/88 (30%), Positives = 46/88 (52%), Gaps = 3/88 (3%)

Query: 6  RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKN-TGLSKGFGFVTFQNKEAVD 64
          +  +KI V N+P+  +  E+++ FS +G++    +      TG  +GFGFV F  K+   
Sbjct: 6  QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 65

Query: 65 KVFST--DSHVLEGSRLSIQPSDSHNRM 90
          K F+    S  L G RL ++ +DS   +
Sbjct: 66 KAFNALCHSTHLYGRRLVLEWADSEVTV 93

>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 = 70.5 bits (172), Expect = 6e-16
 Identities = 22/80 (27%), Positives = 44/80 (55%)

Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
          Q  K+F+G L +  +   L+ ++ ++G++ +  VM D  +  S+GFGFVTF +   VD  
Sbjct: 19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAA 78

Query: 67 FSTDSHVLEGSRLSIQPSDS 86
           +   H ++G  +  + + +
Sbjct: 79 MAARPHSIDGRVVEPKRAVA 98

>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 = 68.5 bits (167), Expect = 2e-15
 Identities = 28/73 (38%), Positives = 46/73 (63%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+F+G L W  +  +LK +FS++G++++ ++  D  TG S+GFGFV F+  E+VDKV   
Sbjct: 1  KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 70 DSHVLEGSRLSIQ 82
            H L G  +  +
Sbjct: 61 KEHKLNGKVIDPK 73

>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 = 68.1 bits (166), Expect = 3e-15
 Identities = 28/86 (32%), Positives = 48/86 (55%), Gaps = 1/86 (1%)

Query: 1  MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
          +  ++++ + + V  LPW  +  +LK++FS +G+++   V  D  TG SKGFGFV F   
Sbjct: 1  VKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEY 60

Query: 61 EAVDKVFSTDSHVLEGSRLSIQPSDS 86
          E   KV S   H+++G     +  +S
Sbjct: 61 ETQVKVMS-QRHMIDGRWCDCKLPNS 85

>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 = 66.7 bits (162), Expect = 1e-14
 Identities = 16/82 (19%), Positives = 38/82 (46%), Gaps = 6/82 (7%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASV-----MFDKNTGLSKGFGFVTFQNKEAVD 64
          +++VGN+P+ ++   +  FF+   ++   +      +        K F F+ F++ +   
Sbjct: 3  RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 65 KVFSTDSHVLEGSRLSIQ-PSD 85
          +  + D  + +G  L I+ P D
Sbjct: 63 QAMAFDGIIFQGQSLKIRRPHD 84

>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 = 64.6 bits (157), Expect = 5e-14
 Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 1/76 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           ++VG+L   V+   L + FS  G I++  V  D  T  S G+ +V FQ     ++   T
Sbjct: 2  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 70 -DSHVLEGSRLSIQPS 84
           +  V++G  + I  S
Sbjct: 62 MNFDVIKGKPVRIMWS 77

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.1 bits (153), Expect = 2e-13
 Identities = 20/84 (23%), Positives = 45/84 (53%), Gaps = 1/84 (1%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          +K+F+G LP  ++ +++K+  + +G +   +++ D  TGLSKG+ F  + +    D+  +
Sbjct: 2  HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

Query: 69 T-DSHVLEGSRLSIQPSDSHNRMA 91
            +   L   +L +Q +    + A
Sbjct: 62 GLNGMQLGDKKLLVQRASVGAKNA 85

>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 = 62.0 bits (150), Expect = 4e-13
 Identities = 25/85 (29%), Positives = 43/85 (50%), Gaps = 4/85 (4%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKN---TGLSKGFGFVTFQNKEAVDKVF 67
          +F+ NL ++ +   LK  FS+ G I + ++   KN     LS GFGFV ++  E   K  
Sbjct: 1  LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 68 ST-DSHVLEGSRLSIQPSDSHNRMA 91
               H ++G +L ++ S+   + A
Sbjct: 61 KQLQGHTVDGHKLEVRISERATKPA 85

>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 = 61.7 bits (149), Expect = 5e-13
 Identities = 24/75 (32%), Positives = 42/75 (56%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          KIFVG +      + L+ +F +YG+I    +M D+ +G  +GF FVTF + ++VDK+   
Sbjct: 4  KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 63

Query: 70 DSHVLEGSRLSIQPS 84
            H + G    ++ +
Sbjct: 64 KYHTVNGHNCEVRKA 78

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 61.5 bits (149), Expect = 6e-13
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           ++V NLP T++ ++L   F +YG I+  +++ DK TG  +G  FV +  +E   +  S 
Sbjct: 8  NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISA 67

Query: 70 -DSHVLEGSRLSIQ 82
           ++ + EG    + 
Sbjct: 68 LNNVIPEGGSQPLS 81

>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 = 60.5 bits (146), Expect = 1e-12
 Identities = 26/73 (35%), Positives = 45/73 (61%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          KIFVG L    +  ++K +F ++G++ +A +MFDK T   +GFGFVTF++++ V+KV   
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 70 DSHVLEGSRLSIQ 82
            H +    +  +
Sbjct: 61 HFHEINNKMVECK 73

>d1wdya_ d.211.1.1 (A:) RNase L, 2-5a-dependent ribonuclease {Human (Homo sapiens) [TaxId: 9606]} Length = 285

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: RNase L, 2-5a-dependent ribonuclease
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 64.6 bits (156), Expect = 2e-12
 Identities = 22/66 (33%), Positives = 34/66 (51%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           ++N   E G   L  A ++ HL +VQ L+E+   ++N TDSDG   L  A  ++   + E
Sbjct: 211 DVNVRGERGKTPLILAVEKKHLGLVQRLLEQEHIEINDTDSDGKTALLLAVELKLKKIAE 270

Query: 341 YLVNSG 346
            L   G
Sbjct: 271 LLCKRG 276

>d1wdya_ d.211.1.1 (A:) RNase L, 2-5a-dependent ribonuclease {Human (Homo sapiens) [TaxId: 9606]} Length = 285

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: RNase L, 2-5a-dependent ribonuclease
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.7 bits (125), Expect = 2e-08
 Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 1/69 (1%)

Query: 252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEK 311
            +  K     A E K   LV++L + +   IN  D +G   L  A +    K+ + L ++
Sbjct: 216 GERGKTPLILAVEKKHLGLVQRLLEQEHIEINDTDSDGKTALLLAVELKLKKIAELLCKR 275

Query: 312 CGADVNVTD 320
            GA  +  D
Sbjct: 276 -GASTDCGD 283

>d1wdya_ d.211.1.1 (A:) RNase L, 2-5a-dependent ribonuclease {Human (Homo sapiens) [TaxId: 9606]} Length = 285

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: RNase L, 2-5a-dependent ribonuclease
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (111), Expect = 9e-07
 Identities = 15/45 (33%), Positives = 28/45 (62%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY 325
           +  +L + G   L  A ++GH++V++ L+++ GADVN  D+ G  
Sbjct: 140 DQERLRKGGATALMDAAEKGHVEVLKILLDEMGADVNACDNMGRN 184

>d1wdya_ d.211.1.1 (A:) RNase L, 2-5a-dependent ribonuclease {Human (Homo sapiens) [TaxId: 9606]} Length = 285

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: RNase L, 2-5a-dependent ribonuclease
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.0 bits (100), Expect = 3e-05
 Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 4/88 (4%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENG---LNCLHWACDRGHLKVVQHLIEKCGADVNV 318
           A++G +++ +K L      ++N  D  G   L     + D   ++ + HL+   GADVNV
Sbjct: 156 AEKGHVEV-LKILLDEMGADVNACDNMGRNALIHALLSSDDSDVEAITHLLLDHGADVNV 214

Query: 319 TDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
               G   L  A   +H  L++ L+   
Sbjct: 215 RGERGKTPLILAVEKKHLGLVQRLLEQE 242

>d1wdya_ d.211.1.1 (A:) RNase L, 2-5a-dependent ribonuclease {Human (Homo sapiens) [TaxId: 9606]} Length = 285

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: RNase L, 2-5a-dependent ribonuclease
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.3 bits (98), Expect = 4e-05
 Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 291 NCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY-GLDYAKAIEHTDLIEYLVN 344
           + L  A     + +VQ L+E  GA+VN  + +G +  L  A  +   D++E L+ 
Sbjct: 7   HLLIKAVQNEDVDLVQQLLEG-GANVNFQEEEGGWTPLHNAVQMSREDIVELLLR 60

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 60.5 bits (146), Expect = 2e-12
 Identities = 25/80 (31%), Positives = 47/80 (58%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          KIFVG LP+  +   L+K+F  +G I  A V+ D+ TG S+G+GFVT  ++ A ++    
Sbjct: 12 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 71

Query: 70 DSHVLEGSRLSIQPSDSHNR 89
           + +++G + ++  +    +
Sbjct: 72 PNPIIDGRKANVNLAYLGAK 91

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.6 bits (144), Expect = 3e-12
 Identities = 15/79 (18%), Positives = 35/79 (44%), Gaps = 1/79 (1%)

Query: 5  IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVD 64
          +++   ++VGNL +  +  ++ + FS+ G I    +  DK    + GF FV + ++   +
Sbjct: 4  LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 63

Query: 65 KVFST-DSHVLEGSRLSIQ 82
                +   L+   +   
Sbjct: 64 NAMRYINGTRLDDRIIRTD 82

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.4 bits (143), Expect = 6e-12
 Identities = 19/82 (23%), Positives = 34/82 (41%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
             F+GNLP+ V+   +K+FF               N    KGFG+  F++ +++    S
Sbjct: 16 YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 69 TDSHVLEGSRLSIQPSDSHNRM 90
           +   L   R+ +  +D     
Sbjct: 76 LNEESLGNKRIRVDVADQAQDK 97

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.5 bits (141), Expect = 7e-12
 Identities = 26/82 (31%), Positives = 47/82 (57%), Gaps = 2/82 (2%)

Query: 2  SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          S SIR  N ++V  LP T++  EL++ FS+YG+I+ + ++ D+ TG+S+G GF+ F  + 
Sbjct: 1  SASIRDAN-LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRI 59

Query: 62 AVDKVFST-DSHVLEGSRLSIQ 82
            ++     +     G+   I 
Sbjct: 60 EAEEAIKGLNGQKPSGATEPIT 81

>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 = 58.4 bits (141), Expect = 7e-12
 Identities = 24/78 (30%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          K+ V NL + VS  ++++ F+E+G +  A+V +D  +G S G   V F+ K    K    
Sbjct: 2  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQ 60

Query: 70 -DSHVLEGSRLSIQPSDS 86
           +   L+G  ++IQ   S
Sbjct: 61 YNGVPLDGRPMNIQLVTS 78

>d2fo1e1 d.211.1.1 (E:1021-1297) Lin-12 {Caenorhabditis elegans [TaxId: 6239]} Length = 277

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Lin-12
species: Caenorhabditis elegans [TaxId: 6239]

 Score = 62.1 bits (149), Expect = 1e-11
 Identities = 38/247 (15%), Positives = 84/247 (34%), Gaps = 14/247 (5%)

Query: 109 VKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMA-------KSE 161
           +    + T+L + A    A   +  I   +   + A +  NA +             +  
Sbjct: 28  IDPRHNRTVLHWIASNSSAEKSEDLIVHEAKECIAAGADVNAMDCDENTPLMLAVLARRR 87

Query: 162 AMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWEDKEQEEINWD 221
            +  Y+         +   E+  ++         M  Y+    ++    E+ ++  +   
Sbjct: 88  RLVAYLMKAGADPTIYNKSERSALHQAAANRDFGMMVYMLNSTKLKGDIEELDRNGMTAL 147

Query: 222 ------ESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLT 275
                 E ++  +       KG          +       +    +A +     +VK L 
Sbjct: 148 MIVAHNEGRDQVASAKLLVEKGAKVDYDGAARKDSEKYKGRTALHYAAQVSNMPIVKYLV 207

Query: 276 KLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEH 335
             K  N ++ DE+G   +  A   G ++VV +LI++ GA V   D+        A+A  H
Sbjct: 208 GEKGSNKDKQDEDGKTPIMLAAQEGRIEVVMYLIQQ-GASVEAVDATDHTARQLAQANNH 266

Query: 336 TDLIEYL 342
            ++++  
Sbjct: 267 HNIVDIF 273

>d2fo1e1 d.211.1.1 (E:1021-1297) Lin-12 {Caenorhabditis elegans [TaxId: 6239]} Length = 277

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Lin-12
species: Caenorhabditis elegans [TaxId: 6239]

 Score = 40.9 bits (94), Expect = 1e-04
 Identities = 14/67 (20%), Positives = 31/67 (46%)

Query: 280 FNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLI 339
              +     G   LH+A    ++ +V++L+ + G++ +  D DG   +  A      +++
Sbjct: 178 ARKDSEKYKGRTALHYAAQVSNMPIVKYLVGEKGSNKDKQDEDGKTPIMLAAQEGRIEVV 237

Query: 340 EYLVNSG 346
            YL+  G
Sbjct: 238 MYLIQQG 244

>d2fo1e1 d.211.1.1 (E:1021-1297) Lin-12 {Caenorhabditis elegans [TaxId: 6239]} Length = 277

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Lin-12
species: Caenorhabditis elegans [TaxId: 6239]

 Score = 40.1 bits (92), Expect = 2e-04
 Identities = 25/207 (12%), Positives = 59/207 (28%), Gaps = 10/207 (4%)

Query: 113 DSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKE 172
           D +T L    L ++  +    +   +   +  KS+ +A +          M   +   K 
Sbjct: 73  DENTPLMLAVLARRRRLVAYLMKAGADPTIYNKSERSALHQAAANRDFGMMVYMLNSTKL 132

Query: 173 VDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWEDKEQEEINWDESQESGS---- 228
                E             + +   +  +    V+   +         D  +  G     
Sbjct: 133 KGDIEELDRNGMTALMIVAHNEGRDQVASAKLLVEKGAKVDYDGAARKDSEKYKGRTALH 192

Query: 229 -KENEGQTKGWVNVSSMINDESQLDDNEKN--IYEWAKEGKLDMLVKQLTKLKDFNINQL 285
                        +           D +    I   A+EG++++ V  L + +  ++  +
Sbjct: 193 YAAQVSNMPIVKYLVGEKGSNKDKQDEDGKTPIMLAAQEGRIEV-VMYLIQ-QGASVEAV 250

Query: 286 DENGLNCLHWACDRGHLKVVQHLIEKC 312
           D         A    H  +V  + ++C
Sbjct: 251 DATDHTARQLAQANNHHNIVD-IFDRC 276

>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 = 57.8 bits (139), Expect = 2e-11
 Identities = 16/75 (21%), Positives = 32/75 (42%), Gaps = 1/75 (1%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
            I V N+P+TVS +E+  FF  Y  I  +  +     G+  G   V F++++       
Sbjct: 10 TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 69

Query: 69 T-DSHVLEGSRLSIQ 82
            +   +   ++ + 
Sbjct: 70 DLNDRPIGSRKVKLV 84

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.7 bits (139), Expect = 2e-11
 Identities = 25/84 (29%), Positives = 42/84 (50%), Gaps = 1/84 (1%)

Query: 7  QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
          Q   ++VG L   VS   L + F + G ++N  +  D+ TG  +G+GFV F ++E  D  
Sbjct: 8  QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 67

Query: 67 FST-DSHVLEGSRLSIQPSDSHNR 89
              D   L G  + +  + +HN+
Sbjct: 68 IKIMDMIKLYGKPIRVNKASAHNK 91

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 56.9 bits (137), Expect = 2e-11
 Identities = 19/76 (25%), Positives = 31/76 (40%), Gaps = 1/76 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           + V  LP  ++  EL   F   G I    +M D  TG S G+ FV F ++    +    
Sbjct: 4  NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 70 -DSHVLEGSRLSIQPS 84
           +   +   RL +  +
Sbjct: 64 LNGITVRNKRLKVSYA 79

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 57.4 bits (138), Expect = 3e-11
 Identities = 29/85 (34%), Positives = 41/85 (48%), Gaps = 1/85 (1%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
           ++FV NL +T S  +L+K FS YG +       D  T   KGF FVTF   E   K ++
Sbjct: 9  GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 69 T-DSHVLEGSRLSIQPSDSHNRMAE 92
            D  V +G  L + PS      ++
Sbjct: 69 EVDGQVFQGRMLHVLPSTIKKEASQ 93

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.2 bits (142), Expect = 3e-11
 Identities = 27/91 (29%), Positives = 47/91 (51%)

Query: 1   MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
              +   + KIFVG +      + L+ +F +YG+I    +M D+ +G  +GF FVTF + 
Sbjct: 90  RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 149

Query: 61  EAVDKVFSTDSHVLEGSRLSIQPSDSHNRMA 91
           ++VDK+     H + G    ++ + S   MA
Sbjct: 150 DSVDKIVIQKYHTVNGHNCEVRKALSKQEMA 180

>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 = 59.2 bits (142), Expect = 4e-11
 Identities = 31/135 (22%), Positives = 60/135 (44%), Gaps = 1/135 (0%)

Query: 7   QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
           QL K+F+G L +  +   L+  F ++G + +  VM D NT  S+GFGFVT+   E VD  
Sbjct: 5   QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64

Query: 67  FSTDSHVLEGSRLSIQPSDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQ 126
            +   H ++G  +  + +      ++           ++  + +  +   L  ++  Y +
Sbjct: 65  MNARPHKVDGRVVEPKRA-VSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 123

Query: 127 ATVGQCNIDKPSWYN 141
             V +   D+ S   
Sbjct: 124 IEVIEIMTDRGSGKK 138

>d1n11a_ d.211.1.1 (A:) Ankyrin-R {Human (Homo sapiens) [TaxId: 9606]} Length = 408

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Ankyrin-R
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.5 bits (148), Expect = 4e-11
 Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 3/83 (3%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS 321
           +  G L + VK L + +  + N  +      LH A   GH +V ++L++   A VN    
Sbjct: 8   SFMGHLPI-VKNLLQ-RGASPNVSNVKVETPLHMAARAGHTEVAKYLLQN-KAKVNAKAK 64

Query: 322 DGDYGLDYAKAIEHTDLIEYLVN 344
           D    L  A  I HT++++ L+ 
Sbjct: 65  DDQTPLHCAARIGHTNMVKLLLE 87

>d1n11a_ d.211.1.1 (A:) Ankyrin-R {Human (Homo sapiens) [TaxId: 9606]} Length = 408

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Ankyrin-R
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.2 bits (142), Expect = 2e-10
 Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 280 FNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLI 339
            ++N   + G + LH A  +GH  +V  L++  GA  N   SDG   L  AK + +  + 
Sbjct: 321 ADVNAKTKLGYSPLHQAAQQGHTDIVTLLLKN-GASPNEVSSDGTTPLAIAKRLGYISVT 379

Query: 340 EYL 342
           + L
Sbjct: 380 DVL 382

>d1n11a_ d.211.1.1 (A:) Ankyrin-R {Human (Homo sapiens) [TaxId: 9606]} Length = 408

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Ankyrin-R
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.6 bits (130), Expect = 6e-09
 Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 1/54 (1%)

Query: 293 LHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           LH A   GHL +V++L+++ GA  NV++   +  L  A    HT++ +YL+ + 
Sbjct: 4   LHVASFMGHLPIVKNLLQR-GASPNVSNVKVETPLHMAARAGHTEVAKYLLQNK 56

>d1n11a_ d.211.1.1 (A:) Ankyrin-R {Human (Homo sapiens) [TaxId: 9606]} Length = 408

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Ankyrin-R
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.5 bits (122), Expect = 6e-08
 Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           +   + + G   LH A   G ++V + L+E+  A  N    +G   L  A    + D+++
Sbjct: 124 SQACMTKKGFTPLHVAAKYGKVRVAELLLER-DAHPNAAGKNGLTPLHVAVHHNNLDIVK 182

Query: 341 YLVNSG 346
            L+  G
Sbjct: 183 LLLPRG 188

>d1n11a_ d.211.1.1 (A:) Ankyrin-R {Human (Homo sapiens) [TaxId: 9606]} Length = 408

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Ankyrin-R
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.7 bits (112), Expect = 1e-06
 Identities = 18/107 (16%), Positives = 40/107 (37%), Gaps = 2/107 (1%)

Query: 238 WVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWAC 297
            + +      ++ +          A +     + + L + +D + N   +NGL  LH A 
Sbjct: 115 VLALLEKEASQACMTKKGFTPLHVAAKYGKVRVAELLLE-RDAHPNAAGKNGLTPLHVAV 173

Query: 298 DRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVN 344
              +L +V+ L+ + G   +    +G   L  A      ++   L+ 
Sbjct: 174 HHNNLDIVKLLLPR-GGSPHSPAWNGYTPLHIAAKQNQVEVARSLLQ 219

>d1n11a_ d.211.1.1 (A:) Ankyrin-R {Human (Homo sapiens) [TaxId: 9606]} Length = 408

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Ankyrin-R
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.6 bits (91), Expect = 4e-04
 Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 4/64 (6%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHL--IEKCGADVNVT 319
           A++G  D+ V  L K    + N++  +G   L  A   G++ V   L  +    + V V+
Sbjct: 338 AQQGHTDI-VTLLLK-NGASPNEVSSDGTTPLAIAKRLGYISVTDVLKVVTDETSFVLVS 395

Query: 320 DSDG 323
           D   
Sbjct: 396 DKHR 399

>d1n11a_ d.211.1.1 (A:) Ankyrin-R {Human (Homo sapiens) [TaxId: 9606]} Length = 408

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Ankyrin-R
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.8 bits (89), Expect = 7e-04
 Identities = 19/118 (16%), Positives = 32/118 (27%), Gaps = 34/118 (28%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEK---------- 311
           A+ G  ++  K L +     +N   ++    LH A   GH  +V+ L+E           
Sbjct: 41  ARAGHTEV-AKYLLQ-NKAKVNAKAKDDQTPLHCAARIGHTNMVKLLLENNANPNLATTA 98

Query: 312 ----------------------CGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
                                   A        G   L  A       + E L+   +
Sbjct: 99  GHTPLHIAAREGHVETVLALLEKEASQACMTKKGFTPLHVAAKYGKVRVAELLLERDA 156

>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 = 4e-11
 Identities = 16/94 (17%), Positives = 39/94 (41%), Gaps = 5/94 (5%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
             +++ NLP+ ++  E+   F +YG I     +   NT  ++G  +V +++         
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNACD 64

Query: 69  T-DSHVLEGSRLSIQPSDSHNRMAENMEDRFNQA 101
                 +    L +   ++ NR  + M+ +  + 
Sbjct: 65  HLSGFNVCNRYLVVLYYNA-NRAFQKMDTKKKEE 97

>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 = 56.8 bits (137), Expect = 4e-11
 Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 10/80 (12%)

Query: 9  NKIFVGNL-PWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
          +++F+GNL    V  ++++  FS+YG+I+  SV          GF FV + N+       
Sbjct: 16 SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFAFVQYVNERNARAAV 67

Query: 68 ST-DSHVLEGSRLSIQPSDS 86
          +  D  ++ G  L I  +  
Sbjct: 68 AGEDGRMIAGQVLDINLAAE 87

>d1sw6a_ d.211.1.1 (A:) Swi6 ankyrin-repeat fragment {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Swi6 ankyrin-repeat fragment
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 58.9 bits (141), Expect = 2e-10
 Identities = 29/148 (19%), Positives = 49/148 (33%), Gaps = 4/148 (2%)

Query: 186 NWDWKPNQKAMSKYIALLNEVDASWEDKEQEEINWDESQESGSKENEGQTKGWVNVSSMI 245
           N+D    +  +      L   D+         I         +            +    
Sbjct: 153 NYDSGTFEALLDYLYPCLILEDSMNRTILHHIIITSGMTGCSAAAKYYLDILMGWIVKKQ 212

Query: 246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDF---NINQLDENGLNCLHWACDRGHL 302
           N   Q   NEK      K G+    + +   LK      +N  D NG  CL+ A   G++
Sbjct: 213 NRPIQSGTNEKESKPNDKNGERKDSILENLDLKWIIANMLNAQDSNGDTCLNIAARLGNI 272

Query: 303 KVVQHLIEKCGADVNVTDSDGDYGLDYA 330
            +V  L++  GAD  + +  G   +D+ 
Sbjct: 273 SIVDALLDY-GADPFIANKSGLRPVDFG 299

>d1sw6a_ d.211.1.1 (A:) Swi6 ankyrin-repeat fragment {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Swi6 ankyrin-repeat fragment
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 53.5 bits (127), Expect = 9e-09
 Identities = 20/92 (21%), Positives = 40/92 (43%), Gaps = 3/92 (3%)

Query: 240 NVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNIN-QLDENGLNCLHWACD 298
             +   N  S+   + +     + +  L  +          N+N  +DE+G   LHW   
Sbjct: 58  LNNDSSNRNSEGGSSNQQQQHVSFDSLLQEVNDAFPN-TQLNLNIPVDEHGNTPLHWLTS 116

Query: 299 RGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA 330
             +L++V+HL++  G++    D+ G+  L  A
Sbjct: 117 IANLELVKHLVKH-GSNRLYGDNMGESCLVKA 147

>d1sw6a_ d.211.1.1 (A:) Swi6 ankyrin-repeat fragment {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 301

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Swi6 ankyrin-repeat fragment
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 44.3 bits (103), Expect = 1e-05
 Identities = 17/95 (17%), Positives = 40/95 (42%), Gaps = 2/95 (2%)

Query: 254 NEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEK-- 311
           +       A +  LD+L+  + K ++  I        +  +         ++++L  K  
Sbjct: 188 SGMTGCSAAAKYYLDILMGWIVKKQNRPIQSGTNEKESKPNDKNGERKDSILENLDLKWI 247

Query: 312 CGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
               +N  DS+GD  L+ A  + +  +++ L++ G
Sbjct: 248 IANMLNAQDSNGDTCLNIAARLGNISIVDALLDYG 282

>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 = 54.3 bits (130), Expect = 2e-10
 Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
            + V  L    +  +L++ FS+YG I + S+++D+ +  S+GF FV F+N +   +   
Sbjct: 10 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 69 T-DSHVLEGSRLSI 81
            +   L+G R+ +
Sbjct: 70 RANGMELDGRRIRV 83

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.3 bits (130), Expect = 3e-10
 Identities = 20/85 (23%), Positives = 33/85 (38%), Gaps = 4/85 (4%)

Query: 1  MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
          M+ + R    ++VG L   V    L   F  +G I +  +  D  T   +GF FV F+  
Sbjct: 1  MATTKR---VLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 57

Query: 61 EAVDKVFST-DSHVLEGSRLSIQPS 84
          E         +   L G  + +  +
Sbjct: 58 EDAAAAIDNMNESELFGRTIRVNLA 82

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.9 bits (129), Expect = 4e-10
 Identities = 18/78 (23%), Positives = 39/78 (50%), Gaps = 6/78 (7%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          + +FVG     ++ +EL++FFS+YG +M+  +           F FVTF + +    +  
Sbjct: 6  SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQIAQSLCG 60

Query: 69 TDSHVLEGSRLSIQPSDS 86
           +  +++G  + I  ++ 
Sbjct: 61 -EDLIIKGISVHISNAEP 77

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.6 bits (128), Expect = 4e-10
 Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 2/78 (2%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNAS-VMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
          IF+GNL   +    L   FS +G I+    +M D +TG SKG+ F+ F + +A D     
Sbjct: 1  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 70 -DSHVLEGSRLSIQPSDS 86
           +   L    +++  +  
Sbjct: 61 MNGQYLCNRPITVSYAFK 78

>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 = 54.1 bits (129), Expect = 5e-10
 Identities = 18/76 (23%), Positives = 30/76 (39%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
            + +  LP+  S  E+ +FFS    + N   +     G S G  FV F ++E  +K   
Sbjct: 16 GFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK 75

Query: 69 TDSHVLEGSRLSIQPS 84
               +    + I  S
Sbjct: 76 KHKERIGHRYIEIFKS 91

>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 = 53.3 bits (127), Expect = 8e-10
 Identities = 14/75 (18%), Positives = 28/75 (37%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
             + N+P++++  ++ +F        NA  +   N G   G   V F+N++   K    
Sbjct: 10 CAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERL 69

Query: 70 DSHVLEGSRLSIQPS 84
              L G    +   
Sbjct: 70 HRKKLNGREAFVHVV 84

>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 = 52.7 bits (126), Expect = 1e-09
 Identities = 17/86 (19%), Positives = 37/86 (43%), Gaps = 6/86 (6%)

Query: 2  SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          S  +R    +   NL + ++ +ELK+ F +  +I           G SKG  ++ F+++ 
Sbjct: 10 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEA 64

Query: 62 AVDKVFST-DSHVLEGSRLSIQPSDS 86
            +K         ++G  +S+  +  
Sbjct: 65 DAEKNLEEKQGAEIDGRSVSLYYTGE 90

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.8 bits (126), Expect = 1e-09
 Identities = 19/79 (24%), Positives = 36/79 (45%), Gaps = 4/79 (5%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
           +I+VGNLP  +   +++  F +YG I +  +   +       F FV F++    +    
Sbjct: 15 CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG---PPFAFVEFEDPRDAEDAVY 71

Query: 69 T-DSHVLEGSRLSIQPSDS 86
            D +  +G RL ++   S
Sbjct: 72 GRDGYDYDGYRLRVEFPRS 90

>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 = 52.3 bits (125), Expect = 1e-09
 Identities = 23/79 (29%), Positives = 42/79 (53%), Gaps = 3/79 (3%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
            IF+ NL  ++ +  L   FS +G I++  V+ D+N   SKG+GFV F+ +EA ++   
Sbjct: 9  GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIE 66

Query: 69 T-DSHVLEGSRLSIQPSDS 86
            +  +L   ++ +    S
Sbjct: 67 KMNGMLLNDRKVFVGRFKS 85

>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 = 52.0 bits (124), Expect = 1e-09
 Identities = 19/76 (25%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           + V  LP  ++  E +  F   G+I +  ++ DK TG S G+GFV + + +  +K  +T
Sbjct: 4  NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINT 63

Query: 70 -DSHVLEGSRLSIQPS 84
           +   L+   + +  +
Sbjct: 64 LNGLRLQTKTIKVSYA 79

>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 = 52.0 bits (124), Expect = 2e-09
 Identities = 12/89 (13%), Positives = 36/89 (40%), Gaps = 5/89 (5%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNA--SVMFDKNTGLSKGFGFVTFQNKEAVDKV- 66
          ++F+G +P      E+ +  ++  + +          +   ++GF FV +++  A     
Sbjct: 3  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 67 --FSTDSHVLEGSRLSIQPSDSHNRMAEN 93
                   L G ++++  ++    + E+
Sbjct: 63 RKLMPGRIQLWGHQIAVDWAEPEIDVDED 91

>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 = 51.6 bits (123), Expect = 2e-09
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 1/77 (1%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
            I V NL       +L++ F  +G I    +  DK TG SKGF F++F  +E   +  +
Sbjct: 9  ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 69 T-DSHVLEGSRLSIQPS 84
                 +   L+++ +
Sbjct: 69 GVSGFGYDHLILNVEWA 85

>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 = 51.2 bits (122), Expect = 3e-09
 Identities = 17/81 (20%), Positives = 35/81 (43%), Gaps = 8/81 (9%)

Query: 8  LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
          +NK+++GNL   V+ ++L++ F +    +           L  G+ FV + ++    +  
Sbjct: 1  MNKLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAI 54

Query: 68 ST--DSHVLEGSRLSIQPSDS 86
           T      L G  + +  S S
Sbjct: 55 ETLSGKVELHGKIMEVDYSVS 75

>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 = 51.0 bits (121), Expect = 4e-09
 Identities = 19/98 (19%), Positives = 39/98 (39%), Gaps = 7/98 (7%)

Query: 1  MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
          + + + +   +F+ NL +      L +   ++G +    V+   +T  SKG  F  F  +
Sbjct: 1  LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQ 60

Query: 61 EAVDKV-------FSTDSHVLEGSRLSIQPSDSHNRMA 91
          EA  K               L+G +L +  + + +  A
Sbjct: 61 EAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA 98

>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 = 50.8 bits (121), Expect = 4e-09
 Identities = 24/86 (27%), Positives = 48/86 (55%), Gaps = 3/86 (3%)

Query: 2  SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
          S S     ++ V N+P+     +L++ F ++G+I++  ++F++    SKGFGFVTF+N  
Sbjct: 5  SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSA 62

Query: 62 AVDKVFST-DSHVLEGSRLSIQPSDS 86
            D+        V+EG ++ +  + +
Sbjct: 63 DADRAREKLHGTVVEGRKIEVNNATA 88

>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 = 50.3 bits (120), Expect = 6e-09
 Identities = 21/84 (25%), Positives = 41/84 (48%), Gaps = 7/84 (8%)

Query: 4  SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAV 63
          +  Q +++FVGNLP  ++  E++K F +YG+     +  DK       FGF+  + +   
Sbjct: 4  TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLA 57

Query: 64 DKVFST-DSHVLEGSRLSIQPSDS 86
          +      D+  L G +L ++ +  
Sbjct: 58 EIAKVELDNMPLRGKQLRVRFACH 81

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.9 bits (121), Expect = 6e-09
 Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 1/82 (1%)

Query: 9   NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
             +F+ +LP      +L + F  +G +++A V  DK T LSK FGFV++ N  +      
Sbjct: 19  ANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQ 78

Query: 69  T-DSHVLEGSRLSIQPSDSHNR 89
           + +   +   RL +Q   S N 
Sbjct: 79  SMNGFQIGMKRLKVQLKRSKND 100

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 49.8 bits (118), Expect = 9e-09
 Identities = 10/77 (12%), Positives = 29/77 (37%), Gaps = 1/77 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           +++ N P + +   ++    +   +  +  +       S+ F ++   +KE        
Sbjct: 3  TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEK 62

Query: 70 -DSHVLEGSRLSIQPSD 85
           +   +EG  L  + S+
Sbjct: 63 LNGLKIEGYTLVTKVSN 79

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.7 bits (118), Expect = 2e-08
 Identities = 12/76 (15%), Positives = 27/76 (35%), Gaps = 2/76 (2%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
          + + +  LP+  + N++  FFS    +     +     G   G   V F   E      +
Sbjct: 16 HCVHMRGLPYRATENDIYNFFSPLNPMRV--HIEIGPDGRVTGEADVEFATHEDAVAAMA 73

Query: 69 TDSHVLEGSRLSIQPS 84
           D   ++   + +  +
Sbjct: 74 KDKANMQHRYVELFLN 89

>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 = 48.5 bits (115), Expect = 3e-08
 Identities = 14/88 (15%), Positives = 31/88 (35%), Gaps = 2/88 (2%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEY-GQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
          + I++ NL   +  +ELKK       +      +    +   +G  FV F+   +     
Sbjct: 4  HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNAL 63

Query: 68 ST-DSHVLEGSRLSIQPSDSHNRMAENM 94
           +          + IQ + + + +   M
Sbjct: 64 RSMQGFPFYDKPMRIQYAKTDSDIIAKM 91

>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 = 48.2 bits (114), Expect = 4e-08
 Identities = 25/77 (32%), Positives = 45/77 (58%), Gaps = 1/77 (1%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK-VF 67
           K+FVG L +  +   L++ FS+YGQI    V+ D+ T  S+GFGFVTF+N +     + 
Sbjct: 6  GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 65

Query: 68 STDSHVLEGSRLSIQPS 84
          + +   ++G ++ +  +
Sbjct: 66 AMNGKSVDGRQIRVDQA 82

>d2ajaa1 a.118.24.1 (A:3-348) Hypothetical protein LPG2416 {Legionella pneumophila [TaxId: 446]} Length = 346

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Pseudo ankyrin repeat-like
family: Pseudo ankyrin repeat
domain: Hypothetical protein LPG2416
species: Legionella pneumophila [TaxId: 446]

 Score = 51.8 bits (123), Expect = 4e-08
 Identities = 18/125 (14%), Positives = 33/125 (26%), Gaps = 12/125 (9%)

Query: 227 GSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDML--VKQLTKLKDFNINQ 284
            +  N    + W +         +   +E   +  A  G    L  +  L    D  +  
Sbjct: 69  YAHYNRNAKQLWSDA------HKKGIKSEVICFVAAITGCSSALDTLCLLLT-SDEIVKV 121

Query: 285 LDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSD--GDYGLDYAKAIEHTDLIEYL 342
           +          A + GHL V+  L E       +        +    A    H  ++  L
Sbjct: 122 IQAENYQAFRLAAENGHLHVLNRLCEL-APTEIMAMIQAENYHAFRLAAENGHLHVLNRL 180

Query: 343 VNSGS 347
                
Sbjct: 181 CELAP 185

>d2ajaa1 a.118.24.1 (A:3-348) Hypothetical protein LPG2416 {Legionella pneumophila [TaxId: 446]} Length = 346

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Pseudo ankyrin repeat-like
family: Pseudo ankyrin repeat
domain: Hypothetical protein LPG2416
species: Legionella pneumophila [TaxId: 446]

 Score = 44.9 bits (105), Expect = 7e-06
 Identities = 16/111 (14%), Positives = 30/111 (27%), Gaps = 12/111 (10%)

Query: 241 VSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRG 300
              +    ++L +          +G  D        L   +        L  L    D  
Sbjct: 239 NPFIARHVNRLKEMHDAFKLSNPDGVFD--------LVTKSECLQGFYMLRNLIRRNDEV 290

Query: 301 HLKVVQHLIE----KCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSGS 347
            L  ++ L+     K  A       D +  L  A  + +      L++  S
Sbjct: 291 LLDDIRFLLSIPGIKALAPTATIPGDANELLRLALRLGNQGACALLLSIPS 341

>d2ajaa1 a.118.24.1 (A:3-348) Hypothetical protein LPG2416 {Legionella pneumophila [TaxId: 446]} Length = 346

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Pseudo ankyrin repeat-like
family: Pseudo ankyrin repeat
domain: Hypothetical protein LPG2416
species: Legionella pneumophila [TaxId: 446]

 Score = 39.5 bits (91), Expect = 4e-04
 Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 2/87 (2%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCG--ADVNVT 319
           A+ G L +L +         +  +     +    A + GHL V+  L E     A   + 
Sbjct: 134 AENGHLHVLNRLCELAPTEIMAMIQAENYHAFRLAAENGHLHVLNRLCELAPTEATAMIQ 193

Query: 320 DSDGDYGLDYAKAIEHTDLIEYLVNSG 346
             +       A    H ++I +L++  
Sbjct: 194 AENYYAFRWAAVGRGHHNVINFLLDCP 220

>d1k1aa_ d.211.1.1 (A:) bcl-3 {Human (Homo sapiens) [TaxId: 9606]} Length = 228

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: bcl-3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.6 bits (119), Expect = 5e-08
 Identities = 33/194 (17%), Positives = 61/194 (31%), Gaps = 4/194 (2%)

Query: 149 NAWNSLGQMAKSEAMSKYIALLKEVDAGWEDKEQEEINWDWKPNQKAM---SKYIALLNE 205
           + +N+L Q     A+   +  +  +                     A    S        
Sbjct: 34  DIYNNLRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALL 93

Query: 206 VDASWEDKEQEEINWDESQESGSKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEG 265
             A+    + E  N+D         N    +    +     D   +D             
Sbjct: 94  DSAAPGTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAVE 153

Query: 266 KLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY 325
              + + QL      N+N    +G + LH A  RG L +V+ L+   GAD ++ +   D 
Sbjct: 154 NNSLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPLVRTLVRS-GADSSLKNCHNDT 212

Query: 326 GLDYAKAIEHTDLI 339
            L  A++    D++
Sbjct: 213 PLMVARSRRVIDIL 226

>d1k1aa_ d.211.1.1 (A:) bcl-3 {Human (Homo sapiens) [TaxId: 9606]} Length = 228

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: bcl-3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.4 bits (108), Expect = 2e-06
 Identities = 12/47 (25%), Positives = 23/47 (48%), Gaps = 3/47 (6%)

Query: 287 ENGLNCLHWACDRGHLKVVQHLIE---KCGADVNVTDSDGDYGLDYA 330
           E+G   LH A  +G+L  V  L+    + G ++++ ++     L  A
Sbjct: 1   EDGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLA 47

>d1k1aa_ d.211.1.1 (A:) bcl-3 {Human (Homo sapiens) [TaxId: 9606]} Length = 228

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: bcl-3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.4 bits (82), Expect = 0.003
 Identities = 20/194 (10%), Positives = 57/194 (29%), Gaps = 5/194 (2%)

Query: 113 DSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKE 172
              T L    +    +V +  +   +      +    A +   +      +   +     
Sbjct: 39  LRQTPLHLAVITTLPSVVRLLVTAGASPMALDRHGQTAAHLACEHRSPTCLRALLDSAAP 98

Query: 173 VDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWEDKEQEEINWDESQESGSKENE 232
                E +  + +            + + LL E  A  +  + +             EN 
Sbjct: 99  GTLDLEARNYDGLTALHVAVNTECQETVQLLLERGADIDAVDIKSGRSPLIHAV---ENN 155

Query: 233 GQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNC 292
             +   + +    N  +Q+      ++  +  G L + V+ L +    + +  + +    
Sbjct: 156 SLSMVQLLLQHGANVNAQMYSGSSALHSASGRGLLPL-VRTLVR-SGADSSLKNCHNDTP 213

Query: 293 LHWACDRGHLKVVQ 306
           L  A  R  + +++
Sbjct: 214 LMVARSRRVIDILR 227

>d1s70b_ d.211.1.1 (B:) Myosin phosphatase targeting subunit 1, MYPT1 {Chicken (Gallus gallus) [TaxId: 9031]} Length = 291

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Myosin phosphatase targeting subunit 1, MYPT1
species: Chicken (Gallus gallus) [TaxId: 9031]

 Score = 50.9 bits (120), Expect = 7e-08
 Identities = 27/166 (16%), Positives = 56/166 (33%), Gaps = 7/166 (4%)

Query: 177 WEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWEDKEQEEINWDESQESGSKENEGQTK 236
            E    +  +     ++      IA    ++   +++   +    E+     +    +  
Sbjct: 122 AEYLISQGAHVGAVNSEGDTPLDIAEEEAMEELLQNEVNRQGVDIEAARKEEERIMLRDA 181

Query: 237 GWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWA 296
                S  IND          ++  A +G  ++L         +++N  D +G   LH A
Sbjct: 182 RQWLNSGHINDVRHAKSGGTALHVAAAKGYTEVLKLL--IQARYDVNIKDYDGWTPLHAA 239

Query: 297 CDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYL 342
              G  +  + L+E    D+   +  G    D A      D++ YL
Sbjct: 240 AHWGKEEACRILVEN-LCDMEAVNKVGQTAFDVADE----DILGYL 280

>d1s70b_ d.211.1.1 (B:) Myosin phosphatase targeting subunit 1, MYPT1 {Chicken (Gallus gallus) [TaxId: 9031]} Length = 291

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Myosin phosphatase targeting subunit 1, MYPT1
species: Chicken (Gallus gallus) [TaxId: 9031]

 Score = 46.6 bits (109), Expect = 2e-06
 Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 8/87 (9%)

Query: 262 AKEGKLDMLVKQLTKLKDFNINQLDEN-------GLNCLHWACDRGHLKVVQHLIEKCGA 314
           AK+ + + L + +    D     +                 AC  G  + V  L+E+ GA
Sbjct: 6   AKQKRNEQLKRWIGSETDLEPPVVKRKKTKVKFDDGAVFLAACSSGDTEEVLRLLER-GA 64

Query: 315 DVNVTDSDGDYGLDYAKAIEHTDLIEY 341
           D+N  + DG   L  A   ++ D++++
Sbjct: 65  DINYANVDGLTALHQACIDDNVDMVKF 91

>d1s70b_ d.211.1.1 (B:) Myosin phosphatase targeting subunit 1, MYPT1 {Chicken (Gallus gallus) [TaxId: 9031]} Length = 291

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Myosin phosphatase targeting subunit 1, MYPT1
species: Chicken (Gallus gallus) [TaxId: 9031]

 Score = 44.7 bits (104), Expect = 6e-06
 Identities = 35/181 (19%), Positives = 65/181 (35%), Gaps = 3/181 (1%)

Query: 168 ALLKEVDAGWEDKEQEEINWDWKPNQKAMSKYIALLNEVDASWEDKEQEEINWDESQESG 227
           AL +       D  +  +      NQ     +I L       + D  +  I+      + 
Sbjct: 76  ALHQACIDDNVDMVKFLVENGANINQPDNEGWIPLHAAASCGYLDIAEYLISQGAHVGAV 135

Query: 228 SKENEGQTKGWVNVSSMINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKL--KDFNINQL 285
           + E +         +     +++++    +I    KE +  ML      L     N  + 
Sbjct: 136 NSEGDTPLDIAEEEAMEELLQNEVNRQGVDIEAARKEEERIMLRDARQWLNSGHINDVRH 195

Query: 286 DENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNS 345
            ++G   LH A  +G+ +V++ LI+    DVN+ D DG   L  A      +    LV +
Sbjct: 196 AKSGGTALHVAAAKGYTEVLKLLIQAR-YDVNIKDYDGWTPLHAAAHWGKEEACRILVEN 254

Query: 346 G 346
            
Sbjct: 255 L 255

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 47.0 bits (111), Expect = 8e-08
 Identities = 15/79 (18%), Positives = 33/79 (41%), Gaps = 2/79 (2%)

Query: 9  NKIFVGNLPWTVSHNE-LKKFFSEYGQI-MNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
           +I + NL   +     L++ F  +G I         K    +    F+ F+NK++ ++ 
Sbjct: 5  REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 67 FSTDSHVLEGSRLSIQPSD 85
             +  +L    +S+  +D
Sbjct: 65 LQMNRSLLGNREISVSLAD 83

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.0 bits (113), Expect = 9e-08
 Identities = 13/92 (14%), Positives = 32/92 (34%)

Query: 6   RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
                +++  LP+   +  +  FF +   + ++  +     G + G GFV F+N+     
Sbjct: 16  EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKA 75

Query: 66  VFSTDSHVLEGSRLSIQPSDSHNRMAENMEDR 97
                   +    + + P      + +    R
Sbjct: 76  ALCRHKQYMGNRFIQVHPITKKGMLEKIDMIR 107

>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 = 47.0 bits (111), Expect = 1e-07
 Identities = 16/75 (21%), Positives = 35/75 (46%), Gaps = 1/75 (1%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
            +FV ++      +E+++ F +YG+I N  +  D+ TG SKG+  V ++  +       
Sbjct: 8  WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 69 T-DSHVLEGSRLSIQ 82
            +   + G  + + 
Sbjct: 68 ALNGAEIMGQTIQVD 82

>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 = 47.4 bits (112), Expect = 1e-07
 Identities = 26/88 (29%), Positives = 45/88 (51%), Gaps = 1/88 (1%)

Query: 6  RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          R L  +FVGN+P+  +  +LK  FSE G +++  +++D+ TG  KG+GF  +Q++E    
Sbjct: 6  RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65

Query: 66 VFST-DSHVLEGSRLSIQPSDSHNRMAE 92
               +     G  L +  + S     E
Sbjct: 66 AMRNLNGREFSGRALRVDNAASEKNKEE 93

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.1 bits (111), Expect = 1e-07
 Identities = 19/85 (22%), Positives = 35/85 (41%), Gaps = 9/85 (10%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMF--------DKNTGLSKGFGFVTFQNK 60
          + I+V  L  +V+ ++L  FF + G +               DK TG  KG   V++++ 
Sbjct: 9  SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 68

Query: 61 EAVDKVFST-DSHVLEGSRLSIQPS 84
                    D    +GS+L +  +
Sbjct: 69 PTAKAAVEWFDGKDFQGSKLKVSLA 93

>d1ixva_ d.211.1.1 (A:) 26S proteasome non-ATPase regulatory subunit 10, gankyrin {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 229

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: 26S proteasome non-ATPase regulatory subunit 10, gankyrin
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 49.0 bits (115), Expect = 2e-07
 Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 3/67 (4%)

Query: 280 FNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLI 339
             +N  D+ G   L  A   GH      L+EK GA+ ++ D+ G    D A    +  + 
Sbjct: 163 SAVNWQDKQGWTPLFHALAEGHGDAAVLLVEKYGAEYDLVDNKGAKAEDVAL---NEQVK 219

Query: 340 EYLVNSG 346
           ++ +N+ 
Sbjct: 220 KFFLNNV 226

>d1ixva_ d.211.1.1 (A:) 26S proteasome non-ATPase regulatory subunit 10, gankyrin {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 229

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: 26S proteasome non-ATPase regulatory subunit 10, gankyrin
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 46.7 bits (109), Expect = 1e-06
 Identities = 12/54 (22%), Positives = 24/54 (44%)

Query: 293 LHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           LH AC       VQ L+    + +   D DG   L ++ + +  ++  +L++  
Sbjct: 4   LHQACMENEFFKVQELLHSKPSLLLQKDQDGRIPLHWSVSFQAHEITSFLLSKM 57

>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 = 46.3 bits (109), Expect = 2e-07
 Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 1/79 (1%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
            +++ NL   V+  +L   F+ + +     + F   TG  +G  F+TF NKE   +   
Sbjct: 19 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 69 T-DSHVLEGSRLSIQPSDS 86
            + + L G  L I+   +
Sbjct: 79 LVNGYKLYGKILVIEFGKN 97

>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 = 46.2 bits (109), Expect = 3e-07
 Identities = 17/104 (16%), Positives = 39/104 (37%), Gaps = 12/104 (11%)

Query: 10  KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           +I V NL + V+ + L + FS++G ++            ++    + + +  +      +
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLS 64

Query: 70  -DSHVL--EGSRLSIQPSDSHNRMAENMEDR---FNQACDYLPS 107
            D   +      L I  S   +   +   D+   + +    LPS
Sbjct: 65  LDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTR--PDLPS 106

>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 = 45.5 bits (107), Expect = 3e-07
 Identities = 17/76 (22%), Positives = 33/76 (43%), Gaps = 1/76 (1%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           +++   P   + +++K++  + GQ++N   M        KG  FV F + E+  K   T
Sbjct: 8  SVYIKGFPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIESAKKFVET 66

Query: 70 DSHVLEGSRLSIQPSD 85
               + + L I   D
Sbjct: 67 PGQKYKETDLLILFKD 82

>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 = 45.2 bits (106), Expect = 3e-07
 Identities = 13/73 (17%), Positives = 30/73 (41%), Gaps = 2/73 (2%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           + V NLP + + N++ K+F   G I++  V    +   +  F  + F   +      + 
Sbjct: 2  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGALAAITK 59

Query: 70 DSHVLEGSRLSIQ 82
             V+  + + + 
Sbjct: 60 THKVVGQNEIIVS 72

>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 = 45.7 bits (107), Expect = 3e-07
 Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
            +F+GNL    S  ELK   SE     + +V+  + TG ++ FG+V F++ E ++K   
Sbjct: 14 FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKALE 72

Query: 69 TDSHVLEGSRLSIQPSDS 86
               + G+ + ++    
Sbjct: 73 LTGLKVFGNEIKLEKPKG 90

>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 = 45.6 bits (107), Expect = 3e-07
 Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 9/85 (10%)

Query: 4  SIR--QLNKIFVGNLPWTVSHNELKKFF---SEYGQIMNASVMFDKNTGLSKGFGFVTFQ 58
          S+R  Q N +FV  L   ++  E+ K      ++G+I    +    +   S+G     + 
Sbjct: 2  SVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYV 61

Query: 59 N----KEAVDKVFSTDSHVLEGSRL 79
               ++A+  +   ++ V++G  L
Sbjct: 62 TYIRSEDALRAIQCVNNVVVDGRTL 86

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.4 bits (107), Expect = 3e-07
 Identities = 16/89 (17%), Positives = 37/89 (41%), Gaps = 7/89 (7%)

Query: 2  SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKE 61
           +++  +  ++V NL  + S   ++K F+         V         + + FV F N+E
Sbjct: 2  EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNRE 55

Query: 62 AVDKVFST-DSHVLEGSRLSIQPSDSHNR 89
             +     +  VL+GS + +  +   ++
Sbjct: 56 DAVEAMKALNGKVLDGSPIEVTLAKPVDK 84

>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 = 45.7 bits (108), Expect = 3e-07
 Identities = 15/74 (20%), Positives = 31/74 (41%), Gaps = 7/74 (9%)

Query: 10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST 69
           ++ G +   ++   +++ FS +GQIM   V  +K       + FV F   E+      +
Sbjct: 20 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESAAHAIVS 73

Query: 70 -DSHVLEGSRLSIQ 82
           +   +EG  +   
Sbjct: 74 VNGTTIEGHVVKCY 87

>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 = 45.4 bits (107), Expect = 4e-07
 Identities = 14/87 (16%), Positives = 34/87 (39%), Gaps = 3/87 (3%)

Query: 1  MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK 60
          M     Q   ++VGNL   V+   + + FS+ G   +  ++ +  +  +  + FV F   
Sbjct: 1  MMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEH 58

Query: 61 EAVDKVFST-DSHVLEGSRLSIQPSDS 86
                 +  +   + G  + +  + +
Sbjct: 59 RDAAAALAAMNGRKILGKEVKVNWATT 85

>d1uoha_ d.211.1.1 (A:) 26S proteasome non-ATPase regulatory subunit 10, gankyrin {Human (Homo sapiens) [TaxId: 9606]} Length = 223

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: 26S proteasome non-ATPase regulatory subunit 10, gankyrin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (111), Expect = 6e-07
 Identities = 15/64 (23%), Positives = 29/64 (45%), Gaps = 2/64 (3%)

Query: 280 FNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLI 339
            + N  D  G   LH ACD   ++  + L+ + GA + + + +    L  AK      ++
Sbjct: 160 ASTNIQDTEGNTPLHLACDEERVEEAKLLVSQ-GASIYIENKEEKTPLQVAKG-GLGLIL 217

Query: 340 EYLV 343
           + +V
Sbjct: 218 KRMV 221

>d1uoha_ d.211.1.1 (A:) 26S proteasome non-ATPase regulatory subunit 10, gankyrin {Human (Homo sapiens) [TaxId: 9606]} Length = 223

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: 26S proteasome non-ATPase regulatory subunit 10, gankyrin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.0 bits (100), Expect = 2e-05
 Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
            +N +++NG   LH+A  +   ++   L+E  GA+ +  D      +  A A  +  +I 
Sbjct: 95  QVNAVNQNGCTPLHYAASKNRHEIAVMLLEG-GANPDAKDHYEATAMHRAAAKGNLKMIH 153

Query: 341 YL 342
            L
Sbjct: 154 IL 155

>d1uoha_ d.211.1.1 (A:) 26S proteasome non-ATPase regulatory subunit 10, gankyrin {Human (Homo sapiens) [TaxId: 9606]} Length = 223

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: 26S proteasome non-ATPase regulatory subunit 10, gankyrin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.6 bits (91), Expect = 2e-04
 Identities = 23/122 (18%), Positives = 38/122 (31%), Gaps = 33/122 (27%)

Query: 257 NIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRG---------------- 300
            +   A  GKL+ L + +   K     + D++    LHWAC  G                
Sbjct: 6   MVCNLAYSGKLEELKESILADKS-LATRTDQDSRTALHWACSAGHTEIVEFLLQLGVPVN 64

Query: 301 ----------------HLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVN 344
                               +   +   GA VN  + +G   L YA +    ++   L+ 
Sbjct: 65  DKDDAGWSPLHIAASAGRDEIVKALLGKGAQVNAVNQNGCTPLHYAASKNRHEIAVMLLE 124

Query: 345 SG 346
            G
Sbjct: 125 GG 126

>d1uoha_ d.211.1.1 (A:) 26S proteasome non-ATPase regulatory subunit 10, gankyrin {Human (Homo sapiens) [TaxId: 9606]} Length = 223

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: 26S proteasome non-ATPase regulatory subunit 10, gankyrin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.9 bits (84), Expect = 0.002
 Identities = 19/89 (21%), Positives = 40/89 (44%), Gaps = 3/89 (3%)

Query: 258 IYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVN 317
           ++  A + + ++    L +    N +  D      +H A  +G+LK++  L+       N
Sbjct: 107 LHYAASKNRHEI-AVMLLE-GGANPDAKDHYEATAMHRAAAKGNLKMIHILLYYKA-STN 163

Query: 318 VTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           + D++G+  L  A   E  +  + LV+ G
Sbjct: 164 IQDTEGNTPLHLACDEERVEEAKLLVSQG 192

>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 = 45.3 bits (106), Expect = 1e-06
 Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 1/81 (1%)

Query: 7   QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV 66
            L  + V  +P TV   +L++ F  YG I +  ++ D+ T  S+G+GFV FQ+  +  + 
Sbjct: 41  VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQA 100

Query: 67  FST-DSHVLEGSRLSIQPSDS 86
            +  +   +   RL +  + S
Sbjct: 101 IAGLNGFNILNKRLKVALAAS 121

>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 = 43.1 bits (101), Expect = 2e-06
 Identities = 16/80 (20%), Positives = 37/80 (46%), Gaps = 9/80 (11%)

Query: 6  RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          R+ N ++V      ++   L+  FS +G I++ S+         +   FVT++  E+ D+
Sbjct: 3  RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQ 54

Query: 66 VFST-DSHVLEGSRLSIQPS 84
            +  +   +E  +L +  +
Sbjct: 55 AVAELNGTQVESVQLKVNIA 74

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.4 bits (102), Expect = 2e-06
 Identities = 13/71 (18%), Positives = 27/71 (38%), Gaps = 7/71 (9%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
            + V   P   + + +   F++YG I+   +    N      +  + +Q+K    K  S
Sbjct: 5  TWVTVFGFPQASA-SYILLQFAQYGNILKHVMSNTGN------WMHIRYQSKLQARKALS 57

Query: 69 TDSHVLEGSRL 79
           D  +   S +
Sbjct: 58 KDGRIFGESIM 68

>d1oy3d_ d.211.1.1 (D:) Transcription factor inhibitor I-kappa-B-beta, IKBB {Mouse (Mus musculus) [TaxId: 10090]} Length = 255

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Transcription factor inhibitor I-kappa-B-beta, IKBB
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.2 bits (108), Expect = 2e-06
 Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 1/56 (1%)

Query: 291 NCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
             LH A +     V++ L++  GAD       G   L  A    +  L   L   G
Sbjct: 194 TPLHLAVEAQAASVLELLLKA-GADPTARMYGGRTPLGSALLRPNPILARLLRAHG 248

>d1oy3d_ d.211.1.1 (D:) Transcription factor inhibitor I-kappa-B-beta, IKBB {Mouse (Mus musculus) [TaxId: 10090]} Length = 255

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Transcription factor inhibitor I-kappa-B-beta, IKBB
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 45.9 bits (107), Expect = 2e-06
 Identities = 11/52 (21%), Positives = 19/52 (36%), Gaps = 4/52 (7%)

Query: 282 INQLDENGLNCLHWACDRGHLKVVQHLIEKCGAD---VNVTDSDGDYGLDYA 330
              + E+G   LH A    H   +  L+    A    +++ +  G   L  A
Sbjct: 2   FGYVTEDGDTALHLAVIHQHEPFLDFLLGF-SAGHEYLDLQNDLGQTALHLA 52

>d1oy3d_ d.211.1.1 (D:) Transcription factor inhibitor I-kappa-B-beta, IKBB {Mouse (Mus musculus) [TaxId: 10090]} Length = 255

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Transcription factor inhibitor I-kappa-B-beta, IKBB
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.8 bits (94), Expect = 1e-04
 Identities = 25/211 (11%), Positives = 59/211 (27%), Gaps = 19/211 (9%)

Query: 122 ALYKQATVGQCNIDKPSW-YNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWEDK 180
           AL+  A +G+ +  +  +             ++   +A          +L +        
Sbjct: 48  ALHLAAILGEASTVEKLYAAGAGVLVAERGGHTALHLACRVRAHTCACVLLQPRPSHPRD 107

Query: 181 EQEEINWDWKPNQKAMSKYIALLNEVDASWEDKEQEEINWDESQESGSKENEGQTKGWVN 240
             +      +      S   A ++       ++E  + +W    E+  +  +G T   V 
Sbjct: 108 ASDTYLTQSQDCTPDTSHAPAAVDSQPNPENEEEPRDEDWRLQLEA--ENYDGHTPLHVA 165

Query: 241 VSSMINDESQL-------------DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDE 287
           V     +  +L                   ++   +     + ++ L K    +      
Sbjct: 166 VIHKDAEMVRLLRDAGADLNKPEPTCGRTPLHLAVEAQAASV-LELLLK-AGADPTARMY 223

Query: 288 NGLNCLHWACDRGHLKVVQHLIEKCGADVNV 318
            G   L  A  R +  + + L    GA    
Sbjct: 224 GGRTPLGSALLRPNPILARLLRAH-GAPEPE 253

>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 = 41.7 bits (97), Expect = 1e-05
 Identities = 7/92 (7%), Positives = 22/92 (23%), Gaps = 12/92 (13%)

Query: 9  NKIFVGNLPWTVSH-----NELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAV 63
          + +        V        + +  F  Y +              S     + F N  + 
Sbjct: 6  SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYF------KSFKRVRINFSNPLSA 59

Query: 64 DK-VFSTDSHVLEGSRLSIQPSDSHNRMAENM 94
                       G  + +  + + +  + ++
Sbjct: 60 ADARLRLHKTEFLGKEMKLYFAQTLHIGSSHL 91

>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 = 41.3 bits (96), Expect = 1e-05
 Identities = 17/78 (21%), Positives = 25/78 (32%), Gaps = 8/78 (10%)

Query: 6  RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDK 65
          R   ++ V  LP + S  +LK    E G +  A V  D         G V +  KE ++ 
Sbjct: 13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG-------MGMVEYLRKEDMEY 65

Query: 66 VFST-DSHVLEGSRLSIQ 82
               D            
Sbjct: 66 ALRKLDDTKFRSHEGETS 83

>d1ot8a_ d.211.1.1 (A:) Neurogenic locus notch receptor domain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 209

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Neurogenic locus notch receptor domain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 43.2 bits (100), Expect = 1e-05
 Identities = 14/63 (22%), Positives = 24/63 (38%), Gaps = 1/63 (1%)

Query: 280 FNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLI 339
            N +  D+     L  A   G  +  + L++   A+  +TD       D A    H D++
Sbjct: 147 ANRDAQDDKDETPLFLAAREGSYEASKALLDN-FANREITDHMDRLPRDVASERLHHDIV 205

Query: 340 EYL 342
             L
Sbjct: 206 RLL 208

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.1 bits (93), Expect = 2e-05
 Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 1/70 (1%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST- 69
          +++  L    +  +L K    YG+I++   + DK T   KG+GFV F +  A  K  +  
Sbjct: 1  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 70 DSHVLEGSRL 79
           +  ++    
Sbjct: 61 KASGVQAQMA 70

>d1ihba_ d.211.1.1 (A:) p18ink4C(ink6) {Human (Homo sapiens) [TaxId: 9606]} Length = 156

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: p18ink4C(ink6)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.4 bits (95), Expect = 4e-05
 Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 1/35 (2%)

Query: 291 NCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY 325
           N L  A  RG L+ +  L++    +VN  +  G  
Sbjct: 3   NELASAAARGDLEQLTSLLQN-NVNVNAQNGFGRT 36

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.3 bits (91), Expect = 5e-05
 Identities = 16/84 (19%), Positives = 28/84 (33%), Gaps = 8/84 (9%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK-EAVDKVF 67
          + I V NLP   +  E+     +Y                +K   FVT  N  +A + + 
Sbjct: 6  SGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDR-------NKRTAFVTLLNGEQAQNAIQ 58

Query: 68 STDSHVLEGSRLSIQPSDSHNRMA 91
              +   G  L +Q   +   + 
Sbjct: 59 MFHQYSFRGKDLIVQLQPTDALLC 82

>d1bd8a_ d.211.1.1 (A:) Cell cycle inhibitor p19ink4D {Human (Homo sapiens) [TaxId: 9606]} Length = 156

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Cell cycle inhibitor p19ink4D
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.6 bits (93), Expect = 7e-05
 Identities = 7/31 (22%), Positives = 14/31 (45%)

Query: 293 LHWACDRGHLKVVQHLIEKCGADVNVTDSDG 323
           L  A  RG ++ V+ L+ +     +  +  G
Sbjct: 6   LSGAAARGDVQEVRRLLHRELVHPDALNRFG 36

>d1bd8a_ d.211.1.1 (A:) Cell cycle inhibitor p19ink4D {Human (Homo sapiens) [TaxId: 9606]} Length = 156

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Cell cycle inhibitor p19ink4D
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.3 bits (82), Expect = 0.002
 Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 2/65 (3%)

Query: 280 FNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLI 339
            ++N  D  G   +H A   GH  VV  L  +  +D++  D+ G   L+ A      DL+
Sbjct: 92  ADVNVPDGTGALPIHLAVQEGHTAVVSFLAAE--SDLHRRDARGLTPLELALQRGAQDLV 149

Query: 340 EYLVN 344
           + L  
Sbjct: 150 DILQG 154

>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 = 39.2 bits (91), Expect = 7e-05
 Identities = 11/78 (14%), Positives = 28/78 (35%), Gaps = 2/78 (2%)

Query: 8   LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
           ++ + +             +   +YG++   +V  D       G  +V F+ +E  +K  
Sbjct: 27  VSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVC-DNLGDHLVGNVYVKFRREEDAEKAV 85

Query: 68  ST-DSHVLEGSRLSIQPS 84
              ++    G  +  + S
Sbjct: 86  IDLNNRWFNGQPIHAELS 103

>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 = 37.7 bits (87), Expect = 2e-04
 Identities = 12/75 (16%), Positives = 28/75 (37%), Gaps = 7/75 (9%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
           +++VG L    S   L + F  +G I     +   +      F ++ +++ +A     +
Sbjct: 18 TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS------FAYIQYESLDAAQAACA 71

Query: 69 T-DSHVLEGSRLSIQ 82
                L G    ++
Sbjct: 72 KMRGFPLGGPDRRLR 86

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.2 bits (85), Expect = 2e-04
 Identities = 21/79 (26%), Positives = 32/79 (40%), Gaps = 10/79 (12%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST- 69
          I +  LP  V++ E+    S+Y        +        KG  FVT  N E  +   +T 
Sbjct: 1  ILIRGLPGDVTNQEVHDLLSDY-------ELKYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 70 DSHVLEGSRLSIQ--PSDS 86
              L    LS+Q  P+D+
Sbjct: 54 HQSRLRERELSVQLQPTDA 72

>d1iknd_ d.211.1.1 (D:) I-kappa-B-alpha {Human (Homo sapiens) [TaxId: 9606]} Length = 221

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: I-kappa-B-alpha
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.5 bits (90), Expect = 3e-04
 Identities = 24/93 (25%), Positives = 31/93 (33%), Gaps = 1/93 (1%)

Query: 254 NEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCG 313
           N       A       +V+ L  L      Q   NG   LH A D  +  +V  L+ KCG
Sbjct: 110 NGHTCLHLASIHGYLGIVELLVSLGADVNAQEPCNGRTALHLAVDLQNPDLVSLLL-KCG 168

Query: 314 ADVNVTDSDGDYGLDYAKAIEHTDLIEYLVNSG 346
           ADVN     G            T + + L    
Sbjct: 169 ADVNRVTYQGYSPYQLTWGRPSTRIQQQLGQLT 201

>d1iknd_ d.211.1.1 (D:) I-kappa-B-alpha {Human (Homo sapiens) [TaxId: 9606]} Length = 221

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: I-kappa-B-alpha
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.5 bits (90), Expect = 3e-04
 Identities = 9/51 (17%), Positives = 17/51 (33%), Gaps = 3/51 (5%)

Query: 288 NGLNCLHWACDRGHLKVVQHLIEKC---GADVNVTDSDGDYGLDYAKAIEH 335
           +G + LH A       +   +I +     A +N  ++     L  A     
Sbjct: 1   DGDSFLHLAIIHEEKALTMEVIRQVKGDLAFLNFQNNLQQTPLHLAVITNQ 51

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.4 bits (86), Expect = 3e-04
 Identities = 11/84 (13%), Positives = 28/84 (33%), Gaps = 10/84 (11%)

Query: 11 IFVGNLP-WTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVD---KV 66
          + + +         +L +    +G I N  ++   N        F+     E        
Sbjct: 11 VHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN------EAFIEMATTEDAQAAVDY 64

Query: 67 FSTDSHVLEGSRLSIQPSDSHNRM 90
          ++T   ++ G  + +  S  + R+
Sbjct: 65 YTTTPALVFGKPVRVHLSQKYKRI 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 = 37.0 bits (85), Expect = 5e-04
 Identities = 22/102 (21%), Positives = 36/102 (35%), Gaps = 8/102 (7%)

Query: 9   NKIFVGNL-PWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVF 67
           + + V NL P  V+   L   F  YG +    ++F+K          V   +        
Sbjct: 3   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQLAM 57

Query: 68  ST-DSHVLEGSRLSIQPSDSHN-RMAENMEDRFNQACDYLPS 107
           S  + H L G  + I  S   N ++    ++      DY  S
Sbjct: 58  SHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNS 99

>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 = 36.1 bits (83), Expect = 0.001
 Identities = 15/64 (23%), Positives = 26/64 (40%), Gaps = 5/64 (7%)

Query: 23 NELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI 81
           +L+   S++GQI    +          G   V+F++ E  D    T D     G +++ 
Sbjct: 34 EDLRVECSKFGQIRKLLLFDRHP----DGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 89

Query: 82 QPSD 85
          Q  D
Sbjct: 90 QAWD 93

>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 = 35.5 bits (81), Expect = 0.001
 Identities = 16/80 (20%), Positives = 29/80 (36%), Gaps = 6/80 (7%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKV-- 66
            + + N+P +VS  +LK  FS  G +    V   K     +    +   + E   +   
Sbjct: 11 ATLHLSNIPPSVSEEDLKVLFSSNGGV----VKGFKFFQKDRKMALIQMGSVEEAVQALI 66

Query: 67 FSTDSHVLEGSRLSIQPSDS 86
             +  + E   L +  S S
Sbjct: 67 DLHNHDLGENHHLRVSFSKS 86

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.5 bits (81), Expect = 0.001
 Identities = 15/77 (19%), Positives = 37/77 (48%), Gaps = 2/77 (2%)

Query: 9  NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS 68
            +++ NLP ++   EL+     +GQ+++ + +   ++G S+G GF   ++ E  + V  
Sbjct: 19 TNLYISNLPLSMDEQELENMLKPFGQVIS-TRILRDSSGTSRGVGFARMESTEKCEAVIG 77

Query: 69 T-DSHVLEGSRLSIQPS 84
            +   ++       P+
Sbjct: 78 HFNGKFIKTPPGVSAPT 94

>d1awcb_ d.211.1.1 (B:) GA bindinig protein (GABP) beta 1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 153

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: GA bindinig protein (GABP) beta 1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.4 bits (82), Expect = 0.002
 Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 281 NINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHTDLIE 340
           ++N  D   +  LHWA +  H +VV+ L+ K GADV+          D +    + DL E
Sbjct: 92  DVNAKDMLKMTALHWATEHNHQEVVE-LLIKYGADVHTQSKFCKTAFDISIDNGNEDLAE 150

Query: 341 YL 342
            L
Sbjct: 151 IL 152

>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 = 35.1 bits (80), Expect = 0.002
 Identities = 13/73 (17%), Positives = 26/73 (35%), Gaps = 8/73 (10%)

Query: 11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST- 69
          +  G L   VS N+L     + G +    +  +K       + F  ++  E   + + T 
Sbjct: 23 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKRAYVTL 76

Query: 70 -DSHVLEGSRLSI 81
              V++     I
Sbjct: 77 NGKEVVDDLGQKI 89

>d1ycsb1 d.211.1.1 (B:327-456) 53BP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 130

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: 53BP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.4 bits (80), Expect = 0.003
 Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 4/60 (6%)

Query: 288 NGLNCLHWACDRGHLKVVQHLIEKCGADVN-VTDSDGDYGLDYAKAIE--HTDLIEYLVN 344
           +G   LH A    +++V + L+E  GA V  +T SD     D  + +E  +T   ++L  
Sbjct: 66  DGWTPLHCAASCNNVQVCKFLVES-GAAVFAMTYSDMQTAADKCEEMEEGYTQCSQFLYG 124

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	347
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.87
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.86
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.85
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.84
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.84
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.84
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.84
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.83
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.83
d1hbka_	89	Acyl-CoA binding protein {Plasmodium falciparum [T	99.83
d1hb6a_	86	Acyl-CoA binding protein {Cow (Bos taurus) [TaxId:	99.83
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.83
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.83
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.82
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.82
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.82
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.82
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.82
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.82
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.82
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.81
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.81
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.81
d1ycsb1	130	53BP2 {Human (Homo sapiens) [TaxId: 9606]}	99.81
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.81
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.81
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.81
d1dcqa1	154	Pyk2-associated protein beta {Mouse (Mus musculus)	99.8
d1myoa_	118	Myotrophin {Rat (Rattus norvegicus) [TaxId: 10116]	99.8
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.8
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.8
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.8
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.79
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.79
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.79
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.79
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.78
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.78
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.77
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.77
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.76
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.76
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.75
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.75
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.75
d1bi7b_	125	Cell cycle inhibitor p16ink4A {Human (Homo sapiens	99.74
d1oy3d_	255	Transcription factor inhibitor I-kappa-B-beta, IKB	99.74
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.73
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.73
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.72
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.72
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.71
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.71
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.71
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.7
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.7
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.7
d1ycsb1	130	53BP2 {Human (Homo sapiens) [TaxId: 9606]}	99.69
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.69
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.69
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.69
d1ot8a_	209	Neurogenic locus notch receptor domain {Fruit fly	99.69
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.69
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.69
d1bd8a_	156	Cell cycle inhibitor p19ink4D {Human (Homo sapiens	99.69
d1myoa_	118	Myotrophin {Rat (Rattus norvegicus) [TaxId: 10116]	99.68
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.68
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.68
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.68
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.67
d1uoha_	223	26S proteasome non-ATPase regulatory subunit 10, g	99.67
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.67
d1bi7b_	125	Cell cycle inhibitor p16ink4A {Human (Homo sapiens	99.67
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.66
d1oy3d_	255	Transcription factor inhibitor I-kappa-B-beta, IKB	99.66
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.65
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.65
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.65
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.65
d1ixva_	229	26S proteasome non-ATPase regulatory subunit 10, g	99.65
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.64
d1wdya_	285	RNase L, 2-5a-dependent ribonuclease {Human (Homo	99.64
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.64
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.64
d1awcb_	153	GA bindinig protein (GABP) beta 1 {Mouse (Mus musc	99.64
d1dcqa1	154	Pyk2-associated protein beta {Mouse (Mus musculus)	99.63
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.63
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.63
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.62
d1uoha_	223	26S proteasome non-ATPase regulatory subunit 10, g	99.62
d2ajaa1	346	Hypothetical protein LPG2416 {Legionella pneumophi	99.62
d2fo1e1	277	Lin-12 {Caenorhabditis elegans [TaxId: 6239]}	99.62
d1n11a_	408	Ankyrin-R {Human (Homo sapiens) [TaxId: 9606]}	99.62
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.6
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.59
d1n11a_	408	Ankyrin-R {Human (Homo sapiens) [TaxId: 9606]}	99.59
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.58
d1sw6a_	301	Swi6 ankyrin-repeat fragment {Baker's yeast (Sacch	99.58
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.58
d1k1aa_	228	bcl-3 {Human (Homo sapiens) [TaxId: 9606]}	99.58
d2fo1e1	277	Lin-12 {Caenorhabditis elegans [TaxId: 6239]}	99.57
d1bd8a_	156	Cell cycle inhibitor p19ink4D {Human (Homo sapiens	99.56
d1ihba_	156	p18ink4C(ink6) {Human (Homo sapiens) [TaxId: 9606]	99.56
d1awcb_	153	GA bindinig protein (GABP) beta 1 {Mouse (Mus musc	99.55
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.54
d1s70b_	291	Myosin phosphatase targeting subunit 1, MYPT1 {Chi	99.53
d1iknd_	221	I-kappa-B-alpha {Human (Homo sapiens) [TaxId: 9606	99.52
d2ajaa1	346	Hypothetical protein LPG2416 {Legionella pneumophi	99.52
d1iknd_	221	I-kappa-B-alpha {Human (Homo sapiens) [TaxId: 9606	99.51
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.49
d1ixva_	229	26S proteasome non-ATPase regulatory subunit 10, g	99.47
d1k1aa_	228	bcl-3 {Human (Homo sapiens) [TaxId: 9606]}	99.46
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.46
d1s70b_	291	Myosin phosphatase targeting subunit 1, MYPT1 {Chi	99.45
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	99.43
d1ihba_	156	p18ink4C(ink6) {Human (Homo sapiens) [TaxId: 9606]	99.42
d1ot8a_	209	Neurogenic locus notch receptor domain {Fruit fly	99.38
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.34
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.34
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.26
d1wdya_	285	RNase L, 2-5a-dependent ribonuclease {Human (Homo	99.24
d1sw6a_	301	Swi6 ankyrin-repeat fragment {Baker's yeast (Sacch	99.21
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.07
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	97.95
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	97.85
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	97.84
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	97.83
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	97.76
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	97.75
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	97.75
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	97.74
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	97.74
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	97.72
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	97.67
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	97.67
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	97.66
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	97.66
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	97.64
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	97.63
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	97.63
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	97.62
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	97.61
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	97.59
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	97.59
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	97.57
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	97.54
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	97.53
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.52
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	97.5
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	97.48
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	97.43
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	97.43
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	97.36
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	97.35
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	97.34
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	97.33
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	97.29
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	97.29
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	97.27
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	97.27
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	97.23
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	97.18
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	97.14
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	97.11
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	97.1
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	97.09
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	97.08
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	97.05
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.05
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	97.03
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	97.02
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	97.0
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	97.0
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	97.0
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	96.95
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	96.93
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	96.92
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	96.9
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	96.89
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	96.85
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	96.84
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	96.82
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	96.8
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	96.77
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	96.75
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	96.74
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	96.69
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	96.69
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	96.67
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	96.64
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	96.58
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	96.57
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	96.53
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	96.52
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	96.5
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	96.4
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	96.33
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	96.31
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	96.27
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	96.13
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	96.05
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	96.04
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	96.0
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	95.66
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.21
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	94.8
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	94.19
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	93.79
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	93.31
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	92.57
d1gg3a1	106	Erythroid membrane protein 4.1R {Human (Homo sapie	88.8
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	83.23
d1h4ra1	111	Merlin {Human (Homo sapiens) [TaxId: 9606]}	81.43
d1mixa1	114	Talin {Chicken (Gallus gallus) [TaxId: 9031]}	80.17

>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=2.2e-23  Score=171.69  Aligned_cols=154  Identities=21%  Similarity=0.364  Sum_probs=123.9

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccC
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP   83 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~   83 (347)
                      +|++.|+|||||||+++|+++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|.+|+...+..+.++.+.+.+
T Consensus         2 ep~~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~   81 (183)
T d1u1qa_           2 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKR   81 (183)
T ss_dssp             CCHHHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhh
Confidence            46778999999999999999999999999999999999999999999999999999999999999988888888888776


Q ss_pred             CCcccccchhhhhhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHH
Q psy630           84 SDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAM  163 (347)
Q Consensus        84 ~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~  163 (347)
                      ..+...... ........++||+|||..+++++|+++|+.||.+....+..+++     .++.|+.|+..  ..+.++|.
T Consensus        82 ~~~~~~~~~-~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~-----~~~~~g~~fV~--f~~~e~A~  153 (183)
T d1u1qa_          82 AVSREDSQR-PGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRG-----SGKKRGFAFVT--FDDHDSVD  153 (183)
T ss_dssp             CCCTTGGGS-TTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----TCCEEEEEEEE--ESCHHHHH
T ss_pred             hhhcccccc-cccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccc-----cCccceeEEEE--ECCHHHHH
Confidence            655443221 12234457899999999999999999999999998877766543     12233333433  44577777


Q ss_pred             HH
Q psy630          164 SK  165 (347)
Q Consensus       164 ~~  165 (347)
                      ++
T Consensus       154 ~A  155 (183)
T d1u1qa_         154 KI  155 (183)
T ss_dssp             HH
T ss_pred             HH
Confidence            65

>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=99.86  E-value=3.9e-22  Score=141.79  Aligned_cols=82  Identities=32%  Similarity=0.604  Sum_probs=78.0

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccC
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP   83 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~   83 (347)
                      +|++.++|||+|||+++|+++|+++|++||.|..+.|++++.+|+++|||||+|.+.++|++|++.+++.+.|+.|.|.+
T Consensus         2 epe~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~~   81 (84)
T d1l3ka1           2 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKR   81 (84)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEE
T ss_pred             CCCCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEe
Confidence            46778999999999999999999999999999999999999999999999999999999999999899999999999987


Q ss_pred             CC
Q psy630           84 SD   85 (347)
Q Consensus        84 ~~   85 (347)
                      |.
T Consensus        82 A~   83 (84)
T d1l3ka1          82 AV   83 (84)
T ss_dssp             CC
T ss_pred             ee
Confidence            74

>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=99.85  E-value=1.7e-21  Score=140.10  Aligned_cols=87  Identities=32%  Similarity=0.628  Sum_probs=80.0

Q ss_pred             CccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccc
Q psy630            2 SNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSI   81 (347)
Q Consensus         2 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v   81 (347)
                      ....+..++|||+|||+++|+++|+++|++||.|..|+|++|+.+|.++|||||+|.+.++|.+|++. .+.++|+.|.|
T Consensus         2 k~~~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~-~~~l~Gr~i~v   80 (90)
T d2cqga1           2 KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ-RHMIDGRWCDC   80 (90)
T ss_dssp             SCCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS-CEEETTEEEEE
T ss_pred             CCCCcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc-CCccCCEEeEE
Confidence            45677889999999999999999999999999999999999999999999999999999999999984 45899999999


Q ss_pred             cCCCcccc
Q psy630           82 QPSDSHNR   89 (347)
Q Consensus        82 ~~~~~~~~   89 (347)
                      .++.++..
T Consensus        81 ~~a~~k~~   88 (90)
T d2cqga1          81 KLPNSKQS   88 (90)
T ss_dssp             ECCCTTCC
T ss_pred             EeCCCCCC
Confidence            99987653

>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=99.84  E-value=2.5e-21  Score=134.55  Aligned_cols=75  Identities=37%  Similarity=0.823  Sum_probs=72.2

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630           10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus        10 ~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      +|||+|||+++|+++|+++|++||.|..+.+++++.+++++|||||+|.+.++|++|+..+++.+.|+.|.|++|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeEC
Confidence            599999999999999999999999999999999999999999999999999999999999999999999999765

>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=99.84  E-value=7.1e-22  Score=137.85  Aligned_cols=76  Identities=34%  Similarity=0.713  Sum_probs=73.1

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      ++|||+|||+++|+++|+++|++||.|.+++|++|+.||+++|||||+|.+.++|++|+..+++.++|+.|.|+.|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            5799999999999999999999999999999999999999999999999999999999999999999999998765

>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=99.84  E-value=1.9e-21  Score=134.72  Aligned_cols=75  Identities=28%  Similarity=0.573  Sum_probs=71.7

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630           10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus        10 ~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      +|||||||+++|+++|+++|++||.|..++|++++.|++++|||||+|.+.++|++|++.+++.++|+.+.|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEEC
Confidence            699999999999999999999999999999999999999999999999999999999998888999999988764

>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=99.84  E-value=1.9e-21  Score=143.52  Aligned_cols=84  Identities=26%  Similarity=0.610  Sum_probs=79.2

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSD   85 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~   85 (347)
                      .+.++|||+|||+++++++|+++|++||.|..+.|++++.++.++|||||+|.+.++|++|++.+++.|.|+.|.|.++.
T Consensus        18 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          18 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCS
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECc
Confidence            34589999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cccc
Q psy630           86 SHNR   89 (347)
Q Consensus        86 ~~~~   89 (347)
                      ++..
T Consensus        98 ~ke~  101 (103)
T d1x4ba1          98 AREE  101 (103)
T ss_dssp             SCCC
T ss_pred             ccCC
Confidence            7654

>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=99.83  E-value=6e-21  Score=138.41  Aligned_cols=85  Identities=29%  Similarity=0.471  Sum_probs=79.3

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~   83 (347)
                      .++.++|||+|||+++|+++|+++|++||.|.++++++++.||.++|||||+|.+.++|++|++ +++..+.|+.|+|.+
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4556899999999999999999999999999999999999999999999999999999999997 599999999999999


Q ss_pred             CCcccc
Q psy630           84 SDSHNR   89 (347)
Q Consensus        84 ~~~~~~   89 (347)
                      |.++..
T Consensus        86 A~~~~~   91 (93)
T d1x5ua1          86 ASAHNK   91 (93)
T ss_dssp             TTTTSC
T ss_pred             cCCCCC
Confidence            987653

>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=99.83  E-value=1e-20  Score=133.09  Aligned_cols=77  Identities=31%  Similarity=0.682  Sum_probs=74.2

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      .|+|||+|||+++|+++|+++|++||.|..+.++.++.++.++|||||+|.+.+++.+|+.++++.++|++|.|++|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999865

>d1hbka_ a.11.1.1 (A:) Acyl-CoA binding protein {Plasmodium falciparum [TaxId: 5833]}

class: All alpha proteins
fold: Acyl-CoA binding protein-like
superfamily: Acyl-CoA binding protein
family: Acyl-CoA binding protein
domain: Acyl-CoA binding protein
species: Plasmodium falciparum [TaxId: 5833]

Probab=99.83  E-value=1.3e-21  Score=137.85  Aligned_cols=86  Identities=30%  Similarity=0.675  Sum_probs=80.0

Q ss_pred             hhhhcccccccccCCccc--ccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Q psy630           94 MEDRFNQACDYLPSLVKK--LDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLK  171 (347)
Q Consensus        94 ~~~~f~~~~~~v~~l~~~--~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~  171 (347)
                      +...|..++.+|++++..  ++.++.+.||++|+|+++|+|+.++|+++++.+++||+||.++++||+++||+.||++++
T Consensus         2 L~~~F~~A~~~v~~~~~~~~~~~~~~L~lY~lyKQat~G~~~~~~P~~~~~~~~~Kw~AW~~l~gms~~eA~~~Yi~~v~   81 (89)
T d1hbka_           2 MAQVFEECVSFINGLPRTINLPNELKLDLYKYYKQSTIGNCNIKEPSAHKYIDRKKYEAWKSVENLNREDAQKRYVDIVS   81 (89)
T ss_dssp             HHHHHHHHHHHHHHSCTTCCCCHHHHHHHHHHHHHHHTCSCCSCCCCTTSHHHHHHHHHHHHTTTCCHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCCCCCccCHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            345688899999998754  678999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhccCCh
Q psy630          172 EVDAGWED  179 (347)
Q Consensus       172 ~l~~~~~~  179 (347)
                      +|.|+|.+
T Consensus        82 ~l~p~w~~   89 (89)
T d1hbka_          82 EIFPYWQD   89 (89)
T ss_dssp             HHCTTTTC
T ss_pred             HHcccccC
Confidence            99999974

>d1hb6a_ a.11.1.1 (A:) Acyl-CoA binding protein {Cow (Bos taurus) [TaxId: 9913]}

class: All alpha proteins
fold: Acyl-CoA binding protein-like
superfamily: Acyl-CoA binding protein
family: Acyl-CoA binding protein
domain: Acyl-CoA binding protein
species: Cow (Bos taurus) [TaxId: 9913]

Probab=99.83  E-value=1.5e-21  Score=137.02  Aligned_cols=83  Identities=33%  Similarity=0.598  Sum_probs=79.5

Q ss_pred             hhcccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhhc
Q psy630           96 DRFNQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDA  175 (347)
Q Consensus        96 ~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~l~~  175 (347)
                      ..|..+..+|++++..++.++++.||++|+|+++|+|+.++|+++++.+++||+||.++++|++++||+.||+++++|.+
T Consensus         3 ~~F~~A~~~v~~~~~~~~~~~~L~LYalyKQat~Gd~~~~~P~~~~~~~~aKw~AW~~~~gms~~eA~~~YI~~v~~l~~   82 (86)
T d1hb6a_           3 AEFDKAAEEVKHLKTKPADEEMLFIYSHYKQATVGDINTERPGMLDFKGKAKWDAWNELKGTSKEDAMKAYIDKVEELKK   82 (86)
T ss_dssp             HHHHHHHHHGGGCSSCCCHHHHHHHHHHHHHHHTCSCCSCCCCTTCHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHhcCCCCCCCCCcchHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Confidence            46888999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCC
Q psy630          176 GWE  178 (347)
Q Consensus       176 ~~~  178 (347)
                      +|-
T Consensus        83 k~g   85 (86)
T d1hb6a_          83 KYG   85 (86)
T ss_dssp             HHC
T ss_pred             HhC
Confidence            873

>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=99.83  E-value=7.4e-21  Score=134.82  Aligned_cols=79  Identities=24%  Similarity=0.434  Sum_probs=75.4

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCc
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~   86 (347)
                      .++|||+|||+++++++|+++|++||.|..+++++++.+|+++|||||+|.+.++|++|+.. |+..+.|++|+|.++.|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            46899999999999999999999999999999999999999999999999999999999975 99999999999999875

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.7e-20  Score=132.15  Aligned_cols=76  Identities=29%  Similarity=0.425  Sum_probs=73.3

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630           10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus        10 ~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      +|||+|||+++|+++|+++|++||+|.+++|++++.||+++|||||+|.+.++|..|++. ++..+.|++|+|.++.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            699999999999999999999999999999999999999999999999999999999975 9999999999999874

>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=99.82  E-value=1.1e-20  Score=134.52  Aligned_cols=80  Identities=24%  Similarity=0.527  Sum_probs=76.2

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCcc
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDSH   87 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~~   87 (347)
                      .+|||+|||+++|+++|+++|++||+|..++|++|+.||+++|||||+|.+.++|..|+.. ++..+.|++|.|.++.+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            4799999999999999999999999999999999999999999999999999999999985 999999999999999765


Q ss_pred             c
Q psy630           88 N   88 (347)
Q Consensus        88 ~   88 (347)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.82  E-value=1.3e-21  Score=143.89  Aligned_cols=83  Identities=24%  Similarity=0.425  Sum_probs=77.4

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      ..+.++|||+|||+++++++|+++|++||.|.+|+|++++.+|+++|||||+|.+.++|.+|+.+++..+.|+.|.|.++
T Consensus        15 ~~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l~V~~a   94 (101)
T d2cq4a1          15 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQAS   94 (101)
T ss_dssp             HHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEH
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEEC
Confidence            34467999999999999999999999999999999999999999999999999999999999988999999999999887


Q ss_pred             Ccc
Q psy630           85 DSH   87 (347)
Q Consensus        85 ~~~   87 (347)
                      .++
T Consensus        95 ~~~   97 (101)
T d2cq4a1          95 QAE   97 (101)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            543

>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=99.82  E-value=4.2e-21  Score=138.18  Aligned_cols=82  Identities=22%  Similarity=0.394  Sum_probs=77.5

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      ..++|||+|||+++++++|+++|++||+|.++.+++++.+|.++|||||+|.+.++|.+|+.. ++..+.|++|.|.++.
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            457999999999999999999999999999999999999999999999999999999999975 9999999999999997


Q ss_pred             ccc
Q psy630           86 SHN   88 (347)
Q Consensus        86 ~~~   88 (347)
                      ++.
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.82  E-value=2.1e-20  Score=134.12  Aligned_cols=83  Identities=19%  Similarity=0.355  Sum_probs=77.2

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      ..+.++|||+|||+++++++|+++|++||.|.++++++++.+|+++|||||+|.+.++|++|+.. |+..+.|+.|+|.+
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999985 99999999999999


Q ss_pred             CCcc
Q psy630           84 SDSH   87 (347)
Q Consensus        84 ~~~~   87 (347)
                      +.++
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            8764

>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=99.82  E-value=2.9e-20  Score=131.79  Aligned_cols=79  Identities=24%  Similarity=0.486  Sum_probs=74.9

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCc
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~   86 (347)
                      .++|||+|||+++++++|+++|++||.|..++++++..+|.++|||||+|.+.++|+.|+.. ++..+.|++|.|.++.|
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            35799999999999999999999999999999999999999999999999999999999975 99999999999998865

>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=99.82  E-value=3.2e-20  Score=134.53  Aligned_cols=83  Identities=18%  Similarity=0.379  Sum_probs=77.8

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~   83 (347)
                      ....++|||+|||+++|+++|+++|++||.|.+|.+++++.+|.++|||||+|.+.++|..|++ +|+..+.|++|.|.+
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~   83 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW   83 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3567899999999999999999999999999999999999999999999999999999999998 599999999999998


Q ss_pred             CCcc
Q psy630           84 SDSH   87 (347)
Q Consensus        84 ~~~~   87 (347)
                      +.+.
T Consensus        84 a~~~   87 (93)
T d1h2vz_          84 DAGF   87 (93)
T ss_dssp             ESCC
T ss_pred             cCCC
Confidence            7553

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=2.3e-20  Score=132.50  Aligned_cols=79  Identities=25%  Similarity=0.470  Sum_probs=74.2

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSI   81 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v   81 (347)
                      ++|...++|||+|||+++|+++|+++|++||.|.+++|++++.+|+++|||||+|.+.++|..|+. +++..+.|++|+|
T Consensus         4 ~~p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           4 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            456677899999999999999999999999999999999999999999999999999999999997 4999999999876

>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=99.81  E-value=2.1e-20  Score=134.78  Aligned_cols=84  Identities=24%  Similarity=0.391  Sum_probs=78.5

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      ..+.++|||+|||+++++++|+++|++||.|..+++++++.+|.++|||||+|.+.++|.+|++. ++..+.|+.|.|.+
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            34567899999999999999999999999999999999999999999999999999999999985 99999999999999


Q ss_pred             CCccc
Q psy630           84 SDSHN   88 (347)
Q Consensus        84 ~~~~~   88 (347)
                      +.++.
T Consensus        85 akp~~   89 (90)
T d2cq0a1          85 AKPST   89 (90)
T ss_dssp             SSCCC
T ss_pred             eeCCC
Confidence            97653

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=4.8e-20  Score=131.25  Aligned_cols=79  Identities=25%  Similarity=0.613  Sum_probs=72.1

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCc--ccccc
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGS--RLSIQ   82 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~--~l~v~   82 (347)
                      -+.++|||+|||+++|+++|+++|++||+|.++++++++.+|.++|||||+|.+.++|.+|++. |+..+.|+  +|.|.
T Consensus         4 ~k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           4 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK   83 (85)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEE
Confidence            4457899999999999999999999999999999999999999999999999999999999985 99999984  47776


Q ss_pred             CC
Q psy630           83 PS   84 (347)
Q Consensus        83 ~~   84 (347)
                      +|
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            54

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.81  E-value=2e-20  Score=137.49  Aligned_cols=86  Identities=34%  Similarity=0.541  Sum_probs=79.6

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~   82 (347)
                      .+...++|||+|||+++++++|+++|++||.|..++|++++.+++++|||||+|.+.++|+.|++ +|+..+.|++|+|.
T Consensus         4 ~~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~   83 (99)
T d1whwa_           4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVL   83 (99)
T ss_dssp             CCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34566789999999999999999999999999999999999999999999999999999999997 49999999999999


Q ss_pred             CCCcccc
Q psy630           83 PSDSHNR   89 (347)
Q Consensus        83 ~~~~~~~   89 (347)
                      ++.++..
T Consensus        84 ~a~~~~~   90 (99)
T d1whwa_          84 PSTIKKE   90 (99)
T ss_dssp             ECCCCST
T ss_pred             ECCCCCc
Confidence            9887654

>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=99.81  E-value=3.2e-20  Score=137.15  Aligned_cols=83  Identities=30%  Similarity=0.657  Sum_probs=75.8

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSD   85 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~   85 (347)
                      ...++|||+|||+++++++|+++|++||.|.+++|++++.||+++|||||+|.+.++|++|++.....+.|+.|.|.++.
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l~V~~a~   87 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAY   87 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEEST
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEcC
Confidence            44578999999999999999999999999999999999999999999999999999999999974457999999998876


Q ss_pred             ccc
Q psy630           86 SHN   88 (347)
Q Consensus        86 ~~~   88 (347)
                      .+.
T Consensus        88 ~~~   90 (103)
T d2cqda1          88 LGA   90 (103)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            543

>d1ycsb1 d.211.1.1 (B:327-456) 53BP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: 53BP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=3.1e-20  Score=143.80  Aligned_cols=89  Identities=26%  Similarity=0.345  Sum_probs=64.6

Q ss_pred             cHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCCH
Q psy630          257 NIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHT  336 (347)
Q Consensus       257 ~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~  336 (347)
                      ++|+.|+..+..+++++|++ .|+++|.+|..|+||||+||..|+.+++++|++ +|++++.+|.+|+||||+|+..|+.
T Consensus         3 ~lL~~A~~~G~~~~v~~Ll~-~g~d~n~~d~~g~t~Lh~A~~~~~~~~~~~ll~-~g~~~~~~d~~g~tpLh~A~~~g~~   80 (130)
T d1ycsb1           3 ALLLDSSLEGEFDLVQRIIY-EVDDPSLPNDEGITALHNAVCAGHTEIVKFLVQ-FGVNVNAADSDGWTPLHCAASCNNV   80 (130)
T ss_dssp             HHHHHHHHHTCHHHHHHHTS-TTSSCCCCCTTSCCHHHHHHHHTCHHHHHHHHH-HTCCTTCCCTTCCCHHHHHHHTTCH
T ss_pred             HHHHHHHHcCCHHHHHHHHH-cCCCccccccccccccccccccccccccccccc-cccccccccccCcccccccchhhHH
Confidence            45555554444556666666 577777777777777777777777777777777 5777777777777777777777777


Q ss_pred             HHHHHHHhCCC
Q psy630          337 DLIEYLVNSGS  347 (347)
Q Consensus       337 ~~v~~Ll~~GA  347 (347)
                      +++++|+++||
T Consensus        81 ~~v~~Ll~~ga   91 (130)
T d1ycsb1          81 QVCKFLVESGA   91 (130)
T ss_dssp             HHHHHHHHTTC
T ss_pred             HHHHHHHHcCC
Confidence            77777777775

>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=99.81  E-value=6.5e-20  Score=130.69  Aligned_cols=78  Identities=29%  Similarity=0.619  Sum_probs=72.7

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCC--ccccccC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEG--SRLSIQP   83 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g--~~l~v~~   83 (347)
                      +.++|||+|||+++++++|+++|++||.|..+++++++.+|+++|||||+|.+.++|.+|++. |+..+.|  ++|.|++
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            456799999999999999999999999999999999999999999999999999999999985 9988876  8899876


Q ss_pred             C
Q psy630           84 S   84 (347)
Q Consensus        84 ~   84 (347)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.81  E-value=5.9e-20  Score=135.48  Aligned_cols=83  Identities=29%  Similarity=0.522  Sum_probs=78.2

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~~~   85 (347)
                      +.++|||+|||+++++++|+++|++||.|.++.++.++.+|.++|||||+|.+.++|+.|+. +|+..+.|++|+|.++.
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~   96 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR   96 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            45789999999999999999999999999999999999999999999999999999999997 59999999999999998


Q ss_pred             cccc
Q psy630           86 SHNR   89 (347)
Q Consensus        86 ~~~~   89 (347)
                      ++..
T Consensus        97 ~k~~  100 (102)
T d2cpza1          97 SKND  100 (102)
T ss_dssp             CSCC
T ss_pred             CCCC
Confidence            7654

>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=99.81  E-value=2.5e-20  Score=134.50  Aligned_cols=84  Identities=30%  Similarity=0.610  Sum_probs=77.7

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      .+.++|||+|||+++++++|+++|++||.|..+.+++++.+|.++|||||+|.+.++|+.|+.. ++..+.|++|.|.++
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            3567899999999999999999999999999999999999999999999999999999999975 999999999999988


Q ss_pred             Ccccc
Q psy630           85 DSHNR   89 (347)
Q Consensus        85 ~~~~~   89 (347)
                      .++..
T Consensus        83 ~~~~~   87 (90)
T d1x5sa1          83 GKSSD   87 (90)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            76543

>d1dcqa1 d.211.1.1 (A:369-522) Pyk2-associated protein beta {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Pyk2-associated protein beta
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=6.6e-20  Score=145.89  Aligned_cols=94  Identities=20%  Similarity=0.329  Sum_probs=85.6

Q ss_pred             CCCCCcHHHHHHc---CChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHH
Q psy630          252 DDNEKNIYEWAKE---GKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLD  328 (347)
Q Consensus       252 ~~~~~~~l~~a~~---~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh  328 (347)
                      +..|.|+||+|+.   .+..+++++|++ .|+++|.+|..|+||||+||..|+.+++++|++ +|++++.+|..|+||||
T Consensus        42 ~~~g~t~Lh~A~~~~~~~~~~iv~~Ll~-~gadin~~d~~g~TpLh~A~~~~~~~~v~~Ll~-~gad~~~~d~~g~tpL~  119 (154)
T d1dcqa1          42 HEPDETALHLAVRSVDRTSLHIVDFLVQ-NSGNLDKQTGKGSTALHYCCLTDNAECLKLLLR-GKASIEIANESGETPLD  119 (154)
T ss_dssp             SSTTCBHHHHHHHHCCTTTHHHHHHHHH-HCSCTTCCCTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCHHH
T ss_pred             CCCCCchHHHHHHhcCCCCHHHHHHHHH-cCCChhhhhhhhccccccccccccccccccccc-cCccccccCCCCCCHHH
Confidence            4568899999885   355678888888 699999999999999999999999999999999 79999999999999999


Q ss_pred             HHHHcCCHHHHHHHHhCCC
Q psy630          329 YAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       329 ~A~~~~~~~~v~~Ll~~GA  347 (347)
                      +|+..|+.+++++|++.|+
T Consensus       120 ~A~~~~~~~i~~~L~~~~~  138 (154)
T d1dcqa1         120 IAKRLKHEHCEELLTQALS  138 (154)
T ss_dssp             HHHHTTCHHHHHHHHHHHT
T ss_pred             HHHHcCCHHHHHHHHHhCC
Confidence            9999999999999998764

>d1myoa_ d.211.1.1 (A:) Myotrophin {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Myotrophin
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.80  E-value=2.7e-20  Score=141.55  Aligned_cols=89  Identities=28%  Similarity=0.356  Sum_probs=82.7

Q ss_pred             cHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCCH
Q psy630          257 NIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEHT  336 (347)
Q Consensus       257 ~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~~  336 (347)
                      |+|.+|+..+..+++++|++ .|++++.+|..|+||||+||..|+.+++++|++ .|+++|.+|..|+||||+|+..|+.
T Consensus         4 tpL~~A~~~g~~~~v~~Ll~-~g~d~n~~~~~g~t~lh~A~~~~~~~~~~~ll~-~g~din~~d~~g~tpLh~A~~~~~~   81 (118)
T d1myoa_           4 KEFMWALKNGDLDEVKDYVA-KGEDVNRTLEGGRKPLHYAADCGQLEILEFLLL-KGADINAPDKHHITPLLSAVYEGHV   81 (118)
T ss_dssp             HHHHHHHHTTCHHHHHHHHT-TTCCCCCCSSSSCCTTHHHHHHSTTTHHHHHHH-SSCTTTCCSSSCSCHHHHHHTTTCC
T ss_pred             hHHHHHHHCCCHHHHHHHHH-hhhcccccccccccccccccccccccccccccc-ccceeeecccccccchhhhhhcCch
Confidence            67888888888888888888 799999999999999999999999999999999 7999999999999999999999999


Q ss_pred             HHHHHHHhCCC
Q psy630          337 DLIEYLVNSGS  347 (347)
Q Consensus       337 ~~v~~Ll~~GA  347 (347)
                      +++++|+++||
T Consensus        82 ~~v~~Ll~~Ga   92 (118)
T d1myoa_          82 SCVKLLLSKGA   92 (118)
T ss_dssp             HHHHHHHTTCC
T ss_pred             hhhhhhhcccc
Confidence            99999999996

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

Probab=99.80  E-value=6.7e-20  Score=143.38  Aligned_cols=86  Identities=26%  Similarity=0.507  Sum_probs=79.7

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~   82 (347)
                      .+...++|||+|||+++|+++|+++|++||.|.+|+|++++.||+++|||||+|.+.++|..|++ +|+..|.|+.|+|.
T Consensus        38 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~  117 (139)
T d1u6fa1          38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            44556789999999999999999999999999999999999999999999999999999999998 49999999999999


Q ss_pred             CCCcccc
Q psy630           83 PSDSHNR   89 (347)
Q Consensus        83 ~~~~~~~   89 (347)
                      ++.++..
T Consensus       118 ~a~~~~~  124 (139)
T d1u6fa1         118 LAASGHQ  124 (139)
T ss_dssp             ESSCCCC
T ss_pred             EcCCCCC
Confidence            9876554

>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=99.80  E-value=3.4e-20  Score=129.05  Aligned_cols=75  Identities=35%  Similarity=0.690  Sum_probs=72.2

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630           10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus        10 ~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      +|||+|||+++|+++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++++++.++|++|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEEC
Confidence            599999999999999999999999999999999999999999999999999999999999999999999999765

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=8.8e-20  Score=132.42  Aligned_cols=85  Identities=32%  Similarity=0.575  Sum_probs=77.5

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCC-CCCceeEEEEEEcCHHHHHHHHh-c-CCCccCCcccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKN-TGLSKGFGFVTFQNKEAVDKVFS-T-DSHVLEGSRLS   80 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~-t~~~~g~afV~f~~~~~a~~a~~-~-~~~~~~g~~l~   80 (347)
                      .....++|||+|||+++++++|+++|++||.|..++|++++. +|+++|||||+|.+.++|.+|+. + ++..+.|++|.
T Consensus         4 ~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~   83 (94)
T d2cpha1           4 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   83 (94)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEE
Confidence            345678899999999999999999999999999999998754 79999999999999999999997 4 89999999999


Q ss_pred             ccCCCccc
Q psy630           81 IQPSDSHN   88 (347)
Q Consensus        81 v~~~~~~~   88 (347)
                      |.++.+..
T Consensus        84 V~~A~~~~   91 (94)
T d2cpha1          84 LEWADSEV   91 (94)
T ss_dssp             EEECCCCC
T ss_pred             EEEcCCCC
Confidence            99997754

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=6.3e-20  Score=136.04  Aligned_cols=84  Identities=30%  Similarity=0.672  Sum_probs=78.2

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      +..++|||+|||+++++++|+++|++||.|.+|++++++.||+++|||||+|.+.++|..|+.. ++..+.|+.|.|.++
T Consensus         6 ~~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a   85 (104)
T d1p1ta_           6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4457899999999999999999999999999999999999999999999999999999999975 999999999999998


Q ss_pred             Ccccc
Q psy630           85 DSHNR   89 (347)
Q Consensus        85 ~~~~~   89 (347)
                      .+...
T Consensus        86 ~~~~~   90 (104)
T d1p1ta_          86 ASEKN   90 (104)
T ss_dssp             TCTTH
T ss_pred             CCCCC
Confidence            76543

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=1.2e-19  Score=130.72  Aligned_cols=85  Identities=15%  Similarity=0.329  Sum_probs=76.6

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI   81 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v   81 (347)
                      ++..+.++|||+|||+++|+++|+++|++||.|..+++++++.++  +|||||+|.+.++|..|+.. ++..+.|+.|+|
T Consensus         3 ~d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v   80 (90)
T d2cqia1           3 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKV   80 (90)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            455677899999999999999999999999999999999987544  79999999999999999985 999999999999


Q ss_pred             cCCCcccc
Q psy630           82 QPSDSHNR   89 (347)
Q Consensus        82 ~~~~~~~~   89 (347)
                      .++.++..
T Consensus        81 ~~a~~~~~   88 (90)
T d2cqia1          81 NWATTPSS   88 (90)
T ss_dssp             EECCCTTC
T ss_pred             EEcCCCCC
Confidence            99876543

>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=99.79  E-value=1.5e-19  Score=132.63  Aligned_cols=89  Identities=20%  Similarity=0.452  Sum_probs=80.7

Q ss_pred             CCccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-------CCCc
Q psy630            1 MSNSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-------DSHV   73 (347)
Q Consensus         1 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-------~~~~   73 (347)
                      |.++..+.++|||+|||+++|+++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|+..       ++..
T Consensus         1 ~P~~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~   80 (98)
T d1x4ha1           1 LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLK   80 (98)
T ss_dssp             CCCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEE
T ss_pred             CccCCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcE
Confidence            456778889999999999999999999999999999999999999999999999999999999999974       3677


Q ss_pred             cCCccccccCCCcccc
Q psy630           74 LEGSRLSIQPSDSHNR   89 (347)
Q Consensus        74 ~~g~~l~v~~~~~~~~   89 (347)
                      +.|+.|+|.++.++.+
T Consensus        81 ~~gr~l~v~~a~~k~~   96 (98)
T d1x4ha1          81 LDGRQLKVDLAVTRDE   96 (98)
T ss_dssp             SSSCEEEEECCCCCCC
T ss_pred             ECCEEEEEEECCCCCc
Confidence            8999999999987543

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.79  E-value=9.7e-20  Score=127.44  Aligned_cols=75  Identities=31%  Similarity=0.541  Sum_probs=71.2

Q ss_pred             eEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630           10 KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus        10 ~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      +|||+|||+++++++|+++|++||.|.+++++.++ +|+++|||||+|.+.++|+.|+.. |+..+.|++|+|.++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            69999999999999999999999999999999987 799999999999999999999985 9999999999998764

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=7.9e-20  Score=129.70  Aligned_cols=79  Identities=28%  Similarity=0.501  Sum_probs=73.3

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCeeE-EEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCccc
Q psy630           11 IFVGNLPWTVSHNELKKFFSEYGQIMN-ASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDSHN   88 (347)
Q Consensus        11 l~V~nLp~~~t~~~l~~~f~~~G~i~~-~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~~~   88 (347)
                      |||+|||+++|+++|+++|++||.|.. +++++++.+|+++|||||+|.+.++|.+|++. ++..+.|++|+|.++.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            799999999999999999999999976 47899999999999999999999999999974 9999999999999988765


Q ss_pred             c
Q psy630           89 R   89 (347)
Q Consensus        89 ~   89 (347)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.79  E-value=2.1e-19  Score=128.03  Aligned_cols=78  Identities=31%  Similarity=0.615  Sum_probs=71.7

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCC---CceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCc
Q psy630           11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTG---LSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDS   86 (347)
Q Consensus        11 l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~---~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~   86 (347)
                      |||+|||+++|+++|+++|++||.|.+++|++++.++   .++|||||+|.+.++|.+|+.. ++..+.|+.|.|.++.+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            7999999999999999999999999999999987765   4789999999999999999975 99999999999999865


Q ss_pred             cc
Q psy630           87 HN   88 (347)
Q Consensus        87 ~~   88 (347)
                      ..
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>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=99.79  E-value=6.8e-20  Score=130.78  Aligned_cols=81  Identities=20%  Similarity=0.404  Sum_probs=71.0

Q ss_pred             CCCeEEEeCCCCCCC-HHHHHHHHhccCCeeEEEEeee-CCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630            7 QLNKIFVGNLPWTVS-HNELKKFFSEYGQIMNASVMFD-KNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t-~~~l~~~f~~~G~i~~~~i~~~-~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      +.++|||+|||++++ +++|+++|++||.|.+++|+++ +.+++++|||||+|.+.++|.+|+++|+..+.|+.|.|.++
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEEc
Confidence            568999999999986 5569999999999999998764 56799999999999999999999988999999999999998


Q ss_pred             Ccc
Q psy630           85 DSH   87 (347)
Q Consensus        85 ~~~   87 (347)
                      .++
T Consensus        83 ~~k   85 (86)
T d2ghpa3          83 DKK   85 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            764

>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=99.78  E-value=1e-19  Score=128.50  Aligned_cols=78  Identities=13%  Similarity=0.268  Sum_probs=67.6

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCc
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDS   86 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~   86 (347)
                      ++|||+|||+++|+++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|++|+.. |+..+.|++|.|.++.|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            6899999999999999999999999999998888888899999999999999999999985 99999999999998875

>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=99.78  E-value=3.4e-19  Score=126.64  Aligned_cols=77  Identities=19%  Similarity=0.321  Sum_probs=72.6

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      ..++|||+|||+++|+++|+++|++||.|..|++++++ +|+++|||||+|.+.++|.+|++.++..+.|+.|.|.++
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~   81 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFK   81 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEc
Confidence            46899999999999999999999999999999998876 799999999999999999999999999999999999765

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=6.5e-19  Score=127.55  Aligned_cols=84  Identities=27%  Similarity=0.638  Sum_probs=76.4

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI   81 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v   81 (347)
                      +.....++|||+|||+++++++|+++|++||.|..|++++++  +.++|||||+|.+.++|.+|+.. ++..+.|+.|.|
T Consensus         6 ~~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V   83 (93)
T d2cq3a1           6 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV   83 (93)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            445667899999999999999999999999999999999886  44799999999999999999975 999999999999


Q ss_pred             cCCCccc
Q psy630           82 QPSDSHN   88 (347)
Q Consensus        82 ~~~~~~~   88 (347)
                      .++.++.
T Consensus        84 ~~A~~r~   90 (93)
T d2cq3a1          84 NNATARV   90 (93)
T ss_dssp             EECCSSC
T ss_pred             EecCcCC
Confidence            9998754

>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=99.77  E-value=3.2e-19  Score=128.13  Aligned_cols=81  Identities=27%  Similarity=0.543  Sum_probs=74.0

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      ...+|||+|||+++++++|+++|++||.|..++|+.++  +.++|||||+|.+.++|++|+.. ++..+.|+.|.|.++.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~   84 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   84 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            35689999999999999999999999999999999886  45789999999999999999975 9999999999999998


Q ss_pred             cccc
Q psy630           86 SHNR   89 (347)
Q Consensus        86 ~~~~   89 (347)
                      ++.+
T Consensus        85 ~~~~   88 (89)
T d1cvja2          85 SRKE   88 (89)
T ss_dssp             CTTT
T ss_pred             CCCC
Confidence            7643

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=5.8e-19  Score=133.10  Aligned_cols=105  Identities=14%  Similarity=0.240  Sum_probs=85.1

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      ++..++|||+|||+++++++|+++|++||.|.+|++..+   +.++|||||+|.+.++|..|++. ++..|.|+.|.|.+
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~   80 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLY   80 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            456789999999999999999999999999999998754   66789999999999999999975 99999999999998


Q ss_pred             CCcccccchhhhhhcccccccccCCcccccchhhHHHHhhcccc
Q psy630           84 SDSHNRMAENMEDRFNQACDYLPSLVKKLDSSTLLKFYALYKQA  127 (347)
Q Consensus        84 ~~~~~~~~~~~~~~f~~~~~~v~~l~~~~~~e~l~~~f~~fg~v  127 (347)
                      +.+....               .........+.+..+...||.-
T Consensus        81 a~~~~~~---------------~~~~~~~~~~~~~~~~~~~g~~  109 (114)
T d2f9da1          81 YNANRAF---------------QKMDTKKKEEQLKLLKEKYGIN  109 (114)
T ss_dssp             CCHHHHT---------------TTSCHHHHHHHHHHHHHHHCCC
T ss_pred             cCCCchh---------------hhhHHHHHHHHHHHHHHHhCCC
Confidence            7653221               1122234456677777777753

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.76  E-value=5e-20  Score=132.76  Aligned_cols=82  Identities=24%  Similarity=0.334  Sum_probs=74.9

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccC
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQP   83 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~   83 (347)
                      .+...++|||+|||+++++++|+++|++||.|..+.++.+ .+|+++|||||+|.+.++|++|+++++..+.|++|+|.+
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~   87 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEK   87 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEe
Confidence            3455678999999999999999999999999999888765 479999999999999999999998899999999999998


Q ss_pred             CCc
Q psy630           84 SDS   86 (347)
Q Consensus        84 ~~~   86 (347)
                      +.+
T Consensus        88 ak~   90 (91)
T d1fjeb1          88 PKG   90 (91)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            865

>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=99.75  E-value=1.4e-18  Score=120.29  Aligned_cols=74  Identities=18%  Similarity=0.313  Sum_probs=68.2

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      ++|||+|||+++++++|+++|++||.|..+++++++.  .+++||||+|.+.++|.+|+.++++.|+|++|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            5899999999999999999999999999999999874  3457999999999999999998999999999998754

>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=99.75  E-value=1.4e-18  Score=128.14  Aligned_cols=86  Identities=22%  Similarity=0.369  Sum_probs=77.1

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCee--------EEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCcc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIM--------NASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVL   74 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~--------~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~   74 (347)
                      +..+.++|||+|||+++|+++|+++|++||.|.        .+.+.+++.+|+++|||||+|.+.++|.+|++. ++..+
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            445678999999999999999999999999874        567778888999999999999999999999985 99999


Q ss_pred             CCccccccCCCcccc
Q psy630           75 EGSRLSIQPSDSHNR   89 (347)
Q Consensus        75 ~g~~l~v~~~~~~~~   89 (347)
                      .|+.|+|.++.++..
T Consensus        84 ~gr~i~V~~a~~~~p   98 (101)
T d2cpea1          84 QGSKLKVSLARKKPP   98 (101)
T ss_dssp             TTEECEEECSSCCCC
T ss_pred             CCEEEEEEEcCCCCC
Confidence            999999999977543

>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=99.75  E-value=3.2e-18  Score=125.82  Aligned_cols=80  Identities=20%  Similarity=0.544  Sum_probs=73.8

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      .+.++|||+|||+++++++|+++|++||.|..+.+..+. ++.++|||||+|.+.++|.+|++. ||..+.|+++.|.++
T Consensus        16 ~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          16 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            445799999999999999999999999999999998885 789999999999999999999985 999999999999877


Q ss_pred             Cc
Q psy630           85 DS   86 (347)
Q Consensus        85 ~~   86 (347)
                      .|
T Consensus        95 ~P   96 (101)
T d1x5oa1          95 EP   96 (101)
T ss_dssp             SC
T ss_pred             CC
Confidence            65

>d1bi7b_ d.211.1.1 (B:) Cell cycle inhibitor p16ink4A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Cell cycle inhibitor p16ink4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=9.3e-19  Score=134.34  Aligned_cols=96  Identities=22%  Similarity=0.259  Sum_probs=86.4

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCc-hHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGL-NCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~-tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      +++..+..|.+++|+|+.| +.+++++|++ .|++++.++..|. ||||+||.+|+.+++++|++ .|++++.+|..|+|
T Consensus        28 d~n~~~~~g~t~l~~a~~g-~~~~v~~Ll~-~ga~~~~~~~~~~~~~L~~A~~~g~~~~v~~Ll~-~ga~~~~~d~~G~T  104 (125)
T d1bi7b_          28 NPNAPNSYGRRPIQVMMMG-SARVAELLLL-HGAEPNCADPATLTRPVHDAAREGFLDTLVVLHR-AGARLDVRDAWGRL  104 (125)
T ss_dssp             CTTCCCSSSCCTTTSSCTT-CHHHHHHHHT-TTCCCCCCCTTTCCCHHHHHHHHTCHHHHHHHHH-HTCCSSCCCTTCCC
T ss_pred             ccccccccccccccccccc-cccccccccc-cccccccccccccccccccccccccccccccccc-cccccccccCCCCC
Confidence            5677888999999988765 5668888888 7999999998876 69999999999999999999 69999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHHhC
Q psy630          326 GLDYAKAIEHTDLIEYLVNS  345 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~  345 (347)
                      |||+|+..|+.+++++|++.
T Consensus       105 ~l~~A~~~g~~~~v~~Llsa  124 (125)
T d1bi7b_         105 PVDLAEELGHRDVARYLRAA  124 (125)
T ss_dssp             HHHHHHHHTCHHHHHHHSSC
T ss_pred             HHHHHHHcCCHHHHHHHHhc
Confidence            99999999999999999853

>d1oy3d_ d.211.1.1 (D:) Transcription factor inhibitor I-kappa-B-beta, IKBB {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Transcription factor inhibitor I-kappa-B-beta, IKBB
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=5.2e-18  Score=145.86  Aligned_cols=99  Identities=20%  Similarity=0.154  Sum_probs=90.4

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccc-cCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQ-LDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~-~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      ..+..+..|.|+||+|+..+..+++++|++ .+.+.+. .+..|.||||+||..|+.+++++|++ +|++++.+|..|.|
T Consensus       150 ~in~~d~~g~TpLh~A~~~~~~~~v~~Ll~-~~~~~~~~~~~~g~TpL~~A~~~~~~~~v~~Ll~-~gadin~~d~~g~t  227 (255)
T d1oy3d_         150 QLEAENYDGHTPLHVAVIHKDAEMVRLLRD-AGADLNKPEPTCGRTPLHLAVEAQAASVLELLLK-AGADPTARMYGGRT  227 (255)
T ss_dssp             GTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-HTCCTTCCCTTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCC
T ss_pred             ccccccccCcccccccccccccccccchhc-ccccccccccccccccccccccccHHHHHHHHHH-CCCCCCCCCCCCCC
Confidence            456677889999999999889899999988 5666665 46789999999999999999999999 79999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|+..++.+++++|+++||
T Consensus       228 ~L~~A~~~~~~~i~~~Ll~~Ga  249 (255)
T d1oy3d_         228 PLGSALLRPNPILARLLRAHGA  249 (255)
T ss_dssp             HHHHHHTSSCHHHHHHHHHTTC
T ss_pred             HHHHHHHCCCHHHHHHHHHcCC
Confidence            9999999999999999999998

>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=99.73  E-value=8.1e-19  Score=129.57  Aligned_cols=84  Identities=23%  Similarity=0.360  Sum_probs=78.0

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ...++|||+|||+++++++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|..|++. ++..+.|++|.|.++
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            3467999999999999999999999999999999998888899999999999999999999975 999999999999999


Q ss_pred             Ccccc
Q psy630           85 DSHNR   89 (347)
Q Consensus        85 ~~~~~   89 (347)
                      .++..
T Consensus        96 k~k~~  100 (102)
T d2cpxa1          96 KNKKQ  100 (102)
T ss_dssp             CCCSC
T ss_pred             CCccc
Confidence            87654

>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=99.73  E-value=6.9e-18  Score=124.74  Aligned_cols=86  Identities=21%  Similarity=0.279  Sum_probs=76.7

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCcccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ   82 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~   82 (347)
                      ++..+...|||+|||+++|+++|+++|+.+|.+....++.+..+++++|||||+|.+.++|++|+++++..|.||.|.|.
T Consensus        10 ~~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~   89 (104)
T d1wg5a_          10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIF   89 (104)
T ss_dssp             SSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEE
Confidence            34455668999999999999999999999999988777777778999999999999999999999989999999999998


Q ss_pred             CCCccc
Q psy630           83 PSDSHN   88 (347)
Q Consensus        83 ~~~~~~   88 (347)
                      ++.+..
T Consensus        90 ~~~~~~   95 (104)
T d1wg5a_          90 KSSRAE   95 (104)
T ss_dssp             EECTTT
T ss_pred             ECCHHH
Confidence            876654

>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=99.72  E-value=9.9e-18  Score=121.76  Aligned_cols=82  Identities=23%  Similarity=0.387  Sum_probs=73.2

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI   81 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v   81 (347)
                      +..+..++|||+|||+++|+++|+++|++||.|..+.+..+   +.++|||||+|.+.++|+.|++. +++.+.|++|+|
T Consensus         9 p~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V   85 (95)
T d1x4aa1           9 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV   85 (95)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            44567789999999999999999999999999999887543   56789999999999999999985 999999999999


Q ss_pred             cCCCcc
Q psy630           82 QPSDSH   87 (347)
Q Consensus        82 ~~~~~~   87 (347)
                      .++.+.
T Consensus        86 ~~a~~~   91 (95)
T d1x4aa1          86 EFPRSG   91 (95)
T ss_dssp             ECCCCC
T ss_pred             EeccCC
Confidence            998764

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=2.2e-18  Score=118.57  Aligned_cols=70  Identities=24%  Similarity=0.503  Sum_probs=66.9

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccc
Q psy630           11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLS   80 (347)
Q Consensus        11 l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~   80 (347)
                      |||+|||+++|+++|+++|++||.|..+++++++.++.++|||||+|.+.++|++|+.. |+..+.|+.++
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999999999999999999999999999999999999999999999999975 99999998874

>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=99.71  E-value=7e-18  Score=124.85  Aligned_cols=82  Identities=24%  Similarity=0.485  Sum_probs=73.1

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeC-CCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDK-NTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~-~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~   85 (347)
                      ..++|||+|||+++|+++|+++|++|| +..+.++.++ .++.++|||||+|.+.++|++|+.+++..+.|+.|+|.++.
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~a~   92 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVAD   92 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            347999999999999999999999999 7788877665 46889999999999999999998889999999999999987


Q ss_pred             cccc
Q psy630           86 SHNR   89 (347)
Q Consensus        86 ~~~~   89 (347)
                      ++..
T Consensus        93 ~~~~   96 (104)
T d1wi8a_          93 QAQD   96 (104)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7544

>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=99.71  E-value=9.5e-18  Score=122.13  Aligned_cols=81  Identities=15%  Similarity=0.322  Sum_probs=72.1

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCC-eeEEEEeeeC-CCCCceeEEEEEEcCHHHHHHHHhc---CCCccCCccccccC
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQ-IMNASVMFDK-NTGLSKGFGFVTFQNKEAVDKVFST---DSHVLEGSRLSIQP   83 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~-i~~~~i~~~~-~t~~~~g~afV~f~~~~~a~~a~~~---~~~~~~g~~l~v~~   83 (347)
                      ++|||+|||+++++++|+++|++||. |..+.++++. .+|+++|||||+|.+.++|..|++.   ++..+.|++|.|.+
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            58999999999999999999999996 8899998875 4688999999999999999999974   45667899999999


Q ss_pred             CCcccc
Q psy630           84 SDSHNR   89 (347)
Q Consensus        84 ~~~~~~   89 (347)
                      +.++..
T Consensus        82 A~p~~~   87 (96)
T d2disa1          82 AEPEID   87 (96)
T ss_dssp             SCSSCS
T ss_pred             cCCCCC
Confidence            987654

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=3.4e-18  Score=122.50  Aligned_cols=76  Identities=21%  Similarity=0.354  Sum_probs=69.0

Q ss_pred             cCCCeEEEeCCCCCCCHHHH---HHHHhccCCeeEEEEeeeCCCCCc---eeEEEEEEcCHHHHHHHHhc-CCCccCCcc
Q psy630            6 RQLNKIFVGNLPWTVSHNEL---KKFFSEYGQIMNASVMFDKNTGLS---KGFGFVTFQNKEAVDKVFST-DSHVLEGSR   78 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l---~~~f~~~G~i~~~~i~~~~~t~~~---~g~afV~f~~~~~a~~a~~~-~~~~~~g~~   78 (347)
                      -+.++|||+|||+++++++|   +++|++||.|..|.+++++.++.+   +|||||+|.+.++|.+|++. |+..+.|++
T Consensus         6 iq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~   85 (89)
T d2cpia1           6 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   85 (89)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             EecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEE
Confidence            45678999999999999999   778999999999999999877654   49999999999999999985 999999999


Q ss_pred             ccc
Q psy630           79 LSI   81 (347)
Q Consensus        79 l~v   81 (347)
                      |+|
T Consensus        86 lkv   88 (89)
T d2cpia1          86 LKA   88 (89)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            987

>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=99.70  E-value=5.7e-18  Score=121.18  Aligned_cols=78  Identities=23%  Similarity=0.531  Sum_probs=69.7

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSD   85 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~   85 (347)
                      ...++|||+|||+++|+++|+++|++||.|..++++     ..++|||||+|.+.++|++|+. +++.+.|++|.|.++.
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG-EDLIIKGISVHISNAE   76 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT-CEEEETTEEEEEECCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh-CCCEECCEEeEEEeCC
Confidence            456899999999999999999999999999998764     4568999999999999999986 7889999999999997


Q ss_pred             cccc
Q psy630           86 SHNR   89 (347)
Q Consensus        86 ~~~~   89 (347)
                      ++..
T Consensus        77 ~k~~   80 (88)
T d1wf0a_          77 PKHN   80 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.70  E-value=7.5e-18  Score=122.66  Aligned_cols=82  Identities=21%  Similarity=0.427  Sum_probs=72.7

Q ss_pred             ccccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccc
Q psy630            3 NSIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSI   81 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v   81 (347)
                      ...++.++|||+|||+++|+++|+++|++||.|..++.     ++.++|||||+|.+.++|.+|+. +++..+.|++|.|
T Consensus        11 ~~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V   85 (96)
T d1fjca_          11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL   85 (96)
T ss_dssp             STTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEE
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEE
Confidence            34566789999999999999999999999998766542     68899999999999999999997 5999999999999


Q ss_pred             cCCCcccc
Q psy630           82 QPSDSHNR   89 (347)
Q Consensus        82 ~~~~~~~~   89 (347)
                      .++.++..
T Consensus        86 ~~a~~k~~   93 (96)
T d1fjca_          86 YYTGEKGG   93 (96)
T ss_dssp             EECSSSCC
T ss_pred             EEeCCCCC
Confidence            99988654

>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=99.70  E-value=2.3e-17  Score=119.84  Aligned_cols=77  Identities=21%  Similarity=0.430  Sum_probs=70.3

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ...++|||+|||+++++++|+++|++||.|.+|+++++      +|||||+|.+.++|..|+.. ++..+.|+.|+|.++
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~a   89 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   89 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            44578999999999999999999999999999999865      58999999999999999975 999999999999998


Q ss_pred             Cccc
Q psy630           85 DSHN   88 (347)
Q Consensus        85 ~~~~   88 (347)
                      .++.
T Consensus        90 k~~p   93 (96)
T d1x4ga1          90 KESP   93 (96)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7643

>d1ycsb1 d.211.1.1 (B:327-456) 53BP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: 53BP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=1.2e-17  Score=128.92  Aligned_cols=98  Identities=24%  Similarity=0.241  Sum_probs=88.4

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCC-CCC
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS-DGD  324 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~-~g~  324 (347)
                      .+++..+..|.|+||+|+..+...++++|++ .+++++.+|..|+||||+||.+|+.+++++|++ +|++++.++. .|+
T Consensus        25 ~d~n~~d~~g~t~Lh~A~~~~~~~~~~~ll~-~g~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~-~ga~v~~~~~~~~~  102 (130)
T d1ycsb1          25 DDPSLPNDEGITALHNAVCAGHTEIVKFLVQ-FGVNVNAADSDGWTPLHCAASCNNVQVCKFLVE-SGAAVFAMTYSDMQ  102 (130)
T ss_dssp             SSCCCCCTTSCCHHHHHHHHTCHHHHHHHHH-HTCCTTCCCTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCSSSCC
T ss_pred             CCccccccccccccccccccccccccccccc-cccccccccccCcccccccchhhHHHHHHHHHH-cCCCcccccCCCCC
Confidence            4677888999999999999999999999998 799999999999999999999999999999999 7999998875 588


Q ss_pred             cHHHHH--HHcCCHHHHHHHHhC
Q psy630          325 YGLDYA--KAIEHTDLIEYLVNS  345 (347)
Q Consensus       325 TpLh~A--~~~~~~~~v~~Ll~~  345 (347)
                      ||++++  +..|+.+++++|+..
T Consensus       103 ~~~~~~~a~~~g~~eiv~~L~~~  125 (130)
T d1ycsb1         103 TAADKCEEMEEGYTQCSQFLYGV  125 (130)
T ss_dssp             CHHHHCCSSSTTCCCHHHHHHHH
T ss_pred             CHHHHHHHHHcChHHHHHHHHhH
Confidence            987766  567899999999875

>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=99.69  E-value=1.8e-17  Score=121.91  Aligned_cols=82  Identities=16%  Similarity=0.257  Sum_probs=73.4

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      .....+|||+|||+++|+++|+++|..|| +..+.++.+. ++.++|||||+|.+.++|++|++++++.|.||.|+|.++
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~s   89 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            45567999999999999999999999998 5578888876 589999999999999999999989999999999999887


Q ss_pred             Cccc
Q psy630           85 DSHN   88 (347)
Q Consensus        85 ~~~~   88 (347)
                      .+..
T Consensus        90 ~~~~   93 (102)
T d1weza_          90 STAG   93 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6654

>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=99.69  E-value=8.1e-18  Score=118.02  Aligned_cols=77  Identities=22%  Similarity=0.466  Sum_probs=67.8

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCC-ccCCccccccCCC
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSH-VLEGSRLSIQPSD   85 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~-~~~g~~l~v~~~~   85 (347)
                      +++|||+|||+++|+++|+++|++||.|..+.+.+      ++|||||+|.+.++|.+|++. ||. .+.|++|.|.++.
T Consensus         1 mn~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~   74 (80)
T d2cqha1           1 MNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSV   74 (80)
T ss_dssp             CCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcC
Confidence            46799999999999999999999999988776654      468999999999999999985 875 6999999999998


Q ss_pred             ccccc
Q psy630           86 SHNRM   90 (347)
Q Consensus        86 ~~~~~   90 (347)
                      ++..+
T Consensus        75 ~k~~r   79 (80)
T d2cqha1          75 SKKLR   79 (80)
T ss_dssp             CCCCC
T ss_pred             CcCcC
Confidence            86653

>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=99.69  E-value=2.6e-17  Score=117.25  Aligned_cols=78  Identities=21%  Similarity=0.366  Sum_probs=69.6

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ...++|||+|||+++++++|+++|++||.|..+.+.      +++|||||+|.+.++|..|+.. ++..+.|+.|.|.++
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~a   79 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA   79 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            445899999999999999999999999999887763      4578999999999999999985 999999999999998


Q ss_pred             Ccccc
Q psy630           85 DSHNR   89 (347)
Q Consensus        85 ~~~~~   89 (347)
                      .|+.+
T Consensus        80 kP~~~   84 (86)
T d2cpda1          80 KPVDK   84 (86)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            87543

>d1ot8a_ d.211.1.1 (A:) Neurogenic locus notch receptor domain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Neurogenic locus notch receptor domain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.69  E-value=7e-17  Score=134.39  Aligned_cols=94  Identities=22%  Similarity=0.252  Sum_probs=87.0

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..+.|+++.++..+...++..+.. .+.+++.+|..|.||||+||..|+.+++++||+ +|++++.+|..|+||
T Consensus       115 ~~~~~~~~~~t~l~~~~~~~~~~~~~~l~~-~~~~~~~~d~~g~TpL~~A~~~g~~~~v~~Ll~-~gad~n~~d~~g~Tp  192 (209)
T d1ot8a_         115 DINAADNSGKTALHWAAAVNNTEAVNILLM-HHANRDAQDDKDETPLFLAAREGSYEASKALLD-NFANREITDHMDRLP  192 (209)
T ss_dssp             CTTCBCTTSCBHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCH
T ss_pred             cccccCCCCCCcchhhcccCcceeeeeecc-ccccccccccccccccchhccccHHHHHHHHHH-CCCCCCCcCCCCCCH
Confidence            345667888999999998888888888888 789999999999999999999999999999999 799999999999999


Q ss_pred             HHHHHHcCCHHHHHHH
Q psy630          327 LDYAKAIEHTDLIEYL  342 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~L  342 (347)
                      ||+|+..|+.++|++|
T Consensus       193 l~~A~~~~~~~iv~lL  208 (209)
T d1ot8a_         193 RDVASERLHHDIVRLL  208 (209)
T ss_dssp             HHHHHHTTCHHHHHHH
T ss_pred             HHHHHHcCCHHHHhhc
Confidence            9999999999999987

>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=99.69  E-value=1.4e-17  Score=118.63  Aligned_cols=79  Identities=20%  Similarity=0.359  Sum_probs=69.2

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ....+|||+|||+++++++|+++|+.||.+....++.+..+|+++|||||+|.+.++|++|+.. |+..+.||+|+|..+
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3455799999999999999999999999987654455556899999999999999999999985 999999999998753

>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=99.69  E-value=2.8e-17  Score=116.86  Aligned_cols=77  Identities=29%  Similarity=0.554  Sum_probs=70.0

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      ...++|||+|||+++++++|+++|++||.|.+|++.++      +|||||+|.+.++|++|+.. ++..+.|+.|+|.++
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A   79 (86)
T d2cpja1           6 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA   79 (86)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            34568999999999999999999999999999999754      57999999999999999985 999999999999998


Q ss_pred             Cccc
Q psy630           85 DSHN   88 (347)
Q Consensus        85 ~~~~   88 (347)
                      .+..
T Consensus        80 ~~~~   83 (86)
T d2cpja1          80 CHSA   83 (86)
T ss_dssp             SCCS
T ss_pred             CCcC
Confidence            7654

>d1bd8a_ d.211.1.1 (A:) Cell cycle inhibitor p19ink4D {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Cell cycle inhibitor p19ink4D
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=6.9e-17  Score=128.52  Aligned_cols=97  Identities=23%  Similarity=0.233  Sum_probs=89.1

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      .+.+..+..+.++++.++..+...+.+++.+ .++++|.+|..|.||||+||..|+.+++++|+.  |++++.+|..|+|
T Consensus        59 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~-~~~~~n~~~~~~~t~L~~A~~~~~~~i~~~L~~--~~~~~~~d~~G~T  135 (156)
T d1bd8a_          59 ASPNVQDTSGTSPVHDAARTGFLDTLKVLVE-HGADVNVPDGTGALPIHLAVQEGHTAVVSFLAA--ESDLHRRDARGLT  135 (156)
T ss_dssp             CCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCSCCCCTTSCCHHHHHHHHTCHHHHHHHHT--TSCTTCCCTTSCC
T ss_pred             ccccccccccccccccccccccccccccccc-cccccccccCCCCeeeccccccccccccccccc--cccccccCCCCCC
Confidence            3456667788999999999999999999998 789999999999999999999999999998884  8999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHHhC
Q psy630          326 GLDYAKAIEHTDLIEYLVNS  345 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~  345 (347)
                      |||+|+..|+.+++++|+++
T Consensus       136 pL~~A~~~g~~~iv~~Ll~h  155 (156)
T d1bd8a_         136 PLELALQRGAQDLVDILQGH  155 (156)
T ss_dssp             HHHHHHHSCCHHHHHHHHTT
T ss_pred             HHHHHHHcCCHHHHHHHHhh
Confidence            99999999999999999986

>d1myoa_ d.211.1.1 (A:) Myotrophin {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Myotrophin
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.68  E-value=1.5e-18  Score=131.72  Aligned_cols=92  Identities=24%  Similarity=0.282  Sum_probs=81.7

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      .+++..+..|.|++|+|+..+...++++|.. .|+++|.+|..|+||||+|+.+|+.+++++|++ +|++++.+|..|.|
T Consensus        26 ~d~n~~~~~g~t~lh~A~~~~~~~~~~~ll~-~g~din~~d~~g~tpLh~A~~~~~~~~v~~Ll~-~Gad~~~~d~~G~t  103 (118)
T d1myoa_          26 EDVNRTLEGGRKPLHYAADCGQLEILEFLLL-KGADINAPDKHHITPLLSAVYEGHVSCVKLLLS-KGADKTVKGPDGLT  103 (118)
T ss_dssp             CCCCCCSSSSCCTTHHHHHHSTTTHHHHHHH-SSCTTTCCSSSCSCHHHHHHTTTCCHHHHHHHT-TCCCSSSSSSSTCC
T ss_pred             hcccccccccccccccccccccccccccccc-ccceeeecccccccchhhhhhcCchhhhhhhhc-ccccceeeCCCCCC
Confidence            3567778899999999998888889999888 899999999999999999999999999999999 79999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHH
Q psy630          326 GLDYAKAIEHTDLIEYLV  343 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll  343 (347)
                      |||+|..    +.++.||
T Consensus       104 ~l~~a~~----~~i~~LL  117 (118)
T d1myoa_         104 ALEATDN----QAIKALL  117 (118)
T ss_dssp             CCCTCSS----TTTGGGG
T ss_pred             HHHHHhH----HHHHHhc
Confidence            9999843    3455554

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=3.5e-17  Score=114.45  Aligned_cols=76  Identities=21%  Similarity=0.378  Sum_probs=68.7

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCcccccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQ   82 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~   82 (347)
                      +|+..++|||+|+|  +|+++|+++|++||.|.++.+.+      .+|||||+|.+.++|..|+.. |+..+.|++|+|.
T Consensus         1 ap~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~   72 (79)
T d2bz2a1           1 APRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDP------PRNCAFVTYEKMESADQAVAELNGTQVESVQLKVN   72 (79)
T ss_dssp             CCCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEET------TTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEECCC--CCHHHHHHHHhccCccceeeecc------CCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEE
Confidence            46788999999996  89999999999999999999864      357999999999999999975 9999999999999


Q ss_pred             CCCcc
Q psy630           83 PSDSH   87 (347)
Q Consensus        83 ~~~~~   87 (347)
                      ++.++
T Consensus        73 ~a~~~   77 (79)
T d2bz2a1          73 IARKQ   77 (79)
T ss_dssp             ECCSS
T ss_pred             EecCC
Confidence            98654

>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=99.68  E-value=1.6e-17  Score=124.43  Aligned_cols=83  Identities=14%  Similarity=0.318  Sum_probs=74.8

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      .....+|||+|||+++|+++|+++|+.||.+..+.++.+..+|.++|||||+|.+.++|++|+.+|+..|+||.|.|.++
T Consensus        15 ~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEE
T ss_pred             CCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEc
Confidence            45567999999999999999999999999998766666777899999999999999999999999999999999999877


Q ss_pred             Ccc
Q psy630           85 DSH   87 (347)
Q Consensus        85 ~~~   87 (347)
                      ...
T Consensus        95 ~~~   97 (112)
T d1wela1          95 TKK   97 (112)
T ss_dssp             CHH
T ss_pred             ChH
Confidence            654

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=1.2e-17  Score=123.32  Aligned_cols=81  Identities=17%  Similarity=0.245  Sum_probs=72.0

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPSD   85 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~~   85 (347)
                      ...++|||+|||+++|+++|+++|+.||.+..+.++....+|.++|||||+|.+.++|++|+.+++..|+|+.|.|.++.
T Consensus         6 ~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           6 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEEC
T ss_pred             CCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEECC
Confidence            34467999999999999999999999999887555555568999999999999999999999889999999999998765


Q ss_pred             c
Q psy630           86 S   86 (347)
Q Consensus        86 ~   86 (347)
                      .
T Consensus        86 ~   86 (103)
T d2cpya1          86 L   86 (103)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=99.67  E-value=1.9e-17  Score=119.17  Aligned_cols=80  Identities=23%  Similarity=0.384  Sum_probs=70.8

Q ss_pred             CCCeEEEeCCCCCCCHHHHH----HHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccc
Q psy630            7 QLNKIFVGNLPWTVSHNELK----KFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSI   81 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~----~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v   81 (347)
                      +.++|||+|||+++++++|+    ++|++||.|.+|++.+   +++++|||||+|.+.++|..|+.. ++..+.|+.|.|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            46899999999999999886    4689999999988754   477899999999999999999985 999999999999


Q ss_pred             cCCCcccc
Q psy630           82 QPSDSHNR   89 (347)
Q Consensus        82 ~~~~~~~~   89 (347)
                      .++.++..
T Consensus        79 ~~ak~~~~   86 (91)
T d1nu4a_          79 QYAKTDSD   86 (91)
T ss_dssp             EECSSCCT
T ss_pred             EEeCCCch
Confidence            99987654

>d1uoha_ d.211.1.1 (A:) 26S proteasome non-ATPase regulatory subunit 10, gankyrin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: 26S proteasome non-ATPase regulatory subunit 10, gankyrin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.1e-16  Score=135.09  Aligned_cols=95  Identities=20%  Similarity=0.224  Sum_probs=59.0

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +++..+..+.+++|+|+..+...+.++|.. .+.+++.+|..|+||||+|+..|+.+++++||+ .|++++.+|..|+||
T Consensus       128 d~~~~~~~~~t~L~~a~~~~~~~~~~~L~~-~~~~i~~~d~~g~TpL~~Aa~~g~~~~v~~LL~-~Gad~~~~d~~g~tp  205 (223)
T d1uoha_         128 NPDAKDHYEATAMHRAAAKGNLKMIHILLY-YKASTNIQDTEGNTPLHLACDEERVEEAKLLVS-QGASIYIENKEEKTP  205 (223)
T ss_dssp             CTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCSCCCCTTCCCHHHHHHHTTCHHHHHHHHH-TTCCSCCCCTTSCCH
T ss_pred             CCCCcCCCCCccchhhhhcCCcchhhhhcc-ccceeeeccCCCCceeccccccCcHHHHHHHHH-CCCCCCCCCCCCCCH
Confidence            445555566666666666666666666655 566666666666666666666666666666666 466666666666666


Q ss_pred             HHHHHHcCCHHHHHHHHh
Q psy630          327 LDYAKAIEHTDLIEYLVN  344 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~  344 (347)
                      ||+|. .|+.+++++||+
T Consensus       206 l~~A~-~~~~~i~~~Ll~  222 (223)
T d1uoha_         206 LQVAK-GGLGLILKRMVE  222 (223)
T ss_dssp             HHHCC-TTHHHHHHHHHC
T ss_pred             HHHHH-CCCHHHHhcccC
Confidence            66653 466666666653

>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=99.67  E-value=2.7e-17  Score=123.26  Aligned_cols=76  Identities=18%  Similarity=0.166  Sum_probs=68.1

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      .+..++|||+|||+++++++|+++|++||.|..|.|.      .++|||||+|.+.++|.+|+.. |+..|.|++|.|.+
T Consensus         7 ~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~   80 (111)
T d1whxa_           7 GRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEW   80 (111)
T ss_dssp             SEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEE
Confidence            4455789999999999999999999999999999874      3578999999999999999985 99999999999987


Q ss_pred             CCc
Q psy630           84 SDS   86 (347)
Q Consensus        84 ~~~   86 (347)
                      +..
T Consensus        81 a~~   83 (111)
T d1whxa_          81 API   83 (111)
T ss_dssp             EET
T ss_pred             CCC
Confidence            644

>d1bi7b_ d.211.1.1 (B:) Cell cycle inhibitor p16ink4A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Cell cycle inhibitor p16ink4A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=2.9e-17  Score=125.85  Aligned_cols=90  Identities=19%  Similarity=0.120  Sum_probs=79.3

Q ss_pred             CCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCC-cHHHHHHHc
Q psy630          255 EKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGD-YGLDYAKAI  333 (347)
Q Consensus       255 ~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~-TpLh~A~~~  333 (347)
                      +.++||.|+..++.+++++|++ .|+++|.+|..|.||||+|+ .|+.+++++|++ .|++++.++..|. ||||+|+..
T Consensus         3 ~~~~L~~Aa~~G~~~~v~~Ll~-~gad~n~~~~~g~t~l~~a~-~g~~~~v~~Ll~-~ga~~~~~~~~~~~~~L~~A~~~   79 (125)
T d1bi7b_           3 SADWLATAAARGRVEEVRALLE-AGANPNAPNSYGRRPIQVMM-MGSARVAELLLL-HGAEPNCADPATLTRPVHDAARE   79 (125)
T ss_dssp             STTHHHHHHHHTCHHHHHHHHT-TTCCTTCCCSSSCCTTTSSC-TTCHHHHHHHHT-TTCCCCCCCTTTCCCHHHHHHHH
T ss_pred             ChhHHHHHHHCCCHHHHHHHHH-cCCccccccccccccccccc-cccccccccccc-ccccccccccccccccccccccc
Confidence            3467777776666778888888 79999999999999999775 799999999999 7999999999876 699999999


Q ss_pred             CCHHHHHHHHhCCC
Q psy630          334 EHTDLIEYLVNSGS  347 (347)
Q Consensus       334 ~~~~~v~~Ll~~GA  347 (347)
                      |+.+++++|+++||
T Consensus        80 g~~~~v~~Ll~~ga   93 (125)
T d1bi7b_          80 GFLDTLVVLHRAGA   93 (125)
T ss_dssp             TCHHHHHHHHHHTC
T ss_pred             cccccccccccccc
Confidence            99999999999986

>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=99.66  E-value=4.6e-17  Score=116.07  Aligned_cols=72  Identities=26%  Similarity=0.329  Sum_probs=65.6

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh-cCCCccCCccccccCCCcc
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS-TDSHVLEGSRLSIQPSDSH   87 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~~~~~   87 (347)
                      ++|||+|||+++++++|+++|++||.|..++++++       |||||+|.+.++|+.|+. +++..|.|+.+.|.++..+
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            47999999999999999999999999999998643       899999999999999997 5999999999999887554

>d1oy3d_ d.211.1.1 (D:) Transcription factor inhibitor I-kappa-B-beta, IKBB {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Transcription factor inhibitor I-kappa-B-beta, IKBB
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.66  E-value=7.7e-17  Score=138.40  Aligned_cols=94  Identities=18%  Similarity=0.212  Sum_probs=87.0

Q ss_pred             cCCCCCcHHHHHHcCChHHHHHHHhhcCCCC---ccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHH
Q psy630          251 LDDNEKNIYEWAKEGKLDMLVKQLTKLKDFN---INQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGL  327 (347)
Q Consensus       251 ~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~---~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpL  327 (347)
                      .+.+|.||||+|+..+...++++|+. .+++   ++.+|..|.||||+||..|+.+++++|++ .|++++.+|..|.|||
T Consensus         5 i~~~G~t~Lh~A~~~~~~~~v~~Ll~-~~a~~~~i~~~~~~g~TpL~~A~~~g~~~iv~~Ll~-~ga~i~~~d~~g~tpL   82 (255)
T d1oy3d_           5 VTEDGDTALHLAVIHQHEPFLDFLLG-FSAGHEYLDLQNDLGQTALHLAAILGEASTVEKLYA-AGAGVLVAERGGHTAL   82 (255)
T ss_dssp             CCTTCCCHHHHHHHTTCHHHHHHHHH-HHTTSGGGGCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCSSCCCTTSCCHH
T ss_pred             CCcCCCCHHHHHHHcCCHHHHHHHHH-cCCCcccccCcCCCCCCccchHHhhccccccccccc-ccccccccccccchhh
Confidence            56889999999999999999999987 5655   67788999999999999999999999999 7999999999999999


Q ss_pred             HHHHHcCCHHHHHHHHhCC
Q psy630          328 DYAKAIEHTDLIEYLVNSG  346 (347)
Q Consensus       328 h~A~~~~~~~~v~~Ll~~G  346 (347)
                      |+|+..++.+++++|++.+
T Consensus        83 ~~A~~~~~~~~~~~Ll~~~  101 (255)
T d1oy3d_          83 HLACRVRAHTCACVLLQPR  101 (255)
T ss_dssp             HHHTTTTCHHHHHHHSSSC
T ss_pred             hhhhccCchHHHHHHHhhc
Confidence            9999999999999998765

>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=99.65  E-value=1.7e-16  Score=112.02  Aligned_cols=75  Identities=13%  Similarity=0.238  Sum_probs=66.6

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCcc-CCccccccC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVL-EGSRLSIQP   83 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~-~g~~l~v~~   83 (347)
                      .+.++|||+|||+++++++|+++|++||.|..++++++     .+|||||+|.+.++|..|+.. ++..+ +|++|.|.+
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~   80 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITF   80 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEE
Confidence            44679999999999999999999999999999999754     368999999999999999985 88888 568999988


Q ss_pred             CC
Q psy630           84 SD   85 (347)
Q Consensus        84 ~~   85 (347)
                      +.
T Consensus        81 ak   82 (83)
T d2b0ga1          81 AK   82 (83)
T ss_dssp             CC
T ss_pred             ec
Confidence            74

>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=99.65  E-value=2.1e-16  Score=112.92  Aligned_cols=77  Identities=22%  Similarity=0.359  Sum_probs=67.4

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCcc-CCccccccC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVL-EGSRLSIQP   83 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~-~g~~l~v~~   83 (347)
                      .+.++|||+|||+++++++|+++|++||.|..+.+..    ++++|||||+|.+.++|.+|+.. ++..+ +|++|+|.+
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~   83 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            3467999999999999999999999999998877654    45678999999999999999975 88877 589999998


Q ss_pred             CCc
Q psy630           84 SDS   86 (347)
Q Consensus        84 ~~~   86 (347)
                      +.+
T Consensus        84 sk~   86 (88)
T d2adca2          84 SKS   86 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            765

>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=99.65  E-value=1.5e-16  Score=118.72  Aligned_cols=75  Identities=24%  Similarity=0.399  Sum_probs=68.0

Q ss_pred             CCeEEEeCCCC-CCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630            8 LNKIFVGNLPW-TVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus         8 ~~~l~V~nLp~-~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      .++|||+|||+ .+|+++|+++|++||.|..|.|++++     +|||||+|.+.++|.+|+.. ++..+.|+.|.|.++.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            46899999976 59999999999999999999998764     68999999999999999985 9999999999999876


Q ss_pred             cc
Q psy630           86 SH   87 (347)
Q Consensus        86 ~~   87 (347)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.65  E-value=5.4e-18  Score=121.97  Aligned_cols=79  Identities=18%  Similarity=0.470  Sum_probs=69.4

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEe-----eeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCcccccc
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVM-----FDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQ   82 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~-----~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~   82 (347)
                      .|+|||+|||+++|+++|+++|++||.+..+.+.     .+..+++++|||||+|.+.++|++|+.+|+..+.|+.|+|.
T Consensus         1 aRrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIR   80 (90)
T ss_dssp             CCEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCCB
T ss_pred             CCEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEEC
Confidence            3789999999999999999999999987766543     45567889999999999999999999889999999999998


Q ss_pred             CCCc
Q psy630           83 PSDS   86 (347)
Q Consensus        83 ~~~~   86 (347)
                      ++..
T Consensus        81 r~k~   84 (90)
T d1u2fa_          81 RPHD   84 (90)
T ss_dssp             CTTC
T ss_pred             CCCC
Confidence            6543

>d1ixva_ d.211.1.1 (A:) 26S proteasome non-ATPase regulatory subunit 10, gankyrin {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: 26S proteasome non-ATPase regulatory subunit 10, gankyrin
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.65  E-value=6.9e-17  Score=136.42  Aligned_cols=98  Identities=22%  Similarity=0.227  Sum_probs=87.1

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      .....+..|.+++|+|+..+...++++|+...+.+++.+|..|+||||+|+..|+.+++++||++.|++++.+|..|+||
T Consensus       130 ~~~~~~~~g~t~l~~a~~~~~~~~~~~Ll~~~~~~in~~d~~g~TpLh~A~~~~~~~~v~~Ll~~~gad~~~~d~~g~t~  209 (229)
T d1ixva_         130 SVRIKDKFNQIPLHRAASVGSLKLIELLCGLGKSAVNWQDKQGWTPLFHALAEGHGDAAVLLVEKYGAEYDLVDNKGAKA  209 (229)
T ss_dssp             CSCCCCTTSCCHHHHHHHHTCHHHHHHHHTTTCCCSCCCCTTSCCHHHHHHHTTCHHHHHHHHHHHCCCSCCCCTTSCCT
T ss_pred             cccccCCCCCCccchhhhcccccccccccccccccccccccccCCchhhhcccccHHHHHHHHHhcCCCCCCcCCCCCCH
Confidence            34556788899999998888888888888855688999999999999999999999999999975699999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+   +.+++++|+++||
T Consensus       210 l~~A~---~~~~~~~Ll~~g~  227 (229)
T d1ixva_         210 EDVAL---NEQVKKFFLNNVV  227 (229)
T ss_dssp             GGGCS---CHHHHHHHHHHCC
T ss_pred             HHHHh---hHHHHHHHHHcCC
Confidence            99998   3589999999997

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=1.4e-16  Score=115.98  Aligned_cols=74  Identities=30%  Similarity=0.585  Sum_probs=66.1

Q ss_pred             cCCCeEEEeCCCC-CCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccC
Q psy630            6 RQLNKIFVGNLPW-TVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQP   83 (347)
Q Consensus         6 ~~~~~l~V~nLp~-~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~   83 (347)
                      ...++|||+|||+ .+++++|+++|++||.|..+.|        ++|||||+|.+.++|++|+.. |+..+.|++|+|.+
T Consensus        13 ~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   84 (98)
T d1wf2a_          13 SMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINL   84 (98)
T ss_dssp             SCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3456899999975 6888999999999999999988        368999999999999999985 99999999999999


Q ss_pred             CCcc
Q psy630           84 SDSH   87 (347)
Q Consensus        84 ~~~~   87 (347)
                      +.++
T Consensus        85 a~~~   88 (98)
T d1wf2a_          85 AAEP   88 (98)
T ss_dssp             TTSC
T ss_pred             CCCC
Confidence            8654

>d1wdya_ d.211.1.1 (A:) RNase L, 2-5a-dependent ribonuclease {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: RNase L, 2-5a-dependent ribonuclease
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=2.6e-16  Score=137.07  Aligned_cols=100  Identities=26%  Similarity=0.373  Sum_probs=86.7

Q ss_pred             CCcccCCCCCcHHHH----HHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCC
Q psy630          247 DESQLDDNEKNIYEW----AKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSD  322 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~----a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~  322 (347)
                      +.+..+..+.++.+.    +..++...+++.|.+ .|++++.+|..|.||||+|+..|+.+++++||++.|+++|.+|.+
T Consensus       174 ~i~~~~~~~~~~~~~~~~~~~~~~~~~i~~~Li~-~ga~~n~~~~~g~t~L~~a~~~~~~~~v~~lL~~~g~din~~d~~  252 (285)
T d1wdya_         174 DVNACDNMGRNALIHALLSSDDSDVEAITHLLLD-HGADVNVRGERGKTPLILAVEKKHLGLVQRLLEQEHIEINDTDSD  252 (285)
T ss_dssp             CTTCCCTTSCCHHHHHHHCSCTTTHHHHHHHHHH-TTCCSSCCCTTSCCHHHHHHHTTCHHHHHHHHHSSSCCTTCCCTT
T ss_pred             CcccccCCCCcccccccccccchHHHHHHHHHHH-CCCCCCccCCCCCCccchhhhcCcHHHHHHHHHcCCCCCcCCCCC
Confidence            445555666554443    345666788888888 799999999999999999999999999999997569999999999


Q ss_pred             CCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          323 GDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       323 g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |.||||+|+..|+.++|++||++||
T Consensus       253 G~TpL~~A~~~~~~eiv~~Ll~~GA  277 (285)
T d1wdya_         253 GKTALLLAVELKLKKIAELLCKRGA  277 (285)
T ss_dssp             SCCHHHHHHHTTCHHHHHHHHHHSS
T ss_pred             CCCHHHHHHHcCCHHHHHHHHHCCC
Confidence            9999999999999999999999998

>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=99.64  E-value=2.6e-16  Score=128.63  Aligned_cols=85  Identities=29%  Similarity=0.600  Sum_probs=79.3

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCccccccCC
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSRLSIQPS   84 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~~   84 (347)
                      ....++|||+|||+.+|+++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|.+|++.+++.+.|+.|.|.++
T Consensus        94 ~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~~~~~~~~G~~i~V~~A  173 (183)
T d1u1qa_          94 HLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA  173 (183)
T ss_dssp             TCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHTSSCEEETTEEEEEEEC
T ss_pred             ccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHHhCCCeECCEEEEEEec
Confidence            45568999999999999999999999999999999999999999999999999999999999998888999999999998


Q ss_pred             Ccccc
Q psy630           85 DSHNR   89 (347)
Q Consensus        85 ~~~~~   89 (347)
                      .++.+
T Consensus       174 ~~k~e  178 (183)
T d1u1qa_         174 LSKQE  178 (183)
T ss_dssp             CCHHH
T ss_pred             CCccc
Confidence            87654

>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=99.64  E-value=1.8e-16  Score=109.42  Aligned_cols=71  Identities=28%  Similarity=0.423  Sum_probs=62.7

Q ss_pred             EEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCCccc
Q psy630           11 IFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSDSHN   88 (347)
Q Consensus        11 l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~~~~   88 (347)
                      |||+|||+++++++|+++|++|| +..+.+      ++++|||||+|.+.++|.+|+.. |+..+.|++|.|+++....
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d~   72 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTDA   72 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCSTT
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCCC
Confidence            79999999999999999999999 444443      55789999999999999999975 9999999999999986543

>d1awcb_ d.211.1.1 (B:) GA bindinig protein (GABP) beta 1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: GA bindinig protein (GABP) beta 1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=6.1e-16  Score=122.20  Aligned_cols=90  Identities=27%  Similarity=0.347  Sum_probs=80.9

Q ss_pred             cCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHH
Q psy630          251 LDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA  330 (347)
Q Consensus       251 ~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A  330 (347)
                      ....+.+.++.++......+++++.. .+.+++.+|..|+||||+||..|+.+++++|++ +|++++.+|..|.||||+|
T Consensus        63 ~~~~~~~~~~~~~~~~~~~~~~~l~~-~~~~~~~~~~~g~T~L~~A~~~g~~~iv~~ll~-~gad~~~~d~~g~Tpl~~A  140 (153)
T d1awcb_          63 RTKVDRTPLHMAASEGHANIVEVLLK-HGADVNAKDMLKMTALHWATEHNHQEVVELLIK-YGADVHTQSKFCKTAFDIS  140 (153)
T ss_dssp             CCTTCCCHHHHHHHHTCHHHHHHHHT-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHH
T ss_pred             cccccccccccccccccceeeecccc-cCCccccccccCchHHHhhhhcchhheeeeccc-cccCCcccCCCCCCHHHHH
Confidence            34555677777777777778888877 789999999999999999999999999999999 7999999999999999999


Q ss_pred             HHcCCHHHHHHH
Q psy630          331 KAIEHTDLIEYL  342 (347)
Q Consensus       331 ~~~~~~~~v~~L  342 (347)
                      +.+|+.+++++|
T Consensus       141 ~~~g~~eiv~lL  152 (153)
T d1awcb_         141 IDNGNEDLAEIL  152 (153)
T ss_dssp             HHTTCHHHHHHH
T ss_pred             HHcCCHHHHHhC
Confidence            999999999987

>d1dcqa1 d.211.1.1 (A:369-522) Pyk2-associated protein beta {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Pyk2-associated protein beta
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.63  E-value=6.3e-16  Score=122.52  Aligned_cols=88  Identities=16%  Similarity=0.307  Sum_probs=75.8

Q ss_pred             cHHHHHHcCChHHHHHHHhhcCCCCcccc------CCCCchHHHHHHHc---CCHHHHHHHHhhcCCCccccCCCCCcHH
Q psy630          257 NIYEWAKEGKLDMLVKQLTKLKDFNINQL------DENGLNCLHWACDR---GHLKVVQHLIEKCGADVNVTDSDGDYGL  327 (347)
Q Consensus       257 ~~l~~a~~~~~~~~~~lL~~~~~~~~~~~------d~~g~tpLh~A~~~---g~~~~v~~Ll~~~ga~i~~~d~~g~TpL  327 (347)
                      .++.++..++...+.+++..  |.+++..      +..|+||||+|+..   ++.+++++|++ +|+++|.+|..|+|||
T Consensus         9 ~L~~Av~~~dl~~l~~~~~~--g~d~~~~~~~~~~~~~g~t~Lh~A~~~~~~~~~~iv~~Ll~-~gadin~~d~~g~TpL   85 (154)
T d1dcqa1           9 SLCEAVKTRDIFGLLQAYAD--GVDLTEKIPLANGHEPDETALHLAVRSVDRTSLHIVDFLVQ-NSGNLDKQTGKGSTAL   85 (154)
T ss_dssp             HHHHHHHTTCHHHHHHHHHT--TCCTTSBCCCSSCSSTTCBHHHHHHHHCCTTTHHHHHHHHH-HCSCTTCCCTTCCCHH
T ss_pred             HHHHHHHhCCHHHHHHHHHc--CCCcCCCCCcccCCCCCCchHHHHHHhcCCCCHHHHHHHHH-cCCChhhhhhhhcccc
Confidence            35566778888888877766  6665543      67899999999974   68899999999 7999999999999999


Q ss_pred             HHHHHcCCHHHHHHHHhCCC
Q psy630          328 DYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       328 h~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |+||..|+.+++++|+++||
T Consensus        86 h~A~~~~~~~~v~~Ll~~ga  105 (154)
T d1dcqa1          86 HYCCLTDNAECLKLLLRGKA  105 (154)
T ss_dssp             HHHHHTTCHHHHHHHHHTTC
T ss_pred             ccccccccccccccccccCc
Confidence            99999999999999999986

>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=99.63  E-value=3.8e-16  Score=111.52  Aligned_cols=78  Identities=18%  Similarity=0.221  Sum_probs=69.9

Q ss_pred             cccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc---CCCccCCcccc
Q psy630            4 SIRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST---DSHVLEGSRLS   80 (347)
Q Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~---~~~~~~g~~l~   80 (347)
                      +....++|||+|||+++++++|+++|++||.|..+++.++      +|||||+|.+.++|.+|+..   ++..+.|++|.
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            4567889999999999999999999999999999998754      47999999999999999973   78899999999


Q ss_pred             ccCCCcc
Q psy630           81 IQPSDSH   87 (347)
Q Consensus        81 v~~~~~~   87 (347)
                      |.++..+
T Consensus        78 v~~sk~~   84 (88)
T d2cq1a1          78 IQYSNHK   84 (88)
T ss_dssp             EEECSCS
T ss_pred             EEECCCC
Confidence            9988654

>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=99.63  E-value=1.2e-16  Score=114.11  Aligned_cols=75  Identities=23%  Similarity=0.332  Sum_probs=65.0

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      ..++|||+|||+++++++|+++|++|| +..+.+      +.++|||||+|.+.++|++|+.. |+..+.|+.|.|.++.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            457899999999999999999999999 333333      45689999999999999999975 9999999999999886


Q ss_pred             ccc
Q psy630           86 SHN   88 (347)
Q Consensus        86 ~~~   88 (347)
                      ++.
T Consensus        77 ~~~   79 (88)
T d1wg1a_          77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            644

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=3.7e-16  Score=116.13  Aligned_cols=79  Identities=16%  Similarity=0.275  Sum_probs=69.2

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCcc--CCccccc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVL--EGSRLSI   81 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~--~g~~l~v   81 (347)
                      +....+|||+|||+.+|+++|+++|++||.|..+.+++++    ++|||||+|.+.++|+.|+.. ++..+  .|+.|.|
T Consensus         4 ~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v   79 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI   79 (108)
T ss_dssp             CCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEE
T ss_pred             CCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEE
Confidence            4566789999999999999999999999999999998764    489999999999999999985 88877  4678888


Q ss_pred             cCCCcc
Q psy630           82 QPSDSH   87 (347)
Q Consensus        82 ~~~~~~   87 (347)
                      .++.++
T Consensus        80 ~~s~~~   85 (108)
T d2adba1          80 DFSKLT   85 (108)
T ss_dssp             EECSSC
T ss_pred             EecCCc
Confidence            777654

>d1uoha_ d.211.1.1 (A:) 26S proteasome non-ATPase regulatory subunit 10, gankyrin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: 26S proteasome non-ATPase regulatory subunit 10, gankyrin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=4.3e-16  Score=131.39  Aligned_cols=99  Identities=21%  Similarity=0.302  Sum_probs=93.2

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +.+..+..|.||||.|+..+..+++++|++ .|++++.+|..|.||||+|+..++..++++|+. .|++++.+|..|+||
T Consensus        95 d~~~~d~~g~tpL~~A~~~~~~e~~~~Ll~-~g~d~~~~~~~~~t~L~~a~~~~~~~~~~~L~~-~~~~i~~~d~~g~Tp  172 (223)
T d1uoha_          95 QVNAVNQNGCTPLHYAASKNRHEIAVMLLE-GGANPDAKDHYEATAMHRAAAKGNLKMIHILLY-YKASTNIQDTEGNTP  172 (223)
T ss_dssp             CTTCCCTTCCCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCSCCCCTTCCCH
T ss_pred             eeEeeCCCCCchhhHHHHcCCHHHHHHHHH-CCCCCCCcCCCCCccchhhhhcCCcchhhhhcc-ccceeeeccCCCCce
Confidence            456678889999999998888899999998 799999999999999999999999999999998 799999999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||+|+..|+.++|++||++||
T Consensus       173 L~~Aa~~g~~~~v~~LL~~Ga  193 (223)
T d1uoha_         173 LHLACDEERVEEAKLLVSQGA  193 (223)
T ss_dssp             HHHHHHTTCHHHHHHHHHTTC
T ss_pred             eccccccCcHHHHHHHHHCCC
Confidence            999999999999999999997

>d2ajaa1 a.118.24.1 (A:3-348) Hypothetical protein LPG2416 {Legionella pneumophila [TaxId: 446]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Pseudo ankyrin repeat-like
family: Pseudo ankyrin repeat
domain: Hypothetical protein LPG2416
species: Legionella pneumophila [TaxId: 446]

Probab=99.62  E-value=4.7e-17  Score=146.69  Aligned_cols=95  Identities=15%  Similarity=0.145  Sum_probs=63.1

Q ss_pred             cCCCCCcHHHHHHcCChHHHHHH---HhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccC--CCCCc
Q psy630          251 LDDNEKNIYEWAKEGKLDMLVKQ---LTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTD--SDGDY  325 (347)
Q Consensus       251 ~~~~~~~~l~~a~~~~~~~~~~l---L~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d--~~g~T  325 (347)
                      .+..+.|+|++|+..++.+++++   |.. .++++|.+|..|+||||+||.+||.++|++|++ .|++++..+  .+|+|
T Consensus        86 ~~~~~~t~L~~Aa~~g~~~~~~~~~~L~~-~~~~in~~~~~g~taL~~Aa~~G~~~~v~~Ll~-~g~~~~~~~~~~~g~t  163 (346)
T d2ajaa1          86 KGIKSEVICFVAAITGCSSALDTLCLLLT-SDEIVKVIQAENYQAFRLAAENGHLHVLNRLCE-LAPTEIMAMIQAENYH  163 (346)
T ss_dssp             HTCCHHHHHHHHHHHCCHHHHHHHTTC---CCSSCC--CHHHHHHHHHHHHTTCHHHHHHHHH-SCTTTHHHHHSHHHHH
T ss_pred             ccCCCCcHHHHHHHhCCHHHHHHHHHHHh-CCCcccccCCCCCCHHHHHHHCCCHHHHHHHHH-cCCCccccccccCCCC
Confidence            34456677777666666555443   344 677777777777777777777777777777777 577777654  34777


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|+..||.++|++|+++|+
T Consensus       164 ~L~~Aa~~g~~~iv~~Ll~~~~  185 (346)
T d2ajaa1         164 AFRLAAENGHLHVLNRLCELAP  185 (346)
T ss_dssp             HHHHHHHTTCHHHHHHHHHSCG
T ss_pred             hhHHHHHHhhHHHHHHHHHcCC
Confidence            7777777777777777777663

>d2fo1e1 d.211.1.1 (E:1021-1297) Lin-12 {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Lin-12
species: Caenorhabditis elegans [TaxId: 6239]

Probab=99.62  E-value=1.1e-15  Score=132.51  Aligned_cols=97  Identities=23%  Similarity=0.292  Sum_probs=86.7

Q ss_pred             CcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHH
Q psy630          248 ESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGL  327 (347)
Q Consensus       248 ~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpL  327 (347)
                      .+..+..+.+++|.++..+...+..++....+.+++.+|..|+||||+||..|+.+++++|++ +|+++|.+|..|+|||
T Consensus       180 ~~~~~~~g~t~L~~~~~~~~~~~~~~~l~~~~~~~~~~d~~g~tpL~~A~~~g~~~iv~~Ll~-~gadin~~d~~G~T~L  258 (277)
T d2fo1e1         180 KDSEKYKGRTALHYAAQVSNMPIVKYLVGEKGSNKDKQDEDGKTPIMLAAQEGRIEVVMYLIQ-QGASVEAVDATDHTAR  258 (277)
T ss_dssp             TSSSSCCCCCTHHHHHSSCCHHHHHHHHHHSCCCTTCCCTTCCCHHHHHHHHTCHHHHHHHHH-TTCCSSCCCSSSCCHH
T ss_pred             ccccccCCCCccccccccccccccccccccccccccccCCCCCCHHHHHHHcCCHHHHHHHHH-CcCCCCCcCCCCCCHH
Confidence            445567889999998888877777765554889999999999999999999999999999999 7999999999999999


Q ss_pred             HHHHHcCCHHHHHHHHhC
Q psy630          328 DYAKAIEHTDLIEYLVNS  345 (347)
Q Consensus       328 h~A~~~~~~~~v~~Ll~~  345 (347)
                      |+|+..|+.++|++|++.
T Consensus       259 ~~A~~~~~~~iv~lL~~c  276 (277)
T d2fo1e1         259 QLAQANNHHNIVDIFDRC  276 (277)
T ss_dssp             HHHHHTTCHHHHHHHHTT
T ss_pred             HHHHHcCCHHHHHHHHHh
Confidence            999999999999999863

>d1n11a_ d.211.1.1 (A:) Ankyrin-R {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Ankyrin-R
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=7.9e-16  Score=140.80  Aligned_cols=96  Identities=25%  Similarity=0.213  Sum_probs=87.5

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      .+.+..+..+.++++.+...+...++++++. .|+++|.+|..|+||||+||.+|+.++|++||+ +||++|.+|.+|+|
T Consensus       288 ~~~~~~~~~~~t~L~~~~~~~~~~~~~~ll~-~g~~in~~d~~G~T~Lh~A~~~g~~~iv~~Ll~-~GAd~n~~d~~G~t  365 (408)
T d1n11a_         288 VMVDATTRMGYTPLHVASHYGNIKLVKFLLQ-HQADVNAKTKLGYSPLHQAAQQGHTDIVTLLLK-NGASPNEVSSDGTT  365 (408)
T ss_dssp             CCTTCCCSSCCCHHHHHHHSSCSHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCSCCCCSSSCC
T ss_pred             CccccccccccccchhhcccCcceeeeeecc-ccccccccCCCCCCHHHHHHHcCCHHHHHHHHH-CCCCCCCCCCCCCC
Confidence            3566677788899999888888888888888 799999999999999999999999999999999 79999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHH
Q psy630          326 GLDYAKAIEHTDLIEYLV  343 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll  343 (347)
                      |||+|+..|+.++|++|.
T Consensus       366 ~L~~A~~~~~~~iv~~L~  383 (408)
T d1n11a_         366 PLAIAKRLGYISVTDVLK  383 (408)
T ss_dssp             HHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHH
Confidence            999999999999998774

>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=99.60  E-value=6.8e-16  Score=112.26  Aligned_cols=76  Identities=22%  Similarity=0.296  Sum_probs=67.8

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      +..++|||+|||+++++++|+++|++||.|..+.+.+       +|||||+|.+.++|++|++. |+..|.|+.|.|.++
T Consensus        13 ~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~   85 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYI   85 (98)
T ss_dssp             SCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEE
Confidence            4456899999999999999999999999999998853       48999999999999999975 999999999999877


Q ss_pred             Cccc
Q psy630           85 DSHN   88 (347)
Q Consensus        85 ~~~~   88 (347)
                      ..+.
T Consensus        86 ~~~~   89 (98)
T d1wg4a_          86 RVYP   89 (98)
T ss_dssp             EEEC
T ss_pred             ecCC
Confidence            5543

>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=99.59  E-value=1.7e-15  Score=110.05  Aligned_cols=77  Identities=19%  Similarity=0.366  Sum_probs=67.7

Q ss_pred             cCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCC--cccccc
Q psy630            6 RQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEG--SRLSIQ   82 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g--~~l~v~   82 (347)
                      .+.++|||+|||+++++++|+++|++||.|..+++.++      ++||||+|.+.++|..|++. ++..+.|  ++|+|.
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~   88 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEE
Confidence            45689999999999999999999999999999998654      57999999999999999985 9999976  478888


Q ss_pred             CCCccc
Q psy630           83 PSDSHN   88 (347)
Q Consensus        83 ~~~~~~   88 (347)
                      ++.+..
T Consensus        89 ~ak~~~   94 (97)
T d1whya_          89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             eCCCCC
Confidence            887643

>d1n11a_ d.211.1.1 (A:) Ankyrin-R {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Ankyrin-R
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=1.2e-15  Score=139.65  Aligned_cols=89  Identities=25%  Similarity=0.240  Sum_probs=82.5

Q ss_pred             CcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCC
Q psy630          256 KNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEH  335 (347)
Q Consensus       256 ~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~  335 (347)
                      .||||.|+..+..+++++|++ .|+++|..|..|+||||+||..|+.+++++||+ +|++++.+|..|+||||+|+..|+
T Consensus         1 ~TpL~~Aa~~g~~~~v~~Ll~-~g~~in~~d~~g~TpL~~A~~~g~~~iv~~Ll~-~gadi~~~~~~g~t~L~~A~~~g~   78 (408)
T d1n11a_           1 LTPLHVASFMGHLPIVKNLLQ-RGASPNVSNVKVETPLHMAARAGHTEVAKYLLQ-NKAKVNAKAKDDQTPLHCAARIGH   78 (408)
T ss_dssp             CCHHHHHHHHTCHHHHHHHHH-TTCCSCCSSSCCCCHHHHHHHHTCHHHHHHHHH-HTCCSSCCCTTSCCHHHHHHHHTC
T ss_pred             CChHHHHHHCcCHHHHHHHHH-CCCCCCCCCCCCCCHHHHHHHcCCHHHHHHHHH-CcCCCCCCCCCCCCHHHHHHHcCC
Confidence            378998888777888888888 799999999999999999999999999999999 699999999999999999999999


Q ss_pred             HHHHHHHHhCC
Q psy630          336 TDLIEYLVNSG  346 (347)
Q Consensus       336 ~~~v~~Ll~~G  346 (347)
                      .+++++|+..+
T Consensus        79 ~~~~~~Ll~~~   89 (408)
T d1n11a_          79 TNMVKLLLENN   89 (408)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHhh
Confidence            99999998754

>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=99.58  E-value=7.3e-16  Score=112.40  Aligned_cols=80  Identities=20%  Similarity=0.291  Sum_probs=69.9

Q ss_pred             ccccCCCeEEEeCCCCC-CCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh---cCCCccCCcc
Q psy630            3 NSIRQLNKIFVGNLPWT-VSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS---TDSHVLEGSR   78 (347)
Q Consensus         3 ~~~~~~~~l~V~nLp~~-~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~---~~~~~~~g~~   78 (347)
                      +.....++|||+|||.+ +|+++|.++|++||.|..+.++++      +|||||+|.+.++|.+|+.   .++..+.|+.
T Consensus        13 ~~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~   86 (99)
T d1x4fa1          13 QKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRC   86 (99)
T ss_dssp             CSSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSC
T ss_pred             cCCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEE
Confidence            34456689999999986 899999999999999999999754      5799999999999999996   3889999999


Q ss_pred             ccccCCCccc
Q psy630           79 LSIQPSDSHN   88 (347)
Q Consensus        79 l~v~~~~~~~   88 (347)
                      |.|.++..+.
T Consensus        87 l~V~~s~~~~   96 (99)
T d1x4fa1          87 VKVDLSEKYK   96 (99)
T ss_dssp             CEEEEECSCS
T ss_pred             EEEEEcCCcc
Confidence            9999886554

>d1sw6a_ d.211.1.1 (A:) Swi6 ankyrin-repeat fragment {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Swi6 ankyrin-repeat fragment
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.58  E-value=2.8e-15  Score=132.25  Aligned_cols=95  Identities=24%  Similarity=0.312  Sum_probs=78.1

Q ss_pred             cCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCH-------HHHHHH---------------
Q psy630          251 LDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHL-------KVVQHL---------------  308 (347)
Q Consensus       251 ~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~-------~~v~~L---------------  308 (347)
                      .|..|.|+||+|+..+..+++++|++ .|++++.+|..|+||||+||..++.       +++.+|               
T Consensus       103 ~D~~G~T~LH~Aa~~g~~~~v~~Ll~-~gad~~~~d~~G~TpL~~A~~~~~~~~~~~~~~ll~~l~~~~~~~d~~g~t~l  181 (301)
T d1sw6a_         103 VDEHGNTPLHWLTSIANLELVKHLVK-HGSNRLYGDNMGESCLVKAVKSVNNYDSGTFEALLDYLYPCLILEDSMNRTIL  181 (301)
T ss_dssp             CSTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTBCCTTCCCHHHHHHHSSHHHHTTCHHHHHHHHGGGGGEECTTCCCHH
T ss_pred             cCCCCCCHHHHHHHcCCHHHHHHHHH-CCCCCCcCCcccccHHHHhhhcccchhhhhHHHHHHHHhhhhhhcccccCCHH
Confidence            37889999999998888889999998 7999999999999999999975531       222222               


Q ss_pred             ---------------------------HhhcCC-------------------------------------CccccCCCCC
Q psy630          309 ---------------------------IEKCGA-------------------------------------DVNVTDSDGD  324 (347)
Q Consensus       309 ---------------------------l~~~ga-------------------------------------~i~~~d~~g~  324 (347)
                                                 +. .+.                                     .+|.+|..|+
T Consensus       182 h~~~~~~~~~~~~~~~~~~~~~~~~~l~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~in~~D~~G~  260 (301)
T d1sw6a_         182 HHIIITSGMTGCSAAAKYYLDILMGWIVK-KQNRPIQSGTNEKESKPNDKNGERKDSILENLDLKWIIANMLNAQDSNGD  260 (301)
T ss_dssp             HHHHHHHTSTTCHHHHHHHHHHHHHHHHH-GGGCCEEEC----------------CHHHHHCSHHHHHHHTTTCCCTTSC
T ss_pred             HHHHHHhCccccHHHHHHHHHHHHHHHHh-cCCcchhcccccccchhHHHHhcchHHHHHHHhhHHHHhcCccCCCCCCC
Confidence                                       22 111                                     1688899999


Q ss_pred             cHHHHHHHcCCHHHHHHHHhCCC
Q psy630          325 YGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       325 TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ||||+|++.|+.++|++||++||
T Consensus       261 TpLh~A~~~g~~~iv~~Ll~~GA  283 (301)
T d1sw6a_         261 TCLNIAARLGNISIVDALLDYGA  283 (301)
T ss_dssp             CHHHHHHHHCCHHHHHHHHHTTC
T ss_pred             CHHHHHHHcCCHHHHHHHHHCCC
Confidence            99999999999999999999997

>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=99.58  E-value=3.3e-15  Score=110.05  Aligned_cols=78  Identities=18%  Similarity=0.200  Sum_probs=69.0

Q ss_pred             ccCCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc---CCCccCCccccc
Q psy630            5 IRQLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST---DSHVLEGSRLSI   81 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~---~~~~~~g~~l~v   81 (347)
                      ....++|||+|||+.+|+++|+++|++||.|..+++.++      +|+|||+|.+.++|+.|+..   ++..+.|++|+|
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v   85 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEE
Confidence            456789999999999999999999999999999998643      57999999999999999974   677899999999


Q ss_pred             cCCCccc
Q psy630           82 QPSDSHN   88 (347)
Q Consensus        82 ~~~~~~~   88 (347)
                      .++..+.
T Consensus        86 ~~s~~~~   92 (104)
T d1wexa_          86 NYSTSKR   92 (104)
T ss_dssp             EECSSSS
T ss_pred             EEcCCCc
Confidence            9886643

>d1k1aa_ d.211.1.1 (A:) bcl-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: bcl-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.58  E-value=4.9e-15  Score=123.14  Aligned_cols=87  Identities=16%  Similarity=0.064  Sum_probs=58.5

Q ss_pred             CCCcHHHHHHcCChHHHHHHHhh---cCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHH
Q psy630          254 NEKNIYEWAKEGKLDMLVKQLTK---LKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA  330 (347)
Q Consensus       254 ~~~~~l~~a~~~~~~~~~~lL~~---~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A  330 (347)
                      +|.||||.|+..+..++++.|+.   ..|+++|.+|..|+||||+||..|+.+++++|++ +|++++..+..|.++++.|
T Consensus         2 dG~TpLh~A~~~g~~~~v~~Ll~~~~~~g~~in~~d~~g~TpL~~A~~~~~~~iv~~Ll~-~ga~~~~~~~~~~~~~~~a   80 (228)
T d1k1aa_           2 DGDTPLHIAVVQGNLPAVHRLVNLFQQGGRELDIYNNLRQTPLHLAVITTLPSVVRLLVT-AGASPMALDRHGQTAAHLA   80 (228)
T ss_dssp             TTCCHHHHHHHTTCHHHHHHHHHHHHHTTCCSCCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHH
T ss_pred             CCccHHHHHHHcCCHHHHHHHHHHHHHCCCCCCccCCCCCccceehhccccccccccccc-ccccccccccccccccccc
Confidence            57788888877777766665542   2577888888888888888888888888888887 4555555555555555555


Q ss_pred             HHcCCHHHHHH
Q psy630          331 KAIEHTDLIEY  341 (347)
Q Consensus       331 ~~~~~~~~v~~  341 (347)
                      ...++..+++.
T Consensus        81 ~~~~~~~~~~~   91 (228)
T d1k1aa_          81 CEHRSPTCLRA   91 (228)
T ss_dssp             HHTTCHHHHHH
T ss_pred             cccccccchhh
Confidence            55554444443

>d2fo1e1 d.211.1.1 (E:1021-1297) Lin-12 {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Lin-12
species: Caenorhabditis elegans [TaxId: 6239]

Probab=99.57  E-value=1e-15  Score=132.58  Aligned_cols=91  Identities=19%  Similarity=0.280  Sum_probs=82.4

Q ss_pred             CCCCcHHHHHHcCChHHHHHHHh--------hcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCC
Q psy630          253 DNEKNIYEWAKEGKLDMLVKQLT--------KLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGD  324 (347)
Q Consensus       253 ~~~~~~l~~a~~~~~~~~~~lL~--------~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~  324 (347)
                      ..|+||||+|+..+..+++++|+        . .|+++|.+|..|+||||+|+.+|+.+++++||+ .|++++.+|..|.
T Consensus        31 ~~g~T~Lh~A~~~g~~~~v~~Ll~~~~~~~l~-~Gadvn~~d~~G~TpLh~A~~~g~~~iv~~Ll~-~Gad~n~~~~~g~  108 (277)
T d2fo1e1          31 RHNRTVLHWIASNSSAEKSEDLIVHEAKECIA-AGADVNAMDCDENTPLMLAVLARRRRLVAYLMK-AGADPTIYNKSER  108 (277)
T ss_dssp             SSCCCHHHHHHCTTCCSCCTTHHHHHHHHHHH-TCCCTTCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCSCCCCTTCC
T ss_pred             CCCccHHHHHHHcCCHHHHHHHHhcchhHHHH-cCCCccccCCCCCeeeccccccccccccccccc-ccccccccccccc
Confidence            35899999999998887776653        3 589999999999999999999999999999999 7999999999999


Q ss_pred             cHHHHHHHcCCHHHHHHHHhC
Q psy630          325 YGLDYAKAIEHTDLIEYLVNS  345 (347)
Q Consensus       325 TpLh~A~~~~~~~~v~~Ll~~  345 (347)
                      ||||+|+..++.+++.+++..
T Consensus       109 t~l~~a~~~~~~~~~~~l~~~  129 (277)
T d2fo1e1         109 SALHQAAANRDFGMMVYMLNS  129 (277)
T ss_dssp             CHHHHHHHTTCHHHHHHHTTS
T ss_pred             ccccchhhhcchhhhhhhhhc
Confidence            999999999999999888654

>d1bd8a_ d.211.1.1 (A:) Cell cycle inhibitor p19ink4D {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Cell cycle inhibitor p19ink4D
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=5.7e-15  Score=117.18  Aligned_cols=98  Identities=28%  Similarity=0.345  Sum_probs=86.6

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      .+++..|..|.||+|+|+.++...+ ..|+. .+.+++..+..|.+||++++..++.++++++++ .|+++|.+|..|.|
T Consensus        27 ~~~n~~d~~g~t~L~~A~~~~~~~v-~~Ll~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~-~~~~~n~~~~~~~t  103 (156)
T d1bd8a_          27 VHPDALNRFGKTALQVMMFGSTAIA-LELLK-QGASPNVQDTSGTSPVHDAARTGFLDTLKVLVE-HGADVNVPDGTGAL  103 (156)
T ss_dssp             CCTTCCCTTSCCHHHHSCTTCHHHH-HHHHH-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCSCCCCTTSCC
T ss_pred             CCCCccCCCCCcccccccccccccc-ccccc-ccccccccccccccccccccccccccccccccc-cccccccccCCCCe
Confidence            3567778899999999998877655 45555 588999999999999999999999999999999 69999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|+..|+.+++++|+ .||
T Consensus       104 ~L~~A~~~~~~~i~~~L~-~~~  124 (156)
T d1bd8a_         104 PIHLAVQEGHTAVVSFLA-AES  124 (156)
T ss_dssp             HHHHHHHHTCHHHHHHHH-TTS
T ss_pred             eecccccccccccccccc-ccc
Confidence            999999999999999887 443

>d1ihba_ d.211.1.1 (A:) p18ink4C(ink6) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: p18ink4C(ink6)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=1.3e-14  Score=114.74  Aligned_cols=99  Identities=21%  Similarity=0.315  Sum_probs=88.8

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcH
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYG  326 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~Tp  326 (347)
                      +++..+..+.++++.++..+...+...|.. .+.+++..|..|.+|||+|+..++.+++++|+++.+.+++.+|..|+||
T Consensus        58 ~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~-~~~~~~~~~~~~~~~l~~a~~~~~~~~~~~Ll~~~~~~~~~~d~~g~Tp  136 (156)
T d1ihba_          58 NPDLKDRTGFAVIHDAARAGFLDTLQTLLE-FQADVNIEDNEGNLPLHLAAKEGHLRVVEFLVKHTASNVGHRNHKGDTA  136 (156)
T ss_dssp             CTTCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHHHSCCCTTCCCTTSCCH
T ss_pred             ccccccccCccccccccccccccccccccc-ccccccccccccccccccccccccccccccccccccccccccCCCCCCH
Confidence            456677788899998888888888888887 7888999999999999999999999999999995334899999999999


Q ss_pred             HHHHHHcCCHHHHHHHHhCC
Q psy630          327 LDYAKAIEHTDLIEYLVNSG  346 (347)
Q Consensus       327 Lh~A~~~~~~~~v~~Ll~~G  346 (347)
                      ||+|+..++.+++++|+++|
T Consensus       137 L~~A~~~~~~~iv~~Ll~~G  156 (156)
T d1ihba_         137 CDLARLYGRNEVVSLMQANG  156 (156)
T ss_dssp             HHHHHHTTCHHHHHHHHHTC
T ss_pred             HHHHHHcCCHHHHHHHHhcC
Confidence            99999999999999999998

>d1awcb_ d.211.1.1 (B:) GA bindinig protein (GABP) beta 1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: GA bindinig protein (GABP) beta 1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.55  E-value=7e-15  Score=115.94  Aligned_cols=95  Identities=23%  Similarity=0.258  Sum_probs=67.0

Q ss_pred             cCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHH
Q psy630          251 LDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA  330 (347)
Q Consensus       251 ~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A  330 (347)
                      .+..|.|+||+|+..+...++..+.. ........+..+.+++|+++...+.+++++|+. .|++++.+|..|+||||+|
T Consensus        30 ~~~~g~t~L~~a~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-~~~~~~~~~~~g~T~L~~A  107 (153)
T d1awcb_          30 TDWLGTSPLHLAAQYGHFSTTEVLLR-AGVSRDARTKVDRTPLHMAASEGHANIVEVLLK-HGADVNAKDMLKMTALHWA  107 (153)
T ss_dssp             CCTTCCCHHHHHHHHTCHHHHHHHHT-TTCCTTCCCTTCCCHHHHHHHHTCHHHHHHHHT-TTCCTTCCCTTSCCHHHHH
T ss_pred             cccCCCcccccccccccccccccccc-ccccccccccccccccccccccccceeeecccc-cCCccccccccCchHHHhh
Confidence            34555555555555555555544444 333334444455555555555556777777776 7999999999999999999


Q ss_pred             HHcCCHHHHHHHHhCCC
Q psy630          331 KAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       331 ~~~~~~~~v~~Ll~~GA  347 (347)
                      +..|+.+++++|+++||
T Consensus       108 ~~~g~~~iv~~ll~~ga  124 (153)
T d1awcb_         108 TEHNHQEVVELLIKYGA  124 (153)
T ss_dssp             HHTTCHHHHHHHHHTTC
T ss_pred             hhcchhheeeecccccc
Confidence            99999999999999986

>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=99.54  E-value=3.7e-15  Score=106.26  Aligned_cols=78  Identities=10%  Similarity=0.184  Sum_probs=69.0

Q ss_pred             ccCCCeEEEeCCCCC-CCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc---CCCccCCcccc
Q psy630            5 IRQLNKIFVGNLPWT-VSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST---DSHVLEGSRLS   80 (347)
Q Consensus         5 ~~~~~~l~V~nLp~~-~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~---~~~~~~g~~l~   80 (347)
                      .+..+.|||+|||.. +|+++|.++|++||.|..+.++.+      +++|||+|.+.++|..|+..   ++..+.|++|.
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~   78 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVR   78 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEE
Confidence            456789999999996 789999999999999999999765      36899999999999999973   78889999999


Q ss_pred             ccCCCccc
Q psy630           81 IQPSDSHN   88 (347)
Q Consensus        81 v~~~~~~~   88 (347)
                      |.++.+..
T Consensus        79 V~~s~~~~   86 (89)
T d1x4da1          79 VHLSQKYK   86 (89)
T ss_dssp             EEEECCCT
T ss_pred             EEECCCcc
Confidence            99987644

>d1s70b_ d.211.1.1 (B:) Myosin phosphatase targeting subunit 1, MYPT1 {Chicken (Gallus gallus) [TaxId: 9031]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Myosin phosphatase targeting subunit 1, MYPT1
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=99.53  E-value=2.6e-15  Score=131.24  Aligned_cols=90  Identities=21%  Similarity=0.298  Sum_probs=80.0

Q ss_pred             cccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHH
Q psy630          249 SQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLD  328 (347)
Q Consensus       249 ~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh  328 (347)
                      ...+..+.+++|.|+..+...+++.|+. .|+++|.+|..|+||||+||..|+.++|++||+ +|++++.+|..|+||||
T Consensus       193 ~~~~~~g~t~L~~a~~~~~~~~~~~Ll~-~g~din~~~~~g~TpL~~A~~~g~~~iv~lLl~-~Gadv~~~d~~G~TaL~  270 (291)
T d1s70b_         193 VRHAKSGGTALHVAAAKGYTEVLKLLIQ-ARYDVNIKDYDGWTPLHAAAHWGKEEACRILVE-NLCDMEAVNKVGQTAFD  270 (291)
T ss_dssp             CCCTTTCCCHHHHHHHHTCHHHHHHHHT-TTCCTTCCCTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCTTT
T ss_pred             ccccCCCCChhhHHHHcCChhhhccccc-ceecccccccCCCCHHHHHHHcCCHHHHHHHHH-CCCCCCCcCCCCCCHHH
Confidence            3445678899999888888888888888 899999999999999999999999999999999 79999999999999999


Q ss_pred             HHHHcCCHHHHHHHHh
Q psy630          329 YAKAIEHTDLIEYLVN  344 (347)
Q Consensus       329 ~A~~~~~~~~v~~Ll~  344 (347)
                      +|+.    +++++|.+
T Consensus       271 ~A~e----~~~~~L~~  282 (291)
T d1s70b_         271 VADE----DILGYLEE  282 (291)
T ss_dssp             SCCS----GGGHHHHH
T ss_pred             HHHH----HHHHHHHH
Confidence            9975    56777654

>d1iknd_ d.211.1.1 (D:) I-kappa-B-alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: I-kappa-B-alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=7.8e-15  Score=123.18  Aligned_cols=93  Identities=24%  Similarity=0.232  Sum_probs=83.0

Q ss_pred             CCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccC-CCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHH
Q psy630          252 DDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLD-ENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA  330 (347)
Q Consensus       252 ~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d-~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A  330 (347)
                      ...+.+++|.|+..+...++.+|.. .+..++..+ ..|.||||+|+..|+.+++++||+ +|+|++.+|..|+||||+|
T Consensus       108 ~~~~~t~l~~a~~~~~~~~~~~l~~-~~~~~~~~~~~~G~T~L~~A~~~g~~~~v~~Ll~-~gad~~~~~~~G~tpl~~A  185 (221)
T d1iknd_         108 NYNGHTCLHLASIHGYLGIVELLVS-LGADVNAQEPCNGRTALHLAVDLQNPDLVSLLLK-CGADVNRVTYQGYSPYQLT  185 (221)
T ss_dssp             CTTCCCHHHHHHHTTCHHHHHHHHH-HTCCTTCCCTTTCCCHHHHHHHTTCHHHHHHHHT-TTCCSCCCCTTCCCGGGGC
T ss_pred             ccccchhhhHHhhcCChhheeeecc-cCcccccccccCCCCccccccccccHHHHHHHHh-cCCcccccCCCCCCHHHHH
Confidence            3457799999888888888888877 677777765 579999999999999999999999 7999999999999999999


Q ss_pred             HHcCCHHHHHHHHhCC
Q psy630          331 KAIEHTDLIEYLVNSG  346 (347)
Q Consensus       331 ~~~~~~~~v~~Ll~~G  346 (347)
                      +..++.+++++|++.+
T Consensus       186 ~~~~~~~~~~~l~~~~  201 (221)
T d1iknd_         186 WGRPSTRIQQQLGQLT  201 (221)
T ss_dssp             TTSSCHHHHHHHHTTS
T ss_pred             HHCCCHHHHHHHHHcC
Confidence            9999999999998865

>d2ajaa1 a.118.24.1 (A:3-348) Hypothetical protein LPG2416 {Legionella pneumophila [TaxId: 446]}

class: All alpha proteins
fold: alpha-alpha superhelix
superfamily: Pseudo ankyrin repeat-like
family: Pseudo ankyrin repeat
domain: Hypothetical protein LPG2416
species: Legionella pneumophila [TaxId: 446]

Probab=99.52  E-value=4.4e-16  Score=140.22  Aligned_cols=102  Identities=14%  Similarity=0.097  Sum_probs=87.1

Q ss_pred             cccCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccC--CCCchHHHHHHHcCCHHHHHHHHhhcCCCc---cc
Q psy630          244 MINDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLD--ENGLNCLHWACDRGHLKVVQHLIEKCGADV---NV  318 (347)
Q Consensus       244 ~~~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d--~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i---~~  318 (347)
                      ...+.+..+..|.|+||+|+..++.+++++|++ .|++++..+  ..|+||||+||.+||.++|++|++ .|++.   +.
T Consensus       115 ~~~~in~~~~~g~taL~~Aa~~G~~~~v~~Ll~-~g~~~~~~~~~~~g~t~L~~Aa~~g~~~iv~~Ll~-~~~~~~~~~~  192 (346)
T d2ajaa1         115 SDEIVKVIQAENYQAFRLAAENGHLHVLNRLCE-LAPTEIMAMIQAENYHAFRLAAENGHLHVLNRLCE-LAPTEATAMI  192 (346)
T ss_dssp             CCSSCC--CHHHHHHHHHHHHTTCHHHHHHHHH-SCTTTHHHHHSHHHHHHHHHHHHTTCHHHHHHHHH-SCGGGHHHHH
T ss_pred             CCCcccccCCCCCCHHHHHHHCCCHHHHHHHHH-cCCCccccccccCCCChhHHHHHHhhHHHHHHHHH-cCCccccccc
Confidence            334577788899999999999999999999999 789998876  469999999999999999999999 68765   34


Q ss_pred             cCCCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          319 TDSDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       319 ~d~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      .+..|.||||.|+..|+.++|++|+++||
T Consensus       193 ~~~~~~t~l~~A~~~g~~~iv~~Ll~~ga  221 (346)
T d2ajaa1         193 QAENYYAFRWAAVGRGHHNVINFLLDCPV  221 (346)
T ss_dssp             HHHHHHHHHHHHSTTCCHHHHHHHTTSHH
T ss_pred             ccCCCcchhhHHhhcCHHHHHHHHHhCCC
Confidence            45667888999999999999999999875

>d1iknd_ d.211.1.1 (D:) I-kappa-B-alpha {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: I-kappa-B-alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=2.7e-15  Score=126.03  Aligned_cols=99  Identities=20%  Similarity=0.197  Sum_probs=68.6

Q ss_pred             CCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCc------cccC
Q psy630          247 DESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADV------NVTD  320 (347)
Q Consensus       247 ~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i------~~~d  320 (347)
                      +++..+..|.||||+|+..+...++++|.+ .|++++.+|..|.||||+|+..++.++++.|+. .+...      +...
T Consensus        31 ~in~~d~~g~TpLh~A~~~~~~~iv~~L~~-~g~d~~~~d~~g~t~l~~~~~~~~~~~~~~l~~-~~~~~~~~~~~~~~~  108 (221)
T d1iknd_          31 FLNFQNNLQQTPLHLAVITNQPEIAEALLG-AGCDPELRDFRGNTPLHLACEQGCLASVGVLTQ-SCTTPHLHSILKATN  108 (221)
T ss_dssp             CCCCCCTTCCCHHHHHHHTTCHHHHHCCCS-CCCCSCCCCTTCCCHHHHHHHHTCHHHHHHHHH-STTTTSSSCGGGCCC
T ss_pred             CcccCCCCCCcccccccccccccccccccc-ccccccccccccccccccccccccccccchhhh-hcccccccccccccc
Confidence            456667777777777777777777777776 677777777777777777777777777777776 44442      2234


Q ss_pred             CCCCcHHHHHHHcCCHHHHHHHHhCCC
Q psy630          321 SDGDYGLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       321 ~~g~TpLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      ..|.||||+|+..++.+++.+|+..|+
T Consensus       109 ~~~~t~l~~a~~~~~~~~~~~l~~~~~  135 (221)
T d1iknd_         109 YNGHTCLHLASIHGYLGIVELLVSLGA  135 (221)
T ss_dssp             TTCCCHHHHHHHTTCHHHHHHHHHHTC
T ss_pred             cccchhhhHHhhcCChhheeeecccCc
Confidence            457777777777777777777776654

>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=99.49  E-value=2.1e-14  Score=99.94  Aligned_cols=74  Identities=19%  Similarity=0.297  Sum_probs=63.1

Q ss_pred             CCCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCcc-ccccCCC
Q psy630            7 QLNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSR-LSIQPSD   85 (347)
Q Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~-l~v~~~~   85 (347)
                      +.+.|+|+++|++.+++.| ++|++||.|.++++.      +++|||||+|.+.++|++|+.+||..++|+. +.|.++.
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCC
Confidence            4568999999999987655 579999999999873      4568999999999999999988999999984 5688776


Q ss_pred             cc
Q psy630           86 SH   87 (347)
Q Consensus        86 ~~   87 (347)
                      .+
T Consensus        76 ~k   77 (81)
T d1wwha1          76 DK   77 (81)
T ss_dssp             CH
T ss_pred             Ch
Confidence            54

>d1ixva_ d.211.1.1 (A:) 26S proteasome non-ATPase regulatory subunit 10, gankyrin {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: 26S proteasome non-ATPase regulatory subunit 10, gankyrin
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.47  E-value=1.2e-13  Score=116.04  Aligned_cols=97  Identities=24%  Similarity=0.166  Sum_probs=86.4

Q ss_pred             ccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHH
Q psy630          250 QLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDY  329 (347)
Q Consensus       250 ~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~  329 (347)
                      ..+..+.++++.++..+...+..+|.. .+...+.+|..|+||||+|+..|+.+++++|++..+.++|.+|..|+||||+
T Consensus       100 ~~~~~~~~~l~~~~~~~~~~~~~~l~~-~~~~~~~~~~~g~t~l~~a~~~~~~~~~~~Ll~~~~~~in~~d~~g~TpLh~  178 (229)
T d1ixva_         100 KITNQGVTCLHLAVGKKWFEVSQFLIE-NGASVRIKDKFNQIPLHRAASVGSLKLIELLCGLGKSAVNWQDKQGWTPLFH  178 (229)
T ss_dssp             CCCTTSCCHHHHHHHTTCHHHHHHHHH-TTCCSCCCCTTSCCHHHHHHHHTCHHHHHHHHTTTCCCSCCCCTTSCCHHHH
T ss_pred             ccccccccccccccccchhhhhhhhhh-hcccccccCCCCCCccchhhhcccccccccccccccccccccccccCCchhh
Confidence            345667788998888888888888888 7899999999999999999999999999999984337899999999999999


Q ss_pred             HHHcCCHHHHHHHHh-CCC
Q psy630          330 AKAIEHTDLIEYLVN-SGS  347 (347)
Q Consensus       330 A~~~~~~~~v~~Ll~-~GA  347 (347)
                      |+..|+.++|++||+ .||
T Consensus       179 A~~~~~~~~v~~Ll~~~ga  197 (229)
T d1ixva_         179 ALAEGHGDAAVLLVEKYGA  197 (229)
T ss_dssp             HHHTTCHHHHHHHHHHHCC
T ss_pred             hcccccHHHHHHHHHhcCC
Confidence            999999999999996 475

>d1k1aa_ d.211.1.1 (A:) bcl-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: bcl-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.46  E-value=1.2e-14  Score=120.61  Aligned_cols=88  Identities=25%  Similarity=0.286  Sum_probs=80.6

Q ss_pred             cCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHH
Q psy630          251 LDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA  330 (347)
Q Consensus       251 ~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A  330 (347)
                      ....+.++++.|+..+...+.+.+.. .+..++.+|..|.||||+||.+|+.+++++|++ .|+|+|.+|.+|+||||+|
T Consensus       140 ~~~~~~~~l~~a~~~~~~~~~~~~~~-~~~~~~~~d~~g~t~L~~A~~~g~~~~v~~Ll~-~Gad~n~~d~~G~TpL~~A  217 (228)
T d1k1aa_         140 DIKSGRSPLIHAVENNSLSMVQLLLQ-HGANVNAQMYSGSSALHSASGRGLLPLVRTLVR-SGADSSLKNCHNDTPLMVA  217 (228)
T ss_dssp             CTTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTCBCTTSCBHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTSCCTTTTC
T ss_pred             cccchhhHHHHHHHhhhhhhhhhhhh-hccccccccccCcchHHHHHHcCCHHHHHHHHH-CCCCCCCCCCCCCCHHHHH
Confidence            34567889999988888888888888 789999999999999999999999999999999 7999999999999999999


Q ss_pred             HHcCCHHHHH
Q psy630          331 KAIEHTDLIE  340 (347)
Q Consensus       331 ~~~~~~~~v~  340 (347)
                      +..|+.++|+
T Consensus       218 ~~~~~~divk  227 (228)
T d1k1aa_         218 RSRRVIDILR  227 (228)
T ss_dssp             SSHHHHHHHT
T ss_pred             HhCCCccccC
Confidence            9999998874

>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=99.46  E-value=2.3e-14  Score=105.08  Aligned_cols=78  Identities=10%  Similarity=0.040  Sum_probs=67.8

Q ss_pred             cCCCeEEEeCCCCCC-CH----HHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccc
Q psy630            6 RQLNKIFVGNLPWTV-SH----NELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRL   79 (347)
Q Consensus         6 ~~~~~l~V~nLp~~~-t~----~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l   79 (347)
                      ...++|||+||+.++ ++    ++|+++|++||.|.++++++      +++||||+|.+.++|.+|+.. |+..+.|+.|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            456789999999987 43    56899999999999999874      467999999999999999986 9999999999


Q ss_pred             cccCCCcccc
Q psy630           80 SIQPSDSHNR   89 (347)
Q Consensus        80 ~v~~~~~~~~   89 (347)
                      +|.++.+...
T Consensus        77 ~v~~a~~~~~   86 (104)
T d1weya_          77 KLYFAQTLHI   86 (104)
T ss_dssp             EEECCCCSSC
T ss_pred             EEeecccCCC
Confidence            9999876543

>d1s70b_ d.211.1.1 (B:) Myosin phosphatase targeting subunit 1, MYPT1 {Chicken (Gallus gallus) [TaxId: 9031]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Myosin phosphatase targeting subunit 1, MYPT1
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=99.45  E-value=6.8e-14  Score=121.99  Aligned_cols=92  Identities=28%  Similarity=0.429  Sum_probs=81.1

Q ss_pred             CCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHc
Q psy630          254 NEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAI  333 (347)
Q Consensus       254 ~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~  333 (347)
                      .+.|+|+.|+..+..+++++|++ .|+++|.+|..|.||||+|+..|+.+++++|++ .|++++..+..+.||||+|+..
T Consensus        39 ~~~t~l~~A~~~G~~~~v~~Ll~-~Gadvn~~d~~G~T~L~~A~~~g~~eiv~~Ll~-~~~~~~~~~~~~~~~L~~a~~~  116 (291)
T d1s70b_          39 DDGAVFLAACSSGDTEEVLRLLE-RGADINYANVDGLTALHQACIDDNVDMVKFLVE-NGANINQPDNEGWIPLHAAASC  116 (291)
T ss_dssp             CHHHHHHHHHHHTCHHHHHHHHH-HCCCTTCBCTTCCBHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHH
T ss_pred             CCchHHHHHHHcCCHHHHHHHHH-CCCCCCccCCCCCcHHHHHHhcCCceeeeeecc-cccccccccccccccccccccc
Confidence            45577777666555556666666 699999999999999999999999999999999 7999999999999999999999


Q ss_pred             CCHHHHHHHHhCCC
Q psy630          334 EHTDLIEYLVNSGS  347 (347)
Q Consensus       334 ~~~~~v~~Ll~~GA  347 (347)
                      ++.++++.|+++|+
T Consensus       117 ~~~~~~~~l~~~~~  130 (291)
T d1s70b_         117 GYLDIAEYLISQGA  130 (291)
T ss_dssp             TCHHHHHHHHHTTC
T ss_pred             cccchhhcccccCc
Confidence            99999999999875

>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=99.43  E-value=5.9e-15  Score=108.27  Aligned_cols=75  Identities=13%  Similarity=0.182  Sum_probs=68.3

Q ss_pred             CeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCC
Q psy630            9 NKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPS   84 (347)
Q Consensus         9 ~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~   84 (347)
                      +.++|++++.++++++|+++|++||+|.+|+|+++. +|+++|||||+|.+.++|.+|+.. ||..++||+|.|.++
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            357788888889999999999999999999998775 799999999999999999999985 999999999998764

>d1ihba_ d.211.1.1 (A:) p18ink4C(ink6) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: p18ink4C(ink6)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.42  E-value=3e-13  Score=106.63  Aligned_cols=99  Identities=25%  Similarity=0.385  Sum_probs=88.6

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCc
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDY  325 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~T  325 (347)
                      .+++..|..|.||||+|+.++ .+++++|++ .+++++.++..|.+||++++..++..++.+|+. .+.+++..|..|.+
T Consensus        25 ~d~n~~d~~g~TpL~~A~~~~-~ei~~~Ll~-~~a~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~-~~~~~~~~~~~~~~  101 (156)
T d1ihba_          25 VNVNAQNGFGRTALQVMKLGN-PEIARRLLL-RGANPDLKDRTGFAVIHDAARAGFLDTLQTLLE-FQADVNIEDNEGNL  101 (156)
T ss_dssp             CCTTCCCTTSCCHHHHCCSSC-HHHHHHHHH-TTCCTTCCCTTSCCHHHHHHHHTCHHHHHHHHH-TTCCTTCCCTTSCC
T ss_pred             CCcCccCCccccccccccccc-ccccccccc-cccccccccccCccccccccccccccccccccc-cccccccccccccc
Confidence            356777889999999998665 557777777 799999999999999999999999999999998 79999999999999


Q ss_pred             HHHHHHHcCCHHHHHHHHhCCC
Q psy630          326 GLDYAKAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       326 pLh~A~~~~~~~~v~~Ll~~GA  347 (347)
                      |||+|+..++.+++++|+++|+
T Consensus       102 ~l~~a~~~~~~~~~~~Ll~~~~  123 (156)
T d1ihba_         102 PLHLAAKEGHLRVVEFLVKHTA  123 (156)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHSC
T ss_pred             cccccccccccccccccccccc
Confidence            9999999999999999998874

>d1ot8a_ d.211.1.1 (A:) Neurogenic locus notch receptor domain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Neurogenic locus notch receptor domain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.38  E-value=1.2e-12  Score=108.06  Aligned_cols=95  Identities=20%  Similarity=0.227  Sum_probs=87.4

Q ss_pred             cCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHH
Q psy630          251 LDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYA  330 (347)
Q Consensus       251 ~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A  330 (347)
                      ....+.+..+.+.......+..+|.. .+.+++.++..|.||||+|+.++...++..|+. .+++++.+|..|.||||+|
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~L~~-~~~~~~~~~~~~~t~l~~~~~~~~~~~~~~l~~-~~~~~~~~d~~g~TpL~~A  163 (209)
T d1ot8a_          86 RMHDGTTPLILAARLAIEGMVEDLIT-ADADINAADNSGKTALHWAAAVNNTEAVNILLM-HHANRDAQDDKDETPLFLA  163 (209)
T ss_dssp             CCTTCCCHHHHHHHTTCTTHHHHHHH-TTCCTTCBCTTSCBHHHHHHHTTCHHHHHHHHH-TTCCTTCCCTTCCCHHHHH
T ss_pred             ccccccccccccccccchhhhhhhhh-hcccccccCCCCCCcchhhcccCcceeeeeecc-ccccccccccccccccchh
Confidence            34566788888888888888888888 799999999999999999999999999999999 7999999999999999999


Q ss_pred             HHcCCHHHHHHHHhCCC
Q psy630          331 KAIEHTDLIEYLVNSGS  347 (347)
Q Consensus       331 ~~~~~~~~v~~Ll~~GA  347 (347)
                      +..|+.++|++||++||
T Consensus       164 ~~~g~~~~v~~Ll~~ga  180 (209)
T d1ot8a_         164 AREGSYEASKALLDNFA  180 (209)
T ss_dssp             HHTTCHHHHHHHHHTTC
T ss_pred             ccccHHHHHHHHHHCCC
Confidence            99999999999999997

>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=99.34  E-value=4.8e-13  Score=99.60  Aligned_cols=73  Identities=16%  Similarity=0.129  Sum_probs=61.6

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCH-HHHHHHHhc-CCCccCCccccccCCC
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNK-EAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~-~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      ...+||||||+.+|+++|+++|++||+|.+|.|+++      +|||||.|.+. ++|..|+.. ++..+.++.+.|.+..
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            446799999999999999999999999999999754      68999999985 677777764 8888888877776654


Q ss_pred             c
Q psy630           86 S   86 (347)
Q Consensus        86 ~   86 (347)
                      .
T Consensus        85 ~   85 (113)
T d1owxa_          85 L   85 (113)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.34  E-value=7.5e-13  Score=96.30  Aligned_cols=73  Identities=18%  Similarity=0.265  Sum_probs=59.8

Q ss_pred             ccccCCCeEEEeC--CCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCcc-CCcc
Q psy630            3 NSIRQLNKIFVGN--LPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVL-EGSR   78 (347)
Q Consensus         3 ~~~~~~~~l~V~n--Lp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~-~g~~   78 (347)
                      ....+.+++||.|  ||+++|+++|+++|++||.|..++++.+      ++||||+|.+.++|..|+.. ||..+ .+..
T Consensus        13 ~~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i~~~~~   86 (101)
T d2cq2a1          13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLG   86 (101)
T ss_dssp             CCSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTS
T ss_pred             cCCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCCCCCCC
Confidence            3456678899955  9999999999999999999999988654      57999999999999999975 87766 3443


Q ss_pred             ccc
Q psy630           79 LSI   81 (347)
Q Consensus        79 l~v   81 (347)
                      +.+
T Consensus        87 ~~i   89 (101)
T d2cq2a1          87 QKI   89 (101)
T ss_dssp             CEE
T ss_pred             cEE
Confidence            333

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.26  E-value=4.4e-12  Score=91.83  Aligned_cols=82  Identities=22%  Similarity=0.385  Sum_probs=69.0

Q ss_pred             ccccCCCeEEEeCC--CCCCC---------HHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-C
Q psy630            3 NSIRQLNKIFVGNL--PWTVS---------HNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-D   70 (347)
Q Consensus         3 ~~~~~~~~l~V~nL--p~~~t---------~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~   70 (347)
                      +..+..+.|+|+||  |.++.         .++|++.|++||.|..+.+..+    .++|||||+|.+.++|.+|+.. |
T Consensus         3 ~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~ln   78 (99)
T d2dita1           3 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLD   78 (99)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHST
T ss_pred             CCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhC
Confidence            34567889999999  65432         2578999999999999988654    4679999999999999999985 9


Q ss_pred             CCccCCccccccCCCccc
Q psy630           71 SHVLEGSRLSIQPSDSHN   88 (347)
Q Consensus        71 ~~~~~g~~l~v~~~~~~~   88 (347)
                      |..++||+|.|.++.++.
T Consensus        79 g~~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          79 GRWFGGRQITAQAWDGTT   96 (99)
T ss_dssp             TCEETTEECEEEECCSCC
T ss_pred             CcEECCEEEEEEEeCCcC
Confidence            999999999999887654

>d1wdya_ d.211.1.1 (A:) RNase L, 2-5a-dependent ribonuclease {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: RNase L, 2-5a-dependent ribonuclease
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.24  E-value=5.5e-12  Score=109.00  Aligned_cols=75  Identities=25%  Similarity=0.239  Sum_probs=68.5

Q ss_pred             cCCcccCCCCCcHHHHHHcCChHHHHHHHhhcCCCCccccCCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCC
Q psy630          246 NDESQLDDNEKNIYEWAKEGKLDMLVKQLTKLKDFNINQLDENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDS  321 (347)
Q Consensus       246 ~~~~~~~~~~~~~l~~a~~~~~~~~~~lL~~~~~~~~~~~d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~  321 (347)
                      .+.+..+..|.|+||+|+..+..+++++|+...++++|.+|..|.||||+|+.+|+.+++++||+ +|||+|++|.
T Consensus       210 a~~n~~~~~g~t~L~~a~~~~~~~~v~~lL~~~g~din~~d~~G~TpL~~A~~~~~~eiv~~Ll~-~GAd~n~~d~  284 (285)
T d1wdya_         210 ADVNVRGERGKTPLILAVEKKHLGLVQRLLEQEHIEINDTDSDGKTALLLAVELKLKKIAELLCK-RGASTDCGDL  284 (285)
T ss_dssp             CCSSCCCTTSCCHHHHHHHTTCHHHHHHHHHSSSCCTTCCCTTSCCHHHHHHHTTCHHHHHHHHH-HSSCSCCSSC
T ss_pred             CCCCccCCCCCCccchhhhcCcHHHHHHHHHcCCCCCcCCCCCCCCHHHHHHHcCCHHHHHHHHH-CCCCCCcccC
Confidence            45677788999999999998888899988876799999999999999999999999999999999 7999999884

>d1sw6a_ d.211.1.1 (A:) Swi6 ankyrin-repeat fragment {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: beta-hairpin-alpha-hairpin repeat
superfamily: Ankyrin repeat
family: Ankyrin repeat
domain: Swi6 ankyrin-repeat fragment
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.21  E-value=6e-12  Score=110.45  Aligned_cols=57  Identities=30%  Similarity=0.436  Sum_probs=52.8

Q ss_pred             CCCCcccc-CCCCchHHHHHHHcCCHHHHHHHHhhcCCCccccCCCCCcHHHHHHHcCC
Q psy630          278 KDFNINQL-DENGLNCLHWACDRGHLKVVQHLIEKCGADVNVTDSDGDYGLDYAKAIEH  335 (347)
Q Consensus       278 ~~~~~~~~-d~~g~tpLh~A~~~g~~~~v~~Ll~~~ga~i~~~d~~g~TpLh~A~~~~~  335 (347)
                      .+.++|.+ |..|+||||+||..|+.++|++||+ .|++++.+|..|+||||+||..++
T Consensus        95 ~~~dvn~~~D~~G~T~LH~Aa~~g~~~~v~~Ll~-~gad~~~~d~~G~TpL~~A~~~~~  152 (301)
T d1sw6a_          95 TQLNLNIPVDEHGNTPLHWLTSIANLELVKHLVK-HGSNRLYGDNMGESCLVKAVKSVN  152 (301)
T ss_dssp             SCCCSCSCCSTTCCCHHHHHHHTTCHHHHHHHHH-TTCCTTBCCTTCCCHHHHHHHSSH
T ss_pred             cCCCcCcCcCCCCCCHHHHHHHcCCHHHHHHHHH-CCCCCCcCCcccccHHHHhhhccc
Confidence            56788876 9999999999999999999999999 799999999999999999998765

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.07  E-value=4.1e-11  Score=87.48  Aligned_cols=80  Identities=14%  Similarity=0.148  Sum_probs=67.2

Q ss_pred             CCCeEEEeCC--CCCCC--------HHHHHHHHhccCCeeEEEEeeeCCCC--CceeEEEEEEcCHHHHHHHHhc-CCCc
Q psy630            7 QLNKIFVGNL--PWTVS--------HNELKKFFSEYGQIMNASVMFDKNTG--LSKGFGFVTFQNKEAVDKVFST-DSHV   73 (347)
Q Consensus         7 ~~~~l~V~nL--p~~~t--------~~~l~~~f~~~G~i~~~~i~~~~~t~--~~~g~afV~f~~~~~a~~a~~~-~~~~   73 (347)
                      +++.|.++|+  |....        .++|++.|++||.|.+|.|+++..+.  ...|++||+|.+.++|.+|+.. +|..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            4678999999  55543        24689999999999999998876543  3569999999999999999985 9999


Q ss_pred             cCCccccccCCCc
Q psy630           74 LEGSRLSIQPSDS   86 (347)
Q Consensus        74 ~~g~~l~v~~~~~   86 (347)
                      ++||+|.+.+...
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999988754

>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=97.95  E-value=2.3e-07  Score=64.34  Aligned_cols=60  Identities=17%  Similarity=0.194  Sum_probs=44.3

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..+++||+|||..+++++|+++|+.||+|....+..++.     .|+.|+.||.  ...+.++|..+
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~-----~g~~kg~afV--~f~~~~~a~~A   64 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQV-----TGVSRGVGFI--RFDKRIEAEEA   64 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----TCCEEEEEEE--EESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccc-----cccCCCeeEE--EEcCHHHHHHH
Confidence            456799999999999999999999999999877766542     2233333443  35567777666

>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=97.85  E-value=5.3e-07  Score=61.97  Aligned_cols=58  Identities=9%  Similarity=0.002  Sum_probs=43.9

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      .++||+|||..+++++|+++|+.||.+....+..++.     .|+.|+.||..  ..+.++|+++
T Consensus         3 t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~-----~g~~~g~afV~--f~~~~~A~~a   60 (82)
T d1b7fa1           3 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYK-----TGYSYGYAFVD--FTSEMDSQRA   60 (82)
T ss_dssp             SEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETT-----TTEECSEEEEE--ESSHHHHHHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecc-----cCCccccceEE--ECCHHHHHHH
Confidence            4699999999999999999999999998766655432     23444445444  4578888777

>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=97.84  E-value=3.7e-07  Score=62.50  Aligned_cols=58  Identities=14%  Similarity=0.032  Sum_probs=43.8

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      |.+||+|||+.+++++|+++|+.||++....+..++.     .|+.|+.|+..  ..+.++|+.+
T Consensus         1 aslfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~-----tg~~~g~aFV~--f~~~~~a~~a   58 (80)
T d1cvja1           1 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMI-----TRRSLGYAYVN--FQQPADAERA   58 (80)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----TCCEEEEEEEE--ESSHHHHHHH
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEeccc-----ccCCCCceEEE--ECCHHHHHHH
Confidence            5789999999999999999999999998877766543     23334444444  4567777766

>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=97.83  E-value=9.3e-07  Score=61.74  Aligned_cols=59  Identities=17%  Similarity=0.153  Sum_probs=43.9

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||++....+..++.     .|+.|+.||..  ..+.++|..+
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~-----~~~~kg~afV~--f~~~~~A~~a   63 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYE-----TEKHRGFAFVE--FELAEDAAAA   63 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSS-----SCCCSSEEEEC--CSSHHHHHHH
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccc-----cccccceeEEE--ECCHHHHHHH
Confidence            46899999999999999999999999998776655442     23344444443  5567777766

>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=97.76  E-value=6.5e-07  Score=60.32  Aligned_cols=57  Identities=5%  Similarity=0.100  Sum_probs=41.7

Q ss_pred             cccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          102 CDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       102 ~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ++||+|||.++++++|+++|+.||+|....+..++.     .++.|+.||..+..  .++|.++
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~-----t~~~rG~~FV~f~~--~~~a~~a   57 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNK-----TNKRRGFCFITFKE--EEPVKKI   57 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTT-----TCCTTCCEEEEESS--SHHHHHH
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCccccccccccc-----ccccccEEEEEECC--HHHHHHH
Confidence            479999999999999999999999998777766543     34455555555443  4444444

>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=97.75  E-value=1.2e-06  Score=61.75  Aligned_cols=65  Identities=6%  Similarity=0.091  Sum_probs=47.6

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIAL  169 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~  169 (347)
                      ...++||+|||..+++++|+++|+.||+|....+..+...    .|+.|+.||..  ..+.++|..+...+
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~----~g~~rg~afV~--f~~~~~A~~Ai~~l   71 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTG----TGAHRGFGFVD--FITKQDAKKAFNAL   71 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSS----SCSSCSEEEEE--ESSHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEecccc----CCCcccEEEEE--ECCHHHHHHHHHHc
Confidence            3468999999999999999999999999987766544321    23445555554  56688888775443

>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=97.75  E-value=9.7e-07  Score=59.48  Aligned_cols=57  Identities=7%  Similarity=0.053  Sum_probs=41.8

Q ss_pred             cccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          102 CDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       102 ~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ++||+|||..+++++|.++|+.||++....+..++.     .++.|+.||..  ..+.++|..+
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~-----t~~~kg~afV~--f~~~~~a~~A   57 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPI-----TGRSRGFGFVL--FKESESVDKV   57 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTT-----TTBCCSEEEEE--ESSHHHHHHH
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCC-----CCCcCceEEEE--ECCHHHHHHH
Confidence            479999999999999999999999999877766543     23444445544  3456666555

>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=97.74  E-value=8.2e-07  Score=60.98  Aligned_cols=58  Identities=9%  Similarity=0.031  Sum_probs=42.9

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      .++||+|||..+++++|+++|+.||.+....+..+..     .++.|+.||..  ..+.++|+.+
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~-----~~~~~g~afv~--f~~~~~a~~a   60 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKI-----TGQSLGYGFVN--YIDPKDAEKA   60 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTT-----TCCEEEEEEEE--ESSHHHHHHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeecc-----CCCceeeEEEE--ECCHHHHHHH
Confidence            4699999999999999999999999998766654433     23344445554  4567777766

>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=97.74  E-value=1e-06  Score=59.66  Aligned_cols=58  Identities=9%  Similarity=0.099  Sum_probs=43.4

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      +++||+|||.++++++|+++|+.||.|....+..++.     .|+.|+.||..+  .+.++|.++
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~-----tg~~kG~aFV~f--~~~~~a~~a   58 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL-----TKRSRGFGFVTF--MDQAGVDKV   58 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCC-----SSSCSSEEEECC--CCTTHHHHH
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccC-----CCCccceEEEEE--CCHHHHHHH
Confidence            4689999999999999999999999998777766543     244555566554  445566555

>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=97.72  E-value=1.6e-06  Score=60.64  Aligned_cols=60  Identities=12%  Similarity=0.101  Sum_probs=43.3

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ..++||+|||..+++++|.++|+.||.|....+..++.     .++.|+.||..  ..+.++|+++.
T Consensus         5 ~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~-----~~~~~g~afV~--f~~~~~a~~Ai   64 (90)
T d1x5sa1           5 EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRE-----TQRSRGFGFVT--FENIDDAKDAM   64 (90)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSS-----SCSCCSEEEEE--CSSHHHHHHHH
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccceeeccccc-----cccccceEEEE--ECCHHHHHHHH
Confidence            35689999999999999999999999998665544332     22334444443  55778887774

>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=97.67  E-value=1e-06  Score=61.66  Aligned_cols=59  Identities=12%  Similarity=0.053  Sum_probs=44.5

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.|....+..++.     .|+.|+.||..  ..+.++|.++
T Consensus         8 ~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~-----tg~srG~aFV~--f~~~~~a~~a   66 (90)
T d2cqga1           8 TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLK-----TGHSKGFGFVR--FTEYETQVKV   66 (90)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSS-----SCSEEEEEEEE--ESSHHHHHHH
T ss_pred             CCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCC-----CcccCCEEEEE--ECCHHHHHHH
Confidence            35799999999999999999999999998877776543     23445555555  3456666665

>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=97.67  E-value=2.3e-06  Score=57.48  Aligned_cols=57  Identities=5%  Similarity=0.053  Sum_probs=41.8

Q ss_pred             cccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          102 CDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       102 ~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ++||+|||..+++++|+++|+.||.+....+..++.     .++.++.||..  ..+.++|..+
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~-----~~~~~~~afV~--F~~~~~a~~a   57 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKT-----TNRHRGFGFVT--FESEDIVEKV   57 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTT-----CTTSCCEEEEE--CSCHHHHHHH
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecc-----ccccCceeEEE--ECCHHHHHHH
Confidence            479999999999999999999999998777666543     23344445554  3456666554

>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=97.66  E-value=2.9e-06  Score=57.95  Aligned_cols=58  Identities=7%  Similarity=-0.035  Sum_probs=39.5

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      +++||+|||..+++++|+++|+.||.+....+..++.     .|+.|+.||..  ..+.++|.++
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~-----~~~~~g~afV~--f~~~e~A~~A   59 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLR-----FNTSRRFAYID--VTSKEDARYC   59 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC------------CCEEEEE--CSSHHHHHHH
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccc-----cccccceeEEE--ECCHHHHHHH
Confidence            5799999999999999999999999987544433321     33444445544  5567777666

>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=97.66  E-value=1.2e-06  Score=60.48  Aligned_cols=60  Identities=15%  Similarity=0.169  Sum_probs=44.9

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||.+....+..++.     .|+.|+.||.  ...+.++|..+
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~-----~g~~~g~afV--~f~~~~~A~~A   64 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKL-----TGRPRGVAFV--RYNKREEAQEA   64 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTT-----TCCEEEEEEE--EESSHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccc-----cccCceeEEE--EECCHHHHHHH
Confidence            345799999999999999999999999998777665543     2334444553  35577787766

>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=97.64  E-value=2e-06  Score=61.68  Aligned_cols=59  Identities=17%  Similarity=0.187  Sum_probs=44.3

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      .+++||+|||..+++++|+++|+.||.+....+..++.     .|+.|+.||.  ...+.++|..+
T Consensus        18 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~-----~g~~kG~afV--~f~~~~~A~~A   76 (102)
T d2cpza1          18 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQ-----TNLSKCFGFV--SYDNPVSAQAA   76 (102)
T ss_dssp             TCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSS-----SCSEEEEEEE--ECSSHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecc-----cCCCccceEE--EeCCHHHHHHH
Confidence            46799999999999999999999999998777666543     2233333444  35678888776

>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=97.63  E-value=1.4e-06  Score=60.60  Aligned_cols=61  Identities=13%  Similarity=0.102  Sum_probs=44.7

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ...++||+|||..+++++|.++|+.||.+....+..++.     .|+.|+.||..  ..+.++|.++.
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~-----tg~~~g~afV~--f~~~~~A~~A~   66 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR-----TGFSKGYALVE--YETHKQALAAK   66 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----TSSEEEEEEEE--ESSHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCccccccccccc-----ccccccceeEE--ECCHHHHHHHH
Confidence            446899999999999999999999999998777665432     23334334443  45688887774

>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=97.63  E-value=1.1e-06  Score=58.65  Aligned_cols=57  Identities=19%  Similarity=0.174  Sum_probs=41.4

Q ss_pred             ccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          103 DYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       103 ~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      +||+|||..+++++|+++|+.||.+....+..+++     .++.|+.|+.  ...+.++|..++
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~-----~~~~~g~afV--~f~~~~~A~~Ai   57 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKT-----TNKCKGYGFV--DFDSPSAAQKAV   57 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSS-----SCSCCSEEEE--EESCHHHHHHHH
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccc-----cccccceeEE--EECCHHHHHHHH
Confidence            68999999999999999999999998776655443     2223333433  355777777664

>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=97.62  E-value=1.3e-05  Score=54.12  Aligned_cols=57  Identities=12%  Similarity=0.100  Sum_probs=43.8

Q ss_pred             cccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          102 CDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       102 ~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ++||+|||+.+++++|+++|+.||++....+..++.+      +.|+.||..  ..+.++|.++.
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g------~~~g~afV~--f~~~~~A~~Ai   58 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSG------RSLGTADVH--FERKADALKAM   58 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCC------CSCCEEEEE--ESCHHHHHHHH
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeecc------ccceeEEEE--ECCHHHHHHHH
Confidence            4899999999999999999999999998777766543      334444443  55778887763

>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=97.61  E-value=1.7e-06  Score=60.88  Aligned_cols=59  Identities=12%  Similarity=0.131  Sum_probs=43.4

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      .+++||+|||..+++++|+++|+.||++....+..++.     .|+.|+.||..  ..+.++|..+
T Consensus         9 ~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~-----tg~~kg~afV~--f~~~~~A~~A   67 (93)
T d1x5ua1           9 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRV-----TGQHQGYGFVE--FLSEEDADYA   67 (93)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSS-----SCSBCSCEEEE--ESSHHHHHHH
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeeccc-----ccccccceEEE--ECCHHHHHHH
Confidence            36899999999999999999999999998777655433     23344445554  3456666655

>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=97.59  E-value=1.3e-06  Score=60.41  Aligned_cols=57  Identities=11%  Similarity=0.023  Sum_probs=42.8

Q ss_pred             cccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          102 CDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       102 ~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ++||+|||..+++++|+++|+.||+|....+..++.     .|+.|..||..  ..+.++|..+
T Consensus         3 rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~-----tg~~rg~aFV~--f~~~~~A~~a   59 (85)
T d2u2fa_           3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSA-----TGLSKGYAFCE--YVDINVTDQA   59 (85)
T ss_dssp             CEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCS-----SSCCCCEEEEE--ESSSHHHHHH
T ss_pred             EEEEECCCCCCCHHHHHHHHHhcCccceEEeecccc-----ccccceeEEEE--ECCHHHHHHH
Confidence            689999999999999999999999998777766543     23444445544  4566666665

>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=97.59  E-value=1.6e-06  Score=61.04  Aligned_cols=61  Identities=8%  Similarity=0.041  Sum_probs=44.6

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYI  167 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi  167 (347)
                      .+++||+|||..+++++|+++|+.||+|....+..++.     .++.|+.|+..  ..+.++|..+..
T Consensus         7 s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~-----~~~~kg~afV~--f~~~~~A~~Ai~   67 (93)
T d1h2vz_           7 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKM-----KKTACGFCFVE--YYSRADAENAMR   67 (93)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----TCCEEEEEEEE--ESSHHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccc-----cccccceEEEE--ECCHHHHHHHHH
Confidence            46899999999999999999999999998777655433     22333334433  457778877743

>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=97.57  E-value=2.8e-06  Score=60.87  Aligned_cols=58  Identities=12%  Similarity=0.093  Sum_probs=43.3

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      .++||+|||..+++++|+++|+.||.|....+..++.     .++.|+.||..  ..+.++|..+
T Consensus        21 ~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~-----~~~~kg~aFV~--f~~~~~a~~a   78 (103)
T d1x4ba1          21 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPA-----SKRSRGFGFVT--FSSMAEVDAA   78 (103)
T ss_dssp             TEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTT-----TSSCCSEEEEE--CSSHHHHHHH
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHhhCcccceeeccccc-----CCCccCeEEEE--ECCHHHHHHH
Confidence            5799999999999999999999999999887766543     22334445554  3466666554

>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=97.54  E-value=2.6e-06  Score=61.14  Aligned_cols=58  Identities=12%  Similarity=0.151  Sum_probs=43.9

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      .++||+|||..+++++|+++|+.||.|....+..++.     .|+.|+.||..  ..+.++|..+
T Consensus        11 ~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~-----tg~~kg~afV~--f~~~~~A~~A   68 (103)
T d2cqda1          11 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQ-----TGKSRGYGFVT--MADRAAAERA   68 (103)
T ss_dssp             SEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSS-----SCCCCSEEEEE--ESSHHHHHHH
T ss_pred             cEEEEeCCCCcCcHHHHHHHHhhcccccceecccccc-----ccccCCeEEEE--ECCHHHHHHH
Confidence            5699999999999999999999999998877766543     23444445544  3467777665

>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=97.53  E-value=2.6e-06  Score=58.51  Aligned_cols=59  Identities=14%  Similarity=0.056  Sum_probs=42.0

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.+....+..++.     .++.|..|+..  ..+.++|..+
T Consensus         9 ~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~-----~~~~~g~afV~--f~~~~~A~~A   67 (83)
T d2cqca1           9 NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQ-----SRRSRGFAFVY--FENVDDAKEA   67 (83)
T ss_dssp             GGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSS-----SSSEEEEEEEE--ESSHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCCcccccccccc-----ccccccceEEE--ECCHHHHHHH
Confidence            35899999999999999999999999998777655432     12223334443  4456666655

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.52  E-value=0.00018  Score=49.18  Aligned_cols=69  Identities=16%  Similarity=0.243  Sum_probs=56.0

Q ss_pred             CCeEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCc--eeEEEEEEcCHHHHHHHHhc-CCCccCC
Q psy630            8 LNKIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLS--KGFGFVTFQNKEAVDKVFST-DSHVLEG   76 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~--~g~afV~f~~~~~a~~a~~~-~~~~~~g   76 (347)
                      .++|.|++|||..|++++.+.+...|.+........+.+.++  -.-|||.|.+.++...-... +|+.+.+
T Consensus         1 ~tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           1 LSKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CCEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             CceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            368999999999999999999999998887777766555432  35699999999988877765 8888754

>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=97.50  E-value=3.5e-06  Score=59.96  Aligned_cols=59  Identities=19%  Similarity=0.180  Sum_probs=43.5

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.|....+..++.     .++.|..||..+  .+.++|.++
T Consensus         8 ~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~-----tg~~~g~afV~f--~~~~~a~~A   66 (99)
T d1whwa_           8 SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSL-----TKKPKGFAFVTF--MFPEHAVKA   66 (99)
T ss_dssp             CEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTT-----TCCCCSEEEEEE--SSHHHHHHH
T ss_pred             CCEEEEECCCCcCCHHHHHHHHHhcCCceeeeeccccc-----ccccCcceEEEE--CCHHHHHHH
Confidence            35799999999999999999999999998766655432     233444455553  456777765

>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=97.48  E-value=2.6e-06  Score=58.66  Aligned_cols=58  Identities=10%  Similarity=0.044  Sum_probs=42.9

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      .++||+|||..+++++|.++|+.||++....+..++.     .|+.|+.||..+.  +.++|..+
T Consensus         7 ~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~-----tg~~kG~afV~f~--~~~~a~~a   64 (84)
T d1l3ka1           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPN-----TKRSRGFGFVTYA--TVEEVDAA   64 (84)
T ss_dssp             GEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-----TCCEEEEEEEEES--SHHHHHHH
T ss_pred             cEEEEECCCCCCCHHHHHHHHHhhccccceeeccccc-----CCCcccEEEEEEc--CHHHHHHH
Confidence            5799999999999999999999999998877766543     2344555555543  45555554

>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=97.43  E-value=3.8e-06  Score=60.34  Aligned_cols=58  Identities=10%  Similarity=0.084  Sum_probs=43.4

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      .++||+|||..+++++|+++|+.||.|....+..++.     .|+.|+.||..  ..+.++|..+
T Consensus         9 rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~-----tg~~~g~afV~--f~~~~~a~~a   66 (104)
T d1p1ta_           9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRE-----TGKPKGYGFCE--YQDQETALSA   66 (104)
T ss_dssp             SCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETT-----TTEEEEEEEEE--CSCHHHHHHH
T ss_pred             CEEEEECCCCcCCHHHHHHhhhccccccccccccccc-----eeccCCceEEE--ECCHHHHHHH
Confidence            5799999999999999999999999998776655432     23344445544  4567777765

>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=97.43  E-value=1.7e-06  Score=60.55  Aligned_cols=60  Identities=17%  Similarity=0.131  Sum_probs=44.1

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|.++|+.||.+....+..++.     .|+.|+.||..  ..+.++|.++
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~-----t~~~rg~afV~--f~~~~~A~~A   66 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKT-----TGQSKGFAFIS--FHRREDAARA   66 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSS-----SCSEEEEEEEE--ESSHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhccccccccccccc-----ccccccceeEE--ECCHHHHHHH
Confidence            346899999999999999999999999998766655432     23334444444  4467777776

>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=97.36  E-value=1.1e-05  Score=56.63  Aligned_cols=59  Identities=7%  Similarity=0.020  Sum_probs=43.6

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ...++||+|||..+++++|+++|+.||.|....+..++.+       .|..||..  ..+.++|..+.
T Consensus        10 ~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~-------~kg~afV~--f~~~~~a~~Ai   68 (93)
T d2cq3a1          10 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-------SKGFGFVT--FENSADADRAR   68 (93)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT-------TCCEEEEE--ESCHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC-------CcceeEEE--ECCHHHHHHHH
Confidence            3457999999999999999999999999987776655322       23334444  44677777763

>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=97.35  E-value=6.9e-06  Score=56.28  Aligned_cols=56  Identities=13%  Similarity=0.092  Sum_probs=39.4

Q ss_pred             ccccCCcccccchhhHHHHhhcccccee-cccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          103 DYLPSLVKKLDSSTLLKFYALYKQATVG-QCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       103 ~~v~~l~~~~~~e~l~~~f~~fg~v~~g-~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      +||+|||..+++++|.++|+.||.+... .+..++.     .|+.|+.||..  ..+.++|+++
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~-----~g~~~g~afV~--f~~~~~a~~A   57 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPD-----TGNSKGYAFIN--FASFDASDAA   57 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTT-----TCSCCSEEEEE--BSSHHHHHHH
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeecc-----ccccCceEEEE--ECCHHHHHHH
Confidence            6899999999999999999999998643 3333321     23344445544  5567777776

>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=97.34  E-value=8.9e-06  Score=57.57  Aligned_cols=59  Identities=12%  Similarity=0.077  Sum_probs=42.3

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||++....+..++.     .++.|+.||..  ..+.++|.++
T Consensus         8 ~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~-----~~~~~g~afV~--F~~~~~a~~a   66 (98)
T d1x4ha1           8 GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPD-----TEHSKGCAFAQ--FMTQEAAQKC   66 (98)
T ss_dssp             CCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSS-----SCCBCSEEEEE--ESSHHHHHHH
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccc-----cccccceEEEE--EcCHHHHHHH
Confidence            46899999999999999999999999987666655432     12233344444  3467777666

>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=97.33  E-value=6.9e-06  Score=58.56  Aligned_cols=59  Identities=12%  Similarity=0.092  Sum_probs=44.4

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.|....+..++.     .|+.|+.||..+..  .++|..+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~-----tg~~kG~afV~F~~--~e~a~~A   76 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRN-----SRRSKGIAYVEFCE--IQSVPLA   76 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCC-----SSSCCCCEEEEESC--GGGHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCC-----CccccceEEEEECC--HHHHHHH
Confidence            35799999999999999999999999998777766543     24455556666533  5556554

>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=97.29  E-value=6.7e-05  Score=54.14  Aligned_cols=54  Identities=7%  Similarity=-0.009  Sum_probs=40.1

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ..+|||+|||..+++++|+++|+.||.|....+.  +.         |+.||  +.....++|.+++
T Consensus        10 ~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~--~~---------kg~af--V~f~~~~~A~~A~   63 (111)
T d1whxa_          10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP--EG---------GITAI--VEFLEPLEARKAF   63 (111)
T ss_dssp             EEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC--SS---------SSCEE--EEESCHHHHHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHhhhhccCCccEEEee--cc---------CceEE--EEEcCHHHHHHHH
Confidence            3689999999999999999999999999865553  22         12233  3455677777763

>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=97.29  E-value=3.6e-05  Score=52.78  Aligned_cols=59  Identities=8%  Similarity=-0.089  Sum_probs=44.2

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||..+++++|+++|+.||++....+..++.      |+.|+.|+..  ..+.++|.++
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~------~~~kG~afV~--f~~~e~a~~a   63 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH------KAFKGSIFVV--FDSIESAKKF   63 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTT------CCEEEEEEEE--ESCHHHHHHH
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeecc------CCcceEEEEE--EcCHHHHHHH
Confidence            456899999999999999999999999998777655443      3344445554  4467777666

>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=97.27  E-value=1.4e-05  Score=56.81  Aligned_cols=65  Identities=14%  Similarity=0.074  Sum_probs=44.4

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCC---ccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPS---WYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~---~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...+|||+|||..+++++|+++|+.||++....+.....-   .....|+.|..||..  ..+.++|..+
T Consensus         7 ~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~--f~~~~~a~~A   74 (101)
T d2cpea1           7 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS--YEDPPTAKAA   74 (101)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEE--BSSHHHHHHH
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEE--ecCHHHHHHH
Confidence            3468999999999999999999999999865444332110   011234555556665  4567777766

>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=97.27  E-value=1.2e-05  Score=56.76  Aligned_cols=60  Identities=10%  Similarity=-0.039  Sum_probs=43.2

Q ss_pred             ccccccCCcccccchhhHHHHhhccc-cceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQ-ATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~-v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      +++||+|||..+++++|+++|+.||. +....+..+..    ..++.|+.||..  ..+.++|+.+.
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~----~~~~~rg~aFV~--F~~~~~A~~Ai   62 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAA----DKMKNRGFAFVE--YESHRAAAMAR   62 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSC----TTTTTCCEEEEE--ESSHHHHHHHH
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeecc----ccccCCCeEEEE--EcCHHHHHHHH
Confidence            57899999999999999999999996 66555544322    134455555554  55677887773

>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=97.23  E-value=5.2e-05  Score=54.53  Aligned_cols=55  Identities=7%  Similarity=-0.027  Sum_probs=41.9

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ..+||+|||..+++++|.++|+.||.|....+...+.         |+.|+.  ...+.++|..+.
T Consensus         8 ~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~---------~g~aFV--~f~~~e~A~~Ai   62 (108)
T d2adba1           8 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN---------QFQALL--QYADPVSAQHAK   62 (108)
T ss_dssp             EEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETT---------EEEEEE--EESCHHHHHHHH
T ss_pred             EEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCC---------CCeEEE--EECCHHHHHHHH
Confidence            4689999999999999999999999998766655432         222333  356788888774

>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=97.18  E-value=0.00014  Score=50.02  Aligned_cols=57  Identities=16%  Similarity=0.099  Sum_probs=41.2

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYI  167 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi  167 (347)
                      ..++||+|||..+++++|+++|+.||.+.......++.         |..|+  ++..+.++|.++..
T Consensus        10 s~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~---------~~~af--V~f~~~~~A~~A~~   66 (88)
T d2adca2          10 SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD---------RKMAL--IQMGSVEEAVQALI   66 (88)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSS---------TTCEE--EEESSHHHHHHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecc---------cceeE--EEECCHHHHHHHHH
Confidence            35799999999999999999999999987655444332         11233  23556788887743

>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=97.14  E-value=1.4e-05  Score=55.02  Aligned_cols=61  Identities=10%  Similarity=-0.011  Sum_probs=40.5

Q ss_pred             ccccccccCCcccccch-hhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSS-TLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e-~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...++||+|||.+++++ .|+++|+.||.|....+.....    -.++.|+.||..+  .+.++|..+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~----~~~~~kg~afV~f--~~~~~a~~A   64 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQK----EHSFNNCCAFMVF--ENKDSAERA   64 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC-------CCCEEEEEEE--SSHHHHHHH
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccC----CccccceeeeEEE--CCHHHHHHH
Confidence            45689999999998765 5899999999998776644321    1233344455443  456777665

>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=97.11  E-value=6.1e-06  Score=57.64  Aligned_cols=58  Identities=3%  Similarity=-0.114  Sum_probs=43.5

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.+....+..++      .|+.|+.||..+  .+.++|.++
T Consensus        13 ~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~------~g~~kg~afv~F--~~~e~a~~A   70 (91)
T d1fjeb1          13 PFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR------TGTNRKFGYVDF--ESAEDLEKA   70 (91)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEE------EETTTTEEEEEE--SSHHHHHHH
T ss_pred             CcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecC------CCCccEEeEEee--CCHHHHHHH
Confidence            3579999999999999999999999998765553322      455666666654  467777766

>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=97.10  E-value=6.2e-05  Score=51.76  Aligned_cols=51  Identities=8%  Similarity=-0.103  Sum_probs=38.5

Q ss_pred             cccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          102 CDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       102 ~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ++||+|||..+++++|.++|+.||.|....+..+  |+          |+  +...+.++|.++.
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~--g~----------af--V~f~~~~~a~~Ai   52 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD--GT----------GV--VEFVRKEDMTYAV   52 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT--SE----------EE--EEESSHHHHHHHH
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc--ce----------ee--EEeCCHHHHHHHH
Confidence            5899999999999999999999999987665433  21          22  3355677777763

>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=97.09  E-value=0.00012  Score=50.46  Aligned_cols=35  Identities=9%  Similarity=0.113  Sum_probs=30.5

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccC
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNI  134 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~  134 (347)
                      ..++||+|||..+++++|+++|+.||.+....+..
T Consensus         5 s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~   39 (88)
T d1wf0a_           5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK   39 (88)
T ss_dssp             CCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee
Confidence            46899999999999999999999999998655543

>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=97.08  E-value=1.1e-05  Score=61.08  Aligned_cols=58  Identities=12%  Similarity=0.089  Sum_probs=42.5

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      .++||+|||..+++++|+++|+.||.|....+..++.     .|+.|+.||..  ..+.++|.++
T Consensus        43 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~-----t~~~rg~afV~--f~~~~~A~~A  100 (139)
T d1u6fa1          43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRE-----TRQSRGYGFVK--FQSGSSAQQA  100 (139)
T ss_dssp             SEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETT-----TTEEEEEEEEE--ESSHHHHHHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhhccccccccccccc-----cccccceeeEE--ECCHHHHHHH
Confidence            5799999999999999999999999998777765432     22333334433  4567777666

>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=97.05  E-value=1e-05  Score=56.20  Aligned_cols=64  Identities=8%  Similarity=0.136  Sum_probs=42.1

Q ss_pred             ccccccccCCcccccchhh---HHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTL---LKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l---~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ....+||+|||+.++++++   .++|+.||.|....+..+++..-  ....++.||  +...+.++|.++.
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~--~~~~~g~aF--V~f~~~~~A~~Ai   73 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAG--SQGPSASAY--VTYIRSEDALRAI   73 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCS--SSCCCEEEE--EEESSHHHHHHHH
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCC--CCCcceEEE--EecccchhHHHHH
Confidence            3457899999999999999   67899999999777665432110  000111222  3355778887773

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.05  E-value=0.00024  Score=47.81  Aligned_cols=71  Identities=21%  Similarity=0.262  Sum_probs=55.9

Q ss_pred             CCeEEEeCCCCCCCH---------HHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhcCCCccCCcc
Q psy630            8 LNKIFVGNLPWTVSH---------NELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFSTDSHVLEGSR   78 (347)
Q Consensus         8 ~~~l~V~nLp~~~t~---------~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~   78 (347)
                      ..+|.|.=..++..+         .+|.+.|..||+|.-+|++.+        -..|+|.+-.+|..|+..++..+.|+.
T Consensus        15 DgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~l~g~~v~G~~   86 (95)
T d1ufwa_          15 DATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLDVDGMKVKGRA   86 (95)
T ss_dssp             TCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHHGGGSEETTEE
T ss_pred             CcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhccCCeEEcceE
Confidence            346767544433322         356788899999999999865        479999999999999999999999999


Q ss_pred             ccccCCCc
Q psy630           79 LSIQPSDS   86 (347)
Q Consensus        79 l~v~~~~~   86 (347)
                      |.|....+
T Consensus        87 l~It~~~~   94 (95)
T d1ufwa_          87 VKISGPSS   94 (95)
T ss_dssp             EEEECCCC
T ss_pred             EEEecCCC
Confidence            99876543

>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=97.03  E-value=9.5e-05  Score=49.22  Aligned_cols=55  Identities=9%  Similarity=0.009  Sum_probs=40.2

Q ss_pred             cccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          102 CDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       102 ~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ++||+|||..+++++|+++|+.||.|....+..++.+..       ..|+.+  ..+.++|.++
T Consensus         2 tv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~-------~~afV~--F~~~~~a~~A   56 (75)
T d2ghpa2           2 TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNF-------RFARIE--FARYDGALAA   56 (75)
T ss_dssp             EEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSS-------EEEEEE--ESSHHHHHHH
T ss_pred             EEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccc-------eEEEEE--EcchHHhHHH
Confidence            689999999999999999999999998777665544321       123333  4456666666

>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=97.02  E-value=0.0001  Score=49.55  Aligned_cols=36  Identities=11%  Similarity=0.232  Sum_probs=31.8

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCC
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDK  136 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~  136 (347)
                      .++||+|||..+++++|+++|+.||.+....+..++
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~   38 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR   38 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECT
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCC
Confidence            578999999999999999999999999877766543

>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=97.00  E-value=0.00028  Score=49.40  Aligned_cols=54  Identities=7%  Similarity=0.006  Sum_probs=39.8

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ..++||+|||+.+++++|+++|+.||.|....+...+.           .||  +...+.++|..+.
T Consensus        17 s~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~-----------~af--V~f~~~~~A~~A~   70 (97)
T d1whya_          17 TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS-----------FAY--IQYESLDAAQAAC   70 (97)
T ss_dssp             CSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSC-----------CEE--EEESSHHHHHHHH
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecccc-----------EEE--eccCCHHHHHHHH
Confidence            36899999999999999999999999998766544322           122  2345677777663

>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=97.00  E-value=1.3e-05  Score=55.72  Aligned_cols=61  Identities=10%  Similarity=0.052  Sum_probs=41.8

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAM  163 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~  163 (347)
                      .++||+|||..+++++|+++|+.||.+....+....+....-.++.|..|+..+.  +.++|.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~--~~e~a~   62 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFR--SVDETT   62 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEES--SCTTTT
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeC--CHHHHH
Confidence            4689999999999999999999999987655544433333334455555555443  344443

>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=97.00  E-value=5.7e-05  Score=54.87  Aligned_cols=56  Identities=11%  Similarity=0.116  Sum_probs=41.3

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|.++|+.||.|....+..+.        +.|+.||..  ..+.++|..+
T Consensus         7 ~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~--------~~kG~afV~--f~~~~~A~~A   62 (114)
T d2f9da1           7 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP--------ETRGTAYVV--YEDIFDAKNA   62 (114)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECST--------TTTTEEEEE--ESSHHHHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccC--------CcCCeEEEE--ECCHHHHHHH
Confidence            3579999999999999999999999999876554322        234445444  4467777766

>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=96.95  E-value=0.00029  Score=47.36  Aligned_cols=52  Identities=15%  Similarity=0.157  Sum_probs=38.4

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      .++||+|||..+++++|+++|+.||.+....+...+           ..|+  +...+.++|.++
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~r-----------g~aF--V~f~~~~~A~~A   53 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS-----------GYAF--VDYPDQNWAIRA   53 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEET-----------TEEE--ECCSCHHHHHHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEeccc-----------ceEE--EEECCHHHHHHH
Confidence            368999999999999999999999988654443322           2222  345677888777

>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=96.93  E-value=0.00018  Score=49.72  Aligned_cols=58  Identities=9%  Similarity=0.134  Sum_probs=42.4

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ..++||+|||..+++++|+++|+.||++....+..++.+.       |..||  +...+.++|..+.
T Consensus         8 ~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~-------~~~af--V~f~~~~~A~~A~   65 (90)
T d2cqia1           8 PRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN-------DPYCF--VEFYEHRDAAAAL   65 (90)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS-------CCEEE--EEESSHHHHHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc-------ceeeE--EEECCHHHHHHHH
Confidence            3579999999999999999999999999877666554321       11233  3345677777663

>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=96.92  E-value=0.00013  Score=51.61  Aligned_cols=58  Identities=12%  Similarity=0.113  Sum_probs=42.0

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.+....+..+..+      +.++.||.  ...+.++|.++
T Consensus        18 ~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~------~~~g~afV--~f~~~~~A~~A   75 (101)
T d1x5oa1          18 PTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSG------TSRGVGFA--RMESTEKCEAV   75 (101)
T ss_dssp             TTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSS------CEEEEEEE--EESCHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccccc------ccccceeE--EeCCHHHHHHH
Confidence            357999999999999999999999999976655544322      22333333  35567777776

>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=96.90  E-value=0.00026  Score=49.50  Aligned_cols=54  Identities=9%  Similarity=0.044  Sum_probs=40.5

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ..++||+|||..+++++|+++|+.||.|....+..++           +.||.  ...+.++|..+.
T Consensus        18 ~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~k-----------g~afV--~f~~~~~A~~Ai   71 (96)
T d1x4ga1          18 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK-----------GYSFV--RFSTHESAAHAI   71 (96)
T ss_dssp             CCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTT-----------TEEEE--EESSHHHHHHHH
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEecc-----------eEEEE--EECCHHHHHHHH
Confidence            3579999999999999999999999999876665442           22222  345677777664

>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=96.89  E-value=0.00022  Score=49.08  Aligned_cols=57  Identities=14%  Similarity=0.140  Sum_probs=41.8

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.|....+..++.+       .|+.||.  ...+.++|+++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~-------~kg~afV--~f~~~~~A~~A   64 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-------SKGYGFV--HFETQEAAERA   64 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTB-------CCSCEEE--EESCHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCC-------CcceeEE--EECCHHHHHHH
Confidence            457999999999999999999999999987777655321       2223333  34567777666

>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=96.85  E-value=3.7e-05  Score=54.79  Aligned_cols=58  Identities=10%  Similarity=0.122  Sum_probs=41.3

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceeccc-CCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCN-IDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~-~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..+|||+|||..+++++|+++|..||.+...... ...      .|+.|+.|+..  ..+.++|..+
T Consensus         8 ~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~------~g~~~G~afV~--F~s~~~a~~A   66 (103)
T d2cpya1           8 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN------NGQGLGQALVQ--FKNEDDARKS   66 (103)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT------TSSCSSCEEEE--CSSHHHHHHH
T ss_pred             ceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCC------CCCcCccEEEE--ECCHHHHHHH
Confidence            3579999999999999999999999988643222 222      33445555554  5567777765

>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=96.84  E-value=0.00031  Score=47.92  Aligned_cols=52  Identities=13%  Similarity=0.145  Sum_probs=39.0

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      .++||+|||..+++++|+++|+.||.+....+...+.           .|+  +...+.++|..+
T Consensus         9 k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~rg-----------~af--V~f~~~~~A~~A   60 (86)
T d2cpda1           9 KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD-----------YAF--VHFSNREDAVEA   60 (86)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECSS-----------EEE--EEESSHHHHHHH
T ss_pred             CEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccccE-----------EEE--EEeCCHHHHHHH
Confidence            5799999999999999999999999987666543321           222  234567777766

>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=96.82  E-value=0.00021  Score=48.83  Aligned_cols=35  Identities=14%  Similarity=0.188  Sum_probs=30.7

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCC
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                      .++||+|||..+++++|+++|+.||.|....+..+
T Consensus         9 ~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~   43 (86)
T d2cpja1           9 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD   43 (86)
T ss_dssp             TEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc
Confidence            46999999999999999999999999987666543

>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=96.80  E-value=1.5e-05  Score=56.86  Aligned_cols=59  Identities=14%  Similarity=0.190  Sum_probs=42.0

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.+....+..+..     .|+.++.||  +...+.++|.++
T Consensus        18 s~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~-----~g~~~g~~f--V~f~~~~~A~~A   76 (102)
T d2cpxa1          18 NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM-----TGRMRGQAF--ITFPNKEIAWQA   76 (102)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE-----CSSSCSEEE--EECSSHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccc-----cccccccce--EEeccHHHHHHH
Confidence            35799999999999999999999999987655543221     122333333  335578888876

>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=96.77  E-value=0.00017  Score=49.12  Aligned_cols=59  Identities=10%  Similarity=-0.075  Sum_probs=41.5

Q ss_pred             ccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          103 DYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       103 ~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      +||+|||..+++++|+++|+.||.|....+..++...  ..++.|+.||..  ..+.++|.++
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~--~~~~~kG~afV~--f~~~~~A~~A   59 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKA--GVLLSMGFGFVE--YKKPEQAQKA   59 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTT--CCEEEEEEEEEE--ESSHHHHHHH
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccc--cccccceEEEEE--ECCHHHHHHH
Confidence            6899999999999999999999999887776543211  111223334444  4467777776

>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=96.75  E-value=4e-05  Score=54.73  Aligned_cols=60  Identities=13%  Similarity=0.062  Sum_probs=40.9

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ...+|||+|||..+++++|+++|..||.+..........     .++.|+.||..  ..+.++|.++
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~-----~~~~kG~afV~--F~~~e~a~~a   73 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDF-----QGRSTGEAFVQ--FASQEIAEKA   73 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCS-----SSCBCSEEEEE--ESSHHHHHHH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCC-----CCCcceEEEEE--eCCHHHHHHH
Confidence            445799999999999999999999999887543333322     23344445554  3456777543

>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=96.74  E-value=0.00043  Score=49.09  Aligned_cols=56  Identities=9%  Similarity=-0.105  Sum_probs=41.2

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYI  167 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi  167 (347)
                      ...++||+|||..+++++|+.+|+.||.|....+..+           |..||.+  ..+.++|..+..
T Consensus        14 ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~-----------k~~AfV~--f~~~e~A~~ai~   69 (104)
T d1wexa_          14 VSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF-----------KRQALVE--FENIDSAKECVT   69 (104)
T ss_dssp             CCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT-----------TTEEEEE--ESSHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec-----------ceeEEEE--eCCHHHHHHHHH
Confidence            3468999999999999999999999999986555432           2234444  456677766643

>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=96.69  E-value=0.00041  Score=46.93  Aligned_cols=55  Identities=7%  Similarity=0.065  Sum_probs=40.8

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ..++||+|||..+++++|..+|+.||.+....+..++.|          .|+  +...+.++|..+.
T Consensus         8 ~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g----------~af--V~f~~~~~A~~A~   62 (83)
T d2b0ga1           8 NQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHD----------IAF--VEFTTELQSNAAK   62 (83)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCS----------CEE--EEESSHHHHHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccce----------eEE--EecCCHHHHHHHH
Confidence            368999999999999999999999999987666443322          122  3355677777774

>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=96.69  E-value=2.6e-05  Score=53.64  Aligned_cols=58  Identities=12%  Similarity=0.106  Sum_probs=39.1

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..+||+|||..+++++|+++|+.||.+.........+     .++.|+.|+..  ..+.++|+++
T Consensus        10 ~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~-----~g~~~G~afV~--f~~~e~a~~A   67 (86)
T d2cqpa1          10 TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE-----KGMPTGEAMVA--FESRDEATAA   67 (86)
T ss_dssp             EEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECS-----SSCEEEEEEEE--ESCHHHHHHH
T ss_pred             CEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCC-----CCCcceEEEEE--EcCcHHHHHH
Confidence            4699999999999999999999999885422222211     23344444444  3456677666

>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=96.67  E-value=0.00015  Score=51.96  Aligned_cols=37  Identities=11%  Similarity=0.244  Sum_probs=31.7

Q ss_pred             ccccccCCcc-cccchhhHHHHhhccccceecccCCCC
Q psy630          101 ACDYLPSLVK-KLDSSTLLKFYALYKQATVGQCNIDKP  137 (347)
Q Consensus       101 ~~~~v~~l~~-~~~~e~l~~~f~~fg~v~~g~~~~~~p  137 (347)
                      .++||+||++ .+++++|+++|+.||.|....+..++.
T Consensus         3 ~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~k   40 (109)
T d2adca1           3 SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK   40 (109)
T ss_dssp             SEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTS
T ss_pred             CEEEEeCCCcccCCHHHHHHHHhhccccceEEEEeccc
Confidence            5789999965 599999999999999999888776653

>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=96.64  E-value=0.00048  Score=47.91  Aligned_cols=56  Identities=9%  Similarity=0.040  Sum_probs=40.3

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      .+++||+|||..+++++|+++|+.||.+....+.....        .|+.|+  +...+.++|+.+
T Consensus        14 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~--------~~g~af--V~f~~~e~a~~A   69 (95)
T d1x4aa1          14 DCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG--------GPPFAF--VEFEDPRDAEDA   69 (95)
T ss_dssp             SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSS--------SSCCEE--EEESCHHHHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccccc--------ccceEE--EEECCHHHHHHH
Confidence            35799999999999999999999999998765543322        122233  334567777766

>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=96.58  E-value=0.00064  Score=45.46  Aligned_cols=51  Identities=8%  Similarity=-0.026  Sum_probs=36.3

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|++  +++++|+++|+.||+|....+..++           ..||  +...+.++|..+
T Consensus         5 ~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~~-----------~~af--V~f~~~~~A~~A   55 (79)
T d2bz2a1           5 GNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR-----------NCAF--VTYEKMESADQA   55 (79)
T ss_dssp             CCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETTT-----------TEEE--EECSSHHHHHHH
T ss_pred             CCEEEEECCC--CCHHHHHHHHhccCccceeeeccCC-----------CEEE--EEEcccHHHHHH
Confidence            3579999985  8999999999999999865543322           1232  335567777766

>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=96.57  E-value=0.00073  Score=46.24  Aligned_cols=53  Identities=9%  Similarity=0.108  Sum_probs=37.5

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ..+|||+|||..+++++|+++|+.||. ....+           ++.|..||  +...+.++|..+.
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G~-~~~~~-----------~~~kg~af--V~f~~~~~A~~Ai   57 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYDL-KYCYV-----------DRNKRTAF--VTLLNGEQAQNAI   57 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSCC-CCEEE-----------EGGGTEEE--ECCSCHHHHHHHH
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcCc-eeeee-----------eccCCceE--EEECCHHHHHHHH
Confidence            357999999999999999999999992 21121           22333444  3466788888763

>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=96.53  E-value=4.5e-05  Score=54.45  Aligned_cols=56  Identities=7%  Similarity=0.087  Sum_probs=37.1

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAM  163 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~  163 (347)
                      .++||+|||..+++++|+++|+.||.+ ...+...+.    ..++.|+.||..+.  +.++|+
T Consensus        16 ~~v~V~nLp~~~te~~l~~~f~~~g~~-~~~~~~~~~----~~g~~~g~afV~f~--~~e~a~   71 (104)
T d1wi8a_          16 YTAFLGNLPYDVTEESIKEFFRGLNIS-AVRLPREPS----NPERLKGFGYAEFE--DLDSLL   71 (104)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTTTSCEE-EEECCBCSS----CTTSBCSCEEEEES--SHHHHH
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhccc-cceeeeeec----cCCCcceeeeEEEC--CHHHHH
Confidence            689999999999999999999999944 333322211    13344555665543  466663

>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=96.52  E-value=0.00023  Score=49.21  Aligned_cols=56  Identities=16%  Similarity=0.133  Sum_probs=39.1

Q ss_pred             ccccccCCcccccchhhH----HHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          101 ACDYLPSLVKKLDSSTLL----KFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~----~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      .++||+|||..+++++|+    .+|+.||+|....+  .+      .++.|+.|+..  ..+.++|.++.
T Consensus         4 ~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~--~~------~~~~~g~afV~--F~~~~~A~~A~   63 (91)
T d1nu4a_           4 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILV--SR------SLKMRGQAFVI--FKEVSSATNAL   63 (91)
T ss_dssp             SEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEEC--CH------HHHHTTCEEEE--ESSHHHHHHHH
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEE--ee------eccCCCceEEE--ECCHHHHHHHH
Confidence            579999999999999885    46899999875443  21      34455555543  55677777663

>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=96.50  E-value=0.00058  Score=45.20  Aligned_cols=23  Identities=9%  Similarity=0.167  Sum_probs=22.3

Q ss_pred             ccccCCcccccchhhHHHHhhcc
Q psy630          103 DYLPSLVKKLDSSTLLKFYALYK  125 (347)
Q Consensus       103 ~~v~~l~~~~~~e~l~~~f~~fg  125 (347)
                      +||+|||+++++++|.++|+.||
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g   23 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE   23 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc
Confidence            68999999999999999999999

>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=96.40  E-value=0.00051  Score=47.02  Aligned_cols=37  Identities=5%  Similarity=-0.062  Sum_probs=31.7

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCC
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                      ...++||+|||..+++++|.++|+.||.+....+...
T Consensus         7 Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~   43 (88)
T d2cq1a1           7 PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG   43 (88)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc
Confidence            3468999999999999999999999999987665543

>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=96.33  E-value=0.00047  Score=48.32  Aligned_cols=52  Identities=8%  Similarity=-0.058  Sum_probs=39.2

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|.++|+.||.+....+..+  |          .||  +...+.++|.++
T Consensus        15 ~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~~--g----------~af--V~f~~~~~a~~A   66 (98)
T d1wg4a_          15 DFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKD--G----------MGM--VEYLRKEDMEYA   66 (98)
T ss_dssp             SCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEETT--T----------EEE--EEESSHHHHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHhhccccccccccc--c----------eEE--EEECCHHHHHHH
Confidence            457999999999999999999999999987665432  2          233  335567777765

>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=96.31  E-value=6.2e-05  Score=54.49  Aligned_cols=59  Identities=10%  Similarity=0.145  Sum_probs=39.7

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+|||..+++++|+++|+.||.+.........     ..|+.++.|+..+.  +.++|..+
T Consensus        18 ~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~-----~~g~~~G~afVeF~--~~e~a~~a   76 (112)
T d1wela1          18 GFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYG-----PNGKATGEGFVEFR--NEADYKAA   76 (112)
T ss_dssp             CCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEEC-----TTSSEEEEEEEEBS--SSHHHHHH
T ss_pred             CeEEEEecCCCcCcHHHHhhHHhhccccccceeeecC-----cccceeeEEEEEEC--CHHHHHHH
Confidence            4589999999999999999999999988643332221     13344455555544  45666533

>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=96.27  E-value=0.00071  Score=48.71  Aligned_cols=35  Identities=6%  Similarity=-0.095  Sum_probs=30.8

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCC
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                      ...||+|||+.+++++|+++|+.||+|...++..+
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~   46 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG   46 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC
Confidence            45699999999999999999999999997777644

>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=96.13  E-value=0.0016  Score=45.65  Aligned_cols=54  Identities=13%  Similarity=0.101  Sum_probs=38.6

Q ss_pred             ccccc--cCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHH
Q psy630          101 ACDYL--PSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYI  167 (347)
Q Consensus       101 ~~~~v--~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi  167 (347)
                      .+++|  ++||..+++++|+++|+.||.+....+..++.           .|+  +...+.++|..++.
T Consensus        19 ~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k~-----------~aF--V~f~~~e~A~~A~~   74 (101)
T d2cq2a1          19 QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP-----------YSF--ARYRTTEESKRAYV   74 (101)
T ss_dssp             SEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCS-----------CEE--EEESSHHHHHHHHH
T ss_pred             ceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCcc-----------EEE--EEECCHHHHHHHHH
Confidence            34556  56999999999999999999998655554332           122  33567888887743

>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=96.05  E-value=0.001  Score=46.62  Aligned_cols=36  Identities=17%  Similarity=0.014  Sum_probs=30.4

Q ss_pred             cccccccCCccc-ccchhhHHHHhhccccceecccCC
Q psy630          100 QACDYLPSLVKK-LDSSTLLKFYALYKQATVGQCNID  135 (347)
Q Consensus       100 ~~~~~v~~l~~~-~~~e~l~~~f~~fg~v~~g~~~~~  135 (347)
                      ..++||+|||.+ +++++|.++|+.||.|....+..+
T Consensus        18 ~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~   54 (99)
T d1x4fa1          18 GRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM   54 (99)
T ss_dssp             CCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT
T ss_pred             CCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec
Confidence            468999999975 899999999999999987666433

>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=96.04  E-value=0.00097  Score=45.68  Aligned_cols=37  Identities=5%  Similarity=-0.112  Sum_probs=31.3

Q ss_pred             cccccccCCccc-ccchhhHHHHhhccccceecccCCC
Q psy630          100 QACDYLPSLVKK-LDSSTLLKFYALYKQATVGQCNIDK  136 (347)
Q Consensus       100 ~~~~~v~~l~~~-~~~e~l~~~f~~fg~v~~g~~~~~~  136 (347)
                      ..++||+|||.. .++++|+++|+.||.|....+...+
T Consensus         8 sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k   45 (89)
T d1x4da1           8 RRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI   45 (89)
T ss_dssp             CCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS
T ss_pred             CcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc
Confidence            457999999985 8899999999999999977665543

>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=96.00  E-value=0.00029  Score=49.20  Aligned_cols=55  Identities=13%  Similarity=0.045  Sum_probs=38.9

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKY  166 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~y  166 (347)
                      ..++||+|||..+++++|+++|+.||.+.....          .++.|+.||..  ..+.++|..++
T Consensus        16 ~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~----------~~~~~~~afV~--f~~~~~A~~A~   70 (96)
T d1fjca_          16 ARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ----------DGKSKGIAYIE--FKSEADAEKNL   70 (96)
T ss_dssp             GGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE----------TTEEEEEEEEE--ESSHHHHHHHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcccceeeee----------cCccccEEEEE--eCCHHHHHHHH
Confidence            468999999999999999999999998764321          12233334433  44677777663

>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=95.66  E-value=0.00019  Score=50.88  Aligned_cols=57  Identities=11%  Similarity=0.144  Sum_probs=38.8

Q ss_pred             cccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..+|||+|||..+++++|+++|+.|+.+. ..+..+..      ++.|..||.+  ..+.++|+.+
T Consensus        15 ~~~v~v~nLp~~~te~dl~~~F~~~~~~~-v~~~~~~~------g~~~G~afVe--F~~~~~a~~A   71 (102)
T d1weza_          15 GHCVHMRGLPYRATENDIYNFFSPLNPMR-VHIEIGPD------GRVTGEADVE--FATHEDAVAA   71 (102)
T ss_dssp             SCEEEEESCCTTCCHHHHHHSSCSCCCSE-EEEEESSS------SCEEEEEEEE--CSSSHHHHHH
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHhccCcce-eeeEEecC------CcceEEEEEE--ECCHHHHHHH
Confidence            35899999999999999999999998553 23333322      3334445554  4456677664

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.21  E-value=0.033  Score=37.77  Aligned_cols=57  Identities=21%  Similarity=0.356  Sum_probs=45.5

Q ss_pred             cccCCC-eEEEeCCCCCCCHHHHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHh
Q psy630            4 SIRQLN-KIFVGNLPWTVSHNELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFS   68 (347)
Q Consensus         4 ~~~~~~-~l~V~nLp~~~t~~~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~   68 (347)
                      ++...| .||.=..|......+|.++|+.||.|. |..+-+.       -|||...+.+.++.++.
T Consensus        10 d~~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-------Sa~V~L~~~e~~~~v~~   67 (100)
T d1whva_          10 DLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCCCCCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHHHHHHHH
T ss_pred             CCCCCcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-------eEEEEecCHHHHHHHHH
Confidence            344444 799999999999999999999999874 4444332       69999999999888875

>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=94.80  E-value=0.0031  Score=43.90  Aligned_cols=34  Identities=9%  Similarity=0.125  Sum_probs=28.1

Q ss_pred             ccccccccCCcc-cccchhhHHHHhhccccceecc
Q psy630           99 NQACDYLPSLVK-KLDSSTLLKFYALYKQATVGQC  132 (347)
Q Consensus        99 ~~~~~~v~~l~~-~~~~e~l~~~f~~fg~v~~g~~  132 (347)
                      ..++|||+||++ .+++++|+++|+.||.|....+
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i   48 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV   48 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE
Confidence            346799999974 6778899999999999986655

>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=94.19  E-value=0.0029  Score=44.60  Aligned_cols=68  Identities=6%  Similarity=0.008  Sum_probs=48.3

Q ss_pred             ccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhhccCChh
Q psy630          101 ACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVDAGWEDK  180 (347)
Q Consensus       101 ~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~l~~~~~~~  180 (347)
                      ..++|.+++..++++.+.++|+.||+|....+..+.+      |+.|+.++..  ..+.++|+++    ++.|...|...
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~------~~~~G~~fV~--f~~~~~A~~A----i~~lng~~~~g   95 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG------DHLVGNVYVK--FRREEDAEKA----VIDLNNRWFNG   95 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS------SSSEEEEEEE--ESCHHHHHHH----HHHHTTCEETT
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCC------CCEeeEEEEE--EechhHHHHH----HHHHCCCEECC
Confidence            4678899999999999999999999999777654443      3334444443  5568888877    45556665543

>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=93.79  E-value=0.059  Score=34.03  Aligned_cols=59  Identities=8%  Similarity=0.118  Sum_probs=47.8

Q ss_pred             HHHHHHhccCCeeEEEEeeeCCCCCceeEEEEEEcCHHHHHHHHhc-CCCccCCccccccCCC
Q psy630           24 ELKKFFSEYGQIMNASVMFDKNTGLSKGFGFVTFQNKEAVDKVFST-DSHVLEGSRLSIQPSD   85 (347)
Q Consensus        24 ~l~~~f~~~G~i~~~~i~~~~~t~~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~v~~~~   85 (347)
                      .|...|.++|.|.++.+..... |  .-.|-|...+..+|..|+.. +...++++.|.|.++.
T Consensus        12 ~L~~~f~~h~~V~sv~l~~~~d-g--~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          12 LLQEAFARHGKVKSVELSPHTD-Y--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHSCEEEEEECSCCS-T--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHhheeEEEEEEEeccC-C--cEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            4567788999999998854322 2  34689999999999999986 9999999999987664

>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=93.31  E-value=0.01  Score=39.47  Aligned_cols=53  Identities=13%  Similarity=0.105  Sum_probs=36.1

Q ss_pred             ccccccccCCcccccchhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630           99 NQACDYLPSLVKKLDSSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus        99 ~~~~~~v~~l~~~~~~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      +...++|.++|+..++ +++++|+.||.|.......++ +            |.-++.-++++|.++
T Consensus         3 ~~~wV~V~G~p~~~~~-~il~~F~~~G~I~~~~~~~~~-~------------~~fV~f~~~~~A~~A   55 (81)
T d1wwha1           3 DDTWVTVFGFPQASAS-YILLQFAQYGNILKHVMSNTG-N------------WMHIRYQSKLQARKA   55 (81)
T ss_dssp             GGGEEEEECCCGGGHH-HHHHHHHTTSCEEEEEECSSS-S------------EEEEEESSHHHHHHH
T ss_pred             cccEEEEECCChHHHH-HHHHHHHhhhhhheEEecCCC-C------------EEEEEEcccHHHHHH
Confidence            3456899999999885 455689999999865543222 1            223445567777777

>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=92.57  E-value=0.023  Score=39.65  Aligned_cols=53  Identities=9%  Similarity=-0.073  Sum_probs=36.2

Q ss_pred             cccccccCCcccccc-----hhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHH
Q psy630          100 QACDYLPSLVKKLDS-----STLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSK  165 (347)
Q Consensus       100 ~~~~~v~~l~~~~~~-----e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~  165 (347)
                      ..++||+||+..+..     +++..+|+.||.+....+...+           ..||  +...+.++|.++
T Consensus         5 ~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~~-----------~~af--V~f~~~~~A~~A   62 (104)
T d1weya_           5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF-----------KRVR--INFSNPLSAADA   62 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT-----------TEEE--EECSSTTHHHHH
T ss_pred             CceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecCC-----------CEEE--EEECCHHHHHHH
Confidence            357899999988633     4588899999999865554221           1133  345667777777

>d1gg3a1 a.11.2.1 (A:82-187) Erythroid membrane protein 4.1R {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Acyl-CoA binding protein-like
superfamily: Second domain of FERM
family: Second domain of FERM
domain: Erythroid membrane protein 4.1R
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.80  E-value=0.36  Score=33.29  Aligned_cols=63  Identities=14%  Similarity=0.133  Sum_probs=40.9

Q ss_pred             ccchhhHHHHhhccccceecccCCC------------CCccchhHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhh
Q psy630          112 LDSSTLLKFYALYKQATVGQCNIDK------------PSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIALLKEVD  174 (347)
Q Consensus       112 ~~~e~l~~~f~~fg~v~~g~~~~~~------------p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~~~l~  174 (347)
                      ++.++...+-+..-|+..|+.....            |....-....=...|+.+.||++.+|+..|++.++.|.
T Consensus        30 ~~~~~a~~Laal~~Qae~GD~~~~~~~~~yl~~~~~~p~~~~~~~~~I~~~h~~l~G~s~~~A~~~fL~~~~~l~  104 (106)
T d1gg3a1          30 CSFATLALLGSYTIQSELGDYDPELHGVDYVSDFKLAPNQTKELEEKVMELHKSYRSMTPAQADLEFLENAKKLS  104 (106)
T ss_dssp             CCHHHHHHHHHHHHHHHHCSCCTTSCSSCCGGGSCCCSSCCHHHHHHHHHHHHHCCSCCHHHHHHHHHHHHHHST
T ss_pred             CCHHHHHHHHHHHHHHHhCCCCccccchhhhhHHhcCCccHHHHHHHHHHHHHHccCcCHHHHHHHHHHHHhcCC
Confidence            5555555666666666666665432            11111122222467899999999999999999999874

>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=83.23  E-value=0.37  Score=32.77  Aligned_cols=66  Identities=12%  Similarity=0.038  Sum_probs=41.8

Q ss_pred             cccccccCC--ccccc---------chhhHHHHhhccccceecccCCCCCccchhHHHHHHHHHHcCCCCHHHHHHHHHH
Q psy630          100 QACDYLPSL--VKKLD---------SSTLLKFYALYKQATVGQCNIDKPSWYNMEAKSKYNAWNSLGQMAKSEAMSKYIA  168 (347)
Q Consensus       100 ~~~~~v~~l--~~~~~---------~e~l~~~f~~fg~v~~g~~~~~~p~~~~~~~~~K~~aw~~~~~~~~~eA~~~yi~  168 (347)
                      ..+++|+|+  |.++.         .+++++.|+.||.|....+..+++..+         ++  +...+.++|.++   
T Consensus         8 ~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~---------~f--V~f~~~e~A~~A---   73 (99)
T d2dita1           8 ERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGV---------AS--VSFRDPEEADYC---   73 (99)
T ss_dssp             CCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCE---------EE--EECSCHHHHHHH---
T ss_pred             ccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccE---------EE--EEECCHHHHHHH---
Confidence            356788887  44321         257889999999999776665554222         22  345567777777   


Q ss_pred             HHHHhhccCChh
Q psy630          169 LLKEVDAGWEDK  180 (347)
Q Consensus       169 ~~~~l~~~~~~~  180 (347)
                       ++.|...|...
T Consensus        74 -~~~lng~~~~g   84 (99)
T d2dita1          74 -IQTLDGRWFGG   84 (99)
T ss_dssp             -HHHSTTCEETT
T ss_pred             -HHHhCCcEECC
Confidence             45555555544

>d1h4ra1 a.11.2.1 (A:104-214) Merlin {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Acyl-CoA binding protein-like
superfamily: Second domain of FERM
family: Second domain of FERM
domain: Merlin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.43  E-value=0.73  Score=31.85  Aligned_cols=63  Identities=13%  Similarity=0.128  Sum_probs=41.5

Q ss_pred             cccchhhHHHHhhccccceecccCCC--CCc------c------------chhHHHHHHHHHHcCCCCHHHHHHHHHHHH
Q psy630          111 KLDSSTLLKFYALYKQATVGQCNIDK--PSW------Y------------NMEAKSKYNAWNSLGQMAKSEAMSKYIALL  170 (347)
Q Consensus       111 ~~~~e~l~~~f~~fg~v~~g~~~~~~--p~~------~------------~~~~~~K~~aw~~~~~~~~~eA~~~yi~~~  170 (347)
                      .+++++...|-+..-|+..|+.....  ++.      +            ...-..=-..|+.+.||++.+|+..|++.+
T Consensus        29 ~~~~~~a~~LAal~~Qae~GD~~~~~~~~~~~~~~~~~P~~~~~~~~~~~~~~~~~I~~~hk~l~G~s~~~A~~~yL~~~  108 (111)
T d1h4ra1          29 YCPPEASVLLASYAVQAKYGDYDPSVHKRGFLAQEELLPKRVINLYQMTPEMWEERITAWYAEHRGRARDEAEMEYLKIA  108 (111)
T ss_dssp             CCCHHHHHHHHHHHHHHHHCSCCTTTSCTTTTTTCCCSCHHHHTTSCCCHHHHHHHHHHHHHTTTTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHhCCCChhhcccchhhhhhcCCchHHHHhhccHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            36667777777777777777765432  111      1            001111234789999999999999999998


Q ss_pred             HHh
Q psy630          171 KEV  173 (347)
Q Consensus       171 ~~l  173 (347)
                      +.|
T Consensus       109 ~~L  111 (111)
T d1h4ra1         109 QDL  111 (111)
T ss_dssp             TTS
T ss_pred             hhC
Confidence            754

>d1mixa1 a.11.2.1 (A:195-308) Talin {Chicken (Gallus gallus) [TaxId: 9031]}

class: All alpha proteins
fold: Acyl-CoA binding protein-like
superfamily: Second domain of FERM
family: Second domain of FERM
domain: Talin
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=80.17  E-value=1.1  Score=30.89  Aligned_cols=27  Identities=26%  Similarity=0.514  Sum_probs=24.1

Q ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHHhh
Q psy630          148 YNAWNSLGQMAKSEAMSKYIALLKEVD  174 (347)
Q Consensus       148 ~~aw~~~~~~~~~eA~~~yi~~~~~l~  174 (347)
                      -..|..+++|++.+|+..|++.++.|.
T Consensus        86 ~~~h~~l~g~s~~~A~~~yL~~~~~l~  112 (114)
T d1mixa1          86 FMAHKNCGNMSEIEAKVRYVKLARSLK  112 (114)
T ss_dssp             HHHHHHTTTCCHHHHHHHHHHHHHHST
T ss_pred             HHHHHHccCCCHHHHHHHHHHHHhcCC
Confidence            367999999999999999999999864